[med-svn] [r-cran-adegenet] 10/12: New upstream version 2.0.1
Andreas Tille
tille at debian.org
Mon Oct 2 17:04:34 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-adegenet.
commit 268adf1e80f186e12f77519f9a00cabc08450a6b
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 2 18:59:05 2017 +0200
New upstream version 2.0.1
---
ChangeLog | 723 ++
DESCRIPTION | 43 +
MD5 | 185 +
NAMESPACE | 181 +
R/HWE.R | 53 +
R/Hs.R | 132 +
R/PCtest.R | 51 +
R/SNPbin.R | 1208 ++++
R/accessors.R | 409 ++
R/adegenet.package.R | 300 +
R/auxil.R | 386 ++
R/basicMethods.R | 552 ++
R/chooseCN.R | 288 +
R/classes.R | 253 +
R/colorplot.R | 76 +
R/constructors.R | 329 +
R/coords.monmonier.R | 58 +
R/dapc.R | 1198 ++++
R/datasets.R | 745 +++
R/dist.genpop.R | 109 +
R/export.R | 171 +
R/find.clust.R | 357 +
R/fstat.R | 97 +
R/gengraph.R | 232 +
R/genind2genpop.R | 149 +
R/glFunctions.R | 774 +++
R/glHandle.R | 461 ++
R/glPlot.R | 42 +
R/glSim.R | 227 +
R/gstat.randtest.R | 63 +
R/handling.R | 663 ++
R/haploGen.R | 723 ++
R/haploPop.R | 946 +++
R/hierarchyMethods.R | 198 +
R/hybridize.R | 235 +
R/import.R | 1733 +++++
R/inbreeding.R | 122 +
R/loadingplot.R | 92 +
R/makefreq.R | 118 +
R/minorAllele.R | 47 +
R/monmonier.R | 666 ++
R/mutations.R | 111 +
R/old2new.R | 161 +
R/orthobasis.R | 366 +
R/pairDist.R | 171 +
R/propShared.R | 41 +
R/propTyped.R | 140 +
R/scale.R | 123 +
R/seqTrack.R | 1145 ++++
R/sequences.R | 317 +
R/servers.R | 51 +
R/setAs.R | 105 +
R/simOutbreak.R | 367 +
R/snpposi.R | 129 +
R/snpzip.R | 340 +
R/spca.R | 442 ++
R/spca.rtests.R | 89 +
R/strataMethods.R | 686 ++
R/xvalDapc.R | 257 +
R/zzz.R | 10 +
README.md | 18 +
data/H3N2.rda | Bin 0 -> 45216 bytes
data/dapcIllus.rda | Bin 0 -> 38831 bytes
data/datalist | 8 +
data/eHGDP.rda | Bin 0 -> 1126695 bytes
data/microbov.rda | Bin 0 -> 28194 bytes
data/nancycats.rda | Bin 0 -> 4889 bytes
data/rupica.rda | Bin 0 -> 30800 bytes
data/sim2pop.rda | Bin 0 -> 6451 bytes
data/spcaIllus.rda | Bin 0 -> 16449 bytes
debian/README.source | 66 -
debian/README.test | 8 -
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 52 -
debian/copyright | 47 -
debian/docs | 3 -
debian/rules | 6 -
debian/source/format | 1 -
debian/tests/control | 3 -
debian/tests/run-unit-test | 12 -
debian/upstream/metadata | 12 -
debian/watch | 3 -
inst/CITATION | 26 +
inst/dapcServer/server.R | 436 ++
inst/dapcServer/ui.R | 501 ++
inst/files/AFLP.txt | 8 +
inst/files/exampleSnpDat.snp | 55 +
inst/files/mondata1.rda | Bin 0 -> 1554 bytes
inst/files/mondata2.rda | Bin 0 -> 1557 bytes
inst/files/nancycats.dat | 247 +
inst/files/nancycats.gen | 264 +
inst/files/nancycats.gtx | 293 +
inst/files/nancycats.str | 475 ++
inst/files/pdH1N1-HA.fasta | 12557 +++++++++++++++++++++++++++++++++++
inst/files/pdH1N1-NA.fasta | 10392 +++++++++++++++++++++++++++++
inst/files/pdH1N1-data.csv | 434 ++
inst/files/usflu.fasta | 2400 +++++++
man/H3N2.Rd | 88 +
man/HWE.Rd | 70 +
man/Hs.Rd | 45 +
man/Hs.test.Rd | 52 +
man/SNPbin.Rd | 164 +
man/accessors.Rd | 243 +
man/adegenet.package.Rd | 210 +
man/as-methods.Rd | 75 +
man/as.SNPbin.Rd | 56 +
man/as.genlight.Rd | 65 +
man/ascore.Rd | 94 +
man/auxil.Rd | 151 +
man/chooseCN.Rd | 96 +
man/colorplot.Rd | 65 +
man/coords.monmonier.Rd | 49 +
man/dapc.Rd | 332 +
man/dapcGraphics.Rd | 204 +
man/dapcIllus.Rd | 91 +
man/df2genind.Rd | 94 +
man/dist.genpop.Rd | 121 +
man/eHGDP.Rd | 148 +
man/fasta2DNAbin.Rd | 61 +
man/fasta2genlight.Rd | 96 +
man/find.clusters.Rd | 280 +
man/gengraph.Rd | 118 +
man/genind.Rd | 104 +
man/genind2df.Rd | 56 +
man/genind2genpop.Rd | 102 +
man/genlight.Rd | 348 +
man/genpop.Rd | 84 +
man/glAux.Rd | 122 +
man/glPca.Rd | 184 +
man/glPlot.Rd | 65 +
man/glSim.Rd | 130 +
man/haploGen.Rd | 194 +
man/hierarchy-methods.Rd | 80 +
man/hybridize.Rd | 104 +
man/import2genind.Rd | 85 +
man/inbreeding.Rd | 113 +
man/isPoly.Rd | 37 +
man/loadingplot.Rd | 71 +
man/makefreq.Rd | 82 +
man/microbov.Rd | 103 +
man/minorAllele.Rd | 37 +
man/monmonier.Rd | 199 +
man/mutations.Rd | 82 +
man/nancycats.Rd | 59 +
man/new.genind.Rd | 62 +
man/new.genpop.Rd | 45 +
man/old2new.Rd | 33 +
man/pairDist.Rd | 99 +
man/population-methods.Rd | 52 +
man/propShared.Rd | 49 +
man/propTyped.Rd | 48 +
man/read.PLINK.Rd | 104 +
man/read.fstat.Rd | 48 +
man/read.genepop.Rd | 51 +
man/read.genetix.Rd | 50 +
man/read.snp.Rd | 99 +
man/read.structure.Rd | 90 +
man/repool.Rd | 47 +
man/rupica.Rd | 80 +
man/scaleGen.Rd | 93 +
man/selpopsize.Rd | 41 +
man/seploc.Rd | 78 +
man/seppop.Rd | 83 +
man/seqTrack.Rd | 270 +
man/sequences.Rd | 69 +
man/servers.Rd | 39 +
man/sim2pop.Rd | 65 +
man/snpposi.Rd | 107 +
man/snpzip.rd | 109 +
man/spca.Rd | 189 +
man/spca.rtests.Rd | 65 +
man/spcaIllus.Rd | 130 +
man/strata-methods.Rd | 169 +
man/tab.Rd | 47 +
man/truenames.Rd | 36 +
man/virClasses.Rd | 18 +
man/web.Rd | 41 +
man/xvalDapc.Rd | 132 +
src/GLfunctions.c | 236 +
src/GLfunctions.h | 5 +
src/adesub.c | 1152 ++++
src/adesub.h | 44 +
src/monmonier-utils.c | 267 +
src/sharedAll.c | 159 +
src/snpbin.c | 564 ++
src/snpbin.h | 102 +
tests/testthat.R | 3 +
tests/testthat/test-prop.R | 18 +
tests/testthat/test-seppop.R | 63 +
tests/testthat/test_accessors.R | 149 +
tests/testthat/test_constructors.R | 15 +
tests/testthat/test_genlight.R | 106 +
tests/testthat/test_hierarchy.R | 50 +
tests/testthat/test_import.R | 131 +
tests/testthat/test_repool.R | 35 +
tests/testthat/test_subset.R | 20 +
tests/testthat/test_summary.R | 13 +
tests/testthat/test_xval.R | 31 +
199 files changed, 59970 insertions(+), 219 deletions(-)
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..5fc0771
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,723 @@
+ CHANGES IN ADEGENET VERSION 2.0.1
+NEW FEATURES
+ o Hs is now much faster and will scale better for large number of
+ loci
+
+ o Hs.test allows for testing differences in expected
+ heterozygosity between two groups of individuals
+
+ o strata tutorial is now available via
+ adegenetTutorial(which="strata")
+
+ o repool can now handle objects with no population information,
+ and can return a list of repooled genind (argument 'list'
+ defauling to FALSE)
+
+ o read.fstat can now handle missing data coded by any number of
+ "0"
+
+ o `scatter.dapc` function can now label individuals using `orditorp`
+ function from `vegan` package, which takes care of overlapping
+ (See issue #100)
+
+ o df2genind is now faster at handling missing data (See issue #114)
+
+ o the summary method has better formatting
+
+BUG FIXES
+ o Hs no longer returns NaN if one locus has not been typed;
+ instead, computations are done using all available loci
+
+ o adegenetTutorial now opens up-to-date tutorials
+
+ o subsetting genlight objects now treats missing data appropriately
+ when given logical, character, or negative subscripts.
+ (See issue #83 (https://github.com/thibautjombart/adegenet/issues/83))
+
+ o fixed occasional spurious warning about duplicated individual
+ labels in df2genind
+
+ o fixed issues with mis-placed missing data in df2genind when samples
+ were labeled with numbers (See issue #96)
+
+ o frequencies can now be obtained from P/A genpop objects (See issue #105)
+
+ o Windows no longer throws an error with as.genlight (See issue #109)
+
+ o read.genpop now returns individual names (See issue #117)
+
+
+
+ CHANGES IN ADEGENET VERSION 2.0.0
+CHANGES IN GENIND/GENPOP/GENLIGHT OBJECTS
+ o generic labels are no longer used; therefore, 'truenames' is now
+ deprecated
+
+ o @tab now stores integers representing counts of alleles, as
+ opposed to the former numeric for allele frequencies
+
+ o @ploidy is now a vector with one value per individual; ploidy
+ can differ across individuals
+
+ o @loc.names, @ind.names, @pop.names have been removed
+
+ o accessors locNames, indNames and popNames can be used to replace
+ calls to the removed slots
+
+ o hierarchical structure is implemented in genind and genlight
+ objects, by the addition of two new slots @strata and @hierarchy.
+
+ o subsetting genlight objects is now up to 10x faster.
+
+
+NEW FEATURES
+ o ploidy can now vary across individuals
+
+ o printing is now consistent across objects classes
+
+ o summary methods now get a verbose argument
+
+ o df2genind is more flexible and faster
+
+ o genind objects size is roughly divided by 2
+
+ o adegenet is now better integrated alongside other packages
+ including pegas and hierfstat; functions for HW test and F
+ statistics have been migrated into these packages and removed from
+ adegenet or deprecated
+
+ o new accessor tab(...) replaces 'truenames' and should be used to
+ get tables of allele counts, frequencies, and optionally replace
+ missing data
+
+ o new accessor locNames<- can be used to rename loci in
+ genind/genpop
+
+ o new accessors 'strata' and 'hier' can be used to get/set
+ hierarchical clustering information!
+
+ o genind2genpop can now take a formula argument for pop to
+ specify strata.
+
+ o subsetting of genind/genpop is more powerful, allowing:
+ x[loc=a , pop=b] where a and b are any subset of loci and
+ populations (characters, integers, logicals)
+
+ o dapc can now store loadings of original variables (argument
+ var.loadings=TRUE)
+
+ o hybridize is now more tolerant towards heterogeneous parent
+ populations and repools data systematically
+
+ o xvalDapc can now run in parallel!
+
+ o roxygen2 is now used for part of the documentation, and
+ mandatory for new contributions
+
+ o new tutorials (distributed on github and on the adegenet
+ website) are now available, including one on strata
+
+ o adegenetIssues() will take you to the issues page of the project
+ on github
+
+ o new welcoming message upon loading the package!
+
+ o a hidden function for listening to music
+
+
+
+ CHANGES IN ADEGENET VERSION 1.4-3
+NEW FEATURES
+ o the generic function pairDist has been added; it plots pairwise
+ distance distributions for different group combinations. Method
+ for objects of class: dist, matrix, genind, DNAbin.
+
+ o 'inbreeding' can now return the maximum likelihood estimate via the
+ stats function 'optimize'.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.4-2
+FIXES
+ o fixed adegenetServer; this should now work on any platform.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.4-1
+NEW FEATURES
+ o the adegenet website is now indicated in CRAN
+
+FIXES
+ o fix to adegenetTutorial: the basics tutorial would not be opened
+ by the function
+
+
+
+ CHANGES IN ADEGENET VERSION 1.4-0
+NEW FEATURES
+ o adegenet now incorporates a web interface for DAPC, started by
+ the command adegenetServer("DAPC")
+
+ o 'xvalDapc' has been modified to incorporate heterogeneous sample
+ sizes
+
+ o the new function 'snpzip' implements feature selection using DAPC
+
+ o 'snpposi.plot' plots SNP density across a DNA sequence
+
+ o 'snpposi.test' tests for randomness in the distribution of SNPs
+ across a DNA sequence
+
+ o the package is no longer distributed with vignettes; instead,
+ tutorials are available from the adegenet website, and can be
+ accessed from R directly by the function 'adegenetTutorial'.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.3-9.2
+FIXES
+ o fixed NAMESPACE to get rid of a warning due to conflicting
+ imports in ape and igraph
+
+ o fixed seploc and seppop, which were loosing some of the
+ attributes of the objects (ploidy, type)
+
+
+ CHANGES IN ADEGENET VERSION 1.3-8
+
+NEW FEATURES
+
+ o new palettes: azur, wasp
+
+ o new function any2col translates (numeric, factor, character)
+ vectors into colors, also providing information for a legend
+
+ o new function xvalDapc which performs cross-validation for a dapc
+ analysis.
+
+
+ CHANGES IN ADEGENET VERSION 1.3-7
+
+NEW FEATURES
+
+ o entirely new version of DNAbin2genind, much faster than before
+ and suitable for large alignments
+
+
+
+ CHANGES IN ADEGENET VERSION 1.3-6
+
+NEW FEATURES
+
+ o findMutations: a new procedure to identify the location and
+ nature of mutations between pairs of DNA sequences
+
+ o graphMutations: a graphical representation for findMutations
+
+ o improved graphics for gengraph
+
+
+
+ CHANGES IN ADEGENET VERSION 1.3-5
+
+NEW FEATURES
+
+ o seqTrack and haploGen now have export functions to igraph class.
+
+ o seqTrack and haploGen now have default plot methods relying on
+ igraph conversion.
+
+ o fstat and gstat.randtest have been restored.
+
+ o gengraph implements graph-based approaches for representing
+ genetic diversity (e-burst type of approaches for any time of
+ genetic data).
+
+
+BUG FIXES
+
+ o mutation rates have been fixed in haploGen
+
+ o calls to printf replaced by Rprintf in C procedures
+
+ o seqTrack example fixed (conversion to graphNEL removed, now
+ using igraph)
+
+ o DLL is now loaded within the NAMESPACE, .First.lib is no longer
+ used.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.3-3
+
+BUG FIXES
+
+ o fixed a bug of propShared, which gave wrong results under weird
+ circumstances. The new implementation is entirely different, uses
+ C code, and is now applicable to data with any level of ploidy.
+
+ o tried making the package smaller by removing unnecessary files.
+
+
+
+
+ CHANGES IN ADEGENET VERSION 1.3-2
+
+BUG FIXES
+
+ o replaced calls to multicore:::detectCores with
+ parallel:::detectCores (the former gives unexpected results on
+ some platforms).
+
+ o documentation update: fstat function is no longer available due
+ to removal of hierfstat package from CRAN. An example shows how to
+ use Fst function from the pegas package instead.
+
+ o documentation update: doc now specifies that read.genepop and
+ read.fstat are meant for diploid data only, with guidelines for
+ haploid data.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.3-1
+
+BUG FIXES
+
+ o removed all dependency with graph package, which was still
+ causing errors on some systems - whenever Bioconductor was not by
+ default one of the accessible repositories (used to be FAQ #4).
+
+NEW FEATURES
+
+ o legend in scatter.dapc now matches to the type and size of
+ symbols used in the plot.
+
+ o the package has been made smaller (from 20MB to 8.5MB).
+
+ o a warning has been added to read.structure: the function is made
+ for diploid data only.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.3-0
+
+BUG FIXES
+
+ o fixed broken dependencies with hierfstat and graph packages
+ (used to be FAQ #4).
+
+ o fixed a minor bug in loadingplot regarding possible label errors.
+
+NEW FEATURES
+
+ o genome-wide SNP data support using the new class genlight,
+ supported by compiled C routines and parallelized computations on
+ multicore architectures.
+
+ o dedicated find.clusters and dapc methods for genlight objects.
+
+ o read.PLINK to read SNP data with PLINK format into genlight
+ objects.
+
+ o read.snp to read SNP data with adegenet's own format into genlight
+ objects.
+
+ o fasta2genlight to extract SNP from FASTA files into genlight
+ objects.
+
+ o new method 'predict' for DAPC objects, allowing for using
+ supplementary individuals.
+
+ o many new options of DAPC scatterplots (scatter.dapc).
+
+ o new plotting method 'compoplot' for DAPC objects, displaying
+ group memberships in a STRUCTURE-like way... only prettier.
+
+ o many new accessors for the classes genind and genpop.
+
+ o 4 new tutorial vignettes: adegenet-basics, adegenet-dapc,
+ adegenet-spca, adegenet-genomics.
+
+ o last but not least: Ismail Ahmed has joined the project as a
+ developper.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-8
+
+BUG FIXES
+
+ o fixed a major issue in the conversion of genind objects to
+ hierfstat data format. In some cases, this issue biased the
+ results of the wrapper function "fstat".
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-7
+
+
+NEW FEATURES
+
+ o dapc and find.clusters are now stable versions for the published methods.
+
+ o a.score and optim.a.score are released in their beta versions.
+
+ o scatter.dapc is now adapted to representation 1-dimensional DAPC results.
+
+
+BUG FIXES
+
+ o fixed a major issue in the ape package causing haploGen to
+ bug. This is a temporary replacement, waiting for ape to implement
+ the changes (currently, adegenet replaces ape's as.list.DNAbin
+ function with a corrected version).
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-6
+
+
+NEW FEATURES
+
+ o pairwise.fst: computes Nei's pairwise Fst between populations
+
+ o alignment2genind: extract polymorphism from nucleic and proteic
+ aligned sequences with the 'alignment' format, returning a genind object.
+
+
+BUG FIXES
+
+ o fixed a minor issue in Hs, occuring in fixed loci for a given population.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-5
+
+
+NEW FEATURES
+
+ o SeqTrack, an algorithm for the reconstruction of genealogies, is
+ now fully implemented and documented.
+
+ o haploGen, a system for simulating genealogies, is now fully
+ implemented and documented.
+
+
+BUG FIXES
+
+ o summary methods for genind and genpop are fixed (again) for the
+ new R version 2.11.1.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-4
+
+
+NEW FEATURES
+
+ o Hs computes the theoretical heterozygosity by populations for
+ genpop object
+
+ o propShared is now available for haploid data
+
+ o Discriminant Analysis of Principal Component (DAPC) is
+ implemented by the function DAPC, although the method itself is
+ still under review.
+
+ o The SeqTrack algorithm for reconstructing genealogies is
+ implemented by the function seqTrack, although the method itself
+ is still under review.
+
+ o Pre-release of new simulation tools, still undocumented
+ (haploPop and haploGen).
+
+ o New datasets eHGDP and H3N2
+
+
+BUG FIXES
+
+ o minor bug fixes in df2genind, propShared, and seploc
+
+ o summary issue arised in certain conditions, depending on which
+ package was loaded before adegenet; in some cases, the summary
+ procedure was not found for genind/genpop objects. Fixed now.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-3
+
+
+NEW FEATURES
+
+ o implement handling of presence/absence markers. genind and
+ genpop object now have a 'type' attribute to differentiate between
+ codominant markers (e.g. microsatellite), which is the default
+ type, and presence/absence data (e.g. AFLP). Functions in adegenet
+ now behave according to the type of markers being used.
+
+ o SNP can now be obtained from sequence data, stored as DNAbin
+ (see E. Paradis's package 'ape'). They can be selected to verify
+ any given degree of polymorphism.
+
+ o 'hybridize' can now be used for genotypes having any even degree
+ of ploidy (e.g. tetraploid genotypes).
+
+ o the new function 'isPoly' checks which loci are polymorphic, or
+ which alleles contribute to polymorphism.
+
+ o the new function 'pop' can be used to retrieve and set the pop
+ slot of genind object.
+
+ o the new function 'selPopSize' allows one to select a subset of
+ genotypes belonging to well-sampled populations, as defined by a
+ threshold sample size.
+
+ o the new accessor 'locNames' can be used to retrieve real labels
+ of markers and/or alleles.
+
+ o the loadingplot has been modified to allow specifying x axis, so
+ that scoring SNPs along their sequence is now possible.
+
+
+BUG FIXES
+
+ o no bug to fix this version!
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-2
+
+
+NEW FEATURES
+
+ o implement different levels of ploidy in genind / genpop objects
+ (new slot @ploidy). Now, any level of ploidy can be handled by
+ input function df2genind, which has been recoded almost
+ entierely. Different levels of ploidy are now handled by different
+ functions.
+
+ o a "sep" argument is now handled by df2genind: this allows
+ reading many data formats.
+
+ o implemented a method "scaleGen" for genind / genpop objects,
+ which scales allelic data using different methods.
+
+ o colorplot: a generic function, with a method for spca
+ objects. Represents up to three principal components based on RGB
+ representation of Cavalli-Sforza.
+
+ o loadingplot for plotting loadings of one axis
+
+ o adegenetTutorial function which opens the online tutorials
+
+ o allow for the use of na.replace and scaleGen in spca function
+
+ o added rupica dataset
+
+ o enable reading data from URL (import2genind, read.[...])
+
+ o permit specification of a matrix of spatial weights in spca
+
+
+BUG FIXES
+
+ o fixed bug 1.2-2.01 (read.structure issue): was due to the
+ default of "onerowperind" argument.
+
+ o fixed bug 1.2-2.02 (read.genetix issue): was due to an
+ error in the data file (wrong nloc); now read.genetix corrects
+ that automatically and issues a warning.
+
+ o fixed bug 1.2-2.03 (monmonier issue): was a non-detected
+ code 2 due to intersection check with previously drawn segment
+ (was not always removed).
+
+ o fixed bug 1.2-2.05 (a few fixes/improvement for monmonier)
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-1
+
+
+NEW FEATURES
+
+ o documentation of scaleGen provides an example of usefulness of
+ an appropriate scaling in PCA
+
+BUG FIXES
+
+ o fixed the recognition of NAs in df2genind
+
+ o fixed the call to inherits in spca (returned value changes in R-devel)
+
+
+
+ CHANGES IN ADEGENET VERSION 1.2-0
+
+
+NEW FEATURES
+
+ o implement different levels of ploidy in genind / genpop
+ objects. Make necessary adaptations throughout the package.
+
+ o put some stop where needed when ploidy!=2 is not handled.
+
+ o implement a "sep" argument in df2genind.
+
+ o implement accessor for genind/genpop: nLoc.
+
+ o implement "scaleGen" for genind/genpop, which allows for
+ different types of scaling.
+
+ o added several coercion methods, from genind/genpop to
+ data.frame, matrix and ktab objects.
+
+ o implemented propTyped, a function giving the proportion of
+ non-missing data in different ways.
+
+BUG FIXES
+
+ o missing data indicated in summary corrected (loci with more
+ alleles had more weight in the computations).
+
+
+
+
+ CHANGES IN ADEGENET VERSION 1.1-3
+
+
+NEW FEATURES
+
+ o 'as' methods for genind/genpop objects to matrix, data.frame,
+ and ktab objects. Now, ordination implemented as dudi functions in
+ ade4 (like dudi.pca) can be performed directly using genind/genpop
+ as inputs.
+
+
+
+
+ CHANGES IN ADEGENET VERSION 1.1-2
+
+
+NEW FEATURES
+
+ o significant improvement in the speed of genind2df (more than
+ twice as fast as before).
+
+ o function propShared added: computes the proportion of shared
+ alleles among a set of genotypes (core computations in C).
+
+ o A warning is issued when NAs exist in the input of sPCA.
+
+ o improvement of the validity checking for genind/genpop:
+ validObject now detects duplicates in any kind of names (ind.names,
+ pop.names, etc.) and prints the corresponding items.
+
+BUG FIXES
+
+ o genind2df does now handles the pop argument correctly.
+
+ o df2genind does no longer bug when there is an entirely non-typed
+ locus.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.1-1
+
+
+NEW FEATURES
+
+ o I/O: df2genind no longer fails when entirely non-type
+ individuals exist.
+
+ o Monmonier: optimize.monmonier now computes the 'best'
+ boundary only once instead of twice. The whole code was re-thought
+ and optimized for speed. Monmonier's boundaries can now form
+ loops. Instead of stoping at a given threshold, it is also
+ possible to ask for a given length of boundary (argument
+ bd.length).
+
+ o The function chooseCN has a new option to return a list of
+ spatial weights defined as the inverse of spatial distances, at a
+ given exponent.
+
+ o A wrapper for glob.varcomp has been implemented for genind
+ objects, through the new function fstat.
+
+ o The elements of the @other slot are now proceeded wisely when
+ objects are subsetted using the '[' operator.
+
+
+BUG FIXES
+
+ o I/O: df2genind no longer fails when entirely non-type
+ individuals exist.
+
+ o monmonier no longer fails when coordinates are drawn from a
+ regular grid. The matched call of the returned object has been
+ fixed.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.1-0
+
+NEW FEATURES
+ o Data representation: S4 classes in replacement of old S3
+ classes.
+
+ o Spatial genetics: the spatial Principal Component Analysis
+ (Jombart et al, 2008, Heredity), two multivariate spatial
+ tests, and new functionalities for Monmonier's algorithm.
+
+ o I/O: functions to import data are now 'read' functions;
+ available for formats of GENETIX, Fstat, Genepop, STRUCTURE and
+ from data.frames of genotypes. Export from genind to data.frame of
+ genotypes.
+
+ o Data: five new simulated geo-referenced datasets
+
+ o Simulations: a hybridize function, which creates hybrids from
+ two parent datasets. Can output to STRUCTURE format.
+
+ o Data manipulation: new function to separate data by
+ population. Accessors to genind and genpop object like with
+ matrices using 'foo[ chosenGenotypes, chosenAlleles]'.
+
+
+
+ CHANGES IN ADEGENET VERSION 1.0-2
+
+NEW FEATURES
+
+ o adegenetWeb is a simple function opening the adegenet website in
+ the default web browser.
+
+ o sim2pop is a dataset obtained by simulation using the software
+ Easypop. It contains 130 georeferenced genotypes sampled from two
+ distinct populations.
+
+ o monmonier documentation was improved by adding a genetic
+ example, using sim2pop data.
+
+BUG FIXES
+
+ o some bugs corrected in optimize.monmonier
+
+
+ CHANGES IN ADEGENET VERSION 1.0-1
+
+NEW FEATURES
+
+ o chooseCN is a simple interactive tool for choosing and building
+ a connection network from spatial coordinates. This tool is called
+ by monmonier function.
+
+ o monmonier, optimize.monmonier, plot.monmonier and print.monmonier
+ implement the Monmonier algorithm. While not restrained to genetic
+ data analysis, this method can be used to find genetic boundaries
+ among individuals or populations based on their allelic
+ frequencies and spatial coordinates.
+
+BUG FIXES
+
+ o several bugs fixed in I/O functions
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..2dd559b
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,43 @@
+Package: adegenet
+Version: 2.0.1
+Encoding: UTF-8
+Date: 2016-02-15
+Title: Exploratory Analysis of Genetic and Genomic Data
+Author: Thibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie-
+ Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne
+ Cori, Federico Calboli
+Maintainer: Thibaut Jombart <thibautjombart at gmail.com>
+Suggests: pegas, hierfstat, akima, maps, splancs, adehabitat, tripack,
+ testthat
+Depends: R (>= 2.14), methods, ade4
+Imports: utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2,
+ seqinr, parallel, spdep, boot, reshape2, dplyr (>= 0.4.1),
+ vegan
+URL: http://adegenet.r-forge.r-project.org/
+Description: Toolset for the exploration of genetic and genomic data. Adegenet
+ provides formal (S4) classes for storing and handling various genetic data,
+ including genetic markers with varying ploidy and hierarchical population
+ structure ('genind' class), alleles counts by populations ('genpop'), and
+ genome-wide SNP data ('genlight'). It also implements original multivariate
+ methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance
+ and similarity measures, and several spatial methods. A range of both empirical
+ and simulated datasets is also provided to illustrate various methods.
+Collate: adegenet.package.R datasets.R orthobasis.R classes.R
+ constructors.R accessors.R basicMethods.R handling.R auxil.R
+ minorAllele.R setAs.R SNPbin.R strataMethods.R
+ hierarchyMethods.R glHandle.R glFunctions.R glSim.R
+ find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R
+ chooseCN.R genind2genpop.R loadingplot.R sequences.R
+ gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R
+ coords.monmonier.R haploGen.R old2new.R spca.rtests.R dapc.R
+ xvalDapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R
+ export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R
+ simOutbreak.R mutations.R snpposi.R snpzip.R pairDist.R
+ servers.R zzz.R
+License: GPL (>= 2)
+LazyLoad: yes
+RoxygenNote: 5.0.1
+NeedsCompilation: yes
+Packaged: 2016-02-15 13:36:45 UTC; thibaut
+Repository: CRAN
+Date/Publication: 2016-02-15 16:12:41
diff --git a/MD5 b/MD5
new file mode 100644
index 0000000..1a976ee
--- /dev/null
+++ b/MD5
@@ -0,0 +1,185 @@
+043721630a5ac2124992db79e1f647f3 *ChangeLog
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diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..8db6ef9
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,181 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(as.POSIXct,haploGen)
+S3method(as.data.frame,genind)
+S3method(as.data.frame,genlight)
+S3method(as.data.frame,genpop)
+S3method(as.integer,SNPbin)
+S3method(as.lda,dapc)
+S3method(as.list,genlight)
+S3method(as.matrix,genind)
+S3method(as.matrix,genlight)
+S3method(as.matrix,genpop)
+S3method(c,SNPbin)
+S3method(colorplot,default)
+S3method(colorplot,spca)
+S3method(dapc,data.frame)
+S3method(dapc,dudi)
+S3method(dapc,genind)
+S3method(dapc,genlight)
+S3method(dapc,matrix)
+S3method(find.clusters,data.frame)
+S3method(find.clusters,genind)
+S3method(find.clusters,genlight)
+S3method(find.clusters,matrix)
+S3method(findMutations,DNAbin)
+S3method(gengraph,DNAbin)
+S3method(gengraph,default)
+S3method(gengraph,dist)
+S3method(gengraph,genind)
+S3method(gengraph,genpop)
+S3method(gengraph,matrix)
+S3method(get.likelihood,seqTrack)
+S3method(graphMutations,DNAbin)
+S3method(labels,haploGen)
+S3method(loadingplot,default)
+S3method(loadingplot,glPca)
+S3method(pairDistPlot,DNAbin)
+S3method(pairDistPlot,default)
+S3method(pairDistPlot,dist)
+S3method(pairDistPlot,genind)
+S3method(pairDistPlot,matrix)
+S3method(plot,haploGen)
+S3method(plot,monmonier)
+S3method(plot,seqTrack)
+S3method(plot,spca)
+S3method(predict,dapc)
+S3method(print,dapc)
+S3method(print,genindSummary)
+S3method(print,genpopSummary)
+S3method(print,glPca)
+S3method(print,haploGen)
+S3method(print,monmonier)
+S3method(print,spca)
+S3method(scatter,dapc)
+S3method(scatter,glPca)
+S3method(screeplot,spca)
+S3method(seqTrack,default)
+S3method(seqTrack,haploGen)
+S3method(seqTrack,matrix)
+S3method(snpposi.plot,DNAbin)
+S3method(snpposi.plot,integer)
+S3method(snpposi.plot,numeric)
+S3method(snpposi.test,DNAbin)
+S3method(snpposi.test,integer)
+S3method(snpposi.test,numeric)
+S3method(summary,dapc)
+S3method(summary,spca)
+export("addStrata<-")
+export("hier<-")
+export("nameStrata<-")
+export("setPop<-")
+export("splitStrata<-")
+export("strata<-")
+export(.genlab)
+export(.readExt)
+export(.render.server.info)
+export(.rmspaces)
+export(Hs)
+export(Hs.test)
+export(addStrata)
+export(adegenetIssues)
+export(adegenetTutorial)
+export(adegenetWeb)
+export(as.genind)
+export(as.genpop)
+export(chooseCN)
+export(df2genind)
+export(extract.PLINKmap)
+export(genind)
+export(genind2df)
+export(genind2genpop)
+export(genpop)
+export(hier)
+export(hybridize)
+export(makefreq)
+export(minorAllele)
+export(nameStrata)
+export(old2new_genind)
+export(old2new_genlight)
+export(old2new_genpop)
+export(read.PLINK)
+export(read.fstat)
+export(read.genepop)
+export(read.genetix)
+export(read.snp)
+export(read.structure)
+export(repool)
+export(scaleGen)
+export(setPop)
+export(splitStrata)
+export(strata)
+export(tab)
+exportMethods(initialize)
+exportMethods(makefreq)
+exportMethods(scaleGen)
+exportPattern("^[^\\.]")
+import(ade4)
+import(grDevices)
+import(graphics)
+import(methods)
+import(parallel)
+import(stats)
+import(utils)
+importFrom(MASS,"lda")
+importFrom(ape,"[.DNAbin")
+importFrom(ape,"as.DNAbin")
+importFrom(ape,"as.DNAbin.alignment")
+importFrom(ape,"as.DNAbin.character")
+importFrom(ape,"as.DNAbin.list")
+importFrom(ape,"as.character.DNAbin")
+importFrom(ape,"as.list.DNAbin")
+importFrom(ape,"as.matrix.DNAbin")
+importFrom(ape,"c.DNAbin")
+importFrom(ape,"cbind.DNAbin")
+importFrom(ape,"dist.dna")
+importFrom(ape,"labels.DNAbin")
+importFrom(ape,"print.DNAbin")
+importFrom(ape,"rbind.DNAbin")
+importFrom(ape,"seg.sites")
+importFrom(dplyr,bind_rows)
+importFrom(ggplot2,"aes")
+importFrom(ggplot2,"coord_flip")
+importFrom(ggplot2,"geom_boxplot")
+importFrom(ggplot2,"geom_density")
+importFrom(ggplot2,"geom_jitter")
+importFrom(ggplot2,"geom_rug")
+importFrom(ggplot2,"geom_violin")
+importFrom(ggplot2,"ggplot")
+importFrom(ggplot2,"guide_legend")
+importFrom(ggplot2,"guides")
+importFrom(ggplot2,"labs")
+importFrom(ggplot2,"xlim")
+importFrom(igraph,"E")
+importFrom(igraph,"E<-")
+importFrom(igraph,"V")
+importFrom(igraph,"V<-")
+importFrom(igraph,"as.igraph")
+importFrom(igraph,"clusters")
+importFrom(igraph,"graph.adjacency")
+importFrom(igraph,"graph.data.frame")
+importFrom(igraph,"layout.fruchterman.reingold")
+importFrom(igraph,"plot.igraph")
+importFrom(igraph,"print.igraph")
+importFrom(reshape2,colsplit)
+importFrom(seqinr,s2c)
+importFrom(shiny,"renderPrint")
+importFrom(shiny,"runApp")
+importFrom(spdep,"card")
+importFrom(spdep,"dnearneigh")
+importFrom(spdep,"gabrielneigh")
+importFrom(spdep,"graph2nb")
+importFrom(spdep,"knearneigh")
+importFrom(spdep,"knn2nb")
+importFrom(spdep,"lag.listw")
+importFrom(spdep,"listw2mat")
+importFrom(spdep,"mat2listw")
+importFrom(spdep,"nb2listw")
+importFrom(spdep,"relativeneigh")
+importFrom(spdep,"tri2nb")
+importFrom(vegan,orditorp)
+useDynLib(adegenet)
diff --git a/R/HWE.R b/R/HWE.R
new file mode 100644
index 0000000..c368dc7
--- /dev/null
+++ b/R/HWE.R
@@ -0,0 +1,53 @@
+##################
+# HWE.test.genind
+##################
+
+HWE.test.genind <- function(x,pop=NULL,permut=FALSE,nsim=1999,hide.NA=TRUE,res.type=c("full","matrix")){
+
+ message("As of adegenet_1.5-0, this function has been removed and is replaced by 'hw.test' in the package 'pegas'")
+
+ ## if(!is.genind(x)) stop("x is not a valid genind object")
+ ## if(x at ploidy != as.integer(2)) stop("not implemented for non-diploid genotypes")
+ ## checkType(x)
+
+ ## if(is.null(pop)) pop <- x at pop
+ ## if(is.null(pop)) pop <- as.factor(rep("P1",nrow(x at tab)))
+ ## res.type <- tolower(res.type[1])
+ ## if(res.type != "full" && res.type != "matrix") stop("unknown res.type specified.")
+
+ ## kGen <- genind2genotype(x,pop=pop,res.type="list")
+
+ ## # ftest tests HWE for a locus and a population
+ ## ftest <- function(vec,permut=permut,nperm=nsim){
+ ## temp <- unique(vec)
+ ## temp <- temp[!is.na(temp)]
+ ## if(length(temp) < 2) return(NA)
+ ## if(res.type=="full") {
+ ## res <- HWE.chisq(vec, simulate.p.value=permut, B=nperm)
+ ## } else {
+ ## res <- HWE.chisq(genotype(vec), simulate.p.value=permut, B=nperm)$p.value
+ ## }
+ ## return(res)
+ ## }
+
+ ## res <- lapply(kGen,function(e) lapply(e,ftest,permut,nsim))
+
+ ## # clean non-tested elements in the results list
+ ## if(hide.NA && res.type=="full"){
+ ## newres=list()
+ ## tokeep <- which(unlist(lapply(res,function(e) !all(is.na(e)))))
+ ## if(length(tokeep) > 0) for(i in 1:length(tokeep)) {newres[[i]] <- res[[tokeep[i]]]}
+ ## newres <- lapply(newres,function(e) {e[!is.na(e)] })
+ ## names(newres) <- names(res)[tokeep]
+ ## res <- newres
+ ## }
+
+ ## if(res.type=="matrix"){
+ ## res <- as.data.frame(lapply(res,unlist))
+ ## rnam <- rownames(res)
+ ## rownames(res) <- gsub(".X-squared","",rnam)
+ ## res <- as.matrix(res)
+ ## }
+
+ ## return(res)
+}
diff --git a/R/Hs.R b/R/Hs.R
new file mode 100644
index 0000000..27a748f
--- /dev/null
+++ b/R/Hs.R
@@ -0,0 +1,132 @@
+#'
+#' Expected heterozygosity (Hs)
+#'
+#' This function computes the expected heterozygosity (Hs) within
+#' populations of a \linkS4class{genpop} object. This function is
+#' available for codominant markers (\code{@@type="codom"}) only. Hs is
+#' commonly used for measuring within population genetic diversity (and
+#' as such, it still has sense when computed from haploid data).
+#'
+#' @aliases Hs
+#'
+#' @rdname Hs
+#'
+#' @export
+#'
+#' @details
+#' Let \emph{m(k)} be the number of alleles of locus \emph{k}, with a
+#' total of \emph{K} loci. We note \eqn{f_i} the allele frequency of
+#' allele \emph{i} in a given population. Then, \eqn{Hs} is given for a
+#' given population by:\cr
+#'
+#' \eqn{\frac{1}{K} \sum_{k=1}^K (1 - \sum_{i=1}^{m(k)} f_i^2)}
+#'
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#'
+#' @param x a \linkS4class{genind} or \linkS4class{genpop} object.
+#' @param pop only used if x is a \linkS4class{genind}; an optional factor to be used as population; if not provided, pop(x) is used.
+#'
+#' @seealso \code{\link{Hs.test}} to test differences in Hs between two groups
+#' @return a vector of Hs values (one value per population)
+#' @examples
+#' \dontrun{
+#' data(nancycats)
+#' Hs(genind2genpop(nancycats))
+#' }
+#'
+Hs <- function(x, pop=NULL) {
+
+ ## CHECKS
+ if(is.genind(x)){
+ if(!is.null(pop)) pop(x) <- pop
+ x <- genind2genpop(x, quiet=TRUE)
+ }
+ if(!is.genpop(x)) stop("x is not a valid genpop object")
+ if(x at type=="PA") stop("not implemented for presence/absence markers")
+
+
+ ## MAIN COMPUTATIONS
+ ## get number of typed loci per pop
+ if(any(is.na(tab(x)))){
+ temp <- apply(tab(x),1,tapply, locFac(x), function(e) !any(is.na(e)))
+ nLoc.typed <- apply(temp,2,sum)
+ } else {
+ nLoc.typed <- nLoc(x)
+ }
+
+ F <- tab(x, freq=TRUE, NA.method="asis")
+ res <- 1-(apply(F^2,1,sum, na.rm=TRUE))/nLoc.typed
+
+ return(res)
+} # end Hs
+
+
+#'
+#' Test differences in expected heterozygosity (Hs)
+#'
+#' This procedure permits to test if two groups have
+#' significant differences in expected heterozygosity (Hs).
+#' The test statistic used is simply the difference in Hs
+#' between the two groups 'x' and 'y':
+#'
+#' \eqn{Hs(x) - Hs(y)}
+#'
+#' Individuals are randomly permuted between groups to obtain
+#' a reference distribution of the test statistics.
+#'
+#' @rdname Hs.test
+#' @aliases Hs.test
+#'
+#' @export
+#'
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#'
+#' @param x a \linkS4class{genind} object.
+#' @param y a \linkS4class{genind} object.
+#' @param n.sim the number of permutations to be used to generate the reference distribution.
+#' @param alter a character string indicating the alternative hypothesis
+#'
+#' @seealso \code{\link{Hs}} to compute Hs for different populations;
+#' \code{\link[ade4]{as.randtest}} for the class of Monte Carlo tests.
+#'
+#' @return an object of the class randtest
+#'
+#' @examples
+#' \dontrun{
+#' data(microbov)
+#' Hs(microbov)
+#' test <- Hs.test(microbov[pop="Borgou"],
+#' microbov[pop="Lagunaire"],
+#' n.sim=499)
+#' test
+#' plot(test)
+#' }
+#'
+Hs.test <- function(x, y, n.sim=999, alter=c("two-sided", "greater", "less")){
+ ## CHECKS ##
+ if(!is.genind(x)) stop("x is not a valid genind object")
+ if(!is.genind(y)) stop("y is not a valid genind object")
+ if(x at type=="PA" || y at type=="PA") stop("not implemented for presence/absence markers")
+ alter <- match.arg(alter)
+
+ ## POOL DATA ##
+ xy <- repool(x,y)
+ pop(xy) <- rep(c("x","y"), c(nInd(x), nInd(y)))
+
+ ## AUXIL FUNCTION ##
+ f1 <- function(x, pop) -diff(Hs(x, pop))
+
+ ## COMPUTE STATS
+ ## observed value
+ obs <- f1(xy, pop(xy))
+
+ ## permuted
+ sim <- replicate(n.sim, f1(xy, sample(pop(xy))))
+
+ ## randtest
+ res <- as.randtest(sim=sim, obs=obs, alter=alter)
+ res$call <- match.call()
+
+ return(res)
+
+} # end Hs.test
diff --git a/R/PCtest.R b/R/PCtest.R
new file mode 100644
index 0000000..6a47ef6
--- /dev/null
+++ b/R/PCtest.R
@@ -0,0 +1,51 @@
+## pctest <- function(x, nperm=99, center=TRUE, scale=TRUE, method=c("sigma", "binom"), quiet=FALSE, plot=TRUE){
+## ## check x
+## if(!is.genind(x) & !is.genpop(x)){
+## stop("x is not a genind or a genpop object")
+## }
+
+## ## a few general variables
+## N <- nrow(x at tab)
+## P <- ncol(x at tab)
+
+## ## make tables of allele frequencies
+## X <- scaleGen(x, center=center, scale=scale, method=method, missing="mean")
+## fac.loc <- factor(sub("[.][^.]*$","",colnames(X)))
+## lX <- lapply(levels(fac.loc), function(id) X[,fac.loc==id,drop=FALSE])
+
+## ## auxil function to compute the first eigenvalue
+## if(N > P){ # N > P
+## f1 <- function(A){
+## Z <- t(A) %*% A / N
+## return(eigen(Z, symmetric=TRUE, only.values=TRUE)$values[1])
+## }
+## } else { #p <= n
+## f1 <- function(A){
+## Z <- A %*% t(A) / N
+## return(eigen(Z, symmetric=TRUE, only.values=TRUE)$values[1])
+## }
+## }
+
+
+## ## Monte Carlo procedure
+## makeOnePerm <- function(listX){
+## return(as.matrix(data.frame(lapply(listX, function(e) e[sample(N),,drop=FALSE]))))
+## }
+
+## if(quiet){
+## sim <- sapply(1:nperm, function(i) f1(makeOnePerm(lX)))
+## } else {
+## cat("\n Computing", nperm, "simulated eigenvalues ")
+## sim <- sapply(1:nperm, function(i) {cat(ifelse(i%%10==0, i, "."));return(f1(makeOnePerm(lX)))} )
+## cat(" done.\n")
+## }
+## ini <- f1(X)
+
+## ## return res
+## myCall <- match.call()
+## res <- as.randtest(sim=sim, obs=ini, alter="greater", call=myCall)
+## if(plot) {
+## plot(res, nclass=NULL, main="1st eigenvalue vs simulated eigenvalues (histogram)")
+## }
+## return(res)
+## }
diff --git a/R/SNPbin.R b/R/SNPbin.R
new file mode 100644
index 0000000..c6ca07a
--- /dev/null
+++ b/R/SNPbin.R
@@ -0,0 +1,1208 @@
+
+
+###############
+##
+## CLASSES
+##
+###############
+
+###############
+## SNPbin class
+###############
+setClass("SNPbin", representation(snp = "list",
+ n.loc = "integer",
+ NA.posi = "integer",
+ label = "charOrNULL",
+ ploidy = "integer"),
+ prototype(snp = list(), n.loc = 0L, label = NULL, ploidy = 1L))
+
+
+
+
+###############
+## genlight class
+###############
+setClass("genlight", representation(gen = "list",
+ n.loc = "integer",
+ ind.names = "charOrNULL",
+ loc.names = "charOrNULL",
+ loc.all = "charOrNULL",
+ chromosome = "factorOrNULL",
+ position = "intOrNULL",
+ ploidy = "intOrNULL",
+ pop = "factorOrNULL",
+ strata = "dfOrNULL",
+ hierarchy = "formOrNULL",
+ other = "list"),
+ prototype(gen = list(), n.loc = 0L, ind.names = NULL, loc.names = NULL, loc.all = NULL,
+ chromosome = NULL, position = NULL, strata = NULL, hierarchy = NULL, ploidy=NULL, pop=NULL, other=list()))
+
+
+
+
+
+
+
+
+#####################
+##
+## CONSTRUCTORS
+##
+#####################
+
+####################
+## SNPbin constructor
+####################
+setMethod("initialize", "SNPbin", function(.Object, ...) {
+ x <- .Object
+ input <- list(...)
+ if(length(input)==1) names(input) <- "snp"
+ if(length(input)>1 && ! "snp" %in% names(input)) names(input)[1] <- "snp"
+
+ ## handle snp data ##
+ if(!is.null(input$snp) && length(input$snp)>0 && !all(is.na(input$snp))){
+ ## a vector of raw is provided
+ if(is.raw(input$snp)){
+ x at snp <-list(input$snp)
+ }
+
+ ## a list of raw vectors is provided
+ if(is.list(input$snp)){
+ if(all(sapply(input$snp, class)=="raw")){
+ x at snp <- input$snp
+ }
+ }
+
+ ## a numeric/integer vector is provided
+ ## conversion from a vector of 0/1 (integers)
+ if(is.numeric(input$snp) | is.integer(input$snp)){
+ input$snp <- as.integer(input$snp)
+ ## determine ploidy
+ if(is.null(input$ploidy)){
+ input$ploidy <- max(input$snp, na.rm=TRUE)
+ if(input$ploidy==0) input$ploidy <- 1
+ }
+ input$ploidy <- as.integer(input$ploidy)
+ if(input$ploidy<1) stop("Ploidy is less than 1")
+
+ ## check values in the vector
+ if(any(input$snp<0 | input$snp>input$ploidy, na.rm=TRUE)){
+ stop("Values of SNPs < 0 or > ploidy")
+ }
+
+
+ ## handle ploidy (may have to split info into binary vectors)
+ x at snp <- list()
+ i <- max(input$snp, na.rm=TRUE) # determine max nb of alleles
+ if(i > 1){ # haplotype can be 0/1/2/...
+ j <- 0 # index for the length of the list @snp
+ while(i > 0){
+ j <- j+1 # update length of the result
+ temp <- as.integer(input$snp==i)
+ x at snp[[j]] <- .bin2raw(temp)$snp # make a vector of 1
+ input$snp <- input$snp-temp # deflate data (subtract the recoded alleles)
+ i <- max(input$snp, na.rm=TRUE) # update the max nb of alleles
+ }
+ } else { # haplotype is only 0/1/NA
+ x at snp[[1]] <- .bin2raw(input$snp)$snp
+ }
+ x at n.loc <- length(input$snp)
+ x at NA.posi <- which(is.na(input$snp))
+ x at ploidy <- as.integer(input$ploidy)
+ return(x)
+ }
+ }
+
+ ## handle full-NA data
+ if(!is.null(input$snp) && all(is.na(input$snp))){
+ x at snp <- list()
+ x at n.loc <- length(input$snp)
+ x at snp[[1]] <- .bin2raw(rep(0L, length(input$snp)))$snp
+ x at NA.posi <- 1:length(input$snp)
+ if(!is.null(input$ploidy)){
+ x at ploidy <- as.integer(input$ploidy)
+ } else {
+ x at ploidy <- as.integer(NA)
+ }
+ return(x)
+ }
+
+
+ ## handle n.loc ##
+ if(!is.null(input$n.loc)){
+ x at n.loc <- as.integer(input$n.loc)
+ } else {
+ if(!is.null(input$snp)){
+ warning("number of SNPs (n.loc) not provided to the genlight constructor - using the maximum number given data coding.")
+ x at n.loc <- as.integer(length(x at snp)*8)
+ } else {
+ x at n.loc <- 0L
+ }
+ }
+
+
+ ## handle NA.posi ##
+ if(!is.null(input$NA.posi)){
+ x at NA.posi <- as.integer(input$NA.posi)
+ }
+
+
+ ## handle ploidy ##
+ if(!is.null(input$ploidy)){
+ x at ploidy <- as.integer(input$ploidy)
+ }
+
+
+ return(x)
+}) # end SNPbin constructor
+
+
+
+
+
+
+
+########################
+## genlight constructor
+########################
+setMethod("initialize", "genlight", function(.Object, ..., parallel=require("parallel"), n.cores=NULL) {
+ if(parallel && !require(parallel)) stop("parallel package requested but not installed")
+ if(parallel && is.null(n.cores)){
+ n.cores <- parallel::detectCores()
+ }
+ if( .Platform$OS.type == "windows" ){
+ n.cores <- 1
+ }
+
+ x <- .Object
+ input <- list(...)
+ if(length(input)==1 && is.null(names(input))) names(input) <- "gen"
+ if(length(input)>1 && ! "gen" %in% names(input)) names(input)[1] <- "gen"
+
+
+ ## HANDLE INPUT$GEN ##
+ if(!is.null(input$gen)){
+ ## input$gen is a list of SNPbin ##
+ if(is.list(input$gen) && all(sapply(input$gen, class)=="SNPbin")){
+ ## check nb of loci in each SNPbin
+ if(length(unique(sapply(input$gen, nLoc)))>1) {
+ warning("SNPbin objects have different numbers of loci")
+ input$gen <- lapply(input$gen, as.integer)
+ } else { # all seems fine
+ x at gen <- input$gen
+ if(is.null(input$ind.names)){
+ input$ind.names <- names(input$gen)
+ }
+ }
+ }
+
+
+ ## input$gen is a matrix or a data.frame
+ if((is.matrix(input$gen) & !inherits(input$gen,"snp.matrix")) | is.data.frame(input$gen)){
+ if(is.null(input$ind.names)){
+ input$ind.names <- rownames(input$gen)
+ }
+ if(is.null(input$loc.names)){
+ input$loc.names <- colnames(input$gen)
+ if(is.data.frame(input$gen)){ # do not use names if these are the default names of a data.frame
+ if(identical(colnames(input$gen), paste("V", 1:ncol(input$gen), sep=""))){
+ input$loc.names <- NULL
+ }
+ }
+ }
+ ##input$gen <- lapply(1:nrow(input$gen), function(i) as.integer(input$gen[i,]))
+ if(parallel){
+ x at gen <- mclapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i,])),
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE)
+ } else {
+ x at gen <- lapply(1:nrow(input$gen), function(i) new("SNPbin", as.integer(input$gen[i,])) )
+ }
+ }
+
+
+ ## input$gen is a list of integers/numeric ##
+ if(is.list(input$gen) && !is.data.frame(input$gen) && all(sapply(input$gen, class) %in% c("integer","numeric"))){
+ ## check length consistency
+ lengthvec <- sapply(input$gen, length)
+
+ ## complete with NA is necessary
+ if(length(unique(lengthvec))>1) {
+ warning("Genotypes have variable length; completing shorter ones with NAs.")
+ for(i in 1:length(input$gen)){
+ input$gen[[i]] <- c(input$gen[[i]], rep(NA, max(lengthvec)-length(input$gen[[i]])))
+ }
+ }
+
+ ## name individuals if needed
+ if(is.null(input$ind.names)){
+ input$ind.names <- names(input$gen)
+ }
+
+ ## create SNPbin list
+ if(parallel){
+ x at gen <- mclapply(input$gen, function(e) new("SNPbin",e), mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE)
+ } else {
+ x at gen <- lapply(input$gen, function(e) new("SNPbin",e))
+ }
+ }
+
+
+ ## input$gen is a snp.matrix object ##
+ if(inherits(input$gen,"snp.matrix")){
+ if(!require(snpMatrix)){
+ cat("\nThe package snp.matrix is needed for this conversion.")
+ cat("\nTo install it, type:")
+ cat("\n source(\"http://bioconductor.org/biocLite.R\")")
+ cat("\n biocLite(\"snpMatrix\")\n")
+ x at gen <- NULL
+ } else {
+
+ ## function to convert one indiv
+ f1 <- function(x){
+ res <- as.integer(x)
+ res[res==0] <- NA
+ res <- res-1
+ return(new("SNPbin", as.integer(res), ploidy=2L))
+ }
+
+ ## create SNPbin list
+ if(parallel){
+ x at gen <- mclapply(1:nrow(input$gen), function(i) f1(input$gen[i,]), mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE)
+ } else {
+ x at gen <- lapply(1:nrow(input$gen), function(i) f1(input$gen[i,]))
+ }
+
+ ## handle names
+ if(is.null(input$ind.names)) {input$ind.names <- rownames(input$gen)}
+ if(is.null(input$loc.names)) {input$loc.names <- colnames(input$gen)}
+ }
+ }
+ }
+
+
+ if(length(x at gen) > 0) { # if non-emtpy object
+ ## HANDLE INPUT$IND.NAMES ##
+ if(!is.null(input$ind.names)){
+ input$ind.names <- as.character(input$ind.names)
+
+ ## check length consistency
+ if(length(input$ind.names) != nInd(x)){
+ warning("Inconsistent length for ind.names - storing this argument in @other.")
+ if(is.null(input$other)) {
+ input$other <- list(ind.names.wrong.length=input$ind.names)
+ } else {
+ input$other$ind.names.wrong.length <- input$ind.names
+ }
+
+ } else {
+ ## assign value to the output object
+ x at ind.names <- input$ind.names
+ ## ## name list and each SNPbin ## THIS DUPLICATES THE INFORMATION
+ ## names(x at gen) <- input$ind.names
+ ## for(i in 1:length(x at gen)){
+ ## x at gen[[i]]@label <- input$ind.names[i]
+ ## }
+
+ }
+
+
+ }
+
+
+ ## HANDLE INPUT$N.LOC ##
+ if(!is.null(input$n.loc)){ # n.loc is provided
+ input$n.loc <- as.integer(input$n.loc)
+
+ ## check length consistency
+ if(input$n.loc != nLoc(x at gen[[1]])) {
+ warning("Inconsistent number of loci (n.loc) - ignoring this argument.")
+ } else {
+ x at n.loc <- input$n.loc
+ }
+ } else { # n.loc is not provided
+ x at n.loc <- nLoc(x at gen[[1]])
+ }
+
+
+ ## HANDLE INPUT$PLOIDY ##
+ ## note: if not provided, @ploidy is NULL (saves some space)
+ if(!is.null(input$ploidy)){ # ploidy is provided
+ input$ploidy <- as.integer(input$ploidy)
+ input$ploidy <- rep(input$ploidy, length=length(x at gen))
+ x at ploidy <- input$ploidy
+ }
+
+
+ ## HANDLE INPUT$LOC.NAMES ##
+ if(!is.null(input$loc.names) && length(input$loc.names)>0){ # ploidy is provided
+ input$loc.names <- as.character(input$loc.names)
+
+ ## check length consistency
+ if(length(input$loc.names) != x at n.loc){ # if problem, store in @other
+ warning("Inconsistent length for loc.names - storing this argument in @other.")
+ if(is.null(input$other)) {
+ input$other <- list(loc.names.wrong.length=input$loc.names)
+ } else {
+ input$other$loc.names.wrong.length <- input$loc.names
+ }
+ } else {
+ x at loc.names <- input$loc.names
+ }
+ }
+
+
+ ## HANDLE INPUT$LOC.ALL ##
+ if(!is.null(input$loc.all) && length(input$loc.all)>0){ # ploidy is provided
+ input$loc.all <- as.character(input$loc.all)
+
+ ## check length consistency
+ if(length(input$loc.all) != x at n.loc){
+ warning("Inconsistent length for loc.all - storing this argument in @other.")
+ if(is.null(input$other)) {
+ input$other <- list(loc.all.wrong.length=input$loc.all)
+ } else {
+ input$other$loc.all.wrong.length <- input$loc.all
+ }
+ } else {
+ ## check string consistency (format is e.g. "a/t")
+ temp <- grep("^[[:alpha:]]{1}/[[:alpha:]]{1}$", input$loc.all)
+ if(any(! 1:nLoc(x at gen[[1]]) %in% temp)){ # if problem, store in @other
+ ## input$loc.all <- gsub("[[:space:]]","", input$loc.all)
+ warning("Miss-formed strings in loc.all (must be e.g. 'c/g') - storing this argument in @other.")
+ if(is.null(input$other)) {
+ input$other <- list(loc.all.misformed=input$loc.all)
+ } else {
+ input$other$loc.all.misformed <- input$loc.all
+ }
+ } else {
+ x at loc.all <- input$loc.all
+ }
+ }
+ }
+
+
+ ## HANDLE CHROMOSOME ##
+ if(!is.null(input$chromosome)){
+ if(length(input$chromosome) != x at n.loc) { # if wrong length, store in @other
+ warning("chromosome argument has inconsistent length - storing this argument in @other")
+ if(is.null(input$other)) {
+ input$other <- list(chromosome.wrong.length=input$chromosome)
+ } else {
+ input$other$chromosome.wrong.length <- input$chromosome
+ }
+ } else {
+ x at chromosome <- factor(input$chromosome)
+ }
+ }
+
+
+ ## HANDLE POSITION ##
+ if(!is.null(input$position)){
+ if(length(input$position) != x at n.loc) { # if wrong length, store in @other
+ warning("position argument has inconsistent length - storing this argument in @other")
+ if(is.null(input$other)) {
+ input$other <- list(position.wrong.length=input$position)
+ } else {
+ input$other$position.wrong.length <- input$position
+ }
+ } else {
+ x at position <- as.integer(input$position)
+ }
+ }
+
+
+ ## HANDLE INPUT$POP ##
+ if(!is.null(input$pop)){
+ ## check length consistency
+ if(length(input$pop) != nInd(x)){
+ warning("Inconsistent length for pop - ignoring this argument.")
+ if(is.null(input$other)) {
+ input$other <- list(pop.wrong.length=input$pop)
+ } else {
+ input$other$pop.wrong.length <- input$pop
+ }
+ } else {
+ x at pop <- factor(input$pop)
+ }
+ }
+
+ ## HANDLE INPUT$STRATA ##
+ if(!is.null(input$strata)){
+ ## check length consistency
+ if(nrow(input$strata) != nInd(x)){
+ warning("Inconsistent length for strata - ignoring this argument.")
+ if(is.null(input$other)) {
+ input$other <- list(strata.wrong.length=input$strata)
+ } else {
+ input$other$strata.wrong.length <- input$strata
+ }
+ } else {
+ # Make sure that the hierarchies are factors.
+ x at strata <- data.frame(lapply(input$strata, function(f) factor(f, unique(f))))
+ if(!is.null(x at ind.names)){
+ rownames(x at strata) <- x at ind.names
+ }
+ }
+ }
+ ## HANDLE INPUT$HIERARCHY ##
+ if (!is.null(x at strata) && !is.null(input$hierarchy)){
+
+ if (is.language(input$hierarchy)){
+ the_names <- all.vars(input$hierarchy)
+ if (all(the_names %in% names(x at strata))){
+ ## TODO: CHECK HIERARCHY HERE
+ x at hierarchy <- input$hierarchy
+ } else {
+ warning("hierarchy names do not match names of strata. Setting slot to NULL")
+ x at hierarchy <- NULL
+ }
+ } else {
+ warning("hierarchy must be a formula. Setting slot to NULL.")
+ x at hierarchy <- NULL
+ }
+ }
+
+
+ } # end if non-empty @gen
+
+
+ ## HANDLE INPUT$OTHER ##
+ if(!is.null(input$other)){
+ x at other <- input$other
+ }
+
+
+ ## RETURN OBJECT ##
+ names(x at gen) <- NULL # do not store ind.names twice
+ return(x)
+}) # end genlight constructor
+
+
+
+
+
+
+
+
+
+
+################################
+##
+## METHODS AND ACCESSORS
+##
+################################
+
+###############
+## show SNPbin
+###############
+setMethod ("show", "SNPbin", function(object){
+ cat("/// SNPBIN OBJECT /////////")
+ if(!is.null(object at label)) {
+ cat("\n", object at label)
+ }
+ cat("\n", format(nLoc(object), big.mark=","), "SNPs coded as bits, size:", format(object.size(object), units="auto"))
+ cat("\n Ploidy:", object at ploidy)
+ temp <- round(length(object at NA.posi)/nLoc(object) *100,2)
+ cat("\n ", length(object at NA.posi), " (", temp," %) missing data\n", sep="")
+}) # end show method
+
+
+
+
+
+#################
+## show genlight
+#################
+setMethod ("show", "genlight", function(object){
+ ## HEADER
+ cat(" /// GENLIGHT OBJECT /////////")
+ cat("\n\n //", format(nInd(object), big.mark=","), "genotypes, ",
+ format(nLoc(object), big.mark=","), "binary SNPs, size:", format(object.size(object), units="auto"))
+
+ temp <- sapply(object at gen, function(e) length(e at NA.posi))
+ if(length(temp>1)){
+ cat("\n ", sum(temp), " (", round((sum(temp)/(nInd(object)*nLoc(object))) *100,2)," %) missing data", sep="")
+ }
+
+ ## BASIC CONTENT
+ cat("\n\n // Basic content")
+ cat("\n @gen: list of", length(object at gen), "SNPbin")
+
+ if(!is.null(object at ploidy)){
+ ploidytxt <- paste("(range: ", paste(range(object at ploidy), collapse="-"), ")", sep="")
+ cat("\n @ploidy: ploidy of each individual ", ploidytxt)
+ }
+
+ ## OPTIONAL CONTENT
+ cat("\n\n // Optional content")
+ optional <- FALSE
+
+ if(!is.null(object at ind.names)){
+ optional <- TRUE
+ cat("\n @ind.names: ", length(object at ind.names), "individual labels")
+ }
+
+ if(!is.null(object at loc.names)){
+ optional <- TRUE
+ cat("\n @loc.names: ", length(object at loc.names), "locus labels")
+ }
+
+ if(!is.null(object at loc.all)){
+ optional <- TRUE
+ cat("\n @loc.all: ", length(object at loc.all), "alleles")
+ }
+
+ if(!is.null(object at chromosome)){
+ optional <- TRUE
+ cat("\n @chromosome: factor storing chromosomes of the SNPs")
+ }
+
+ if(!is.null(object at position)){
+ optional <- TRUE
+ cat("\n @position: integer storing positions of the SNPs")
+ }
+
+ if(!is.null(object at pop)){
+ optional <- TRUE
+ poptxt <- paste("(group size range: ", paste(range(table(object at pop)), collapse="-"), ")", sep="")
+ cat("\n @pop:", paste("population of each individual", poptxt))
+ }
+
+ if (!is.null(object at strata)){
+ optional <- TRUE
+ cat("\n @strata: ")
+ levs <- names(object at strata)
+ if (length(levs) > 6){
+ levs <- paste(paste(head(levs), collapse = ", "), "...", sep = ", ")
+ } else {
+ levs <- paste(levs, collapse = ", ")
+ }
+ cat("a data frame with", length(object at strata), "columns (", levs, ")")
+ }
+
+ if (!is.null(object at hierarchy)){
+ optional <- TRUE
+ cat("\n @hierarchy:", paste(object at hierarchy, collapse = ""))
+ }
+
+ if(!is.null(object at other)){
+ optional <- TRUE
+ cat("\n @other: ")
+ cat("a list containing: ")
+ cat(ifelse(is.null(names(object at other)), "elements without names", paste(names(object at other), collapse= " ")), "\n")
+ }
+
+ if(!optional) cat("\n - empty -")
+
+ cat("\n")
+}) # end show method
+
+
+
+
+
+
+############
+## accessors
+############
+
+## nLoc
+setMethod("nLoc","SNPbin", function(x,...){
+ return(x at n.loc)
+})
+
+setMethod("nLoc","genlight", function(x,...){
+ return(x at n.loc)
+})
+
+
+## nInd
+setMethod("nInd","genlight", function(x,...){
+ return(length(x at gen))
+})
+
+## nPop
+setMethod("nPop","genlight", function(x,...){
+ return(length(levels(pop(x))))
+})
+
+setMethod("dim", "genlight", function(x){
+ return(c(nInd(x), nLoc(x)))
+})
+
+## $
+setMethod("$","SNPbin",function(x,name) {
+ return(slot(x,name))
+})
+
+setMethod("$","genlight",function(x,name) {
+ return(slot(x,name))
+})
+
+
+setMethod("$<-","SNPbin",function(x,name,value) {
+ slot(x,name,check=TRUE) <- value
+ return(x)
+})
+
+setMethod("$<-","genlight",function(x,name,value) {
+ slot(x,name,check=TRUE) <- value
+ return(x)
+})
+
+
+## names
+setMethod("names", signature(x = "SNPbin"), function(x){
+ return(slotNames(x))
+})
+
+setMethod("names", signature(x = "genlight"), function(x){
+ return(slotNames(x))
+})
+
+
+## ploidy
+setMethod("ploidy","SNPbin", function(x,...){
+ return(x at ploidy)
+})
+
+setMethod("ploidy","genlight", function(x,...){
+ if(nInd(x)>0){
+ if(!is.null(x at ploidy)){
+ res <- x at ploidy
+ } else {
+ res <- sapply(x at gen, function(e) e at ploidy)
+ }
+ names(res) <- x at ind.names
+ return(res)
+ } else {
+ return(NULL)
+ }
+})
+
+
+setReplaceMethod("ploidy","SNPbin",function(x,value) {
+ if(is.null(value)){
+ slot(x, "ploidy", check=TRUE) <- value
+ return(x)
+ }
+ value <- as.integer(value)
+ if(any(value)<1) stop("Negative or null values provided")
+ if(any(is.na(value))) stop("NA values provided")
+ if(length(value)>1) warning("Several ploidy numbers provided; using only the first integer")
+ slot(x,"ploidy",check=TRUE) <- value[1]
+ return(x)
+})
+
+setReplaceMethod("ploidy","genlight",function(x,value) {
+ if(is.null(value)){
+ slot(x, "ploidy", check=TRUE) <- value
+ return(x)
+ }
+ value <- as.integer(value)
+ if(any(value)<1) stop("Negative or null values provided")
+ if(any(is.na(value))) stop("NA values provided")
+ if(length(value) == 1) value <- rep(value, length=nInd(x))
+ if(length(value) != nInd(x)) stop("Length of the provided vector does not match nInd(x)")
+ slot(x,"ploidy",check=TRUE) <- value
+ return(x)
+})
+
+
+## locNames
+setMethod("locNames","genlight", function(x,...){
+ ## if loc names provided, return them
+ if(!is.null(x at loc.names)) return(x at loc.names)
+
+ ## otherwise, look for position / alleles
+ if(!is.null(res <- position(x))){
+ if(!is.null(alleles(x))){
+ res <- paste(res, alleles(x), sep=".")
+ } else { # force position to be character
+ res <- as.character(res)
+ }
+ return(res)
+ }
+})
+
+
+setReplaceMethod("locNames","genlight",function(x,value) {
+ if(is.null(value)){
+ slot(x, "loc.names", check=TRUE) <- value
+ return(x)
+ }
+ if(length(value) != nLoc(x)) stop("Vector length does no match number of loci")
+ slot(x,"loc.names",check=TRUE) <- as.character(value)
+ return(x)
+})
+
+
+## indNames
+setMethod("indNames","genlight", function(x,...){
+ if(length(x at ind.names)==0) return(NULL)
+ return(x at ind.names)
+})
+
+
+setReplaceMethod("indNames","genlight",function(x,value) {
+ if(is.null(value)){
+ slot(x, "ind.names", check=TRUE) <- value
+ return(x)
+ }
+ value <- as.character(value)
+ if(length(value) != nInd(x)) stop("Vector length does no match number of individuals")
+ slot(x,"ind.names",check=TRUE) <- value
+ return(x)
+})
+
+## popNames
+setMethod("popNames","genlight", function(x,...){
+ if(length(levels(pop(x)))==0) return(NULL)
+ return(levels(pop(x)))
+})
+
+
+setReplaceMethod("popNames","genlight",function(x,value) {
+ if (is.null(value) || any(is.na(value))){
+ stop("Can't set population names to NULL or NA")
+ return(x)
+ }
+ value <- as.character(value)
+ if(length(value) != length(levels(pop(x)))){
+ stop("Vector length does no match number of populations")
+ }
+ levels(pop(x)) <- value
+ return(x)
+})
+
+## alleles
+setMethod("alleles","genlight", function(x,...){
+ if(length(x at loc.all)==0) return(NULL)
+ return(x at loc.all)
+})
+
+setReplaceMethod("alleles","genlight", function(x, value){
+ if(is.null(value)){
+ slot(x, "loc.all", check=TRUE) <- value
+ return(x)
+ }
+ value <- as.character(value)
+ if(length(value)!=nLoc(x)) stop("replacement vector must be of length nLoc(x)")
+ temp <- grep("^[[:alpha:]]{1}/[[:alpha:]]{1}$", value)
+ if(any(! 1:nLoc(x) %in% temp)) stop("Miss-formed strings in replacement (must be e.g. 'c/g')")
+ slot(x, "loc.all", check=TRUE) <- value
+ return(x)
+})
+
+
+## chromosome
+setGeneric("chromosome", function(x, ...) standardGeneric("chromosome"))
+setGeneric("chromosome<-", function(x, value) standardGeneric("chromosome<-"))
+setGeneric("chr", function(x,...) standardGeneric("chr"))
+setGeneric("chr<-", function(x, value) standardGeneric("chr<-"))
+
+setMethod("chromosome","genlight", function(x,...){
+ if(length(x at chromosome)==0) return(NULL)
+ return(x at chromosome)
+})
+
+setMethod("chr","genlight", function(x,...){
+ return(chromosome(x))
+})
+
+
+setReplaceMethod("chromosome","genlight",function(x,value) {
+ if(is.null(value)){
+ slot(x, "chromosome", check=TRUE) <- value
+ return(x)
+ }
+ if(length(value) != nLoc(x)) stop("Vector length does no match number of loci")
+ slot(x,"chromosome",check=TRUE) <- factor(value)
+ return(x)
+})
+
+setReplaceMethod("chr","genlight",function(x,value) {
+ chromosome(x) <- value
+ return(x)
+})
+
+
+
+## position
+setGeneric("position", function(x, ...) standardGeneric("position"))
+setGeneric("position<-", function(x, value) standardGeneric("position<-"))
+
+setMethod("position","genlight", function(x,...){
+ if(length(x at position)==0) return(NULL)
+ return(x at position)
+})
+
+
+setReplaceMethod("position","genlight",function(x,value) {
+ if(is.null(value)){
+ slot(x, "position", check=TRUE) <- value
+ return(x)
+ }
+ if(length(value) != nLoc(x)) stop("Vector length does no match number of loci")
+ slot(x,"position",check=TRUE) <- as.integer(value)
+ return(x)
+})
+
+
+
+## NA.posi
+setGeneric("NA.posi", function(x, ...) standardGeneric("NA.posi"))
+
+setMethod("NA.posi","SNPbin", function(x,...){
+ return(x at NA.posi)
+})
+
+setMethod("NA.posi","genlight", function(x,...){
+ res <- lapply(x at gen, function(e) e at NA.posi)
+ names(res) <- indNames(x)
+ return(res)
+})
+
+
+## pop
+setMethod("pop","genlight", function(x){
+ return(x at pop)
+})
+
+
+setReplaceMethod("pop","genlight",function(x,value) {
+ if(is.null(value) | length(value)==0){
+ slot(x, "pop", check=TRUE) <- NULL
+ return(x)
+ }
+ if(length(value) != nInd(x)) stop("Vector length does no match number of individuals")
+ slot(x,"pop", check=TRUE) <- factor(value)
+ return(x)
+})
+
+
+
+## other
+setMethod("other","genlight", function(x,...){
+ if(length(x at other)==0) return(NULL)
+ return(x at other)
+})
+
+
+setReplaceMethod("other","genlight",function(x,value) {
+ if( !is.null(value) && (!is.list(value) | is.data.frame(value)) ) {
+ value <- list(value)
+ }
+ slot(x,"other",check=TRUE) <- value
+ return(x)
+})
+
+
+
+
+
+
+
+
+###################
+##
+## CONVERSIONS
+##
+###################
+
+############
+## .bin2raw
+###########
+## each byte takes a value on [0,255]
+
+## function to code multiple SNPs on a byte
+## 8 combinations of SNPs can be coded onto a single byte (0->255)
+.bin2raw <- function(vecSnp){
+ ## handle missing data
+ NAposi <- which(is.na(vecSnp))
+ if(length(NAposi)>0){
+ vecSnp[is.na(vecSnp)] <- 0L
+ }
+
+
+ nbBytes <- length(vecSnp) %/% 8
+ if(length(vecSnp) %% 8 > 0) {nbBytes <- nbBytes +1}
+ ori.length <- length(vecSnp)
+ new.length <- 8*nbBytes
+ vecSnp <- c(vecSnp, rep(0, new.length-ori.length)) # fill the end with 0 of necessary
+
+
+ ## map info to bytes (0:255)
+ vecSnp <- as.integer(vecSnp)
+ ##vecRaw <- integer(nbBytes) # no longer needed - sending raw type directly
+ vecRaw <- raw(nbBytes)
+
+ vecRaw <- .C("binIntToBytes", vecSnp, length(vecSnp), vecRaw, nbBytes, PACKAGE="adegenet")[[3]]
+ ## vecraw <- sapply(seq(1, by=8, length=nbBytes), function(i) which(apply(SNPCOMB,1, function(e) all(temp[i:(i+7)]==e))) ) # old R version
+
+ ## return result
+ res <- list(snp=vecRaw, n.loc=as.integer(ori.length), NA.posi=as.integer(NAposi))
+ return(res)
+} # end .bin2raw
+
+
+
+
+
+
+###########
+## .raw2bin
+###########
+## convert vector of raw to 0/1 integers
+.raw2bin <- function(x){
+ if(!is.raw(x)) stop("x is not of class raw")
+ ## SNPCOMB <- as.matrix(expand.grid(rep(list(c(0,1)), 8)))
+ ## colnames(SNPCOMB) <- NULL
+ ## res <- unlist(lapply(as.integer(x), function(i) SNPCOMB[i+1,]))
+ res <- .C("bytesToBinInt", x, length(x), integer(length(x)*8), PACKAGE="adegenet")[[3]]
+ return(res)
+} # end .raw2bin
+
+
+#############
+## .SNPbin2int
+#############
+## convert SNPbin to integers (0/1/2...)
+.SNPbin2int <- function(x){
+ ##res <- lapply(x at snp, .raw2bin)
+ resSize <- length(x at snp[[1]])*8
+ res <- .C("bytesToInt", unlist(x at snp), length(x at snp[[1]]), length(x at snp), integer(resSize), as.integer(resSize), PACKAGE="adegenet")[[4]][1:nLoc(x)]
+ ##res <- lapply(res, function(e) e[1:x at n.loc])
+ ##res <- as.integer(Reduce("+", res))
+ if(length(x at NA.posi)>0){
+ res[x at NA.posi] <- NA
+ }
+ return(res)
+} # end .SNPbin2int
+
+
+
+
+
+
+#############
+## as methods
+#############
+## KLUDGE - needed for as.matrix.genlight to be dispatched correctly (R-2.12.1)
+setGeneric("as.matrix")
+
+
+## SNPbin/genlight -> other
+setAs("SNPbin", "integer", def=function(from){
+ res <- .SNPbin2int(from)
+ return(res)
+})
+
+
+as.integer.SNPbin <- function(x, ...){
+ return(as(x, "integer"))
+}
+
+
+setAs("genlight", "matrix", def=function(from){
+ res <- unlist(lapply(from at gen, as.integer))
+ res <- matrix(res, ncol=nLoc(from), nrow=nInd(from), byrow=TRUE)
+ colnames(res) <- locNames(from)
+ ## if(!is.null(alleles(from))){
+ ## colnames(res) <- paste(locNames(from), alleles(from), sep=ifelse(is.null(locNames(from)), "", "."))
+ ## }
+ rownames(res) <- indNames(from)
+ return(res)
+})
+
+
+as.matrix.genlight <- function(x, ...){
+ return(as(x, "matrix"))
+}
+
+
+setAs("genlight", "data.frame", def=function(from){
+ return(as.data.frame(as.matrix(from)))
+})
+
+
+as.data.frame.genlight <- function(x, ...){
+ return(as(x, "data.frame"))
+}
+
+
+setAs("genlight", "list", def=function(from){
+ res <- lapply(from at gen, as.integer)
+ names(res) <- indNames(from)
+ return(res)
+})
+
+
+as.list.genlight <- function(x, ...){
+ return(as(x, "list"))
+}
+
+
+
+
+## other -> SNPbin/genlight
+setGeneric("as.SNPbin", function(x, ...) standardGeneric("as.SNPbin"))
+setGeneric("as.genlight", function(x, ...) standardGeneric("as.genlight"))
+
+setAs("integer", "SNPbin", def=function(from){
+ res <- new("SNPbin", from)
+ return(res)
+})
+
+setAs("numeric", "SNPbin", def=function(from){
+ res <- new("SNPbin", from)
+ return(res)
+})
+
+
+setMethod("as.SNPbin", "integer", function(x, ...) as(x, "SNPbin"))
+setMethod("as.SNPbin", "numeric", function(x, ...) as(x, "SNPbin"))
+
+
+setAs("matrix", "genlight", def=function(from){
+ return(new("genlight", from))
+})
+
+
+setAs("data.frame", "genlight", def=function(from){
+ return(new("genlight", from))
+})
+
+
+setAs("list", "genlight", def=function(from){
+ return(new("genlight", from))
+})
+
+
+## setAs("snp.matrix", "genlight", def=function(from){
+## return(new("genlight", from))
+## })
+
+
+
+
+setMethod("as.genlight", "matrix", function(x, ...) as(x, "genlight"))
+setMethod("as.genlight", "data.frame", function(x, ...) as(x, "genlight"))
+setMethod("as.genlight", "list", function(x, ...) as(x, "genlight"))
+## setMethod("as.genlight", "snp.matrix", function(x, ...) as(x, "genlight"))
+
+
+
+
+
+
+################################
+## testing SNPbin
+##
+##
+## library(adegenet)
+## dat <- c(1,0,0,1,0,NA,1,0,0,0,0,1)
+## x <- new("SNPbin",dat)
+## as.integer(x)
+
+
+## HAPLOID DATA - NO NA
+## dat <- sample(c(0L,1L), 1e6, replace=TRUE)
+## x <- new("SNPbin", dat)
+## identical(as(x, "integer"),dat) # SHOULD NORMALLY BE TRUE
+## all(as(x, "integer") == dat, na.rm=TRUE) # MUST BE TRUE
+## object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
+
+
+## HAPLOID DATA - WITH NAs
+## dat <- sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE)
+## x <- new("SNPbin", dat)
+## identical(as(x, "integer"),dat) # SHOULD NORMALLY BE TRUE
+## all(as(x, "integer") == dat, na.rm=TRUE) # MUST BE TRUE
+## object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
+
+
+
+ ## DIPLOID DATA
+## dat <- sample(c(0:2,NA), 1e6, prob=c(.4, .4, .195 ,.005), replace=TRUE)
+## x <- new("SNPbin", dat)
+
+## identical(as(x, "integer"),dat) # MUST BE TRUE
+
+## object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
+
+
+
+ ## POLYLOID DATA
+## dat <- sample(c(0:5,NA), 1e6, prob=c(rep(.995/6,6), 0.005), replace=TRUE)
+## x <- new("SNPbin", dat)
+
+## identical(as(x, "integer"),dat) # MUST BE TRUE
+
+## object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
+
+
+
+
+################################
+## testing genlight
+##
+##
+
+
+## SIMPLE TESTS
+## dat <- c(1,0,0,1,0,0,1,1,1,0,1)
+## x <- new("SNPbin",dat)$snp[[1]]
+## as.integer(x)==dat
+
+
+## library(adegenet)
+## dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA))
+## x <- new("genlight", dat)
+## x
+## as.list(x)
+## as.matrix(x)
+
+## identical(x, new("genlight", as.list(x))) # round trip - list - MUST BE TRUE
+## identical(x, new("genlight", as.matrix(x))) # round trip - matrix - MUST BE TRUE
+## identical(x, new("genlight", as.data.frame(x))) # round trip - data.frame - MUST BE TRUE
+
+## ## test subsetting
+## identical(as.list(x[c(1,3)]), as.list(x)[c(1,3)]) # MUST BE TRUE
+## identical(x, x[]) # MUST BE TRUE
+## all.equal(t(as.matrix(as.data.frame(dat)))[,1:3], as.matrix(x[,1:3])) # MUST BE TRUE
+
+
+
+
+## ## ## BIG SCALE TEST - HAPLOID DATA WITH NA
+## library(adegenet)
+## dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE))
+## names(dat) <- paste("indiv", 1:length(dat))
+## print(object.size(dat), unit="aut")
+
+## system.time(x <- new("genlight", dat)) # conversion + time taken
+## print(object.size(x), unit="au")
+## object.size(dat)/object.size(x) # conversion efficiency
+
+
+## ## time taken by subsetting (quite long, +- 35sec)
+## system.time(y <- x[1:10, 1:5e5])
+
+
+
+## c, cbind, rbind ##
+## a <- new("genlight", list(c(1,0,1), c(0,0,1,0)) )
+## b <- new("genlight", list(c(1,0,1,1,1,1), c(1,0)) )
+## locNames(a) <- letters[1:4]
+## locNames(b) <- 1:6
+## c <- cbind(a,b)
+## identical(as.matrix(c),cbind(as.matrix(a), as.matrix(b))) # MUST BE TRUE
+## identical(as.matrix(rbind(a,a)),rbind(as.matrix(a),as.matrix(a)))
+
+
+
+
+## test subsetting with/without @other ##
+## x <- new("genlight", list(a=1,b=0,c=1), other=list(1:3, letters, data.frame(2:4)))
+## pop(x) <- c("pop1","pop1", "pop2")
diff --git a/R/accessors.R b/R/accessors.R
new file mode 100644
index 0000000..3d557f6
--- /dev/null
+++ b/R/accessors.R
@@ -0,0 +1,409 @@
+#######
+# nLoc
+#######
+setGeneric("nLoc", function(x,...){
+ standardGeneric("nLoc")
+})
+
+
+
+# setMethod("nLoc","genind", function(x,...){
+# if (x at type == "PA"){
+# return(ncol(x at tab))
+# } else {
+# return(length(levels(x at loc.fac)))
+# }
+# })
+#
+#
+#
+# setMethod("nLoc","genpop", function(x,...){
+# if (x at type == "PA"){
+# return(ncol(x at tab))
+# } else {
+# return(length(levels(x at loc.fac)))
+# }
+#
+# })
+
+setMethod("nLoc","gen", function(x,...){
+ if (x at type == "PA"){
+ return(ncol(x at tab))
+ } else {
+ return(length(levels(x at loc.fac)))
+ }
+})
+
+setMethod("nLoc", "genind", function(x, ...){
+ callNextMethod()
+})
+
+setMethod("nLoc", "genpop", function(x, ...){
+ callNextMethod()
+})
+
+#########
+# locFac
+#########
+setGeneric("locFac", function(x, ...){
+ standardGeneric("locFac")
+})
+
+setMethod("locFac","gen", function(x,...){
+ return(x at loc.fac)
+})
+
+setMethod("locFac","genind", function(x,...){
+ callNextMethod()
+})
+
+setMethod("locFac","genpop", function(x,...){
+ callNextMethod()
+})
+
+
+#######
+# nAll
+#######
+setGeneric("nAll", function(x,...){
+ standardGeneric("nAll")
+})
+
+
+setMethod("nAll","gen", function(x,...){
+ if (x at type == "PA"){
+ return(ncol(x at tab))
+ } else {
+ return(x at loc.n.all)
+ }
+})
+
+setMethod("nAll","genind", function(x,...){
+ callNextMethod()
+})
+
+setMethod("nAll","genpop", function(x,...){
+ callNextMethod()
+})
+
+
+#######
+# nPop (no gen method)
+#######
+setGeneric("nPop", function(x,...){
+ standardGeneric("nPop")
+})
+
+setMethod("nPop","genind", function(x,...){
+ return(length(levels(x at pop)))
+})
+
+setMethod("nPop","genpop", function(x,...){
+ return(nrow(x at tab))
+})
+
+
+#######
+# nInd (no gen method)
+#######
+setGeneric("nInd", function(x,...){
+ standardGeneric("nInd")
+})
+
+
+
+setMethod("nInd","genind", function(x,...){
+ return(nrow(x at tab))
+})
+
+
+
+
+
+######
+# pop (no gen method)
+######
+setGeneric("pop", function(x) {
+ standardGeneric("pop")
+})
+
+
+
+setGeneric("pop<-",
+ function(x, value) {
+ standardGeneric("pop<-")
+ })
+
+
+
+setMethod("pop","genind", function(x){
+ return(x at pop)
+})
+
+
+
+setReplaceMethod("pop", "genind", function(x, value) {
+ if(is.null(value)){
+ x at pop <- NULL
+ return(x)
+ }
+
+ if(length(value) != nrow(x$tab)) stop("wrong length for population factor")
+
+ ## coerce to factor (put levels in their order of appearance)
+ newPop <- as.character(value)
+ newPop <- factor(newPop, levels=unique(newPop))
+
+ ## construct output
+ x$pop <- newPop
+
+ return(x)
+})
+
+
+
+
+
+###########
+# locNames
+###########
+setGeneric("locNames", function(x,...){
+ standardGeneric("locNames")
+})
+
+setGeneric("locNames<-", function(x, value) {
+ standardGeneric("locNames<-")
+})
+
+
+setMethod("locNames","gen", function(x, withAlleles=FALSE, ...){
+ if (withAlleles){
+ res <- colnames(x at tab)
+ } else {
+ res <- unique(sub("[.][^.]*$","",colnames(x at tab)))
+ }
+ return(res)
+})
+
+
+setReplaceMethod("locNames","gen",function(x,value) {
+ ## check input
+ value <- as.character(value)
+ if(length(value) != nLoc(x)) stop("Vector length does no match number of loci")
+
+ ## make changes in the object
+ names(x at all.names) <- value
+ levels(x at loc.fac) <- value
+ names(x at loc.n.all) <- value
+ newColNames <- paste(rep(value, x at loc.n.all), unlist(x at all.names), sep=".")
+ colnames(x at tab) <- newColNames
+
+ ## return
+ return(x)
+})
+
+
+setMethod("locNames","genpop", function(x, withAlleles=FALSE, ...){
+ callNextMethod()
+})
+setReplaceMethod("locNames", "genpop", function(x, value) {
+ callNextMethod()
+})
+
+
+setMethod("locNames","genind", function(x, withAlleles=FALSE, ...){
+ callNextMethod()
+})
+setReplaceMethod("locNames", "genind", function(x, value) {
+ callNextMethod()
+})
+
+
+###########
+# indNames (no gen method)
+###########
+setGeneric("indNames", function(x,...){
+ standardGeneric("indNames")
+})
+
+setGeneric("indNames<-", function(x, value){
+ standardGeneric("indNames<-")
+})
+
+setMethod("indNames","genind", function(x, ...){
+ return(rownames(x at tab))
+})
+
+
+setReplaceMethod("indNames","genind",function(x,value) {
+ if(length(value) != nrow(x at tab)) stop("Vector length does not match number of individuals")
+ rownames(x at tab) <- as.character(value)
+ return(x)
+})
+
+###########
+# popNames (no gen method)
+###########
+setGeneric("popNames", function(x,...){
+ standardGeneric("popNames")
+})
+
+setGeneric("popNames<-", function(x, value){
+ standardGeneric("popNames<-")
+})
+
+setMethod("popNames","genind", function(x, ...){
+ return(levels(pop(x)))
+})
+
+
+setReplaceMethod("popNames","genind",function(x, value) {
+ value <- as.character(value)
+ if(length(value) != length(levels(pop(x)))){
+ stop("Vector length does not match number of populations")
+ }
+ levels(pop(x)) <- value
+ return(x)
+})
+
+setMethod("popNames","genpop", function(x, ...){
+ return(rownames(x at tab))
+})
+
+
+setReplaceMethod("popNames","genpop",function(x, value) {
+ value <- as.character(value)
+ if (length(value) != nrow(x at tab)){
+ stop("Vector length does not match number of populations")
+ }
+ rownames(x at tab) <- value
+ return(x)
+})
+
+
+##########
+# alleles
+##########
+setGeneric("alleles", function(x,...){
+ standardGeneric("alleles")
+})
+
+setGeneric("alleles<-", function(x, value){
+ standardGeneric("alleles<-")
+})
+
+setMethod("alleles","gen", function(x, ...){
+ return(x at all.names)
+})
+
+setReplaceMethod("alleles","gen", function(x, value){
+ if(!is.list(value)) stop("replacement value must be a list")
+ if(length(value)!=nLoc(x)) stop("replacement list must be of length nLoc(x)")
+ if(any(sapply(value, length) != x$loc.n.all)) stop("number of replacement alleles do not match that of the object")
+ x at all.names <- value
+ names(x at all.names) <- locNames(x)
+ return(x)
+})
+
+setMethod("alleles","genind", function(x, ...){
+ callNextMethod()
+})
+setReplaceMethod("alleles","genind", function(x, value){
+ callNextMethod()
+})
+
+setMethod("alleles","genpop", function(x, ...){
+ callNextMethod()
+})
+setReplaceMethod("alleles","genpop", function(x, value){
+ callNextMethod()
+})
+
+
+
+##########
+## ploidy (no gen method)
+##########
+setGeneric("ploidy", function(x,...){
+ standardGeneric("ploidy")
+})
+
+setGeneric("ploidy<-", function(x, value){
+ standardGeneric("ploidy<-")
+})
+
+setMethod("ploidy","genind", function(x,...){
+ return(x at ploidy)
+})
+
+
+setReplaceMethod("ploidy","genind",function(x,value) {
+ value <- as.integer(value)
+ if(any(value)<1) stop("Negative or null values provided")
+ if(any(is.na(value))) stop("NA values provided")
+ if(length(value)!=nInd(x)) value <- rep(value, length=nInd(x))
+ slot(x,"ploidy",check=TRUE) <- value
+ return(x)
+})
+
+
+setMethod("ploidy","genpop", function(x,...){
+ return(x at ploidy)
+})
+
+
+setReplaceMethod("ploidy","genpop",function(x,value) {
+ value <- as.integer(value)
+ if(any(value)<1) stop("Negative or null values provided")
+ if(any(is.na(value))) stop("NA values provided")
+ if(length(value)>1) warning("Several ploidy numbers provided; using only the first integer")
+ slot(x,"ploidy",check=TRUE) <- value[1]
+ return(x)
+})
+
+
+
+
+
+
+##########
+## other
+#########
+setGeneric("other", function(x,...){
+ standardGeneric("other")
+})
+
+setGeneric("other<-", function(x, value){
+ standardGeneric("other<-")
+})
+
+setMethod("other","gen", function(x,...){
+ if(length(x at other)==0) return(NULL)
+ return(x at other)
+})
+
+
+setReplaceMethod("other","gen",function(x,value) {
+ if( !is.null(value) && (!is.list(value) | is.data.frame(value)) ) {
+ value <- list(value)
+ }
+ slot(x,"other",check=TRUE) <- value
+ return(x)
+})
+
+
+setMethod("other","genind", function(x,...){
+ callNextMethod()
+})
+setReplaceMethod("other","genind",function(x,value) {
+ callNextMethod()
+})
+
+setMethod("other","genpop", function(x,...){
+ callNextMethod()
+})
+setReplaceMethod("other","genpop",function(x,value) {
+ callNextMethod()
+})
+
+
diff --git a/R/adegenet.package.R b/R/adegenet.package.R
new file mode 100644
index 0000000..303aaba
--- /dev/null
+++ b/R/adegenet.package.R
@@ -0,0 +1,300 @@
+#' The adegenet package
+#'
+#'
+#' This package is devoted to the multivariate analysis of genetic markers
+#' data. These data can be codominant markers (e.g. microsatellites) or
+#' presence/absence data (e.g. AFLP), and have any level of ploidy. 'adegenet'
+#' defines three formal (S4) classes:\cr - \linkS4class{genind}: a class for
+#' data of individuals ("genind" stands for genotypes-individuals).\cr -
+#' \linkS4class{genpop}: a class for data of groups of individuals ("genpop"
+#' stands for genotypes-populations)\cr - \linkS4class{genlight}: a class for
+#' genome-wide SNP data\cr
+#'
+#' For more information about these classes, type "class ? genind", "class ?
+#' genpop", or "?genlight".\cr
+#'
+#' Essential functionalities of the package are presented througout 4
+#' tutorials, accessible using \code{adegenetTutorial(which="name-below")}:\cr
+#' - \code{basics}: introduction to the package.\cr - \code{spca}: multivariate
+#' analysis of spatial genetic patterns.\cr - \code{dapc}: population structure
+#' and group assignment using DAPC.\cr - \code{genomics}: introduction to the
+#' class \linkS4class{genlight} for the handling and analysis of genome-wide
+#' SNP data.\cr
+#'
+#' Note: In older versions of adegenet, these tutorials were avilable as
+#' vignettes, accessible through the function \code{vignette("name-below",
+#' package="adegenet")}:\cr - \code{adegenet-basics}.\cr -
+#' \code{adegenet-spca}.\cr - \code{adegenet-dapc}.\cr -
+#' \code{adegenet-genomics}.\cr
+#'
+#' Important functions are also summarized below.\cr
+#'
+#' === IMPORTING DATA ===\cr = TO GENIND OBJECTS = \cr \code{adegenet} imports
+#' data to \linkS4class{genind} object from the following softwares:\cr -
+#' STRUCTURE: see \code{\link{read.structure}}\cr - GENETIX: see
+#' \code{\link{read.genetix}}\cr - FSTAT: see \code{\link{read.fstat}}\cr -
+#' Genepop: see \code{\link{read.genepop}}\cr To import data from any of these
+#' formats, you can also use the general function
+#' \code{\link{import2genind}}.\cr
+#'
+#' In addition, it can extract polymorphic sites from nucleotide and amino-acid
+#' alignments:\cr - DNA files: use \code{\link[ape]{read.dna}} from the ape
+#' package, and then extract SNPs from DNA alignments using
+#' \code{\link{DNAbin2genind}}. \cr
+#'
+#' - protein sequences alignments: polymorphic sites can be extracted from
+#' protein sequences alignments in \code{alignment} format (package
+#' \code{seqinr}, see \code{\link[seqinr]{as.alignment}}) using the function
+#' \code{\link{alignment2genind}}. \cr
+#'
+#' The function \code{\link{fasta2DNAbin}} allows for reading fasta files into
+#' DNAbin object with minimum RAM requirements.\cr
+#'
+#' It is also possible to read genotypes coded by character strings from a
+#' data.frame in which genotypes are in rows, markers in columns. For this, use
+#' \code{\link{df2genind}}. Note that \code{\link{df2genind}} can be used for
+#' any level of ploidy.\cr
+#'
+#' = TO GENLIGHT OBJECTS = \cr SNP data can be read from the following
+#' formats:\cr - PLINK: see function \code{\link{read.PLINK}}\cr - .snp
+#' (adegenet's own format): see function \code{\link{read.snp}}\cr
+#'
+#' SNP can also be extracted from aligned DNA sequences with the fasta format,
+#' using \code{\link{fasta2genlight}}\cr
+#'
+#' === EXPORTING DATA ===\cr \code{adegenet} exports data from
+#'
+#' Genotypes can also be recoded from a \linkS4class{genind} object into a
+#' data.frame of character strings, using any separator between alleles. This
+#' covers formats from many softwares like GENETIX or STRUCTURE. For this, see
+#' \code{\link{genind2df}}.\cr
+#'
+#' Also note that the \code{pegas} package imports \linkS4class{genind} objects
+#' using the function \code{as.loci}.
+#'
+#' === MANIPULATING DATA ===\cr Several functions allow one to manipulate
+#' \linkS4class{genind} or \linkS4class{genpop} objects\cr -
+#' \code{\link{genind2genpop}}: convert a \linkS4class{genind} object to a
+#' \linkS4class{genpop} \cr - \code{\link{seploc}}: creates one object per
+#' marker; for \linkS4class{genlight} objects, creates blocks of SNPs.\cr -
+#' \code{\link{seppop}}: creates one object per population \cr -
+#' - \code{\link{tab}}: access the allele data (counts or frequencies) of an object
+#' (\linkS4class{genind} and \linkS4class{genpop}) \cr -
+#' x[i,j]: create a new object keeping only genotypes (or populations) indexed
+#' by 'i' and the alleles indexed by 'j'.\cr - \code{\link{makefreq}}: returns
+#' a table of allelic frequencies from a \linkS4class{genpop} object.\cr -
+#' \code{\link{repool}} merges genoptypes from different gene pools into one
+#' single \linkS4class{genind} object.\cr - \code{\link{propTyped}} returns the
+#' proportion of available (typed) data, by individual, population, and/or
+#' locus.\cr - \code{\link{selPopSize}} subsets data, retaining only genotypes
+#' from a population whose sample size is above a given level.\cr -
+#' \code{\link{pop}} sets the population of a set of genotypes.\cr
+#'
+#' === ANALYZING DATA ===\cr Several functions allow to use usual, and less
+#' usual analyses:\cr - \code{\link{HWE.test.genind}}: performs HWE test for
+#' all populations and loci combinations \cr - \code{\link{dist.genpop}}: computes 5 genetic distances among populations.
+#' \cr - \code{\link{monmonier}}: implementation of the Monmonier algorithm,
+#' used to seek genetic boundaries among individuals or populations. Optimized
+#' boundaries can be obtained using \code{\link{optimize.monmonier}}. Object of
+#' the class \code{monmonier} can be plotted and printed using the
+#' corresponding methods. \cr - \code{\link{spca}}: implements Jombart et al.
+#' (2008) spatial Principal Component Analysis \cr -
+#' \code{\link{global.rtest}}: implements Jombart et al. (2008) test for global
+#' spatial structures \cr - \code{\link{local.rtest}}: implements Jombart et
+#' al. (2008) test for local spatial structures \cr - \code{\link{propShared}}:
+#' computes the proportion of shared alleles in a set of genotypes (i.e. from a
+#' genind object)\cr - \code{\link{propTyped}}: function to investigate missing
+#' data in several ways \cr - \code{\link{scaleGen}}: generic method to scale
+#' \linkS4class{genind} or \linkS4class{genpop} before a principal component
+#' analysis \cr - \code{\link{Hs}}: computes the average expected
+#' heterozygosity by population in a \linkS4class{genpop}. Classically Used as
+#' a measure of genetic diversity.\cr - \code{\link{find.clusters}} and
+#' \code{\link{dapc}}: implement the Discriminant Analysis of Principal
+#' Component (DAPC, Jombart et al., 2010).\cr - \code{\link{seqTrack}}:
+#' implements the SeqTrack algorithm for recontructing transmission trees of
+#' pathogens (Jombart et al., 2010) .\cr \code{\link{glPca}}: implements PCA
+#' for \linkS4class{genlight} objects.\cr - \code{\link{gengraph}}: implements
+#' some simple graph-based clustering using genetic data. -
+#' \code{\link{snpposi.plot}} and \code{\link{snpposi.test}}: visualize the
+#' distribution of SNPs on a genetic sequence and test their randomness. -
+#' \code{\link{adegenetServer}}: opens up a web interface for some
+#' functionalities of the package (DAPC with cross validation and feature
+#' selection).\cr
+#'
+#' === GRAPHICS ===\cr - \code{\link{colorplot}}: plots points with associated
+#' values for up to three variables represented by colors using the RGB system;
+#' useful for spatial mapping of principal components.\cr -
+#' \code{\link{loadingplot}}: plots loadings of variables. Useful for
+#' representing the contribution of alleles to a given principal component in a
+#' multivariate method. \cr - \code{\link{scatter.dapc}}: scatterplots for DAPC
+#' results.\cr - \code{\link{compoplot}}: plots membership probabilities from a
+#' DAPC object. \cr
+#'
+#' === SIMULATING DATA ===\cr - \code{\link{hybridize}}: implements
+#' hybridization between two populations. \cr - \code{\link{haploGen}}:
+#' simulates genealogies of haplotypes, storing full genomes. \cr
+#' \code{\link{glSim}}: simulates simple \linkS4class{genlight} objects.\cr
+#'
+#' === DATASETS ===\cr - \code{\link{H3N2}}: Seasonal influenza (H3N2) HA
+#' segment data. \cr - \code{\link{dapcIllus}}: Simulated data illustrating the
+#' DAPC. \cr - \code{\link{eHGDP}}: Extended HGDP-CEPH dataset. \cr -
+#' \code{\link{microbov}}: Microsatellites genotypes of 15 cattle breeds. \cr -
+#' \code{\link{nancycats}}: Microsatellites genotypes of 237 cats from 17
+#' colonies of Nancy (France). \cr - \code{\link{rupica}}: Microsatellites
+#' genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains
+#' (France).\cr - \code{\link{sim2pop}}: Simulated genotypes of two
+#' georeferenced populations.\cr - \code{\link{spcaIllus}}: Simulated data
+#' illustrating the sPCA. \cr
+#'
+#' For more information, visit the adegenet website using the function
+#' \code{\link{adegenetWeb}}.\cr
+#'
+#' Tutorials are available via the command \code{adegenetTutorial}.\cr
+#'
+#' To cite adegenet, please use the reference given by
+#' \code{citation("adegenet")} (or see references below).
+#'
+#' @name adegenet.package
+#' @encoding utf-8
+#' @aliases adegenet.package adegenet
+#' @docType package
+#' @author Thibaut Jombart <t.jombart@@imperial.ac.uk>\cr
+#' Developers: Zhian N. Kamvar <zkamvar@@gmail.com>,
+#' Caitlin Collins <caitiecollins17@@gmail.com>,
+#' Ismail Ahmed <ismail.ahmed@@inserm.fr>,
+#' Federico Calboli, Tobias Erik Reiners, Peter
+#' Solymos, Anne Cori, \cr Contributed datasets from: Katayoun
+#' Moazami-Goudarzi, Denis Laloë, Dominique Pontier, Daniel Maillard, Francois
+#' Balloux.
+#' @seealso adegenet is related to several packages, in particular:\cr -
+#' \code{ade4} for multivariate analysis\cr - \code{pegas} for population
+#' genetics tools\cr - \code{ape} for phylogenetics and DNA data handling\cr -
+#' \code{seqinr} for handling nucleic and proteic sequences\cr - \code{shiny}
+#' for R-based web interfaces\cr
+#' @references Jombart T. (2008) adegenet: a R package for the multivariate
+#' analysis of genetic markers \emph{Bioinformatics} 24: 1403-1405. doi:
+#' 10.1093/bioinformatics/btn129\cr
+#'
+#' Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of
+#' genome-wide SNP data. \emph{Bioinformatics}. doi:
+#' 10.1093/bioinformatics/btr521
+#'
+#' Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+#' principal components: a new method for the analysis of genetically
+#' structured populations. BMC Genetics 11:94. doi:10.1186/1471-2156-11-94\cr
+#'
+#' Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease outbreaks
+#' from genetic data: a graph approach. \emph{Heredity}. doi:
+#' 10.1038/hdy.2010.78.\cr
+#'
+#' Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. (2008) Revealing
+#' cryptic spatial patterns in genetic variability by a new multivariate
+#' method. \emph{Heredity}, \bold{101}, 92--103.\cr
+#'
+#' See adegenet website: \url{http://adegenet.r-forge.r-project.org/}\cr
+#'
+#' Please post your questions on 'the adegenet forum':
+#' adegenet-forum@@lists.r-forge.r-project.org
+#' @keywords manip multivariate
+#'
+#' @exportPattern "^[^\\.]"
+#'
+#' @export .rmspaces .readExt .genlab .render.server.info
+#'
+#' @S3method as.POSIXct haploGen
+#' @S3method as.data.frame genind
+#' @S3method as.data.frame genlight
+#' @S3method as.data.frame genpop
+#' @S3method as.integer SNPbin
+#' @S3method as.lda dapc
+#' @S3method as.list genlight
+#' @S3method as.matrix genind
+#' @S3method as.matrix genlight
+#' @S3method as.matrix genpop
+#' @S3method c SNPbin
+#' @S3method colorplot default
+#' @S3method colorplot spca
+#' @S3method dapc data.frame
+#' @S3method dapc dudi
+#' @S3method dapc genind
+#' @S3method dapc genlight
+#' @S3method dapc matrix
+#' @S3method find.clusters data.frame
+#' @S3method find.clusters genind
+#' @S3method find.clusters genlight
+#' @S3method find.clusters matrix
+#' @S3method findMutations DNAbin
+#' @S3method gengraph DNAbin
+#' @S3method gengraph default
+#' @S3method gengraph dist
+#' @S3method gengraph genind
+#' @S3method gengraph genpop
+#' @S3method gengraph matrix
+#' @S3method get.likelihood seqTrack
+#' @S3method graphMutations DNAbin
+#' @S3method labels haploGen
+#' @S3method loadingplot default
+#' @S3method loadingplot glPca
+#' @S3method pairDistPlot DNAbin
+#' @S3method pairDistPlot default
+#' @S3method pairDistPlot dist
+#' @S3method pairDistPlot genind
+#' @S3method pairDistPlot matrix
+#' @S3method plot haploGen
+#' @S3method plot monmonier
+#' @S3method plot seqTrack
+#' @S3method plot spca
+#' @S3method predict dapc
+#' @S3method print dapc
+#' @S3method print glPca
+#' @S3method print haploGen
+#' @S3method print monmonier
+#' @S3method print spca
+#' @S3method scatter dapc
+#' @S3method scatter glPca
+#' @S3method screeplot spca
+#' @S3method seqTrack default
+#' @S3method seqTrack haploGen
+#' @S3method seqTrack matrix
+#' @S3method snpposi.plot DNAbin
+#' @S3method snpposi.plot integer
+#' @S3method snpposi.plot numeric
+#' @S3method snpposi.test DNAbin
+#' @S3method snpposi.test integer
+#' @S3method snpposi.test numeric
+#' @S3method summary dapc
+#' @S3method summary spca
+#' @S3method print genindSummary
+#' @S3method print genpopSummary
+#'
+#' @import methods
+#'
+#' @import parallel
+#'
+#' @import utils
+#'
+#' @import stats
+#'
+#' @import graphics
+#'
+#' @import grDevices
+#'
+#' @import ade4
+#'
+#' @importFrom seqinr s2c
+#'
+#' @importFrom MASS "lda"
+#'
+#' @importFrom ape "as.character.DNAbin" "as.DNAbin" "as.DNAbin.alignment" "as.DNAbin.character" "as.DNAbin.list" "as.list.DNAbin" "as.matrix.DNAbin" "cbind.DNAbin" "c.DNAbin" "[.DNAbin" "labels.DNAbin" "print.DNAbin" "rbind.DNAbin" "dist.dna" "seg.sites"
+#'
+#' @importFrom igraph "graph.data.frame" "V" "V<-" "E" "E<-" "layout.fruchterman.reingold" "as.igraph" "plot.igraph" "print.igraph" "graph.adjacency" "clusters"
+#'
+#' @importFrom shiny "runApp" "renderPrint"
+#'
+#' @importFrom ggplot2 "ggplot" "geom_density" "geom_rug" "labs" "aes" "xlim" "guides" "guide_legend" "geom_boxplot" "geom_violin" "geom_jitter" "coord_flip"
+#'
+#' @useDynLib adegenet
+#'
+
+
+NULL
diff --git a/R/auxil.R b/R/auxil.R
new file mode 100644
index 0000000..6250ecb
--- /dev/null
+++ b/R/auxil.R
@@ -0,0 +1,386 @@
+###########################
+#
+# Auxiliary functions for
+# adegenet objects
+#
+# T. Jombart
+###########################
+
+
+#######################
+# Function rmspaces
+#######################
+# removes spaces and tab at the begining and the end of each element of charvec
+.rmspaces <- function(charvec){
+ charvec <- gsub("^([[:blank:]]*)([[:space:]]*)","",charvec)
+ charvec <- gsub("([[:blank:]]*)([[:space:]]*)$","",charvec)
+ return(charvec)
+}
+
+
+
+
+
+###################
+# Function readExt
+###################
+.readExt <- function(char){
+ temp <- as.character(char)
+ temp <- unlist(strsplit(char,"[.]"))
+ res <- temp[length(temp)]
+ return(res)
+}
+
+
+
+
+
+###################
+# Function .genlab
+###################
+# recursive function to have labels of constant length
+# base = a character string
+# n = number of labels
+.genlab <- function(base, n) {
+ f1 <- function(cha,n){
+ if(nchar(cha)<n){
+ cha <- paste("0",cha,sep="")
+ return(f1(cha,n))
+ } else {return(cha)}
+ }
+ w <- as.character(1:n)
+ max0 <- max(nchar(w))
+ w <- sapply(w, function(cha) f1(cha,max0))
+ return(paste(base,w,sep=""))
+}
+
+
+
+
+
+#'
+#' Functions to access online resources for adegenet
+#'
+#' These functions simply open websites or documents
+#' available online providing resources for adegenet.
+#'
+#' \itemize{
+#' \item adegenetWeb opens adegenet's website
+#' \item adegenetTutorial opens adegenet tutorials
+#' \item adegenetIssues opens the issue page on github;
+#' this is used to report a bug or post a feature request.
+#' }
+#'
+#' @param which a character string indicating which tutorial to open (see details)
+#'
+#' @details
+#'
+#' Available tutorials are:
+#' \itemize{
+#' \item 'basics': general introduction to adegenet; covers basic data structures, import/export, handling, and a number of population genetics methods
+#' \item 'spca': spatial genetic structures using the spatial Principal Component Analysis
+#' \item 'dapc': population structure using the Discriminant Analysis of Principal Components
+#' \item 'genomics': handling large genome-wide SNP data using adegenet
+#' \item 'strata': introduction to hierarchical population structure in adegenet
+#' }
+#'
+#' @export
+#'
+#' @rdname web
+#'
+adegenetWeb <- function(){
+ cat("Opening url \"http://adegenet.r-forge.r-project.org/\" ...\n")
+ browseURL("http://adegenet.r-forge.r-project.org/")
+}
+
+
+
+
+#' @rdname web
+#' @export
+adegenetTutorial <- function(which=c("basics","spca","dapc","genomics","strata")){
+ which <- match.arg(which)
+ if(which=="basics"){
+ url <- "https://github.com/thibautjombart/adegenet/raw/master/tutorials/tutorial-basics.pdf"
+ cat("\n")
+ cat(" >> Opening the general introduction to adegenet.\n")
+ cat(" >> Seeking url: ",url,"\n ", sep="")
+ cat("\n")
+ }
+ if(which=="spca"){
+ url <- "https://github.com/thibautjombart/adegenet/raw/master/tutorials/tutorial-spca.pdf"
+ cat("\n")
+ cat(" >> Opening the sPCA tutorial.\n")
+ cat(" >> Seeking url: ",url,"\n ", sep="")
+ cat("\n")
+ }
+ if(which=="dapc"){
+ url <- "https://github.com/thibautjombart/adegenet/raw/master/tutorials/tutorial-dapc.pdf"
+ cat("\n")
+ cat(" >> Opening the DAPC tutorial.\n")
+ cat(" >> Seeking url: ",url,"\n ", sep="")
+ cat("\n")
+ }
+ if(which=="genomics"){
+ url <- "https://github.com/thibautjombart/adegenet/raw/master/tutorials/tutorial-genomics.pdf"
+ cat("\n")
+ cat(" >> Opening the genomics tutorial.\n")
+ cat(" >> Seeking url: ",url,"\n ", sep="")
+ cat("\n")
+ }
+ if(which=="strata"){
+ url <- "https://github.com/thibautjombart/adegenet/raw/master/tutorials/tutorial-strata.pdf"
+ cat("\n")
+ cat(" >> Opening the strata tutorial.\n")
+ cat(" >> Seeking url: ",url,"\n ", sep="")
+ cat("\n")
+ }
+
+ browseURL(url)
+
+ return(invisible(NULL))
+}
+
+
+
+
+#' @rdname web
+#' @export
+adegenetIssues <- function(){
+ cat("Opening url \"https://github.com/thibautjombart/adegenet/issues\" ...\n")
+ browseURL("https://github.com/thibautjombart/adegenet/issues")
+}
+
+
+
+
+
+############
+# checkType
+############
+##
+## WARNING: this does not work with S4 methods
+##
+checkType <- function(x){
+ if(is.character(x)){
+ markType <- x
+ } else {
+ markType <- x at type
+ }
+
+ if(markType=="codom") return() # always ok for codominant markers
+
+ currCall <- as.character(sys.call(sys.parent()))[1]
+ currFunction <- sub("[[:space:]]*[(].*","",currCall)
+ if(currFunction==".local"){
+ warning("Current call not found - stopping check (please report this warning).")
+ return()
+ }
+
+ ## names of functions which are ok for dominant markers
+ PAOk <- c("genind","genpop","genind2genpop","summary","df2genind", "genind2df",
+ "truenames","seppop","na.replace","nLoc","scaleGen","spca","selpop")
+
+ PAWarn <- c("df2genind")
+
+ ## function exists but is experimental
+ if(currFunction %in% PAWarn){
+ msg <- paste(currFunction,"is implemented but experimental presence/absence markers")
+ warning(msg)
+ return()
+ }
+
+ ## function not implemented
+ if(! currFunction %in% PAOk){
+ msgError <- paste(currFunction,"is not implemented for presence/absence markers")
+ stop(msgError)
+ } else return() # else, ok.
+} # end checkType
+
+
+
+
+
+
+##########
+## transp
+##########
+## AUXIL FUNCTION TO USE TRANSPARENT COLORS
+transp <- function(col, alpha=.5){
+ res <- apply(col2rgb(col),2, function(c) rgb(c[1]/255, c[2]/255, c[3]/255, alpha))
+ return(res)
+}
+
+
+
+##########
+## corner
+##########
+## AUXIL FUNCTION TO ADD LETTER TO A PLOT
+corner <- function(text, posi="topleft", inset=0.1, ...){
+ oxpd <- par("xpd")
+ on.exit(par(xpd=oxpd))
+ par(xpd=TRUE)
+ myUsr <- par("usr")
+ xrange <- myUsr[1:2]
+ yrange <- myUsr[3:4]
+ x.size <- abs(diff(xrange))
+ y.size <- abs(diff(yrange))
+ inset <- rep(inset, length=2)
+ x.inset <- inset[1]
+ y.inset <- inset[2]
+
+ if(length(grep("top", posi))==1){
+ y <- yrange[2] - y.size*y.inset
+ } else {
+ y <- yrange[1] + y.size*y.inset
+ }
+
+ if(length(grep("right", posi))==1){
+ x <- xrange[2] - x.size*x.inset
+ } else {
+ x <- xrange[1] + x.size*x.inset
+ }
+
+ text(x, y, lab=text, ...)
+}
+
+
+
+.listenToTheBrood <- function(){
+ char <- c("?","??","?!?!?")
+ for(i in 1:3){
+ cat("\nGrind", char[i], " (y/N): ")
+ x <- readLines(n=1)
+ if(x!="y") {
+ cat("\n =( \n")
+ return(invisible())
+ }
+ }
+
+ cat("\nGRIIIINNND !!!\n")
+ cat("\n\\m/ ^o^ \\m/\n\n")
+ url.vec <- c("http://thebrooduk.bandcamp.com/album/swallowed-by-the-earth-single",
+ "http://thebrooduk.bandcamp.com/album/the-brood")
+ Sys.sleep(2)
+ browseURL(sample(url.vec,1))
+}
+
+
+
+###########
+## num2col
+###########
+## translate numeric values into colors of a palette
+num2col <- function(x, col.pal=heat.colors, reverse=FALSE,
+ x.min=min(x,na.rm=TRUE), x.max=max(x,na.rm=TRUE),
+ na.col="transparent"){
+ ## if(any(is.na(x))) warning("NAs detected in x")
+ x[x < x.min] <- x.min
+ x[x > x.max] <- x.max
+ x <- x-x.min # min=0
+ x.max <- x.max-x.min # update x.max
+ x <- x/x.max # max=1
+ x <- round(x*100)
+ x[x<=0] <- 1
+ if(!reverse) {
+ pal <- col.pal(100)
+ } else {
+ pal <- rev(col.pal(100))
+ }
+
+ res <- pal[x]
+ res[is.na(res)] <- na.col
+ return(res)
+}
+
+
+
+
+
+###########
+## fac2col
+###########
+## translate a factor into colors of a palette
+## colors are randomized based on the provided seed
+fac2col <- function(x, col.pal=funky, na.col="transparent", seed=NULL){
+ ## get factors and levels
+ x <- factor(x)
+ lev <- levels(x)
+ nlev <- length(lev)
+
+ ## get colors corresponding to levels
+ if(!is.null(seed)){
+ set.seed(seed)
+ newseed <- round(runif(1,1,1e9))
+ on.exit(set.seed(newseed))
+ col <- sample(col.pal(nlev))
+ } else {
+ col <- col.pal(nlev)
+ }
+
+ ## get output colors
+ res <- rep(na.col, length(x))
+ res[!is.na(x)] <- col[as.integer(x[!is.na(x)])]
+
+ ## return
+ return(res)
+}
+
+
+###########
+## any2col
+###########
+any2col <- function(x, col.pal=seasun, na.col="transparent"){
+ ## handle numeric data
+ if(is.numeric(x)){
+ col <- num2col(x, col.pal=col.pal, na.col=na.col)
+ leg.col <- num2col(pretty(x), x.min=min(x, na.rm=TRUE),
+ x.max=max(x, na.rm=TRUE), col.pal=col.pal,
+ na.col=na.col)
+ leg.txt <- pretty(x)
+ } else{ ## handle factor
+ x <- factor(x)
+ col <- fac2col(x, col.pal=col.pal, na.col=na.col)
+ leg.col <- col.pal(length(levels(x)))
+ leg.txt <- levels(x)
+ }
+
+ return(list(col=col, leg.col=leg.col, leg.txt=leg.txt))
+} # end any2col
+
+
+
+## pre-defined palettes ##
+## mono color
+bluepal <- colorRampPalette(c("#F7FBFF","#DEEBF7","#C6DBEF",
+ "#9ECAE1","#6BAED6","#4292C6",
+ "#2171B5","#08519C","#08306B"))
+redpal <- colorRampPalette(c("#FFF5F0","#FEE0D2","#FCBBA1",
+ "#FC9272","#FB6A4A","#EF3B2C",
+ "#CB181D","#A50F15","#67000D"))
+greenpal <- colorRampPalette(c("#F7FCF5","#E5F5E0","#C7E9C0",
+ "#A1D99B","#74C476","#41AB5D",
+ "#238B45","#006D2C","#00441B"))
+greypal <- colorRampPalette(c("#FFFFFF","#F0F0F0","#D9D9D9",
+ "#BDBDBD","#969696","#737373",
+ "#525252","#252525","#000000"))
+
+## bi-color
+flame <- colorRampPalette(c("gold","red3"))
+azur <- colorRampPalette(c("gold","royalblue"))
+
+## tri-color
+seasun <- colorRampPalette(c("blue","gold","red"))
+lightseasun <- colorRampPalette(c("deepskyblue2","gold","red1"))
+deepseasun <- colorRampPalette(c("blue2","gold","red2"))
+wasp <- colorRampPalette(c("yellow2","brown", "black"))
+spectral <- colorRampPalette(c("#D53E4F","#F46D43","#FDAE61",
+ "#FEE08B","#FFFFBF","#E6F598",
+ "#ABDDA4","#66C2A5","#3288BD"))
+
+## psychedelic
+funky <- colorRampPalette(c("#A6CEE3","#1F78B4","#B2DF8A",
+ "#33A02C","#FB9A99","#E31A1C",
+ "#FDBF6F","#FF7F00","#CAB2D6",
+ "#6A3D9A","#FFFF99","#B15928"))
diff --git a/R/basicMethods.R b/R/basicMethods.R
new file mode 100644
index 0000000..f54e864
--- /dev/null
+++ b/R/basicMethods.R
@@ -0,0 +1,552 @@
+
+
+setMethod("$","genpop",function(x,name) {
+ return(slot(x,name))
+})
+
+
+setMethod("$<-","genpop",function(x,name,value) {
+ slot(x,name,check=TRUE) <- value
+ return(x)
+})
+
+
+.drop_alleles <- function(x, toKeep){
+ all.vec <- unlist(alleles(x), use.names = FALSE)[toKeep]
+ loc.fac <- factor(locFac(x)[toKeep])
+
+ x at all.names <- split(all.vec, loc.fac)
+ x at loc.n.all <- setNames(tabulate(loc.fac), levels(loc.fac))
+ x at loc.fac <- loc.fac
+ return(x)
+}
+
+
+###############
+# '[' operator
+###############
+## genind
+setMethod("[", signature(x="genind", i="ANY", j="ANY", drop="ANY"), function(x, i, j, ..., pop=NULL, loc=NULL, treatOther=TRUE, quiet=TRUE, drop=FALSE) {
+
+ if (missing(i)) i <- TRUE
+ if (missing(j)) j <- TRUE
+
+ ## HANDLE 'i' as character
+ if(is.factor(i)) i <- as.character(i)
+ if(is.character(i)){
+ old.i <- i
+ i <- match(i, indNames(x))
+ if(any(is.na(i))){
+ warning(paste("the following specified individuals do not exist:", old.i[is.na(i)]))
+ i <- i[!is.na(i)]
+ if(length(i)==0) {
+ warning("no individual selected - ignoring")
+ i <- TRUE
+ }
+ }
+ }
+
+ ## HANDLE 'POP'
+ if(!is.null(pop) && !is.null(pop(x))){
+ if(is.factor(pop)) pop <- as.character(pop)
+ if(!is.character(pop)) pop <- popNames(x)[pop]
+ temp <- !pop %in% pop(x)
+ if (any(temp)) { # if wrong population specified
+ warning(paste("the following specified populations do not exist:", pop[temp]))
+ }
+ i <- pop(x) %in% pop
+ }
+
+ ## handle population factor
+ if(!is.null(pop(x))) {
+ pop <- factor(pop(x)[i])
+ } else {
+ pop <- NULL
+ }
+
+ tab <- tab(x)
+ old.other <- other(x)
+ hier <- x at strata
+ prevcall <- match.call()
+
+ if (x at type == "codom"){
+ ## handle loc argument
+ if(!is.null(loc)){
+ if(is.factor(loc)) loc <- as.character(loc)
+ if(!is.character(loc)) loc <- locNames(x)[loc]
+ temp <- !loc %in% locFac(x)
+ if (any(temp)) { # if wrong loci specified
+ warning(paste("the following specified loci do not exist:", loc[temp]))
+ }
+ j <- x$loc.fac %in% loc
+ } # end loc argument
+ if (drop){
+ tab <- tab[i, , ..., drop = FALSE]
+ allNb <- colSums(tab, na.rm=TRUE) # allele absolute frequencies
+ toKeep <- (allNb > 1e-10)
+ j <- j & toKeep
+ tab <- tab[, j, ..., drop=FALSE]
+ } else {
+ tab <- tab[i, j, ..., drop=FALSE]
+ }
+ } else { # PA case
+ tab <- tab[i, j, ..., drop = FALSE]
+ }
+
+
+ ## handle 'other' slot
+ nOther <- length(other(x))
+ namesOther <- names(other(x))
+ counter <- 0
+ if(treatOther){
+ f1 <- function(obj,n=nrow(tab(x))){
+ counter <<- counter+1
+ if(!is.null(dim(obj)) && nrow(obj)==n) { # if the element is a matrix-like obj
+ obj <- obj[i,,drop=FALSE]
+ } else if(length(obj) == n) { # if the element is not a matrix but has a length == n
+ obj <- obj[i]
+ if(is.factor(obj)) {obj <- factor(obj)}
+ } else {if(!quiet) warning(paste("cannot treat the object",namesOther[counter]))}
+
+ return(obj)
+ } # end f1
+
+ x at other <- lapply(other(x), f1) # treat all elements
+
+ } else {
+ other(x) <- old.other
+ } # end treatOther
+
+ x at tab <- tab
+ x at pop <- pop
+ x at call <- prevcall
+ x at type <- x at type
+
+ # Treat sample and strata
+ x at ploidy <- ploidy(x)[i]
+ x at hierarchy <- x at hierarchy
+ x at strata <- hier[i, , drop = FALSE]
+
+ if (x at type == "codom"){
+ # Treat locus items
+ x <- .drop_alleles(x, j)
+ }
+ return(x)
+})
+
+
+
+
+
+## genpop
+setMethod("[", "genpop", function(x, i, j, ..., loc=NULL, treatOther=TRUE, drop=FALSE) {
+
+ if (missing(i)) i <- TRUE
+ if (missing(j)) j <- TRUE
+
+ tab <- tab(x)
+ old.other <- other(x)
+
+
+ ## HANDLE 'i' as character
+ if(is.factor(i)) i <- as.character(i)
+ if(is.character(i)){
+ old.i <- i
+ i <- match(i, popNames(x))
+ if(any(is.na(i))){
+ warning(paste("the following specified populations do not exist:", old.i[is.na(i)]))
+ i <- i[!is.na(i)]
+ if(length(i)==0) {
+ warning("no population selected - ignoring")
+ i <- TRUE
+ }
+ }
+ }
+
+ ## handle loc argument
+ if(!is.null(loc)){
+ if(is.factor(loc)) loc <- as.character(loc)
+ if(!is.character(loc)) loc <- locNames(x)[loc]
+ temp <- !loc %in% locFac(x)
+ if(any(temp)) { # si mauvais loci
+ warning(paste("the following specified loci do not exist:", loc[temp]))
+ }
+ j <- x$loc.fac %in% loc
+ } # end loc argument
+
+ prevcall <- match.call()
+ # tab <- tab[i, j, ...,drop=FALSE]
+
+ # if(drop){
+ # allNb <- apply(tab, 2, sum, na.rm=TRUE) # allele absolute frequencies
+ # toKeep <- (allNb > 1e-10)
+ # tab <- tab[,toKeep, drop=FALSE]
+ # }
+ if (drop){
+ tab <- tab[i, , ..., drop = FALSE]
+ allNb <- colSums(tab, na.rm=TRUE) # allele absolute frequencies
+ toKeep <- (allNb > 1e-10)
+ j <- j & toKeep
+ tab <- tab[, j, ..., drop=FALSE]
+ } else {
+ tab <- tab[i, j, ..., drop=FALSE]
+ }
+
+ # res <- genpop(tab,prevcall=prevcall,ploidy=x at ploidy)
+
+ ## handle 'other' slot
+ nOther <- length(other(x))
+ namesOther <- names(other(x))
+ counter <- 0
+ if(treatOther){
+ f1 <- function(obj,n=nrow(tab(x))){
+ counter <<- counter+1
+ if(!is.null(dim(obj)) && nrow(obj)==n) { # if the element is a matrix-like obj
+ obj <- obj[i,,drop=FALSE]
+ } else if(length(obj) == n) { # if the element is not a matrix but has a length == n
+ obj <- obj[i]
+ if(is.factor(obj)) {obj <- factor(obj)}
+ } else {warning(paste("cannot treat the object",namesOther[counter]))}
+
+ return(obj)
+ } # end f1
+
+ x at other <- lapply(other(x), f1) # treat all elements
+
+ } else {
+ other(x) <- old.other
+ } # end treatOther
+
+ x at tab <- tab
+ x at call <- prevcall
+ x at type <- x at type
+
+ # Treat populations
+ x at ploidy <- ploidy(x)
+
+ # Treat locus items
+ x <- .drop_alleles(x, j)
+
+ return(x)
+})
+
+
+##########################
+## Method show for genind
+##########################
+setMethod ("show", "genind", function(object){
+ ## GET USEFUL VARIABLES
+ x <- object
+ indTxt <- ifelse(nInd(x)>1, "individuals;", "individual;")
+ locTxt <- ifelse(nLoc(x)>1, "loci;", "locus;")
+ allTxt <- ifelse(ncol(tab((x)))>1, "alleles;", "allele;")
+
+ ## HEADER
+ cat("/// GENIND OBJECT /////////")
+
+ cat("\n\n //", format(nInd(x), big.mark=","), indTxt,
+ format(nLoc(x), big.mark=","), locTxt,
+ format(ncol(tab(x)), big.mark=","), allTxt,
+ "size:", format(object.size(x), units="auto"))
+
+ ## BASIC CONTENT
+ cat("\n\n // Basic content")
+ p <- ncol(tab(x))
+ len <- 7
+
+ cat("\n @tab: ", nrow(tab(x)), "x", ncol(tab(x)), "matrix of allele counts" )
+
+ if(!is.null(nAll(x))){
+ alleletxt <- paste("(range: ", paste(range(nAll(x)), collapse="-"), ")", sep="")
+ cat("\n @loc.n.all: number of alleles per locus", alleletxt)
+ }
+
+ if(!is.null(locFac(x))){
+ cat("\n @loc.fac: locus factor for the", ncol(tab(x)), "columns of @tab")
+ }
+ if(!is.null(alleles(x))){
+ cat("\n @all.names: list of allele names for each locus")
+ }
+
+ ploidytxt <- paste("(range: ", paste(range(ploidy(x)), collapse="-"), ")", sep="")
+ cat("\n @ploidy: ploidy of each individual ", ploidytxt)
+ cat("\n @type: ",x at type)
+ cat("\n @call: ")
+ print(x at call)
+
+ ## OPTIONAL CONTENT
+ cat("\n // Optional content")
+ optional <- FALSE
+ if(!is.null(pop(x))){
+ optional <- TRUE
+ poptxt <- paste("(group size range: ", paste(range(table(pop(x))), collapse="-"), ")", sep="")
+ cat("\n @pop:", paste("population of each individual", poptxt))
+ }
+
+ if (!is.null(x at strata)){
+ optional <- TRUE
+ cat("\n @strata: ")
+ levs <- names(x at strata)
+ if (length(levs) > 6){
+ levs <- paste(paste(head(levs), collapse = ", "), "...", sep = ", ")
+ } else {
+ levs <- paste(levs, collapse = ", ")
+ }
+ cat("a data frame with", length(x at strata), "columns (", levs, ")")
+ }
+
+ if (!is.null(x at hierarchy)){
+ optional <- TRUE
+ cat("\n @hierarchy:", paste(x at hierarchy, collapse = ""))
+ }
+
+ if(!is.null(other(x))){
+ optional <- TRUE
+ cat("\n @other: ")
+ cat("a list containing: ")
+ cat(ifelse(is.null(names(other(x))), "elements without names", paste(names(other(x)), collapse= " ")), "\n")
+ }
+
+ if(!optional) cat("\n - empty -")
+
+ cat("\n")
+}
+) # end show method for genind
+
+
+
+
+##########################
+## Method show for genpop
+##########################
+setMethod ("show", "genpop", function(object){
+ ## GET USEFUL VARIABLES
+ x <- object
+ popTxt <- ifelse(nPop(x)>1, "populations;", "population;")
+ locTxt <- ifelse(nLoc(x)>1, "loci;", "locus;")
+ allTxt <- ifelse(ncol(tab((x)))>1, "alleles;", "allele;")
+
+ ## HEADER
+ cat("/// GENPOP OBJECT /////////")
+
+ cat("\n\n //", format(nPop(x), big.mark=","), popTxt,
+ format(nLoc(x), big.mark=","), locTxt,
+ format(ncol(tab(x)), big.mark=","), allTxt,
+ "size:", format(object.size(x), units="auto"))
+
+ ## BASIC CONTENT
+ cat("\n\n // Basic content")
+ p <- ncol(tab(x))
+ len <- 7
+
+ cat("\n @tab: ", nrow(tab(x)), "x", ncol(tab(x)), "matrix of allele counts" )
+
+ if(!is.null(nAll(x))){
+ alleletxt <- paste("(range: ", paste(range(nAll(x)), collapse="-"), ")", sep="")
+ cat("\n @loc.n.all: number of alleles per locus", alleletxt)
+ }
+
+ if(!is.null(locFac(x))){
+ cat("\n @loc.fac: locus factor for the", ncol(tab(x)), "columns of @tab")
+ }
+ if(!is.null(alleles(x))){
+ cat("\n @all.names: list of allele names for each locus")
+ }
+
+ ploidytxt <- paste("(range: ", paste(range(ploidy(x)), collapse="-"), ")", sep="")
+ cat("\n @ploidy: ploidy of each individual ", ploidytxt)
+ cat("\n @type: ",x at type)
+ cat("\n @call: ")
+ print(x at call)
+
+ ## OPTIONAL CONTENT
+ cat("\n // Optional content")
+ optional <- FALSE
+ if(!is.null(other(x))){
+ optional <- TRUE
+ cat("\n @other: ")
+ cat("a list containing: ")
+ cat(ifelse(is.null(names(other(x))), "elements without names", paste(names(other(x)), collapse= " ")), "\n")
+ }
+
+ if(!optional) cat("\n - empty -")
+
+ cat("\n")
+
+}
+) # end show method for genpop
+
+
+
+
+
+############################
+# Method summary for genind
+############################
+if(!isGeneric("summary")){
+ setGeneric("summary", function(object, ...) standardGeneric("summary"))
+}
+setMethod ("summary", signature(object="genind"), function(object, verbose = TRUE, ...){
+ x <- object
+ if(!is.genind(x)) stop("Provided object is not a valid genind.")
+
+
+ if(is.null(pop(x))){
+ pop(x) <- rep("P1", nInd(x))
+ }
+
+ ## BUILD THE OUTPUT ##
+ ## type-independent stuff
+ res <- list()
+
+ res$n <- nrow(tab(x))
+
+ res$n.by.pop <- as.numeric(table(pop(x)))
+ names(res$n.by.pop) <- popNames(x)
+
+ ## PA case ##
+ if(x at type=="PA"){
+ ## % of missing data
+ res$NA.perc <- 100*sum(is.na(tab(x)))/prod(dim(tab(x)))
+
+ return(invisible(res))
+ }
+
+
+ ## codom case ##
+ res$loc.n.all <- nAll(x)
+
+ temp <- tab(genind2genpop(x,quiet=TRUE))
+
+ res$pop.n.all <- apply(temp,1,function(r) sum(r!=0,na.rm=TRUE))
+
+ res$NA.perc <- 100*(1-mean(propTyped(x,by="both")))
+
+ ## handle heterozygosity
+ if(any(ploidy(x) > 1)){
+ ## auxiliary function to compute observed heterozygosity
+ temp <- lapply(seploc(x),tab, freq=TRUE)
+ f1 <- function(tab){
+ H <- apply(tab, 1, function(vec) any(vec > 0 & vec < 1))
+ H <- mean(H,na.rm=TRUE)
+ return(H)
+ }
+
+ res$Hobs <- unlist(lapply(temp,f1))
+
+ ## auxiliary function to compute expected heterozygosity
+ ## freq is a vector of frequencies
+ f2 <- function(freq){
+ H <- 1-sum(freq*freq,na.rm=TRUE)
+ return(H)
+ }
+
+ temp <- genind2genpop(x,pop=rep(1,nInd(x)),quiet=TRUE)
+ temp <- tab(temp, freq=TRUE, quiet=TRUE)
+ res$Hexp <-tapply(temp^2, locFac(x), function(e) 1-sum(e, na.rm=TRUE))
+ } else { # no possible heterozygosity for haploid genotypes
+ res$Hobs <- 0
+ res$Xexp <- 0
+ }
+
+ ## add class and return
+ class(res) <- "genindSummary"
+ return(res)
+}) # end summary.genind
+
+
+
+
+
+############################
+# Method summary for genpop
+############################
+setMethod ("summary", signature(object="genpop"), function(object, verbose = TRUE, ...){
+ x <- object
+ if(!inherits(x,"genpop")) stop("To be used with a genpop object")
+
+ ## BUILD THE OUTPUT ##
+ ## type-independent stuff
+ res <- list()
+
+ res$n.pop <- nrow(tab(x))
+
+ ## PA case ##
+ if(x at type=="PA"){
+ ## % of missing data
+ res$NA.perc <- 100*sum(is.na(tab(x)))/prod(dim(tab(x)))
+
+ ## add class and return
+ class(res) <- "genpopSummary"
+ return(res)
+ }
+
+
+ ## codom case ##
+ res$loc.n.all <- nAll(x)
+
+ res$pop.n.all <- apply(tab(x),1,function(r) sum(r>0,na.rm=TRUE))
+
+ ## res$NA.perc <- 100*sum(is.na(x at tab))/prod(dim(x at tab)) <- old version
+ mean.w <- function(x,w=rep(1/length(x),length(x))){
+ x <- x[!is.na(x)]
+ w <- w[!is.na(x)]
+ w <- w/sum(w)
+ return(sum(x*w))
+ }
+
+ w <- apply(tab(x),1,sum,na.rm=TRUE) # weights for populations
+ res$NA.perc <- 100*(1-mean.w(propTyped(x), w=w))
+
+ ## add class and return
+ class(res) <- "genpopSummary"
+ return(res)
+}
+)# end summary.genpop
+
+
+
+
+#######################
+## print for summaries
+#######################
+print.genindSummary <- function(x, ...){
+ if(!is.null(x$n)) cat("\n// Number of individuals:", x$n)
+ if(!is.null(x$n.by.pop)) cat("\n// Group sizes:", x$n.by.pop)
+ if(!is.null(x$loc.n.all)) cat("\n// Number of alleles per locus:", x$loc.n.all)
+ if(!is.null(x$pop.n.all)) cat("\n// Number of alleles per group:", x$pop.n.all)
+ if(!is.null(x$NA.perc)) cat("\n// Percentage of missing data:", round(x$NA.perc,2), "%")
+ if(!is.null(x$Hobs)) cat("\n// Observed heterozygosity:", round(x$Hobs,2))
+ if(!is.null(x$Hexp)) cat("\n// Expected heterozygosity:", round(x$Hexp,2))
+ cat("\n")
+} # end print.genindSummary
+
+
+print.genpopSummary <- function(x, ...){
+ if(!is.null(x$n.pop)) cat("\n// Number of populations:", x$n.pop)
+ if(!is.null(x$loc.n.all)) cat("\n// Number of alleles per locus:", x$loc.n.all)
+ if(!is.null(x$pop.n.all)) cat("\n// Number of alleles per group:", x$pop.n.all)
+ if(!is.null(x$NA.perc)) cat("\n// Percentage of missing data:", round(x$NA.perc,2), "%")
+ cat("\n")
+} # end print.genpopSummary
+
+
+
+###############
+# Methods "is"
+###############
+is.genind <- function(x){
+ res <- ( is(x, "genind") & validObject(x))
+ return(res)
+}
+
+is.genpop <- function(x){
+ res <- ( is(x, "genpop") & validObject(x))
+ return(res)
+}
+
+
+
+.hasUniquePloidy <- function(x){
+ return(length(unique(ploidy(x)))==1)
+}
diff --git a/R/chooseCN.R b/R/chooseCN.R
new file mode 100644
index 0000000..b8e6a42
--- /dev/null
+++ b/R/chooseCN.R
@@ -0,0 +1,288 @@
+#####################
+# Function chooseCN
+#####################
+
+
+#' Function to choose a connection network
+#'
+#' The function \code{chooseCN} is a simple interface to build a connection
+#' network (CN) from xy coordinates. The user chooses from 6 types of graph and
+#' one additional weighting scheme. \code{chooseCN} calls functions from
+#' appropriate packages, handles non-unique coordinates and returns a
+#' connection network either with classe \code{nb} or \code{listw}. For graph
+#' types 1-4, duplicated locations are not accepted and will issue an error.
+#'
+#' There are 7 kinds of graphs proposed: \cr Delaunay triangulation (type 1)\cr
+#' Gabriel graph (type 2)\cr Relative neighbours (type 3)\cr Minimum spanning
+#' tree (type 4)\cr Neighbourhood by distance (type 5)\cr K nearests neighbours
+#' (type 6)\cr Inverse distances (type 7)\cr
+#'
+#' The last option (type=7) is not a true neighbouring graph: all sites are
+#' neighbours, but the spatial weights are directly proportional to the
+#' inversed spatial distances.\cr Also not that in this case, the output of the
+#' function is always a \code{listw} object, even if \code{nb} was
+#' requested.\cr
+#'
+#' The choice of the connection network has been discuted on the adegenet
+#' forum. Please search the archives from adegenet website (section 'contact')
+#' using 'graph' as keyword.
+#'
+#' @param xy an matrix or data.frame with two columns for x and y coordinates.
+#' @param ask a logical stating whether graph should be chosen interactively
+#' (TRUE,default) or not (FALSE). Set to FALSE if \code{type} is provided.
+#' @param type an integer giving the type of graph (see details).
+#' @param result.type a character giving the class of the returned object.
+#' Either "nb" (default) or "listw", both from \code{spdep} package. See
+#' details.
+#' @param d1 the minimum distance between any two neighbours. Used if
+#' \code{type=5.}
+#' @param d2 the maximum distance between any two neighbours. Used if
+#' \code{type=5}. Can also be a character: "dmin" for the minimum distance so
+#' that each site has at least one connection, or "dmax" to have all sites
+#' connected (despite the later has no sense).
+#' @param k the number of neighbours per point. Used if \code{type=6}.
+#' @param a the exponent of the inverse distance matrix. Used if \code{type=7}.
+#' @param dmin the minimum distance between any two distinct points. Used to
+#' avoid infinite spatial proximities (defined as the inversed spatial
+#' distances). Used if \code{type=7}.
+#' @param plot.nb a logical stating whether the resulting graph should be
+#' plotted (TRUE, default) or not (FALSE).
+#' @param edit.nb a logical stating whether the resulting graph should be
+#' edited manually for corrections (TRUE) or not (FALSE, default).
+#' @return Returns a connection network having the class \code{nb} or
+#' \code{listw}. The xy coordinates are passed as attribute to the created
+#' object.
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{spca}}
+#' @keywords spatial utilities
+#' @examples
+#'
+#' \dontrun{
+#' data(nancycats)
+#'
+#' par(mfrow=c(2,2))
+#' cn1 <- chooseCN(nancycats@@other$xy,ask=FALSE,type=1)
+#' cn2 <- chooseCN(nancycats@@other$xy,ask=FALSE,type=2)
+#' cn3 <- chooseCN(nancycats@@other$xy,ask=FALSE,type=3)
+#' cn4 <- chooseCN(nancycats@@other$xy,ask=FALSE,type=4)
+#' par(mfrow=c(1,1))
+#' }
+#'
+#' @export chooseCN
+#' @importFrom spdep "tri2nb" "gabrielneigh" "graph2nb" "relativeneigh" "dnearneigh" "knearneigh" "knn2nb" "nb2listw" "mat2listw" "listw2mat" "lag.listw" "card"
+#' @import ade4
+#'
+chooseCN <- function(xy,ask=TRUE, type=NULL, result.type="nb", d1=NULL, d2=NULL, k=NULL,
+ a=NULL, dmin=NULL, plot.nb=TRUE, edit.nb=FALSE){
+
+ if(is.data.frame(xy)) xy <- as.matrix(xy)
+ if(ncol(xy) != 2) stop("xy does not have two columns.")
+ if(any(is.na(xy))) stop("NA entries in xy.")
+ result.type <- tolower(result.type)
+ if(is.null(type) & !ask) stop("Non-interactive mode but no graph chosen; please provide a value for 'type' argument.")
+
+ ## if(!require(spdep, quietly=TRUE)) stop("spdep library is required.")
+
+ res <- list()
+
+ if(!is.null(d2)){
+ if(d2=="dmin"){
+ tempmat <- as.matrix(dist(xy))
+ d2min <- max(apply(tempmat, 1, function(r) min(r[r>1e-12])))
+ d2min <- d2min * 1.0001 # to avoid exact number problem
+ d2 <- d2min
+ } else if(d2=="dmax"){
+ d2max <- max(dist(xy))
+ d2max <- d2max * 1.0001 # to avoid exact number problem
+ d2 <- d2max
+ }
+ } # end handle d2
+
+ d1.first <- d1
+ d2.first <- d2
+ k.first <- k
+
+ ## handle type argument
+ if(!is.null(type)){
+ type <- as.integer(type)
+ if(type < 1 |type > 7) stop("type must be between 1 and 7")
+ ask <- FALSE
+ }
+
+ ## check for uniqueness of coordinates
+ if(any(xyTable(xy)$number>1)){ # if duplicate coords
+ DUPLICATE.XY <- TRUE
+ } else {
+ DUPLICATE.XY <- FALSE
+ }
+
+
+ ## if(is.null(type) & !ask) { type <- 1 }
+
+ ### begin large while ###
+ chooseAgain <- TRUE
+ while(chooseAgain){
+ # re-initialisation of some variables
+ d1 <- d1.first
+ d2 <- d2.first
+ k <- k.first
+
+ ## read type from console
+ if(ask){
+ temp <- TRUE
+ while(temp){
+ cat("\nChoose a connection network:\n")
+ cat("\t Delaunay triangulation (type 1)\n")
+ cat("\t Gabriel graph (type 2)\n")
+ cat("\t Relative neighbours (type 3)\n")
+ cat("\t Minimum spanning tree (type 4)\n")
+ cat("\t Neighbourhood by distance (type 5)\n")
+ cat("\t K nearest neighbours (type 6)\n")
+ cat("\t Inverse distances (type 7)\n")
+ cat("Answer: ")
+
+ type <- as.integer(readLines(n = 1))
+ temp <- type < 1 |type > 7
+ if(temp) cat("\nWrong answer\n")
+
+ if(type %in% 1:4 & DUPLICATE.XY){
+ cat("\n\n== PROBLEM DETECTED ==")
+ cat("\nDuplicate locations detected\nPlease choose another graph (5-7) or add random noise to locations (see ?jitter).\n")
+ temp <- TRUE
+ }
+
+ } # end while
+ }
+ ##
+
+ ## warning about duplicate xy coords
+ if(type %in% 1:4 & DUPLICATE.XY){
+ stop("Duplicate locations detected and incompatible with graph type 1-4.\nPlease choose another graph (5-7) or add random noise to locations (see ?jitter).")
+ }
+
+ ## graph types
+ ## type 1: Delaunay
+ if(type==1){
+ ## if(!require(tripack, quietly=TRUE)) stop("tripack library is required.")
+ cn <- tri2nb(xy)
+ }
+
+ # type 2: Gabriel
+ if(type==2){
+ cn <- gabrielneigh(xy)
+ cn <- graph2nb(cn, sym=TRUE)
+ }
+
+ ## type 3: Relative neighbours
+ if(type==3){
+ cn <- relativeneigh(xy)
+ cn <- graph2nb(cn, sym=TRUE)
+ }
+
+ ## type 4: Minimum spanning tree
+ if(type==4){
+ cn <- ade4::mstree(dist(xy)) # there is also a spdep::mstree
+ cn <- neig2nb(cn)
+ }
+
+ ## type 5: Neighbourhood by distance
+ if(type==5){
+ if(is.null(d1) |is.null(d2)){
+ tempmat <- as.matrix(dist(xy))
+ d2min <- max(apply(tempmat, 1, function(r) min(r[r>1e-12])))
+ d2min <- d2min * 1.0001 # to avoid exact number problem
+ d2max <- max(dist(xy))
+ d2max <- d2max * 1.0001 # to avoid exact number problem
+ dig <- options("digits")
+ options("digits=5")
+ cat("\n Enter minimum distance: ")
+ d1 <- as.numeric(readLines(n = 1))
+ cat("\n Enter maximum distance \n(dmin=", d2min, ", dmax=", d2max, "): ")
+ d2 <- readLines(n = 1)
+ ## handle character
+ if(d2=="dmin") {
+ d2 <- d2min
+ } else if(d2=="dmax") {
+ d2 <- d2max
+ } else {
+ d2 <- as.numeric(d2)
+ }
+ ## restore initial digit option
+ options(dig)
+ }
+ # avoid that a point is its neighbour
+ dmin <- mean(dist(xy))/100000
+ if(d1<dmin) d1 <- dmin
+ if(d2<d1) stop("d2 < d1")
+ cn <- dnearneigh(x=xy, d1=d1, d2=d2)
+ }
+
+ ## type 6: K nearests
+ if(type==6){
+ if(is.null(k)) {
+ cat("\n Enter the number of neighbours: ")
+ k <- as.numeric(readLines(n = 1))
+ }
+ cn <- knearneigh(x=xy, k=k)
+ cn <- knn2nb(cn, sym=TRUE)
+ }
+
+ ## type 7: inverse distances
+ if(type==7){
+ if(is.null(a)) {
+ cat("\n Enter the exponent: ")
+ a <- as.numeric(readLines(n = 1))
+ }
+ cn <- as.matrix(dist(xy))
+ if(is.null(dmin)) {
+ cat("\n Enter the minimum distance \n(range = 0 -", max(cn),"): ")
+ dmin <- as.numeric(readLines(n = 1))
+ }
+ if(a<1) { a <- 1 }
+ thres <- mean(cn)/1e8
+ if(dmin > thres) dmin <- thres
+ cn[cn < dmin] <- dmin
+ cn <- 1/(cn^a)
+ diag(cn) <- 0
+ cn <- prop.table(cn,1)
+ plot.nb <- FALSE
+ edit.nb <- FALSE
+ result.type <- "listw"
+ } # end type 7
+
+ ## end graph types
+
+ if(ask & plot.nb) {
+ plot(cn,xy)
+ cat("\nKeep this graph (y/n)? ")
+ ans <- tolower(readLines(n=1))
+ if(ans=="n") {chooseAgain <- TRUE} else {chooseAgain <- FALSE}
+ }
+ else if(plot.nb){
+ plot(cn,xy)
+ chooseAgain <- FALSE
+ }
+ else {chooseAgain <- FALSE}
+
+ }
+### end large while
+
+ if(edit.nb) {cn <- edit(cn,xy)}
+
+ if(result.type == "listw") {
+ if(type!=7) {
+ cn <- nb2listw(cn, style="W", zero.policy=TRUE)
+ } else {
+ cn <- mat2listw(cn)
+ cn$style <- "W"
+ }
+ }
+
+ res <- cn
+
+ attr(res,"xy") <- xy
+
+ return(res)
+
+} # end chooseCN
+
diff --git a/R/classes.R b/R/classes.R
new file mode 100644
index 0000000..68f2d5f
--- /dev/null
+++ b/R/classes.R
@@ -0,0 +1,253 @@
+########################################################################
+## adegenet classes definitions. All classes are S4.
+##
+## Initial development: Thibaut Jombart, November 2007
+##
+## Major reform for adegenet 2.0.0 (March-August 2015)
+##
+## t.jombart at imperial.ac.uk
+########################################################################
+
+###############################
+# Two classes of R object are
+# defined :
+# gen - common part to genind and genpop
+# genind - allele counts for individuals
+# genpop - allele counts for populations
+###############################
+
+
+###############################################################
+###############################################################
+# AUXILIARY FUNCTIONS
+###############################################################
+###############################################################
+
+
+
+
+###############################################################
+###############################################################
+# CLASSES DEFINITION
+###############################################################
+###############################################################
+
+##.initAdegenetClasses <- function(){
+
+
+####################
+# Unions of classes
+####################
+setClassUnion("listOrNULL", c("list","NULL"))
+setClassUnion("factorOrNULL", c("factor","NULL"))
+setClassUnion("charOrNULL", c("character","NULL"))
+setClassUnion("callOrNULL", c("call","NULL"))
+setClassUnion("intOrNum", c("integer","numeric","NULL"))
+setClassUnion("intOrNULL", c("integer","NULL"))
+setClassUnion("dfOrNULL", c("data.frame", "NULL"))
+setClassUnion("formOrNULL", c("formula", "NULL"))
+
+
+####################
+# virtual class gen
+####################
+.gen.valid <- function(object){
+ # this function tests only the consistency
+ # of the length of each component
+ p <- ncol(object at tab)
+ k <- length(levels(object at loc.fac))
+
+
+ if(!is.null(object at loc.fac)){
+ if(length(object at loc.fac) != p) {
+ cat("\ninvalid length for loc.fac\n")
+ return(FALSE)
+ }
+
+ if(length(levels(object at loc.fac)) != k) {
+ cat("\ninvalid number of levels in loc.fac\n")
+ return(FALSE)
+ }
+ }
+
+ if(!is.null(object at loc.n.all)){
+ if(length(object at loc.n.all) != k) {
+ cat("\ninvalid length in loc.n.all\n")
+ return(FALSE)
+ }
+ }
+
+ if(!is.null(object at all.names)){
+ if(length(unlist(object at all.names)) != p) {
+ cat("\ninvalid length in all.names\n")
+ return(FALSE)
+ }
+ }
+
+ return(TRUE)
+
+}# end .gen.valid
+
+
+setClass("gen", representation(tab = "matrix",
+ loc.fac = "factorOrNULL",
+ loc.n.all = "intOrNum",
+ all.names = "listOrNULL",
+ ploidy = "integer",
+ type = "character",
+ other = "listOrNULL",
+ call = "callOrNULL",
+ "VIRTUAL"),
+ prototype(tab=matrix(0L, ncol=0,nrow=0),
+ loc.fac=NULL,
+ loc.n.all=integer(0),
+ all.names=NULL,
+ ploidy=integer(0),
+ type=character(0),
+ other=NULL,
+ call=NULL))
+
+setValidity("gen", .gen.valid)
+
+
+
+
+########################
+# virtual class indInfo
+########################
+setClass("indInfo", representation(pop = "factorOrNULL",
+ strata = "dfOrNULL",
+ hierarchy = "formOrNULL",
+ "VIRTUAL"),
+ prototype(pop=NULL, stata=NULL, hierarchy=NULL))
+
+
+
+
+
+###############
+# Class genind
+###############
+
+setClass("genind", contains=c("gen", "indInfo"))
+
+.genind.valid <- function(object){
+
+ validation <- TRUE
+ if(!.gen.valid(object)) return(FALSE)
+
+ if(typeof(object at tab) != "integer"){
+ warning("@tab does not contain integers; as of adegenet_2.0-0, numeric values are no longer used")
+ ## message("\ntab does not contain integers; as of adegenet_1.5-0, numeric values are no longer used")
+ ## validation <- FALSE
+ }
+
+
+ if(!is.null(object at pop)){ # check pop
+
+ if(length(object at pop) != nrow(object at tab)) {
+ message("\npop is given but has invalid length\n")
+ validation <- FALSE
+ }
+
+ } # end check pop
+
+ # Check population strata
+ if (!is.null(object at strata)){
+ if (nrow(object at strata) != nrow(object at tab)){
+ message("\na strata is defined has invalid length\n")
+ validation <- FALSE
+ }
+
+ dups <- duplicated(colnames(object at strata))
+ if (any(dups)){
+ message("\nduplicated names found in @strata slot:\n")
+ dups <- colnames(object at strata)[dups]
+ message(paste0(dups, collapse = ", "))
+ validation <- FALSE
+ }
+ }
+
+ # TODO: CHECK HIERARCHY FORMULA
+
+ ## check ploidy
+ if(any(object at ploidy < 1L)){
+ message("\nploidy inferior to 1\n")
+ validation <- FALSE
+ }
+ if(length(object at ploidy)!= nrow(object at tab)){
+ warning("as of adegenet_2.0-0, @ploidy should contain one value per individual")
+ }
+
+ ## check type of marker
+ if(!object at type %in% c("codom","PA") ){
+ message("\nunknown type of marker\n")
+ validation <- FALSE
+ }
+
+
+ return(validation)
+} #end .genind.valid
+
+setValidity("genind", .genind.valid)
+
+
+
+########################
+# virtual class popInfo
+########################
+setClass("genpop", contains=c("gen"))
+
+
+
+###############
+# Class genpop
+###############
+.genpop.valid <- function(object){
+
+ validation <- TRUE
+
+ if(!.gen.valid(object)) return(FALSE)
+
+ ## check ploidy
+ if(length(object at ploidy) > 1 && object at ploidy < 1L){
+ message("\nploidy inferior to 1\n")
+ validation <- FALSE
+ }
+
+ ## check type of marker
+ if(!object at type %in% c("codom","PA") ){
+ message("\nunknown type of marker\n")
+ validation <- FALSE
+ }
+
+ return(validation)
+} #end .genpop.valid
+
+setValidity("genpop", .genpop.valid)
+
+
+
+
+
+
+
+###############################################################
+###############################################################
+## MISCELLANEOUS METHODS
+###############################################################
+###############################################################
+
+
+
+#################
+# Function names
+#################
+setMethod("names", signature(x = "genind"), function(x){
+ return(slotNames(x))
+})
+
+setMethod("names", signature(x = "genpop"), function(x){
+ return(slotNames(x))
+})
+
diff --git a/R/colorplot.R b/R/colorplot.R
new file mode 100644
index 0000000..fc3a92a
--- /dev/null
+++ b/R/colorplot.R
@@ -0,0 +1,76 @@
+##
+## COLOR PLOT
+##
+## used to plot up to 3 variables in space using RGB system
+##
+## all coded in S3 method (arguments vary largely)
+##
+
+
+##########
+# generic
+##########
+colorplot <- function(...){
+ UseMethod("colorplot")
+}
+
+
+
+#################
+# default method
+#################
+colorplot.default <- function(xy, X, axes=NULL, add.plot=FALSE, defaultLevel=0, transp=FALSE, alpha=.5, ...){
+
+ ## some checks
+ if(any(is.na(xy))) stop("NAs exist in xy")
+ xy <- as.matrix(xy)
+ if(!is.numeric(xy)) stop("xy is not numeric")
+ if(nrow(xy) != nrow(X)) stop("xy and X have different row numbers")
+ if(is.null(axes)) {
+ axes <- 1:min(ncol(X),3)
+ }
+ X <- as.matrix(X[,axes,drop=FALSE])
+ if(any(is.na(X))) stop("NAs exist in X")
+ if(!is.numeric(X)) stop("X is not numeric")
+ if(defaultLevel < 0 | defaultLevel>1) stop("defaultLevel must be between 0 and 1")
+
+ ## function mapping x to [0,+inf[
+ f1 <- function(x){
+ if(any(x<0)) {
+ x <- x + abs(min(x))
+ }
+ return(x)
+ }
+
+ ## apply f1 to X
+ X <- apply(X, 2, f1)
+
+ v1 <- X[,1]
+ if(ncol(X)>=2) {v2 <- X[,2]} else {v2 <- defaultLevel}
+ if(ncol(X)>=3) {v3 <- X[,3]} else {v3 <- defaultLevel}
+
+ ## make colors
+ if(transp){
+ col <- rgb(v1/max(X), v2/max(X), v3/max(X), alpha)
+ } else {
+ col <- rgb(v1, v2, v3, maxColorValue=max(X))
+ }
+
+ ## handle ...
+ listArgs <- list(...)
+ if(is.null(listArgs$pch)) {listArgs$pch <- 20}
+
+ ## build list of arguments
+ listArgs$x <- xy
+ listArgs$col <- col
+
+ ## plot data
+ if(!add.plot) {
+ do.call(plot,listArgs)
+ } else {
+ do.call(points,listArgs)
+ }
+
+ ##return(invisible(match.call()))
+ return(invisible(col))
+} # end colorplot.default
diff --git a/R/constructors.R b/R/constructors.R
new file mode 100644
index 0000000..1ee32b3
--- /dev/null
+++ b/R/constructors.R
@@ -0,0 +1,329 @@
+
+#' genind constructor
+#'
+#' The function \code{new} has a method for building \linkS4class{genind} objects.
+#' See the class description of \linkS4class{genind} for more information on this data structure.
+#' The functions \code{genind} and \code{as.genind} are aliases for \code{new("genind", ...)}.
+#'
+#' Most users do not need using the constructor, but merely to convert raw allele data using \code{\link{df2genind}} and related functions.
+#'
+#' @export
+#' @docType methods
+#'
+#' @aliases initialize,genind-methods
+#' @aliases genind
+#' @aliases as.genind
+#'
+#' @rdname new.genind
+#'
+#' @param .Object prototyped object (generated automatically when calling 'new')
+#' @param tab A matrix of integers corresponding to the @@tab slot of a genind
+#' object, with individuals in rows and alleles in columns, and containing
+#' either allele counts (if type="codom") or allele presence/absence (if
+#' type="PA")
+#' @param pop an optional factor with one value per row in \code{tab} indicating
+#' the population of each individual
+#' @param prevcall an optional call to be stored in the object
+#' @param ploidy an integer vector indicating the ploidy of the individual; each
+#' individual can have a different value; if only one value is provided, it is
+#' recycled to generate a vector of the right length.
+#' @param type a character string indicating the type of marker: codominant
+#' ("codom") or presence/absence ("PA")
+#' @param strata a data frame containing population hierarchies or
+#' stratifications in columns. This must be the same length as the number of
+#' individuals in the data set.
+#' @param hierarchy a hierarchical formula defining the columns of the strata
+#' slot that are hierarchical. Defaults to NULL.
+#' @param ... further arguments passed to other methods (currently not used)
+#'
+#' @return a \linkS4class{genind} object
+#'
+#' @seealso the description of the \linkS4class{genind} class; \code{\link{df2genind}}
+#'
+setMethod("initialize", "genind", function(.Object, tab, pop=NULL, prevcall=NULL, ploidy=2L, type=c("codom","PA"), strata = NULL, hierarchy = NULL, ...){
+ ## HANDLE ARGUMENTS ##
+ out <- .Object
+ if (missing(tab)){
+ .Object at tab <- matrix(0L, ncol = 0, nrow = 0)
+ .Object at pop <- NULL
+ .Object at strata <- NULL
+ .Object at hierarchy <- NULL
+ .Object at call <- NULL
+ .Object at loc.n.all <- integer(0)
+ .Object at loc.fac <- NULL
+ .Object at ploidy <- integer(0)
+ .Object at other <- NULL
+ .Object at type <- "codom"
+ return(.Object)
+ }
+ if(is.null(colnames(tab))) {colnames(tab) <- seq(ncol(tab))}
+ if(is.null(rownames(tab))) {rownames(tab) <- seq(nrow(tab))}
+
+ ## force matrix & integer
+ if(!is.matrix(tab)) tab <- as.matrix(tab)
+ old.rownames <- rownames(tab)
+ old.colnames <- colnames(tab)
+ old.dim <- dim(tab)
+ if(typeof(tab)!="integer"){
+ tab <- as.integer(tab)
+ dim(tab) <- old.dim
+ rownames(tab) <- old.rownames
+ colnames(tab) <- old.colnames
+ }
+ type <- match.arg(type)
+ nind <- nrow(tab)
+ ploidy <- as.integer(ploidy)
+ ploidy <- rep(ploidy, length=nind)
+
+ ## HANDLE LABELS ##
+ ## loc names is not type-dependent
+ if(length(grep("([.][^.]*){2,}", old.colnames))>0L){
+ stop("more than one '.' in column names; please name column as [LOCUS].[ALLELE]")
+ }
+ temp <- sub("[.].*$", "", old.colnames)
+ temp <- .rmspaces(temp)
+ loc.names <- unique(temp)
+ nloc <- length(loc.names)
+
+ ## ind names is not type-dependent either
+ ## only use generic label if no name or duplicates
+ if(is.null(rownames(tab))) {
+ rownames(tab) <- .genlab("", nind)
+ }
+ ind.names <- rownames(tab)
+ if(length(unique(ind.names))!=length(ind.names)) {
+ warning("duplicate labels detected for some individuals; using generic labels")
+ rownames(tab) <- ind.names <- .genlab("", nind)
+ }
+
+ if (!is.null(strata)){
+ # Make sure that the hierarchies are factors.
+ strata <- data.frame(lapply(strata, function(f) factor(f, unique(f))))
+ rownames(strata) <- rownames(tab)
+ }
+
+ if (!is.null(strata) && !is.null(hierarchy)){
+ if (is.language(hierarchy)){
+ the_names <- all.vars(hierarchy)
+ if (all(the_names %in% names(strata))){
+ ## TODO: CHECK HIERARCHY HERE
+ } else {
+ warning("hierarchy names do not match names of strata. Setting slot to NULL")
+ hierarchy <- NULL
+ }
+ } else {
+ warning("hierarchy must be a formula. Setting slot to NULL.")
+ hierarchy <- NULL
+ }
+ }
+
+
+ if(type=="codom"){
+ ## loc.n.all
+ loc.n.all <- table(temp)[match(loc.names,names(table(temp)))]
+ loc.n.all <- as.integer(loc.n.all)
+ names(loc.n.all) <- loc.names
+
+ ## loc.fac
+ loc.fac <- factor(rep(loc.names,loc.n.all),levels=loc.names)
+
+ ## alleles name
+ temp <- colnames(tab)
+ temp <- sub("^[^.]*[.]","",temp)
+ temp <- .rmspaces(temp)
+ all.names <- split(temp,loc.fac)
+ all.names <- all.names[loc.names]
+
+ } else { # end if type=="codom" <=> if type=="PA"
+ loc.fac <- NULL
+ all.names <- NULL
+ loc.n.all <- NULL
+ }
+
+ ## Ideally I should use an 'initialize' method here
+ out at tab <- tab
+ out at loc.n.all <- loc.n.all
+ out at loc.fac <- loc.fac
+ out at all.names <- all.names
+ out at strata <- strata
+ out at hierarchy <- hierarchy
+ ## populations name (optional)
+ ## beware, keep levels of pop sorted in
+ ## there order of appearance
+ if(!is.null(pop)) {
+ # convert pop to a factor if it is not
+ if(!is.factor(pop)) {pop <- factor(pop)}
+ out at pop <- pop
+ }
+
+ ## ploidy
+ plo <- as.integer(ploidy)
+ if(any(plo < 1L)) stop("ploidy inferior to 1")
+ out at ploidy <- plo
+
+ ## type of marker
+ out at type <- as.character(type)
+
+ if(is.null(prevcall)) {prevcall <- match.call()}
+ out at call <- prevcall
+
+ return(out)
+})
+
+
+#' @export
+#' @rdname new.genind
+genind <- function(...){
+ out <- new("genind", ...)
+ return(out)
+} # end genind
+
+#' @export
+#' @rdname new.genind
+as.genind <- function(...){
+ out <- new("genind", ...)
+ return(out)
+} # end genind
+
+
+
+
+
+
+#' genpop constructor
+#'
+#' The function \code{new} has a method for building \linkS4class{genpop} objects.
+#' See the class description of \linkS4class{genpop} for more information on this data structure.
+#' The functions \code{genpop} and \code{as.genpop} are aliases for \code{new("genpop", ...)}.
+#'
+#' Most users do not need using the constructor, but merely to convert raw allele data using \code{\link{genind2genpop}}.
+#'
+#' @export
+#' @docType methods
+#'
+#' @aliases initialize,genpop-methods
+#' @aliases genpop
+#' @aliases as.genpop
+#'
+#' @rdname new.genpop
+#'
+#' @param .Object prototyped object (generated automatically when calling 'new')
+#' @param tab A matrix of integers corresponding to the @@tab slot of a genpop object, with individuals in rows and alleles in columns, and containing either allele counts
+#' @param prevcall an optional call to be stored in the object
+#' @param ploidy an integer vector indicating the ploidy of the individual; each individual can have a different value; if only one value is provided, it is recycled to generate a vector of the right length.
+#' @param type a character string indicating the type of marker: codominant ("codom") or presence/absence ("PA")
+#' @param ... further arguments passed to other methods (currently not used)
+#'
+#' @return a \linkS4class{genpop} object
+#'
+#' @seealso the description of the \linkS4class{genpop} class; \code{\link{df2genind}} and related functions for reading raw allele data
+#'
+##################
+# Function genpop
+##################
+setMethod("initialize", "genpop", function(.Object, tab, prevcall=NULL, ploidy=2L, type=c("codom","PA"), ...){
+ ## HANDLE ARGS ##
+ out <- .Object
+ if (missing(tab)){
+ .Object at tab <- matrix(0L, ncol = 0, nrow = 0)
+ .Object at call <- NULL
+ .Object at loc.n.all <- integer(0)
+ .Object at loc.fac <- NULL
+ .Object at ploidy <- integer(0)
+ .Object at other <- NULL
+ .Object at type <- "codom"
+ return(.Object)
+ }
+ if(is.null(colnames(tab))) stop("tab columns have no name.")
+ if(is.null(rownames(tab))) {rownames(tab) <- 1:nrow(tab)}
+
+ ## force matrix & integer
+ if(!is.matrix(tab)) tab <- as.matrix(tab)
+ old.rownames <- rownames(tab)
+ old.colnames <- colnames(tab)
+ old.dim <- dim(tab)
+ if(typeof(tab)!="integer"){
+ tab <- as.integer(tab)
+ dim(tab) <- old.dim
+ rownames(tab) <- old.rownames
+ colnames(tab) <- old.colnames
+ }
+ type <- match.arg(type)
+ ploidy <- as.integer(ploidy)
+ npop <- nrow(tab)
+
+
+ ## HANDLE LABELS ##
+
+ ## loc names is not type-dependent
+ if(length(grep("([.][^.]*){2,}", old.colnames))>0L){
+ stop("more than one '.' in column names; please name column as [LOCUS].[ALLELE]")
+ }
+ temp <- sub("[.].*$", "", old.colnames)
+ temp <- .rmspaces(temp)
+ loc.names <- unique(temp)
+ nloc <- length(loc.names)
+
+ ## pop names is not type-dependent either
+ ## only use generic label if no name or duplicates
+ if(is.null(rownames(tab))) {
+ rownames(tab) <- .genlab("", npop)
+ }
+ pop.names <- rownames(tab)
+ if(length(unique(pop.names))!=length(pop.names)) {
+ warning("duplicate labels detected for some populations; using generic labels")
+ rownames(tab) <- pop.names <- .genlab("", npop)
+ }
+
+ if(type=="codom"){
+ ## loc.n.all
+ loc.n.all <- table(temp)[match(loc.names,names(table(temp)))]
+ loc.n.all <- as.integer(loc.n.all)
+ names(loc.n.all) <- loc.names
+
+ ## loc.fac
+ loc.fac <- factor(rep(loc.names,loc.n.all),levels=loc.names)
+
+ ## alleles name
+ temp <- colnames(tab)
+ temp <- sub("^[^.]*[.]","",temp)
+ temp <- .rmspaces(temp)
+ all.names <- split(temp,loc.fac)
+ all.names <- all.names[loc.names]
+ loc.fac <- as.factor(loc.fac)
+
+ } else { # end if type=="codom" <=> if type=="PA"
+ loc.fac <- NULL
+ all.names <- NULL
+ loc.n.all <- NULL
+ }
+
+ ## build final output
+ out at tab <- tab
+ out at loc.n.all <- loc.n.all
+ out at loc.fac <- loc.fac
+ out at all.names <- all.names
+ out at ploidy <- ploidy
+ out at type <- as.character(type)
+
+ if(is.null(prevcall)) {prevcall <- match.call()}
+ out at call <- prevcall
+
+ return(out)
+})
+
+
+
+#' @export
+#' @rdname new.genpop
+genpop <- function(...){
+ out <- new("genpop", ...)
+ return(out)
+} # end genpop
+
+#' @export
+#' @rdname new.genpop
+as.genpop <- function(...){
+ out <- new("genpop", ...)
+ return(out)
+} # end genpop
diff --git a/R/coords.monmonier.R b/R/coords.monmonier.R
new file mode 100644
index 0000000..1b21860
--- /dev/null
+++ b/R/coords.monmonier.R
@@ -0,0 +1,58 @@
+coords.monmonier <- function(x){
+
+if (!inherits(x, "monmonier")) stop("Use only with 'monmonier' objects")
+
+xy.full <- x$xy
+n.points <- nrow(xy.full)
+k <- 1
+
+#cn list to cn matrix
+cn.matr <- matrix(data = 0, nrow = n.points, ncol = n.points)
+
+for(i in 1:n.points){
+ eval <- is.element(c(1:n.points), x$cn[[i]])
+ cn.matr[i,which(eval == TRUE)] <- 1
+ }
+
+#halfway <- matrix(data = NA, nrow = (n.points^2-n.points)/2, ncol = 4)
+halfway <- matrix(data = NA, nrow = sum(cn.matr)/2, ncol = 4)
+colnames(halfway) <- c("x.hw","y.hw","first","second")
+
+for(first in 1:(n.points-1)){
+for(second in (first+1):n.points){
+ if(cn.matr[first,second] == 1){
+ halfway[k,] <- c(
+ (xy.full[first,1]+xy.full[second,1])/2,
+ (xy.full[first,2]+xy.full[second,2])/2,
+ first, second)
+ k <- k+1}
+ }}
+
+output=list()
+for(run in 1:x$nrun){
+ runname <- paste('run',run,sep='')
+ output[[runname]] <- list(dir1=list(),dir2=list())
+
+dir1.in <- x[[runname]]$dir1$path
+output[[runname]]$dir1 <- matrix(data = NA, nrow = nrow(dir1.in), ncol = 4)
+colnames(output[[runname]]$dir1) <- c("x.hw","y.hw","first","second")
+rownames(output[[runname]]$dir1) <- rownames(x[[runname]]$dir1$path)
+for(i in 1:nrow(dir1.in)){
+ eval.x <- is.element(halfway[,1], dir1.in[i,1])
+ eval.y <- is.element(halfway[,2], dir1.in[i,2])
+ output[[runname]]$dir1[i,] <- halfway[which(eval.x == TRUE & eval.y == TRUE),]
+ }
+
+dir2.in <- x[[runname]]$dir2$path
+output[[runname]]$dir2 <- matrix(data = NA, nrow = nrow(dir2.in), ncol = 4)
+colnames(output[[runname]]$dir2) <- c("x.hw","y.hw","first","second")
+rownames(output[[runname]]$dir2) <- rownames(x[[runname]]$dir2$path)
+for(i in 1:nrow(dir2.in)){
+ eval.x <- is.element(halfway[,1], dir2.in[i,1])
+ eval.y <- is.element(halfway[,2], dir2.in[i,2])
+ output[[runname]]$dir2[i,] <- halfway[which(eval.x == TRUE & eval.y == TRUE),]
+ }
+}
+
+return(output)
+}
diff --git a/R/dapc.R b/R/dapc.R
new file mode 100644
index 0000000..76fc410
--- /dev/null
+++ b/R/dapc.R
@@ -0,0 +1,1198 @@
+#######
+## dapc
+########
+dapc <- function (x, ...) UseMethod("dapc")
+
+###################
+## dapc.data.frame
+###################
+dapc.data.frame <- function(x, grp, n.pca=NULL, n.da=NULL,
+ center=TRUE, scale=FALSE, var.contrib=TRUE, var.loadings=FALSE,
+ pca.info=TRUE, pca.select=c("nbEig","percVar"), perc.pca=NULL, ..., dudi=NULL){
+
+ ## FIRST CHECKS
+ grp <- as.factor(grp)
+ if(length(grp) != nrow(x)) stop("Inconsistent length for grp")
+ pca.select <- match.arg(pca.select)
+ if(!is.null(perc.pca) & is.null(n.pca)) pca.select <- "percVar"
+ if(is.null(perc.pca) & !is.null(n.pca)) pca.select <- "nbEig"
+ if(!is.null(dudi) && !inherits(dudi, "dudi")) stop("dudi provided, but not of class 'dudi'")
+
+
+ ## SOME GENERAL VARIABLES
+ N <- nrow(x)
+ REDUCEDIM <- is.null(dudi)
+
+ if(REDUCEDIM){ # if no dudi provided
+ ## PERFORM PCA ##
+ maxRank <- min(dim(x))
+ pcaX <- dudi.pca(x, center = center, scale = scale, scannf = FALSE, nf=maxRank)
+ } else { # else use the provided dudi
+ pcaX <- dudi
+ }
+ cumVar <- 100 * cumsum(pcaX$eig)/sum(pcaX$eig)
+
+ if(!REDUCEDIM){
+ myCol <- rep(c("black", "lightgrey"), c(ncol(pcaX$li),length(pcaX$eig)))
+ } else {
+ myCol <- "black"
+ }
+
+ ## select the number of retained PC for PCA
+ if(is.null(n.pca) & pca.select=="nbEig"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the number PCs to retain (>=1): ")
+ n.pca <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(perc.pca) & pca.select=="percVar"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the percentage of variance to retain (0-100): ")
+ nperc.pca <- as.numeric(readLines(n = 1))
+ }
+
+ ## get n.pca from the % of variance to conserve
+ if(!is.null(perc.pca)){
+ n.pca <- min(which(cumVar >= perc.pca))
+ if(perc.pca > 99.999) n.pca <- length(pcaX$eig)
+ if(n.pca<1) n.pca <- 1
+ }
+
+
+ ## keep relevant PCs - stored in XU
+ X.rank <- sum(pcaX$eig > 1e-14)
+ n.pca <- min(X.rank, n.pca)
+ if(n.pca >= N) n.pca <- N-1
+ if(n.pca > N/3) warning("number of retained PCs of PCA may be too large (> N /3)\n results may be unstable ")
+ n.pca <- round(n.pca)
+
+ U <- pcaX$c1[, 1:n.pca, drop=FALSE] # principal axes
+ rownames(U) <- colnames(x) # force to restore names
+ XU <- pcaX$li[, 1:n.pca, drop=FALSE] # principal components
+ XU.lambda <- sum(pcaX$eig[1:n.pca])/sum(pcaX$eig) # sum of retained eigenvalues
+ names(U) <- paste("PCA-pa", 1:ncol(U), sep=".")
+ names(XU) <- paste("PCA-pc", 1:ncol(XU), sep=".")
+
+
+ ## PERFORM DA ##
+ ldaX <- lda(XU, grp, tol=1e-30) # tol=1e-30 is a kludge, but a safe (?) one to avoid fancy rescaling by lda.default
+ lda.dim <- sum(ldaX$svd^2 > 1e-10)
+ ldaX$svd <- ldaX$svd[1:lda.dim]
+ ldaX$scaling <- ldaX$scaling[,1:lda.dim,drop=FALSE]
+
+ if(is.null(n.da)){
+ barplot(ldaX$svd^2, xlab="Linear Discriminants", ylab="F-statistic", main="Discriminant analysis eigenvalues", col=heat.colors(length(levels(grp))) )
+ cat("Choose the number discriminant functions to retain (>=1): ")
+ n.da <- as.integer(readLines(n = 1))
+ }
+
+ ##n.da <- min(n.da, length(levels(grp))-1, n.pca) # can't be more than K-1 disc. func., or more than n.pca
+ n.da <- round(min(n.da, lda.dim)) # can't be more than K-1 disc. func., or more than n.pca
+ predX <- predict(ldaX, dimen=n.da)
+
+
+ ## BUILD RESULT
+ res <- list()
+ res$n.pca <- n.pca
+ res$n.da <- n.da
+ res$tab <- XU
+ res$grp <- grp
+ res$var <- XU.lambda
+ res$eig <- ldaX$svd^2
+ res$loadings <- ldaX$scaling[, 1:n.da, drop=FALSE]
+ res$means <- ldaX$means
+ res$ind.coord <-predX$x
+ res$grp.coord <- apply(res$ind.coord, 2, tapply, grp, mean)
+ res$prior <- ldaX$prior
+ res$posterior <- predX$posterior
+ res$assign <- predX$class
+ res$call <- match.call()
+
+
+ ## optional: store loadings of variables
+ if(pca.info){
+ res$pca.loadings <- as.matrix(U)
+ res$pca.cent <- pcaX$cent
+ res$pca.norm <- pcaX$norm
+ res$pca.eig <- pcaX$eig
+ }
+
+ ## optional: get loadings of variables
+ if(var.contrib || var.loadings){
+ var.load <- as.matrix(U) %*% as.matrix(ldaX$scaling[,1:n.da,drop=FALSE])
+
+ if(var.contrib){
+ f1 <- function(x){
+ temp <- sum(x*x)
+ if(temp < 1e-12) return(rep(0, length(x)))
+ return(x*x / temp)
+ }
+ res$var.contr <- apply(var.load, 2, f1)
+ }
+ if(var.loadings) res$var.load <- var.load
+ }
+
+ class(res) <- "dapc"
+ return(res)
+} # end dapc.data.frame
+
+
+
+
+
+#############
+## dapc.matrix
+#############
+dapc.matrix <- function(x, ...){
+ return(dapc(as.data.frame(x), ...))
+}
+
+
+
+
+#############
+## dapc.genind
+#############
+dapc.genind <- function(x, pop=NULL, n.pca=NULL, n.da=NULL,
+ scale=FALSE, truenames=TRUE, var.contrib=TRUE, var.loadings=FALSE,
+ pca.info=TRUE, pca.select=c("nbEig","percVar"), perc.pca=NULL, ...){
+
+ ## FIRST CHECKS
+ if(!is.genind(x)) stop("x must be a genind object.")
+
+ if(is.null(pop)) {
+ pop.fac <- pop(x)
+ } else {
+ pop.fac <- pop
+ }
+
+ if(is.null(pop.fac)) stop("x does not include pre-defined populations, and `pop' is not provided")
+
+
+ ## SOME GENERAL VARIABLES
+ N <- nrow(x at tab)
+
+ ## PERFORM PCA ##
+ maxRank <- min(dim(x at tab))
+
+ X <- scaleGen(x, center = TRUE, scale = scale,
+ NA.method = "mean")
+
+ ## CALL DATA.FRAME METHOD ##
+ res <- dapc(X, grp=pop.fac, n.pca=n.pca, n.da=n.da,
+ center=FALSE, scale=FALSE, var.contrib=var.contrib,
+ var.loadings=var.loadings, pca.select=pca.select, perc.pca=perc.pca)
+
+ res$call <- match.call()
+
+ ## restore centring/scaling
+ res$pca.cent <- attr(X, "scaled:center")
+
+ if(scale) {
+ res$pca.norm <- attr(X, "scaled:scale")
+ }
+
+ return(res)
+} # end dapc.genind
+
+
+
+
+
+
+######################
+## Function dapc.dudi
+######################
+dapc.dudi <- function(x, grp, ...){
+ return(dapc.data.frame(x$li, grp, dudi=x, ...))
+}
+
+
+
+
+
+#################
+## dapc.genlight
+#################
+dapc.genlight <- function(x, pop=NULL, n.pca=NULL, n.da=NULL,
+ scale=FALSE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE,
+ pca.select=c("nbEig","percVar"), perc.pca=NULL, glPca=NULL, ...){
+ ## FIRST CHECKS ##
+ if(!inherits(x, "genlight")) stop("x must be a genlight object.")
+
+ pca.select <- match.arg(pca.select)
+
+ if(is.null(pop)) {
+ pop.fac <- pop(x)
+ } else {
+ pop.fac <- pop
+ }
+
+ if(is.null(pop.fac)) stop("x does not include pre-defined populations, and `pop' is not provided")
+
+
+
+ ## PERFORM PCA ##
+ REDUCEDIM <- is.null(glPca)
+
+ if(REDUCEDIM){ # if no glPca provided
+ maxRank <- min(c(nInd(x), nLoc(x)))
+ pcaX <- glPca(x, center = TRUE, scale = scale, nf=maxRank, loadings=FALSE, returnDotProd = TRUE, ...)
+ }
+
+ if(!REDUCEDIM){ # else use the provided glPca object
+ if(is.null(glPca$loadings) & var.contrib) {
+ warning("Contribution of variables requested but glPca object provided without loadings.")
+ var.contrib <- FALSE
+ }
+ pcaX <- glPca
+ }
+
+ if(is.null(n.pca)){
+ cumVar <- 100 * cumsum(pcaX$eig)/sum(pcaX$eig)
+ }
+
+
+ ## select the number of retained PC for PCA
+ if(!REDUCEDIM){
+ myCol <- rep(c("black", "lightgrey"), c(ncol(pcaX$scores),length(pcaX$eig)))
+ } else {
+ myCol <- "black"
+ }
+
+ if(is.null(n.pca) & pca.select=="nbEig"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the number PCs to retain (>=1): ")
+ n.pca <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(perc.pca) & pca.select=="percVar"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the percentage of variance to retain (0-100): ")
+ nperc.pca <- as.numeric(readLines(n = 1))
+ }
+
+ ## get n.pca from the % of variance to conserve
+ if(!is.null(perc.pca)){
+ n.pca <- min(which(cumVar >= perc.pca))
+ if(perc.pca > 99.999) n.pca <- length(pcaX$eig)
+ if(n.pca<1) n.pca <- 1
+ }
+
+ if(!REDUCEDIM){
+ if(n.pca > ncol(pcaX$scores)) {
+ n.pca <- ncol(pcaX$scores)
+ }
+ }
+
+
+ ## recompute PCA with loadings if needed
+ if(REDUCEDIM){
+ pcaX <- glPca(x, center = TRUE, scale = scale, nf=n.pca, loadings=var.contrib, matDotProd = pcaX$dotProd)
+ }
+
+
+ ## keep relevant PCs - stored in XU
+ N <- nInd(x)
+ X.rank <- sum(pcaX$eig > 1e-14)
+ n.pca <- min(X.rank, n.pca)
+ if(n.pca >= N) n.pca <- N-1
+ if(n.pca > N/3) warning("number of retained PCs of PCA may be too large (> N /3)\n results may be unstable ")
+
+ U <- pcaX$loadings[, 1:n.pca, drop=FALSE] # principal axes
+ XU <- pcaX$scores[, 1:n.pca, drop=FALSE] # principal components
+ XU.lambda <- sum(pcaX$eig[1:n.pca])/sum(pcaX$eig) # sum of retained eigenvalues
+ names(U) <- paste("PCA-pa", 1:ncol(U), sep=".")
+ names(XU) <- paste("PCA-pc", 1:ncol(XU), sep=".")
+
+
+ ## PERFORM DA ##
+ ldaX <- lda(XU, pop.fac, tol=1e-30) # tol=1e-30 is a kludge, but a safe (?) one to avoid fancy rescaling by lda.default
+ lda.dim <- sum(ldaX$svd^2 > 1e-10)
+ ldaX$svd <- ldaX$svd[1:lda.dim]
+ ldaX$scaling <- ldaX$scaling[,1:lda.dim,drop=FALSE]
+
+ if(is.null(n.da)){
+ barplot(ldaX$svd^2, xlab="Linear Discriminants", ylab="F-statistic", main="Discriminant analysis eigenvalues", col=heat.colors(length(levels(pop.fac))) )
+ cat("Choose the number discriminant functions to retain (>=1): ")
+ n.da <- as.integer(readLines(n = 1))
+ }
+
+ n.da <- min(n.da, length(levels(pop.fac))-1, n.pca, sum(ldaX$svd>1e-10)) # can't be more than K-1 disc. func., or more than n.pca
+ n.da <- round(n.da)
+ predX <- predict(ldaX, dimen=n.da)
+
+
+ ## BUILD RESULT
+ res <- list()
+ res$n.pca <- n.pca
+ res$n.da <- n.da
+ res$tab <- XU
+ res$grp <- pop.fac
+ res$var <- XU.lambda
+ res$eig <- ldaX$svd^2
+ res$loadings <- ldaX$scaling[, 1:n.da, drop=FALSE]
+ res$means <- ldaX$means
+ res$ind.coord <-predX$x
+ res$grp.coord <- apply(res$ind.coord, 2, tapply, pop.fac, mean)
+ res$prior <- ldaX$prior
+ res$posterior <- predX$posterior
+ res$assign <- predX$class
+ res$call <- match.call()
+
+
+ ## optional: store loadings of variables
+ if(pca.info){
+ res$pca.loadings <- as.matrix(U)
+ res$pca.cent <- glMean(x,alleleAsUnit=FALSE)
+ if(scale) {
+ res$pca.norm <- sqrt(glVar(x,alleleAsUnit=FALSE))
+ } else {
+ res$pca.norm <- rep(1, nLoc(x))
+ }
+ res$pca.eig <- pcaX$eig
+ }
+
+ ## optional: get loadings of variables
+ if(var.contrib || var.loadings){
+ var.load <- as.matrix(U) %*% as.matrix(ldaX$scaling[,1:n.da,drop=FALSE])
+
+ if(var.contrib){
+ f1 <- function(x){
+ temp <- sum(x*x)
+ if(temp < 1e-12) return(rep(0, length(x)))
+ return(x*x / temp)
+ }
+ res$var.contr <- apply(var.load, 2, f1)
+ }
+ if(var.loadings) res$var.load <- var.load
+ }
+
+ class(res) <- "dapc"
+ return(res)
+} # end dapc.genlight
+
+
+
+
+
+
+######################
+# Function print.dapc
+######################
+print.dapc <- function(x, ...){
+ cat("\t#################################################\n")
+ cat("\t# Discriminant Analysis of Principal Components #\n")
+ cat("\t#################################################\n")
+ cat("class: ")
+ cat(class(x))
+ cat("\n$call: ")
+ print(x$call)
+ cat("\n$n.pca:", x$n.pca, "first PCs of PCA used")
+ cat("\n$n.da:", x$n.da, "discriminant functions saved")
+ cat("\n$var (proportion of conserved variance):", round(x$var,3))
+ cat("\n\n$eig (eigenvalues): ")
+ l0 <- sum(x$eig >= 0)
+ cat(signif(x$eig, 4)[1:(min(5, l0))])
+ if (l0 > 5)
+ cat(" ...\n\n")
+
+ ## vectors
+ TABDIM <- 4
+ if(!is.null(x$pca.loadings)){
+ TABDIM <- TABDIM + 3
+ }
+ sumry <- array("", c(TABDIM, 3), list(1:TABDIM, c("vector", "length", "content")))
+ sumry[1, ] <- c('$eig', length(x$eig), 'eigenvalues')
+ sumry[2, ] <- c('$grp', length(x$grp), 'prior group assignment')
+ sumry[3, ] <- c('$prior', length(x$prior), 'prior group probabilities')
+ sumry[4, ] <- c('$assign', length(x$assign), 'posterior group assignment')
+ if(!is.null(x$pca.loadings)){
+ sumry[5, ] <- c('$pca.cent', length(x$pca.cent), 'centring vector of PCA')
+ sumry[6, ] <- c('$pca.norm', length(x$pca.norm), 'scaling vector of PCA')
+ sumry[7, ] <- c('$pca.eig', length(x$pca.eig), 'eigenvalues of PCA')
+ }
+ class(sumry) <- "table"
+ print(sumry)
+
+ ## data.frames
+ cat("\n")
+ TABDIM <- 6
+ if(!is.null(x$pca.loadings)){
+ TABDIM <- TABDIM + 1
+ }
+ if(!is.null(x$var.contr)){
+ TABDIM <- TABDIM + 1
+ }
+ if(!is.null(x$var.load)){
+ TABDIM <- TABDIM + 1
+ }
+
+ sumry <- array("", c(TABDIM, 4), list(1:TABDIM, c("data.frame", "nrow", "ncol", "content")))
+
+ sumry[1, ] <- c("$tab", nrow(x$tab), ncol(x$tab), "retained PCs of PCA")
+ sumry[2, ] <- c("$means", nrow(x$means), ncol(x$means), "group means")
+ sumry[3, ] <- c("$loadings", nrow(x$loadings), ncol(x$loadings), "loadings of variables")
+ sumry[4, ] <- c("$ind.coord", nrow(x$ind.coord), ncol(x$ind.coord), "coordinates of individuals (principal components)")
+ sumry[5, ] <- c("$grp.coord", nrow(x$grp.coord), ncol(x$grp.coord), "coordinates of groups")
+ sumry[6, ] <- c("$posterior", nrow(x$posterior), ncol(x$posterior), "posterior membership probabilities")
+ count <- 6
+ if(!is.null(x$pca.loadings)){
+ count <- count+1
+ sumry[count, ] <- c("$pca.loadings", nrow(x$pca.loadings), ncol(x$pca.loadings), "PCA loadings of original variables")
+ }
+ if(!is.null(x$var.contr)){
+ count <- count+1
+ sumry[count, ] <- c("$var.contr", nrow(x$var.contr), ncol(x$var.contr), "contribution of original variables")
+ }
+ if(!is.null(x$var.load)){
+ count <- count+1
+ sumry[count, ] <- c("$var.load", nrow(x$var.load), ncol(x$var.load), "loadings of original variables")
+ }
+ class(sumry) <- "table"
+ print(sumry)
+
+ ## cat("\nother elements: ")
+ ## if (length(names(x)) > 15)
+ ## cat(names(x)[15:(length(names(x)))], "\n")
+ ## else cat("NULL\n")
+ cat("\n")
+} # end print.dapc
+
+
+
+
+
+
+##############
+## summary.dapc
+##############
+summary.dapc <- function(object, ...){
+ x <- object
+ res <- list()
+
+ ## number of dimensions
+ res$n.dim <- ncol(x$loadings)
+ res$n.pop <- length(levels(x$grp))
+
+ ## assignment success
+ temp <- as.character(x$grp)==as.character(x$assign)
+ res$assign.prop <- mean(temp)
+ res$assign.per.pop <- tapply(temp, x$grp, mean)
+
+ ## group sizes
+ res$prior.grp.size <- table(x$grp)
+ res$post.grp.size <- table(x$assign)
+
+ return(res)
+} # end summary.dapc
+
+
+
+
+
+
+##############
+## scatter.dapc
+##############
+#' @importFrom vegan orditorp
+scatter.dapc <- function(x, xax=1, yax=2, grp=x$grp, col=seasun(length(levels(grp))), pch=20, bg="white", solid=.7,
+ scree.da=TRUE, scree.pca=FALSE, posi.da="bottomright", posi.pca="bottomleft", bg.inset="white",
+ ratio.da=.25, ratio.pca=.25, inset.da=0.02, inset.pca=0.02, inset.solid=.5,
+ onedim.filled=TRUE, mstree=FALSE, lwd=1, lty=1, segcol="black",
+ legend=FALSE, posi.leg="topright", cleg=1, txt.leg=levels(grp),
+ cstar = 1, cellipse = 1.5, axesell = FALSE, label = levels(grp), clabel = 1, xlim = NULL, ylim = NULL,
+ grid = FALSE, addaxes = TRUE, origin = c(0,0), include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft",
+ cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, label.inds = NULL, ...){
+ ONEDIM <- xax==yax | ncol(x$ind.coord)==1
+
+
+ ## recycle color and pch
+ col <- rep(col, length(levels(grp)))
+ pch <- rep(pch, length(levels(grp)))
+ col <- transp(col, solid)
+ bg.inset <- transp(bg.inset, inset.solid)
+
+ ## handle grp
+ if(is.null(grp)){
+ grp <- x$grp
+ }
+
+ ## handle xax or yax NULL
+ if(is.null(xax)||is.null(yax)){
+ xax <- 1L
+ yax <- ifelse(ncol(x$ind.coord)==1L, 1L, 2L)
+ ONEDIM <- TRUE
+ }
+
+ ## handle 1 dimensional plot
+ if(!ONEDIM){
+ ## set par
+ opar <- par(mar = par("mar"))
+ par(mar = c(0.1, 0.1, 0.1, 0.1), bg=bg)
+ on.exit(par(opar))
+ axes <- c(xax,yax)
+
+ ## basic empty plot
+ s.class(x$ind.coord[,axes], fac=grp, col=col, cpoint=0, cstar = cstar, cellipse = cellipse, axesell = axesell, label = label,
+ clabel = clabel, xlim = xlim, ylim = ylim, grid = grid, addaxes = addaxes, origin = origin, include.origin = include.origin,
+ sub = sub, csub = csub, possub = possub, cgrid = cgrid, pixmap = pixmap, contour = contour, area = area)
+
+ ## add points
+ colfac <- pchfac <- grp
+ levels(colfac) <- col
+ levels(pchfac) <- pch
+ colfac <- as.character(colfac)
+ pchfac <- as.character(pchfac)
+ if(is.numeric(col)) colfac <- as.numeric(colfac)
+ if(is.numeric(pch)) pchfac <- as.numeric(pchfac)
+
+ points(x$ind.coord[,xax], x$ind.coord[,yax], col=colfac, pch=pchfac, ...)
+ s.class(x$ind.coord[,axes], fac=grp, col=col, cpoint=0, add.plot=TRUE, cstar = cstar, cellipse = cellipse, axesell = axesell, label = label,
+ clabel = clabel, xlim = xlim, ylim = ylim, grid = grid, addaxes = addaxes, origin = origin, include.origin = include.origin,
+ sub = sub, csub = csub, possub = possub, cgrid = cgrid, pixmap = pixmap, contour = contour, area = area)
+
+ # Add labels of individuals if specified. Play around with "air" to get
+ # a satisfactory result.
+ if (!is.null(label.inds) & is.list(label.inds)) {
+ appendList <- function (x, val) {
+ # recursevly "bind" a list into a longer list,
+ # from http://stackoverflow.com/a/9519964/322912
+ stopifnot(is.list(x), is.list(val))
+ xnames <- names(x)
+ for (v in names(val)) {
+ x[[v]] <- if (v %in% xnames && is.list(x[[v]]) && is.list(val[[v]]))
+ appendList(x[[v]], val[[v]])
+ else c(x[[v]], val[[v]])
+ }
+ x
+ }
+
+ do.call("orditorp", c(appendList(list(x = x$ind.coord[, c(xax, yax)], display = "species"),
+ label.inds)))
+ }
+
+ ## add minimum spanning tree if needed
+ if(mstree){
+ meanposi <- apply(x$tab,2, tapply, grp, mean)
+ D <- dist(meanposi)^2
+ tre <- ade4::mstree(D)
+ x0 <- x$grp.coord[tre[,1], axes[1]]
+ y0 <- x$grp.coord[tre[,1], axes[2]]
+ x1 <- x$grp.coord[tre[,2], axes[1]]
+ y1 <- x$grp.coord[tre[,2], axes[2]]
+ segments(x0, y0, x1, y1, lwd=lwd, lty=lty, col=segcol)
+ }
+
+ } else {
+ ## set screeplot of DA to FALSE (just 1 bar)
+ scree.da <- FALSE
+
+ ## get plotted axis
+ if(ncol(x$ind.coord)==1) {
+ pcLab <- 1
+ } else{
+ pcLab <- xax
+ }
+ ## get densities
+ ldens <- tapply(x$ind.coord[,pcLab], grp, density)
+ allx <- unlist(lapply(ldens, function(e) e$x))
+ ally <- unlist(lapply(ldens, function(e) e$y))
+ par(bg=bg)
+ plot(allx, ally, type="n", xlab=paste("Discriminant function", pcLab), ylab="Density")
+ for(i in 1:length(ldens)){
+ if(!onedim.filled) {
+ lines(ldens[[i]]$x,ldens[[i]]$y, col=col[i], lwd=2) # add lines
+ } else {
+ polygon(c(ldens[[i]]$x,rev(ldens[[i]]$x)),c(ldens[[i]]$y,rep(0,length(ldens[[i]]$x))), col=col[i], lwd=2, border=col[i]) # add lines
+ }
+ points(x=x$ind.coord[grp==levels(grp)[i],pcLab], y=rep(0, sum(grp==levels(grp)[i])), pch="|", col=col[i]) # add points for indiv
+ }
+ }
+
+ ## ADD INSETS ##
+ ## group legend
+ if(legend){
+ ## add a legend
+ temp <- list(...)$cex
+ if(is.null(temp)) temp <- 1
+ if(ONEDIM | temp<0.5 | all(pch=="")) {
+ legend(posi.leg, fill=col, legend=txt.leg, cex=cleg, bg=bg.inset)
+ } else {
+ legend(posi.leg, col=col, legend=txt.leg, cex=cleg, bg=bg.inset, pch=pch, pt.cex=temp)
+ }
+ }
+
+ ## eigenvalues discriminant analysis
+ if(scree.da && ratio.da>.01) {
+ inset <- function(){
+ myCol <- rep("white", length(x$eig))
+ myCol[1:x$n.da] <- "grey"
+ myCol[c(xax, yax)] <- "black"
+ myCol <- transp(myCol, inset.solid)
+ barplot(x$eig, col=myCol, xaxt="n", yaxt="n", ylim=c(0, x$eig[1]*1.1))
+ mtext(side=3, "DA eigenvalues", line=-1.2, adj=.8)
+ box()
+ }
+
+ add.scatter(inset(), posi=posi.da, ratio=ratio.da, bg.col=bg.inset, inset=inset.da)
+ ##add.scatter.eig(x$eig, ncol(x$loadings), axes[1], axes[2], posi=posi, ratio=ratio, csub=csub) # does not allow for bg
+ }
+
+ ## eigenvalues PCA
+ if(scree.pca && !is.null(x$pca.eig) && ratio.pca>.01) {
+ inset <- function(){
+ temp <- 100* cumsum(x$pca.eig) / sum(x$pca.eig)
+ myCol <- rep(c("black","grey"), c(x$n.pca, length(x$pca.eig)))
+ myCol <- transp(myCol, inset.solid)
+ plot(temp, col=myCol, ylim=c(0,115),
+ type="h", xaxt="n", yaxt="n", xlab="", ylab="", lwd=2)
+ mtext(side=3, "PCA eigenvalues", line=-1.2, adj=.1)
+ }
+ add.scatter(inset(), posi=posi.pca, ratio=ratio.pca, bg.col=bg.inset, inset=inset.pca)
+ }
+
+
+ return(invisible(match.call()))
+} # end scatter.dapc
+
+
+
+
+
+
+############
+## assignplot
+############
+assignplot <- function(x, only.grp=NULL, subset=NULL, new.pred=NULL, cex.lab=.75, pch=3){
+ if(!inherits(x, "dapc")) stop("x is not a dapc object")
+
+ ## handle data from predict.dapc ##
+ if(!is.null(new.pred)){
+ n.new <- length(new.pred$assign)
+ x$grp <- c(as.character(x$grp), rep("unknown", n.new))
+ x$assign <- c(as.character(x$assign), as.character(new.pred$assign))
+ x$posterior <- rbind(x$posterior, new.pred$posterior)
+ }
+
+
+ ## treat other arguments ##
+ if(!is.null(only.grp)){
+ only.grp <- as.character(only.grp)
+ ori.grp <- as.character(x$grp)
+ x$grp <- x$grp[only.grp==ori.grp]
+ x$assign <- x$assign[only.grp==ori.grp]
+ x$posterior <- x$posterior[only.grp==ori.grp, , drop=FALSE]
+ } else if(!is.null(subset)){
+ x$grp <- x$grp[subset]
+ x$assign <- x$assign[subset]
+ x$posterior <- x$posterior[subset, , drop=FALSE]
+ }
+
+
+ ##table.paint(x$posterior, col.lab=ori.grp, ...)
+ ## symbols(x$posterior)
+
+
+ ## FIND PLOT PARAMETERS
+ n.grp <- ncol(x$posterior)
+ n.ind <- nrow(x$posterior)
+ Z <- t(x$posterior)
+ Z <- Z[,ncol(Z):1,drop=FALSE ]
+
+ image(x=1:n.grp, y=seq(.5, by=1, le=n.ind), Z, col=rev(heat.colors(100)), yaxt="n", ylab="", xaxt="n", xlab="Clusters")
+ axis(side=1, at=1:n.grp,tick=FALSE, labels=colnames(x$posterior))
+ axis(side=2, at=seq(.5, by=1, le=n.ind), labels=rev(rownames(x$posterior)), las=1, cex.axis=cex.lab)
+ abline(h=1:n.ind, col="lightgrey")
+ abline(v=seq(0.5, by=1, le=n.grp))
+ box()
+
+ newGrp <- colnames(x$posterior)
+ x.real.coord <- rev(match(x$grp, newGrp))
+ y.real.coord <- seq(.5, by=1, le=n.ind)
+
+ points(x.real.coord, y.real.coord, col="deepskyblue2", pch=pch)
+
+ return(invisible(match.call()))
+} # end assignplot
+
+
+
+
+
+############
+## compoplot
+############
+compoplot <- function(x, only.grp=NULL, subset=NULL, new.pred=NULL, col=NULL, lab=NULL,
+ legend=TRUE, txt.leg=NULL, ncol=4, posi=NULL, cleg=.8, bg=transp("white"), ...){
+ if(!inherits(x, "dapc")) stop("x is not a dapc object")
+
+
+ ## HANDLE ARGUMENTS ##
+ ngrp <- length(levels(x$grp))
+
+ ## col
+ if(is.null(col)){
+ col <- rainbow(ngrp)
+ }
+
+ ## lab
+ if(is.null(lab)){
+ lab <- rownames(x$tab)
+ } else {
+ ## recycle labels
+ lab <- rep(lab, le=nrow(x$tab))
+ }
+
+ ## posi
+ if(is.null(posi)){
+ posi <- list(x=0, y=-.01)
+ }
+
+ ## txt.leg
+ if(is.null(txt.leg)){
+ txt.leg <- levels(x$grp)
+ }
+
+ ## HANDLE DATA FROM PREDICT.DAPC ##
+ if(!is.null(new.pred)){
+ n.new <- length(new.pred$assign)
+ x$grp <- c(as.character(x$grp), rep("unknown", n.new))
+ x$assign <- c(as.character(x$assign), as.character(new.pred$assign))
+ x$posterior <- rbind(x$posterior, new.pred$posterior)
+ lab <- c(lab, rownames(new.pred$posterior))
+ }
+
+
+ ## TREAT OTHER ARGUMENTS ##
+ if(!is.null(only.grp)){
+ only.grp <- as.character(only.grp)
+ ori.grp <- as.character(x$grp)
+ x$grp <- x$grp[only.grp==ori.grp]
+ x$assign <- x$assign[only.grp==ori.grp]
+ x$posterior <- x$posterior[only.grp==ori.grp, , drop=FALSE]
+ lab <- lab[only.grp==ori.grp]
+ } else if(!is.null(subset)){
+ x$grp <- x$grp[subset]
+ x$assign <- x$assign[subset]
+ x$posterior <- x$posterior[subset, , drop=FALSE]
+ lab <- lab[subset]
+ }
+
+
+ ## MAKE THE PLOT ##
+ Z <- t(x$posterior)
+ barplot(Z, border=NA, col=col, ylab="membership probability", names=lab, las=3, ...)
+
+ if(legend){
+ oxpd <- par("xpd")
+ par(xpd=TRUE)
+ legend(posi, fill=col, leg=txt.leg, cex=cleg, ncol=ncol, bg=bg)
+ on.exit(par(xpd=oxpd))
+ }
+
+ return(invisible(match.call()))
+} # end compoplot
+
+
+
+
+
+###############
+## a.score
+###############
+a.score <- function(x, n.sim=10, ...){
+ if(!inherits(x,"dapc")) stop("x is not a dapc object")
+
+ ## perform DAPC based on permuted groups
+ lsim <- lapply(1:n.sim, function(i) summary(dapc(x$tab, sample(x$grp), n.pca=x$n.pca, n.da=x$n.da))$assign.per.pop)
+ sumry <- summary(x)
+
+ ## get the a-scores
+ f1 <- function(Pt, Pf){
+ tol <- 1e-7
+ ##res <- (Pt-Pf) / (1-Pf)
+ ##res[Pf > (1-tol)] <- 0
+ res <- Pt-Pf
+ return(res)
+ }
+
+ lscores <- lapply(lsim, function(e) f1(sumry$assign.per.pop, e))
+
+ ## make a table of a-scores
+ tab <- data.frame(lscores)
+ colnames(tab) <- paste("sim", 1:n.sim, sep=".")
+ rownames(tab) <- names(sumry$assign.per.pop)
+ tab <- t(as.matrix(tab))
+
+ ## make result
+ res <- list()
+ res$tab <- tab
+ res$pop.score <- apply(tab, 2, mean)
+ res$mean <- mean(tab)
+
+ return(res)
+
+} # end a.score
+
+
+
+
+
+
+
+##############
+## optim.a.score
+##############
+optim.a.score <- function(x, n.pca=1:ncol(x$tab), smart=TRUE, n=10, plot=TRUE,
+ n.sim=10, n.da=length(levels(x$grp)), ...){
+ ## A FEW CHECKS ##
+ if(!inherits(x,"dapc")) stop("x is not a dapc object")
+ if(max(n.pca)>ncol(x$tab)) {
+ n.pca <- min(n.pca):ncol(x$tab)
+ }
+ if(n.da>length(levels(x$grp))){
+ n.da <- min(n.da):length(levels(x$grp))
+ }
+ pred <- NULL
+ if(length(n.pca)==1){
+ n.pca <- 1:n.pca
+ }
+ if(length(n.da)==1){
+ n.da <- 1:n.da
+ }
+
+
+ ## AUXILIARY FUNCTION ##
+ f1 <- function(ndim){
+ temp <- dapc(x$tab[,1:ndim,drop=FALSE], x$grp, n.pca=ndim, n.da=x$n.da)
+ a.score(temp, n.sim=n.sim)$pop.score
+ }
+
+
+ ## SMART: COMPUTE A FEW VALUES, PREDICT THE BEST PICK ##
+ if(smart){
+ ## if(!require(stats)) stop("the package stats is required for 'smart' option")
+ o.min <- min(n.pca)
+ o.max <- max(n.pca)
+ n.pca <- pretty(n.pca, n) # get evenly spaced nb of retained PCs
+ n.pca <- n.pca[n.pca>0 & n.pca<=ncol(x$tab)]
+ if(!any(o.min==n.pca)) n.pca <- c(o.min, n.pca) # make sure range is OK
+ if(!any(o.max==n.pca)) n.pca <- c(o.max, n.pca) # make sure range is OK
+ lres <- lapply(n.pca, f1)
+ names(lres) <- n.pca
+ means <- sapply(lres, mean)
+ sp1 <- smooth.spline(n.pca, means) # spline smoothing
+ pred <- predict(sp1, x=1:max(n.pca))
+ best <- pred$x[which.max(pred$y)]
+ } else { ## DO NOT TRY TO BE SMART ##
+ lres <- lapply(n.pca, f1)
+ names(lres) <- n.pca
+ best <- which.max(sapply(lres, mean))
+ means <- sapply(lres, mean)
+ }
+
+
+ ## MAKE FINAL OUTPUT ##
+ res <- list()
+ res$pop.score <- lres
+ res$mean <- means
+ if(!is.null(pred)) res$pred <- pred
+ res$best <- best
+
+ ## PLOTTING (OPTIONAL) ##
+ if(plot){
+ if(smart){
+ boxplot(lres, at=n.pca, col="gold", xlab="Number of retained PCs", ylab="a-score", xlim=range(n.pca)+c(-1,1), ylim=c(-.1,1.1))
+ lines(pred, lwd=3)
+ points(pred$x[best], pred$y[best], col="red", lwd=3)
+ title("a-score optimisation - spline interpolation")
+ mtext(paste("Optimal number of PCs:", res$best), side=3)
+ } else {
+ myCol <- rep("gold", length(lres))
+ myCol[best] <- "red"
+ boxplot(lres, at=n.pca, col=myCol, xlab="Number of retained PCs", ylab="a-score", xlim=range(n.pca)+c(-1,1), ylim=c(-.1,1.1))
+ lines(n.pca, sapply(lres, mean), lwd=3, type="b")
+ myCol <- rep("black", length(lres))
+ myCol[best] <- "red"
+ points(n.pca, res$mean, lwd=3, col=myCol)
+ title("a-score optimisation - basic search")
+ mtext(paste("Optimal number of PCs:", res$best), side=3)
+ }
+ }
+
+ return(res)
+} # end optim.a.score
+
+
+
+
+
+
+#############
+## as.lda.dapc
+#############
+as.lda <- function(...){
+ UseMethod("as.lda")
+}
+
+as.lda.dapc <- function(x, ...){
+ if(!inherits(x,"dapc")) stop("x is not a dapc object")
+ res <- list()
+
+ res$N <- nrow(res$ind.coord)
+ res$call <- match.call()
+ res$counts <- as.integer(table(x$grp))
+ res$lev <- names(res$counts) <- levels(x$grp)
+ res$means <- x$means
+ res$prior <- x$prior
+ res$scaling <- x$loadings
+ res$svd <- sqrt(x$eig)
+
+ class(res) <- "lda"
+
+ return(res)
+} # end as.lda.dapc
+
+
+
+
+
+
+##############
+## predict.dapc
+##############
+predict.dapc <- function(object, newdata, prior = object$prior, dimen,
+ method = c("plug-in", "predictive", "debiased"), ...){
+
+ if(!inherits(object,"dapc")) stop("x is not a dapc object")
+ method <- match.arg(method)
+
+ x <- as.lda(object)
+
+
+ ## HANDLE NEW DATA ##
+ if(!missing(newdata)){
+ ## make a few checks
+ if(is.null(object$pca.loadings)) stop("DAPC object does not contain loadings of original variables. \nPlease re-run DAPC using 'pca.loadings=TRUE'.")
+ newdata <- as.matrix(newdata) # to force conversion, notably from genlight objects
+ if(ncol(newdata) != nrow(object$pca.loadings)) stop("Number of variables in newdata does not match original data.")
+
+ ## centre/scale data
+ for(i in 1:nrow(newdata)){ # this is faster for large, flat matrices)
+ newdata[i,] <- (newdata[i,] - object$pca.cent) / object$pca.norm
+ }
+ newdata[is.na(newdata)] <- 0
+
+ ## project as supplementary individuals
+ XU <- newdata %*% as.matrix(object$pca.loadings)
+ } else {
+ XU <- object$tab
+ }
+
+ ## FORCE IDENTICAL VARIABLE NAMES ##
+ colnames(XU) <- colnames(object$tab)
+
+
+ ## HANDLE DIMEN ##
+ if(!missing(dimen)){
+ if(dimen > object$n.da) stop(paste("Too many dimensions requested. \nOnly", object$n.da, "discriminant functions were saved in DAPC."))
+ } else {
+ dimen <- object$n.da
+ }
+
+ ## CALL PREDICT.LDA ##
+ temp <- predict(x, XU, prior, dimen, method, ...)
+
+
+ ## FORMAT OUTPUT ##
+ res <- list()
+ res$assign <- temp$class
+ res$posterior <- temp$posterior
+ res$ind.scores <- temp$x
+
+ return(res)
+
+} # end predict.dapc
+
+
+
+
+
+
+
+############
+## xvalDapc
+############
+
+xvalDapc <- function (x, ...) UseMethod("xvalDapc")
+
+xvalDapc.data.frame <- function(x, grp, n.pca.max, n.da=NULL, training.set = 0.9,
+ result=c("groupMean","overall"),
+ center=TRUE, scale=FALSE, n.pca=NULL, n.rep=10, ...){
+
+ ## CHECKS ##
+ grp <- factor(grp)
+ n.pca <- n.pca[n.pca>0]
+ result <- match.arg(result)
+ if(is.null(n.da)) {
+ n.da <- length(levels(grp))-1
+ }
+
+ ## GET TRAINING SET SIZE ##
+ N <- nrow(x)
+ N.training <- round(N*training.set)
+
+ ## GET FULL PCA ##
+ if(missing(n.pca.max)) n.pca.max <- min(dim(x))
+ pcaX <- dudi.pca(x, nf=n.pca.max, scannf=FALSE, center=center, scale=scale)
+ n.pca.max <- min(n.pca.max,pcaX$rank,N.training-1)
+
+ ## DETERMINE N.PCA IF NEEDED ##
+ if(is.null(n.pca)){
+ n.pca <- round(pretty(1:n.pca.max,10))
+ }
+ n.pca <- n.pca[n.pca>0 & n.pca<(N.training-1)]
+
+ ## FUNCTION GETTING THE % OF ACCURATE PREDICTION FOR ONE NUMBER OF PCA PCs ##
+ ## n.pca is a number of retained PCA PCs
+ VOID.GRP <- FALSE # will be TRUE if empty group happened
+ get.prop.pred <- function(n.pca){
+ f1 <- function(){
+ toKeep <- sample(1:N, N.training)
+ if(!(all(table(grp[toKeep])>0) & all(table(grp[-toKeep])>0))) VOID.GRP <<- TRUE
+ temp.pca <- pcaX
+ temp.pca$li <- temp.pca$li[toKeep,,drop=FALSE]
+ temp.dapc <- suppressWarnings(dapc(x[toKeep,,drop=FALSE], grp[toKeep], n.pca=n.pca, n.da=n.da, dudi=temp.pca))
+ temp.pred <- predict.dapc(temp.dapc, newdata=x[-toKeep,,drop=FALSE])
+ if(result=="overall"){
+ out <- mean(temp.pred$assign==grp[-toKeep])
+ }
+ if(result=="groupMean"){
+ out <- mean(tapply(temp.pred$assign==grp[-toKeep], grp[-toKeep], mean), na.rm=TRUE)
+ }
+ return(out)
+ }
+ return(replicate(n.rep, f1()))
+ }
+
+
+ ## GET %SUCCESSFUL OF ACCURATE PREDICTION FOR ALL VALUES ##
+ res.all <- unlist(lapply(n.pca, get.prop.pred))
+ if(VOID.GRP) warning("At least one group was absent from the training / validating sets.\nTry using smaller training sets.")
+ res <- data.frame(n.pca=rep(n.pca, each=n.rep), success=res.all)
+ return(res)
+} # end xvalDapc.data.frame
+
+
+xvalDapc.matrix <- xvalDapc.data.frame
+
+
+
+
+
+
+## #############
+## ## discriVal
+## #############
+
+## discriVal <- function (x, ...) UseMethod("discriVal")
+
+## discriVal.data.frame <- function(x, grp, n.pca.max, n.da=NULL, center=TRUE, scale=FALSE, n.pca=NULL, ...){
+
+## ## CHECKS ##
+## grp <- factor(grp)
+## n.pca <- n.pca[n.pca>0]
+## if(is.null(n.da)) {
+## n.da <- length(levels(grp))-1
+## }
+
+## ## GET FULL PCA ##
+## if(missing(n.pca.max)) n.pca.max <- min(dim(x))
+## pcaX <- dudi.pca(x, nf=n.pca.max, scannf=FALSE, center=center, scale=scale)
+## n.pca.max <- min(n.pca.max,pcaX$rank)
+
+## ## DETERMINE N.PCA IF NEEDED ##
+## if(is.null(n.pca)){
+## n.pca <- round(pretty(1:n.pca.max,10))
+## }
+## n.pca <- n.pca[n.pca>0 & n.pca<n.pca.max]
+
+## ## FUNCTION GETTING THE TOTAL DISCRIMINATION (SUM OF EIGENVALUES) FOR ONE GIVEN NB OF PCA PCs ##
+## ## n.pca is a number of retained PCA PCs
+## get.totdiscr <- function(n.pca){
+## temp.dapc <- suppressWarnings(dapc(x, grp, n.pca=n.pca, n.da=n.da, dudi=pcaX))
+## return(sum(temp.dapc$eig))
+## }
+
+
+## ## GET %SUCCESSFUL OF ACCURATE PREDICTION FOR ALL VALUES ##
+## res.all <- sapply(n.pca, get.totdiscr)
+## res <- data.frame(n.pca=n.pca, success=res.all)
+## return(res)
+## } # end discriVal.data.frame
+
+
+## discriVal.matrix <- discriVal.data.frame
+
+
+
+
+## There's a bunch of problems down there, commenting it for nowé
+## xval.dapc <- function(object, n.pca, n.da, training.set = 90, ...){
+## training.set = training.set/100
+## kept.id <- unlist(tapply(1:nInd(object), pop(object), function(e) {pop.size = length(e); pop.size.train = round(pop.size * training.set); sample(e, pop.size.train, replace=FALSE)})) # this can't work: nInd/pop not defined for DAPC objects
+## training <- object[kept.id]
+## validating <- object[-kept.id]
+## post = vector(mode = 'list', length = n.pca)
+## asgn = vector(mode = 'list', length = n.pca)
+## ind = vector(mode = 'list', length = n.pca)
+## mtch = vector(mode = 'list', length = n.pca)
+## for(i in 1:n.pca){
+## dapc.base = dapc(training, n.pca = i, n.da = 15) # Why 15??
+## dapc.p = predict.dapc(dapc.base, newdata = validating)
+## match.prp = mean(as.character(dapc.p$assign)==as.character(pop(validating)))
+## post[[i]] = dapc.p$posterior
+## asgn[[i]] = dapc.p$assign
+## ind[[i]] = dapc.p$ind.score
+## mtch[[i]] = match.prp
+## }
+## res = list(assign = asgn, posterior = post, ind.score = ind, match.prp = mtch)
+## return(res)
+## } # end of xval.dapc
+
+## xval.genind <- function(object, n.pca, n.da, training.set = 90, ...){
+## res = xval.dapc(object = object, n.pca = n.pca, n.da = n.da, training.set = training.set)
+## return(res)
+## }
+## ###############
+## ## randtest.dapc
+## ###############
+## ##randtest.dapc <- function(x, nperm = 999, ...){
+
+## ##} # end randtest.dapc
+
+
+
+
+######## TESTS IN R #######
+
+## TEST PREDICT.DAPC ##
+## data(sim2pop)
+## temp <- seppop(sim2pop)
+## temp <- lapply(temp, function(e) hybridize(e,e,n=30)) # force equal pop sizes
+## hyb <- hybridize(temp[[1]], temp[[2]], n=30)
+## newdat <- repool(temp[[1]], temp[[2]], hyb)
+## pop(newdat) <- rep(c("pop A", "popB", "hyb AB"), c(30,30,30))
+
+
+## ##dapc1 <- dapc(newdat[1:61],n.pca=10,n.da=1)
+## dapc1 <- dapc(newdat[1:60],n.pca=2,n.da=1)
+## scatter(dapc1)
+## hyb.pred <- predict(dapc1, newdat[61:90])
+
+## scatter(dapc1)
+## points(hyb.pred$ind.scores, rep(.1, 30))
+
+## assignplot(dapc1, new.pred=hyb.pred)
+## title("30 indiv popA, 30 indiv pop B, 30 hybrids")
diff --git a/R/datasets.R b/R/datasets.R
new file mode 100644
index 0000000..7d798a6
--- /dev/null
+++ b/R/datasets.R
@@ -0,0 +1,745 @@
+
+
+
+
+
+#' Simulated data illustrating the DAPC
+#'
+#' Datasets illustrating the Discriminant Analysis of Principal Components
+#' (DAPC, Jombart et al. submitted).\cr
+#'
+#' These data were simulated using various models using Easypop (2.0.1). The
+#' \code{dapcIllus} is a list containing the following \linkS4class{genind}
+#' objects:\cr - "a": island model with 6 populations \cr - "b": hierarchical
+#' island model with 6 populations (3,2,1) \cr - "c": one-dimensional stepping
+#' stone with 2x6 populations, and a boundary between the two sets of 6
+#' populations\cr - "d": one-dimensional stepping stone with 24 populations\cr
+#'
+#' See "source" for a reference providing simulation details.
+#'
+#'
+#' @name dapcIllus
+#' @docType data
+#' @format \code{dapcIllus} is list of 4 components being all genind objects.
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso - \code{\link{dapc}}: implements the DAPC.
+#'
+#' - \code{\link{eHGDP}}: dataset illustrating the DAPC and
+#' \code{find.clusters}.
+#'
+#' - \code{\link{H3N2}}: dataset illustrating the DAPC.
+#'
+#' - \code{\link{find.clusters}}: to identify clusters without prior.
+#' @references Jombart, T., Devillard, S. and Balloux, F. Discriminant
+#' analysis of principal components: a new method for the analysis of
+#' genetically structured populations. Submitted to \emph{Genetics}.
+#' @source Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of
+#' principal components: a new method for the analysis of genetically
+#' structured populations. Submitted to \emph{BMC genetics}.
+#' @keywords datasets
+#' @examples
+#'
+#' \dontrun{
+#'
+#' data(dapcIllus)
+#' attach(dapcIllus)
+#' a # this is a genind object, like b, c, and d.
+#'
+#'
+#' ## FINS CLUSTERS EX NIHILO
+#' clust.a <- find.clusters(a, n.pca=100, n.clust=6)
+#' clust.b <- find.clusters(b, n.pca=100, n.clust=6)
+#' clust.c <- find.clusters(c, n.pca=100, n.clust=12)
+#' clust.d <- find.clusters(d, n.pca=100, n.clust=24)
+#'
+#' ## examin outputs
+#' names(clust.a)
+#' lapply(clust.a, head)
+#'
+#'
+#' ## PERFORM DAPCs
+#' dapc.a <- dapc(a, pop=clust.a$grp, n.pca=100, n.da=5)
+#' dapc.b <- dapc(b, pop=clust.b$grp, n.pca=100, n.da=5)
+#' dapc.c <- dapc(c, pop=clust.c$grp, n.pca=100, n.da=11)
+#' dapc.d <- dapc(d, pop=clust.d$grp, n.pca=100, n.da=23)
+#'
+#'
+#' ## LOOK AT ONE RESULT
+#' dapc.a
+#' summary(dapc.a)
+#'
+#' ## FORM A LIST OF RESULTS FOR THE 4 DATASETS
+#' lres <- list(dapc.a, dapc.b, dapc.c, dapc.d)
+#'
+#'
+#' ## DRAW 4 SCATTERPLOTS
+#' par(mfrow=c(2,2))
+#' lapply(lres, scatter)
+#'
+#'
+#' # detach data
+#' detach(dapcIllus)
+#' }
+#'
+NULL
+
+
+
+
+
+
+
+#' Extended HGDP-CEPH dataset
+#'
+#' This dataset consists of 1350 individuals from native Human populations
+#' distributed worldwide typed at 678 microsatellite loci. The original
+#' HGDP-CEPH panel [1-3] has been extended by several native American
+#' populations [4]. This dataset was used to illustrate the Discriminant
+#' Analysis of Principal Components (DAPC, [5]).
+#'
+#'
+#' @name eHGDP
+#' @docType data
+#' @format \code{eHGDP} is a genind object with a data frame named
+#' \code{popInfo} as supplementary component (\code{eHGDP@@other$popInfo}),
+#' which contains the following variables: \describe{ \item{Population: }{a
+#' character vector indicating populations.} \item{Region: }{a character vector
+#' indicating the geographic region of each population.} \item{Label: }{a
+#' character vector indicating the correspondence with population labels used
+#' in the genind object (i.e., as output by \code{pop(eHGDP)}).}
+#' \item{Latitude,Longitude: }{geographic coordinates of the populations,
+#' indicated as north and east degrees.} }
+#' @references [1] Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, et
+#' al. (2002) Genetic structure of human populations. \emph{Science} 298:
+#' 2381-2385.
+#'
+#' [2] Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, et
+#' al. (2005) Support from the relationship of genetic and geographic distance
+#' in human populations for a serial founder effect originating in Africa.
+#' \emph{Proc Natl Acad Sci U S A} 102: 15942-15947.
+#'
+#' [3] Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, et al. (2002) A human
+#' genome diversity cell line panel. \emph{Science} 296: 261-262.
+#'
+#' [4] Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, et al. (2007)
+#' Genetic Variation and Population Structure in Native Americans. \emph{PLoS
+#' Genetics} 3: e185.
+#'
+#' [5] Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of
+#' principal components: a new method for the analysis of genetically
+#' structured populations. Submitted to \emph{BMC genetics}.
+#' @source Original panel by Human Genome Diversity Project (HGDP) and Centre
+#' d'Etude du Polymorphisme Humain (CEPH). See reference [4] for Native
+#' American populations.
+#'
+#' This copy of the dataset was prepared by Francois Balloux.
+#' @keywords datasets
+#' @examples
+#'
+#' \dontrun{
+#' ## LOAD DATA
+#' data(eHGDP)
+#' eHGDP
+#'
+#'
+#' ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
+#' ## to reproduce exactly analyses from the paper, use "n.pca=1000"
+#' dapc1 <- dapc(eHGDP, all.contrib=TRUE, scale=FALSE,
+#' n.pca=200, n.da=80) # takes 2 minutes
+#' dapc1
+#'
+#' ## (see ?dapc for details about the output)
+#'
+#'
+#'
+#' ## SCREEPLOT OF EIGENVALUES
+#' barplot(dapc1$eig, main="eHGDP - DAPC eigenvalues",
+#' col=c("red","green","blue", rep("grey", 1000)))
+#'
+#'
+#'
+#' ## SCATTERPLOTS
+#' ## (!) Note: colors may be inverted with respect to [5]
+#' ## as signs of principal components are arbitrary
+#' ## and change from one computer to another
+#' ##
+#' ## axes 1-2
+#' s.label(dapc1$grp.coord[,1:2], clab=0, sub="Axes 1-2")
+#' par(xpd=T)
+#' colorplot(dapc1$grp.coord[,1:2], dapc1$grp.coord, cex=3, add=TRUE)
+#' add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25)
+#'
+#' ## axes 2-3
+#' s.label(dapc1$grp.coord[,2:3], clab=0, sub="Axes 2-3")
+#' par(xpd=T)
+#' colorplot(dapc1$grp.coord[,2:3], dapc1$grp.coord, cex=3, add=TRUE)
+#' add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25)
+#'
+#'
+#'
+#' ## MAP DAPC1 RESULTS
+#' if(require(maps)){
+#'
+#' xy <- cbind(eHGDP$other$popInfo$Longitude, eHGDP$other$popInfo$Latitude)
+#'
+#' par(mar=rep(.1,4))
+#' map(fill=TRUE, col="lightgrey")
+#' colorplot(xy, -dapc1$grp.coord, cex=3, add=TRUE, trans=FALSE)
+#' }
+#'
+#'
+#'
+#' ## LOOK FOR OTHER CLUSTERS
+#' ## to reproduce results of the reference paper, use :
+#' ## grp <- find.clusters(eHGDP, max.n=50, n.pca=200, scale=FALSE)
+#' ## and then
+#' ## plot(grp$Kstat, type="b", col="blue")
+#'
+#' grp <- find.clusters(eHGDP, max.n=30, n.pca=200,
+#' scale=FALSE, n.clust=4) # takes about 2 minutes
+#' names(grp)
+#'
+#' ## (see ?find.clusters for details about the output)
+#'
+#'
+#'
+#' ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
+#' ## to reproduce exactly analyses from the paper, use "n.pca=1000"
+#' dapc2 <- dapc(eHGDP, pop=grp$grp, all.contrib=TRUE,
+#' scale=FALSE, n.pca=200, n.da=80) # takes around a 1 minute
+#' dapc2
+#'
+#'
+#' ## PRODUCE SCATTERPLOT
+#' scatter(dapc2) # axes 1-2
+#' scatter(dapc2,2,3) # axes 2-3
+#'
+#'
+#' ## MAP DAPC2 RESULTS
+#' if(require(maps)){
+#' xy <- cbind(eHGDP$other$popInfo$Longitude,
+#' eHGDP$other$popInfo$Latitude)
+#'
+#' myCoords <- apply(dapc2$ind.coord, 2, tapply, pop(eHGDP), mean)
+#'
+#' par(mar=rep(.1,4))
+#' map(fill=TRUE, col="lightgrey")
+#' colorplot(xy, myCoords, cex=3, add=TRUE, trans=FALSE)
+#' }
+#'
+#' }
+#'
+NULL
+
+
+
+
+
+
+#' Seasonal influenza (H3N2) HA segment data
+#'
+#' The dataset \code{H3N2} consists of 1903 strains of seasonal influenza
+#' (H3N2) distributed worldwide, and typed at 125 SNPs located in the
+#' hemagglutinin (HA) segment. It is stored as an R object with class
+#' \linkS4class{genind} and can be accessed as usual using \code{data(H3N2)}
+#' (see example). These data were gathered from DNA sequences available from
+#' Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).
+#'
+#' The data file \code{usflu.fasta} is a toy dataset also gathered from
+#' Genbank, consisting of the aligned sequences of 80 seasonal influenza
+#' isolates (HA segment) sampled in the US, in \code{fasta} format. This file
+#' is installed alongside the package; the path to this file is automatically
+#' determined by R using \code{system.file} (see example in this manpage and in
+#' ?fasta2genlight) as well.
+#'
+#'
+#' @name H3N2
+#' @aliases H3N2 usflu usflu.fasta USflu USflu.fasta
+#' @docType data
+#' @format \code{H3N2} is a genind object with several data frame as
+#' supplementary components (\code{H3N2@@other) slort}, which contains the
+#' following items: \describe{ \item{x}{a \code{data.frame} containing
+#' miscellaneous annotations of the sequences.} \item{xy}{a matrix with two
+#' columns indicating the geographic coordinates of the strains, as longitudes
+#' and latitudes.} \item{epid}{a character vector indicating the epidemic of
+#' the strains.} }
+#' @references Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis
+#' of principal components: a new method for the analysis of genetically
+#' structured populations. Submitted to \emph{BMC genetics}.
+#' @source This dataset was prepared by Thibaut Jombart
+#' (t.jombart@@imperia.ac.uk), from annotated sequences available on Genbank
+#' (http://www.ncbi.nlm.nih.gov/Genbank/).
+#' @keywords datasets
+#' @examples
+#'
+#' \dontrun{
+#' #### H3N2 ####
+#' ## LOAD DATA
+#' data(H3N2)
+#' H3N2
+#'
+#' ## set population to yearly epidemics
+#' pop(H3N2) <- factor(H3N2$other$epid)
+#'
+#'
+#'
+#' ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
+#' ## to reproduce exactly analyses from the paper, use "n.pca=1000"
+#' dapc1 <- dapc(H3N2, all.contrib=TRUE, scale=FALSE, n.pca=150, n.da=5)
+#' dapc1
+#'
+#' ## (see ?dapc for details about the output)
+#'
+#'
+#' ## SCREEPLOT OF EIGENVALUES
+#' barplot(dapc1$eig, main="H3N2 - DAPC eigenvalues")
+#'
+#'
+#' ## SCATTERPLOT (axes 1-2)
+#' scatter(dapc1, posi.da="topleft", cstar=FALSE, cex=2, pch=17:22,
+#' solid=.5, bg="white")
+#'
+#'
+#'
+#'
+#' #### usflu.fasta ####
+#' myPath <- system.file("files/usflu.fasta",package="adegenet")
+#' myPath
+#'
+#' ## extract SNPs from alignments using fasta2genlight
+#' ## see ?fasta2genlight for more details
+#' obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time
+#' obj
+#' }
+#'
+NULL
+
+
+
+
+
+
+
+#' Microsatellites genotypes of 15 cattle breeds
+#'
+#' This data set gives the genotypes of 704 cattle individuals for 30
+#' microsatellites recommended by the FAO. The individuals are divided into two
+#' countries (Afric, France), two species (Bos taurus, Bos indicus) and 15
+#' breeds. Individuals were chosen in order to avoid pseudoreplication
+#' according to their exact genealogy.
+#'
+#'
+#' @name microbov
+#' @docType data
+#' @format \code{microbov} is a genind object with 3 supplementary components:
+#' \describe{ \item{coun}{a factor giving the country of each individual (AF:
+#' Afric; FR: France).} \item{breed}{a factor giving the breed of each
+#' individual.} \item{spe}{is a factor giving the species of each individual
+#' (BT: Bos taurus; BI: Bos indicus).} }
+#' @references Lalo\"e D., Jombart T., Dufour A.-B. and Moazami-Goudarzi K.
+#' (2007) Consensus genetic structuring and typological value of markers using
+#' Multiple Co-Inertia Analysis. \emph{Genetics Selection Evolution}.
+#' \bold{39}: 545--567.
+#' @source Data prepared by Katayoun Moazami-Goudarzi and Denis Lalo\"e (INRA,
+#' Jouy-en-Josas, France)
+#' @keywords datasets
+#' @examples
+#'
+#' \dontrun{
+#' data(microbov)
+#' microbov
+#' summary(microbov)
+#'
+#' # make Y, a genpop object
+#' Y <- genind2genpop(microbov)
+#'
+#' # make allelic frequency table
+#' temp <- makefreq(Y,missing="mean")
+#' X <- temp$tab
+#' nsamp <- temp$nobs
+#'
+#' # perform 1 PCA per marker
+#'
+#' kX <- ktab.data.frame(data.frame(X),Y@@loc.n.all)
+#'
+#' kpca <- list()
+#' for(i in 1:30) {kpca[[i]] <- dudi.pca(kX[[i]],scannf=FALSE,nf=2,center=TRUE,scale=FALSE)}
+#'
+#'
+#' sel <- sample(1:30,4)
+#' col = rep('red',15)
+#' col[c(2,10)] = 'darkred'
+#' col[c(4,12,14)] = 'deepskyblue4'
+#' col[c(8,15)] = 'darkblue'
+#'
+#' # display %PCA
+#' par(mfrow=c(2,2))
+#' for(i in sel) {
+#' s.multinom(kpca[[i]]$c1,kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i])
+#' add.scatter.eig(kpca[[i]]$eig,3,xax=1,yax=2,posi="top")
+#' }
+#'
+#' # perform a Multiple Coinertia Analysis
+#' kXcent <- kX
+#' for(i in 1:30) kXcent[[i]] <- as.data.frame(scalewt(kX[[i]],center=TRUE,scale=FALSE))
+#' mcoa1 <- mcoa(kXcent,scannf=FALSE,nf=3, option="uniform")
+#'
+#' # coordinated %PCA
+#' mcoa.axes <- split(mcoa1$axis, Y@@loc.fac)
+#' mcoa.coord <- split(mcoa1$Tli,mcoa1$TL[,1])
+#' var.coord <- lapply(mcoa.coord,function(e) apply(e,2,var))
+#'
+#' par(mfrow=c(2,2))
+#' for(i in sel) {
+#' s.multinom(mcoa.axes[[i]][,1:2],kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i])
+#' add.scatter.eig(var.coord[[i]],2,xax=1,yax=2,posi="top")
+#' }
+#'
+#' # reference typology
+#' par(mfrow=c(1,1))
+#' s.label(mcoa1$SynVar,lab=popNames(microbov),sub="Reference typology",csub=1.5)
+#' add.scatter.eig(mcoa1$pseudoeig,nf=3,xax=1,yax=2,posi="top")
+#'
+#' # typologial values
+#' tv <- mcoa1$cov2
+#' tv <- apply(tv,2,function(c) c/sum(c))*100
+#' rownames(tv) <- locNames(Y)
+#' tv <- tv[order(locNames(Y)),]
+#'
+#' par(mfrow=c(3,1),mar=c(5,3,3,4),las=3)
+#' for(i in 1:3){
+#' barplot(round(tv[,i],3),ylim=c(0,12),yaxt="n",main=paste("Typological value -
+#' structure",i))
+#' axis(side=2,at=seq(0,12,by=2),labels=paste(seq(0,12,by=2),"%"),cex=3)
+#' abline(h=seq(0,12,by=2),col="grey",lty=2)
+#' }
+#' }
+#'
+NULL
+
+
+
+
+
+#' Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
+#'
+#' This data set gives the genotypes of 237 cats (\emph{Felis catus} L.) for 9
+#' microsatellites markers. The individuals are divided into 17 colonies whose
+#' spatial coordinates are also provided.
+#'
+#'
+#' @name nancycats
+#' @docType data
+#' @format \code{nancycats} is a genind object with spatial coordinates of the
+#' colonies as a supplementary components (@@xy).
+#' @references Devillard, S.; Jombart, T. & Pontier, D. Disentangling spatial
+#' and genetic structure of stray cat (\emph{Felis catus} L.) colonies in urban
+#' habitat using: not all colonies are equal. submitted to \emph{Molecular
+#' Ecology}
+#' @source Dominique Pontier (UMR CNRS 5558, University Lyon1, France)
+#' @keywords datasets
+#' @examples
+#'
+#' \dontrun{
+#' data(nancycats)
+#' nancycats
+#'
+#' # summary's results are stored in x
+#' x <- summary(nancycats)
+#'
+#' # some useful graphics
+#' barplot(x$loc.n.all,ylab="Alleles numbers",main="Alleles numbers
+#' per locus")
+#'
+#' plot(x$pop.eff,x$pop.nall,type="n",xlab="Sample size",ylab="Number of alleles")
+#' text(x$pop.eff,y=x$pop.nall,lab=names(x$pop.nall))
+#'
+#' par(las=3)
+#' barplot(table(nancycats@@pop),ylab="Number of genotypes",main="Number of genotypes per colony")
+#'
+#' # are cats structured among colonies ?
+#' if(require(hierfstat)){
+#'
+#' gtest <- gstat.randtest(nancycats,nsim=99)
+#' gtest
+#' plot(gtest)
+#'
+#'
+#' dat <- genind2hierfstat(nancycats)
+#'
+#' Fstat <- varcomp.glob(dat$pop,dat[,-1])
+#' Fstat
+#' }
+#' }
+#'
+NULL
+
+
+
+
+
+
+
+#' Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the
+#' Bauges mountains (France)
+#'
+#' This data set contains the genotypes of 335 chamois (\emph{Rupicapra
+#' rupicapra}) from the Bauges mountains, in France. No prior clustering about
+#' individuals is known. Each genotype is georeferenced. These data also
+#' contain a raster map of elevation of the sampling area.
+#'
+#'
+#' @name rupica
+#' @docType data
+#' @encoding utf-8
+#' @format \code{rupica} is a genind object with 3 supplementary components
+#' inside the \code{@@other} slot: \describe{ \item{xy}{a matrix containing the
+#' spatial coordinates of the genotypes.} \item{mnt}{a raster map of elevation,
+#' with the \code{asc} format from the \code{adehabitat} package.}
+#' \item{showBauges}{a function to display the map of elevation with an
+#' appropriate legend (use \code{showBauges()}).} }
+#' @references Cassar S (2008) Organisation spatiale de la variabilité
+#' génétique et phénotypique a l'échelle du paysage: le cas du chamois et du
+#' chevreuil, en milieu de montagne. PhD Thesis. University Claude Bernard -
+#' Lyon 1, France. \cr
+#'
+#' Cassar S, Jombart T, Loison A, Pontier D, Dufour A-B, Jullien J-M, Chevrier
+#' T, Maillard D. Spatial genetic structure of Alpine chamois (\emph{Rupicapra
+#' rupicapra}): a consequence of landscape features and social factors?
+#' submitted to \emph{Molecular Ecology}.
+#' @source Daniel Maillard, 'Office National de la Chasse et de la Faune
+#' Sauvage' (ONCFS), France.
+#' @keywords datasets
+#' @examples
+#'
+#'
+#' data(rupica)
+#' rupica
+#'
+#'
+#' \dontrun{
+#' if(require(adehabitat)){
+#'
+#' ## see the sampling area
+#' showBauges <- rupica$other$showBauges
+#' showBauges()
+#' points(rupica$other$xy,col="red")
+#'
+#' ## perform a sPCA
+#' spca1 <- spca(rupica,type=5,d1=0,d2=2300,plot=FALSE,scannf=FALSE,nfposi=2,nfnega=0)
+#' barplot(spca1$eig,col=rep(c("black","grey"),c(2,100)),main="sPCA eigenvalues")
+#' screeplot(spca1,main="sPCA eigenvalues: decomposition")
+#'
+#' ## data visualization
+#' showBauges(,labcex=1)
+#' s.value(spca1$xy,spca1$ls[,1],add.p=TRUE,csize=.5)
+#' add.scatter.eig(spca1$eig,1,1,1,posi="topleft",sub="Eigenvalues")
+#'
+#' showBauges(,labcex=1)
+#' s.value(spca1$xy,spca1$ls[,2],add.p=TRUE,csize=.5)
+#' add.scatter.eig(spca1$eig,2,2,2,posi="topleft",sub="Eigenvalues")
+#'
+#' rupica$other$showBauges()
+#' colorplot(spca1$xy,spca1$li,cex=1.5,add.plot=TRUE)
+#'
+#' ## global and local tests
+#' Gtest <- global.rtest(rupica@@tab,spca1$lw,nperm=999)
+#' Gtest
+#' plot(Gtest)
+#' Ltest <- local.rtest(rupica@@tab,spca1$lw,nperm=999)
+#' Ltest
+#' plot(Ltest)
+#' }
+#' }
+#'
+NULL
+
+
+
+
+
+
+
+
+#' Simulated genotypes of two georeferenced populations
+#'
+#' This simple data set was obtained by sampling two populations evolving in a
+#' island model, simulated using Easypop (2.0.1). See \code{source} for
+#' simulation details. Sample sizes were respectively 100 and 30 genotypes. The
+#' genotypes were given spatial coordinates so that both populations were
+#' spatially differentiated.
+#'
+#'
+#' @name sim2pop
+#' @docType data
+#' @format \code{sim2pop} is a genind object with a matrix of xy coordinates as
+#' supplementary component.
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @references Balloux F (2001) Easypop (version 1.7): a computer program for
+#' oppulation genetics simulations \emph{Journal of Heredity}, \bold{92}:
+#' 301-302
+#' @source Easypop version 2.0.1 was run with the following parameters:\cr -
+#' two diploid populations, one sex, random mating\cr - 1000 individuals per
+#' population\cr - proportion of migration: 0.002\cr - 20 loci\cr - mutation
+#' rate: 0.0001 (KAM model)\cr - maximum of 50 allelic states\cr - 1000
+#' generations (last one taken)\cr
+#' @keywords datasets
+#' @examples
+#'
+#' \dontrun{
+#' data(sim2pop)
+#'
+#' if(require(hierfstat)){
+#' ## try and find the Fst
+#' temp <- genind2hierfstat(sim2pop)
+#' varcomp.glob(temp[,1],temp[,-1])
+#' # Fst = 0.038
+#' }
+#'
+#' ## run monmonier algorithm
+#'
+#' # build connection network
+#' gab <- chooseCN(sim2pop@@other$xy,ask=FALSE,type=2)
+#'
+#' # filter random noise
+#' pca1 <- dudi.pca(sim2pop@@tab,scale=FALSE, scannf=FALSE, nf=1)
+#'
+#' # run the algorithm
+#' mon1 <- monmonier(sim2pop@@other$xy,dist(pca1$l1[,1]),gab, scanthres=FALSE)
+#'
+#' # graphical display
+#' temp <- sim2pop@@pop
+#' levels(temp) <- c(17,19)
+#' temp <- as.numeric(as.character(temp))
+#' plot(mon1)
+#' points(sim2pop@@other$xy,pch=temp,cex=2)
+#' legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19))
+#' }
+#'
+NULL
+
+
+
+
+
+
+#' Simulated data illustrating the sPCA
+#'
+#' Datasets illustrating the spatial Principal Component Analysis (Jombart et
+#' al. 2009). These data were simulated using various models using Easypop
+#' (2.0.1). Spatial coordinates were defined so that different spatial
+#' patterns existed in the data. The \code{spca-illus} is a list containing the
+#' following \linkS4class{genind} or \linkS4class{genpop} objects:\cr - dat2A:
+#' 2 patches \cr - dat2B: cline between two pop \cr - dat2C: repulsion among
+#' individuals from the same gene pool \cr - dat3: cline and repulsion \cr -
+#' dat4: patches and local alternance \cr
+#'
+#' See "source" for a reference providing simulation details.
+#'
+#'
+#' @name spcaIllus
+#' @docType data
+#' @format \code{spcaIllus} is list of 5 components being either genind or
+#' genpop objects.
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{spca}}
+#' @references Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D.
+#' Revealing cryptic spatial patterns in genetic variability by a new
+#' multivariate method. \emph{Heredity}, \bold{101}, 92--103.
+#'
+#' Balloux F (2001) Easypop (version 1.7): a computer program for oppulation
+#' genetics simulations \emph{Journal of Heredity}, \bold{92}: 301-302
+#' @source Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing
+#' cryptic spatial patterns in genetic variability by a new multivariate
+#' method. \emph{Heredity}, \bold{101}, 92--103.
+#' @keywords datasets spatial
+#' @examples
+#'
+#' data(spcaIllus)
+#' attach(spcaIllus)
+#' opar <- par(no.readonly=TRUE)
+#' ## comparison PCA vs sPCA
+#'
+#' # PCA
+#' pca2A <- dudi.pca(dat2A$tab,center=TRUE,scale=FALSE,scannf=FALSE)
+#' pca2B <- dudi.pca(dat2B$tab,center=TRUE,scale=FALSE,scannf=FALSE)
+#' pca2C <- dudi.pca(dat2C$tab,center=TRUE,scale=FALSE,scannf=FALSE)
+#' pca3 <- dudi.pca(dat3$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)
+#' pca4 <- dudi.pca(dat4$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)
+#'
+#' # sPCA
+#' spca2A <-spca(dat2A,xy=dat2A$other$xy,ask=FALSE,type=1,
+#' plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)
+#'
+#' spca2B <- spca(dat2B,xy=dat2B$other$xy,ask=FALSE,type=1,
+#' plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)
+#'
+#' spca2C <- spca(dat2C,xy=dat2C$other$xy,ask=FALSE,
+#' type=1,plot=FALSE,scannf=FALSE,nfposi=0,nfnega=1)
+#'
+#' spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,
+#' type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
+#'
+#' spca4 <- spca(dat4,xy=dat4$other$xy,ask=FALSE,
+#' type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
+#'
+#' # an auxiliary function for graphics
+#' plotaux <- function(x,analysis,axis=1,lab=NULL,...){
+#' neig <- NULL
+#' if(inherits(analysis,"spca")) neig <- nb2neig(analysis$lw$neighbours)
+#' xrange <- range(x$other$xy[,1])
+#' xlim <- xrange + c(-diff(xrange)*.1 , diff(xrange)*.45)
+#' yrange <- range(x$other$xy[,2])
+#' ylim <- yrange + c(-diff(yrange)*.45 , diff(yrange)*.1)
+#'
+#' s.value(x$other$xy,analysis$li[,axis],include.ori=FALSE,addaxes=FALSE,
+#' cgrid=0,grid=FALSE,neig=neig,cleg=0,xlim=xlim,ylim=ylim,...)
+#'
+#' par(mar=rep(.1,4))
+#' if(is.null(lab)) lab = gsub("[P]","",x$pop)
+#' text(x$other$xy, lab=lab, col="blue", cex=1.2, font=2)
+#' add.scatter({barplot(analysis$eig,col="grey");box();
+#' title("Eigenvalues",line=-1)},posi="bottomright",ratio=.3)
+#' }
+#'
+#' # plots
+#' plotaux(dat2A,pca2A,sub="dat2A - PCA",pos="bottomleft",csub=2)
+#' plotaux(dat2A,spca2A,sub="dat2A - sPCA glob1",pos="bottomleft",csub=2)
+#'
+#' plotaux(dat2B,pca2B,sub="dat2B - PCA",pos="bottomleft",csub=2)
+#' plotaux(dat2B,spca2B,sub="dat2B - sPCA glob1",pos="bottomleft",csub=2)
+#'
+#' plotaux(dat2C,pca2C,sub="dat2C - PCA",pos="bottomleft",csub=2)
+#' plotaux(dat2C,spca2C,sub="dat2C - sPCA loc1",pos="bottomleft",csub=2,axis=2)
+#'
+#' par(mfrow=c(2,2))
+#' plotaux(dat3,pca3,sub="dat3 - PCA axis1",pos="bottomleft",csub=2)
+#' plotaux(dat3,spca3,sub="dat3 - sPCA glob1",pos="bottomleft",csub=2)
+#' plotaux(dat3,pca3,sub="dat3 - PCA axis2",pos="bottomleft",csub=2,axis=2)
+#' plotaux(dat3,spca3,sub="dat3 - sPCA loc1",pos="bottomleft",csub=2,axis=2)
+#'
+#' plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis1",
+#' pos="bottomleft",csub=2)
+#' plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA glob1",
+#' pos="bottomleft",csub=2)
+#' plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis2",
+#' pos="bottomleft",csub=2,axis=2)
+#' plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA loc1",
+#' pos="bottomleft",csub=2,axis=2)
+#'
+#' # color plot
+#' par(opar)
+#' colorplot(spca3, cex=4, main="colorplot sPCA dat3")
+#' text(spca3$xy[,1], spca3$xy[,2], dat3$pop)
+#'
+#' colorplot(spca4, cex=4, main="colorplot sPCA dat4")
+#' text(spca4$xy[,1], spca4$xy[,2], dat4$other$sup.pop)
+#'
+#' # detach data
+#' detach(spcaIllus)
+#'
+#'
+NULL
+
+
+
diff --git a/R/dist.genpop.R b/R/dist.genpop.R
new file mode 100644
index 0000000..d58f596
--- /dev/null
+++ b/R/dist.genpop.R
@@ -0,0 +1,109 @@
+###################################
+#
+# Distances functions
+# based on old ade4 'dist.genet'
+# by Daniel Chessel
+#
+# Thibaut Jombart
+# t.jombart at imperial.ac.uk
+###################################
+
+
+
+############################
+# S3 method dist for genpop
+############################
+dist.genpop <- function(x, method = 1, diag = FALSE, upper = FALSE) {
+
+ if(!is.genpop(x)) stop("x is not a valid genpop object")
+
+ ## haploidy kludge (have to get rid of that later)
+ if(x at ploidy==as.integer(1)){
+ x at tab <- x at tab * 2
+ x at ploidy <- as.integer(2)
+ }
+
+
+ ## check marker type
+ checkType(x)
+
+
+ METHODS = c("Nei","Edwards","Reynolds","Rodgers","Provesti")
+ if (all((1:5)!=method)) {
+ cat("1 = Nei 1972\n")
+ cat("2 = Edwards 1971\n")
+ cat("3 = Reynolds, Weir and Coockerman 1983\n")
+ cat("4 = Rodgers 1972\n")
+ cat("5 = Provesti 1975\n")
+ cat("Select an integer (1-5): ")
+ method <- as.integer(readLines(n = 1))
+ }
+ if (all((1:5)!=method)) (stop ("Non convenient method number"))
+
+ nloc <- length(levels(x at loc.fac))
+ loc.fac <- x at loc.fac
+ X <- makefreq(x,missing="mean",quiet=TRUE)
+ # X is a matrix of allelic frequencies
+ nlig <- nrow(X)
+
+ if (method == 1) { # Nei
+ d <- X%*%t(X)
+ vec <- sqrt(diag(d))
+ d <- d/vec[col(d)]
+ d <- d/vec[row(d)]
+ d <- -log(d)
+ d <- as.dist(d)
+ } else if (method == 2) { # Edward's (angular)
+ X <- sqrt(X)
+ d <- X%*%t(X)
+ d <- 1-d/nloc
+ diag(d) <- 0
+ d <- sqrt(d)
+ d <- as.dist(d)
+ } else if (method == 3) { # Coancestrality coef (Reynold's)
+ denomi <- X%*%t(X)
+ vec <- apply(X,1,function(x) sum(x*x))
+ d <- -2*denomi + vec[col(denomi)] + vec[row(denomi)]
+ diag(d) <- 0
+ denomi <- 2*nloc - 2*denomi
+ diag(denomi) <- 1
+ d <- d/denomi
+ d <- sqrt(d)
+ d <- as.dist(d)
+ } else if (method == 4) { # Rogers' distance
+ # kX is a list of K=nloc matrices
+ kX <- lapply(split(X,loc.fac[col(X)]),matrix,nrow=nlig)
+ dcano <- function(mat) {
+ daux <- mat%*%t(mat)
+ vec <- diag(daux)
+ daux <- -2*daux + vec[col(daux)] + vec[row(daux)]
+ diag(daux) <- 0
+ daux <- sqrt(.5*daux)
+ return(daux)
+ }
+
+ d <- matrix(0,nlig,nlig)
+ for(i in 1:length(kX)) {
+ d <- d + dcano(kX[[i]])
+ }
+ d <- d/length(kX)
+ d <- as.dist(d)
+ } else if (method ==5) { # Provesti (absolute genetic distance)
+ w0 <- 1:(nlig-1)
+ loca <- function(k) {
+ w1 <- (k+1):nlig
+ resloc <- unlist(lapply(w1, function(x) sum(abs(X[k,]-X[x,]))))
+ return(resloc/(2*nloc))
+ }
+ d <- unlist(lapply(w0,loca))
+ }
+ attr(d, "Size") <- nlig
+ attr(d, "Labels") <- popNames(x)
+ attr(d, "Diag") <- diag
+ attr(d, "Upper") <- upper
+ attr(d, "method") <- METHODS[method]
+ attr(d, "call") <- match.call()
+ class(d) <- "dist"
+ return(d)
+
+} # end method dist for genpop
diff --git a/R/export.R b/R/export.R
new file mode 100644
index 0000000..4c73039
--- /dev/null
+++ b/R/export.R
@@ -0,0 +1,171 @@
+############################################
+#
+# Functions to transform a genind object
+# into other R classes
+#
+# Thibaut Jombart
+# t.jombart at imperial.ac.uk
+#
+############################################
+
+
+## ############################
+## # Function genind2hierfstat
+## ############################
+## genind2hierfstat <- function(x,pop=NULL){
+## ## if(!inherits(x,"genind")) stop("x must be a genind object (see ?genind)")
+## ## invisible(validObject(x))
+## if(!is.genind(x)) stop("x is not a valid genind object")
+## if(any(ploidy(x) != 2L)) stop("not implemented for non-diploid genotypes")
+## checkType(x)
+
+## if(is.null(pop)) pop <- pop(x)
+## if(is.null(pop)) pop <- as.factor(rep("P1",nrow(x at tab)))
+
+## ## ## NOTES ON THE CODING IN HIERFSTAT ##
+## ## - interpreting function is genot2al
+## ## - same coding has to be used for all loci
+## ## (i.e., all based on the maximum number of digits to be used)
+## ## - alleles have to be coded as integers
+## ## - alleles have to be sorted by increasing order when coding a genotype
+## ## - for instance, 121 is 1/21, 101 is 1/1, 11 is 1/1
+
+## ## find max number of alleles ##
+## max.nall <- max(nAll(x))
+## x at all.names <- lapply(alleles(x), function(e) .genlab("",max.nall)[1:length(e)])
+
+
+## ## VERSION USING GENIND2DF ##
+## gen <- genind2df(x, sep="", usepop=FALSE)
+## gen <- as.matrix(data.frame(lapply(gen, as.numeric)))
+## res <- cbind(as.numeric(pop),as.data.frame(gen))
+## colnames(res) <- c("pop", locNames(x))
+## if(!any(table(indNames(x))>1)){
+## rownames(res) <- indNames(x)
+## } else {
+## warning("non-unique labels for individuals; using generic labels")
+## rownames(res) <- 1:nrow(res)
+## }
+
+## return(res)
+## } # end genind2hierfstat
+
+
+
+
+
+#####################
+# Function genind2df
+#####################
+#' Convert a genind object to a data.frame.
+#'
+#' The function \code{genind2df} converts a \linkS4class{genind} back to a
+#' data.frame of raw allelic data.
+#'
+#' @aliases genind2df
+#'
+#' @param x a \linkS4class{genind} object
+#' @param pop an optional factor giving the population of each individual.
+#' @param sep a character string separating alleles. See details.
+#' @param usepop a logical stating whether the population (argument \code{pop}
+#' or \code{x@@pop} should be used (TRUE, default) or not (FALSE)).
+#' @param oneColPerAll a logical stating whether or not alleles should be split
+#' into columns (defaults to \code{FALSE}). This will only work with data with
+#' consistent ploidies.
+#'
+#' @return a data.frame of raw allelic data, with individuals in rows and loci in column
+#'
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#'
+#' @seealso \code{\link{df2genind}}, \code{\link{import2genind}}, \code{\link{read.genetix}},
+#' \code{\link{read.fstat}}, \code{\link{read.structure}}
+#' @keywords manip
+#' @examples
+#'
+#' ## simple example
+#' df <- data.frame(locusA=c("11","11","12","32"),
+#' locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22"))
+#' row.names(df) <- .genlab("genotype",4)
+#' df
+#'
+#' obj <- df2genind(df, ploidy=2, ncode=1)
+#' obj
+#' obj@@tab
+#'
+#'
+#' ## converting a genind as data.frame
+#' genind2df(obj)
+#' genind2df(obj, sep="/")
+#'
+#' @export
+#'
+genind2df <- function(x, pop=NULL, sep="", usepop=TRUE, oneColPerAll = FALSE){
+
+ if(!is.genind(x)) stop("x is not a valid genind object")
+ ## checkType(x)
+
+ if(is.null(pop)) {
+ pop <- x at pop
+ }
+
+ ## PA case ##
+ if(x at type=="PA"){
+ res <- tab(x)
+ if(usepop && !is.null(pop)) res <- cbind.data.frame(pop=pop(x),res)
+ return(res) # exit here
+ }
+
+ ## codom case ##
+ # make one table by locus from x at tab
+ kX <- seploc(x,res.type="matrix")
+
+ if (oneColPerAll & all(x at ploidy == x at ploidy[1])){
+ sep <- "/"
+ }
+ ## function to recode a genotype in form "A1[sep]...[sep]Ak" from frequencies
+ recod <- function(vec,lab){
+ if(any(is.na(vec))) return(NA)
+ res <- paste(rep(lab,vec), collapse=sep)
+ return(res)
+ }
+
+
+ # kGen is a list of nloc vectors of genotypes
+ kGen <- lapply(1:length(kX), function(i) apply(kX[[i]],1,recod,x at all.names[[i]]))
+ names(kGen) <- locNames(x)
+
+ ## if use one column per allele
+ if(oneColPerAll){
+ if (all(x at ploidy == x at ploidy[1])){
+ f1 <- function(vec){ # to repeat NA with seperators
+ vec[is.na(vec)] <- paste(rep("NA", x at ploidy[1]), collapse=sep)
+ return(vec)
+ }
+ temp <- lapply(kGen, f1)
+ temp <- lapply(temp, strsplit,sep)
+
+ res <- lapply(temp, function(e) matrix(unlist(e), ncol=x at ploidy[1], byrow=TRUE))
+ res <- data.frame(res,stringsAsFactors=FALSE)
+ names(res) <- paste(rep(locNames(x),each=x at ploidy[1]), 1:x at ploidy[1], sep=".")
+
+ ## handle pop here
+ if(!is.null(pop) & usepop) res <- cbind.data.frame(pop,res,stringsAsFactors=FALSE)
+ rownames(res) <- indNames(x)
+ return(res) # exit here
+ } else {
+ warning("All ploidies must be equal in order to separate the alleles.\nReturning one column per locus")
+ }
+ } # end if oneColPerAll
+
+ ## build the final data.frame
+ ## res <- as.data.frame(cbind(kGen,stringsAsFactors=FALSE))
+ ## faster option
+ res <- as.data.frame(do.call(cbind, kGen), stringsAsFactors=FALSE)
+ rownames(res) <- indNames(x)
+ colnames(res) <- locNames(x)
+
+ ## handle pop here
+ if(!is.null(pop) & usepop) res <- cbind.data.frame(pop,res,stringsAsFactors=FALSE)
+
+ return(res)
+}
diff --git a/R/find.clust.R b/R/find.clust.R
new file mode 100644
index 0000000..b5c636d
--- /dev/null
+++ b/R/find.clust.R
@@ -0,0 +1,357 @@
+#############
+## find.clusters
+#############
+find.clusters <- function (x, ...) UseMethod("find.clusters")
+
+############################
+## find.clusters.data.frame
+############################
+find.clusters.data.frame <- function(x, clust=NULL, n.pca=NULL, n.clust=NULL, stat=c("BIC", "AIC", "WSS"), choose.n.clust=TRUE,
+ criterion=c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"),
+ max.n.clust=round(nrow(x)/10), n.iter=1e5, n.start=10, center=TRUE, scale=TRUE,
+ pca.select=c("nbEig","percVar"), perc.pca=NULL,..., dudi=NULL){
+
+ ## CHECKS ##
+ stat <- match.arg(stat)
+ pca.select <- match.arg(pca.select)
+ criterion <- match.arg(criterion)
+ min.n.clust <- 2
+ max.n.clust <- max(max.n.clust, 2)
+
+ ## KEEP TRACK OF SOME ORIGINAL PARAMETERS
+ ## n.pca.ori <- n.pca
+ ##n.clust.ori <- n.clust
+
+
+ ## ESCAPE IF SUB-CLUST ARE SEEKED ##
+ if(!is.null(clust)){
+ res <- .find.sub.clusters(x=x, clust=clust, n.pca=n.pca, n.clust=n.clust, stat=stat, max.n.clust=max.n.clust, n.iter=n.iter, n.start=n.start,
+ choose.n.clust=choose.n.clust, criterion=criterion, center=center, scale=scale)
+ return(res)
+ }
+ ## END SUB-CLUST
+
+
+ ## PERFORM PCA ##
+ N <- nrow(x)
+ REDUCEDIM <- is.null(dudi)
+
+ if(REDUCEDIM){ # if no dudi provided
+ ## PERFORM PCA ##
+ maxRank <- min(dim(x))
+ pcaX <- dudi.pca(x, center = center, scale = scale, scannf = FALSE, nf=maxRank)
+ } else { # else use the provided dudi
+ pcaX <- dudi
+ }
+ cumVar <- 100 * cumsum(pcaX$eig)/sum(pcaX$eig)
+
+ if(!REDUCEDIM){
+ myCol <- rep(c("black", "lightgrey"), c(ncol(pcaX$li),length(pcaX$eig)))
+ } else {
+ myCol <- "black"
+ }
+
+ ## select the number of retained PC for PCA
+ if(is.null(n.pca) & pca.select=="nbEig"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the number PCs to retain (>=1): ")
+ n.pca <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(perc.pca) & pca.select=="percVar"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the percentage of variance to retain (0-100): ")
+ nperc.pca <- as.numeric(readLines(n = 1))
+ }
+
+ ## get n.pca from the % of variance to conserve
+ if(!is.null(perc.pca)){
+ n.pca <- min(which(cumVar >= perc.pca))
+ if(perc.pca > 99.999) n.pca <- length(pcaX$eig)
+ if(n.pca<1) n.pca <- 1
+ }
+
+
+ ## keep relevant PCs - stored in XU
+ X.rank <- length(pcaX$eig)
+ n.pca <- min(X.rank, n.pca)
+ if(n.pca >= N) warning("number of retained PCs of PCA is greater than N")
+ ##if(n.pca > N/3) warning("number of retained PCs of PCA may be too large (> N /3)")
+
+ XU <- pcaX$li[, 1:n.pca, drop=FALSE] # principal components
+
+ ## PERFORM K-MEANS
+ if(is.null(n.clust)){
+ nbClust <- min.n.clust:max.n.clust
+ WSS <- numeric(0)
+
+ for(i in 1:length(nbClust)){
+ ## temp <- kmeans(XU, centers=nbClust[i], iter.max=min(n.iter, 100), nstart=min(n.start, 1e3))
+ temp <- kmeans(XU, centers=nbClust[i], iter.max=n.iter, nstart=n.start)
+ WSS[i] <- sum(temp$withinss)
+ }
+
+
+ ## DETERMINE THE NUMBER OF GROUPS
+ ##TSS <- sum(pcaX$eig) * N
+ ##betweenVar <- (1 - ((stat/(N-nbClust-1))/(TSS/(N-1)) )) *100
+ ##WSS.ori <- sum(apply(XU, 2, function(v) sum((v-mean(v))^2) ))
+ ##reducWSS <- -diff(c(WSS.ori, stat))
+ ##reducWSS <- reducWSS/max(reducWSS)
+
+ if(stat=="AIC"){
+ WSS.ori <- sum(apply(XU, 2, function(v) sum((v-mean(v))^2) ))
+ k <- nbClust
+ myStat <- N*log(c(WSS.ori,WSS)/N) + 2*c(1,nbClust)
+ myLab <- "AIC"
+ myTitle <- "Value of AIC \nversus number of clusters"
+
+ }
+ if(stat=="BIC"){
+ WSS.ori <- sum(apply(XU, 2, function(v) sum((v-mean(v))^2) ))
+ k <- nbClust
+ myStat <- N*log(c(WSS.ori,WSS)/N) + log(N) *c(1,nbClust)
+ myLab <- "BIC"
+ myTitle <- "Value of BIC \nversus number of clusters"
+ }
+ if(stat=="WSS"){
+ WSS.ori <- sum(apply(XU, 2, function(v) sum((v-mean(v))^2) ))
+ myStat <- c(WSS.ori, WSS)
+ ## reducWSS <- -diff(c(WSS.ori, stat))
+ ## myStat <- reducWSS/max(reducWSS)
+ myLab <- "Within sum of squares"
+ myTitle <- "Value of within SS\nversus number of clusters"
+ }
+
+ if(choose.n.clust){
+ plot(c(1,nbClust), myStat, xlab="Number of clusters", ylab=myLab, main=myTitle, type="o", col="blue")
+ abline(h=0, lty=2, col="red")
+ cat("Choose the number of clusters (>=2: ")
+ n.clust <- NA
+ while(is.na(n.clust)){
+ n.clust <- max(1, as.integer(readLines(n = 1)))
+ }
+ } else {
+ if(criterion=="min") {
+ n.clust <- which.min(myStat)
+ }
+ if(criterion=="goesup") {
+ ## temp <- diff(myStat)
+ ## n.clust <- which.max( which( (temp-min(temp))<max(temp)/1e4))
+ n.clust <- min(which(diff(myStat)>0))
+ }
+ if(criterion=="goodfit") {
+ temp <- min(myStat) + 0.1*(max(myStat) - min(myStat))
+ n.clust <- min( which(myStat < temp))-1
+ }
+ if(criterion=="diffNgroup") {
+ temp <- cutree(hclust(dist(diff(myStat)), method="ward"), k=2)
+ goodgrp <- which.min(tapply(diff(myStat), temp, mean))
+ n.clust <- max(which(temp==goodgrp))+1
+ }
+ if(criterion=="smoothNgoesup") {
+ temp <- myStat
+ temp[2:(length(myStat)-1)] <- sapply(1:(length(myStat)-2), function(i) mean(myStat[c(i,i+1,i+2)]))
+ n.clust <- min(which(diff(temp)>0))
+ }
+
+ }
+ } else { # if n.clust provided
+ myStat <- NULL
+ }
+
+ ## get final groups
+ if(n.clust >1){
+ best <- kmeans(XU, centers=n.clust, iter.max=n.iter, nstart=n.start)
+ } else {
+ best <- list(cluster=factor(rep(1,N)), size=N)
+ }
+
+
+ ## MAKE RESULT ##
+ if(!is.null(myStat)){
+ names(myStat) <- paste("K",c(1,nbClust), sep="=")
+ }
+
+ res <- list(Kstat=myStat, stat=myStat[n.clust], grp=factor(best$cluster), size=best$size)
+
+ return(res)
+} # end find.clusters.data.frame
+
+
+
+
+
+
+########################
+## find.clusters.genind
+########################
+find.clusters.genind <- function(x, clust=NULL, n.pca=NULL, n.clust=NULL, stat=c("BIC", "AIC", "WSS"), choose.n.clust=TRUE,
+ criterion=c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"),
+ max.n.clust=round(nrow(x at tab)/10), n.iter=1e5, n.start=10,
+ scale=FALSE, truenames=TRUE, ...){
+
+ ## CHECKS ##
+ if(!is.genind(x)) stop("x must be a genind object.")
+ stat <- match.arg(stat)
+
+
+ ## SOME GENERAL VARIABLES ##
+ N <- nrow(x at tab)
+ min.n.clust <- 2
+
+ ## PERFORM PCA ##
+ maxRank <- min(dim(x at tab))
+
+ X <- scaleGen(x, center = TRUE, scale = scale,
+ NA.method = "mean")
+
+ ## CALL DATA.FRAME METHOD
+ res <- find.clusters(X, clust=clust, n.pca=n.pca, n.clust=n.clust, stat=stat, max.n.clust=max.n.clust, n.iter=n.iter, n.start=n.start,
+ choose.n.clust=choose.n.clust, criterion=criterion, center=FALSE, scale=FALSE,...)
+ return(res)
+} # end find.clusters.genind
+
+
+
+
+
+###################
+## find.clusters.matrix
+###################
+find.clusters.matrix <- function(x, ...){
+ return(find.clusters(as.data.frame(x), ...))
+}
+
+
+
+
+
+
+
+
+##########################
+## find.clusters.genlight
+##########################
+find.clusters.genlight <- function(x, clust=NULL, n.pca=NULL, n.clust=NULL, stat=c("BIC", "AIC", "WSS"), choose.n.clust=TRUE,
+ criterion=c("diffNgroup", "min","goesup", "smoothNgoesup", "goodfit"),
+ max.n.clust=round(nInd(x)/10), n.iter=1e5, n.start=10,
+ scale=FALSE, pca.select=c("nbEig","percVar"), perc.pca=NULL, glPca=NULL, ...){
+
+ ## CHECKS ##
+ if(!inherits(x, "genlight")) stop("x is not a genlight object.")
+ stat <- match.arg(stat)
+ pca.select <- match.arg(pca.select)
+
+
+ ## SOME GENERAL VARIABLES ##
+ N <- nInd(x)
+ min.n.clust <- 2
+
+
+ ## PERFORM PCA ##
+ REDUCEDIM <- is.null(glPca)
+
+ if(REDUCEDIM){ # if no glPca provided
+ maxRank <- min(c(nInd(x), nLoc(x)))
+ pcaX <- glPca(x, center = TRUE, scale = scale, nf=maxRank, loadings=FALSE, returnDotProd = FALSE, ...)
+ } else {
+ pcaX <- glPca
+ }
+
+ if(is.null(n.pca)){
+ cumVar <- 100 * cumsum(pcaX$eig)/sum(pcaX$eig)
+ }
+
+
+ ## select the number of retained PC for PCA
+ if(!REDUCEDIM){
+ myCol <- rep(c("black", "lightgrey"), c(ncol(pcaX$scores),length(pcaX$eig)))
+ } else {
+ myCol <- "black"
+ }
+
+ if(is.null(n.pca) & pca.select=="nbEig"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the number PCs to retain (>=1): ")
+ n.pca <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(perc.pca) & pca.select=="percVar"){
+ plot(cumVar, xlab="Number of retained PCs", ylab="Cumulative variance (%)", main="Variance explained by PCA", col=myCol)
+ cat("Choose the percentage of variance to retain (0-100): ")
+ nperc.pca <- as.numeric(readLines(n = 1))
+ }
+
+ ## get n.pca from the % of variance to conserve
+ if(!is.null(perc.pca)){
+ n.pca <- min(which(cumVar >= perc.pca))
+ if(perc.pca > 99.999) n.pca <- length(pcaX$eig)
+ if(n.pca<1) n.pca <- 1
+ }
+
+ if(!REDUCEDIM){
+ if(n.pca > ncol(pcaX$scores)) {
+ n.pca <- ncol(pcaX$scores)
+ }
+ }
+
+
+ ## convert PCA
+ pcaX <- .glPca2dudi(pcaX)
+
+
+ ## CALL DATA.FRAME METHOD
+ res <- find.clusters(pcaX$li, clust=clust, n.pca=n.pca, n.clust=n.clust, stat=stat, max.n.clust=max.n.clust, n.iter=n.iter, n.start=n.start,
+ choose.n.clust=choose.n.clust, criterion=criterion, center=FALSE, scale=FALSE, dudi=pcaX)
+ return(res)
+} # end find.clusters.genlight
+
+
+
+
+
+
+
+
+
+
+###################
+## .find.sub.clusters
+###################
+.find.sub.clusters <- function(x, ...){
+
+ ## GET ... ##
+ myArgs <- list(...)
+ if(!is.null(myArgs$quiet)){
+ quiet <- myArgs$quiet
+ myArgs$quiet <- NULL
+ } else {
+ quiet <- FALSE
+ }
+
+ clust <- myArgs$clust
+ myArgs$clust <- NULL
+
+ if(is.null(clust)) stop("clust is not provided")
+ clust <- as.factor(clust)
+
+ ## temp will store temporary resuts
+ newFac <- character(length(clust))
+
+ ## find sub clusters
+ for(i in levels(clust)){
+ if(!quiet) cat("\nLooking for sub-clusters in cluster",i,"\n")
+ myArgs$x <- x[clust==i, ]
+ temp <- do.call(find.clusters, myArgs)$grp
+ levels(temp) <- paste(i, levels(temp), sep=".")
+ newFac[clust==i] <- as.character(temp)
+ }
+
+ res <- list(stat=NA, grp=factor(newFac), size=as.integer(table(newFac)))
+
+ return(res)
+}
+
+
+
diff --git a/R/fstat.R b/R/fstat.R
new file mode 100644
index 0000000..e4b6e95
--- /dev/null
+++ b/R/fstat.R
@@ -0,0 +1,97 @@
+## #################
+## # fstat function
+## #################
+## #
+## # Wrapper for fst estimator from hierfstat package
+## #
+
+## fstat <- function(x, pop=NULL, fstonly=FALSE){
+## message("Sorry, this function depends on hierfstat, and has been moved to the package hierfstat.")
+## return()
+## ## ## cat("\nSorry, hierfstat package has been disabled - this function will be restored in a future release.\n")
+## ## ## return(invisible())
+## ## ## misc checks
+## ## if(!is.genind(x)) stop("x is not a valid genind object")
+## ## ## if(!require(hierfstat)) stop("hierfstat package is required. Please install it.")
+## ## if(x at ploidy != as.integer(2)) stop("not implemented for non-diploid genotypes")
+## ## checkType(x)
+
+## ## if(is.null(pop)) pop <- x at pop
+## ## if(is.null(pop)) stop("no pop factor provided")
+## ## if(length(pop)!=nrow(x at tab)) stop("pop has a wrong length.")
+
+## ## ## computations
+## ## dat <- genind2hierfstat(x)[,-1]
+## ## res <- varcomp.glob(levels=data.frame(pop), loci=dat)$F
+
+## ## if(fstonly) {res <- res[1,1]}
+## ## return(res)
+## }
+
+
+
+## ###############
+## ## pairwise.fst
+## ###############
+## ##
+## ## pairwise fst sensu Nei (Ht - mean(Hs))/Ht
+## ##
+## pairwise.fst <- function(x, pop=NULL, res.type=c("dist","matrix"), truenames=TRUE){
+## message("This function has been moved to the package hierfstat. You can still use it in adegenet, but this version is deprecated.")
+## ## MISC CHECKS ##
+## if(!is.genind(x)) stop("x is not a valid genind object")
+## if(!is.null(pop)){
+## pop(x) <- pop
+## }
+## temp <- pop(x)
+## if(is.null(temp)) stop("no grouping factor (pop) provided")
+## if(length(levels(temp)) < 2){
+## warning("There is only one pop - returning NULL")
+## return(NULL)
+## }
+
+## res.type <- match.arg(res.type)
+
+
+## ## COMPUTATIONS ##
+
+## ## function to compute one Fst ##
+## f1 <- function(pop1, pop2){ # pop1 and pop2 are genind obj. with a single pop each
+## n1 <- nrow(pop1 at tab)
+## n2 <- nrow(pop2 at tab)
+## temp <- repool(pop1,pop2)
+## b <- weighted.mean(Hs(temp), c(n1,n2)) # mean Hs is weighted for pop sizes
+## pop(temp) <- NULL
+## a <- Hs(temp)
+## return((a-b)/a)
+## }
+
+
+## ## compute pairwise Fst for all pairs
+## lx <- seppop(x,treatOther=FALSE)
+## temp <- pop(x)
+## levPop <- levels(temp)
+## allPairs <- combn(1:length(levPop), 2)
+## if(!is.matrix(allPairs)){
+## allPairs <- matrix(allPairs,nrow=2)
+## }
+
+## vecRes <- numeric()
+## for(i in 1:ncol(allPairs)){
+## vecRes[i] <- f1(lx[[allPairs[1,i]]], lx[[allPairs[2,i]]])
+## }
+
+
+## squelres <- dist(1:length(levPop))
+## res <- vecRes
+## attributes(res) <- attributes(squelres)
+
+## if(res.type=="matrix"){
+## res <- as.matrix(res)
+## lab <- popNames(x)
+
+## colnames(res) <- rownames(res) <- lab
+## }
+
+## return(res)
+## } # end of pairwise.fst
diff --git a/R/gengraph.R b/R/gengraph.R
new file mode 100644
index 0000000..b9ae4e2
--- /dev/null
+++ b/R/gengraph.R
@@ -0,0 +1,232 @@
+#############
+## GENERIC ##
+#############
+gengraph <- function (x, ...) UseMethod("gengraph")
+
+
+
+
+
+#############
+## DEFAULT ##
+#############
+gengraph.default <- function(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE,
+ show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...){
+ stop(paste("No method for objects of class",class(x)))
+} # end gengraph.default
+
+
+
+
+
+############
+## MATRIX ##
+############
+##
+## this is the basic method
+##
+gengraph.matrix <- function(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky,
+ truenames=TRUE, nbreaks=10, ...){
+ ## CHECKS ##
+
+ ## IF COMPUTEALL IS TRUE ##
+ if(computeAll){
+ cutoffvec <- 1:max(x)
+ res <- lapply(cutoffvec, function(i) gengraph.matrix(x, cutoff=i, computeAll=FALSE))
+ temp <- sapply(res, function(e) e$clust$no)
+ if(plot){
+ plot(cutoffvec, temp, xlab="Cut-off Hamming distance chosen", ylab="Number of groups")
+ }
+ return(res)
+ }
+
+
+ ## INTERACTIVE MODE IF BOTH CUTOFF AND NGRP MISSING ##
+ if(is.null(cutoff) & is.null(ngrp)){
+ chooseAgain <- TRUE
+ while (chooseAgain) {
+ if(plot){
+ hist(x, nclass=50, col="deepskyblue1",xlab="Hamming distance",ylab="Frequency",main="Distribution of frequences")
+ }
+ cat("\nPlease choose a cutoff distance: ")
+ ans <- NA
+ while(is.null(ans) || is.na(ans)) suppressWarnings(ans <- as.numeric(readLines(n = 1)))
+ if(plot){
+ abline(v=ans,col="red",lty=2, lwd=2)
+ }
+ res <- gengraph.matrix(x, cutoff=ans, truenames=truenames)
+ if(truenames){
+ V(res$graph)$label <- rownames(x)
+ }
+
+ cat(paste("\nNumber of clusters found: ", res$clust$no, sep=""))
+ if(plot && show.graph) plot(res$graph)
+ ans <- ""
+ while(!ans %in% c("y","n")){
+ cat("\nAre you satisfied with this solution? (yes:y / no:n): ")
+ ans <- tolower(readLines(n = 1))
+ }
+ if(ans=="y") chooseAgain <- FALSE
+ }
+ return(res)
+ }
+
+
+
+ ## MAIN CASE: IF CUT-OFF POINT IS GIVEN ##
+ if(!is.null(cutoff)){
+ x[x>=cutoff] <- 0
+ g <- graph.adjacency(x, mode="undirected", weighted=TRUE, diag=FALSE)
+ clust <- clusters(g)
+ V(g)$color <- col.pal(clust$no)[clust$membership]
+ col <- col.pal(clust$no)[1:clust$no]
+ names(col) <- 1:clust$no
+
+ ## assign labels to vertices
+ if(truenames){
+ V(g)$label <- rownames(x)
+ } else {
+ V(g)$label <- 1:nrow(x)
+ }
+
+ ## assign labels to edges
+ if(length(E(g))>0) {
+ E(g)$label <- E(g)$weight
+ }
+
+ ## graph plotting options ##
+ V(g)$label.dist <- 0.75
+ V(g)$size <- 10
+ V(g)$label.family <- "sans"
+ V(g)$label.color <- "black"
+
+ ## make result
+ res <- list(graph=g, clust=clusters(g), cutoff=cutoff, col=col)
+
+ } else { ## IF CUT-OFF POINT NEEDS TO BE FOUND ##
+ if(ngrp>=nrow(x)) stop("ngrp is greater than or equal to the number of individuals")
+
+ ## FIRST HAVE A LOOK AT A RANGE OF VALUES ##
+ cutToTry <- pretty(x,nbreaks)
+ cutToTry <- cutToTry[cutToTry>0 & cutToTry<max(x)]
+ if(length(cutToTry)==0) cutToTry <- 1
+ tempRes <- lapply(cutToTry, function(i) gengraph.matrix(x,cutoff=i))
+ temp <- sapply(tempRes,function(e) e$clust$no)
+ if(!min(abs(temp-ngrp))<1) warning(paste("The exact number of groups was not found. Tried increasing nbreaks"))
+ cutoff <- cutToTry[which.min(abs(temp-ngrp))]
+ ## if(!any(temp<ngrp)) {
+ ## cutoff <- 1
+ ## } else {
+ ## cutoff <- cutToTry[max(which(temp>ngrp))]
+ ## }
+
+ ## FIND THE LOWEST CUTOFF GIVING NGRP ##
+ res <- gengraph.matrix(x,cutoff=cutoff)
+ while(res$clust$no>ngrp){
+ cutoff <- cutoff+1
+ res <- gengraph.matrix(x,cutoff=cutoff)
+ }
+
+ if(res$clust$no != ngrp) cat("\nNote: the exact number of clusters could not be found.\n")
+ }
+
+
+ ## RETURN ##
+ return(res)
+
+} # end gengraph.matrix
+
+
+
+
+
+
+
+############
+## GENIND ##
+############
+gengraph.dist <- function(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE,
+ show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...){
+ ## CHECKS ##
+
+ ## USE MATRIX METHOD ##
+ res <- gengraph(as.matrix(x), cutoff=cutoff, ngrp=ngrp, computeAll=computeAll, plot=plot, show.graph=show.graph, col.pal=col.pal,
+ truenames=truenames, nbreaks=nbreaks, ...)
+ return(res)
+} # end gengraph.dist
+
+
+
+
+
+
+
+############
+## GENIND ##
+############
+gengraph.genind <- function(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE,
+ show.graph=TRUE, col.pal=funky, truenames=TRUE, nbreaks=10, ...){
+ ## CHECKS ##
+
+ ## COMPUTE DISTANCES ##
+ x$tab[is.na(x$tab)] <- 0
+ D <- (1-propShared(x))*nLoc(x)*ploidy(x)
+
+ ## USE MATRIX METHOD ##
+ res <- gengraph(D, cutoff=cutoff, ngrp=ngrp, computeAll=computeAll, plot=plot, show.graph=show.graph, col.pal=col.pal,
+ truenames=truenames, nbreaks=nbreaks, ...)
+ if(truenames){
+ V(res$graph)$label <- indNames(x)
+ }
+
+ return(res)
+} # end gengraph.genind
+
+
+
+
+
+
+
+
+############
+## GENPOP ##
+############
+gengraph.genpop <- function(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE,
+ col.pal=funky, method=1, truenames=TRUE, nbreaks=10, ...){ ## CHECKS ##
+
+ ## COMPUTE DISTANCES ##
+ x$tab[is.na(x$tab)] <- 0
+ D <- as.matrix(dist.genpop(x, method=method))
+
+ ## USE MATRIX METHOD ##
+ res <- gengraph(D, cutoff=cutoff, ngrp=ngrp, computeAll=computeAll, plot=plot, show.graph=show.graph, col.pal=col.pal,
+ truenames=truenames, nbreaks=nbreaks, ...)
+ if(truenames){
+ V(res$graph)$label <- popNames(x)
+ }
+
+ return(res)
+} # end gengraph.genpop
+
+
+
+
+
+
+
+############
+## DNABIN ##
+############
+gengraph.DNAbin <- function(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE, plot=TRUE, show.graph=TRUE, col.pal=funky,
+ truenames=TRUE, nbreaks=10, ...){
+ ## CHECKS #
+ ## COMPUTE DISTANCES ##
+ D <- as.matrix(round(dist.dna(x,model="raw", pairwise.deletion = TRUE)*ncol(x)))
+
+ ## USE MATRIX METHOD ##
+ res <- gengraph(D, cutoff=cutoff, ngrp=ngrp, computeAll=computeAll, plot=plot, show.graph=show.graph, col.pal=col.pal,
+ truenames=truenames, nbreaks=nbreaks, ...)
+ return(res)
+} # end gengraph.DNAbin
+
diff --git a/R/genind2genpop.R b/R/genind2genpop.R
new file mode 100644
index 0000000..c120f99
--- /dev/null
+++ b/R/genind2genpop.R
@@ -0,0 +1,149 @@
+#########################
+# Function genind2genpop
+#########################
+
+
+#' Conversion from a genind to a genpop object
+#'
+#' The function \code{genind2genpop} converts genotypes data (genind) into
+#' alleles counts per population (genpop).
+#'
+#' === 'missing' argument ===\cr The values of the 'missing' argument in
+#' \code{genind2genpop} have the following effects:\cr - "NA": if all genotypes
+#' of a population for a given allele are missing, count value will be NA\cr
+#'
+#' - "0": if all genotypes of a population for a given allele are missing, count
+#' value will be 0\cr
+#'
+#' - "chi2": if all genotypes of a population for a given allele are missing,
+#' count value will be that of a theoretical count in of a Chi-squared test.
+#' This is obtained by the product of the margins sums divided by the total
+#' number of alleles.\cr
+#'
+#' === processing the \code{@@other} slot ===\cr Essentially,
+#' \code{genind2genpop} is about aggregating data per population. The function
+#' can do the same for all numeric items in the \code{@@other} slot provided
+#' they have the same length (for vectors) or the same number of rows
+#' (matrix-like objects) as the number of genotypes. When the case is
+#' encountered and if \code{process.other} is TRUE, then these objects are
+#' processed using the function defined in \code{other.action} per population.
+#' For instance, spatial coordinates of genotypes would be averaged to obtain
+#' population coordinates.
+#'
+#' @param x an object of class \code{genind}.
+#' @param pop a factor giving the population of each genotype in 'x' OR a
+#' formula specifying which strata are to be used when converting to a genpop
+#' object. If none provided, population factors are sought in x@@pop, but if
+#' given, the argument prevails on x@@pop.
+#' @param quiet logical stating whether a conversion message must be printed
+#' (TRUE,default) or not (FALSE).
+#' @param process.other a logical indicating whether the \code{@@other} slot
+#' should be processed (see details).
+#' @param other.action a function to be used when processing the \code{@@other}
+#' slot. By default, 'mean' is used.
+#' @return A genpop object. The component @@other in 'x' is passed to the
+#' created genpop object.
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \linkS4class{genind}, \linkS4class{genpop}
+#' @keywords classes manip multivariate
+#' @examples
+#'
+#' ## simple conversion
+#' data(nancycats)
+#' nancycats
+#' catpop <- genind2genpop(nancycats)
+#' catpop
+#' summary(catpop)
+#'
+#' ## processing the @@other slot
+#' data(sim2pop)
+#' sim2pop$other$foo <- letters
+#' sim2pop
+#' dim(sim2pop$other$xy) # matches the number of genotypes
+#' sim2pop$other$foo # does not match the number of genotypes
+#'
+#' obj <- genind2genpop(sim2pop, process.other=TRUE)
+#' obj$other # the new xy is the populations' centre
+#'
+#' pch <- as.numeric(pop(sim2pop))
+#' col <- pop(sim2pop)
+#' levels(col) <- c("blue","red")
+#' col <- as.character(col)
+#' plot(sim2pop$other$xy, pch=pch, col=col)
+#' text(obj$other$xy, lab=row.names(obj$other$xy), col=c("blue","red"), cex=2, font=2)
+#' \dontrun{
+#' data(microbov)
+#' strata(microbov) <- data.frame(other(microbov))
+#' summary(genind2genpop(microbov)) # Conversion based on population factor
+#' summary(genind2genpop(microbov, ~coun)) # Conversion based on country
+#' summary(genind2genpop(microbov, ~coun/spe)) # Conversion based on country and species
+#'
+#' }
+#'
+#' @export genind2genpop
+genind2genpop <- function(x, pop = NULL, quiet = FALSE,
+ process.other = FALSE, other.action = mean){
+
+ ## CHECKS ##
+ if (!is.genind(x)) stop("x is not a valid genind object")
+ checkType(x)
+ if (!all(ploidy(x)[1]==ploidy(x))) stop("conversion to genpop not supported for varying ploidy")
+ if (!is.null(pop)){
+ if (is.language(pop)){
+ setPop(x) <- pop
+ } else {
+ pop(x) <- pop
+ }
+ }
+
+ if (is.null(pop(x))) {
+ if(!quiet) warning("\npop is not provided either in x or in pop - assuming one single group")
+ pop(x) <- factor(rep(1, nInd(x)))
+ }
+
+ if (!quiet) cat("\n Converting data from a genind to a genpop object... \n")
+
+ ## tabcount is a matrix pop x alleles, counting alleles per pop
+ tabcount <- apply(tab(x), 2, tapply, pop(x), sum, na.rm=TRUE)
+
+ ## restitute matrix class when only one pop
+ if(is.null(dim(tabcount))) {
+ lab.col <- names(tabcount)
+ tabcount <- matrix(tabcount,nrow=1)
+ colnames(tabcount) <- lab.col
+ rownames(tabcount) <- levels(pop(x))[1]
+ }
+
+ ## MAKE FINAL OBJECT ##
+ prevcall <- match.call()
+ res <- new("genpop", tab=tabcount, prevcall=prevcall, ploidy=x at ploidy[1], type=x at type)
+
+ ## handle @other here
+ res at other <- x at other
+ if(process.other){
+ ## auxiliary function doing the job
+ fOther <- function(e){
+ N <- nrow(x at tab)
+ if(is.vector(e) && is.numeric(e) && length(e)==N){ # numeric vector
+ res <- tapply(e, pop(x), other.action)
+ return(res)
+ } else if(is.matrix(e) && is.numeric(e) && nrow(e)==N){ # numeric matrix
+ res <- apply(e, 2, function(vec) tapply(vec, pop(x), other.action))
+ colnames(res) <- colnames(e)
+ return(res)
+ } else if(is.data.frame(e) && nrow(e)==N && all(sapply(e,is.numeric)) ){ # df of numeric vectors
+ res <- lapply(e, function(vec) tapply(vec, pop(x), other.action))
+ res <- data.frame(res)
+ names(res) <- names(e)
+ return(res)
+ } else return(e)
+ } # end fOther
+
+ res at other <- lapply(res at other, fOther)
+ } # end if(process.other)
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+
+} # end genind2genpop
diff --git a/R/glFunctions.R b/R/glFunctions.R
new file mode 100644
index 0000000..2eb087d
--- /dev/null
+++ b/R/glFunctions.R
@@ -0,0 +1,774 @@
+
+##########
+## glSum
+##########
+## compute col sums
+## removing NAs
+##
+glSum <- function(x, alleleAsUnit=TRUE, useC=FALSE){
+ if(!inherits(x, "genlight")) stop("x is not a genlight object")
+
+ if(useC){
+ ## use ploidy (sum absolute frequencies)
+ if(alleleAsUnit){
+ vecbyte <- unlist(lapply(x at gen, function(e) e$snp))
+ nbVec <- sapply(x at gen, function(e) length(e$snp))
+ nbNa <- sapply(NA.posi(x), length)
+ naPosi <- unlist(NA.posi(x))
+ res <- .C("GLsumInt", vecbyte, nbVec, length(x at gen[[1]]@snp[[1]]), nbNa, naPosi, nInd(x), nLoc(x), ploidy(x),
+ integer(nLoc(x)), PACKAGE="adegenet")[[9]]
+ } else {
+ ## sum relative frequencies
+ vecbyte <- unlist(lapply(x at gen, function(e) e$snp))
+ nbVec <- sapply(x at gen, function(e) length(e$snp))
+ nbNa <- sapply(NA.posi(x), length)
+ naPosi <- unlist(NA.posi(x))
+ res <- .C("GLsumFreq", vecbyte, nbVec, length(x at gen[[1]]@snp[[1]]), nbNa, naPosi, nInd(x), nLoc(x), ploidy(x),
+ double(nLoc(x)), PACKAGE="adegenet")[[9]]
+ }
+ } else {
+ ## use ploidy (sum absolute frequencies)
+ if(alleleAsUnit){
+ res <- integer(nLoc(x))
+ for(e in x at gen){
+ temp <- as.integer(e)
+ temp[is.na(temp)] <- 0L
+ res <- res + temp
+ }
+ } else {
+ ## sum relative frequencies
+ res <- numeric(nLoc(x))
+ myPloidy <- ploidy(x)
+ for(i in 1:nInd(x)){
+ temp <- as.integer(x at gen[[i]]) / myPloidy[i]
+ temp[is.na(temp)] <- 0
+ res <- res + temp
+ }
+ }
+
+ }
+ names(res) <- locNames(x)
+ return(res)
+
+} # glSum
+
+
+
+
+
+##########
+## glNA
+##########
+## counts NB of NAs per column
+##
+## if alleleAsUnit, then effective is the number of alleles sampled (sum(ploidy(x)))
+## otherwise, effective is simply the number of individuals (
+glNA <- function(x, alleleAsUnit=TRUE){
+ if(!inherits(x, "genlight")) stop("x is not a genlight object")
+
+ ## DEFAULT, VECTOR-WISE PROCEDURE ##
+ res <- integer(nLoc(x))
+ temp <- NA.posi(x)
+
+ ## NAs in allele sampling
+ if(alleleAsUnit){
+ for(i in 1:length(temp)){
+ if(length(temp[[i]])>0){
+ res[temp[[i]]] <- res[temp[[i]]] + ploidy(x)[i]
+ }
+ }
+ } else { ## NAs amongst individuals
+ for(e in temp){
+ if(length(e)>0){
+ res[e] <- res[e] + 1
+ }
+ }
+ }
+
+ names(res) <- locNames(x)
+ return(res)
+
+} # glNA
+
+
+
+
+
+##########
+## glMean
+##########
+## computes SNPs means
+## takes NAs into account
+##
+glMean <- function(x, alleleAsUnit=TRUE){
+ if(!inherits(x, "genlight")) stop("x is not a genlight object")
+
+ ## DEFAULT, VECTOR-WISE PROCEDURE ##
+ if(alleleAsUnit){ # use alleles
+ N <- sum(ploidy(x)) - glNA(x, alleleAsUnit=TRUE)
+ res <- glSum(x, alleleAsUnit=TRUE)/N
+ } else { # use relative frequencies of individuals
+ N <- nInd(x) - glNA(x, alleleAsUnit=FALSE)
+ res <- glSum(x, alleleAsUnit=FALSE)/N
+ }
+
+ names(res) <- locNames(x)
+ return(res)
+
+} # glMean
+
+
+
+
+
+########
+## glVar
+########
+## computes SNPs variances
+## takes NAs into account
+##
+glVar <- function(x, alleleAsUnit=TRUE){
+ if(!inherits(x, "genlight")) stop("x is not a genlight object")
+
+ ## DEFAULT, VECTOR-WISE PROCEDURE ##
+ res <- numeric(nLoc(x))
+ myPloidy <- ploidy(x)
+
+ if(alleleAsUnit){ # use alleles
+ N <- sum(ploidy(x)) - glNA(x, alleleAsUnit=TRUE)
+ xbar <- glMean(x, alleleAsUnit=TRUE)
+ for(i in 1:nInd(x)){
+ temp <- (as.integer(x at gen[[i]])/myPloidy[i] - xbar)^2
+ temp[is.na(temp)] <- 0
+ res <- res + temp*myPloidy[i]
+ }
+ res <- res/N
+ } else { # use relative frequencies of individuals
+ N <- nInd(x) - glNA(x, alleleAsUnit=FALSE)
+ xbar <- glMean(x, alleleAsUnit=FALSE)
+
+ for(i in 1:nInd(x)){
+ temp <- (as.integer(x at gen[[i]])/myPloidy[i] - xbar)^2
+ temp[is.na(temp)] <- 0L
+ res <- res + temp
+ }
+ res <- res/N
+ }
+
+ names(res) <- locNames(x)
+ return(res)
+
+} # glVar
+
+
+
+
+
+
+#############
+## glDotProd
+############
+## computes all pairs of dot products
+## between centred/scaled vectors
+## of SNPs
+glDotProd <- function(x, center=FALSE, scale=FALSE, alleleAsUnit=FALSE,
+ parallel=require("parallel"), n.cores=NULL){
+ if(!inherits(x, "genlight")) stop("x is not a genlight object")
+
+ ## SOME CHECKS ##
+ ## if(parallel && !require(parallel)) stop("parallel package requested but not installed")
+ if(parallel && is.null(n.cores)){
+ n.cores <- parallel::detectCores()
+ }
+
+
+ ## STORE USEFUL INFO ##
+ N <- nInd(x)
+ ind.names <- indNames(x)
+
+
+ if(!parallel){ # DO NOT USE MULTIPLE CORES
+ ## GET INPUTS TO C PROCEDURE ##
+ if(center){
+ mu <- glMean(x,alleleAsUnit=alleleAsUnit)
+ } else {
+ mu <- rep(0, nLoc(x))
+ }
+
+ if(scale){
+ s <- sqrt(glVar(x,alleleAsUnit=alleleAsUnit))
+ if(any(s<1e-10)) {
+ warning("Null variances have been detected; corresponding alleles won't be standardized.")
+ }
+ } else {
+ s <- rep(1, nLoc(x))
+ }
+
+ vecbyte <- unlist(lapply(x at gen, function(e) e$snp))
+ nbVec <- sapply(x at gen, function(e) length(e$snp))
+ nbNa <- sapply(NA.posi(x), length)
+ naPosi <- unlist(NA.posi(x))
+ lowerTriSize <- (nInd(x)*(nInd(x)-1))/2
+ resSize <- lowerTriSize + nInd(x)
+
+ ## CALL C FUNCTION ##
+ temp <- .C("GLdotProd", vecbyte, nbVec, length(x at gen[[1]]@snp[[1]]), nbNa, naPosi, nInd(x), nLoc(x), ploidy(x),
+ as.double(mu), as.double(s), as.integer(!alleleAsUnit), double(resSize), PACKAGE="adegenet")[[12]]
+ } else { # USE MULTIPLE CORES
+ x <- seploc(x, n.block = n.cores) # one block per core (x is now a list of genlight)
+ temp <- list()
+ i <- 0
+ for(block in x){
+ i <- i+1
+ ## GET INPUTS TO C PROCEDURE ##
+ if(center){
+ mu <- glMean(block,alleleAsUnit=alleleAsUnit)
+ } else {
+ mu <- rep(0, nLoc(block))
+ }
+
+ if(scale){
+ s <- sqrt(glVar(block,alleleAsUnit=alleleAsUnit))
+ if(any(s<1e-10)) {
+ warning("Null variances have been detected; corresponding alleles won't be standardized.")
+ }
+ } else {
+ s <- rep(1, nLoc(block))
+ }
+
+ vecbyte <- unlist(lapply(block at gen, function(e) e$snp))
+ nbVec <- sapply(block at gen, function(e) length(e$snp))
+ nbNa <- sapply(NA.posi(block), length)
+ naPosi <- unlist(NA.posi(block))
+ lowerTriSize <- (nInd(block)*(nInd(block)-1))/2
+ resSize <- lowerTriSize + nInd(block)
+
+ ## CALL C FUNCTION ##
+ temp[[i]] <- .C("GLdotProd", vecbyte, nbVec, length(block at gen[[1]]@snp[[1]]), nbNa, naPosi, nInd(block), nLoc(block), ploidy(block),
+ as.double(mu), as.double(s), as.integer(!alleleAsUnit), double(resSize), PACKAGE="adegenet")[[12]]
+ }
+
+
+ ## POOL BLOCK RESULTS TOGETHER ##
+ temp <- Reduce("+", temp)
+ }
+
+ res <- temp[1:lowerTriSize]
+ attr(res,"Size") <- N
+ attr(res,"Diag") <- FALSE
+ attr(res,"Upper") <- FALSE
+ class(res) <- "dist"
+ res <- as.matrix(res)
+ diag(res) <- temp[(lowerTriSize+1):length(temp)]
+
+ colnames(res) <- rownames(res) <- ind.names
+ return(res)
+} # end glDotProd
+
+
+
+
+
+
+########
+## glPca
+########
+##
+## PCA for genlight objects
+##
+glPca <- function(x, center=TRUE, scale=FALSE, nf=NULL, loadings=TRUE, alleleAsUnit=FALSE,
+ useC=TRUE, parallel=require("parallel"), n.cores=NULL,
+ returnDotProd=FALSE, matDotProd=NULL){
+ if(!inherits(x, "genlight")) stop("x is not a genlight object")
+
+ ## COMPUTE MEANS AND VARIANCES ##
+ if(center) {
+ vecMeans <- glMean(x, alleleAsUnit=alleleAsUnit)
+ if(any(is.na(vecMeans))) stop("NAs detected in the vector of means")
+ }
+
+ if(scale){
+ vecVar <- glVar(x, alleleAsUnit=alleleAsUnit)
+ if(any(is.na(vecVar))) stop("NAs detected in the vector of variances")
+ }
+
+
+ myPloidy <- ploidy(x)
+
+ ## NEED TO COMPUTE DOT PRODUCTS ##
+ if(is.null(matDotProd)){
+
+ ## == if non-C code is used ==
+ if(!useC){
+ ## if(parallel && !require(parallel)) stop("parallel package requested but not installed")
+ if(parallel && is.null(n.cores)){
+ n.cores <- parallel::detectCores()
+ }
+
+
+ ## COMPUTE DOT PRODUCTS BETWEEN GENOTYPES ##
+ ## to be fast, a particular function is defined for each case of centring/scaling
+
+ ## NO CENTRING / NO SCALING
+ if(!center & !scale){
+ dotProd <- function(a,b, ploid.a, ploid.b){ # a and b are two SNPbin objects
+ a <- as.integer(a) / ploid.a
+ a[is.na(a)] <- 0
+ b <- as.integer(b) / ploid.b
+ b[is.na(b)] <- 0
+ return(sum( a*b, na.rm=TRUE))
+ }
+ }
+
+ ## CENTRING / NO SCALING
+ if(center & !scale){
+ dotProd <- function(a,b, ploid.a, ploid.b){ # a and b are two SNPbin objects
+ a <- as.integer(a) / ploid.a
+ a[is.na(a)] <- vecMeans[is.na(a)]
+ b <- as.integer(b) / ploid.b
+ b[is.na(b)] <- vecMeans[is.na(b)]
+ return(sum( (a-vecMeans) * (b-vecMeans), na.rm=TRUE) )
+ }
+ }
+
+
+ ## NO CENTRING / SCALING (odd option...)
+ if(!center & scale){
+ dotProd <- function(a,b, ploid.a, ploid.b){ # a and b are two SNPbin objects
+ a <- as.integer(a) / ploid.a
+ a[is.na(a)] <- 0
+ b <- as.integer(b) / ploid.b
+ b[is.na(b)] <- 0
+ return(sum( (a*b)/vecVar, na.rm=TRUE))
+ }
+ }
+
+
+ ## CENTRING / SCALING
+ if(center & scale){
+ dotProd <- function(a,b, ploid.a, ploid.b){ # a and b are two SNPbin objects
+ a <- as.integer(a) / ploid.a
+ a[is.na(a)] <- vecMeans[is.na(a)]
+ b <- as.integer(b) / ploid.b
+ a[is.na(a)] <- vecMeans[is.na(a)]
+ return( sum( ((a-vecMeans)*(b-vecMeans))/vecVar, na.rm=TRUE ) )
+ }
+ }
+
+
+ ## COMPUTE ALL POSSIBLE DOT PRODUCTS (XX^T / n) ##
+ allComb <- combn(1:nInd(x), 2)
+ if(parallel){
+ allProd <- unlist(mclapply(1:ncol(allComb), function(i) dotProd(x at gen[[allComb[1,i]]], x at gen[[allComb[2,i]]], myPloidy[allComb[1,i]], myPloidy[allComb[2,i]]),
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE))
+ } else {
+ allProd <- unlist(lapply(1:ncol(allComb), function(i) dotProd(x at gen[[allComb[1,i]]], x at gen[[allComb[2,i]]], myPloidy[allComb[1,i]], myPloidy[allComb[2,i]]) ))
+ }
+ allProd <- allProd / nInd(x) # assume uniform weights
+
+ ## shape result as a matrix
+ attr(allProd,"Size") <- nInd(x)
+ attr(allProd,"Diag") <- FALSE
+ attr(allProd,"Upper") <- FALSE
+ class(allProd) <- "dist"
+ allProd <- as.matrix(allProd)
+
+ ## compute the diagonal
+ if(parallel){
+ temp <- unlist(mclapply(1:nInd(x), function(i) dotProd(x at gen[[i]], x at gen[[i]], myPloidy[i], myPloidy[i]),
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE))/nInd(x)
+ } else {
+ temp <- unlist(lapply(1:nInd(x), function(i) dotProd(x at gen[[i]], x at gen[[i]], myPloidy[i], myPloidy[i]) ))/nInd(x)
+ }
+ diag(allProd) <- temp
+ } else { # === use C computations ====
+ allProd <- glDotProd(x, center=center, scale=scale, alleleAsUnit=alleleAsUnit, parallel=parallel, n.cores=n.cores)/nInd(x)
+ }
+ } else { # END NEED TO COMPUTE DOTPROD
+ if(!all(dim(matDotProd)==nInd(x))) stop("matDotProd has wrong dimensions.")
+ allProd <- matDotProd
+ }
+
+ ## PERFORM THE ANALYSIS ##
+ ## eigenanalysis
+ eigRes <- eigen(allProd, symmetric=TRUE, only.values=FALSE)
+ rank <- sum(eigRes$values > 1e-12)
+ eigRes$values <- eigRes$values[1:rank]
+ eigRes$vectors <- eigRes$vectors[, 1:rank, drop=FALSE]
+
+ ## scan nb of axes retained
+ if(is.null(nf)){
+ barplot(eigRes$values, main="Eigenvalues", col=heat.colors(rank))
+ cat("Select the number of axes: ")
+ nf <- as.integer(readLines(n = 1))
+ }
+
+ ## rescale PCs
+ res <- list()
+ res$eig <- eigRes$values
+ nf <- min(nf, sum(res$eig>1e-10))
+ ##res$matprod <- allProd # for debugging
+
+ ## use: li = XQU = V\Lambda^(1/2)
+ eigRes$vectors <- eigRes$vectors * sqrt(nInd(x)) # D-normalize vectors
+ res$scores <- sweep(eigRes$vectors[, 1:nf, drop=FALSE],2, sqrt(eigRes$values[1:nf]), FUN="*")
+
+
+ ## GET LOADINGS ##
+ ## need to decompose X^TDV into a sum of n matrices of dim p*r
+ ## but only two such matrices are represented at a time
+ if(loadings){
+ if(scale) {
+ vecSd <- sqrt(vecVar)
+ }
+ res$loadings <- matrix(0, nrow=nLoc(x), ncol=nf) # create empty matrix
+ ## use: c1 = X^TDV
+ ## and X^TV = A_1 + ... + A_n
+ ## with A_k = X_[k-]^T v[k-]
+ for(k in 1:nInd(x)){
+ temp <- as.integer(x at gen[[k]]) / myPloidy[k]
+ if(center) {
+ temp[is.na(temp)] <- vecMeans[is.na(temp)]
+ temp <- temp - vecMeans
+ } else {
+ temp[is.na(temp)] <- 0
+ }
+ if(scale){
+ temp <- temp/vecSd
+ }
+
+ res$loadings <- res$loadings + matrix(temp) %*% eigRes$vectors[k, 1:nf, drop=FALSE]
+ }
+
+ res$loadings <- res$loadings / nInd(x) # don't forget the /n of X_tDV
+ res$loadings <- sweep(res$loadings, 2, sqrt(eigRes$values[1:nf]), FUN="/")
+ }
+
+
+ ## FORMAT OUTPUT ##
+ colnames(res$scores) <- paste("PC", 1:nf, sep="")
+ if(!is.null(indNames(x))){
+ rownames(res$scores) <- indNames(x)
+ } else {
+ rownames(res$scores) <- 1:nInd(x)
+ }
+
+ if(!is.null(res$loadings)){
+ colnames(res$loadings) <- paste("Axis", 1:nf, sep="")
+ if(!is.null(locNames(x)) & !is.null(alleles(x))){
+ rownames(res$loadings) <- paste(locNames(x),alleles(x), sep=".")
+ } else {
+ rownames(res$loadings) <- 1:nLoc(x)
+ }
+ }
+
+ if(returnDotProd){
+ res$dotProd <- allProd
+ rownames(res$dotProd) <- colnames(res$dotProd) <- indNames(x)
+ }
+
+ res$call <- match.call()
+
+ class(res) <- "glPca"
+
+ return(res)
+
+} # glPca
+
+
+
+
+
+
+###############
+## print.glPca
+###############
+print.glPca <- function(x, ...){
+ cat(" === PCA of genlight object ===")
+ cat("\nClass: list of type glPca")
+ cat("\nCall ($call):")
+ print(x$call)
+ cat("\nEigenvalues ($eig):\n", round(head(x$eig,6),3), ifelse(length(x$eig)>6, "...\n", "\n") )
+ cat("\nPrincipal components ($scores):\n matrix with", nrow(x$scores), "rows (individuals) and", ncol(x$scores), "columns (axes)", "\n")
+ if(!is.null(x$loadings)){
+ cat("\nPrincipal axes ($loadings):\n matrix with", nrow(x$loadings), "rows (SNPs) and", ncol(x$loadings), "columns (axes)", "\n")
+ }
+ if(!is.null(x$dotProd)){
+ cat("\nDot products between individuals ($dotProd):\n matrix with", nrow(x$dotProd), "rows and", ncol(x$dotProd), "columns", "\n")
+ }
+ cat("\n")
+}
+
+
+
+
+
+#################
+## scatter.glPca
+#################
+scatter.glPca <- function(x, xax=1, yax=2, posi="bottomleft", bg="white", ratio=0.3,
+ label = rownames(x$scores), clabel = 1, xlim = NULL, ylim = NULL,
+ grid = TRUE, addaxes = TRUE, origin = c(0,0), include.origin = TRUE,
+ sub = "", csub = 1, possub = "bottomleft", cgrid = 1,
+ pixmap = NULL, contour = NULL, area = NULL, ...){
+
+ ## set par
+ opar <- par(mar = par("mar"))
+ par(mar = c(0.1, 0.1, 0.1, 0.1), bg=bg)
+ on.exit(par(opar))
+ axes <- c(xax,yax)
+ ## basic empty plot
+ ## s.label(x$ind.coord[,axes], clab=0, cpoint=0, grid=FALSE, addaxes = FALSE, cgrid = 1, include.origin = FALSE, ...)
+ s.label(x$scores[,axes], label = label, clabel = clabel, xlim = xlim, ylim = ylim, grid = grid, addaxes = addaxes,
+ origin = origin, include.origin = include.origin, sub = sub, csub = csub, possub = possub, cgrid = cgrid,
+ pixmap = pixmap, contour = contour, area = area)
+
+
+ if(ratio>0.001) {
+ add.scatter.eig(x$eig, ncol(x$scores), axes[1], axes[2], posi=posi, ratio=ratio, csub=csub)
+ }
+
+ return(invisible(match.call()))
+} # end scatter.glPca
+
+
+
+
+
+
+#####################
+## loadingplot.glPca
+#####################
+loadingplot.glPca <- function(x, at=NULL, threshold=NULL, axis=1, fac=NULL, byfac=FALSE,
+ lab=rownames(x$loadings), cex.lab=0.7, cex.fac=1, lab.jitter=0,
+ main="Loading plot", xlab="SNP positions", ylab="Contributions", srt=90, adj=c(0,0.5), ... ){
+
+ if(is.null(x$loadings)){
+ warning("This object does not contain loadings. Re-run the analysis, specifying 'loadings=TRUE'.")
+ return(invisible())
+ }
+
+ if(is.null(at)){
+ at <- as.integer(gsub("[.]+.+$", "", rownames(x$loadings)))
+ }
+ if(is.null(threshold)){
+ threshold <- quantile(x$loadings[,axis]^2,0.75)
+ }
+
+ res <- loadingplot.default(x$loadings^2, at=at, threshold=threshold, axis=axis, fac=fac, byfac=byfac,
+ lab=lab, cex.lab=cex.lab, cex.fac=cex.fac, lab.jitter=lab.jitter,
+ main=main, xlab=xlab, ylab=ylab, srt=srt, adj=adj, ...)
+
+ axis(1)
+
+ return(invisible(res))
+} # end loadingplot.glPca
+
+
+
+
+
+###############
+## .glPca2dudi
+###############
+.glPca2dudi <- function(x){
+ if(!inherits(x,"glPca")) stop("x is not a glPca object")
+ old.names <- names(x)
+ new.names <- sub("scores","li", old.names)
+ new.names <- sub("loadings","c1", new.names)
+ names(x) <- new.names
+ class(x) <- c("pca","dudi")
+ return(x)
+} # end glPca2dudi
+
+
+
+
+## TESTING ##
+## x <- new("genlight", list(c(0,0,1,1,0), c(1,1,1,0,0,1), c(2,1,1,1,1,NA)))
+## as.matrix(x)
+## glNA(x)
+## glSum(x)
+## glMean(x)
+
+## same ploidy everywhere
+## x <- new("genlight", list(c(0,0,1,1,0), c(1,1,1,0,0,1), c(0,0,0,1,1,1)))
+## f1 <- function(e) {return(mean((e-mean(e, na.rm=TRUE))^2, na.rm=TRUE))}
+## all.equal(glVar(x), apply(as.matrix(x), 2, f1 )) # MUST BE TRUE
+## all.equal(glVar(x,FALSE), apply(as.matrix(x), 2, f1 )) # MUST BE TRUE
+
+## ## differences in ploidy
+## x <- new("genlight", list(c(0,0,1,1,0), c(1,1,1,0,0,1), c(2,1,1,1,1,NA)))
+## temp <- sweep(as.matrix(x), 1, c(1,1,2), "/")
+## f2 <- function(e,w) {
+## mu <- weighted.mean(e, w, na.rm=TRUE)
+## res <- weighted.mean((e-mu)^2, w, na.rm=TRUE)
+## return(res)
+## }
+
+## all.equal(glMean(x), apply(temp,2,weighted.mean, w=c(1,1,2), na.rm=TRUE)) # MUST BE TRUE
+## all.equal(glVar(x), apply(temp, 2, f2,w=c(1,1,2) )) # MUST BE TRUE
+
+## all.equal(glMean(x,FALSE), apply(temp,2,mean,na.rm=TRUE)) # MUST BE TRUE
+## all.equal(glVar(x,FALSE), apply(temp,2,f1)) # MUST BE TRUE
+
+
+
+#### TESTING DOT PRODUCTS ####
+## M <- matrix(sample(c(0,1), 100*1e3, replace=TRUE), nrow=100)
+## rownames(M) <- paste("ind", 1:100)
+## x <- new("genlight",M)
+
+## ## not centred, not scaled
+## res1 <- glDotProd(x,alleleAsUnit=FALSE, center=FALSE, scale=FALSE)
+## res2 <- M %*% t(M)
+## all.equal(res1,res2) # must be TRUE
+
+## ## centred, not scaled
+## res1 <- glDotProd(x,alleleAsUnit=FALSE, center=TRUE, scale=FALSE)
+## M <- scalewt(M,center=TRUE,scale=FALSE)
+## res2 <- M %*% t(M)
+## all.equal(res1,res2) # must be TRUE
+
+## ## centred, scaled
+## res1 <- glDotProd(x,alleleAsUnit=FALSE, center=TRUE, scale=TRUE)
+## M <- scalewt(M,center=TRUE,scale=TRUE)
+## res2 <- M %*% t(M)
+## all.equal(res1,res2) # must be TRUE
+
+
+#### TESTING PCA ####
+## M <- matrix(sample(c(0,1), 20*1000, replace=TRUE), nrow=20)
+## rownames(M) <- paste("ind", 1:20)
+
+## x <- new("genlight",M)
+## res1 <- glPca(x, nf=4)
+## res2 <- glPca(x, useC=FALSE, nf=4)
+## res3 <- dudi.pca(M, center=TRUE,scale=FALSE, scannf=FALSE,nf=4)
+
+## ## all must be TRUE
+## all.equal(res1$eig,res3$eig)
+## all.equal(res2$eig,res3$eig)
+## all.equal(res1$eig,res2$eig)
+
+## all(abs(res1$scores)-abs(res3$li)<1e-8)
+## all(abs(res2$scores)-abs(res3$li)<1e-8)
+## all(abs(res1$scores)-abs(res2$scores)<1e-8)
+
+## all(abs(res1$loadings)-abs(res3$c1)<1e-8)
+## all(abs(res2$loadings)-abs(res3$c1)<1e-8)
+## all(abs(res1$loadings)-abs(res2$loadings)<1e-8)
+
+
+## ## perform ordinary PCA
+## titi <- dudi.pca(M, center=TRUE, scale=FALSE, scannf=FALSE, nf=4)
+
+
+## ## check results
+## all(round(abs(toto$scores), 10) == round(abs(titi$li), 10)) # MUST BE TRUE
+## all.equal(toto$eig, titi$eig) # MUST BE TRUE
+## all(round(abs(toto$loadings), 10)==round(abs(titi$c1), 10)) # MUST BE TRUE
+
+
+## TEST WITH NAS ##
+## M <- matrix(sample(c(0,1, NA), 1e5, replace=TRUE, prob=c(.495,.495,.01)), nrow=100)
+## rownames(M) <- paste("ind", 1:100)
+
+## ## perform glPca
+## x <- new("genlight",M)
+## toto <- glPca(x, nf=4)
+
+## round(cor(toto$scores),10) # must be diag(1,4)
+## round(t(toto$loadings) %*% toto$loadings,10) # must be diag(1,4)
+
+
+
+
+
+## ## SPEED TESTS ##
+## ## perform glPca
+## M <- matrix(sample(c(0,1), 100*1e5, replace=TRUE), nrow=100)
+## x <- new("genlight",M)
+## system.time(titi <- dudi.pca(M,center=TRUE,scale=FALSE, scannf=FALSE, nf=4)) # 92 sec
+## system.time(toto <- glPca(x, ,center=TRUE,scale=FALSE, useC=TRUE, nf=4)) # 102 sec
+
+## M <- matrix(sample(c(0,1), 200*1e5, replace=TRUE), nrow=200)
+## x <- new("genlight",M)
+## system.time(titi <- dudi.pca(M,center=TRUE,scale=FALSE, scannf=FALSE, nf=4)) # 109 sec
+## system.time(toto <- glPca(x, ,center=TRUE,scale=FALSE, useC=TRUE, nf=4)) # 360 sec
+
+## M <- matrix(sample(c(0,1), 100*5e5, replace=TRUE), nrow=500)
+## x <- new("genlight",M)
+## system.time(titi <- dudi.pca(M,center=TRUE,scale=FALSE, scannf=FALSE, nf=4)) # MEM LIMIT ISSUE
+## system.time(toto <- glPca(x, ,center=TRUE,scale=FALSE, useC=TRUE, nf=4)) # sec
+
+## USE R PROFILING ##
+## for glPca
+## M <- matrix(sample(c(0,1), 100*1e5, replace=TRUE), nrow=100)
+## x <- new("genlight",M)
+## Rprof("glPca-prof.log")
+## toto <- glPca(x, ,center=TRUE,scale=FALSE, useC=TRUE, nf=4) # 102 sec
+## Rprof(NULL)
+## res <- summaryRprof("glPca-prof.log")
+## t <- res$by.total$total.time
+## names(t) <- rownames(res$by.total)
+## par(mar=c(7,4,4,2))
+## barplot(t,las=3, cex.names=.7)
+
+
+## ## for dudi.pca
+## M <- matrix(sample(c(0,1), 100*1e5, replace=TRUE), nrow=100)
+## Rprof("dudipca-prof.log")
+## toto <- dudi.pca(M ,center=TRUE,scale=FALSE, scannf=FALSE, nf=4) # 102 sec
+## Rprof(NULL)
+## res <- summaryRprof("dudipca-prof.log")
+## t <- res$by.total$total.time
+## names(t) <- rownames(res$by.total)
+## par(mar=c(7,4,4,2))
+## barplot(t,las=3, cex.names=.7)
+
+
+## test GLsum:
+## library(adegenet)
+## x <- new("genlight", lapply(1:50, function(i) sample(c(0,1,NA), 1e5, prob=c(.5, .49, .01), replace=TRUE)))
+## res1 <- glSum(x, useC=FALSE)
+## res2 <- glSum(x, useC=TRUE)
+## res3 <- apply(as.matrix(x),2,sum,na.rm=TRUE)
+## all(res1==res3) # must be TRUE
+## all(res2==res3) # must be TRUE
+
+## library(adegenet)
+## x <- new("genlight", lapply(1:50, function(i) sample(c(0,1,2,NA), 1e5, prob=c(.5, .40, .09, .01), replace=TRUE)))
+## res1 <- glSum(x, alleleAsUnit=FALSE, useC=FALSE)
+## res2 <- glSum(x, alleleAsUnit=FALSE, useC=TRUE)
+## res3 <- apply(as.matrix(x)/ploidy(x),2,sum,na.rm=TRUE)
+## all.equal(res1,res3)
+## all.equal(res2,res3)
+
+
+## TEST PARALLELE C COMPUTATIONS IN GLDOTPROD
+## system.time(toto <- glDotProd(x,multi=TRUE)) # 58 sec: cool!
+## system.time(titi <- glDotProd(x,multi=FALSE)) # 245 sec
+## all.equal(toto,titi)
+
+
+## TEST PARALLELE C COMPUTATIONS IN GLPCA ##
+## first dataset
+## x <- new("genlight", lapply(1:50, function(i) sample(c(0,1,2,NA), 1e5, prob=c(.5, .40, .09, .01), replace=TRUE)))
+## system.time(pca1 <- glPca(x, multi=FALSE, useC=FALSE, nf=1)) # no C, no parallel: 43 sec
+## system.time(pca2 <- glPca(x, multi=FALSE, useC=TRUE, nf=1)) # just C: 248 sec
+## system.time(pca3 <- glPca(x, multi=TRUE, useC=FALSE, nf=1, n.core=7)) # just parallel: 16 sec
+## system.time(pca4 <- glPca(x, multi=TRUE, useC=TRUE, nf=1, n.core=7)) # C and parallel: 65 sec
+## all.equal(pca1$scores^2, pca2$scores^2) # must be TRUE
+## all.equal(pca1$scores^2, pca3$scores^2) # must be TRUE
+## all.equal(pca1$scores^2, pca4$scores^2) # must be TRUE
+
+## second dataset
+## x <- new("genlight", lapply(1:500, function(i) sample(c(0,1,2,NA), 1e4, prob=c(.5, .40, .09, .01), replace=TRUE)))
+## system.time(pca1 <- glPca(x, multi=FALSE, useC=FALSE, nf=1)) # no C, no parallel: 418 sec
+## system.time(pca2 <- glPca(x, multi=FALSE, useC=TRUE, nf=1)) # just C: 496 sec
+## system.time(pca3 <- glPca(x, multi=TRUE, useC=FALSE, nf=1, n.core=7)) # just parallel: 589 sec
+## system.time(pca4 <- glPca(x, multi=TRUE, useC=TRUE, nf=1, n.core=7)) # C and parallel: 315 sec
+## all.equal(pca1$scores^2, pca2$scores^2) # must be TRUE
+## all.equal(pca1$scores^2, pca3$scores^2) # must be TRUE
+## all.equal(pca1$scores^2, pca4$scores^2) # must be TRUE
diff --git a/R/glHandle.R b/R/glHandle.R
new file mode 100644
index 0000000..055cd1b
--- /dev/null
+++ b/R/glHandle.R
@@ -0,0 +1,461 @@
+
+# Function to subset raw vectors
+.subsetbin <- function(x, i){
+ # Take a raw vector, subset the bits and then convert to integers.
+ xint <- as.integer(rawToBits(x)[i])
+ # Figure out how many zeroes are needed to pad the end.
+ zeroes <- 8 - (length(xint) %% 8)
+ # Convert the integer vector with zeroes on the end back into a raw vector.
+ return(packBits(c(xint, rep(0L, zeroes))))
+}
+
+# old method for [] for SNPbin
+.oldSNPbinset <- function(x, i){
+ if (missing(i)) i <- TRUE
+ temp <- .SNPbin2int(x) # data as integers with NAs
+ x <- new("SNPbin", snp=temp[i], label=x at label, ploidy=x at ploidy)
+ return(x)
+}
+
+# Zhian N. Kamvar
+# Mon Aug 17 09:39:12 2015 ------------------------------
+#
+# This function takes two steps:
+# 1. Subset the missing positions
+# 2. Subset the vectors of raw SNPs
+#
+# Both steps are not exactly straighforward. Because the missing vector only
+# represents the positions of missing data, it must be subset by value as
+# opposed to position.
+.SNPbinset <- function(x, i){
+ if (missing(i)) i <- TRUE
+
+ # Create a logical value indicating whether or not subsetting is necessary.
+ we_take_all <- length(i) == 1 && is.logical(i) && i
+ n.loc <- x at n.loc
+ if (length(x at NA.posi) > 0){
+ if (is.logical(i)){
+ if (we_take_all){
+ # Keep all of the data
+ return(x)
+ } else {
+ # If the positons are logical, perhaps the best way to address this is
+ # to match the TRUE positions to the NA.posi vector. Adding nomatch = 0
+ # avoids introducing NAs.
+ namatches <- match(which(i), x at NA.posi, nomatch = 0)
+ nas.kept <- x at NA.posi[namatches]
+ }
+ } else if (is.character(i)){
+ stop("Cannot subset a SNPbin object with a character vector", call. = FALSE)
+ } else if (all(i < 0)){
+ # For negative subscripts, find which ones they match and then
+ # negate those. Luckily -0 is allowed.
+ namatches <- match(abs(i), x at NA.posi, nomatch = 0)
+ # Unfortunately, if nothing matches, then the default are zeroes. When you
+ # subset a vector in R with only zero, you will get an empty vector. This
+ # conditional makes sure that NA positions are retained.
+ if (all(namatches == 0)){
+ nas.kept <- x at NA.posi
+ } else {
+ nas.kept <- x at NA.posi[-namatches]
+ }
+
+ } else if (all(i > 0)){
+ # Positive subscripts are much easier. First you find where the subscripts
+ # match and then your subset with those positions.
+ namatches <- match(i, x at NA.posi, nomatch = 0)
+ nas.kept <- x at NA.posi[namatches]
+ } else {
+ stop("Cannot subset a SNPbin with mixed subscripts.", call. = FALSE)
+ }
+ # After we find out which missing positions we need to keep, we reset the
+ # missing positions to the subset data.
+ if (length(nas.kept) > 0){
+ old.posi <- 1:n.loc
+ x at NA.posi <- match(nas.kept, old.posi[i])
+ } else {
+ x at NA.posi <- nas.kept
+ }
+ }
+ # Here we calculate the number of loci we will have left in the data.
+ if (we_take_all){
+ return(x)
+ } else if (all(is.logical(i))){
+ n.loc <- sum(i)
+ } else if (any(i < 0)){
+ n.loc <- n.loc - length(i)
+ } else {
+ n.loc <- length(i)
+ }
+ # Now we loop over all chromosomes and subset.
+ x at snp <- lapply(x at snp, .subsetbin, i)
+ # Set the new value of the number of loci and return.
+ x at n.loc <- n.loc
+ return(x)
+}
+
+###############
+## '[' operators
+###############
+## SNPbin
+
+setMethod("[", signature(x="SNPbin", i="ANY"), function(x, i) {
+ .SNPbinset(x, i)
+}) # end [] for SNPbin
+
+
+
+
+## genlight
+setMethod("[", signature(x="genlight", i="ANY", j="ANY", drop="ANY"), function(x, i, j, ..., treatOther=TRUE, quiet=TRUE, drop=FALSE) {
+ if (missing(i)) i <- TRUE
+ if (missing(j)) j <- TRUE
+
+ ori.n <- nInd(x)
+ ori.p <- nLoc(x)
+
+ ## recycle logicals if needed
+ if(!is.null(i) && is.logical(i)) i <- rep(i, length=ori.n)
+ if(!is.null(j) && is.logical(j)) j <- rep(j, length=ori.p)
+
+
+ ## SUBSET INDIVIDUALS ##
+ ## genotypes
+ x at gen <- x at gen[i]
+
+ ## ind names
+ x at ind.names <- x at ind.names[i]
+
+ ## ploidy
+ if(!is.null(x at ploidy)) {
+ ori.ploidy <- ploidy(x) <- ploidy(x)[i]
+ } else {
+ ori.ploidy <- NULL
+ }
+
+ ## pop
+ if(!is.null(pop(x))) {
+ ori.pop <- pop(x) <- factor(pop(x)[i])
+ } else {
+ ori.pop <- NULL
+ }
+ ## strata
+ if(!is.null(x at strata)) {
+ ori.strata <- x at strata <- x at strata[i, , drop = FALSE]
+ } else {
+ ori.strata <- NULL
+ }
+
+
+ ## HANDLE 'OTHER' SLOT ##
+ nOther <- length(other(x))
+ namesOther <- names(other(x))
+ counter <- 0
+ if(treatOther & !(is.logical(i) && all(i))){
+ f1 <- function(obj,n=ori.n){
+ counter <<- counter+1
+ if(!is.null(dim(obj)) && nrow(obj)==ori.n) { # if the element is a matrix-like obj
+ obj <- obj[i,,drop=FALSE]
+ } else if(length(obj) == ori.n) { # if the element is not a matrix but has a length == n
+ obj <- obj[i]
+ if(is.factor(obj)) {obj <- factor(obj)}
+ } else {if(!quiet) warning(paste("cannot treat the object",namesOther[counter]))}
+
+ return(obj)
+ } # end f1
+
+ other(x) <- lapply(x at other, f1) # treat all elements
+
+ } # end treatOther
+
+
+ ## SUBSET LOCI ##
+
+ ## handle ind.names, loc.names, chromosome, position, and alleles
+ if (is.character(j)){
+ j <- match(j, x at loc.names, nomatch = 0)
+ }
+ x at loc.names <- x at loc.names[j]
+ x at chromosome <- chr(x)[j]
+ x at position <- position(x)[j]
+ x at loc.all <- alleles(x)[j]
+ x at gen <- lapply(x at gen, function(e) e[j])
+ x at n.loc <- x at gen[[1]]@n.loc
+
+ return(x)
+}) # end [] for genlight
+
+
+
+
+
+
+
+######################
+##
+## c, cbind, rbind...
+##
+######################
+
+################
+## cbind SNPbin
+################
+##setMethod("cbind", signature("SNPbin"), function(..., deparse.level = 1) {
+cbind.SNPbin <- function(..., checkPloidy=TRUE){
+ myList <- list(...)
+ if(!all(sapply(myList, class)=="SNPbin")) stop("some objects are not SNPbin objects")
+ ## remove empty objects
+ myList <- myList[sapply(myList,nLoc)>0]
+ if(length(myList)==0) {
+ warning("All objects are empty")
+ return(NULL)
+ }
+
+
+ if(checkPloidy && length(unique(sapply(myList, ploidy))) !=1 ) stop("objects have different ploidy levels")
+ if(checkPloidy) {
+ ori.ploidy <- ploidy(myList[[1]])
+ } else {
+ ori.ploidy <- NULL
+ }
+ x <- new("SNPbin", unlist(lapply(myList, as.integer)), ploidy=ori.ploidy)
+ return(x)
+} # end cbind.SNPbin
+##})
+
+
+
+c.SNPbin <- function(...){
+ return(cbind(...))
+}
+
+
+
+
+##################
+## cbind genlight
+##################
+##setMethod("cbind", signature(x="genlight"), function(..., deparse.level = 1) {
+cbind.genlight <- function(...){
+ ## store arguments
+ dots <- list(...)
+
+ ## extract arguments which are genlight objects
+ myList <- dots[sapply(dots, inherits, "genlight")]
+
+ ## keep the rest in 'dots'
+ dots <- dots[!sapply(dots, inherits, "genlight")]
+
+ if(length(myList)==1 && is.list(myList[[1]])) myList <- myList[[1]]
+ if(!all(sapply(myList, class)=="genlight")) stop("some objects are not genlight objects")
+ ## remove empty objects
+ myList <- myList[sapply(myList,nLoc)>0 & sapply(myList,nInd)>0]
+ if(length(myList)==0) {
+ warning("All objects are empty")
+ return(NULL)
+ }
+
+ ## different checks
+ if(length(unique(sapply(myList, nInd))) > 1 ) stop("objects have different numbers of individuals")
+ n.obj <- length(myList)
+ n.ind <- nInd(myList[[1]])
+ if(n.ind==0){
+ warning("All objects are empty")
+ return(NULL)
+ }
+ temp <- as.matrix(as.data.frame(lapply(myList, ploidy)))
+ if(any(apply(temp,1,function(r) length(unique(r)))>1)) stop("non-consistent ploidy across datasets")
+ ori.ploidy <- ploidy(myList[[1]])
+
+
+ ## merge one individual at a time ##
+ res <- list()
+ for(i in 1:n.ind){
+ res[[i]] <- Reduce(function(a,b) {cbind(a,b,checkPloidy=FALSE)}, lapply(myList, function(e) e at gen[[i]]) )
+ }
+
+ dots$gen <- res
+ dots$Class <- "genlight"
+ res <- do.call(new, dots)
+
+ ## handle loc.names, alleles, etc. ##
+ indNames(res) <- indNames(myList[[1]])
+ locNames(res) <- unlist(lapply(myList, locNames))
+ alleles(res) <- unlist(lapply(myList, alleles))
+ pop(res) <- pop(myList[[1]])
+ res at strata <- myList[[1]]@strata
+ ploidy(res) <- ori.ploidy
+
+ ## return object ##
+ return(res)
+} # end cbind.genlight
+##})
+
+
+
+
+
+
+##################
+## rbind genlight
+##################
+##setMethod("cbind", signature(x="genlight"), function(..., deparse.level = 1) {
+#' @importFrom dplyr bind_rows
+rbind.genlight <- function(...){
+ ## store arguments
+ dots <- list(...)
+
+ ## extract arguments which are genlight objects
+ myList <- dots[sapply(dots, inherits, "genlight")]
+
+ ## keep the rest in 'dots'
+ dots <- dots[!sapply(dots, inherits, "genlight")]
+
+ if(!all(sapply(myList, class)=="genlight")) stop("some objects are not genlight objects")
+
+ ## remove empty objects
+ myList <- myList[sapply(myList,nLoc)>0 & sapply(myList,nInd)>0]
+ if(length(myList)==0) {
+ warning("All objects are empty")
+ return(NULL)
+ }
+
+ if(length(unique(sapply(myList, nLoc))) !=1 ) stop("objects have different numbers of SNPs")
+
+ ## build output
+ dots$Class <- "genlight"
+ dots$gen <- Reduce(c, lapply(myList, function(e) e at gen))
+ res <- do.call(new, dots)
+ locNames(res) <- locNames(myList[[1]])
+ alleles(res) <- alleles(myList[[1]])
+ indNames(res) <- unlist(lapply(myList, indNames))
+ pop(res) <- factor(unlist(lapply(myList, pop)))
+
+ # Hierarchies are tricky. Using dplyr's bind_rows.
+ res <- .rbind_strata(myList, res)
+
+ ## return object ##
+ return(res)
+
+} # end rbind.genlight
+
+
+
+
+
+
+##########
+## seppop
+##########
+setMethod("seppop", signature(x="genlight"), function(x, pop=NULL, treatOther=TRUE, quiet=TRUE, ...){
+ ## HANDLE POP ARGUMENT ##
+ if(!is.null(pop)) {
+ if (is.language(pop)){
+ setPop(x) <- pop
+ } else {
+ pop(x) <- pop
+ }
+ }
+
+ if(is.null(pop(x))) stop("pop not provided and pop(x) is NULL")
+
+ ## PERFORM SUBSETTING ##
+ kObj <- lapply(levels(pop(x)), function(lev) x[pop(x)==lev, , treatOther=treatOther, quiet=quiet, ...])
+ names(kObj) <- levels(pop(x))
+
+ return(kObj)
+}) # end seppop
+
+
+
+
+
+
+##########
+## seploc
+##########
+setMethod("seploc", signature(x="genlight"), function(x, n.block=NULL, block.size=NULL, random=FALSE,
+ parallel=require(parallel), n.cores=NULL){
+ ## CHECKS ##
+ if(is.null(n.block) & is.null(block.size)) stop("n.block and block.size are both missing.")
+ if(!is.null(n.block) & !is.null(block.size)) stop("n.block and block.size are both provided.")
+ if(parallel && !require(parallel)) stop("parallel package requested but not installed")
+ if(parallel && is.null(n.cores)){
+ n.cores <- parallel::detectCores()
+ }
+
+
+ ## GET BLOCK SIZE VECTOR ##
+ P <- nLoc(x)
+
+ ## n.block is given
+ if(!is.null(n.block)){
+ vec.blocksize <- rep(P %/% n.block, n.block)
+ if(P %% n.block >0){
+ vec.blocksize[1:(P %% n.block)] <- vec.blocksize[1:(P %% n.block)] + 1
+ }
+
+ }
+
+ ## block.size is given
+ if(!is.null(block.size)){
+ vec.blocksize <- rep(block.size, P %/% block.size)
+ if(P %% block.size >0){
+ vec.blocksize <- c( vec.blocksize, P %% block.size)
+ }
+ }
+
+
+ ## split data by blocks ##
+ fac.block <- factor(rep(1:length(vec.blocksize), vec.blocksize))
+ if(random){
+ fac.block <- sample(fac.block)
+ }
+
+ if(parallel){
+ if(random){
+ res <- mclapply(levels(fac.block), function(lev) x[, sample(which(fac.block==lev))],
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE)
+ } else {
+ res <- mclapply(levels(fac.block), function(lev) x[, which(fac.block==lev)],
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE)
+ }
+ } else {
+ if(random){
+ res <- lapply(levels(fac.block), function(lev) x[, sample(which(fac.block==lev))])
+ } else {
+ res <- lapply(levels(fac.block), function(lev) x[, which(fac.block==lev)])
+ }
+ }
+
+ ## return result ##
+ names(res) <- paste("block", 1:length(res),sep=".")
+
+ return(res)
+}) # end seploc
+
+
+
+
+
+
+###################
+### TESTING
+###################
+
+
+## c, cbind, rbind ##
+## a <- new("genlight", list(c(1,0,1), c(0,0,1,0)) )
+## b <- new("genlight", list(c(1,0,1,1,1,1), c(1,0)) )
+## locNames(a) <- letters[1:4]
+## locNames(b) <- 1:6
+## c <- cbind(a,b)
+## identical(as.matrix(c),cbind(as.matrix(a), as.matrix(b))) # MUST BE TRUE
+## identical(as.matrix(rbind(a,a)),rbind(as.matrix(a),as.matrix(a)))
+
+
+
+
+## test subsetting with/without @other ##
+## x <- new("genlight", list(a=1,b=0,c=1), other=list(1:3, letters, data.frame(2:4)))
+## pop(x) <- c("pop1","pop1", "pop2")
diff --git a/R/glPlot.R b/R/glPlot.R
new file mode 100644
index 0000000..e661916
--- /dev/null
+++ b/R/glPlot.R
@@ -0,0 +1,42 @@
+
+###########
+## glPlot
+############
+glPlot <- function(x, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),...) {
+
+ ## get plotted elements ##
+ X <- t(as.matrix(x))
+ X <- X[,ncol(X):1]
+ ylabpos <- pretty(1:nInd(x),5)
+ if(is.null(col)) {
+ myCol <- colorRampPalette(c("royalblue3", "firebrick1"))(max(X,na.rm=TRUE)+1)
+ } else {
+ myCol <- col
+ }
+
+ ## draw the plot ##
+ ## main plot
+ image(x=1:nLoc(x), y=1:nInd(x), z=X, xlab="SNP index", ylab="Individual index", yaxt="n", col=myCol, ...)
+
+ ## add y axis
+ axis(side=2, at=nInd(x)-ylabpos+1, labels=ylabpos)
+
+ ## add legend
+ if(legend){
+ legend(posi, fill=myCol, legend=0:max(X,na.rm=TRUE), horiz=TRUE, bg=bg, title="Number of 2nd allele")
+ }
+
+ return(invisible())
+} # end plot for glPlot
+
+
+
+## hack to remove the NOTE in R CMD check about:
+## "plot,genlight: no visible binding for global variable ‘y’"
+if(getRversion() >= "2.15.1") utils::globalVariables("y")
+
+## plot method
+setMethod("plot", signature(x="genlight", y="ANY"), function(x, y=NULL, col=NULL, legend=TRUE,
+ posi="bottomleft", bg=rgb(1,1,1,.5),...) {
+ glPlot(x, col=col, legend=legend, posi=posi, bg=bg, ...)
+})
diff --git a/R/glSim.R b/R/glSim.R
new file mode 100644
index 0000000..08dcb3f
--- /dev/null
+++ b/R/glSim.R
@@ -0,0 +1,227 @@
+
+
+##########
+## glSim
+##########
+glSim <- function(n.ind, n.snp.nonstruc, n.snp.struc = 0, grp.size = c(0.5, 0.5), k = NULL,
+ pop.freq = NULL, ploidy = 1, alpha = 0, parallel = FALSE,
+ LD = TRUE, block.minsize = 10, block.maxsize = 1000, theta = NULL,
+ sort.pop = FALSE, ...){
+
+
+
+ ## BASIC CHECKS ##
+ if( any(c(n.ind, n.snp.nonstruc+n.snp.struc) <1)) stop("null numbers of individuals and/or SNPs requested")
+ ## alpha parameter
+ if(alpha>0.5){
+ alpha <- 0.5
+ warning("alpha cannot exceed 0.5 - changing the value to 0.5 (total forced asymmetry)")
+ }
+ if(alpha<0){
+ alpha <- 0
+ warning("alpha cannot be lower than 0 - changing the value to 0 (no forced asymmetry)")
+ }
+
+ ## handle group sizes
+ if(length(grp.size)!=2) stop("grp.size should be a vector of length 2")
+ grp.size <- grp.size/sum(grp.size)
+ grpA.size <- grp.size[[1]]*n.ind
+ if(grpA.size >= n.ind) stop("grpA.size is >= n.ind")
+ grpB.size <- n.ind - grpA.size
+
+
+ # handle pop.freq for k populations
+ if(is.null(k) & is.null(pop.freq)){
+ pop.freq <- 1
+ }
+ if(!is.null(k) & !is.null(pop.freq)){
+ if(k != length(pop.freq)){
+ warning("k != length(pop.freq), length(pop.freq) will be taken as k")
+ }
+ }
+ if(!is.null(k) & is.null(pop.freq)){
+ pops <-c(1:k)
+ popBaseline <- rep(pops, c(10))
+ popBaseline <- factor(sample(popBaseline, length(popBaseline)))
+ popExtra <- factor(sample(pops, (n.ind - length(popBaseline)), replace=TRUE))
+ pop <- c(popBaseline, popExtra)
+ pop <- factor(pop)
+ pop.freq <- as.vector(unlist(sapply(pops, function(e) sum(pop==e))))
+ }
+
+
+ n.all <- n.snp.nonstruc
+
+
+
+
+
+ simNeutralSNPs <- function(n.ind, n.all, pop.freq=1, LD=TRUE, ploidy=1,
+ block.minsize=10, block.maxsize=1000, theta=NULL,
+ sort.pop=FALSE, parallel=parallel){
+ ## CHECKS ##
+ ## force population frequencies to 1
+ pop.freq <- pop.freq/sum(pop.freq)
+ K <- length(pop.freq)
+ if(!is.null(theta) && theta<1e-14) theta <- NULL
+
+
+ ## GET POPULATION FACTOR ##
+ pop <- paste("pop", sample(1:K, n.ind, replace=TRUE, prob=pop.freq),sep=".")
+ if(sort.pop) pop <- sort(pop)
+
+
+ ## AUXILIARY FUNCTIONS ##
+
+ ## this function simulates a block of allele frequencies for K pop
+ ## without linkage
+ ## nbAll is a number of alleles to simulate
+ ## 'pop' is a factor indicating populations
+ simBlock.NOLD <- function(nbAll, pop){
+ ## function to simulate one allele ##
+ simOneAll <- function(){
+ f <- runif(K)
+ names(f) <- unique(pop)
+ return(rbinom(n=n.ind, prob=f[pop], size=ploidy))
+ }
+
+ ## simulate all allele frequencies ##
+ out <- replicate(nbAll, simOneAll())
+ return(new("genlight", out, ploidy=ploidy, parallel=parallel))
+ } # end simBlock.NOLD
+
+
+ ## this function simulates a block of allele frequencies for K pop
+ ## with linkage
+ ## nbAll is a number of alleles to simulate
+ ## 'pop' is a factor indicating populations
+
+ if(is.null(theta)){
+ ## FUNCTION WITHOUT THETA ##
+ simBlock.LD <- function(nbAll, pop){
+ ## get master allele ##
+ f.ori <- runif(K)
+ names(f.ori) <- unique(pop)
+ prob.ori <- f.ori[pop]
+
+ ## function to simulate one allele ##
+ simOneAll <- function(){
+ return(rbinom(n=n.ind, prob=prob.ori, size=ploidy))
+ }
+ ## simulate all allele frequencies ##
+ out <- replicate(nbAll, simOneAll())
+ out <- matrix(out, ncol=nbAll)
+ return(out)
+ } # end simBlock.LD
+ } else {
+ ## FUNCTION WITH THETA ##
+ ## function to alter frequencies ##
+ tweak.freq <- function(f){
+ f[f<.5] <- suppressWarnings(f[f<.5] + runif(length(f[f<.5]), 0, theta))
+ f[f>.5] <- suppressWarnings(f[f>.5] - runif(length(f[f>.5]), 0, theta))
+ f[f<0] <- 0
+ f[f>1] <- 1
+ return(f)
+ }
+
+ simBlock.LD <- function(nbAll, pop){
+ ## get master allele ##
+ f.ori <- runif(K)
+ names(f.ori) <- unique(pop)
+ prob.ori <- f.ori[pop]
+
+ ## function to simulate one allele ##
+ simOneAll <- function(){
+ return(rbinom(n=n.ind, prob=tweak.freq(prob.ori), size=ploidy))
+ }
+
+ ## simulate all allele frequencies ##
+ out <- replicate(nbAll, simOneAll())
+ out <- matrix(out, ncol=nbAll)
+ return(out)
+ }
+ } # end function with theta
+
+
+ ## SIMULATE ALL DATA ##
+ if(!LD){ # no LD
+ out <- simBlock.NOLD(n.all, pop)
+ } else { # with LD IFF n.snp.nonstruc > 0 !
+ if(n.snp.nonstruc > 0){
+ ## determine blocks ##
+ block.sizes <- round(runif(1,min=block.minsize,max=block.maxsize))
+ while(sum(block.sizes)<n.all){
+ block.sizes <- c(block.sizes, round(runif(1,min=block.minsize,max=block.maxsize)))
+ }
+ block.sizes <- block.sizes[-length(block.sizes)]
+ if(sum(block.sizes)<n.all) block.sizes <- c(block.sizes, n.all-sum(block.sizes))
+
+ ## simulate all blocks ##
+ temp <- lapply(block.sizes, simBlock.LD, pop)
+
+ ## put blocks together ##
+ out <- temp[[1]]
+ if(length(temp)>1){
+ for(i in 2:length(temp)){
+ out <- cbind(out, temp[[i]])
+ }
+ }
+ out <- new("genlight", out, ploidy=ploidy, parallel=parallel)
+ }else{
+ out <- simBlock.NOLD(0, pop)
+ }}
+ out at other <- list(factor(pop))
+ names(out at other) <- "ancestral.pops"
+ outpop <- list(out, pop)
+ return(outpop)
+ } # end simNeutralSNPs
+
+
+ ## carry out fn to get non-structural SNPs:
+ res.ns <- simNeutralSNPs(n.ind, n.snp.nonstruc, pop.freq=pop.freq, ploidy=ploidy,
+ LD=LD, block.minsize=block.minsize, block.maxsize=block.maxsize, theta=theta,
+ sort.pop=sort.pop, parallel=FALSE)
+
+
+
+ ## GET STRUCTURAL SNPS:
+
+ ## GET PHEN FACTOR ##
+ phen <- paste("phen", sample(rep(c("A", "B"), c(grpA.size, grpB.size)),
+ n.ind, replace=TRUE), sep=".")
+ if(!sort.pop) phen <- sort(phen)
+
+ ## function simulating structural SNPs for phenotypic groups A and B
+ f2 <- function(){
+ probA <- runif(1, min=0, max=0.5-alpha) # generates probA for SNP p
+ probB <- 1 - probA # generates probB for SNP p
+ # get vector of probabilities by phenotype at SNP p
+ phenProbs <- c(probA, probB)
+ names(phenProbs) <- unique(phen)
+ # draw SNP p for all individuals according to the phenProbs for that SNP
+ rbinom(n=rep(1,n.ind), prob=phenProbs[phen], size=ploidy)
+ }
+
+ if(n.snp.struc > 0){
+ struct <- replicate(n.snp.struc, f2())
+ struct <- matrix(struct, ncol=n.snp.struc)
+ phen <- factor(phen)
+ struct <- new("genlight", struct, ploidy=ploidy, parallel=FALSE)
+ struct at pop <- phen
+ } # end snp.struc
+
+
+ pop <- res.ns[[2]]
+ res.ns <- res.ns[[1]]
+ if(n.snp.struc>0){
+ res <- cbind(res.ns, struct, parallel = parallel)
+ res at pop <- phen
+ }
+ else{
+ res <- res.ns
+ }
+ res at other <- list(factor(pop))
+ names(res at other) <- "ancestral.pops"
+ return(res)
+}
+#
diff --git a/R/gstat.randtest.R b/R/gstat.randtest.R
new file mode 100644
index 0000000..6c8f2c0
--- /dev/null
+++ b/R/gstat.randtest.R
@@ -0,0 +1,63 @@
+## ##########################
+## ## Function gstat.randtest
+## ##########################
+## gstat.randtest <- function(x,pop=NULL, method=c("global","within","between"),
+## sup.pop=NULL, sub.pop=NULL, nsim=499){
+## message("Sorry, this function depends on hierfstat, and has been moved to the package hierfstat.")
+## return()
+
+## ## ## cat("\nSorry, hierfstat package has been disabled - this function will be restored in a future release.\n")
+## ## ## return(invisible())
+
+## ## if(!is.genind(x)) stop("x is not a valid genind object")
+## ## if(x at ploidy != as.integer(2)) stop("not implemented for non-diploid genotypes")
+## ## checkType(x)
+## ## ## if(!require(hierfstat)) stop("hierfstat package is required. Please install it.")
+
+## ## if(is.null(pop)) pop <- x at pop
+## ## if(is.null(pop)) pop <- as.factor(rep("P1",nrow(x at tab)))
+## ## if(length(pop)!=nrow(x at tab)) stop("pop has a wrong length.")
+
+## ## met <- tolower(method[1])
+## ## if(met=="within" && is.null(sup.pop)) stop("Method 'within' chosen but 'sup.pop' is not provided.")
+## ## if(met=="between" && is.null(sub.pop)) stop("Method 'between' chosen but 'sub.pop' is not provided.")
+
+## ## ## make data for hierfstat
+## ## X <- genind2hierfstat(x=x,pop=pop)
+
+## ## ## compute obs gstat
+## ## obs <- g.stats.glob(X)$g.stats
+
+## ## pop <- X[,1]
+## ## X <- X[,-1]
+
+## ## ## simulations according one of the 3 different schemes
+## ## ## note: for, lapply and sapply are all equivalent
+## ## ## recursive functions would require options("expression") to be modified...
+## ## sim <- vector(mode="numeric",length=nsim)
+
+## ## if(met=="global"){
+
+## ## sim <- sapply(1:nsim, function(i) g.stats.glob(cbind(sample(pop),X))$g.stats)
+
+## ## } else if(met=="within"){
+
+## ## if(length(sup.pop) != length(pop)) stop("pop and sup.pop do not have the same length.")
+## ## sim <- sapply(1:nsim, function(i) g.stats.glob(cbind(pop,X[samp.within(sup.pop),]))$g.stats)
+
+## ## } else if(met=="between"){
+
+## ## if(length(sub.pop) != length(pop)) stop("pop and sub.pop do not have the same length.")
+## ## sim <- sapply(1:nsim, function(i) g.stats.glob(cbind(pop,X[samp.between(sub.pop),]))$g.stats)
+
+## ## } else {
+## ## stop("Unknown method requested.")
+## ## }
+
+## ## prevcall <- match.call()
+
+## ## res <- as.randtest(sim=sim, obs=obs, call=prevcall)
+
+## ## return(res)
+
+## }
diff --git a/R/handling.R b/R/handling.R
new file mode 100644
index 0000000..2608806
--- /dev/null
+++ b/R/handling.R
@@ -0,0 +1,663 @@
+###########################
+#
+# Auxiliary functions for
+# adegenet objects
+#
+# T. Jombart
+###########################
+
+##############################
+# Method truenames for genind
+##############################
+setGeneric("truenames", function(x) standardGeneric("truenames"))
+
+setMethod("truenames", signature(x="genind"), function(x){
+ message("This accessor is now deprecated. Please use 'tab' instead.")
+ return(x at tab)
+})
+
+
+
+##############################
+# Method truenames for genpop
+##############################
+setMethod("truenames",signature(x="genpop"), function(x){
+ message("This accessor is now deprecated. Please use 'tab' instead.")
+ return(x at tab)
+})
+
+
+
+
+###########################
+## Generic / methods 'tab'
+###########################
+#'
+#' Access allele counts or frequencies
+#'
+#' This accessor is used to retrieve a matrix of allele data.
+#' By default, a matrix of integers representing allele counts is returned.
+#' If \code{freq} is TRUE, then data are standardised as frequencies, so that for any individual and any locus the data sum to 1.
+#' The argument \code{NA.method} allows to replace missing data (NAs).
+#' This accessor replaces the previous function \code{truenames} as well as the function \code{makefreq}.
+#'
+#' @export
+#'
+#' @aliases tab
+#'
+#' @rdname tab
+#'
+#' @docType methods
+#'
+#' @param x a \linkS4class{genind} or \linkS4class{genpop} object.
+#' @param freq a logical indicating if data should be transformed into relative frequencies (TRUE); defaults to FALSE.
+#' @param NA.method a method to replace NA; asis: leave NAs as is; mean: replace by the mean allele frequencies; zero: replace by zero
+#' @param ... further arguments passed to other methods.
+#' @return a matrix of integers or numeric
+#'
+#' @examples
+#'
+#' data(microbov)
+#' head(tab(microbov))
+#' head(tab(microbov,freq=TRUE))
+#'
+#'
+setGeneric("tab", function(x, ...) standardGeneric("tab"))
+
+.tabGetter <- function(x, freq=FALSE, NA.method=c("asis","mean","zero"), ...){
+ ## handle arguments
+ NA.method <- match.arg(NA.method)
+ # outdim <- dim(x at tab)
+ ## get matrix of data
+ if (!freq){
+ out <- x at tab
+ } else {
+ out <- x at tab/x at ploidy
+ }
+
+ ## replace NAs if needed
+ if(NA.method=="mean"){
+ f1 <- function(vec){
+ m <- mean(vec,na.rm=TRUE)
+ vec[is.na(vec)] <- m
+ return(vec)
+ }
+
+ out <- apply(out, 2, f1)
+
+ }
+ if(NA.method=="zero"){
+ out[is.na(out)] <- ifelse(freq, 0, 0L)
+ }
+ # dim(out) <- outdim
+ ## return output
+ return(out)
+}
+
+#' @rdname tab
+#' @aliases tab,genind-methods
+#' @aliases tab.genind
+setMethod("tab", signature(x = "genind"),
+ function (x, freq = FALSE, NA.method = c("asis","mean","zero"), ...){
+ .tabGetter(x, freq = freq, NA.method = NA.method, ...)
+ })
+
+
+
+#' @rdname tab
+#' @aliases tab,genpop-methods
+#' @aliases tab.genpop
+
+setMethod("tab", signature(x="genpop"), function(x, freq=FALSE, NA.method=c("asis","mean","zero"), ...){
+ ## handle arguments
+ NA.method <- match.arg(NA.method)
+ # outdim <- dim(x at tab)
+ ## get matrix of data
+ if(!freq) {
+ out <- x at tab
+ } else {
+ out <- x at tab
+ f1 <- function(vec) return(vec/sum(vec,na.rm=TRUE))
+ ## compute frequencies
+ fac <- x at loc.fac
+ if (is.null(fac)) fac <- rep(1, nLoc(x))
+ out <- apply(x at tab, 1, tapply, fac, f1)
+ if (ncol(x at tab) > 1){
+ ## reshape into matrix
+ col.names <- do.call(c,lapply(out[[1]],names))
+ row.names <- names(out)
+ out <- matrix(unlist(out), byrow=TRUE, nrow=nrow(x at tab),
+ dimnames=list(row.names, col.names))
+ ## reorder columns
+ out <- out[, colnames(x at tab), drop = FALSE]
+ } else {
+ out <- matrix(out, nrow = length(out), ncol = 1,
+ dimnames = list(rownames(x at tab), colnames(x at tab)))
+ }
+
+ }
+
+ ## replace NAs if needed
+ if(NA.method=="mean"){
+ f1 <- function(vec){
+ m <- mean(vec, na.rm=TRUE)
+ vec[is.na(vec)] <- m
+ return(vec)
+ }
+
+ out <- apply(out, 2, f1)
+ }
+ if(NA.method=="zero"){
+ out[is.na(out)] <- ifelse(freq, 0, 0L)
+ }
+ # dim(out) <- outdim
+ ## return output
+ return(out)
+})
+
+
+
+
+###########################
+# Method seploc for genind
+###########################
+setGeneric("seploc", function(x, ...) standardGeneric("seploc"))
+
+setMethod("seploc", signature(x="genind"), function(x,truenames=TRUE,res.type=c("genind","matrix")){
+ truenames <- TRUE # this argument will be deprecated
+ if(x at type=="PA"){
+ msg <- paste("seploc is not implemented for presence/absence markers")
+ cat("\n",msg,"\n")
+ return(invisible())
+ }
+
+ if(!is.genind(x)) stop("x is not a valid genind object")
+ res.type <- match.arg(res.type)
+
+ ## make separate tables
+ kX <- list()
+ locfac.char <- as.character(x at loc.fac)
+ for(i in locNames(x)){
+ kX[[i]] <- x at tab[, i==locfac.char,drop=FALSE]
+ }
+
+ prevcall <- match.call()
+ if(res.type=="genind"){
+ ## ploidy bug fixed by Zhian N. Kamvar
+ ##kX <- lapply(kX, genind, pop=x at pop, prevcall=prevcall)
+ kX <- lapply(kX, genind, pop=x at pop, prevcall=prevcall, ploidy=x at ploidy, type=x at type)
+ for(i in 1:length(kX)){
+ kX[[i]]@other <- x at other
+ }
+ }
+
+ return(kX)
+})
+
+
+
+###########################
+# Method seploc for genpop
+###########################
+setMethod("seploc", signature(x="genpop"), function(x,truenames=TRUE,res.type=c("genpop","matrix")){
+ truenames <- TRUE # this argument will be deprecated
+ if(x at type=="PA"){
+ msg <- paste("seploc is not implemented for presence/absence markers")
+ cat("\n",msg,"\n")
+ return(invisible())
+ }
+
+
+ if(!is.genpop(x)) stop("x is not a valid genpop object")
+ res.type <- match.arg(res.type)
+ if(res.type=="genpop") { truenames <- TRUE }
+
+ temp <- x at loc.fac
+ nloc <- length(levels(temp))
+ levels(temp) <- 1:nloc
+
+ ## make separate tables
+ kX <- list()
+ locfac.char <- as.character(x at loc.fac)
+ for(i in locNames(x)){
+ kX[[i]] <- x at tab[,i==locfac.char,drop=FALSE]
+ }
+
+ names(kX) <- locNames(x)
+
+ prevcall <- match.call()
+ if(res.type=="genpop"){
+ kX <- lapply(kX, genpop, prevcall=prevcall, ploidy=x at ploidy, type=x at type)
+ for(i in 1:length(kX)){
+ kX[[i]]@other <- x at other
+ }
+ }
+
+ return(kX)
+})
+
+
+
+
+
+###############
+# '$' operator
+###############
+setMethod("$","genind",function(x,name) {
+ return(slot(x,name))
+})
+
+
+setMethod("$<-","genind",function(x,name,value) {
+ slot(x,name,check=TRUE) <- value
+ return(x)
+})
+
+
+
+
+
+
+
+##################
+# Function seppop
+##################
+setGeneric("seppop", function(x, ...) standardGeneric("seppop"))
+
+## genind
+setMethod("seppop", signature(x="genind"), function(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"),
+ drop=FALSE, treatOther=TRUE, quiet=TRUE){
+ ## checkType(x)
+ truenames <- TRUE # this argument will be deprecated
+
+ ## misc checks
+ if(!is.genind(x)) stop("x is not a valid genind object")
+ if(is.null(pop)) { # pop taken from @pop
+ if(is.null(x at pop)) stop("pop not provided and x at pop is empty")
+ pop <- pop(x)
+ } else if (is.language(pop)){
+ setPop(x) <- pop
+ pop <- pop(x)
+ } else {
+ pop <- factor(pop)
+ }
+
+
+ res.type <- match.arg(res.type)
+
+ ## pop <- x at pop # comment to take pop arg into account
+
+ ## make a list of genind objects
+ kObj <- lapply(levels(pop), function(lev) x[pop==lev, , drop=drop, treatOther=treatOther, quiet=quiet])
+ names(kObj) <- levels(pop)
+
+ ## res is a list of genind
+ if(res.type=="genind"){ return(kObj) }
+
+ ## res is list of matrices
+ res <- lapply(kObj, function(obj) tab(obj))
+
+ return(res)
+}) # end seppop
+
+
+
+
+
+
+
+## #####################
+## # Methods na.replace
+## #####################
+## setGeneric("na.replace", function(x, ...) standardGeneric("na.replace"))
+
+## ## genind method
+## setMethod("na.replace", signature(x="genind"), function(x, method, quiet=FALSE){
+## ## checkType(x)
+
+## ## preliminary stuff
+## validObject(x)
+## if(!any(is.na(x at tab))) {
+## if(!quiet) cat("\n Replaced 0 missing values \n")
+## return(x)
+## }
+## method <- tolower(method)
+## method <- match.arg(method, c("0","mean"))
+
+## res <- x
+
+## if(method=="0"){
+## res at tab[is.na(x at tab)] <- 0
+## }
+
+## if(method=="mean"){
+## f1 <- function(vec){
+## m <- mean(vec,na.rm=TRUE)
+## vec[is.na(vec)] <- m
+## return(vec)
+## }
+
+## res at tab <- apply(x at tab, 2, f1)
+## }
+
+## if(!quiet){
+## Nna <- sum(is.na(x at tab))
+## cat("\n Replaced",Nna,"missing values \n")
+## }
+
+## return(res)
+
+## })
+
+
+
+
+## ## genpop method
+## setMethod("na.replace", signature(x="genpop"), function(x,method, quiet=FALSE){
+## ## checkType(x)
+
+## ## preliminary stuff
+## validObject(x)
+## if(!any(is.na(x at tab))) {
+## if(!quiet) cat("\n Replaced 0 missing values \n")
+## return(x)
+## }
+
+## method <- tolower(method)
+## method <- match.arg(method, c("0","chi2"))
+
+## res <- x
+
+## if(method=="0"){
+## res at tab[is.na(x at tab)] <- 0
+## }
+
+## if(method=="chi2"){
+## ## compute theoretical counts
+## ## (same as in a Chi-squared)
+## X <- x at tab
+## sumPop <- apply(X,1,sum,na.rm=TRUE)
+## sumLoc <- apply(X,2,sum,na.rm=TRUE)
+## X.theo <- sumPop %o% sumLoc / sum(X,na.rm=TRUE)
+
+## X[is.na(X)] <- X.theo[is.na(X)]
+## res at tab <- X
+## }
+
+## if(!quiet){
+## Nna <- sum(is.na(x at tab))
+## cat("\n Replaced",Nna,"missing values \n")
+## }
+
+## return(res)
+## })
+
+# Function to bind strata from a list of genind objects and return a single
+# genind object.
+.rbind_strata <- function(myList, res){
+ strata_list <- lapply(myList, slot, "strata")
+ null_strata <- vapply(strata_list, is.null, TRUE)
+ if (!all(null_strata)){
+ # NULL strata must be converted to data frames.
+ # Solution: take the first non-empty strata, and create a new one
+ # with one variable.
+ if (any(null_strata)){
+
+ # Extract the name of the first column of the first full strata
+ fullname <- names(strata_list[[which(!null_strata)[1]]])[1]
+
+ # loop over all the empty strata and replace them with a data
+ # frame that has the same number of elements as the samples in that
+ # genlight object.
+ for (i in which(null_strata)){
+ replace_strata <- data.frame(rep(NA, nInd(myList[[i]])))
+ names(replace_strata) <- fullname
+ strata_list[[i]] <- replace_strata
+ }
+ }
+ strata(res) <- as.data.frame(suppressWarnings(dplyr::bind_rows(strata_list)))
+ } else {
+ res at strata <- NULL
+ }
+ return(res)
+}
+
+
+
+
+#'
+#' Pool several genotypes into a single dataset
+#'
+#' The function \code{repool} allows to merge genotypes from different
+#' \linkS4class{genind} objects into a single 'pool' (i.e. a new \linkS4class{genind}).
+#' The markers have to be the same for all objects to be merged, but
+#' there is no constraint on alleles.\cr
+#'
+#' This function can be useful, for instance, when hybrids are created
+#' using \code{\link{hybridize}}, to merge hybrids with their parent
+#' population for further analyses. Note that \code{repool} can also
+#' reverse the action of \code{\link{seppop}}.
+#'
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#'
+#' @seealso \code{\link{seploc}}, \code{\link{seppop}}
+#'
+#' @examples
+#' \dontrun{
+#' ## use the cattle breeds dataset
+#' data(microbov)
+#' temp <- seppop(microbov)
+#' names(temp)
+
+#' ## hybridize salers and zebu -- nasty cattle
+#' zebler <- hybridize(temp$Salers, temp$Zebu, n=40)
+#' zebler
+
+#' ## now merge zebler with other cattle breeds
+#' nastyCattle <- repool(microbov, zebler)
+#' nastyCattle
+#' }
+#'
+#' @export
+#'
+#' @param ... a list of \linkS4class{genind} objects, or a series of \linkS4class{genind} objects separated by commas
+#' @param list a logical indicating whether a list of objects with matched alleles shall be returned (TRUE), or a single \linkS4class{genind} object (FALSE, default).
+#'
+#'
+#'
+repool <- function(..., list=FALSE){
+
+ ## PRELIMINARY STUFF
+ x <- list(...)
+ old.names <- names(x)
+ if(is.list(x[[1]])) x <- x[[1]] ## if ... is a list, keep this list for x
+ if(!inherits(x,"list")) stop("x must be a list")
+ if(!all(sapply(x,is.genind))) stop("x is does not contain only valid genind objects")
+ temp <- sapply(x,function(e) locNames(e))
+ if(!all(table(temp)==length(x))) stop("markers are not the same for all objects")
+ ## temp <- sapply(x,function(e) e$ploidy)
+ ## if(length(unique(temp)) != as.integer(1)) stop("objects have different levels of ploidy")
+
+
+ ## MAKE A LIST OF OBJECTS
+ listTab <- lapply(x,genind2df,usepop=FALSE,sep="/")
+ newPloidy <- unlist(lapply(x,ploidy))
+
+
+ ## SET POPS IF MISSING
+ ## STORE OLD POP
+ old.pop <- lapply(x, pop)
+
+ for(i in 1:length(x)){
+ if(is.null(pop(x[[i]]))){
+ pop(x[[i]]) <- rep(paste("unknown",i,sep="_"), nInd(x[[i]]))
+ }
+ }
+
+ new.pop <- lapply(x, pop)
+
+
+ ## MERGE RAW DATASETS
+ ## reorder columns like in first dataset
+ markNames <- colnames(listTab[[1]])
+ listTab <- lapply(listTab, function(tab) tab[,markNames,drop=FALSE]) # resorting of the tabs
+
+ ## bind all tabs by rows
+ tab <- listTab[[1]]
+ for(i in 2:length(x)){
+ tab <- rbind(tab,listTab[[i]])
+ }
+
+ ## GET SINGLE GENIND
+ res <- df2genind(tab, ploidy=newPloidy, type=x[[1]]@type, sep="/")
+ pop(res) <- unlist(new.pop)
+ res <- .rbind_strata(x, res)
+ res at hierarchy <- NULL
+ res$call <- match.call()
+
+ ## IF A LIST OF GENIND IS TO BE RETURNED
+ if(list){
+ ## SEPARATE DATASETS
+ old.n <- sapply(x, nInd)
+ new.pop <- rep(1:length(x), old.n)
+ pop(res) <- new.pop
+ res <- seppop(res)
+
+ ## RESTORE OLD OTHER AND POP
+ old.other <- lapply(x, other)
+ for(i in 1:length(res)){
+ other(res[[i]]) <- old.other[[i]]
+ pop(res[[i]]) <- old.pop[[i]]
+ }
+
+ ## SET OBJECT NAMES
+ names(res) <- old.names
+ }
+
+ ## RETURN
+ return(res)
+} # end repool
+
+
+
+
+
+#############
+# selpopsize
+#############
+setGeneric("selPopSize", function(x, ...) standardGeneric("selPopSize"))
+
+## genind method ##
+setMethod("selPopSize", signature(x="genind"), function(x,pop=NULL,nMin=10){
+
+ ## misc checks
+ ## checkType(x)
+ if(!is.genind(x)) stop("x is not a valid genind object")
+ if(is.null(pop)) { # pop taken from @pop
+ if(is.null(x at pop)) stop("pop not provided and x at pop is empty")
+ pop <- pop(x)
+ } else{
+ pop <- factor(pop)
+ }
+
+ ## select retained individuals
+ effPop <- table(pop)
+ popOk <- names(effPop)[effPop >= nMin]
+ toKeep <- pop %in% popOk
+
+ ## build result
+ res <- x[toKeep]
+ pop(res) <- pop[toKeep]
+
+ return(res)
+}) # end selPopSize
+
+
+
+
+
+#########
+# isPoly
+#########
+setGeneric("isPoly", function(x, ...) standardGeneric("isPoly"))
+
+## genind method ##
+setMethod("isPoly", signature(x="genind"), function(x, by=c("locus","allele"), thres=1/100){
+
+ ## misc checks
+ ## checkType(x)
+ if(!is.genind(x)) stop("x is not a valid genind object")
+ by <- match.arg(by)
+
+
+ ## main computations ##
+
+ ## PA case ##
+ if(x at type=="PA") {
+ allNb <- apply(x at tab, 2, mean, na.rm=TRUE) # allele frequencies
+ toKeep <- (allNb >= thres) & (allNb <= (1-thres))
+ return(toKeep)
+ }
+
+
+ ## codom case ##
+ allNb <- apply(x at tab, 2, sum, na.rm=TRUE) # allele absolute frequencies
+
+ if(by=="locus"){
+ f1 <- function(vec){
+ if(sum(vec) < 1e-10) return(FALSE)
+ vec <- vec/sum(vec, na.rm=TRUE)
+ if(sum(vec >= thres) >= 2) return(TRUE)
+ return(FALSE)
+ }
+
+ toKeep <- tapply(allNb, x at loc.fac, f1)
+ } else { # i.e. if mode==allele
+ toKeep <- (allNb >= thres)
+ }
+
+ return(toKeep)
+}) # end isPoly
+
+
+
+
+
+## ## genpop method ##
+## setMethod("isPoly", signature(x="genpop"), function(x, by=c("locus","allele"), thres=1/100){
+
+## ## misc checks
+## checkType(x)
+## if(!is.genpop(x)) stop("x is not a valid genind object")
+## by <- match.arg(by)
+
+
+## ## main computations ##
+## ## ## PA case ##
+## ## if(x at type=="PA") {
+## ## allNb <- apply(x at tab, 2, mean, na.rm=TRUE) # allele frequencies
+## ## toKeep <- (allNb >= thres) & (allNb <= (1-thres))
+## ## return(toKeep)
+## ## }
+
+
+## ## codom case ##
+## allNb <- apply(x at tab, 2, sum, na.rm=TRUE) # alleles absolute frequencies
+
+## if(by=="locus"){
+## f1 <- function(vec){
+## if(sum(vec) < 1e-10) return(FALSE)
+## vec <- vec/sum(vec, na.rm=TRUE)
+## if(sum(vec >= thres) >= 2) return(TRUE)
+## return(FALSE)
+## }
+
+## toKeep <- tapply(allNb, x at loc.fac, f1)
+## } else { # i.e. if mode==allele
+## toKeep <- allNb >= thres
+## }
+
+## return(toKeep)
+## }) # end isPoly
+
+
diff --git a/R/haploGen.R b/R/haploGen.R
new file mode 100644
index 0000000..c47dba1
--- /dev/null
+++ b/R/haploGen.R
@@ -0,0 +1,723 @@
+############
+## haploGen
+############
+##
+## N: number of sequences to simulate
+## mu: mutation rate per nucleotid per generation
+## Tmax: periode of time to simulate
+## mean.gen.time, sd.gen.time: average time for transmission and its standard deviation (normal dist)
+## mean.repro, sd.repro: average number of transmissions and its standard deviation (normal dist)
+##
+haploGen <- function(seq.length=1e4, mu.transi=1e-4, mu.transv=mu.transi/2, t.max=20,
+ gen.time=function(){1+rpois(1,0.5)},
+ repro=function(){rpois(1,1.5)}, max.nb.haplo=200,
+ geo.sim=FALSE, grid.size=10, lambda.xy=0.5,
+ mat.connect=NULL,
+ ini.n=1, ini.xy=NULL){
+
+ ## CHECKS ##
+
+ ## HANDLE ARGUMENTS ##
+ ## if numeric value, make it a function
+ if(is.numeric(gen.time)){
+ gen.time.val <- gen.time[1]
+ gen.time <- function(){return(gen.time.val)}
+ }
+
+ ## if numeric value, make it a function
+ if(is.numeric(repro)){
+ repro.val <- repro[1]
+ repro <- function(){return(repro.val)}
+ }
+
+
+
+ ## GENERAL VARIABLES ##
+ NUCL <- as.DNAbin(c("a","t","c","g"))
+ TRANSISET <- list('a'=as.DNAbin('g'), 'g'=as.DNAbin('a'), 'c'=as.DNAbin('t'), 't'=as.DNAbin('c'))
+ TRANSVSET <- list('a'=as.DNAbin(c('c','t')), 'g'=as.DNAbin(c('c','t')), 'c'=as.DNAbin(c('a','g')), 't'=as.DNAbin(c('a','g')))
+ res <- list(seq=as.matrix(as.DNAbin(character(0))), dates=integer(), ances=character())
+ toExpand <- logical()
+ myGrid <- matrix(1:grid.size^2, ncol=grid.size, nrow=grid.size)
+
+
+ ## AUXILIARY FUNCTIONS ##
+ ## generate sequence from scratch
+ seq.gen <- function(){
+ ##res <- list(sample(NUCL, size=seq.length, replace=TRUE)) # DNAbin are no longer lists by default
+ res <- sample(NUCL, size=seq.length, replace=TRUE)
+ class(res) <- "DNAbin"
+ return(res)
+ }
+
+ ## create substitutions for defined SNPs - no longer used
+ substi <- function(snp){
+ res <- sapply(1:length(snp), function(i) sample(setdiff(NUCL,snp[i]),1)) # ! sapply does not work on DNAbin vectors directly
+ class(res) <- "DNAbin"
+ return(res)
+ }
+
+ ## create transitions for defined SNPs
+ transi <- function(snp){
+ res <- unlist(TRANSISET[as.character(snp)])
+ class(res) <- "DNAbin"
+ return(res)
+ }
+
+ ## create transversions for defined SNPs
+ transv <- function(snp){
+ res <- sapply(TRANSVSET[as.character(snp)],sample,1)
+ class(res) <- "DNAbin"
+ return(res)
+ }
+
+ ## duplicate a sequence (including possible mutations)
+ seq.dupli <- function(seq, T){ # T is the number of time units between ancestor and decendent
+ ## transitions ##
+ n.transi <- rbinom(n=1, size=seq.length*T, prob=mu.transi) # total number of transitions
+ if(n.transi>0) {
+ idx <- sample(1:seq.length, size=n.transi, replace=FALSE)
+ seq[idx] <- transi(seq[idx])
+ }
+
+ ## transversions ##
+ n.transv <- rbinom(n=1, size=seq.length*T, prob=mu.transv) # total number of transitions
+ if(n.transv>0) {
+ idx <- sample(1:seq.length, size=n.transv, replace=FALSE)
+ seq[idx] <- transv(seq[idx])
+ }
+ return(seq)
+ }
+
+ ## what is the name of the new sequences?
+ seqname.gen <- function(nb.new.seq){
+ res <- max(as.integer(rownames(res$seq)), 0) + 1:nb.new.seq
+ return(as.character(res))
+ }
+
+ ## how many days before duplication occurs ?
+ time.dupli <- function(){
+ ##res <- round(rnorm(1, mean=mean.gen.time, sd=sd.gen.time))
+ res <- round(gen.time()) # force integers
+ res[res<0] <- 0
+ return(res)
+ }
+
+ ## when duplication occurs?
+ date.dupli <- function(curDate){
+ res <- curDate + time.dupli()
+ return(res)
+ }
+
+ ## how many duplication/transmission occur?
+ nb.desc <- function(){
+ ##res <- round(rnorm(1, mean=mean.repro, sd=sd.repro))
+ res <- repro()
+ res[res<0] <- 0
+ return(res)
+ }
+
+ ## where does an haplotype emerges in the first place?
+ xy.gen <- function(){
+ return(sample(1:grid.size, size=2, replace=TRUE))
+ }
+
+ ## where does a transmission occur (destination)?
+ if(is.null(mat.connect)){ # use universal lambda param
+ xy.dupli <- function(cur.xy, nbLoc){
+ mvt <- rpois(2*nbLoc, lambda.xy) * sample(c(-1,1), size=2*nbLoc, replace=TRUE)
+ res <- t(matrix(mvt, nrow=2) + as.vector(cur.xy))
+ res[res < 1] <- 1
+ res[res > grid.size] <- grid.size
+ return(res)
+ }
+ } else { # use location-dependent proba of dispersal between locations
+ if(any(mat.connect < 0)) stop("Negative values in mat.connect (probabilities expected!)")
+ mat.connect <- prop.table(mat.connect,1)
+ xy.dupli <- function(cur.xy, nbLoc){
+ idxAncesLoc <- myGrid[cur.xy[1], cur.xy[2]]
+ newLoc <- sample(1:grid.size^2, size=nbLoc, prob=mat.connect[idxAncesLoc,], replace=TRUE) # get new locations
+ res <- cbind(row(myGrid)[newLoc] , col(myGrid)[newLoc]) # get coords of new locations
+ return(res)
+ }
+ }
+
+
+ ## check result size and resize it if needed
+ resize.result <- function(){
+ curSize <- length(res$dates)
+ if(curSize <= max.nb.haplo) return(NULL)
+ toKeep <- rep(FALSE, curSize)
+ toKeep[sample(1:curSize, size=max.nb.haplo, replace=FALSE)] <- TRUE
+ removed.strains <- rownames(res$seq)[!toKeep]
+ res$seq <<- res$seq[toKeep,]
+ res$dates <<- res$dates[toKeep]
+ res$ances <<- res$ances[toKeep]
+ toExpand <<- toExpand[toKeep]
+ temp <- as.character(res$ances) %in% removed.strains
+ if(any(temp)) {
+ res$ances[temp] <<- NA
+ }
+
+ return(NULL)
+ }
+
+ ## check result size and resize it if needed - spatial version
+ resize.result.xy <- function(){
+ curSize <- length(res$dates)
+ if(curSize <= max.nb.haplo) return(NULL)
+ toKeep <- rep(FALSE, curSize)
+ toKeep[sample(1:curSize, size=max.nb.haplo, replace=FALSE)] <- TRUE
+ removed.strains <- rownames(res$seq)[!toKeep]
+ res$seq <<- res$seq[toKeep,]
+ res$dates <<- res$dates[toKeep]
+ res$ances <<- res$ances[toKeep]
+ res$xy <<- res$xy[toKeep,,drop=FALSE]
+ toExpand <<- toExpand[toKeep]
+ temp <- as.character(res$ances) %in% removed.strains
+ if(any(temp)) {
+ res$ances[temp] <<- NA
+ }
+
+ return(NULL)
+ }
+
+
+
+ ## MAIN SUB-FUNCTION: EXPANDING FROM ONE SEQUENCE - NON SPATIAL ##
+ expand.one.strain <- function(seq, date, idx){
+ toExpand[idx] <<- FALSE # this one is no longer to expand
+ nbDes <- nb.desc()
+ if(nbDes==0) return(NULL) # stop if no descendant
+ newDates <- sapply(1:nbDes, function(i) date.dupli(date)) # find dates for descendants
+ newDates <- newDates[newDates <= t.max] # don't store future sequences
+ nbDes <- length(newDates)
+ if(nbDes==0) return(NULL) # stop if no suitable date
+ newSeq <- lapply(1:nbDes, function(i) seq.dupli(seq, newDates[i]-date)) # generate new sequences
+ class(newSeq) <- "DNAbin" # lists of DNAbin vectors must also have class "DNAbin"
+ newSeq <- as.matrix(newSeq) # list DNAbin -> matrix DNAbin with nbDes rows
+ rownames(newSeq) <- seqname.gen(nbDes) # find new labels for these new sequences
+ res$seq <<- rbind(res$seq, newSeq) # append to general output
+ res$dates <<- c(res$dates, newDates) # append to general output
+ res$ances <<- c(res$ances, rep(rownames(res$seq)[idx], nbDes)) # append to general output
+ toExpand <<- c(toExpand, rep(TRUE, nbDes))
+ return(NULL)
+ }
+
+
+ ## 2nd MAIN SUB-FUNCTION: EXPANDING FROM ONE SEQUENCE - SPATIAL ##
+ expand.one.strain.xy <- function(seq, date, idx, cur.xy){
+ toExpand[idx] <<- FALSE # this one is no longer to expand
+ nbDes <- nb.desc()
+ if(nbDes==0) return(NULL) # stop if no descendant
+ newDates <- sapply(1:nbDes, function(i) date.dupli(date)) # find dates for descendants
+ newDates <- newDates[newDates <= t.max] # don't store future sequences
+ nbDes <- length(newDates)
+ if(nbDes==0) return(NULL) # stop if no suitable date
+ newSeq <- lapply(1:nbDes, function(i) seq.dupli(seq, newDates[i]-date)) # generate new sequences
+ class(newSeq) <- "DNAbin" # lists of DNAbin vectors must also have class "DNAbin"
+ newSeq <- as.matrix(newSeq) # list DNAbin -> matrix DNAbin with nbDes rows
+ rownames(newSeq) <- seqname.gen(nbDes) # find new labels for these new sequences
+ res$seq <<- rbind(res$seq, newSeq) # append to general output
+ res$dates <<- c(res$dates, newDates) # append to general output
+ res$ances <<- c(res$ances, rep(rownames(res$seq)[idx], nbDes)) # append to general output
+ res$xy <<- rbind(res$xy, xy.dupli(cur.xy, nbDes))
+ toExpand <<- c(toExpand, rep(TRUE, nbDes))
+ return(NULL)
+ }
+
+
+
+ ## PERFORM SIMULATIONS - NON SPATIAL CASE ##
+ if(!geo.sim){
+ ## initialization
+ res$seq <- matrix(rep(seq.gen(), ini.n), byrow=TRUE, nrow=ini.n)
+ class(res$seq) <- "DNAbin"
+ rownames(res$seq) <- 1:ini.n
+ res$dates[1:ini.n] <- rep(0,ini.n)
+ res$ances[1:ini.n] <- rep(NA,ini.n)
+ toExpand <- rep(TRUE,ini.n)
+
+ ## simulations: isn't simplicity beautiful?
+ while(any(toExpand)){
+ idx <- min(which(toExpand))
+ expand.one.strain(res$seq[idx,], res$dates[idx], idx)
+ resize.result()
+ }
+
+
+ ## SHAPE AND RETURN OUTPUT ##
+ res$id <- as.character(1:length(res$ances))
+ res$ances <- as.character(res$ances)
+ names(res$dates) <- rownames(res$seq)
+ res$call <- match.call()
+ class(res) <- "haploGen"
+ return(res)
+
+ } # END NON-SPATIAL SIMULATIONS
+
+
+
+ ## PERFORM SIMULATIONS - SPATIAL CASE ##
+ if(geo.sim){
+ ## some checks
+ if(!is.null(mat.connect)) {
+ if(nrow(mat.connect) != ncol(mat.connect)) stop("mat.connect is not a square matrix")
+ if(nrow(mat.connect) != grid.size^2) stop("dimension of mat.connect does not match grid size")
+ }
+
+ ## initialization
+ res$seq <- matrix(rep(seq.gen(), ini.n), byrow=TRUE, nrow=ini.n)
+ class(res$seq) <- "DNAbin"
+ rownames(res$seq) <- 1:ini.n
+ res$dates[1:ini.n] <- rep(0,ini.n)
+ res$ances[1:ini.n] <- rep(NA,ini.n)
+ toExpand <- rep(TRUE,ini.n)
+
+ if(is.null(ini.xy)){
+ locStart <- xy.gen()
+ } else{
+ locStart <- as.vector(ini.xy)[1:2]
+ }
+ res$xy <- matrix(rep(locStart, ini.n), byrow=TRUE, nrow=ini.n)
+ colnames(res$xy) <- c("x","y")
+
+ ##cat("nb.strains","iteration.time",file="haploGenTime.out") # for debugging
+
+
+ ## simulations: isn't simplicity beautiful?
+ while(any(toExpand)){
+ ##time.previous <- Sys.time() # FOR DEBUGGING
+ idx <- min(which(toExpand))
+ expand.one.strain.xy(res$seq[idx,], res$dates[idx], idx, res$xy[idx,])
+ resize.result.xy()
+ ## VERBOSE OUTPUT FOR DEBUGGING ##
+ ## cat("\nNb strains:",length(res$ances),"/",max.nb.haplo)
+ ## cat("\nLatest date:", max(res$dates),"/",t.max)
+ ## cat("\nRemaining strains to duplicate", sum(toExpand))
+ ## cat("\n",append=TRUE,file="haploGenTime.out")
+ ## iter.time <- as.numeric(difftime(Sys.time(),time.previous,unit="sec"))
+ ## time.previous <- Sys.time()
+ ## cat(c(length(res$ances), iter.time),append=
+ ##TRUE,file="haploGenTime.out")
+ ## END DEBUGGING VERBOSE ##
+ }
+
+ ## VERBOSE OUTPUT FOR DEBUGGING ##
+ ##cat("\nSimulation time stored in haploGenTime.out\n")
+
+ ## SHAPE AND RETURN OUTPUT ##
+ res$id <- as.character(1:length(res$ances))
+ res$ances <- as.character(res$ances)
+ names(res$dates) <- rownames(res$seq)
+
+ class(res) <- "haploGen"
+ res$call <- match.call()
+ return(res)
+
+ } # end SPATIAL SIMULATIONS
+
+
+} # end haploGen
+
+
+
+
+
+
+
+
+##################
+## print.haploGen
+##################
+print.haploGen <- function(x, ...){
+
+ cat("\t\n========================")
+ cat("\t\n= simulated haplotypes =")
+ cat("\t\n= (haploGen object) =")
+ cat("\t\n========================\n")
+
+ cat("\nSize :", length(x$ances),"haplotypes")
+ cat("\nHaplotype length :", ncol(x$seq),"nucleotids")
+ cat("\nProportion of NA ancestors :", signif(mean(is.na(x$ances)),5))
+ cat("\nNumber of known ancestors :", sum(!is.na(x$ances)))
+ nbAncInSamp <- sum(x$ances %in% labels(x))
+ cat("\nNumber of ancestors within the sample :", nbAncInSamp)
+ cat("\nDate range :", min(x$dates,na.rm=TRUE),"-",max(x$dates,na.rm=TRUE))
+ ##nUniqSeq <- length(unique(apply(as.character(x$seq),1,paste,collapse="")))
+ ##cat("\nNumber of unique haplotypes :", nUniqSeq)
+
+ cat("\n\n= Content =")
+ for(i in 1:length(x)){
+ cat("\n")
+
+ cat(paste("$", names(x)[i], sep=""),"\n")
+ if(names(x)[i] %in% c("seq","call")) {
+ print(x[[i]])
+ } else if(names(x)[i]=="xy"){
+ print(head(x[[i]]))
+ if(nrow(x[[i]]>6)) cat(" ...\n")
+ } else cat(head(x[[i]],6), ifelse(length(x[[i]])>6,"...",""),"\n")
+ }
+
+
+ return(NULL)
+} # end print.haploGen
+
+
+
+
+
+
+##############
+## [.haploGen
+##############
+"[.haploGen" <- function(x,i,j,drop=FALSE){
+ res <- x
+ res$seq <- res$seq[i,,drop=FALSE]
+ res$id <- res$id[i]
+ res$ances <- res$ances[i]
+ res$ances[!res$ances %in% res$id] <- NA
+ res$dates <- res$dates[i]
+ if(!is.null(res$xy)) res$xy <- res$xy[i,,drop=FALSE]
+
+ return(res)
+}
+
+
+
+
+
+
+##################
+## labels.haploGen
+##################
+labels.haploGen <- function(object, ...){
+ return(object$id)
+}
+
+
+
+
+
+#######################
+## as.POSIXct.haploGen
+#######################
+as.POSIXct.haploGen <- function(x, tz="", origin=as.POSIXct("2000/01/01"), ...){
+ res <- as.POSIXct(x$dates*24*3600, origin=origin)
+ return(res)
+}
+
+
+
+
+
+
+#####################
+## seqTrack.haploGen
+#####################
+seqTrack.haploGen <- function(x, best=c("min","max"), prox.mat=NULL, ...){
+ myX <- dist.dna(x$seq, model="raw")
+ x.names <- labels(x)
+ x.dates <- as.POSIXct(x)
+ seq.length <- ncol(x$seq)
+ myX <- myX * seq.length
+ myX <- as.matrix(myX)
+ prevCall <- as.list(x$call)
+ if(is.null(prevCall$mu)){
+ mu0 <- 0.0001
+ } else {
+ mu0 <- eval(prevCall$mu)
+ }
+ res <- seqTrack(myX, x.names=x.names, x.dates=x.dates, best=best, prox.mat=prox.mat,...)
+ return(res)
+}
+
+
+
+
+
+
+########################
+## as.seqTrack.haploGen
+########################
+as.seqTrack.haploGen <- function(x){
+ ## x.ori <- x
+ ## x <- na.omit(x)
+ toSetToNA <- x$dates==min(x$dates)
+ res <- list()
+ res$id <- labels(x)
+ res <- as.data.frame(res)
+ res$ances <- x$ances
+ res$ances[toSetToNA] <- NA
+ res$weight <- 1 # ??? have to recompute that...
+ res$weight[toSetToNA] <- NA
+ res$date <- as.POSIXct(x)[labels(x)]
+ res$ances.date <- as.POSIXct(x)[x$ances]
+
+ ## set results as indices rather than labels
+ res$ances <- match(res$ances, res$id)
+ res$id <- 1:length(res$id)
+
+ ## SET CLASS
+ class(res) <- c("seqTrack", "data.frame")
+
+ return(res)
+}
+
+
+
+
+
+
+################
+## plotHaploGen
+################
+plotHaploGen <- function(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", add=FALSE, ...){
+
+ ## SOME CHECKS ##
+ if(class(x)!="haploGen") stop("x is not a haploGen object")
+ if(is.null(x$xy)) stop("x does not contain xy coordinates - try converting to graphNEL for plotting")
+
+
+ ## ## CONVERSION TO A SEQTRACK-LIKE OBJECT ##
+ xy <- x$xy
+ res <- as.seqTrack.haploGen(x)
+
+ ## res <- list()
+ ## res$id <- labels(x)
+ ## res <- as.data.frame(res)
+ ## res$ances <- x$ances
+ ## res$ances[toSetToNA] <- NA
+ ## res$weight <- 1 # ??? have to recompute that...
+ ## res$weight[toSetToNA] <- NA
+ ## res$date <- as.POSIXct(x.ori)[labels(x)]
+ ## res$ances.date <- as.POSIXct(x.ori)[x$ances]
+ ## ## set results as indices rather than labels
+ ## res$ances <- match(res$ances, res$id)
+ ## res$id <- 1:length(res$id)
+
+
+ ## CALL TO PLOTSEQTRACK ##
+ plotSeqTrack(x=res, xy=xy, annot=annot, date.range=date.range,
+ col=col, bg=bg, add=add, ...)
+
+ return(invisible(res))
+
+} # end plotHaploGen
+
+
+
+
+
+
+###################
+## sample.haploGen
+###################
+sample.haploGen <- function(x, n){
+##sample.haploGen <- function(x, n, rDate=.rTimeSeq, arg.rDate=NULL){
+ ## EXTRACT THE SAMPLE ##
+ res <- x[sample(1:nrow(x$seq), n, replace=FALSE)]
+
+
+ ## RETRIEVE SOME PARAMETERS FROM HAPLOSIM CALL
+ prevCall <- as.list(x$call)
+ if(!is.null(prevCall$mu)){
+ mu0 <- eval(prevCall$mu)
+ } else {
+ mu0 <- 1e-04
+ }
+
+ if(!is.null(prevCall$seq.length)){
+ L <- eval(prevCall$seq.length)
+ } else {
+ L <- 1000
+ }
+
+ ## truedates <- res$dates
+ ## daterange <- diff(range(res$dates,na.rm=TRUE))
+
+ ## if(identical(rDate,.rTimeSeq)){
+ ## sampdates <- .rTimeSeq(n=length(truedates), mu=mu0, L=L, maxNbDays=daterange/2)
+ ## } else{
+ ## arg.rDate$n <- n
+ ## sampdates <- do.call(rDate, arg.rDate)
+ ## }
+ ## sampdates <- truedates + abs(sampdates)
+
+ return(res)
+} # end sample.haploGen
+
+
+
+
+
+
+######################
+## as.igraph.haploGen
+######################
+as.igraph.haploGen <- function(x, col.pal=redpal, ...){
+
+ ## GET DAG ##
+ from <- x$ances
+ to <- x$id
+ isNotNA <- !is.na(from) & !is.na(to)
+ dat <- data.frame(from,to,stringsAsFactors=FALSE)[isNotNA,,drop=FALSE]
+ vnames <- as.character(unique(unlist(dat)))
+ out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(names=vnames, dates=x$dates[vnames]))
+
+ ## SET WEIGHTS ##
+ D <- as.matrix(dist.dna(x$seq,model="raw")*ncol(x$seq))
+ temp <- mapply(function(i,j) return(D[i,j]), as.integer(from), as.integer(to))
+ E(out)$weight <- temp[isNotNA]
+
+
+ ## DATES FOR VERTICES
+ V(out)$dates <- x$date
+
+ ## SET EDGE LABELS ##
+ E(out)$label <- E(out)$weight
+
+ ## SET EDGE COLORS
+ E(out)$color <- num2col(E(out)$weight, col.pal=col.pal, reverse=TRUE)
+
+ ## SET LAYOUT ##
+ ypos <- V(out)$dates
+ ypos <- abs(ypos-max(ypos))
+ attr(out, "layout") <- layout.fruchterman.reingold(out, params=list(miny=ypos, maxy=ypos))
+
+ return(out)
+} # end as.igraph.haploGen
+
+
+
+
+
+
+#################
+## plot.haploGen
+#################
+plot.haploGen <- function(x, y=NULL, col.pal=redpal, ...){
+
+ ## get graph ##
+ g <- as.igraph(x, col.pal=col.pal)
+
+ ## make plot ##
+ plot(g, layout=attr(g,"layout"), ...)
+
+ ## return graph invisibly ##
+ return(invisible(g))
+
+} # end plot.haploGen
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+##########################
+## as("haploGen", "graphNEL")
+##########################
+## if(require(graph)){
+## setOldClass("haploGen")
+
+## setAs("haploGen", "graphNEL", def=function(from){
+## if(!require(ape)) stop("package ape is required")
+## if(!require(graph)) stop("package graph is required")
+
+## N <- length(from$ances)
+## areNA <- is.na(from$ances)
+
+## ## EXTRACT WEIGHTS (nb of mutations)
+## M <- as.matrix(dist.dna(from$seq, model="raw")*ncol(from$seq))
+## rownames(M) <- colnames(M) <- from$id
+## w <- mapply(function(i,j) {M[i, j]}, i=from$ances[!areNA], j=from$id[!areNA])
+
+
+## ## CONVERT TO GRAPH
+## res <- ftM2graphNEL(ft=cbind(from$ances[!areNA], from$id[!areNA]), W=w, edgemode = "directed", V=from$id)
+## return(res)
+## })
+
+## }
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+## #####################
+## ## seqTrackG.haploGen
+## #####################
+## seqTrackG.haploGen <- function(x, optim=c("min","max"), ...){
+## myX <- dist.dna(x$seq, model="raw")
+## x.names <- labels(x)
+## x.dates <- as.POSIXct(x)
+## seq.length <- ncol(x$seq)
+## myX <- myX * seq.length
+## prevCall <- as.list(x$call)
+## if(is.null(prevCall$mu)){
+## mu0 <- 0.0001
+## } else {
+## mu0 <- eval(prevCall$mu)
+## }
+## res <- seqTrackG(myX, x.names=x.names, x.dates=x.dates, best=optim,...)
+## return(res)
+## }
+
+
+
+
+
+
+##############################
+## optimize.seqTrack.haploGen
+##############################
+## optimize.seqTrack.haploGen <- function(x, thres=0.2, optim=c("min","max"),
+## typed.chr=NULL, mu0=NULL, chr.length=NULL,
+## prox.mat=NULL, nstep=10, step.size=1e3,
+## rDate=.rTimeSeq, arg.rDate=NULL, rMissDate=.rUnifTimeSeq, ...){
+
+## x.names <- labels(x)
+## x.dates <- as.POSIXct(x)
+## seq.length <- ncol(x$seq)
+## myX <- dist.dna(x$seq, model="raw") * seq.length
+## prevCall <- as.list(x$call)
+## if(is.null(prevCall$mu)){
+## mu0 <- 0.0001
+## } else {
+## mu0 <- eval(prevCall$mu)
+## }
+
+## res <- optimize.seqTrack.default(x=myX, x.names=x.names, x.dates=x.dates,
+## typed.chr=typed.chr, mu0=mu0, chr.length=chr.length,
+## thres=thres, optim=optim, prox.mat=prox.mat,
+## nstep=nstep, step.size=step.size,
+## rDate=rDate, arg.rDate=arg.rDate, rMissDate=rMissDate, ...)
+## } # end optimize.seqTrack.haploGen
diff --git a/R/haploPop.R b/R/haploPop.R
new file mode 100644
index 0000000..2e56652
--- /dev/null
+++ b/R/haploPop.R
@@ -0,0 +1,946 @@
+## ############
+## ## haploPop
+## ############
+## ##
+## ## Simulate only SNPs, allow reverse mutations.
+## ##
+## ## - haplo.length: length of simulated haplotypes
+## ## - mu: substitution rate / nucleotide / year
+## ## - n.steps: number of generations to simulate
+## ##
+## haploPop <- function(n.steps=20, ini.obj=NULL, ini.haplo=NULL, haplo.length=1e6, mu=1e-5, n.snp.ini=1,
+## birth.func=function(){ sample(0:3, 1, prob=c(.05, .45, .35, .15))},
+## max.pop.size=function(){1e4}, max.nb.pop=30, ini.pop.size=10, regen=FALSE,
+## p.new.pop=function(){1e-4}, death.func=function(age){age>1},
+## quiet=FALSE, allow.reverse=TRUE) {
+
+
+## ## SOME CHECKS
+## ## if(is.numeric(ini.pop.size)){
+## ## ini.pop.size.val <- ini.pop.size
+## ## ini.pop.size <- function(){ini.pop.size.val}
+## ## }
+
+## if(is.numeric(max.pop.size)){
+## max.pop.size.val <- max.pop.size
+## max.pop.size <- function(){max.pop.size.val}
+## }
+
+## if(is.numeric(p.new.pop)){
+## p.new.pop.val <- p.new.pop
+## p.new.pop <- function(){p.new.pop.val}
+## }
+
+## if(is.numeric(birth.func)){
+## birth.func.val <- birth.func[1]
+## birth.func <- function(){birth.func.val}
+## }
+
+## if(is.numeric(death.func)){
+## death.func.val <- death.func[1]
+## death.func <- function(age){age>death.func.val}
+## }
+
+
+## ## GLOBAL VARIABLES ##
+## SNP.POOL <- 1:haplo.length
+## vecS <- 1 # will be redefined later, but needed for evolveOnePop definition
+
+## ## AUXILIARY FUNCTIONS ##
+## if(allow.reverse){
+## createMutations <- function(N){ # L:genome length; N: pop size
+## nb.mutations <- sum(rbinom(N, size=haplo.length, prob=mu))
+## return( sample(SNP.POOL, size=nb.mutations, replace=TRUE) )
+## }
+## } else {
+## createMutations <- function(N){ # L:genome length; N: pop size
+## nb.mutations <- sum(rbinom(N, size=haplo.length, prob=mu))
+## res <- sample(SNP.POOL, size=nb.mutations, replace=TRUE)
+## SNP.POOL <<- setdiff(SNP.POOL, res)# update pool of SNPs
+## return(res)
+## }
+## }
+
+## ## clean reverse mutations
+## cleanRes <- function(vec){
+## temp <- table(vec)
+## return( as.integer(names(temp)[temp %% 2 != 0]) )
+## }
+
+
+## ## assign mutation to haplotypes
+## assignMutations <- function(myPop, mutations){ # mypop: list of `haplotypes'; mutations: vector of SNPs
+## if(length(mutations)==0 | length(myPop)==0) return(myPop)
+## id <- sample(1:length(myPop), size=length(mutations), replace=TRUE)
+## mutations <- split(mutations, id)
+
+## ## function to merge new mutations - handle reverse case
+## f1 <- function(a,b){
+## revMut <- intersect(a,b)
+## if(length(revMut)==0) return(c(a,b))
+## return(setdiff(c(a ,b), revMut))
+## }
+
+## ##myPop[as.integer(names(mutations))] <- mapply(c, myPop[as.integer(names(mutations))], mutations, SIMPLIFY=FALSE)
+## myPop[as.integer(names(mutations))] <- mapply(f1, myPop[as.integer(names(mutations))], mutations, SIMPLIFY=FALSE)
+
+## return(myPop)
+## } # end assignMutations
+
+
+## if(!regen){
+## ## VERSION FOR NO REGENERATION OF SUSCEPTIBLES
+## evolveOnePop <- function(myPop, myS, myAge){ # myPop: pop to evolve; myS: nb of susceptible in the pop; myAge: vector of ages
+## ## strains get older
+## myAge <- myAge + 1
+## ## toKill <- death.func(myAge)
+## ## myPop[toKill] <- NULL
+## ## myAge <- myAge[!toKill]
+
+## ## generate new strains for new generation
+## sampSize <- round(min( length(myPop)*birth.func(), myS)) # number of strains for next step
+## if(sampSize<1){ # if no new strains
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+## return(list(pop=myPop, S=myS, age=myAge))
+## } # if there are new strains, do...
+## newGen <- myPop[sample(1:length(myPop), sampSize, replace=TRUE)] # sample strains for new generations
+## newGen <- assignMutations(newGen, createMutations(sampSize)) # mutate strains
+## newAge <- rep(0, sampSize) # new ages for newborns
+
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+
+## ## merge old and new generation
+## myPop <- c(myPop,newGen)
+## myAge <- c(myAge, newAge)
+
+## ## possibly create one or more new pop
+## if((length(listPop) < max.nb.pop) & (p.new.pop()>0)) { # total number of pop. limitation
+## nbNewPop <- rbinom(1, length(myPop), prob=p.new.pop())
+## } else {
+## nbNewPop <- 0
+## }
+## if(nbNewPop>0){
+## ## newPop <- sample(listPop, size=nbNewPop, replace=TRUE) # wrong
+## newPop <- lapply(sample(myPop, size=nbNewPop, replace=TRUE), as.list)
+## listPop <<- c(listPop, newPop)
+## vecS <<- c(vecS, replicate(nbNewPop, max.pop.size()) )
+## listAges <<- c(listAges, replicate(nbNewPop, 0, simplify=FALSE) )
+## } # end new pop
+## return(list(pop=myPop, S=myS-sampSize, age=myAge))
+## } # end no regen version
+## } else { ## REGEN VERSION
+## evolveOnePop <- function(myPop, myS, myAge){ # myPop: pop to evolve; myS: nb of susceptible in the pop; myAge: vector of ages
+## ## strains get older
+## myAge <- myAge + 1
+## ## toKill <- death.func(myAge)
+## ## myPop[toKill] <- NULL
+## ## myAge <- myAge[!toKill]
+## myS <- max.pop.size() ## DIFFERENCE between the two versions of the function
+
+## ## generate new strains for new generation
+## sampSize <- round(min( length(myPop)*birth.func(), myS)) # number of strains for next step
+## if(sampSize<1){ # if no sample
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+## return(list(pop=myPop, S=myS, age=myAge))
+## }
+## newGen <- myPop[sample(1:length(myPop), sampSize, replace=TRUE)] # sample strains for new generations
+## newGen <- assignMutations(newGen, createMutations(sampSize)) # mutate strains
+## newAge <- rep(0, sampSize) # new ages for newborns
+
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+
+## ## merge old and new generation
+## myPop <- c(myPop,newGen)
+## myAge <- c(myAge, newAge)
+
+## ## possibly create one or more new pop
+## if((length(listPop) < max.nb.pop) & (p.new.pop()>0)) { # total number of pop. limitation
+## nbNewPop <- rbinom(1, length(myPop), prob=p.new.pop())
+## } else {
+## nbNewPop <- 0
+## }
+## if(nbNewPop>0){
+## ## newPop <- sample(listPop, size=nbNewPop, replace=TRUE) # wrong
+## newPop <- lapply(sample(myPop, size=nbNewPop, replace=TRUE), as.list)
+## listPop <<- c(listPop, newPop)
+## vecS <<- c(vecS, replicate(nbNewPop, max.pop.size()) )
+## listAges <<- c(listAges, replicate(nbNewPop, 0, simplify=FALSE) )
+## } # end new pop
+## return(list(pop=myPop, S=myS, age=myAge)) ## DIFFERENCE between the two versions of the function
+## } # end no regen version
+## } ## end evolveOnePop (both versions)
+
+
+
+## ## INITIATE SIMULATIONS ##
+## ## INITIALIZE FROM SCRATCH
+## vecS <- max.pop.size() # susceptibles
+
+## if(is.null(ini.obj)){
+## ##vecS <- max.pop.size() - n.snp.ini # susceptibles
+## if(is.null(ini.haplo)) {
+## haplo.ini <- sample(SNP.POOL, n.snp.ini, replace=TRUE)
+## } else {
+## haplo.ini <- ini.haplo
+## }
+
+## ANCES <- haplo.ini
+## listPop <- list()
+## listPop[[1]] <- lapply(1:ini.pop.size, function(i) haplo.ini) # contains only one population of identical clones to start with
+## listAges <- list() # will contain vectors of ages of haplotypes (a time of appearance, age=0)
+## listAges[[1]] <- rep(0, ini.pop.size)
+## } else { ## INITIALIZE WITH PROVIDED OBJECT
+## if(!inherits(ini.obj, "haploPop")) stop("x is not a haploPop object")
+## ##vecS <- ini.obj$S
+## ANCES <- attr(ini.obj, "ances")
+## listPop <- ini.obj$pop
+## listAges <- ini.obj$ages
+## }
+
+## ## MAKE SIMULATIONS ##
+
+## ## evolve all populations
+## i <- 1L
+## if(!quiet){
+## cat("\nSimulating populations of haplotypes through time: \n")
+## }
+## ##while((sum(vecS)>0) & (i<(n.steps+1))){ # evolve all generations
+## while(i<(n.steps+1)){ # evolve all generations
+## i <- i + 1L # update iterator
+## if(!quiet){
+## catStep <- max(round(n.steps/100), 10)
+## cat(ifelse((i %% catStep)==0, paste(" ...", i), ""))
+## }
+
+
+## ## make populations evolve of one generation
+## ##idx <- which(vecS>0) # make sure that new pop won't evolve this time ! leads to not dying
+## idx <- 1:length(listPop) # make sure that new pop won't evolve this time
+## if(length(idx)>0){
+## for(j in idx){
+## temp <- evolveOnePop(listPop[[j]], vecS[j], listAges[[j]])
+## listPop[[j]] <- temp$pop
+## vecS[j] <- temp$S
+## listAges[[j]] <- temp$age
+## }
+## }
+
+## ## ## purge non-susceptible pop
+## ## listPop <- listPop[vecS>0]
+## ## vecS <- vecS[vecS>0]
+
+## ## purge empty populations
+## toKeep <- sapply(listPop, length)>0
+## listPop <- listPop[toKeep]
+## vecS <- vecS[toKeep]
+## listAges <- listAges[toKeep]
+
+## ## stop if all pop go extinct
+## if(length(listPop)==0L){
+## if(!quiet) cat("\n All populations went extinct at time",i,"\n")
+## return(invisible(NULL))
+## }
+
+## ## FOR DEBUGGING
+## ## cat("\n=== ",i," ===")
+## ## cat("\nlistPop")
+## ## print(listPop)
+## ## cat("\nvecS")
+## ## print(vecS)
+## ## cat("\nlistAges")
+## ## print(listAges)
+## ## END DEBUGGING
+## } # end while
+
+## if(!quiet){
+## cat("\n... done! \n")
+## }
+
+## ## END OF SIMULATIONS ##
+
+
+## ## CLEAN RESULTS ##
+## ## handle reverse mutations
+## ## if(clean.haplo){
+## ## if(!quiet){
+## ## cat("\n... Cleaning haplotypes (handling reverse mutations)\n")
+## ## }
+
+## ## cleanRes <- function(vec){
+## ## temp <- table(vec)
+## ## return(sort(as.integer(names(temp)[temp %% 2 != 0])))
+## ## }
+
+## ## for(i in 1:length(listPop)){
+## ## listPop[[i]] <- lapply(listPop[[i]], cleanRes)
+## ## }
+
+## ## if(!quiet){
+## ## cat("\n... done! \n")
+## ## }
+## ## }
+
+## ## RETURN RESULTS ##
+## res <- list(pop=listPop, ages=listAges, S=vecS)
+## class(res) <- "haploPop"
+## res$call <- match.call()
+## attr(res,"ances") <- ANCES # ancestral genotype
+## return(res)
+
+## } # end haploPop
+
+
+
+
+
+
+## ##################
+## ## print.haploPop
+## ##################
+## print.haploPop <- function(x, ...){
+## myCall <- x$call
+
+## cat("\n== haploPop object ==\n")
+## cat("\nNumber of populations :", length(x$pop))
+
+## N <- sum(sapply(x$pop,length))
+## cat("\nNumber of haplotypes :", N)
+
+## N.mut <- length(unique(unlist(x$pop)))
+## cat("\nNumber of mutations :", N.mut)
+
+## N.empty <- sum(sapply(x$pop, function(e) length(e)==0))
+## cat("\nNumber of unmutated genotypes :", N.empty)
+
+## if( (length(x$pop) == length(x$ages)) & (length(x$pop) == length(x$S)) ){
+## cat("\nSlot lengths consistency: OK\n")
+## } else {
+## cat("\nSlot lengths consistency: !! NOT OK !!\n")
+## }
+## } # end print.haploPop
+
+
+
+
+
+
+## ##################
+## ## summary.haploPop
+## ##################
+## summary.haploPop <- function(object, ...){
+## x <- object$pop
+## myCall <- x$call
+## x$call <- NULL
+## res <- list()
+
+## ## cat("\t\n=======================================")
+## ## cat("\t\n= simulated populations of haplotypes =")
+## ## cat("\t\n= (haploPop object) =")
+## ## cat("\t\n=======================================\n")
+
+## cat("\nNumber of populations :", length(x))
+
+## cat("\nPopulation sizes :\n")
+## temp <- sapply(x,length)
+## names(temp) <- 1:length(temp)
+## print(temp)
+## res$pop.size <- temp
+
+## cat("\nNumber of SNPs per population :\n")
+## temp <- sapply(x,function(e) length(unique(unlist(e))))
+## names(temp) <- 1:length(temp)
+## print(temp)
+## res$n.snp <- temp
+
+## return(invisible(res))
+## } # end print.haploPop
+
+
+
+
+
+
+## ##################
+## ## sample.haploPop
+## ##################
+## sample.haploPop <- function(x, n, n.pop=NULL, keep.pop=TRUE){
+## if(!inherits(x, "haploPop")) stop("x is not a haploPop object")
+## x$call <- NULL
+
+## if(!is.null(n.pop)){ # pre-treatment: reduce to n.pop populations with same size
+## ## kEEP ONLY SOME POP
+## popToKeep <- sample(which(sapply(x$pop, length) > n), n.pop, replace=FALSE) # keep n.pop large enough populations
+## if(length(popToKeep)==0L) stop("No population is big enough for this sampling.")
+## x$pop <- x$pop[popToKeep]
+## x$ages <- x$ages[popToKeep]
+## x$S <- x$S[popToKeep]
+
+## ## MAKE THEM THE SAME SIZE
+## popSizes <- sapply(x$pop, length)
+## for(i in 1:n.pop){
+## idx <- sample(1:popSizes[i], n, replace=FALSE)
+## x$pop[[i]] <- x$pop[[i]][idx]
+## x$ages[[i]] <- x$ages[[i]][idx]
+## }
+
+## } # end pop pre-treatment
+
+## if(keep.pop){
+## popSizes <- sapply(x$pop, length)
+## pop.id <- rep(1:length(x$pop), popSizes)
+## }
+
+## x$pop <- unlist(x$pop, recursive=FALSE)
+## x$ages <- unlist(x$ages, recursive=FALSE)
+
+## idx <- sample(1:length(x$pop), n, replace=FALSE)
+## res <- list(pop=list(), ages=list() )
+
+## if(keep.pop){
+## res$pop <- split(x$pop[idx], pop.id[idx])
+## res$ages <- split(x$ages[idx], pop.id[idx])
+## } else {
+## res$pop[[1]] <- x$pop[idx]
+## res$ages[[1]] <- x$ages[idx]
+## }
+
+## res$S <- rep(n, length(res$pop))
+
+## class(res) <- "haploPop"
+## attr(res, "ances") <- attr(x, "ances")
+## return(res)
+## } # end sample.haploPop
+
+
+
+
+
+
+## ###############
+## ## dist.haploPop
+## ###############
+## dist.haploPop <- function(x, add.root=TRUE, res.type=c("dist","matrix")){
+## if(!inherits(x, "haploPop")) stop("x is not a haploPop object")
+## res.type <- match.arg(res.type)
+## ANCES <- attr(x,"ances")
+
+## x <- unlist(x$pop, recursive=FALSE)
+
+## ## handle root
+## if(add.root){ # add the root
+## x <- c(ANCES, x)
+## }
+
+## n <- length(x)
+
+## f1 <- function(a,b){
+## return(sum(!union(unlist(a),unlist(b)) %in% intersect(unlist(a),unlist(b))))
+## }
+
+## ## res <- outer(x, x, FUN=f1)
+## res <- matrix(0, ncol=n, nrow=n)
+## for(i in 1:(n-1)){
+## for(j in (i+1):n){
+## res[i,j] <- f1(x[[i]], x[[j]])
+## }
+## }
+
+## res <- res+t(res)
+
+## if(res.type=="dist"){
+## res <- as.dist(res)
+## }
+## return(res)
+## } # end dist.haploPop
+
+
+
+
+
+
+## ###############
+## ## plot.haploPop
+## ###############
+## plot.haploPop <- function(x, y=NULL, type="unrooted", size.limit=300, show.pop=TRUE, col=NULL,
+## transp=TRUE, tip.cex=2, method=c("nj", "bionj", "fastme.bal", "fastme.ols"), ...){
+## ## CHECKS ##
+## if(!require(ape)) stop("ape package is required")
+## if(!inherits(x, "haploPop")) stop("x is not a haploPop object")
+## method <- match.arg(method)
+
+## N <- sum(sapply(x$pop,length))
+
+## if(N > size.limit) {
+## stop("tree exceeds size limit")
+## }
+
+
+## ## PLOT TREE ##
+## f1 <- get(method)
+## if(method %in% c("nj","bionj")){
+## tre <- root(f1(dist.haploPop(x)),"1")
+## } else {
+## tre <- f1(dist.haploPop(x))
+## }
+## plot(tre, type=type, ...)
+## xy <- get("last_plot.phylo", envir = .PlotPhyloEnv)
+
+
+## ## SHOW POPULATIONS ##
+## if(!is.null(col)){
+## if(is.integer(col) | is.numeric(col)) {
+## col <- palette()[col]
+## }
+## if(transp){
+## transp <- function(col, alpha=.5){
+## res <- apply(col2rgb(col),2, function(c) rgb(c[1]/255, c[2]/255, c[3]/255, alpha))
+## return(res)
+## }
+
+## col <- transp(col)
+## }
+## points(xy$xx[2:(N+1)], xy$yy[2:(N+1)], pch=20, col=col, cex=tip.cex)
+
+## } else if(show.pop){
+## nPop <- length(x$pop)
+## popSizes <- sapply(x$pop, length)
+## pop.id <- rep(1:length(x$pop), popSizes)
+## opal <- palette()
+## on.exit(palette(opal))
+## if(nPop>1){
+## pop.col <- rainbow(nPop)
+## } else {
+## pop.col <- c("red","red")
+## }
+
+## if(transp){
+## transp <- function(col, alpha=.5){
+## res <- apply(col2rgb(col),2, function(c) rgb(c[1]/255, c[2]/255, c[3]/255, alpha))
+## return(res)
+## }
+
+## pop.col <- transp(pop.col)
+## }
+
+## palette(pop.col)
+## points(xy$xx[2:(N+1)], xy$yy[2:(N+1)], pch=20, col=pop.id, cex=tip.cex)
+## }
+
+
+## ## SHOW ROOT ##
+## points(xy$xx[1], xy$yy[1], pch=20, cex=3)
+
+## return(invisible(tre))
+## } # end plot.haploPop
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+## ##########################################################################
+## ##########################################################################
+## ##########################################################################
+## ##########################################################################
+## ##########################################################################
+## ##########################################################################
+## ##########################################################################
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+## ############
+## ## haploPopDiv
+## ############
+## haploPopDiv <- function(n.steps=20, ini.obj=NULL, ini.haplo=NULL, haplo.length=1e6, mu=1e-5, n.snp.ini=1,
+## birth.func=function(){ sample(0:3, 1, prob=c(.05, .45, .35, .15))},
+## max.pop.size=function(){1e4}, max.nb.pop=30, ini.pop.size=10, regen=FALSE,
+## p.new.pop=function(){1e-4}, death.func=function(age){age>1},
+## quiet=FALSE, allow.reverse=TRUE,
+## track=c("div", "distRoot", "freq","nbMut"), root.haplo=NULL, samp.size=50) {
+
+
+## ## SOME CHECKS
+## ## if(is.numeric(ini.pop.size)){
+## ## ini.pop.size.val <- ini.pop.size
+## ## ini.pop.size <- function(){ini.pop.size.val}
+## ## }
+
+## track <- match.arg(track)
+
+## if(is.numeric(max.pop.size)){
+## max.pop.size.val <- max.pop.size
+## max.pop.size <- function(){max.pop.size.val}
+## }
+
+## if(is.numeric(p.new.pop)){
+## p.new.pop.val <- p.new.pop
+## p.new.pop <- function(){p.new.pop.val}
+## }
+
+## if(is.numeric(birth.func)){
+## birth.func.val <- birth.func[1]
+## birth.func <- function(){birth.func.val}
+## }
+
+## if(is.numeric(death.func)){
+## death.func.val <- death.func[1]
+## death.func <- function(age){age>death.func.val}
+## }
+
+
+## ## GLOBAL VARIABLES ##
+## SNP.POOL <- 1:haplo.length
+## vecS <- 1 # will be redefined later, but needed for evolveOnePop definition
+
+## ## AUXILIARY FUNCTIONS ##
+## if(allow.reverse){
+## createMutations <- function(N){ # L:genome length; N: pop size
+## nb.mutations <- sum(rbinom(N, size=haplo.length, prob=mu))
+## return( sample(SNP.POOL, size=nb.mutations, replace=TRUE) )
+## }
+## } else {
+## createMutations <- function(N){ # L:genome length; N: pop size
+## nb.mutations <- sum(rbinom(N, size=haplo.length, prob=mu))
+## res <- sample(SNP.POOL, size=nb.mutations, replace=TRUE)
+## SNP.POOL <<- setdiff(SNP.POOL, res)# update pool of SNPs
+## return(res)
+## }
+## }
+
+
+## ## assign mutation to haplotypes
+## assignMutations <- function(myPop, mutations){ # mypop: list of `haplotypes'; mutations: vector of SNPs
+## if(length(mutations)==0 | length(myPop)==0) return(myPop)
+## id <- sample(1:length(myPop), size=length(mutations), replace=TRUE)
+## mutations <- split(mutations, id)
+
+## ## function to merge new mutations - handle reverse case
+## f1 <- function(a,b){
+## revMut <- intersect(a,b)
+## if(length(revMut)==0) return(c(a,b))
+## return(setdiff(c(a ,b), revMut))
+## }
+
+## ##myPop[as.integer(names(mutations))] <- mapply(c, myPop[as.integer(names(mutations))], mutations, SIMPLIFY=FALSE)
+## myPop[as.integer(names(mutations))] <- mapply(f1, myPop[as.integer(names(mutations))], mutations, SIMPLIFY=FALSE)
+
+## return(myPop)
+## } # end assignMutations
+
+
+## if(!regen){
+## ## VERSION FOR NO REGENERATION OF SUSCEPTIBLES
+## evolveOnePop <- function(myPop, myS, myAge){ # myPop: pop to evolve; myS: nb of susceptible in the pop; myAge: vector of ages
+## ## strains get older
+## myAge <- myAge + 1
+## ## toKill <- death.func(myAge)
+## ## myPop[toKill] <- NULL
+## ## myAge <- myAge[!toKill]
+
+## ## generate new strains for new generation
+## sampSize <- round(min( length(myPop)*birth.func(), myS)) # number of strains for next step
+## if(sampSize<1){ # if no sample
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+## return(list(pop=myPop, S=myS, age=myAge))
+## }
+## newGen <- myPop[sample(1:length(myPop), sampSize, replace=TRUE)] # sample strains for new generations
+## newGen <- assignMutations(newGen, createMutations(sampSize)) # mutate strains
+## newAge <- rep(0, sampSize) # new ages for newborns
+
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+
+## ## merge old and new generation
+## myPop <- c(myPop,newGen)
+## myAge <- c(myAge, newAge)
+
+## ## possibly create one or more new pop
+## if((length(listPop) < max.nb.pop) & (p.new.pop()>0)) { # total number of pop. limitation
+## nbNewPop <- rbinom(1, length(myPop), prob=p.new.pop())
+## } else {
+## nbNewPop <- 0
+## }
+## if(nbNewPop>0){
+## ## newPop <- sample(listPop, size=nbNewPop, replace=TRUE) # wrong
+## newPop <- lapply(sample(myPop, size=nbNewPop, replace=TRUE), as.list)
+## listPop <<- c(listPop, newPop)
+## vecS <<- c(vecS, replicate(nbNewPop, max.pop.size()) )
+## listAges <<- c(listAges, replicate(nbNewPop, 0, simplify=FALSE) )
+## } # end new pop
+## return(list(pop=myPop, S=myS-sampSize, age=myAge))
+## } # end no regen version
+## } else { ## REGEN VERSION
+## evolveOnePop <- function(myPop, myS, myAge){ # myPop: pop to evolve; myS: nb of susceptible in the pop; myAge: vector of ages
+## ## strains get older
+## myAge <- myAge + 1
+## ## toKill <- death.func(myAge)
+## ## myPop[toKill] <- NULL
+## ## myAge <- myAge[!toKill]
+## myS <- max.pop.size() ## DIFFERENCE between the two versions of the function
+
+## ## generate new strains for new generation
+## sampSize <- round(min( length(myPop)*birth.func(), myS)) # number of strains for next step
+## if(sampSize<1){ # if no sample
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+## return(list(pop=myPop, S=myS, age=myAge))
+## }
+## newGen <- myPop[sample(1:length(myPop), sampSize, replace=TRUE)] # sample strains for new generations
+## newGen <- assignMutations(newGen, createMutations(sampSize)) # mutate strains
+## newAge <- rep(0, sampSize) # new ages for newborns
+
+## ## old strains die
+## toKill <- death.func(myAge)
+## myPop[toKill] <- NULL
+## myAge <- myAge[!toKill]
+
+## ## merge old and new generation
+## myPop <- c(myPop,newGen)
+## myAge <- c(myAge, newAge)
+
+## ## possibly create one or more new pop
+## if((length(listPop) < max.nb.pop) & (p.new.pop()>0)) { # total number of pop. limitation
+## nbNewPop <- rbinom(1, length(myPop), prob=p.new.pop())
+## } else {
+## nbNewPop <- 0
+## }
+## if(nbNewPop>0){
+## ## newPop <- sample(listPop, size=nbNewPop, replace=TRUE) # wrong
+## newPop <- lapply(sample(myPop, size=nbNewPop, replace=TRUE), as.list)
+## listPop <<- c(listPop, newPop)
+## vecS <<- c(vecS, replicate(nbNewPop, max.pop.size()) )
+## listAges <<- c(listAges, replicate(nbNewPop, 0, simplify=FALSE) )
+## } # end new pop
+## return(list(pop=myPop, S=myS, age=myAge)) ## DIFFERENCE between the two versions of the function
+## } # end no regen version
+## } ## end evolveOnePop (both versions)
+
+
+## ## INITIATE SIMULATIONS ##
+## ## INITIALIZE FROM SCRATCH
+## vecS <- max.pop.size() # susceptibles
+
+## if(is.null(ini.obj)){
+## ## vecS <- max.pop.size() - n.snp.ini # susceptibles
+
+## if(is.null(ini.haplo)) {
+## haplo.ini <- sample(SNP.POOL, n.snp.ini, replace=TRUE)
+## } else {
+## haplo.ini <- ini.haplo
+## }
+## ANCES <- haplo.ini
+## listPop <- list()
+## listPop[[1]] <- lapply(1:ini.pop.size, function(i) haplo.ini) # contains only one population of identical clones to start with
+## listAges <- list() # will contain vectors of ages of haplotypes (a time of appearance, age=0)
+## listAges[[1]] <- rep(0, ini.pop.size)
+## } else { ## INITIALIZE WITH PROVIDED OBJECT
+## if(!inherits(ini.obj, "haploPop")) stop("x is not a haploPopDiv object")
+## ## vecS <- ini.obj$S
+## ANCES <- attr(ini.obj, "ances")
+## listPop <- ini.obj$pop
+## listAges <- ini.obj$ages
+## }
+
+## ## function getting pairwise distances
+## if(track=="div"){
+## fRes <- function(list.pop){
+## list.pop <- list(pop=list.pop) # kludge needed for dist.haploPop
+## class(list.pop) <- "haploPop" # kludge needed for dist.haploPop
+## N <- sum(sapply(list.pop$pop, length))
+## if(N<2) return(0)
+## if(N > samp.size){
+## return(dist.haploPop(sample.haploPop(list.pop, samp.size, keep.pop=FALSE), add.root=FALSE)) # do not include the root in distances.
+## } else {
+## return(dist.haploPop(list.pop, add.root=FALSE))
+## }
+## } # end fRes
+## }
+
+## ## function getting distances to the root
+## if(track=="distRoot"){
+## if(is.null(root.haplo)) {
+## root.haplo <- ANCES
+## }
+## fRes <- function(list.pop){
+## list.pop <- list(pop=list.pop) # kludge needed for sample.haploPop
+## class(list.pop) <- "haploPop" # kludge needed for sample.haploPop
+## N <- sum(sapply(list.pop$pop, length))
+## if(N<1) return(0)
+## if(N > samp.size){
+## list.pop <- sample.haploPop(list.pop, samp.size, keep.pop=FALSE)
+## }
+
+## res <- sapply(unlist(list.pop$pop, recursive=FALSE), function(e) sum(!e %in% root.haplo))
+## return(res)
+## } # end fRes
+## }
+
+## ## function getting allele absolute frequencies
+## if(track=="freq"){
+## fRes <- function(list.pop){
+## res <- table(unlist(list.pop))
+## return(res)
+## } # end fRes
+## }
+
+## ## function getting allele absolute frequencies
+## if(track=="nbMut"){
+## fRes <- function(list.pop){
+## list.pop <- list(pop=list.pop) # kludge needed for sample.haploPop
+## class(list.pop) <- "haploPop" # kludge needed for sample.haploPop
+## N <- sum(sapply(list.pop$pop, length))
+## if(N<1) return(0)
+## if(N > samp.size){
+## list.pop <- sample.haploPop(list.pop, samp.size, keep.pop=FALSE)
+## }
+
+## return( length(unique(unlist(list.pop))) )
+## } # end fRes
+
+## }
+
+
+
+## res <- list(div=list(), popSize=integer())
+## res$div[[1]] <- fRes(listPop)
+## res$popSize[1] <- sum(sapply(listPop, length))
+
+
+## ## MAKE SIMULATIONS ##
+
+## ## evolve all populations
+## i <- 1L
+## if(!quiet){
+## cat("\nSimulating populations of haplotypes through time: \n")
+## }
+## ##while((sum(vecS)>0) & (i<(n.steps+1))){ # evolve all generations
+## while(i<(n.steps+1)){ # evolve all generations
+## i <- i + 1L # update iterator
+## if(!quiet){
+## catStep <- max(round(n.steps/100), 10)
+## cat(ifelse((i %% catStep)==0, paste(" ...", i), ""))
+## }
+
+
+## ## make populations evolve of one generation
+## ##idx <- which(vecS>0) # make sure that new pop won't evolve this time ! leads to not dying
+## idx <- 1:length(listPop) # make sure that new pop won't evolve this time
+## if(length(idx)>0){
+## for(j in idx){
+## temp <- evolveOnePop(listPop[[j]], vecS[j], listAges[[j]])
+## listPop[[j]] <- temp$pop
+## vecS[j] <- temp$S
+## listAges[[j]] <- temp$age
+## }
+
+## }
+
+## ## ## purge non-susceptible pop
+## ## listPop <- listPop[vecS>0]
+## ## vecS <- vecS[vecS>0]
+
+## ## purge empty populations
+## toKeep <- sapply(listPop, length)>0
+## listPop <- listPop[toKeep]
+## vecS <- vecS[toKeep]
+## listAges <- listAges[toKeep]
+
+## ## stop if all pop go extinct
+## if(length(listPop)==0L){
+## if(!quiet) cat("\n All populations went extinct at time",i,"\n")
+## return(res)
+## }
+
+## res$div[[i]] <- fRes(listPop)
+## res$popSize[i] <- sum(sapply(listPop, length))
+
+## ## FOR DEBUGGING
+## ## cat("\n=== ",i," ===")
+## ## cat("\nlistPop")
+## ## print(listPop)
+## ## cat("\nvecS")
+## ## print(vecS)
+## ## cat("\nlistAges")
+## ## print(listAges)
+## ## END DEBUGGING
+## } # end while
+
+## if(!quiet){
+## cat("\n... done! \n")
+## }
+
+## ## END OF SIMULATIONS ##
+
+## ## STORE HAPLOPOP OBJECT
+## obj <- list(pop=listPop, ages=listAges, S=vecS)
+## class(obj) <- "haploPop"
+## obj$call <- match.call()
+## attr(obj,"ances") <- ANCES # ancestral genotype
+
+## if(!quiet) cat("\nStored haploPop object in 'last.haploPop'\n")
+## assign("last.haploPop", obj, envir= .GlobalEnv)
+
+
+## ## RETURN RES
+## return(res)
+
+## } # end haploPopDiv
+
+
diff --git a/R/hierarchyMethods.R b/R/hierarchyMethods.R
new file mode 100644
index 0000000..4bddf5c
--- /dev/null
+++ b/R/hierarchyMethods.R
@@ -0,0 +1,198 @@
+########################################################################
+# hierarchy methods definitions.
+#
+# Zhian Kamvar, March 2015
+# kamvarz at science.oregonstate.edu
+########################################################################
+.getHier <- function(x, formula = NULL, combine = TRUE, call = match.call()){
+ if (is.null(x at strata)){
+ warning("Strata must be specified before defining a hierarchy. See ?strata for details.", call. = FALSE)
+ return(NULL)
+ }
+ if (is.null(x at hierarchy)){
+ warning("A hierarchy must be defined before retrieving it.", call. = FALSE)
+ return(NULL)
+ }
+ if (is.null(formula)){
+ if (!is.null(x at hierarchy)){
+ # Returning the base hierarchy
+ return(.getHier(x, formula = x at hierarchy, combine = combine, call = call))
+ } else {
+ return(NULL)
+ }
+ }
+ vars <- all.vars(formula)
+ if (any(!vars %in% names(x at strata))){
+ stop(.strata_incompatible_warning(vars, x at strata), call. = FALSE)
+ }
+ if (!.test_existing_hier(vars, all.vars(x at hierarchy))){
+ callform <- as.character(call["formula"])
+ lines <- paste(rep("-", 78), collapse = "")
+ stop(paste0("\n", lines, "\n", callform, "\nis not a subset of\n",
+ paste(x at hierarchy, collapse = "")), call. = FALSE)
+ }
+ if (combine){
+ strata <- .make_strata(formula, x at strata)
+ } else {
+ strata <- x at strata[all.vars(formula)]
+ }
+ invisible(return(strata))
+}
+
+.setHier <- function(x, value, call = match.call()){
+ if (is.null(value)){
+ x at hierarchy <- value
+ return(x)
+ }
+ if (is.null(x at strata)){
+ warning("Strata must be specified before defining a hierarchy. See ?strata for details.", call. = FALSE)
+ return(NULL)
+ }
+ if (!is.language(value)){
+ callval <- as.character(call["value"])
+ stop(paste(callval, "is not a formula"), call. = FALSE)
+ }
+ vars <- all.vars(value)
+ if (any(!vars %in% names(x at strata))){
+ stop(.strata_incompatible_warning(vars, x at strata), call. = FALSE)
+ }
+
+ ## TODO: Insert Jerome's method of checking whether or not the hierarchy is
+ ## truly hierarchical.
+
+ x at hierarchy <- value
+ return(x)
+}
+
+.test_existing_hier <- function(query, hier){
+ matches <- match(hier, query)
+ matches <- matches[!is.na(matches)]
+ if (all(matches == sort(matches))){
+ return(TRUE)
+ } else {
+ return(FALSE)
+ }
+}
+
+#==============================================================================#
+#' Access and manipulate the population hierarchy for genind or genlight objects.
+#'
+#' The following methods allow the user to quickly change the hierarchy or
+#' population of a genind or genlight object.
+#'
+#' @export
+#' @rdname hierarchy-methods
+#' @aliases hier,genind-method hier,genlight-method
+#' @param x a genind or genlight object
+#' @param formula a nested formula indicating the order of the population
+#' hierarchy to be returned.
+#' @param combine if \code{TRUE} (default), the levels will be combined
+#' according to the formula argument. If it is \code{FALSE}, the levels will
+#' not be combined.
+#' @param value a formula specifying the full hierarchy of columns in the strata
+#' slot. \strong{(See Details below)}
+#' @docType methods
+#'
+#' @details You must first specify your strata before you can specify your
+#' hierarchies. Hierarchies are special cases of strata in that the levels
+#' must be nested within each other. An error will occur if you specify a
+#' hierarchy that is not truly hierarchical.
+#'
+#' \subsection{Details on Formulas}{
+#'
+#' The preferred use of these functions is with a \code{\link{formula}}
+#' object. Specifically, a hierarchical formula argument is used to name which
+#' strata are hierarchical. An example of a hierarchical formula would
+#' be:\tabular{r}{ \code{~Country/City/Neighborhood}} This convention was
+#' chosen as it becomes easier to type and makes intuitive sense when defining
+#' a hierarchy. Note: it is important to use hierarchical formulas when
+#' specifying hierarchies as other types of formulas (eg.
+#' \code{~Country*City*Neighborhood}) will give incorrect results.}
+#'
+#' @seealso \code{\link{strata}} \code{\link{genind}}
+#' \code{\link{as.genind}}
+#'
+#' @author Zhian N. Kamvar
+#' @examples
+#' # let's look at the microbov data set:
+#' data(microbov)
+#' microbov
+#'
+#' # We see that we have three vectors of different names in the 'other' slot.
+#' ?microbov
+#' # These are Country, Breed, and Species
+#' names(other(microbov))
+#'
+#' # Let's set the hierarchy
+#' strata(microbov) <- data.frame(other(microbov))
+#' microbov
+#'
+#' # And change the names so we know what they are
+#' nameStrata(microbov) <- ~Country/Breed/Species
+#'
+#' # let's see what the hierarchy looks like by Species and Breed:
+#' hier(microbov) <- ~Species/Breed
+#' head(hier(microbov, ~Species/Breed))
+#'
+#==============================================================================#
+hier <- function(x, formula = NULL, combine = TRUE, value){
+ standardGeneric("hier")
+}
+
+#' @export
+setGeneric("hier")
+
+setMethod(
+ f = "hier",
+ signature(x = "genind"),
+ definition = function(x, formula = NULL, combine = TRUE, value){
+ theCall <- match.call()
+ if (missing(value)){
+ .getHier(x, formula = formula, combine = combine, theCall)
+ } else {
+ .setHier(x, value, theCall)
+ }
+ })
+
+setMethod(
+ f = "hier",
+ signature(x = "genlight"),
+ definition = function(x, formula = NULL, combine = TRUE, value){
+ theCall <- match.call()
+ if (missing(value)){
+ .getHier(x, formula = formula, combine = combine, theCall)
+ } else {
+ .setHier(x, value, theCall)
+ }
+
+ })
+
+
+#==============================================================================#
+#' @export
+#' @rdname hierarchy-methods
+#' @aliases hier<-,genind-method hier<-,genlight-method
+#' @docType methods
+#==============================================================================#
+"hier<-" <- function(x, value){
+ standardGeneric("hier<-")
+}
+
+#' @export
+setGeneric("hier<-")
+
+setMethod(
+ f = "hier<-",
+ signature(x = "genind"),
+ definition = function(x, value){
+ theCall <- match.call()
+ return(.setHier(x, value, theCall))
+ })
+
+setMethod(
+ f = "hier<-",
+ signature(x = "genlight"),
+ definition = function(x, value){
+ theCall <- match.call()
+ return(.setHier(x, value, theCall))
+ })
diff --git a/R/hybridize.R b/R/hybridize.R
new file mode 100644
index 0000000..2743c8b
--- /dev/null
+++ b/R/hybridize.R
@@ -0,0 +1,235 @@
+#'
+#' Function hybridize takes two genind in inputs
+#' and generates hybrids individuals having one parent
+#' in both objects.
+#'
+#'The function \code{hybridize} performs hybridization between two set
+#' of genotypes stored in \linkS4class{genind} objects (referred as the "2
+#' populations"). Allelic frequencies are derived for each population,
+#' and then gametes are sampled following a multinomial distribution. \cr
+#'
+#' The result consists in a set of 'n' genotypes, with different possible
+#' outputs (see 'res.type' argument).
+#'
+#'
+#' @export
+#'
+#' @param x1 a \linkS4class{genind} object
+#' @param x2 a \linkS4class{genind} object
+#' @param n an integer giving the number of hybrids requested
+#' @param pop a character string giving naming the population of the
+#' created hybrids.
+#' @param res.type a character giving the type of output requested. Must
+#' be "genind" (default), "df" (i.e. data.frame like in
+#' \code{\link{genind2df}}), or "STRUCTURE" to generate a .str file
+#' readable by STRUCTURE (in which case the 'file' must be supplied). See
+#' 'details' for STRUCTURE output.
+#' @param file a character giving the name of the file to be written
+#' when 'res.type' is "STRUCTURE"; if NULL, a the created file is of the
+#' form "hybrids\_[the current date].str".
+#' @param quiet a logical specifying whether the writing to a file (when
+#' 'res.type' is "STRUCTURE") should be announced (FALSE, default) or
+#' not (TRUE).
+#' @param sep a character used to separate two alleles
+#' @param hyb.label a character string used to construct the hybrids
+#' labels; by default, "h", which gives labels: "h01", "h02", "h03",...
+#'
+#' @return
+#' A \linkS4class{genind} object (by default), or a data.frame of alleles
+#' (res.type="df"). No R output if res.type="STRUCTURE" (results written
+#' to the specified file).
+#'
+#' @details
+#' If the output is a STRUCTURE file, this file will have the following
+#' caracteristics:\cr
+#' - file contains the genotypes of the parents, and then the genotypes
+#' of hybrids\cr
+#' - the first column identifies genotypes\cr
+#' - the second column identifies the population (1 and 2 for parents x1 and x2;
+#' 3 for hybrids)\cr
+#' - the first line contains the names of the markers\cr
+#' - one row = one genotype (onerowperind will be true)\cr
+#' - missing values coded by "-9" (the software's default)\cr
+#'
+#' @examples
+#' \dontrun{
+#' ## Let's make some cattle hybrids
+#' data(microbov)
+#'
+#' ## first, isolate each breed
+#' temp <- seppop(microbov)
+#' names(temp)
+#' salers <- temp$Salers
+#' zebu <- temp$Zebu
+#'
+#' ## let's make some... Zeblers
+#' zebler <- hybridize(salers, zebu, n=40,
+#' pop="Zebler")
+#'
+#'
+#' ## now let's merge all data into a single genind
+#' newDat <- repool(microbov, zebler)
+#'
+#' ## make a correspondance analysis
+#' ## and see where hybrids are placed
+#' X <- genind2genpop(newDat, quiet=TRUE)
+#' coa1 <- dudi.coa(tab(X),scannf=FALSE,nf=3)
+#' s.label(coa1$li)
+#' add.scatter.eig(coa1$eig,2,1,2)
+#'
+#' }
+#'
+#'
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#'
+#' @seealso \code{\link{seploc}}, \code{\link{seppop}}, \code{\link{repool}}
+#'
+#'
+#'
+hybridize <- function(x1, x2, n, pop="hybrid",
+ res.type=c("genind","df","STRUCTURE"),
+ file=NULL, quiet=FALSE, sep="/", hyb.label="h"){
+ ## checks
+ if(!is.genind(x1)) stop("x1 is not a valid genind object")
+ if(!is.genind(x2)) stop("x2 is not a valid genind object")
+ if(!all(ploidy(x1)==ploidy(x1)[1])) stop("varying ploidy (in x1) is not supported for this function")
+ if(!all(ploidy(x2)==ploidy(x2)[1])) stop("varying ploidy (in x2) is not supported for this function")
+ if(ploidy(x1)[1] %% 2 != 0) stop("not implemented for odd levels of ploidy")
+ if(ploidy(x1)[1] != ploidy(x2)[1]) stop("x1 and x2 have different ploidy")
+ checkType(x1)
+ checkType(x2)
+
+ ## store a few variables
+ n <- as.integer(n)
+ ploidy <- ploidy(x1)[1]
+ res.type <- match.arg(res.type)
+
+ ## ensure different names for pop
+ popNames(x1) <- "pop1"
+ popNames(x2) <- "pop2"
+
+ ## repool data
+ x1x2 <- repool(x1, x2)
+ x1 <- x1x2[pop=1]
+ x2 <- x1x2[pop=2]
+
+ ## used variables
+ n1 <- nInd(x1)
+ n2 <- nInd(x2)
+ k <- nLoc(x1)
+
+ #### get frequencies for each locus
+ y1 <- genind2genpop(x1,pop=factor(rep(1,n1)),quiet=TRUE)
+ freq1 <- tab(y1, freq=TRUE) # get frequencies
+ freq1 <- split(freq1, y1 at loc.fac) # split by locus
+ freq1 <- freq1[locNames(x1)] # ensure right order
+
+ y2 <- genind2genpop(x2,pop=factor(rep(1,n2)),quiet=TRUE)
+ freq2 <- tab(y2, freq=TRUE) # get frequencies
+ freq2 <- split(freq2, y2 at loc.fac) # split by locus
+ freq2 <- freq2[locNames(x2)] # ensure right order
+
+ #### sampling of gametes
+ ## kX1 / kX2 are lists of tables of sampled gametes
+ kX1 <- lapply(freq1, function(v) t(rmultinom(n,ploidy/2,v)))
+ names(kX1) <- locNames(x1)
+ vec.paste1<-NULL
+ Vec.all1<-NULL
+ for(i in 1:k) {
+ colnames(kX1[[i]]) <- alleles(x1)[[i]]
+ ## Paste the alleles locus after locus
+ vec.paste1<-c(vec.paste1, alleles(x1)[[i]])
+ ## Paste the number of alleles, locus after locus
+ Vec.all1<-c(Vec.all1, length(alleles(x1)[[i]]))
+ }
+ kX2 <- lapply(freq2, function(v) t(rmultinom(n,ploidy/2,v)))
+ names(kX2) <- locNames(x2)
+ vec.paste2<-NULL
+ Vec.all2<-NULL
+ for(i in 1:k) {
+ colnames(kX2[[i]]) <- alleles(x2)[[i]]
+ vec.paste2<-c(vec.paste2, alleles(x2)[[i]])
+ Vec.all2<-c(Vec.all2, length(alleles(x2)[[i]]))
+ }
+
+
+ ## construction of zygotes ##
+ ## individual gamete tables
+ tab1 <- as.matrix(cbind.data.frame(kX1))
+ ## Force the names of the columns for tab1 and tab2 with the pattern "locNames.allele"
+ colnames(tab1)<-paste(rep(locNames(x1), Vec.all1), ".",vec.paste1, sep = "")
+ tab2 <- as.matrix(cbind.data.frame(kX2))
+ colnames(tab2)<-paste(rep(locNames(x2), Vec.all2), ".",vec.paste2, sep = "")
+
+
+ ## make empty matrix with all alleles in tab1 and tab2
+ zyg.rownames <- .genlab(hyb.label,n)
+ zyg.colnames <- sort(unique(c(colnames(tab1),colnames(tab2))))
+ zyg <- matrix(0, nrow=n, ncol=length(zyg.colnames),
+ dimnames=list(zyg.rownames, zyg.colnames))
+
+ ## add in the alleles
+ zyg[, colnames(tab1)] <- zyg[, colnames(tab1)] + tab1
+ zyg[, colnames(tab2)] <- zyg[, colnames(tab2)] + tab2
+ zyg <- zyg
+ zyg <- genind(zyg, type="codom", ploidy=ploidy)
+
+ ## res.type=="STRUCTURE"
+ if(res.type=="STRUCTURE"){
+ ## res <- paste(gam1,gam2,sep=" ") # make df for the hybrids
+ ## res <- as.data.frame(matrix(res,ncol=k))
+ temp <- genind2df(repool(x1,x2,zyg), usepop=FALSE, sep=" ")
+ res <- unlist(apply(temp,1,strsplit," "))
+ res <- as.data.frame(matrix(res, nrow=nrow(temp), byrow=TRUE))
+ colnames(res) <- rep(colnames(temp),each=ploidy)
+ ## df1 <- genind2df(x1,sep=" ",usepop=FALSE) # make df with parents and hybrids
+ ## df2 <- genind2df(x2,sep=" ",usepop=FALSE)
+ ## res <- rbind.data.frame(df1,df2,res) # rbind the three df
+ res[is.na(res)] <- "-9" # this is two missing alleles for STRUCTURE
+ pop <- rep(1:3,c(nrow(x1 at tab), nrow(x2 at tab), n)) # make a pop identifier
+ res <- cbind.data.frame(pop,res, stringsAsFactors = FALSE)
+ names(res)[1] <- ""
+
+ if(is.null(file)) {
+ file <- gsub("[[:space:]]|:","-",date())
+ file <- paste("hybrid",file,sep="_")
+ file <- paste(file,"str",sep=".")
+ }
+ write.table(res, file=file,row.names = TRUE, col.names = TRUE, quote=FALSE)
+ if(!quiet) cat("\nWrote results to file", file, "\n")
+
+ return(invisible())
+ }
+
+
+ ## res.type=="df"
+ if(res.type=="df"){
+ ## res <- paste(gam1,gam2,sep=sep)
+ ## res <- as.data.frame(matrix(res,ncol=k), stringsAsFactors=FALSE)
+ ## names(res) <- x1 at loc.names
+ ## row.names(res) <- .genlab(hyb.label,n)
+
+ res <- genind2df(zyg, sep=sep)
+ return(res)
+ }
+
+
+ ## res.type=="genind"
+ if(res.type=="genind"){
+ ## res <- paste(gam1,gam2,sep="")
+ ## res <- as.data.frame(matrix(res,ncol=k), stringsAsFactors=FALSE)
+ ## names(res) <- x1 at loc.names
+ ## row.names(res) <- .genlab(hyb.label,n)
+ ## if(is.null(pop)){ # if pop is not provided, merge the two parent populations
+ ## pop <- paste(deparse(substitute(x1)) , deparse(substitute(x2)), sep="-")
+ ## }
+ pop <- factor(rep(pop,n))
+
+ res <- zyg
+ pop(res) <- pop
+ res at call <- match.call()
+
+ return(res)
+ }
+
+} # end hybridize
diff --git a/R/import.R b/R/import.R
new file mode 100644
index 0000000..d6fb438
--- /dev/null
+++ b/R/import.R
@@ -0,0 +1,1733 @@
+###################################################################
+## Fonctions designed to import files from other softwares
+## into genind objects
+##
+## currently supported formats are :
+## .gtx (GENETIX)
+## .dat (Fstat)
+## .gen (Genepop)
+## .stru (STRUCTURE)
+##
+## Thibaut Jombart, avril 2006
+## Revised March 2015
+## t.jombart at imperial.ac.uk
+##
+##################################################################
+
+
+######################
+## Function df2genind
+######################
+#' Convert a data.frame of allele data to a genind object.
+#'
+#' The function \code{df2genind} converts a data.frame (or a matrix) into a
+#' \linkS4class{genind} object. The data.frame must meet the following
+#' requirements:\cr
+#' - genotypes are in row (one row per genotype)\cr
+#' - markers/loci are in columns\cr
+#' - each element is a string of characters coding alleles, ideally separated by a character string (argument \code{sep});
+#' if no separator is used, the number of characters coding alleles must be indicated (argument \code{ncode}).\cr
+#'
+#' See \code{\link{genind2df}} to convert \linkS4class{genind} objects back to such a
+#' data.frame.
+#'
+#' === Details for the \code{sep} argument ===\cr this character is directly
+#' used in reguar expressions like \code{gsub}, and thus require some
+#' characters to be preceeded by double backslashes. For instance, "/" works
+#' but "|" must be coded as "\\|".
+#'
+#' @aliases df2genind
+#' @param X a matrix or a data.frame containing allelle data only (see
+#' decription)
+#' @param sep a character string separating alleles. See details.
+#' @param ncode an optional integer giving the number of characters used for
+#' coding one genotype at one locus. If not provided, this is determined from
+#' data.
+#' @param ind.names optinal, a vector giving the individuals names; if NULL, taken
+#' from rownames of X. If factor or numeric, vector is converted to character.
+#' @param loc.names an optional character vector giving the markers names; if
+#' NULL, taken from colnames of X.
+#' @param pop an optional factor giving the population of each individual.
+#' @param NA.char a character string corresponding to missing allele (to be treated as NA)
+#' @param ploidy an integer indicating the degree of ploidy of the genotypes.
+#' @param type a character string indicating the type of marker: 'codom' stands
+#' for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for
+#' 'presence/absence' markers (e.g. AFLP, RAPD).
+#' @param strata an optional data frame that defines population stratifications
+#' for your samples. This is especially useful if you have a hierarchical or
+#' factorial sampling design.
+#' @param hierarchy a hierarchical formula that explicitely defines hierarchical
+#' levels in your strata. see \code{\link{hierarchy}} for details.
+#'
+#' @return an object of the class \linkS4class{genind} for \code{df2genind}; a
+#' matrix of biallelic genotypes for \code{genind2df}
+#'
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}, Zhian N. Kamvar
+#' \email{kamvarz@@science.oregonstate.edu}
+#'
+#' @seealso \code{\link{genind2df}}, \code{\link{import2genind}},
+#' \code{\link{read.genetix}}, \code{\link{read.fstat}},
+#' \code{\link{read.structure}}
+#'
+#' @keywords manip
+#' @examples
+#'
+#' ## simple example
+#' df <- data.frame(locusA=c("11","11","12","32"),
+#' locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22"))
+#' row.names(df) <- .genlab("genotype",4)
+#' df
+#'
+#' obj <- df2genind(df, ploidy=2, ncode=1)
+#' obj
+#' tab(obj)
+#'
+#'
+#' ## converting a genind as data.frame
+#' genind2df(obj)
+#' genind2df(obj, sep="/")
+#'
+#' @export
+#'
+df2genind <- function(X, sep=NULL, ncode=NULL, ind.names=NULL, loc.names=NULL,
+ pop=NULL, NA.char="", ploidy=2, type=c("codom","PA"),
+ strata = NULL, hierarchy = NULL){
+
+ ## CHECKS ##
+ if(is.data.frame(X)) X <- as.matrix(X)
+ if (!inherits(X, "matrix")) stop ("X is not a matrix")
+ res <- list()
+ type <- match.arg(type)
+ if (is.null(sep) && is.null(ncode) && any(ploidy > 1)){
+ stop("Not enough information to convert data: please indicate the separator (sep=...) or the number of characters coding an allele (ncode=...)")
+ }
+ if(length(NA.char)>1) {
+ warning("NA.char has several values; only the first one will be considered")
+ NA.char <- NA.char[1]
+ }
+
+ # If by any chance provided ind.names are of class int/factor, they are (silently?) converted to characters.
+ if (!is.character(ind.names) & !is.null(ind.names)) {
+ ind.names <- as.character(ind.names)
+ }
+
+
+ ## TYPE-INDEPENDENT STUFF ##
+ ## misc variables
+ n <- nrow(X)
+ nloc <- ncol(X)
+ if (length(ploidy) < n){
+ if (length(ploidy) == 1){
+ ploidy <- rep(as.integer(ploidy), length=n)
+ } else {
+ undefined <- length(ploidy)/n
+ msg <- paste0("\nPloidy is undefined for ",
+ undefined*100,
+ "% of data.\n",
+ "This must be a single integer indicating the ploidy of",
+ "the entire data set or vector of integers the same",
+ "length as the number of samples.")
+ stop(msg)
+ }
+
+ }
+ if(any(ploidy < 1L)) stop("ploidy cannot be less than 1")
+
+ ## check individual labels
+ if(is.null(ind.names)) ind.names <- rownames(X)
+ if(is.null(ind.names)) ind.names <- .genlab("",n)
+ if(any(duplicated(ind.names))){
+ warning("duplicate labels detected for some individuals; using generic labels")
+ ind.names <- .genlab("",n)
+ }
+ rownames(X) <- ind.names
+
+ ## check locus labels
+ if(is.null(loc.names)) loc.names <- colnames(X)
+ if(is.null(loc.names)) loc.names <- .genlab("loc",nloc)
+ if(any(duplicated(loc.names))){
+ warning("duplicate labels detected for some loci; using generic labels")
+ loc.names <- .genlab("loc",nloc)
+ }
+ if(length(grep("[.]", loc.names))>0L){
+ warning("character '.' detected in names of loci; replacing with '_'")
+ gsub("[.]","_", loc.names)
+ }
+ colnames(X) <- loc.names
+
+
+ ## pop argument
+ if(!is.null(pop)){
+ if(length(pop)!= n) stop("length of factor pop differs from nrow(X)")
+ pop <- as.factor(pop)
+ }
+
+
+ ## PRESENCE/ABSENCE MARKERS ##
+ if(toupper(type)=="PA"){
+ ## preliminary stuff
+ rownames(X) <- ind.names
+ colnames(X) <- loc.names
+
+ ## Erase entierely non-typed loci
+ temp <- colSums(is.na(X))==nrow(X)
+ if(any(temp)){
+ X <- X[,!temp]
+ warning("entirely non-type marker(s) deleted")
+ }
+
+ ## Erase entierely non-type individuals
+ temp <- rowSums(is.na(X))==ncol(X)
+ if(any(temp)){
+ X <- X[!temp,,drop=FALSE]
+ if(!is.null(pop)) pop <- pop[!temp]
+ ploidy <- ploidy[!temp]
+ ind.names <- ind.names[!temp]
+ warning("entirely non-type individual(s) deleted")
+ }
+
+ ## erase non-polymorphic loci
+ temp <- apply(X, 2, function(loc) length(unique(loc[!is.na(loc)]))==1)
+ if(any(temp)){
+ X <- X[,!temp,drop=FALSE]
+ loc.names <- loc.names[!temp]
+ nloc <- ncol(X)
+ warning("non-polymorphic marker(s) deleted")
+ }
+
+ prevcall <- match.call()
+
+ res <- genind(tab=X, pop=pop, prevcall=prevcall, ploidy=ploidy,
+ type = "PA", strata = strata, hierarchy = hierarchy)
+
+ return(res)
+ } # end type PA
+
+
+ ## CODOMINANT MARKERS ##
+ ## make sure X is in character mode
+ mode(X) <- "character"
+
+
+ ## HANDLE MISSING SEPARATORS
+ if(is.null(sep) && any(ploidy>1)){
+ ## check that ncode is provided
+ if(is.null(ncode)) stop("please indicate either the separator (sep) or the number of characters coding an allele (ncode).")
+
+ ## add "/" as separator
+ X <- gsub(paste("([[:alnum:]]{",ncode,"})",sep=""), "\\1/", X)
+ X <- sub("/$","",X)
+ sep <- "/"
+ }
+
+ ## HANDLE NAs
+ ## find all strings which are in fact NAs
+ NA.list <- unlist(lapply(unique(ploidy), function(nrep) paste(rep(NA.char, nrep), collapse=sep)))
+ NA.list <- unique(c(NA.list, NA.char))
+
+ ## replace NAs
+ X[X %in% NA.list] <- NA
+
+ ## erase entirely non-type loci
+ toRemove <- which(colSums(is.na(X))==nrow(X))
+ if(length(toRemove) > 0){
+ X <- X[,-toRemove, drop = FALSE]
+ loc.names <- loc.names[-toRemove]
+ warning("entirely non-type marker(s) deleted")
+ }
+
+
+ ## erase entierely non-type individuals
+ toRemove <- which(rowSums(is.na(X))==ncol(X))
+ if(length(toRemove) > 0){
+ X <- X[-toRemove, , drop = FALSE]
+ ind.names <- rownames(X)
+ ploidy <- ploidy[-toRemove]
+ if(!is.null(pop)) pop <- pop[-toRemove]
+ warning("entirely non-type individual(s) deleted")
+ }
+
+
+ ## TRANSLATE DATA INTO ALLELE COUNTS ##
+ ## get dimensions of X
+ nloc <- ncol(X)
+ nind <- nrow(X)
+
+ ## unfold data for each cell of the table
+ if (any(ploidy > 1)){
+ allele.data <- strsplit(X, sep)
+ n.items <- sapply(allele.data, length)
+ locus.data <- rep(rep(loc.names, each=nind), n.items)
+ ind.data <- rep(rep(ind.names,ncol(X)), n.items)
+ allele.data <- unlist(allele.data)
+ } else {
+ n.items <- rep(1, length(X))
+ locus.data <- rep(rep(loc.names, each=nind), n.items)
+ ind.data <- rep(rep(ind.names, ncol(X)), n.items)
+ allele.data <- unlist(X)
+ }
+
+
+ ## identify NAs
+ NA.posi <- which(is.na(allele.data))
+ NA.ind <- ind.data[NA.posi]
+ NA.locus <- locus.data[NA.posi]
+
+ ## remove NAs
+ if(length(NA.posi)>0){
+ allele.data <- allele.data[-NA.posi]
+ locus.data <- locus.data[-NA.posi]
+ ind.data <- ind.data[-NA.posi]
+ }
+
+ ## get matrix of allele counts
+ allele.data <- paste(locus.data, allele.data, sep=".")
+ allele.data <- factor(allele.data, levels=unique(allele.data))
+ out <- table(ind.data, allele.data)
+ out <- out[ind.names, , drop = FALSE] # table sorts alphabetically. This resets.
+
+ ## force type 'matrix'
+ class(out) <- NULL
+ dimnames(out) <- list(rownames(out), colnames(out))
+
+ ## restore NAs
+ ##
+ ## Thanks to Klaus Schliep for the proposed speedup:
+ ##
+ # if (length(NA.posi) > 0) {
+ # out.colnames <- colnames(out)
+ # NA.row <- match(NA.ind, rownames(out))
+ # loc <- paste0(NA.locus, "\\.")
+ # uloc <- unique(loc)
+ # loc.list <- lapply(uloc, grep, out.colnames)
+ # NA.col <- match(loc, uloc)
+ # out[cbind(rep(NA.row, unlist(lapply(loc.list, length))[NA.col]), unlist(loc.list[NA.col]))] <- NA
+ # }
+ ## This one is modified from above to make everything more explicit.
+ if (length(NA.posi) > 0) {
+ out.colnames <- colnames(out)
+ NA.row <- match(NA.ind, rownames(out))
+ loc <- paste0(NA.locus, "\\.")
+ uloc <- unique(loc)
+ loc.list <- lapply(uloc, grep, out.colnames)
+ NA.col <- match(loc, uloc)
+
+ # Coordinates for missing rows
+ missing.ind <- vapply(loc.list, length, integer(1))[NA.col]
+ missing.ind <- rep(NA.row, missing.ind)
+ # Coordinates for missing columns
+ missing.loc <- unlist(loc.list[NA.col], use.names = FALSE)
+
+ missing_coordinates <- matrix(0L, nrow = length(missing.ind), ncol = 2L)
+ missing_coordinates[, 1] <- missing.ind
+ missing_coordinates[, 2] <- missing.loc
+
+ out[missing_coordinates] <- NA
+ }
+
+
+ ## call upon genind constructor
+ prevcall <- match.call()
+ out <- genind(tab=out, pop=pop, prevcall=prevcall, ploidy=ploidy, type=type,
+ strata = strata, hierarchy = hierarchy)
+
+ return(out)
+} # end df2genind
+
+
+
+
+
+
+
+########################################
+## Function read.genetix
+## code based on previous ade4 functions
+########################################
+#'
+#' Reading data from GENETIX
+#'
+#' The function \code{read.genetix} reads GENETIX data files (.gtx) and convert
+#' them into a \linkS4class{genind} object.
+#'
+#' Note: \code{read.genetix} is meant for DIPLOID DATA ONLY. Haploid data with
+#' the GENETIX format can be read into R using \code{read.table} or
+#' \code{read.csv} after removing headers and 'POP' lines, and then converted
+#' using \code{\link{df2genind}}.
+#'
+#' @param file a character string giving the path to the file to convert, with
+#' the appropriate extension.
+#' @param quiet logical stating whether a conversion message must be printed
+#' (TRUE,default) or not (FALSE).
+#' @return an object of the class \code{genind}
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{import2genind}}, \code{\link{df2genind}},
+#' \code{\link{read.fstat}}, \code{\link{read.structure}},
+#' \code{\link{read.genepop}}
+#' @references Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F.
+#' (1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la genetique des
+#' populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000,
+#' Universite de Montpellier II, Montpellier (France). \cr
+#' @keywords manip
+#' @examples
+#'
+#' obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"))
+#' obj
+#'
+#' @export read.genetix
+read.genetix <- function(file=NULL,quiet=FALSE) {
+ if(!quiet) cat("\n Converting data from GENETIX to a genind object... \n")
+
+
+ ## read from file
+ ## if(!file.exists(file)) stop("Specified file does not exist.") <- not needed
+
+ if(toupper(.readExt(file)) != "GTX") stop("File extension .gtx expected")
+ ## retrieve first infos
+ nloc <- as.integer(scan(file,nlines=1,what="character",quiet=TRUE)[1])
+ npop <- as.integer(scan(file,nlines=1,skip=1,what="character",quiet=TRUE)[1])
+ txt <- scan(file,skip=2,what="character",sep="\n",quiet=TRUE)
+ txt <- gsub("\t"," ",txt)
+ ## check that nloc is consistent with actual nloc (bug-report 1.2-2.02)
+ temp <- temp <- .rmspaces(txt[length(txt)])
+ nlocbis <- length(unlist(strsplit(temp, "[[:space:]]+")))-1
+ if(nloc != nlocbis) {
+ warning(paste("\n== Genetix file error == \n",
+ "Indicated number of locus (", nloc, ")\n",
+ "does not match actual number (", nlocbis, ").\n",
+ "Using ", nlocbis, " as number of locus.\n",
+ "Please check your file.", sep=""))
+ nloc <- nlocbis
+ }
+ loc.names <- txt[seq(1,by=2,length=nloc)]
+ txt <- txt[-(1:(nloc*2))]
+
+ ## retrieve populations infos
+ pop.names <- vector(mode="character",length=npop)
+ pop.nind <- vector(mode="integer",length=npop)
+ index <- 1
+ temp <- vector(mode="integer",length=npop)
+ for(i in 1:npop){
+ pop.names[i] <- txt[index]
+ pop.nind[i] <- as.numeric(txt[index+1])
+ temp[i] <- index
+ index <- index + pop.nind[i] + 2
+ }
+ pop.names <- .rmspaces(pop.names)
+
+ ## retrieve genotypes infos
+ txt <- txt[-c(temp,temp+1)]
+ txt <- .rmspaces(txt)
+ txt <- sapply(1:length(txt),function(i) unlist(strsplit(txt[i],"([[:space:]]+)|([[:blank:]]+)")) )
+ X <- t(txt)
+ if(ncol(X) == (nloc+1)){
+ rownames(X) <- X[,1]
+ X <- X[,-1]
+ } else{
+ rownames(X) <- 1:nrow(X)
+ }
+
+ colnames(X) <- loc.names
+
+ ## make a factor "pop" if there is more than one population
+ pop <- factor(rep(pop.names,pop.nind))
+
+ ## pass X to df2genind
+ res <- df2genind(X=X, ncode=3, pop=pop, ploidy=2, NA.char="000")
+ res at call <- match.call()
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+} # end read.genetix
+
+
+
+
+
+######################
+## Function read.fstat
+######################
+#' Reading data from Fstat
+#'
+#' The function \code{read.fstat} reads Fstat data files (.dat) and convert
+#' them into a \linkS4class{genind} object.
+#'
+#' Note: \code{read.fstat} is meant for DIPLOID DATA ONLY. Haploid data with
+#' the Hierfstat format can be read into R using \code{read.table} or
+#' \code{read.csv} after removing headers and 'POP' lines, and then converted
+#' using \code{\link{df2genind}}.
+#'
+#' @param file a character string giving the path to the file to convert, with
+#' the appropriate extension.
+#' @param quiet logical stating whether a conversion message must be printed
+#' (TRUE,default) or not (FALSE).
+#' @return an object of the class \code{genind}
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{import2genind}}, \code{\link{df2genind}},
+#' \code{\link{read.genetix}}, \code{\link{read.structure}},
+#' \code{\link{read.genepop}}
+#' @references Fstat (version 2.9.3). Software by Jerome Goudet.
+#' http://www2.unil.ch/popgen/softwares/fstat.htm\cr
+#' @keywords manip
+#' @examples
+#'
+#' obj <- read.fstat(system.file("files/nancycats.dat",package="adegenet"))
+#' obj
+#'
+#' @export read.fstat
+read.fstat <- function(file, quiet=FALSE){
+ ##if(!file.exists(file)) stop("Specified file does not exist.") <- not needed
+ if(toupper(.readExt(file)) != "DAT") stop("File extension .dat expected")
+
+ if(!quiet) cat("\n Converting data from a FSTAT .dat file to a genind object... \n\n")
+
+ call <- match.call()
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE)
+ txt <- gsub("\t"," ",txt)
+
+ ## read length of allele
+ ncode <- as.integer(unlist(strsplit(txt[1], " "))[4])
+ NA.char <- paste(rep("0",ncode),collapse="")
+
+ ## read first infos
+ info <- unlist(strsplit(txt[1],"([[:space:]]+)"))
+ ## npop <- as.numeric(info[1]) ## no longer used
+ nloc <- as.numeric(info[2])
+
+ loc.names <- txt[2:(nloc+1)]
+
+ ## build genotype matrix
+ txt <- txt[-(1:(nloc+1))]
+ txt <- .rmspaces(txt)
+ txt <- sapply(1:length(txt),function(i) unlist(strsplit(txt[i],"([[:space:]]+)|([[:blank:]]+)")) )
+ X <- t(txt)
+ pop <- factor(X[,1])
+ if(length(levels(pop)) == 1 ) pop <- NULL
+ X <- X[,-1]
+
+ colnames(X) <- loc.names
+ rownames(X) <- 1:nrow(X)
+
+ ## replace all possible missing data coding by NA.char
+ allNAs <- sapply(1:8, function(i) paste(rep("0",i),collapse=""))
+ X[X %in% allNAs] <- NA.char
+
+ ## call df2genind
+ res <- df2genind(X=X,pop=pop, ploidy=2, ncode=ncode, NA.char=NA.char)
+ res at call <- call
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+
+} # end read.fstat
+
+
+
+
+
+##########################
+## Function read.genepop
+##########################
+#' Reading data from Genepop
+#'
+#' The function \code{read.genepop} reads Genepop data files (.gen) and convert
+#' them into a \linkS4class{genind} object.
+#'
+#' Note: \code{read.genepop} is meant for DIPLOID DATA ONLY. Haploid data with
+#' the Genepop format can be read into R using \code{read.table} or
+#' \code{read.csv} after removing headers and 'POP' lines, and then converted
+#' using \code{\link{df2genind}}.
+#'
+#' @param file a character string giving the path to the file to convert, with
+#' the appropriate extension.
+#' @param ncode an integer indicating the number of characters used to code an allele.
+#' @param quiet logical stating whether a conversion message must be printed
+#' (TRUE,default) or not (FALSE).
+#' @return an object of the class \code{genind}
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{import2genind}}, \code{\link{df2genind}},
+#' \code{\link{read.fstat}}, \code{\link{read.structure}},
+#' \code{\link{read.genetix}}
+#' @references Raymond M. & Rousset F, (1995). GENEPOP (version 1.2):
+#' population genetics software for exact tests and ecumenicism. \emph{J.
+#' Heredity}, \bold{86}:248-249 \cr
+#' @keywords manip
+#' @examples
+#'
+#' obj <- read.genepop(system.file("files/nancycats.gen",package="adegenet"))
+#' obj
+#'
+#' @export read.genepop
+read.genepop <- function(file, ncode=2L, quiet=FALSE){
+ ## if(!file.exists(file)) stop("Specified file does not exist.") <- not needed
+ if(toupper(.readExt(file)) != "GEN") stop("File extension .gen expected")
+
+ if(!quiet) cat("\n Converting data from a Genepop .gen file to a genind object... \n\n")
+
+ prevcall <- match.call()
+
+ txt <- scan(file,sep="\n",what="character",quiet=TRUE)
+ if(!quiet) cat("\nFile description: ",txt[1], "\n")
+ txt <- txt[-1]
+ txt <- gsub("\t", " ", txt)
+ NA.char <- paste(rep("0",ncode), collapse="")
+
+ ## two cases for locus names:
+ ## 1) all on the same row, separated by ","
+ ## 2) one per row
+ ## ! spaces and tab allowed
+ ## a bug was reported by S. Devillard, occuring
+ ## when the two cases occur together,
+ ## that is:
+ ## loc1,
+ ## loc2,
+ ## ...
+
+
+ ## new strategy (shorter): isolate the 'locus names' part and then parse it.
+ locinfo.idx <- 1:(min(grep("POP",toupper(txt)))-1)
+ locinfo <- txt[locinfo.idx]
+ locinfo <- paste(locinfo,collapse=",")
+ loc.names <- unlist(strsplit(locinfo,"([,]|[\n])+"))
+ loc.names <- .rmspaces(loc.names)
+ nloc <- length(loc.names)
+ txt <- txt[-locinfo.idx]
+
+ ## locus names have been retreived
+
+ ## build the pop factor
+ ## and correct the genotypes splited on more than 1 line
+ pop.idx <- grep("^([[:space:]]*)POP([[:space:]]*)$",toupper(txt))
+ npop <- length(pop.idx)
+ ## correction for splited genotype
+ ## isolated by the absence of comma on a line not containing "pop"
+ nocomma <- which(! (1:length(txt)) %in% grep(",",txt))
+ splited <- nocomma[which(! nocomma %in% pop.idx)]
+ if(length(splited)>0){
+ for(i in sort(splited,decreasing=TRUE)){
+ txt[i-1] <- paste(txt[i-1],txt[i],sep=" ")
+ }
+ txt <- txt[-splited]
+ }
+ ## end correction
+
+ ## reevaluate pop index
+ pop.idx <- grep("^([[:space:]]*)POP([[:space:]]*)$",toupper(txt))
+
+ txt[length(txt)+1] <- "POP"
+ nind.bypop <- diff(grep("^([[:space:]]*)POP([[:space:]]*)$",toupper(txt)))-1
+ pop <- factor(rep(1:npop,nind.bypop))
+
+ txt <- txt[-c(pop.idx,length(txt))]
+
+ temp <- sapply(1:length(txt),function(i) strsplit(txt[i],","))
+ ## temp is a list with nind elements, first being ind. name and 2nd, genotype
+
+ ind.names <- sapply(temp,function(e) e[1])
+ ind.names <- .rmspaces(ind.names)
+ ## individuals' name are now clean
+
+ vec.genot <- sapply(temp,function(e) e[2])
+ vec.genot <- .rmspaces(vec.genot)
+
+ ## X is a individual x locus genotypes matrix
+ X <- matrix(unlist(strsplit(vec.genot,"[[:space:]]+")),ncol=nloc,byrow=TRUE)
+
+ # If there are any duplicate names, make them unique and issue a warning. Else
+ # use existing individual names.
+ if (any(duplicated(ind.names))) {
+ rownames(X) <- .genlab("", nrow(X))
+ warning("Duplicate individual names detected. Coercing them to be unique.")
+ } else {
+ rownames(X) <- ind.names
+ }
+ colnames(X) <- loc.names
+
+ ## give right pop names
+ ## beware: genepop takes the name of the last individual of a sample as this sample's name
+ pop.names.idx <- cumsum(table(pop))
+ pop.names <- ind.names[pop.names.idx]
+ levels(pop) <- pop.names
+
+ ## check that data are consistent with NCODE and ploidy=2
+ if(!all(unique(nchar(X))==(ncode*2))) stop(paste("some alleles are not encoded with", ncode,
+ "characters\nCheck 'ncode' argument"))
+
+ res <- df2genind(X=X,pop=pop, ploidy=2, ncode=ncode, NA.char=NA.char)
+ res at call <- prevcall
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+
+} # end read.genepop
+
+
+
+
+
+############################
+## Function read.structure
+############################
+#' Reading data from STRUCTURE
+#'
+#' The function \code{read.structure} reads STRUCTURE data files (.str ou
+#' .stru) and convert them into a \linkS4class{genind} object. By default, this
+#' function is interactive and asks a few questions about data content. This
+#' can be disabled (for optional questions) by turning the 'ask' argument to
+#' FALSE. However, one has to know the number of genotypes, of markers and if
+#' genotypes are coded on a single or on two rows before importing data.
+#'
+#' Note: \code{read.structure} is meant for DIPLOID DATA ONLY. Haploid data
+#' with the STRUCTURE format can easily be read into R using \code{read.table}
+#' or \code{read.csv} and then converted using \code{\link{df2genind}}.
+#'
+#' @param file a character string giving the path to the file to convert, with
+#' the appropriate extension.
+#' @param n.ind an integer giving the number of genotypes (or 'individuals') in
+#' the dataset
+#' @param n.loc an integer giving the number of markers in the dataset
+#' @param onerowperind a STRUCTURE coding option: are genotypes coded on a
+#' single row (TRUE), or on two rows (FALSE, default)
+#' @param col.lab an integer giving the index of the column containing labels
+#' of genotypes. '0' if absent.
+#' @param col.pop an integer giving the index of the column containing
+#' population to which genotypes belong. '0' if absent.
+#' @param col.others an vector of integers giving the indexes of the columns
+#' containing other informations to be read. Will be available in @@other of the
+#' created object.
+#' @param row.marknames an integer giving the index of the row containing the
+#' names of the markers. '0' if absent.
+#' @param NA.char the character string coding missing data. "-9" by default.
+#' Note that in any case, series of zero (like "000") are interpreted as NA
+#' too.
+#' @param pop an optional factor giving the population of each individual.
+#' @param sep a character string used as separator between alleles.
+#' @param ask a logical specifying if the function should ask for optional
+#' informations about the dataset (TRUE, default), or try to be as quiet as
+#' possible (FALSE).
+#' @param quiet logical stating whether a conversion message must be printed
+#' (TRUE,default) or not (FALSE).
+#' @return an object of the class \code{genind}
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{import2genind}}, \code{\link{df2genind}},
+#' \code{\link{read.fstat}}, \code{\link{read.genetix}},
+#' \code{\link{read.genepop}}
+#' @references Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of
+#' population structure using multilocus genotype data. \emph{Genetics},
+#' \bold{155}: 945-959
+#' @keywords manip
+#' @examples
+#'
+#' obj <- read.structure(system.file("files/nancycats.str",package="adegenet"),
+#' onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)
+#'
+#' obj
+#'
+#' @export read.structure
+read.structure <- function(file, n.ind=NULL, n.loc=NULL, onerowperind=NULL,
+ col.lab=NULL, col.pop=NULL, col.others=NULL,
+ row.marknames=NULL, NA.char="-9", pop=NULL,
+ sep=NULL, ask=TRUE, quiet=FALSE){
+
+ ## if(!file.exists(file)) stop("Specified file does not exist.") <- not needed
+ if(!toupper(.readExt(file)) %in% c("STR","STRU")) stop("File extension .stru expected")
+
+ ## set defaults for non optional arguments without default values
+ if(!ask){
+ if(is.null(col.lab)) col.lab <- as.integer(0)
+ if(is.null(col.pop)) col.pop <- as.integer(0)
+ if(is.null(row.marknames)) row.marknames <- as.integer(0)
+ }
+
+ ## required questions
+ if(is.null(n.ind)){
+ cat("\n How many genotypes are there? ")
+ n.ind <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(n.loc)){
+ cat("\n How many markers are there? ")
+ n.loc <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(col.lab)){
+ cat("\n Which column contains labels for genotypes ('0' if absent)? ")
+ col.lab <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(col.pop)){
+ cat("\n Which column contains the population factor ('0' if absent)? ")
+ col.pop <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(col.others) & ask){
+ cat("\n Which other optional columns should be read (press 'return' when done)? ")
+ col.others <- scan(quiet=TRUE)
+ if(length(col.others) == 0) col.others <- NULL
+ }
+
+ if(is.null(row.marknames)){
+ cat("\n Which row contains the marker names ('0' if absent)? ")
+ row.marknames <- as.integer(readLines(n = 1))
+ }
+
+ if(is.null(onerowperind)){
+ cat("\n Are genotypes coded by a single row (y/n)? ")
+ onerowperind <- toupper(readLines(n = 1))
+ if(onerowperind == "Y") {
+ onerowperind <- TRUE
+ } else {
+ onerowperind <- FALSE
+ }
+ }
+
+ if(is.null(NA.char)){
+ cat("\n What is the code for missing data (default is '-9')? ")
+ NA.char <- as.character(readLines(n = 1))
+ }
+
+ ## message to console
+ if(!quiet) cat("\n Converting data from a STRUCTURE .stru file to a genind object... \n\n")
+
+ ## read the file
+ txt <- scan(file,sep="\n",what="character",quiet=TRUE)
+
+ ## remove empty lines and spaces/tabs at the end of a line
+ temp <- grep("^[[:space:]]*$",txt)
+ if(length(temp) > 0) {
+ txt <- txt[-temp]
+ }
+
+ txt <- gsub("([[:blank:]]+)$","",txt)
+
+ ## isolate each useful component of the file
+ ## matrix of data
+ if(onerowperind) {
+ n <- n.ind
+ p <- 2*n.loc
+ } else{
+ n <- 2*n.ind
+ p <- n.loc
+ }
+
+ lastline <- length(txt)
+ mat <- txt[(lastline-n+1):lastline]
+ mat <- t(as.data.frame(strsplit(mat,"[[:blank:]]+")))
+ rownames(mat) <- 1:n
+ gen <- mat[, (ncol(mat)-p+1):ncol(mat)]
+
+
+ ## markers names
+ if(row.marknames != 0) {
+ loc.names <- .rmspaces(txt[row.marknames])
+ loc.names <- unlist(strsplit(loc.names,"[[:blank:]]+"))
+ } else {
+ loc.names <- .genlab("L",n.loc)
+ }
+
+ ## genotypes labels
+ if(col.lab !=0) {
+ ind.names <- mat[, col.lab]
+ } else {
+ ind.names <- .genlab("",n.ind)
+ }
+
+ ## population factor
+ if(col.pop !=0) {
+ pop <- factor(mat[, col.pop])
+ } else {
+ pop <- NULL
+ }
+
+ ## other variables
+ if(!is.null(col.others)){
+ X.other <- mat[,col.others]
+ }
+
+ ## transformations if onerowperind is FALSE
+ if(!onerowperind) {
+ temp <- seq(1,n,by=2)
+ ind.names <- ind.names[temp]
+ if(length(ind.names) < n.ind) warning("Duplicated identifier for genotypes")
+ pop <- pop[temp]
+ if(exists("X.other")) X.other <- X.other[temp]
+
+ ## make sur that all strings in gen have the same number of characters
+ ncode <- max(nchar(gen))
+ keepCheck <- any(nchar(gen) < ncode)
+
+ while(keepCheck){
+ mat0 <- matrix("", ncol=ncol(gen), nrow=nrow(gen))
+ mat0[nchar(gen) < ncode] <- "0"
+ gen <- matrix(paste(mat0, gen, sep=""), nrow=nrow(mat0))
+ keepCheck <- any(nchar(gen) < ncode)
+ }
+
+ ## reorder matrix of genotypes
+ X <- t(sapply(temp, function(i) paste(gen[i,],gen[i+1,],sep="") ))
+
+ } else { # if onerowperind
+ temp <- seq(1,p-1,by=2)
+ X <- paste(gen[,temp] , gen[,temp+1], sep="/")
+ X <- matrix(X, nrow=n.ind)
+ sep <- "/"
+ }
+
+ ## replace missing values by NAs
+ X <- gsub(NA.char,NA,X)
+ rownames(X) <- ind.names
+ colnames(X) <- loc.names
+
+ res <- df2genind(X=X,pop=pop, ploidy=2,sep=sep,ncode=ncode)
+
+ res at call <- match.call()
+
+ if(exists("X.other")) {res at other <- list(X=X.other)}
+
+ return(res)
+
+}
+
+
+
+
+#########################
+## Function import2genind
+#########################
+#'
+#' Importing data from several softwares to a genind object
+#'
+#' Their are several ways to import genotype data to a \linkS4class{genind}
+#' object: i) from a data.frame with a given format (see
+#' \code{\link{df2genind}}), ii) from a file with a recognized extension, or
+#' iii) from an alignement of sequences (see \code{\link{DNAbin2genind}}).\cr
+#'
+#' The function \code{import2genind} detects the extension of the file given in
+#' argument and seeks for an appropriate import function to create a
+#' \code{genind} object.\cr Current recognized formats are :\cr - GENETIX files
+#' (.gtx) \cr - Genepop files (.gen) \cr - Fstat files (.dat) \cr - STRUCTURE
+#' files (.str or .stru) \cr
+#'
+#' Beware: same data in different formats are not expected to produce exactly
+#' the same \code{genind} objects.\cr For instance, conversions made by GENETIX
+#' to Fstat may change the the sorting of the genotypes; GENETIX stores
+#' individual names whereas Fstat does not; Genepop chooses a sample's name
+#' from the name of its last genotype; etc.
+#'
+#' @aliases import2genind
+#' @param file a character string giving the path to the file to convert, with
+#' the appropriate extension.
+#' @param quiet logical stating whether a conversion message must be printed
+#' (TRUE,default) or not (FALSE).
+#' @param \dots other arguments passed to the appropriate 'read' function
+#' (currently passed to \code{read.structure})
+#' @return an object of the class \code{genind}
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{import2genind}}, \code{\link{read.genetix}},
+#' \code{\link{read.fstat}}, \code{\link{read.structure}},
+#' \code{\link{read.genepop}}
+#' @references Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F.
+#' (1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la genetique des
+#' populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000,
+#' Universite de Montpellier II, Montpellier (France). \cr
+#'
+#' Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of population
+#' structure using multilocus genotype data. \emph{Genetics}, \bold{155}:
+#' 945-959
+#'
+#' Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population genetics
+#' software for exact tests and ecumenicism. \emph{J. Heredity},
+#' \bold{86}:248-249 \cr
+#'
+#' Fstat (version 2.9.3). Software by Jerome Goudet.
+#' http://www2.unil.ch/popgen/softwares/fstat.htm\cr
+#'
+#' Excoffier L. & Heckel G.(2006) Computer programs for population genetics
+#' data analysis: a survival guide \emph{Nature}, \bold{7}: 745-758
+#' @keywords manip
+#' @examples
+#'
+#' import2genind(system.file("files/nancycats.gtx",
+#' package="adegenet"))
+#'
+#' import2genind(system.file("files/nancycats.dat",
+#' package="adegenet"))
+#'
+#' import2genind(system.file("files/nancycats.gen",
+#' package="adegenet"))
+#'
+#' import2genind(system.file("files/nancycats.str",
+#' package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)
+#'
+import2genind <- function(file, quiet=FALSE, ...){
+ ## if(!file.exists(file)) stop("Specified file does not exist.") <- not needed
+ ext <- .readExt(file)
+ ext <- toupper(ext)
+
+ if(ext == "GTX")
+ return(read.genetix(file,quiet=quiet))
+
+ if(ext == "DAT")
+ return(read.fstat(file, quiet=quiet))
+
+ if(ext == "GEN")
+ return(read.genepop(file, quiet=quiet, ...))
+
+ if(ext %in% c("STR","STRU"))
+ return(read.structure(file, quiet=quiet, ...))
+
+ ## evaluated only if extension is not supported
+ cat("\n File format (",ext,") not supported.\n")
+ cat("\nSupported formats are:\nGENETIX (.gtx) \nFSTAT (.dat) \nGenepop (.gen)\n \nSTRUCTURE (.str)\n")
+
+ return(invisible())
+}
+
+
+
+
+
+
+
+#######################
+## Function read.snp
+#######################
+#' Reading Single Nucleotide Polymorphism data
+#'
+#' The function \code{read.snp} reads a SNP data file with extension '.snp' and
+#' converts it into a \linkS4class{genlight} object. This format is devoted to
+#' handle biallelic SNP only, but can accommodate massive datasets such as
+#' complete genomes with considerably less memory than other formats.
+#'
+#' The function reads data by chunks of a few genomes (minimum 1, no maximum)
+#' at a time, which allows one to read massive datasets with negligible RAM
+#' requirements (albeit at a cost of computational time). The argument
+#' \code{chunkSize} indicates the number of genomes read at a time. Increasing
+#' this value decreases the computational time required to read data in, while
+#' increasing memory requirements.
+#'
+#' A description of the .snp format is provided in an example file distributed
+#' with adegenet (see example below).
+#'
+#' === The .snp format ===
+#'
+#' Details of the .snp format can be found in the example file distributed with
+#' adegenet (see below), or on the adegenet website (type \code{adegenetWeb()}
+#' in R).
+#'
+#' @param file a character string giving the path to the file to convert, with
+#' the extension ".snp".
+#' @param quiet logical stating whether a conversion messages should be printed
+#' (TRUE,default) or not (FALSE).
+#' @param chunkSize an integer indicating the number of genomes to be read at a
+#' time; larger values require more RAM but decrease the time needed to read
+#' the data.
+#' @param parallel a logical indicating whether multiple cores -if available-
+#' should be used for the computations (TRUE, default), or not (FALSE);
+#' requires the package \code{parallel} to be installed (see details).
+#' @param n.cores if \code{parallel} is TRUE, the number of cores to be used in
+#' the computations; if NULL, then the maximum number of cores available on the
+#' computer is used.
+#' @param \dots other arguments to be passed to other functions - currently not
+#' used.
+#' @return an object of the class \code{"\linkS4class{genlight}"}
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso - \code{?genlight} for a description of the class
+#' \code{"\linkS4class{genlight}"}.
+#'
+#' - \code{\link{read.PLINK}}: read SNPs in PLINK's '.raw' format.
+#'
+#' - \code{\link{fasta2genlight}}: extract SNPs from alignments with fasta
+#' format.
+#'
+#' - \code{\link{df2genind}}: convert any multiallelic markers into adegenet
+#' \code{"\linkS4class{genlight}"}.
+#'
+#' - \code{\link{import2genind}}: read multiallelic markers from various
+#' software into adegenet.\cr
+#' @keywords manip
+#' @examples
+#'
+#' \dontrun{
+#' ## show the example file ##
+#' ## this is the path to the file:
+#' system.file("files/exampleSnpDat.snp",package="adegenet")
+#'
+#' ## show its content:
+#' file.show(system.file("files/exampleSnpDat.snp",package="adegenet"))
+#'
+#'
+#' ## read the file
+#' obj <-
+#' read.snp(system.file("files/exampleSnpDat.snp",package="adegenet"), chunk=2)
+#' obj
+#' as.matrix(obj)
+#' ploidy(obj)
+#' alleles(obj)
+#' locNames(obj)
+#' }
+#'
+#' @export read.snp
+#'
+read.snp <- function(file, quiet=FALSE, chunkSize=1000,
+ parallel=require("parallel"), n.cores=NULL, ...){
+ ext <- .readExt(file)
+ ext <- toupper(ext)
+ if(ext != "SNP") warning("wrong file extension - '.snp' expected")
+ if(!quiet) cat("\n Reading biallelic SNP data file into a genlight object... \n\n")
+ ## if(parallel && !require(parallel)) stop("parallel package requested but not installed")
+ if(parallel && is.null(n.cores)){
+ n.cores <- parallel::detectCores()
+ }
+
+ call <- match.call()
+
+ ## HANDLE THE COMMENTS ##
+ if(!quiet) cat("\n Reading comments... \n")
+
+ count <- 0L
+ i <- 0
+ while(count < 2L){
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=i, nmax=1, blank.lines.skip=FALSE)
+ if(length(grep(">>>>", txt)>0)){
+ count <- count + 1L
+ }
+ i <- i+1
+ if(count==0L && i>10){
+ warning("No comment section at the beginning of the file. Format may be wrong.")
+ i <- 0
+ break
+ }
+ }
+
+ lines.to.skip <- i
+
+
+ ## READ GENERAL DATA (>>) ##
+ if(!quiet) cat("\n Reading general information... \n")
+
+ misc.info <- list()
+
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=1)
+
+ while(length(grep(">>", txt))>0){
+ itemName <- gsub(">>","", txt)
+ itemName <- gsub("(^[[:space:]]+)|([[:space:]]+$)", "", itemName)
+ misc.info[itemName] <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip + 1, nmax=1)
+ lines.to.skip <-lines.to.skip + 2
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=1)
+ }
+
+ ## transform each character string into a vector
+ misc.info <- sapply(misc.info, function(e) unlist(strsplit(e,"[[:space:]]+")))
+
+ ## READ GENOTYPE DATA ##
+ ## one genotype is read/converted at a time to spare RAM
+ if(!quiet) cat("\n Reading",ifelse(is.null(misc.info$population),"",length(misc.info$population)), "genotypes... \n")
+
+
+ res <- list() # this will be a list of SNPbin objects
+
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=chunkSize*2)
+
+ ID.INDIV <- grep(">", txt)
+
+ COUNT <- 0 # used to count the nb reads
+
+ while(length(ID.INDIV)>0){
+ COUNT <- COUNT + 1
+ if(!quiet) {
+ if(COUNT %% 5 == 0){
+ cat(length(res)+length(ID.INDIV))
+ } else {
+ cat(".")
+ }
+ }
+
+ ind.lab <- gsub(">","", txt[ID.INDIV])
+ ind.lab <- gsub("(^[[:space:]]+)|([[:space:]]+$)", "", ind.lab)
+ temp <- strsplit(txt[ID.INDIV+1], "")
+ temp <- lapply(temp, function(e) suppressWarnings(as.integer(e)))
+ if(parallel){
+ res <- c(res, mclapply(temp, function(e) new("SNPbin", e),
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE) )
+ } else {
+ res <- c(res, lapply(temp, function(e) new("SNPbin", e)) )
+ }
+ names(res)[(length(res)-length(ID.INDIV)+1):length(res)] <- ind.lab
+ lines.to.skip <-lines.to.skip + length(txt)
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=chunkSize*2)
+ ID.INDIV <- grep(">", txt)
+ }
+
+
+ ## CHECK CONSISTENCY ##
+ if(!quiet) cat("\n Checking consistency... \n")
+
+ n.loc <- unique(sapply(res, nLoc))
+ n.ind <- length(res)
+ other <- list()
+
+ if(length(n.loc)>1) {
+ print(n.loc)
+ warning("!!! Differing numbers of loci detected between individuals !!!")
+ }
+
+ if(!is.null(misc.info$position) && length(misc.info$position)!=n.loc) {
+ other$position <- misc.info$position
+ misc.info$position <- NULL
+ warning("vector of positions of the SNPs does not match the number of SNPs - storing this information in @other")
+ }
+ if(!is.null(misc.info$allele) && length(misc.info$allele)!=n.loc) {
+ other$allele <- misc.info$allele
+ misc.info$allele <- NULL
+ warning("vector of alleles of the SNPs does not match the number of SNPs - storing this information in @other")
+ }
+ if(!is.null(misc.info$chromosome) && length(misc.info$chromosome)!=n.loc) {
+ other$chromosome <- misc.info$chromosome
+ misc.info$chromosome <- NULL
+ warning("vector of chromosomes of the SNPs does not match the number of SNPs - storing this information in @other")
+ }
+ if(!is.null(misc.info$population) && length(misc.info$population)!=n.ind) {
+ other$population <- misc.info$population
+ misc.info$population <- NULL
+ warning("vector of population of the individuals does not match the number of individuals - storing this information in @other")
+ }
+ if(!is.null(misc.info$ploidy) && length(misc.info$ploidy)>1 && length(misc.info$ploidy)!=n.ind) {
+ other$ploidy <- misc.info$ploidy
+ misc.info$ploidy <- NULL
+ warning("vector of ploidy of the individuals has more than one value but does not match the number of individuals - storing this information in @other")
+ }
+
+
+ ## BUILD OUTPUT ##
+ if(!quiet) cat("\n Building final object... \n")
+
+ ind.names <- names(res)
+ if(!is.null(misc.info$chromosome)){
+ other <- list(chromosome = misc.info$chromosome)
+ }
+
+ res <- new("genlight", gen=res, ind.names=ind.names, position=misc.info$position, loc.all=misc.info$allele, ploidy=misc.info$ploidy, pop=misc.info$population, other=other, parallel=parallel)
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+
+} # end read.snp
+
+
+
+
+
+
+
+####################
+## extract.PLINKmap
+####################
+#' @export
+#' @rdname read.PLINK
+#' @aliases extract.PLINKmap
+#'
+#' @param x an optional object of the class \code{"\linkS4class{genlight}"}, in which
+#' the information read is stored; if provided, information is matched against
+#' the names of the loci in \code{x}, as returned by \code{locNames(x)}; if not
+#' provided, a list of two components is returned, containing chromosome and
+#' position information.
+#'
+extract.PLINKmap <- function(file, x=NULL){
+ ## CHECK EXTENSION ##
+ ext <- .readExt(file)
+ ext <- toupper(ext)
+ if(ext != "MAP") warning("wrong map.file extension - '.map' expected")
+
+
+ ## READ FILE ##
+ ## find nb of columns
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, nlines=1)
+ nb.col <- length( unlist(strsplit(txt,"[[:blank:]]+")))
+
+ ## read file
+ txt <- scan(file,what="character",sep="\t",quiet=TRUE)
+ txt <- matrix(txt, ncol=4, byrow=TRUE)
+
+
+ ## EXTRACT INFO AND RETURN OBJECT ##
+ ## return a genlight
+ if(!is.null(x)){
+ ## match data
+ ord <- match(locNames(x), txt[,2]) # check that it is the 2nd column
+ if(!inherits(x, "genlight")) stop("x is not a genlight object")
+ other(x)$chromosome <- factor(txt[ord,1])
+ other(x)$position <- as.integer(txt[ord,4])
+
+ return(x)
+ }
+
+ ## return a list
+ res <- list(chromosome=factor(txt[ord,1]), position=as.integer(txt[ord,4]))
+
+ return(res)
+} # end extract.PLINKmap
+
+
+
+
+
+
+
+########################
+## Function read.PLINK
+########################
+#' Reading PLINK Single Nucleotide Polymorphism data
+#'
+#' The function \code{read.PLINK} reads a data file exported by the PLINK
+#' software with extension '.raw' and converts it into a \code{"\linkS4class{genlight}"}
+#' object. Optionally, information about SNPs can be read from a ".map" file,
+#' either by specifying the argument \code{map.file} in \code{read.PLINK}, or
+#' using \code{extract.PLINKmap} to add information to an existing
+#' \code{"\linkS4class{genlight}"} object.
+#'
+#' The function reads data by chunks of several genomes (minimum 1, no maximum)
+#' at a time, which allows one to read massive datasets with negligible RAM
+#' requirements (albeit at a cost of computational time). The argument
+#' \code{chunkSize} indicates the number of genomes read at a time. Increasing
+#' this value decreases the computational time required to read data in, while
+#' increasing memory requirements.
+#'
+#' See details for the documentation about how to export data using PLINK to
+#' the '.raw' format.
+#'
+#' === Exporting data from PLINK ===
+#'
+#' Data need to be exported from PLINK using the option "--recodeA" (and NOT
+#' "--recodeAD"). The PLINK command should therefore look like: \code{plink
+#' --file data --recodeA}. For more information on this topic, please look at
+#' this webpage: \url{http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml}
+#'
+#' @aliases read.PLINK read.plink
+#' @param file for \code{read.PLINK} a character string giving the path to the
+#' file to convert, with the extension ".raw"; for \code{extract.PLINKmap}, a
+#' character string giving the path to a file with extension ".map".
+#' @param map.file an optional character string indicating the path to a ".map"
+#' file, which contains information about the SNPs (chromosome, position). If
+#' provided, this information is processed by \code{extract.PLINKmap} and
+#' stored in the \code{@@other} slot.
+#' @param quiet logical stating whether a conversion messages should be printed
+#' (TRUE,default) or not (FALSE).
+#' @param chunkSize an integer indicating the number of genomes to be read at a
+#' time; larger values require more RAM but decrease the time needed to read
+#' the data.
+#' @param parallel a logical indicating whether multiple cores -if available-
+#' should be used for the computations (TRUE, default), or not (FALSE);
+#' requires the package \code{parallel} to be installed (see details).
+#' @param n.cores if \code{parallel} is TRUE, the number of cores to be used in
+#' the computations; if NULL, then the maximum number of cores available on the
+#' computer is used.
+#' @param \dots other arguments to be passed to other functions - currently not
+#' used.
+#'
+#' @return - read.PLINK: an object of the class \code{"\linkS4class{genlight}"}
+#'
+#' - extract.PLINKmap: if a \code{"\linkS4class{genlight}"} is provided as argument
+#' \code{x}, this object incorporating the new information about SNPs in the
+#' \code{@@other} slot (with new components 'chromosome' and 'position');
+#' otherwise, a list with two components containing chromosome and position
+#' information.
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso - \code{?genlight} for a description of the class
+#' \code{"\linkS4class{genlight}"}.
+#'
+#' - \code{\link{read.snp}}: read SNPs in adegenet's '.snp' format.
+#'
+#' - \code{\link{fasta2genlight}}: extract SNPs from alignments with fasta
+#' format.
+#'
+#' - other import function in adegenet: \code{\link{import2genind}},
+#' \code{\link{df2genind}}, \code{\link{read.genetix}}
+#' \code{\link{read.fstat}}, \code{\link{read.structure}},
+#' \code{\link{read.genepop}}.
+#'
+#' - another function \code{read.plink} is available in the package
+#' \code{snpMatrix}.
+#' @keywords manip
+#' @export
+#' @rdname read.PLINK
+read.PLINK <- function(file, map.file=NULL, quiet=FALSE, chunkSize=1000,
+ parallel=require("parallel"), n.cores=NULL, ...){
+ ## HANDLE ARGUMENTS ##
+ ext <- .readExt(file)
+ ext <- toupper(ext)
+ if(ext != "RAW") warning("wrong file extension - '.raw' expected")
+ if(!quiet) cat("\n Reading PLINK raw format into a genlight object... \n\n")
+ ## if(parallel && !require(parallel)) stop("parallel package requested but not installed")
+ if(parallel && is.null(n.cores)){
+ n.cores <- parallel::detectCores()
+ }
+
+
+ ## READ NAMES OF LOCI ##
+ if(!quiet) cat("\n Reading loci information... \n")
+
+ loc.names <- scan(file,what="character",sep=" ",quiet=TRUE, nlines=1, blank.lines.skip=FALSE)
+ n.loc <- length(loc.names) - 6
+ misc.info <- lapply(1:6,function(i) NULL)
+ names(misc.info) <- loc.names[1:6]
+ loc.names <- loc.names[7:length(loc.names)]
+ loc.names <- gsub("_[1-9]$","",loc.names)
+
+ ## READ GENOTYPES ##
+ if(!quiet) cat("\n Reading and converting genotypes... \n")
+
+ res <- list() # this will be a list of SNPbin objects
+
+ ## initialize reading
+ lines.to.skip <- 1
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=chunkSize)
+ txt <- lapply(txt, function(e) unlist(strsplit(e,"[[:blank:]]+") ))
+
+ COUNT <- 0 # used to count the nb reads
+
+ while(length(txt)>0){
+ COUNT <- COUNT + 1
+ if(!quiet) {
+ if(COUNT %% 5 == 0){
+ cat(length(res)+length(txt))
+ } else {
+ cat(".")
+ }
+ }
+
+
+ ## handle misc info
+ temp <- lapply(txt, function(e) e[1:6])
+ for(i in 1:6){
+ misc.info[[i]] <- c(misc.info[[i]], unlist(lapply(temp, function(e) e[[i]])) )
+ }
+
+
+ ## build SNPbin objects
+ txt <- lapply(txt, function(e) suppressWarnings(as.integer(e[-(1:6)])))
+
+ if(parallel){
+ res <- c(res, mclapply(txt, function(e) new("SNPbin", snp=e, ploidy=2L),
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE) )
+ } else {
+ res <- c(res, lapply(txt, function(e) new("SNPbin", snp=e, ploidy=2L)) )
+ }
+
+ lines.to.skip <-lines.to.skip + length(txt)
+
+ ## read lines
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=chunkSize)
+ txt <- lapply(txt, function(e) unlist(strsplit(e,"[[:blank:]]+") ))
+ }
+
+
+ ## MAKE A FEW CHECKS ##
+ if(!all(sapply(res, nLoc)==n.loc)) stop(paste("some individuals do not have",n.loc,"SNPs."))
+
+
+ ## BUILD FINAL OBJECT ##
+ if(!quiet) cat("\n Building final object... \n")
+
+ res <- new("genlight",res, ploidy=2L, parallel=parallel)
+ indNames(res) <- misc.info$IID
+ pop(res) <- misc.info$FID
+ locNames(res) <- loc.names
+ misc.info <- misc.info[c("SEX", "PHENOTYPE", "PAT","MAT")]
+ names(misc.info) <- tolower(names(misc.info))
+ misc.info$sex[misc.info$sex==1] <- "m"
+ misc.info$sex[misc.info$sex==2] <- "f"
+ misc.info$sex <- factor(misc.info$sex)
+ misc.info$phenotype[misc.info$phenotype==1] <- "control"
+ misc.info$phenotype[misc.info$phenotype==2] <- "case"
+ misc.info$phenotype <- factor(misc.info$phenotype)
+ other(res) <- misc.info
+
+
+ ## HANDLE MAP FILE INFO ##
+ if(!is.null(map.file)){
+ res <- extract.PLINKmap(map.file, res)
+ }
+
+
+ ## RETURN OUTPUT ##
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+} # end read.PLINK
+
+
+
+
+
+
+
+###########################
+## Function fasta2genlight
+###########################
+fasta2genlight <- function(file, quiet=FALSE, chunkSize=1000, saveNbAlleles=FALSE,
+ parallel=require("parallel"), n.cores=NULL, ...){
+ ## HANDLE ARGUMENTS ##
+ ext <- .readExt(file)
+ ext <- toupper(ext)
+ if(!ext %in% c("FASTA", "FA", "FAS")) warning("wrong file extension - '.fasta', '.fa' or '.fas' expected")
+ if(!quiet) cat("\n Converting FASTA alignment into a genlight object... \n\n")
+ ## if(parallel && !require(parallel)) stop("parallel package requested but not installed")
+ if(parallel && is.null(n.cores)){
+ n.cores <- parallel::detectCores()
+ }
+
+
+ ## PRIOR CHECKS ##
+ ## find nb of lines per genome
+ lines.to.skip <- 0
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, nmax=1)
+
+ while(length(grep("^>.+", txt))<2){
+ lines.to.skip <- lines.to.skip + 1
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, nmax=lines.to.skip)
+ }
+
+ LINES.PER.IND <- lines.to.skip-1
+
+
+ ## find length of a genome
+ NLOC <- sum(nchar(txt[2:LINES.PER.IND]))
+
+
+ ## SCAN ALL POSITIONS AND IDENTIFY SNPs ##
+ if(!quiet) cat("\n Looking for polymorphic positions... \n")
+
+ ## read all genomes by chunks
+ ## initialize
+ lines.to.skip <- 0
+ IND.LAB <- NULL
+ POOL <- as.list(rep("-", NLOC))
+ COUNT <- 0 # used to count the nb reads
+
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=LINES.PER.IND*chunkSize)
+
+ ## read and process chunks
+ while(length(txt)>0){
+ COUNT <- COUNT + 1
+ if(!quiet) {
+ for(i in 1:(COUNT*chunkSize)) cat(".")
+ }
+
+
+ nb.ind <- length(grep("^>", txt))
+ IND.LAB <- c(IND.LAB, sub(">","",txt[grep("^>", txt)])) # find individuals' labels
+ txt <- split(txt, rep(1:nb.ind, each=LINES.PER.IND)) # split per individuals
+ if(parallel){
+ txt <- mclapply(txt, function(e) strsplit(paste(e[-1], collapse=""), split=""),
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE) # each genome -> one vector
+ } else {
+ txt <- lapply(txt, function(e) strsplit(paste(e[-1], collapse=""), split="")) # each genome -> one vector
+ }
+
+ ## POOL contains all alleles of each position
+ temp <- as.list(apply(matrix(unlist(txt), byrow=TRUE, nrow=length(txt)),2,unique)) # alleles current genomes
+ POOL <- mapply(function(x,y) unique(c(x,y)), POOL, temp, SIMPLIFY=FALSE) # update global pool
+
+ lines.to.skip <- lines.to.skip + nb.ind*LINES.PER.IND
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=LINES.PER.IND*chunkSize)
+ }
+
+
+ ## analyse pool of alleles
+ letterOK <- c("a","g","c","t","A","G","C","T")
+ POOL <- lapply(POOL, function(e) e[e %in% letterOK]) # keep only proper letters
+ ## POOL <- lapply(POOL, setdiff, "-")
+ nb.alleles <- sapply(POOL, length)
+ snp.posi <- nb.alleles==2
+ if(all(!snp.posi)){
+ warning("No polymorphism in the alignment - returning empty object")
+ return(new("genlight"))
+ }
+ sec.all <- unlist(lapply(POOL[snp.posi], function(e) e[2]))
+
+
+
+ ## RE-READ DATA, CONVERT SNPs TO GENLIGHT ##
+ if(!quiet) cat("\n Extracting SNPs from the alignment... \n")
+
+ ## initialize
+ lines.to.skip <- 0
+ COUNT <- 0 # used to count the nb reads
+ res <- list()
+
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=LINES.PER.IND*chunkSize)
+
+ ## returns a vector of nb of second alleles or NAs
+ f1 <- function(vec){
+ out <- as.integer(vec==sec.all)
+ out[!vec %in% letterOK] <- NA
+ return(out)
+ }
+
+ ## read and process chunks
+ while(length(txt)>0){
+ COUNT <- COUNT + 1
+ if(!quiet) {
+ for(i in 1:(COUNT*chunkSize)) cat(".")
+ }
+
+
+ ## read SNPs
+ nb.ind <- length(grep("^>", txt))
+ txt <- split(txt, rep(1:nb.ind, each=LINES.PER.IND)) # split per individuals
+ if(parallel){
+ txt <- mclapply(txt, function(e) strsplit(paste(e[-1], collapse=""), split="")[[1]][snp.posi],
+ mc.cores=n.cores, mc.silent=TRUE, mc.cleanup=TRUE, mc.preschedule=FALSE) # each genome -> one SNP vector
+ } else {
+ txt <- lapply(txt, function(e) strsplit(paste(e[-1], collapse=""), split="")[[1]][snp.posi]) # each genome -> one SNP vector
+ }
+
+ ## convert to genlight
+ ##res <- c(res, lapply(txt, function(e) new("SNPbin", as.integer(e==sec.all))))
+ res <- c(res, lapply(txt, function(e) new("SNPbin", f1(e))))
+
+ lines.to.skip <- lines.to.skip + nb.ind*LINES.PER.IND
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, nmax=LINES.PER.IND*chunkSize)
+ }
+
+
+
+ ## BUILD FINAL OBJECT ##
+ if(!quiet) cat("\n Building final object... \n")
+
+ res <- new("genlight",res, ploidy=1, parallel=parallel)
+ indNames(res) <- IND.LAB
+ alleles(res) <- sapply(POOL[snp.posi], paste, collapse="/")
+ position(res) <- which(snp.posi)
+ if(saveNbAlleles) other(res) <- list(nb.all.per.loc=nb.alleles)
+
+
+ ## RETURN OUTPUT ##
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+} # end fasta2genlight
+
+
+
+
+
+
+
+
+###########################
+## Function fasta2DNAbin
+###########################
+fasta2DNAbin <- function(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE){
+
+ ## HANDLE ARGUMENTS ##
+ ext <- .readExt(file)
+ ext <- toupper(ext)
+ if(!ext %in% c("FASTA", "FA", "FAS")) warning("wrong file extension - '.fasta', '.fa' or '.fas' expected")
+ if(!quiet) cat("\n Converting FASTA alignment into a DNAbin object... \n\n")
+
+
+ ## PRIOR CHECKS ##
+ ## find nb of lines per genome ##
+
+ ## find length of a single line of sequence
+ if(!quiet) cat("\n Finding the size of a single genome... \n\n")
+ lines.to.skip <- 0
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, nmax=1)
+
+ while(length(grep("^>.+", txt))==1){
+ lines.to.skip <- lines.to.skip + 1
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, n=1)
+ }
+
+ char.per.line <- nchar(txt)
+ nbOfLinesToRead <- max(round(1e6/char.per.line),1)#
+
+ ## read file to find genome size, 1e6 characters at a time
+ nblocks <- 1
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, n=nbOfLinesToRead*nblocks)
+
+ while(length(grep("^>.+", txt))<2){
+ nblocks <- nblocks+1
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, n=nbOfLinesToRead*nblocks)
+ }
+
+ ## this is the nb of lines for one genome
+ ## including the first line of annotation
+ LINES.PER.IND <- diff(grep("^>.+", txt))[1]
+
+ ## this is the length of a genome single
+ GENOMESIZE <- sum(nchar(txt[2:LINES.PER.IND]))
+ if(!quiet) cat("\n genome size is:", format(GENOMESIZE, big.mark=","), "nucleotides \n")
+ if(!quiet) cat("\n(",format(LINES.PER.IND, big.mark=","), " lines per genome )\n")
+
+
+ ## START READING / CONVERTING GENOMES ##
+ if(!quiet) cat("\n Importing sequences... \n")
+
+ ## read all genomes by chunks
+ ## initialize
+ lines.to.skip <- 0
+ IND.LAB <- NULL
+ COUNT <- 0 # used to count the nb reads
+
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, n=LINES.PER.IND*chunkSize)
+ res <- raw()
+
+ ## read and process chunks
+ while(length(txt)>0){
+ ## clean memory ##
+ invisible(gc())
+
+ ## progression... ##
+ COUNT <- COUNT + 1
+ if(!quiet) {
+ for(i in 1:(COUNT*chunkSize)) cat(".")
+ }
+
+ ## process txt ##
+ nb.ind <- length(grep("^>", txt))
+ IND.LAB <- c(IND.LAB, sub(">","",txt[grep("^>", txt)])) # find individuals' labels
+ txt <- split(txt, rep(1:nb.ind, each=LINES.PER.IND)) # split per individuals
+ txt <- lapply(txt, function(e) unlist(strsplit(tolower(paste(e[-1], collapse="")), split=""))) # each genome -> one vector
+
+ ## convert character vectors to DNAbin output
+ res <- c(res, unlist(lapply(txt, as.DNAbin)))
+
+ ## ## POOL contains all alleles of each position
+ ## temp <- as.list(apply(matrix(unlist(txt), byrow=TRUE, nrow=length(txt)),2,unique)) # alleles current genomes
+ ## POOL <- mapply(function(x,y) unique(c(x,y)), POOL, temp, SIMPLIFY=FALSE) # update global pool
+
+ ## scan file further ##
+ lines.to.skip <- lines.to.skip + nb.ind*LINES.PER.IND
+ txt <- scan(file,what="character",sep="\n",quiet=TRUE, skip=lines.to.skip, n=LINES.PER.IND*chunkSize)
+ }
+
+ ## GET FINAL OBJECT ##
+ if(!quiet) cat("\n Forming final object... \n")
+
+ ## form matrix ##
+ res <- matrix(res, nrow=length(IND.LAB), byrow=TRUE)
+ class(res) <- "DNAbin"
+ rownames(res) <- IND.LAB
+
+ ## extract snps if needed ##
+ if(snpOnly){
+ if(!quiet) cat("\n Extracting SNPs... \n")
+ snp.posi <- seg.sites(res)
+ if(length(snp.posi)==0) warning("no polymorphic site in the sequences")
+ res <- res[,seg.sites(res),drop=FALSE]
+ colnames(res) <- snp.posi
+ }
+
+ ## RETURN OUTPUT ##
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(res)
+} # end fasta2DNAbin
diff --git a/R/inbreeding.R b/R/inbreeding.R
new file mode 100644
index 0000000..ee97954
--- /dev/null
+++ b/R/inbreeding.R
@@ -0,0 +1,122 @@
+
+###############
+## inbreeding
+###############
+inbreeding <- function(x, pop=NULL, truenames=TRUE, res.type=c("sample","function","estimate"), N=200, M=N*10){
+ ## CHECKS ##
+ if(!is.genind(x)) stop("x is not a valid genind object")
+ checkType(x)
+ res.type <- match.arg(res.type)[1]
+
+ ## if(x$ploidy != 2) stop("this inbreeding coefficient is designed for diploid genotypes only")
+ PLO <- ploidy(x)
+
+ if(!is.null(pop)) pop(x) <- pop
+ if(is.null(x at pop) && is.null(pop)) {
+ pop(x) <- factor(rep(1, nInd(x)))
+ }
+
+ ## COMPUTATIONS ##
+
+ ## get allele frequencies and \sum p_i^2 by pop and loc ##
+ ## (generalized to any ploidy) ##
+ ## tabfreq2 <- (makefreq(x = genind2genpop(x, quiet = TRUE), quiet=TRUE, truenames=truenames)$tab) ^2
+ ## For genpop objects, a constant ploidy is assumed/needed. This kludge will do for now.
+ tabfreq2 <- tab(genind2genpop(x, quiet = TRUE), freq=TRUE) ^ PLO[1]
+ sumpi2 <- t(apply(tabfreq2, 1, tapply, x$loc.fac, sum))
+
+ ## function to check a 1-locus genotype for homozigosity
+ ## returns 1 if homoz, 0 otherwise
+ ## !!! NOTE : reverse the values returned by f1 to obtain a strange thing !!!
+ f1 <- function(gen){
+ if(any(is.na(gen))) return(NA)
+ return(ifelse(sum(gen > 0) == 1, 1, 0))
+ # if(any(round(gen, 10)==1)) return(1)
+ # return(0)
+ }
+
+ ## get the table of binary hetero/homo data
+ if (truenames) {
+ X <- tab(x)
+ } else
+ X <- tab(x)
+
+ homotab <- t(apply(X, 1, tapply, x at loc.fac, f1))
+
+
+ ## get pi2 for the appropriate pop
+ if(truenames){
+ popx <- pop(x)
+ } else {
+ popx <- x$pop
+ }
+
+ popx <- as.character(popx)
+ tabpi2 <- sumpi2[popx, , drop=FALSE]
+
+
+
+ ## function returning a likelihood function - multi-locus ##
+ ## x is a vector of 1/0 for each locus, with 1=homoz
+ LIK <- function(x, sumpi2){
+ ## return( sum(log( x*(F+(1-F)*sumpi2) + (1-x)*(1-(F+(1-F)*sumpi2)) ) ,na.rm=TRUE) ) # returns the log-likelihood
+ myEnv <- new.env()
+ assign("x", x, envir=myEnv)
+ assign("sumpi2", sumpi2, envir=myEnv)
+ res <- function(F) {
+ ## cat("\nx used:\n") # debugging
+ ## print(x)
+ ## cat("\nsumpi2 used:\n") # debugging
+ ## print(sumpi2)
+
+ return(exp(sum(log( x*(F+(1-F)*sumpi2) + (1-x)*(1-(F+(1-F)*sumpi2)) ) ,na.rm=TRUE)))
+ }
+ environment(res) <- myEnv
+
+ return(res)
+ }
+
+
+ ## get likelihood functions for all individuals
+ res <- lapply(1:nrow(homotab), function(i) LIK(homotab[i,], tabpi2[i,]) )
+ res <- lapply(res, Vectorize)
+
+ ## name output
+ if(truenames) {
+ names(res) <- indNames(x)
+ } else {
+ names(res) <- names(x$tab)
+ }
+
+
+ ## IF WE RETURN FUNCTIONS ##
+ if(res.type=="function"){
+ return(res)
+ }
+
+ if (res.type == "estimate"){
+ opfun <- function(x, ...) optimize(x, ...)[[1]]
+ funval <- numeric(1)
+ res <- vapply(res, FUN = opfun , FUN.VALUE = funval, interval = c(0, 1),
+ maximum = TRUE, tol = .Machine$double.eps^0.75)
+ return(res)
+ }
+
+
+ ## IF WE RETURN SAMPLES ##
+ ## function to get one sample
+ getSample <- function(f){ # f is a vectorized density function
+ x <- runif(M, 0, 1)
+ fx <- f(x)
+ fx <- fx - min(fx)
+ if(sum(fx)<1e-14) {
+ warning("Likelihood uniformly zero likely reflecting precision issue\nreturning uniformly distributed sample")
+ return(runif(N))
+ }
+ fx <- fx/sum(fx)
+ return(sample(x, size=N, prob=fx))
+ }
+
+ res <- lapply(res, getSample)
+ return(res)
+} # end inbreeding
diff --git a/R/loadingplot.R b/R/loadingplot.R
new file mode 100644
index 0000000..2b5928a
--- /dev/null
+++ b/R/loadingplot.R
@@ -0,0 +1,92 @@
+##############
+# loadingplot
+##############
+loadingplot <- function (x, ...) UseMethod("loadingplot")
+
+
+loadingplot.default <- function(x, at=NULL, threshold=quantile(x,0.75), axis=1, fac=NULL, byfac=FALSE,
+ lab=NULL, cex.lab=0.7, cex.fac=1, lab.jitter=0,
+ main="Loading plot", xlab="Variables", ylab="Loadings", srt=0, adj=NULL, ...){
+ ## some checks
+ if(is.data.frame(x) | is.matrix(x)){
+ if(is.null(lab)) {lab <- rownames(x)}
+ x <- x[,axis]
+ } else {
+ if(is.null(lab)) {lab <- names(x)}
+ }
+
+ names(x) <- lab <- rep(lab, length=length(x))
+
+ if(!is.numeric(x)) stop("x is not numeric")
+ if(any(is.na(x))) stop("NA entries in x")
+ if(any(x<0)) {
+ warning("Some values in x are less than 0\n Using abs(x) instead, but this might not be optimal.")
+ x <- abs(x)
+ }
+
+ ## handle lab
+ if(is.null(lab)) {lab <- 1:length(x)}
+
+ ## handle fac
+ if(!is.null(fac)){
+ if(byfac){
+ x <- tapply(x, fac, sum)
+ if(length(lab) != length(x)) lab <- names(x)
+ } else {
+ fac <- factor(fac, levels=unique(fac))
+ grp.idx <- cumsum(table(fac)) + 0.5
+ grp.lab.idx <- tapply(1:length(x), fac, mean)
+ grp.lab <- names(grp.idx)
+ grp.idx <- grp.idx[-length(grp.idx)]
+ }
+ }
+
+ ## preliminary computations
+ y.min <- min(min(x),0)
+ y.max <- max(max(x),0)
+ y.offset <- (y.max-y.min)*0.02
+
+ ## handle 'at'
+ if(is.null(at)){
+ at <- 1:length(x)
+ } else {
+ if(length(at) != length(x)) stop("x and at do not have the same length.")
+ }
+
+
+ ## start the plot
+ dat <- cbind(at, x)
+ plot(dat, type="h", xlab=xlab, ylab=ylab,
+ main=main, xaxt="n", ylim=c(y.min,y.max*1.2), ...)
+
+ ## add groups of variables (optional)
+ if(!is.null(fac) & !byfac) {
+ abline(v=grp.idx,lty=2) # split groups of variables
+ text(x=grp.lab.idx,y=y.max*1.15, labels=grp.lab, cex=cex.fac) # annotate groups
+ }
+
+ ## annotate variables that are above the threshold
+ if(sum(x > threshold)>0){
+ x.ann <- at[x > threshold]
+ x.ann <- jitter(x.ann,factor=lab.jitter)
+
+ y.ann <- x[x > threshold] + y.offset
+ y.ann <- jitter(y.ann,factor=lab.jitter)
+
+ txt.ann <- lab[x > threshold]
+ text(x=x.ann, y=y.ann, label=txt.ann, cex=cex.lab, srt=srt, adj=adj)
+
+ ## indicate the threshold
+ abline(h=threshold, col="grey")
+
+ ## build the result
+
+ res <- list(threshold=threshold,
+ var.names=txt.ann,
+ var.idx=which(x > threshold),
+ var.values=x[x > threshold])
+ return(invisible(res))
+ }
+
+ return(NULL) # if no point above threshold
+} # end loadingplot
diff --git a/R/makefreq.R b/R/makefreq.R
new file mode 100644
index 0000000..c683ae1
--- /dev/null
+++ b/R/makefreq.R
@@ -0,0 +1,118 @@
+
+####################
+# Function makefreq
+####################
+
+#' Compute allelic frequencies
+#'
+#' The function \code{makefreq} is a generic to compute allele frequencies.
+#' These can be derived for \linkS4class{genind} or \linkS4class{genpop} objects.
+#' In the case of \linkS4class{genind} objects, data are kept at the individual level, but standardised so that allele frequencies sum up to 1.
+#'
+#' There are 3 treatments for missing values: \cr - NA: kept as NA.\cr - 0:
+#' missing values are considered as zero. Recommended for a PCA on
+#' compositionnal data.\cr - "mean": missing values are given the mean
+#' frequency of the corresponding allele. Recommended for a centred PCA.
+#'
+#' Note that this function is now a simple wrapper for the accessor \code{\link{tab}}.
+#'
+#' @param x a \linkS4class{genind} or \linkS4class{genpop} object.
+#' @param quiet logical stating whether a conversion message must be printed
+#' (TRUE,default) or not (FALSE).
+#' @param missing treatment for missing values. Can be NA, 0 or "mean" (see
+#' details)
+#' @param truenames deprecated; there for backward compatibility
+#' @param ... further arguments (curently unused)
+#'
+#' @return Returns a list with the following components: \item{tab}{matrix of
+#' allelic frequencies (rows: populations; columns: alleles).}
+#' \item{nobs}{number of observations (i.e. alleles) for each population x
+#' locus combinaison.} \item{call}{the matched call}
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @seealso \code{\link{genpop}}
+#' @keywords manip multivariate
+#'
+#' @examples
+#'
+#' \dontrun{
+#' data(microbov)
+#' obj1 <- microbov
+#' obj2 <- genind2genpop(obj1)
+#'
+#' # perform a correspondance analysis on counts data
+#' Xcount <- tab(obj2, NA.method="zero")
+#' ca1 <- dudi.coa(Xcount,scannf=FALSE)
+#' s.label(ca1$li,sub="Correspondance Analysis",csub=1.2)
+#' add.scatter.eig(ca1$eig,nf=2,xax=1,yax=2,posi="topleft")
+#'
+#' # perform a principal component analysis on frequency data
+#' Xfreq <- makefreq(obj2, missing="mean")
+#' Xfreq <- tab(obj2, NA.method="mean") # equivalent to line above
+#' pca1 <- dudi.pca(Xfreq,scale=FALSE,scannf=FALSE)
+#' s.label(pca1$li,sub="Principal Component Analysis",csub=1.2)
+#' add.scatter.eig(pca1$eig,nf=2,xax=1,yax=2,posi="top")
+#' }
+#'
+#' @export
+#' @docType methods
+#' @rdname makefreq
+#'
+setGeneric("makefreq", function(x, ...) standardGeneric("makefreq"))
+
+#' @export
+#' @rdname makefreq
+#' @aliases makefreq,genind-methods
+#' @aliases makefreq.genind
+setMethod ("makefreq", signature(x="genind"), function(x, quiet=FALSE, missing=NA, truenames=TRUE, ...){
+ if(!quiet) cat("\n Finding allelic frequencies from a genpop object... \n")
+
+ ## treat 'missing' argument for compatibility with 'tab
+ ## NA -> "asis"
+ ## 0 -> "zero"
+ ## "mean" -> "mean"
+ if(is.na(missing)) {
+ NA.method <- "asis"
+ } else if(is.numeric(missing) && missing==0){
+ NA.method <- "zero"
+ } else {
+ NA.method <- "mean"
+ }
+
+ out <- tab(x, freq=TRUE, NA.method=NA.method)
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(out)
+}) #end makefreq for genind
+
+
+
+
+## genpop method
+#' @export
+#' @rdname makefreq
+#' @aliases makefreq,genpop-methods
+#' @aliases makefreq.genpop
+setMethod ("makefreq", signature(x="genpop"), function(x, quiet=FALSE, missing=NA, truenames=TRUE, ...){
+
+ if(!quiet) cat("\n Finding allelic frequencies from a genpop object... \n")
+
+ ## treat 'missing' argument for compatibility with 'tab
+ ## NA -> "asis"
+ ## 0 -> "zero"
+ ## "mean" -> "mean"
+ if(is.na(missing)) {
+ NA.method <- "asis"
+ } else if(is.numeric(missing) && missing==0){
+ NA.method <- "zero"
+ } else {
+ NA.method <- "mean"
+ }
+
+ out <- tab(x, freq=TRUE, NA.method=NA.method)
+
+ if(!quiet) cat("\n...done.\n\n")
+
+ return(out)
+}) #end makefreq for genpop
+
diff --git a/R/minorAllele.R b/R/minorAllele.R
new file mode 100644
index 0000000..d35aea5
--- /dev/null
+++ b/R/minorAllele.R
@@ -0,0 +1,47 @@
+#' Compute minor allele frequency
+#'
+#' This function computes the minor allele frequency for each locus in a \linkS4class{genind} object. To test if loci are polymorphic, see the function \code{\link{isPoly}}.
+#'
+#' @param x a \linkS4class{genind} object
+#'
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#'
+#' ## LOAD DATA
+#' data(nancycats)
+#'
+#' ## COMPUTE ALLELE FREQUENCIES
+#' x <- nancycats
+#' apply(tab(x, freq=TRUE),2,mean, na.rm=TRUE)
+#'
+#' ## GET MINOR ALLELE FREQUENCY
+#' m.freq <- minorAllele(x)
+#' m.freq
+#' }
+#'
+#' @seealso \code{\link{isPoly}}
+#'
+minorAllele <- function(x){
+ ## CHECK INPUT
+ if(!is.genind(x)) stop("x is not a valid genind object")
+
+ ## AUXIL FUNCTION
+ f1 <- function(vec){
+ vec <- sort(vec, decreasing=TRUE)
+ res <- vec[min(2,length(vec))]
+ return(res)
+ }
+
+ ## GET ALLELE FREQUENCIES
+ freq <- apply(tab(x, freq=TRUE),2,mean, na.rm=TRUE)
+
+ ## GET MINOR ALLELE
+ out <- tapply(freq, locFac(x), f1)
+
+ ## RETURN OUTPUT
+ return(out)
+}
diff --git a/R/monmonier.R b/R/monmonier.R
new file mode 100644
index 0000000..f5d8d29
--- /dev/null
+++ b/R/monmonier.R
@@ -0,0 +1,666 @@
+# Algorithm to detect boundaries, based on Monmonier's algorithm
+# Extended to any connection network
+# Thibaut Jombart 2006-2008 (t.jombart at imperial.ac.uk)
+
+
+
+#####################
+# function monmonier
+#####################
+monmonier <- function(xy, dist, cn, threshold=NULL, bd.length=NULL, nrun=1,
+ skip.local.diff=rep(0,nrun), scanthres=is.null(threshold), allowLoop=TRUE){
+if(!inherits(cn,"nb")) stop('cn is not a nb object')
+if(is.data.frame(xy)) xy <- as.matrix(xy)
+if(!is.matrix(xy)) stop('xy must be a matrix')
+if(!inherits(dist,"dist")) stop('Argument \'dist\' must be a distance matrix of class dist')
+if(nrow(xy) != nrow(as.matrix(dist))) stop('Number of sites and number of observations differ')
+
+## set to TRUE to debug
+## DEBUG <- FALSE
+
+## if(DEBUG) {
+## plot.nb(cn, xy, col="grey", points=FALSE)
+## if(exists("x1")) {
+## x1 <<- x1
+## s.value(xy,x1,add.p=TRUE)
+## }
+## text(xy,lab=1:nrow(xy),font=2,col="darkgreen")
+## }
+
+## PRECISION of the xy coordinates (in digits)
+## used when coordinates are inputed in C code.
+PRECISION=12
+
+## conversion of the connection network
+cn.nb <- cn
+cn <- nb2neig(cn)
+## binary matrix of neighbourhood
+M <- neig2mat(cn)
+## distance matrix
+D <- as.matrix(dist)
+## matrix of distances among neighbours
+D <- M*D
+
+## set/check the threshold value of the distances among neighbours
+## default: the median of all distances among neighbours
+if(is.null(threshold) || threshold<0) {Dlim <- summary(unique(D[D>0]))[5]} else {Dlim <- threshold}
+
+## handle 'bd.length' / must prevail over threshold.
+if(!is.null(bd.length)) {
+ if(bd.length < 1) bd.length <- 1
+ Dlim <- 0
+ scanthres <- FALSE
+} else {
+ bd.length <- nrow(xy)^2
+}
+
+
+if(scanthres){
+ plot(sort(unique(D)[unique(D) > 0],decreasing=TRUE),main="Local distances plot",type="l",xlab="rank",ylab="Sorted local distances")
+ abline(h=Dlim,lty=2)
+ mtext("Dashed line indicates present threshold")
+ cat("Indicate the threshold (\'d\' for default): ")
+ temp <- as.character(readLines(n = 1))
+ if(toupper(temp)!="D") { Dlim <- as.numeric(temp) }
+}
+
+#### OLD VERSION ####
+## ## build a data.frame of coords of neighbours, with columns x1 y1 x2 y2
+## listCpl <- neig.util.GtoL(neig2mat(cn))
+## allSeg <- cbind(xy[,1][listCpl[,1]] , xy[,2][listCpl[,1]] , xy[,1][listCpl[,2]] , xy[,2][listCpl[,2]])
+## colnames(allSeg) <- c('xP','yP','xQ','yQ')
+#### END OLD VERSION ####
+
+## Compute once and for all a matrix matSegVal with columns A, B and val
+## A: index of one vertex
+## B: index if another vertex, connected (beighbour) to B
+## val: distance between A and B
+## This table is such that "val" is sorted in decreasing order.
+matSegVal <- which(D>0,arr.ind=TRUE)
+matSegVal.names <- apply(matSegVal,1,function(vec) paste(sort(vec),collapse="-"))
+rownames(matSegVal) <- matSegVal.names # used to get unique segments (cause D is symmetric)
+matSegVal <- matSegVal[unique(rownames(matSegVal)),]
+temp <- apply(matSegVal,1,function(vec) D[vec[1],vec[2]])
+matSegVal <- cbind(matSegVal,temp) # matSegVal has its 3 colums
+idx <- order(matSegVal[,3], decreasing=TRUE)
+matSegVal <- matSegVal[idx,]
+
+## allSeg is a matrix giving the coordinates of all edges (in row), x1 y1 x2 y2.
+allSeg <- cbind(xy[matSegVal[,1],] , xy[matSegVal[,2],])
+rownames(allSeg) <- rownames(matSegVal)
+colnames(allSeg) <- c("x1","y1","x2","y2")
+
+## auxiliary function used to remove a segment from matSegVal (A,B: indices of vertices of the removed edge)
+rmFromMatSegVal <- function(A,B){
+ AB.name <- paste(sort(c(A,B)), collapse="-")
+ toRemove <- match(AB.name, rownames(matSegVal))
+ matSegVal <<- matSegVal[-toRemove,]
+}
+
+## Given a rank 'rang', getNext retrieves the two corresponding neighbours (A and B),
+## their middle (M), and the corresponding value.
+## A is the index of the vertex, xA and yA are its coordinates
+getNext <- function(rang){
+ ## ## ## OLD VERSION ## ## ##
+ ## val <- unique(sort(D,decreasing=TRUE))[rang]
+ ## A <- which(round(D,10)==round(val,10),TRUE)[1,1] # beware: == used on doubles
+ ## B <- which(round(D,10)==round(val,10),TRUE)[1,2] # beware: == used on doubles
+ ## xA <- xy[A,1]
+ ## yA <- xy[A,2]
+ ## xB <- xy[B,1]
+ ## yB <- xy[B,2]
+ ## xM <- (xA + xB)/2
+ ## yM <- (yA + yB)/2
+ ## ## ## END OLD VERSION ## ## ##
+
+ #### Must take into account that the some local distances occur for different segments
+ #### Create a table with columns A, B and val
+
+ temp <- matSegVal[rang,]
+ A <- temp[1]
+ B <- temp[2]
+ val <- temp[3]
+ xA <- xy[A,1]
+ yA <- xy[A,2]
+ xB <- xy[B,1]
+ yB <- xy[B,2]
+ xM <- mean(c(xA,xB))
+ yM <- mean(c(yA,yB))
+
+ return( list(A=c(A,xA,yA), B=c(B,xB,yB), M=c(xM,yM), val=val) )
+}
+
+## checkNext returns TRUE if it is ok to draw the segment MN, i.e. if MN does not cross another edge,
+## and FALSE otherwise
+## - M and N define the segment of interest
+## M = c(xM,yM) ; N=c(xN,yN)
+## -segMat is the matrix of all known edges
+## A,B,C,D are not coordinates, but indices of vertices
+## -AB is the edge whose middle is M ; given to avoid checking MN vs AB
+## -CD is the edge whose middle is N ; given to avoid checking MN vs CD
+## - toRemove: a vector of characters naming other edges in segMat to be removed before checking
+checkNext <- function(M,N,A,B,C,D,segMat=allSeg,toRemove=NULL,curDir=NULL){
+ ## orientation of the segment MN
+ xmin <- min(M[1],N[1])
+ xmax <- max(M[1],N[1])
+ ymin <- min(M[2],N[2])
+ ymax <- max(M[2],N[2])
+
+### From here segment that would be difficult to check for crossing are removed
+### If MN is the segment of interest, with M middle of AB and N middle of CD,
+
+ subsetSeg <- segMat
+ ## The segment that was just drawn before is removed from the checks for crossing (messy code 2)
+ if(!is.null(curDir)){
+ prevSeg <- grep(paste("dir",curDir,sep=""),rownames(subsetSeg))
+ if(length(prevSeg)>0){ # this is not the 1st seg. in this dir
+ prevSeg <- prevSeg[length(prevSeg)]
+ subsetSeg <- segMat[-prevSeg,,drop=FALSE]
+ } else { # this is the 1st seg. in this direction -> rm 1st seg of other dir
+ otherDir <- ifelse(curDir==1L, 2, 1)
+ prevSeg <- grep(paste("dir",otherDir,"-1-2",sep=""),rownames(subsetSeg))
+ if(length(prevSeg)>0) { subsetSeg <- segMat[-prevSeg,,drop=FALSE] }
+ }
+ }
+
+ ## AB and CD are now taken out (doubtful code 2 returned by the C procedure CheckAllSeg)
+ AB.name <- paste(sort(c(A,B)),collapse="-")
+ AB.idx <- match(AB.name, rownames(subsetSeg))
+ CD.name <- paste(sort(c(C,D)),collapse="-")
+ CD.idx <- match(CD.name, rownames(subsetSeg))
+ subsetSeg <- subsetSeg[-c(AB.idx,CD.idx),,drop=FALSE]
+
+ ## subsetSeg is a matrix, each of its rows being a segment: xP,yP,xQ,yQ
+ ## edges out of the square of diagonal MN cannot be crossed, so they are removed from
+ ## the checks for crossing
+ subsetSeg <- subsetSeg[!(subsetSeg[,1] < xmin & subsetSeg[,3] < xmin),,drop=FALSE]
+ subsetSeg <- subsetSeg[!(subsetSeg[,1] > xmax & subsetSeg[,3] > xmax),,drop=FALSE]
+ subsetSeg <- subsetSeg[!(subsetSeg[,2] < ymin & subsetSeg[,4] < ymin),,drop=FALSE]
+ subsetSeg <- subsetSeg[!(subsetSeg[,2] > ymax & subsetSeg[,4] > ymax),,drop=FALSE]
+
+ ## handle toRemove here
+ if(!is.null(toRemove)){
+ idx <- match(toRemove, rownames(subsetSeg))
+ idx <- idx[!is.na(idx)]
+ if(length(idx)>0) { subsetSeg <- subsetSeg[-idx,,drop=FALSE] }
+ }
+
+ ## temp is used for the output of CheckAllSeg
+ ## initialized at 10, which is never returned by CheckAllSeg
+ temp <- as.integer(10)
+
+ ## call to CheckAllSeg
+ ## =======================
+ ## output code for CheckAllSeg:
+ ## - 0: no intersection
+ ## - 1: all kind of intersection, including the codes from SegSeg function
+ ## (a C function inside monmonier-utils.C):
+ ## - 3 : The segments collinearly overlap, sharing at least a point.
+ ## - 2 : An endpoint (vertex) of one segment is on the other segment,
+ ## but segments aren't collinear.
+ ## - 1 : The segments intersect properly (i.e. not case 2 or 3)
+ ## =======================
+ ##
+ ## restore the matrix type if there is only one segment to check for crossing in subsetSeg
+
+ ## round down coordinates in subsetSeg
+ subsetSeg <- round(subsetSeg, digits=PRECISION)
+
+ if(nrow(subsetSeg)>0) {
+ temp <- .C("CheckAllSeg",as.integer(nrow(subsetSeg)),as.integer(ncol(subsetSeg)),
+ as.double(as.matrix(subsetSeg)), as.double(M), as.double(N), temp,PACKAGE="adegenet")[[6]]
+ } else {temp <- 0}
+
+ ## for debugging
+ ## if(DEBUG) {
+ ## if(temp==1) cat("\n can't go there (code",temp,")") else cat("\n new segment ok (code",temp,")")
+ ## }
+
+ ## if a code 1 or 3 is returned, CheckAllSeg returns FALSE
+ ## else it returns TRUE
+ ## additional control used (code 10, CheckAllSeg failed)
+ if(temp==10) stop("CheckAllSeg failure (returned value=10, i.e. unchanged, not computed). Please report the bug.")
+ if(temp==1 | temp==2 | temp==3) return(FALSE) else return(TRUE)
+} # end of checkNext
+
+## result object is created
+## this is a list with one component per run (a run = a boundary)
+result <-list()
+for(run in 1:nrun){
+ result[[run]] <- list(dir1=list(),dir2=list())
+}
+
+
+#### MAIN FUNCTION HERE
+#### a for loop is used to handle several runs
+## each boundary seeks one starting point, and then expands both sides (dir1 / dir2)
+for(run in 1:nrun){
+
+ ## handle skip.local.diff here
+ ## the corresponding values of distance are set definitely to -1
+ ## if(skip.local.diff[run] >0)
+ ## for(i in 1:skip.local.diff[run]){
+ ## temp <- getNext(1)
+ ## ## D[temp$A[1],temp$B[1] ] <- -1
+ ## ## D[temp$B[1],temp$A[1] ] <- -1
+ ## rmFromMatSegVal(temp$A[1],temp$B[1])
+ ## }
+
+ ## starting point: find the highest distance among neighbours
+ ## then expand
+ currentDir1 <- getNext(1 + skip.local.diff[run])
+ currentDir2 <- currentDir1
+ current.bd.length <- 1
+ if(currentDir1$val<=Dlim) stop(paste('Algorithm reached the threshold value at the first step of run',run))
+ result[[run]]$dir1[[1]] <- currentDir1 # first point dir1
+ result[[run]]$dir2[[1]] <- currentDir2 # first point dir2 (same as dir1)
+ ## D[result[[run]]$dir1[[1]]$A[1],result[[run]]$dir1[[1]]$B[1]] <- -1 # update D matrix
+ ## D[result[[run]]$dir1[[1]]$B[1],result[[run]]$dir1[[1]]$A[1]] <- -1 # update D matrix
+ rmFromMatSegVal(result[[run]]$dir1[[1]]$A[1], result[[run]]$dir1[[1]]$B[1]) # update matSegVal
+
+ ## dir1 => i1: result index; s1: index for the rank of the distance between neighbours (decreasing order)
+ ## dir2 => i2: result index; s2: index for the rank of the distance between neighbours (decreasing order)
+ i1 <- 1
+ s1 <- 1
+ i2 <- 1
+ s2 <- 2
+ n <- nrow(D)
+
+ ## logical handling the expansion of a boundary
+ keepExpanding <- ((current.bd.length < bd.length)
+ && ((currentDir1$val>Dlim)|(currentDir2$val>Dlim))
+ && (s1 < nrow(matSegVal) | s2 < nrow(matSegVal)) )
+
+ #### This while loop has the following behavior:
+ ## as long as the keepExpanding is true, we try to expand the boundary by
+ ## 1) finding the highest next distance among neighbours
+ ## 2) test if we can draw the corresponding segment
+ ## 3) - if we can, store the result, increment i1 or i2, reset s1 and s2, erase the edge
+ ## 3) - if we can't, take the next distance among neighbours (incrementing s1 and s2)
+ ## 4) get back to 1)
+ while(keepExpanding){
+ hasExpanded <- FALSE # used to test if it is relevant to check for looping
+ ## if(DEBUG){
+ ## points(currentDir1$M[1],currentDir1$M[2],col="white",pch=20)
+ ## points(currentDir2$M[1],currentDir2$M[2],col="white",pch=20)
+ ## }
+ if(s1 <= nrow(matSegVal)) { currentDir1 <- getNext(s1) }
+ if(s2 <= nrow(matSegVal)) { currentDir2 <- getNext(s2) }
+ ## if(DEBUG){
+ ## cat("\n\n ## dir1: trying edge",currentDir1$A[1],"-",currentDir1$B[1])
+ ## points(currentDir1$M[1],currentDir1$M[2],col="blue",pch=20)
+ ## readline("\npress enter")
+ ## }
+
+ ## first direction (dir1)
+ if( currentDir1$val > Dlim && s1 <= nrow(matSegVal)) {
+ if(checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M,
+ currentDir1$M,
+ result[[run]]$dir1[[length(result[[run]]$dir1)]]$A[1],
+ result[[run]]$dir1[[length(result[[run]]$dir1)]]$B[1],
+ currentDir1$A[1],
+ currentDir1$B[1], curDir=as.integer(1))) {
+ i1 <- i1+1
+ result[[run]]$dir1[[i1]] <- currentDir1
+ ## update the matrix of diff. between neighbours
+ ## D[result[[run]]$dir1[[i1]]$A[1],result[[run]]$dir1[[i1]]$B[1]] <- -1
+ ## D[result[[run]]$dir1[[i1]]$B[1],result[[run]]$dir1[[i1]]$A[1]] <- -1
+ rmFromMatSegVal(result[[run]]$dir1[[i1]]$A[1],result[[run]]$dir1[[i1]]$B[1] ) # update matSegVal
+
+ s1 <- 1
+ ## update existing segments
+ allSeg <- rbind(allSeg,c(result[[run]]$dir1[[i1-1]]$M,result[[run]]$dir1[[i1]]$M) )
+ rownames(allSeg) <- c(rownames(allSeg)[-nrow(allSeg)] , paste("dir1",i1-1,i1,sep="-"))
+ ## add 1 to the boundary length
+ current.bd.length <- current.bd.length + 1
+ hasExpanded <- TRUE
+ ## if(DEBUG) {
+ ## arrows(result[[run]]$dir1[[i1-1]]$M[1], result[[run]]$dir1[[i1-1]]$M[2],
+ ## result[[run]]$dir1[[i1]]$M[1], result[[run]]$dir1[[i1]]$M[2],col="blue")
+ ## }
+
+ } else{ s1 <- s1+1 }
+ } # end "if( currentDir1$val>Dlim)"
+
+ ## if(DEBUG){
+ ## cat("\n\n ## dir2: trying edge",currentDir2$A[1],"-",currentDir2$B[1])
+ ## points(currentDir2$M[1],currentDir2$M[2],col="red",pch=20)
+ ## readline("\npress enter")
+ ## }
+
+ ## second direction (dir2)
+ if( currentDir2$val > Dlim && s2 <= nrow(matSegVal)) {
+ if(checkNext(result[[run]]$dir2[[length(result[[run]]$dir2)]]$M,
+ currentDir2$M,
+ result[[run]]$dir2[[length(result[[run]]$dir2)]]$A[1],
+ result[[run]]$dir2[[length(result[[run]]$dir2)]]$B[1],
+ currentDir2$A[1],
+ currentDir2$B[1], curDir=as.integer(2))) {
+ i2 <- i2+1
+ result[[run]]$dir2[[i2]] <- currentDir2
+ ## update the matrix of diff. between neighbours
+ ## D[result[[run]]$dir2[[i2]]$A[1],result[[run]]$dir2[[i2]]$B[1]] <- -1
+ ## D[result[[run]]$dir2[[i2]]$B[1],result[[run]]$dir2[[i2]]$A[1]] <- -1
+ rmFromMatSegVal(result[[run]]$dir2[[i2]]$A[1],result[[run]]$dir2[[i2]]$B[1])
+ s2 <- 1
+ ## update existing segments
+ allSeg <- rbind(allSeg,c(result[[run]]$dir2[[i2-1]]$M,result[[run]]$dir2[[i2]]$M) )
+ rownames(allSeg) <- c(rownames(allSeg)[-nrow(allSeg)] , paste("dir2",i2-1,i2,sep="-"))
+ ## add 1 to the boundary length
+ current.bd.length <- current.bd.length + 1
+ hasExpanded <- TRUE
+ ## if(DEBUG){
+ ## arrows(result[[run]]$dir2[[i2-1]]$M[1], result[[run]]$dir2[[i2-1]]$M[2],
+ ## result[[run]]$dir2[[i2]]$M[1], result[[run]]$dir2[[i2]]$M[2],col="red",cex=2)
+ ## }
+
+ } else{ s2 <- s2+1 }
+ } # end "if( currentDir2$val>Dlim)"
+
+ ## update the logical for the while loop
+ keepExpanding <- ((current.bd.length < bd.length)
+ && ((currentDir1$val>Dlim)|(currentDir2$val>Dlim))
+ && (s1 <= nrow(matSegVal) | s2 <= nrow(matSegVal)) )
+
+ ## handle the looping of a boundary
+ if(hasExpanded && (current.bd.length>3) && allowLoop){
+ ## check if the two ends of the boundary can be joined
+ ## remove segments ending each direction (to avoid messy code 2 in checkNext)
+ terminalEdges <- c(paste("dir1",i1-1,i1,sep="-"),
+ paste("dir2",i2-1,i2,sep="-"))
+
+ canLoop <- checkNext(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M,
+ result[[run]]$dir2[[length(result[[run]]$dir2)]]$M,
+ result[[run]]$dir1[[length(result[[run]]$dir1)]]$A[1],
+ result[[run]]$dir1[[length(result[[run]]$dir1)]]$B[1],
+ result[[run]]$dir2[[length(result[[run]]$dir2)]]$A[1],
+ result[[run]]$dir2[[length(result[[run]]$dir2)]]$B[1],
+ toRemove=terminalEdges
+ )
+
+ if(canLoop) {
+ ## add the last, closing segment
+ result[[run]]$dir1[[length(result[[run]]$dir1)+1]] <- result[[run]]$dir2[[length(result[[run]]$dir2)]]
+ ## stop expanding
+ keepExpanding <- FALSE
+ ## update existing segments
+ allSeg <- rbind(allSeg,c(result[[run]]$dir1[[length(result[[run]]$dir1)]]$M,
+ result[[run]]$dir2[[length(result[[run]]$dir2)]]$M) )
+ } # end looping of the boundary
+
+ }
+
+ ## output for debugging
+ ## if(DEBUG) {
+ ## cat("\n","s1:",s1,"s2:",s2,"i1:",i1,"i2:",i2,"D1:",
+ ## currentDir1$val,"D2:",currentDir2$val,"Dlim:",Dlim,
+ ## "nrow(matSegVal)",nrow(matSegVal),"\n")
+ ## cat("\n","D1:",currentDir1$val,"D2:",currentDir2$val,"Dlim:",Dlim,
+ ## "cur.bd.le:", current.bd.length,"max length:", bd.length,"\n",
+ ## "s1:",s1,"s2:",s2,"maxS:",nrow(matSegVal))
+ ## }
+
+ } # end of one given run
+
+} # end for all run
+
+# build the final output
+# this is a list of class monmonier
+# each element correspond to a run, i.e. to a potential boundary
+# the output also contains the number of runs ($nrun) and the matched call ($call).
+output=list()
+for(run in 1:nrun){
+ runname <- paste('run',run,sep='')
+ output[[runname]] <- list(dir1=list(),dir2=list())
+ # dir 1 #
+ output[[runname]]$dir1$path <- matrix(-1, ncol=2,nrow=length(result[[run]]$dir1))
+ colnames(output[[runname]]$dir1$path) <- c('x','y')
+ rownames(output[[runname]]$dir1$path) <- paste('Point',1:nrow(output[[run]]$dir1$path),sep='_')
+
+ for(i in 1:length(result[[run]]$dir1)) {
+ output[[runname]]$dir1$path[i,] <- result[[run]]$dir1[[i]]$M
+ output[[runname]]$dir1$values[i] <- result[[run]]$dir1[[i]]$val
+ }
+
+ # dir 2 #
+ output[[runname]]$dir2$path <- matrix(-1, ncol=2,nrow=length(result[[run]]$dir2))
+ colnames(output[[runname]]$dir2$path) <- c('x','y')
+ rownames(output[[runname]]$dir2$path) <- paste('Point',1:nrow(output[[run]]$dir2$path),sep='_')
+ for(i in 1:length(result[[run]]$dir2)) {
+ output[[runname]]$dir2$path[i,] <- result[[run]]$dir2[[i]]$M
+ output[[runname]]$dir2$values[i] <- result[[run]]$dir2[[i]]$val
+ }
+
+}
+
+output$nrun <- nrun
+output$threshold <- Dlim
+output$xy <- xy
+output$cn <- cn.nb
+output$call <- match.call()
+class(output) <- 'monmonier'
+return(output)
+}
+
+
+
+
+##########################
+# function plot.monmonier
+##########################
+plot.monmonier <- function(x, variable=NULL,displayed.runs=1:x$nrun,
+ add.arrows=TRUE, col='blue',lty=1,bwd=4, clegend=1,csize=0.7,
+ method = c('squaresize','greylevel'),sub='',csub=1,possub='topleft',
+ cneig=1,pixmap=NULL,contour=NULL,area=NULL,add.plot=FALSE,...){
+
+ if (!inherits(x, "monmonier")) stop("Use only with 'monmonier' objects")
+ if(!is.null(variable) & !is.numeric(variable)) stop('If provided, variable must be numeric.\n')
+
+
+ xy <- x$xy
+ cpoint <- 0
+
+ if(cneig>0) {neig <- nb2neig(x$cn)} else {neig <- NULL}
+ if(is.null(variable)){
+ variable <- rep(1,nrow(xy))
+ csize <- 0
+ cpoint <- 1
+ clegend <- 0
+ }
+ s.value(xy,variable,grid=FALSE,include.origin=FALSE,addaxes=FALSE,neig=neig,
+ cneig=cneig,clegend=clegend,csize=csize,cpoint=cpoint,pch=20,pixmap=pixmap,
+ method=method,sub=sub,csub=csub,possub=possub,add.plot=add.plot)
+ opar <- par(no.readonly=TRUE)
+ on.exit(par(mar=opar$mar))
+ par(mar=c(0,0,0,0))
+
+ for(run in displayed.runs){
+ obj <- x[[run]]
+ if(length(col)!=x$nrun) col <- rep(col,x$nrun)
+ if(length(lty)!=x$nrun) lty <- rep(lty,x$nrun)
+ if(length(obj$dir1$values) == 0) stop(paste('Monmonier object of run', run, 'is empty (no point in the path)\n'))
+
+ if(length(obj$dir1$values) == 1 && length(obj$dir2$values) == 1) {
+ points(obj$dir1$path[1],obj$dir1$path[2],pch=20,col=col[run],...)
+ } else{
+ ## handle boundary width
+ ## the largest part corresponds to the highest distance among neighbours
+ val.1 <- obj$dir1$values
+ val.2 <- obj$dir2$values
+ n1 <- length(val.1)
+ n2 <- length(val.2)
+ cex.bwd.1 <- ( val.1[1:(n1-1)] + val.1[2:n1] )/2
+ cex.bwd.2 <- ( val.2[1:(n2-1)] + val.2[2:n2] )/2
+ cex.bwd.max <- max(c(cex.bwd.1,cex.bwd.2), na.rm=TRUE)
+ cex.bwd.1 <- cex.bwd.1/max(cex.bwd.max)
+ cex.bwd.2 <- cex.bwd.2/max(cex.bwd.max)
+ ## amplify the differences
+ ## cex.bwd.1 <- cex.bwd.1^1.5
+ ## cex.bwd.2 <- cex.bwd.2^1.5
+
+
+ if(add.arrows) {
+ if(n1>1) arrows(obj$dir1$path[1:(nrow(obj$dir1$path)-1),1],
+ obj$dir1$path[1:(nrow(obj$dir1$path)-1),2],
+ obj$dir1$path[2:nrow(obj$dir1$path),1],
+ obj$dir1$path[2:nrow(obj$dir1$path),2],
+ lwd=bwd*cex.bwd.1,angle=20,length=0.2,col=col[run],lty=lty[run],...)
+
+ if(n2>1) arrows(obj$dir2$path[1:(nrow(obj$dir2$path)-1),1],
+ obj$dir2$path[1:(nrow(obj$dir2$path)-1),2],
+ obj$dir2$path[2:nrow(obj$dir2$path),1],
+ obj$dir2$path[2:nrow(obj$dir2$path),2],
+ lwd=bwd*cex.bwd.2,angle=20,length=0.2,col=col[run],lty=lty[run],...)
+ } else {
+ if(n1>1) segments(obj$dir1$path[1:(nrow(obj$dir1$path)-1),1],
+ obj$dir1$path[1:(nrow(obj$dir1$path)-1),2],
+ obj$dir1$path[2:nrow(obj$dir1$path),1],
+ obj$dir1$path[2:nrow(obj$dir1$path),2],
+ lwd=bwd*cex.bwd.1,col=col[run],lty=lty[run],...)
+
+ if(n2>1)segments(obj$dir2$path[1:(nrow(obj$dir2$path)-1),1],
+ obj$dir2$path[1:(nrow(obj$dir2$path)-1),2],
+ obj$dir2$path[2:nrow(obj$dir2$path),1],
+ obj$dir2$path[2:nrow(obj$dir2$path),2],
+ lwd=bwd*cex.bwd.2,col=col[run],lty=lty[run],...)
+ }
+ } # end else
+ } # end for
+
+} # end function
+
+
+
+#####################
+# print function
+#####################
+print.monmonier <- function(x, ...){
+cat("\t\n###########################################################")
+cat("\t\n# List of paths of maximum differences between neighbours #")
+cat("\t\n# Using a Monmonier based algorithm #")
+cat("\t\n###########################################################\n")
+cat('\n$call:')
+print(x$call)
+
+cat('\n # Object content #')
+cat("\nClass: ", class(x))
+cat('\n$nrun (number of successive runs): ', x$nrun)
+if(x$nrun==1)
+cat('\n$run1: run of the algorithm')
+else if(x$nrun==2)
+cat('\n$run1, $run2: runs of the algorithm')
+else cat('\n$run1 ... $run',x$nrun, ': runs of the algorithm',sep='')
+cat('\n$threshold (minimum difference between neighbours): ', x$threshold)
+cat("\n$xy: spatial coordinates")
+cat("\n$cn: connection network")
+
+cat('\n\n # Runs content #')
+for(i in 1:x$nrun){
+ cat('\n# Run',i)
+ # dir 1 #
+ cat('\n# First direction')
+ cat('\nClass: ', class(x$run1$dir1))
+ cat('\n$path:\n')
+ print(head(x[[i]]$dir1$path,n=3))
+ if(nrow(x[[i]]$dir1$path) >3) cat('...\n')
+ cat('\n$values:\n',head(x[[i]]$dir1$values,n=3))
+ if(length(x[[i]]$dir1$values)>3) cat(' ...')
+ # dir 2 #
+ cat('\n# Second direction')
+ cat('\nClass: ', class(x$run1$dir2))
+ cat('\n$path:\n')
+ print(head(x[[i]]$dir2$path,n=3))
+ if(nrow(x[[i]]$dir2$path) >3) cat('...\n')
+ cat('\n$values:\n',head(x[[i]]$dir2$values,n=3))
+ if(length(x[[i]]$dir2$values)>3) cat(' ...')
+
+ cat('\n')
+ lenTheo <- x$nrun + 5
+ if(length(names(x))> lenTheo) {
+ cat('Other elements: \n')
+ cat(names(x)[(lenTheo+1) : length(x)])
+ }
+ cat('\n')
+ }
+}
+
+
+
+##############################
+# function optimize.monmonier
+##############################
+optimize.monmonier <- function(xy,dist,cn,ntry=10, bd.length=NULL, return.best=TRUE,
+ display.graph=TRUE,threshold=NULL,scanthres=is.null(threshold),allowLoop=TRUE){
+
+## move X to the arguments if we want to optimize an already created object
+X <- NULL
+#if( any(is.null(xy), is.null(dist), is.null(cn)) & is.null(X) ) stop("Please provide either xy, dist and cn or a monmonier object (X)")
+
+## if X is a monmonier object...
+if(inherits(X,what="monmonier")){
+ obj <- as.list(X$call)
+ xy <- obj$xy
+ dist <- obj$dist
+ cn <- obj$cn
+}
+
+cn.nb <- cn
+cn <- nb2neig(cn)
+M <- neig2mat(cn)
+D <- as.matrix(dist)
+D <- M*D
+if(is.null(threshold) || (threshold<0)) {Dlim <- summary(unique(D[D>0]))[5]} else {Dlim <- threshold}
+
+if(scanthres){
+ plot(sort(unique(D)[unique(D) > 0],decreasing=TRUE),main="Local distances plot", type="l", xlab="rank",ylab="Sorted local distances")
+ abline(h=Dlim,lty=2)
+ mtext("Dashed line indicates present threshold")
+ cat("Indicate the threshold (\'d\' for default): ")
+ temp <- as.character(readLines(n = 1))
+ if(toupper(temp)!="D") { Dlim <- as.numeric(temp) }
+}
+
+## start the series if computations
+cat(paste("Boundaries computed (required: ",ntry,")\n",sep=""))
+
+## for loop
+bdr.values <- -1 # used so that the first boundary is automatically the best
+
+for(i in 0:(ntry-1)){
+ temp <- monmonier(xy, dist, cn.nb,skip.local.diff=i,scanthres=FALSE,
+ threshold=Dlim, bd.length=bd.length, allowLoop=allowLoop)
+ current.bdr.value <- sum(c(temp$run1$dir1$values, temp$run1$dir2$values))
+
+ if(all(current.bdr.value > bdr.values)) {
+ bdr.best <- temp
+ bdr.skip <- i
+ }
+
+ bdr.values <- c(bdr.values , current.bdr.value)
+ cat(paste(1+i," ")) # print progression in live
+}
+
+## remove the first value (-1) in bdr.value
+bdr.values <- bdr.values[-1]
+
+## graphical display
+if(display.graph) barplot(bdr.values,xlab="Local differences skipped",ylab="Sum of all local differences",names.arg=0:(ntry-1))
+
+## return the best value of skip.local.diff, or the corresponding object
+if(!return.best) {
+ return(bdr.skip)
+ } else {
+ cat(paste("\nOptimal number of skipped local differences: ",bdr.skip,"\n"))
+ prevcall <- as.list(match.call())
+ newcall <- bquote( monmonier(xy=.(prevcall$xy), dist=.(prevcall$dist), cn=.(prevcall$cn),
+ threshold=.(bdr.best$threshold), bd.length=.(bd.length),
+ nrun=1, skip.local.diff=.(as.numeric(bdr.skip)), scanthres=FALSE, allowLoop=.(allowLoop)) )
+
+ ## assign the appropriate call to the result
+ bdr.best$call <- newcall
+
+ ## exp <- bquote( monmonier(xy=.(prevcall$xy),dist=.(prevcall$dist),cn=.(prevcall$cn),skip=.(bdr.skip),
+ ## ,scan=FALSE,thres=.(Dlim),bd.length=.(bd.length),allowLoop=.(allowLoop)) )
+ return(bdr.best)
+ }
+}
diff --git a/R/mutations.R b/R/mutations.R
new file mode 100644
index 0000000..b297887
--- /dev/null
+++ b/R/mutations.R
@@ -0,0 +1,111 @@
+
+
+#################
+## findMutations
+#################
+
+## GENERIC
+findMutations <- function(...){
+ UseMethod("findMutations")
+}
+
+
+
+## METHOD FOR DNABIN
+findMutations.DNAbin <- function(x, from=NULL, to=NULL, allcomb=TRUE, ...){
+ ## CHECKS ##
+ if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
+ x <- as.matrix(x)
+
+ ## function to pull out mutations from sequence a to b ##
+ NUCL <- c('a','t','g','c')
+ f1 <- function(a,b){
+ seqa <- as.character(x[a,])
+ seqb <- as.character(x[b,])
+ temp <- which(seqa != seqb)
+ ori <- seqa[temp]
+ mut <- seqb[temp]
+ names(ori) <- names(mut) <- temp
+ toRemove <- !ori %in% NUCL | !mut %in% NUCL
+ ori <- ori[!toRemove]
+ mut <- mut[!toRemove]
+ if(all(toRemove)) return(NULL)
+ res <- data.frame(ori,mut)
+ names(res) <- rownames(x)[c(a,b)]
+ res$short <- paste(row.names(res),":",res[,1],"->",res[,2],sep="")
+ return(res)
+ }
+
+ ## GET LIST OF PAIRS TO COMPARE ##
+ ## handle from/to as character
+ if(is.character(from)) from <- match(from, rownames(x))
+ if(is.character(to)) to <- match(to, rownames(x))
+
+ ## handle NULL
+ if(is.null(from)) from <- 1:nrow(x)
+ if(is.null(to)) to <- 1:nrow(x)
+
+ ## get pairs
+ if(allcomb){
+ pairs <- expand.grid(to, from)[,2:1,drop=FALSE]
+ } else {
+ N <- max(length(from),length(to))
+ from <- rep(from, length=N)
+ to <- rep(to, length=N)
+ pairs <- cbind(from, to)
+ }
+
+ ## remove unwanted comparisons
+ pairs <- pairs[pairs[,1]!=pairs[,2],,drop=FALSE]
+
+ ## GET NUMBER OF MUTATIONS ##
+ out <- lapply(1:nrow(pairs), function(i) f1(pairs[i,1], pairs[i,2]))
+ names(out) <- paste(rownames(x)[pairs[,1]], rownames(x)[pairs[,2]],sep="->")
+
+ return(out)
+
+} # end findMutations
+
+
+
+
+
+
+
+##################
+## graphMutations
+##################
+
+## GENERIC
+graphMutations <- function(...){
+ UseMethod("graphMutations")
+}
+
+
+
+## METHOD FOR DNABIN
+graphMutations.DNAbin <- function(x, from=NULL, to=NULL, allcomb=TRUE, plot=TRUE, curved.edges=TRUE, ...){
+
+ ## GET MUTATIONS ##
+ x <- findMutations(x, from=from, to=to, allcomb=allcomb)
+
+ ## GET GRAPH ##
+ from <- gsub("->.*","",names(x))
+ to <- gsub(".*->","",names(x))
+ vnames <- sort(unique(c(from,to)))
+ dat <- data.frame(from,to,stringsAsFactors=FALSE)
+ out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(vnames, label=vnames))
+
+ ## SET ANNOTATIONS FOR THE BRANCHES ##
+ annot <- unlist(lapply(x, function(e) paste(e$short, collapse="\n")))
+ E(out)$label <- annot
+ E(out)$curved <- curved.edges
+
+ ## PLOT / RETURN ##
+ if(plot) plot(out, ...)
+
+ return(out)
+} # end graphMutations
+
+
+
diff --git a/R/old2new.R b/R/old2new.R
new file mode 100644
index 0000000..a33f06b
--- /dev/null
+++ b/R/old2new.R
@@ -0,0 +1,161 @@
+##################
+# Methods old2new
+##################
+.get_slot <- function(object, theslot = "strata"){
+ if (.hasSlot(object, theslot)) slot(object, theslot)
+ else NULL
+}
+#' Convert objects with obsolete classes into new objects
+#'
+#' The genind and genlight objects have changed in Adegenet version 2.0. They
+#' have each gained strata and hierarchy slots. What's more is that the genind
+#' objects have been optimized for storage and now store the tab slot as
+#' integers instead of numerics. This function will convert old genind or
+#' genlight objects to new ones seamlessly.
+#'
+#' @rdname old2new
+#' @param object a genind or genlight object from version 1.4 or earlier.
+#' @param donor a new object to place all the data into.
+#' @aliases old2new
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}\cr
+#' Zhian N. Kamvar \email{kamvarz@@science.oregonstate.edu}
+#' @keywords manip
+#' @export
+old2new_genind <- function(object, donor = new("genind")){
+ if (missing(donor) || !is(donor, "genind")){
+ donor <- new("genind")
+ }
+ donor_tab <- slot(object, "tab")
+ donor_loc.fac <- slot(object, "loc.fac")
+ donor_all.names <- slot(object, "all.names")
+ donor_ind.names <- slot(object, "ind.names")
+ donor_loc.names <- slot(object, "loc.names")
+ donor_loc.n.all <- slot(object, "loc.nall")
+ donor_all.names <- slot(object, "all.names")
+ donor_ploidy <- slot(object, "ploidy")
+ donor_type <- slot(object, "type")
+ donor_other <- slot(object, "other")
+ donor_call <- slot(object, "call")
+ donor_pop <- slot(object, "pop")
+ donor_pop.names <- slot(object, "pop.names")
+
+ if (donor_type == "codom"){
+
+ if (!is.integer(donor_tab) && length(donor_ploidy == 1)){
+ xtab <- donor_tab
+ newtab <- as.integer(donor_tab * donor_ploidy)
+ donor_tab <- matrix(newtab, nrow = nrow(xtab), ncol = ncol(xtab),
+ dimnames = dimnames(xtab))
+ donor_ploidy <- rep(donor_ploidy, nrow(donor_tab))
+ }
+
+ names(donor_loc.names) <- NULL
+ rownames(donor_tab) <- donor_ind.names
+ names(donor_all.names) <- donor_loc.names
+ donor_all.names <- lapply(donor_all.names, setNames, NULL)
+ colnames(donor_tab) <- unlist(lapply(donor_loc.names,
+ function(i) paste(i, donor_all.names[[i]],
+ sep = ".")),
+ use.names = FALSE)
+ levels(donor_loc.fac) <- donor_loc.names
+ names(donor_loc.n.all) <- donor_loc.names
+ }
+
+ if (!is.null(donor_pop)){
+ levels(donor_pop) <- donor_pop.names
+ }
+ donor_call <- match.call()
+ donor at tab <- donor_tab
+ donor at loc.fac <- donor_loc.fac
+ donor at all.names <- donor_all.names
+ donor at loc.n.all <- donor_loc.n.all
+ donor at all.names <- donor_all.names
+ donor at ploidy <- donor_ploidy
+ donor at type <- donor_type
+ donor at other <- donor_other
+ donor at call <- donor_call
+ donor at pop <- donor_pop
+ donor at strata <- .get_slot(object, "strata")
+ donor at hierarchy <- .get_slot(object, "hierarchy")
+ return(donor)
+}
+
+
+
+#' @rdname old2new
+#' @export
+old2new_genlight <- function(object, donor = new("genlight")){
+ if (missing(donor) || !is(donor, "genlight")){
+ donor <- new("genlight")
+ }
+ slot(donor, "gen") <- slot(object, "gen")
+ slot(donor, "n.loc") <- slot(object, "n.loc")
+ slot(donor, "ind.names") <- slot(object, "ind.names")
+ slot(donor, "loc.names") <- slot(object, "loc.names")
+ slot(donor, "loc.all") <- slot(object, "loc.all")
+ slot(donor, "chromosome") <- slot(object, "chromosome")
+ slot(donor, "position") <- slot(object, "position")
+ slot(donor, "ploidy") <- slot(object, "ploidy")
+ slot(donor, "pop") <- slot(object, "pop")
+ slot(donor, "other") <- slot(object, "other")
+ donor at strata <- .get_slot(object, "strata")
+ donor at hierarchy <- .get_slot(object, "hierarchy")
+ return(donor)
+}
+
+#' @rdname old2new
+#' @export
+old2new_genpop <- function(object, donor = new("genpop")){
+
+ ## names(donor_pop.names) <- NULL
+ ## names(donor_loc.names) <- NULL
+ donor_tab <- object at tab
+ donor_loc.fac <- object at loc.fac
+ donor_all.names <- object at all.names
+ donor_loc.n.all <- object at loc.nall
+ donor_all.names <- object at all.names
+ donor_ploidy <- object at ploidy
+ donor_type <- object at type
+ donor_other <- object at other
+ donor_call <- object at call
+
+ donor_pop.names <- object at pop.names
+ donor_loc.names <- object at loc.names
+
+ rownames(donor_tab) <- donor_pop.names
+ colnames(donor_tab) <- unlist(lapply(donor_loc.names,
+ function(i) paste(i, donor_all.names[[i]],
+ sep = ".")),
+ use.names = FALSE)
+ names(donor_all.names) <- donor_loc.names
+ donor_all.names <- lapply(donor_all.names, setNames, NULL)
+ donor_call <- match.call()
+
+ donor at tab <- donor_tab
+ donor at loc.fac <- donor_loc.fac
+ donor at all.names <- donor_all.names
+ donor at loc.n.all <- donor_loc.n.all
+ donor at all.names <- donor_all.names
+ donor at ploidy <- donor_ploidy
+ donor at type <- donor_type
+ donor at other <- donor_other
+ donor at call <- donor_call
+ return(object)
+ # x <- object
+# res <- new("genpop")
+#
+# res at tab <- as.matrix(x$tab)
+# res at pop.names <- as.character(x$pop.names)
+# res at loc.names <- as.character(x$loc.names)
+# res at loc.n.all <- as.integer(x$loc.n.all)
+# res at loc.fac <- as.factor(x$loc.fac)
+# res at all.names <- as.list(x$all.names)
+# res at ploidy <- as.integer(2)
+# res at type <- "codom"
+#
+# res at call <- match.call()
+#
+# if(length(object)>7) warning("optional content was not converted")
+#
+# return(res)
+}
diff --git a/R/orthobasis.R b/R/orthobasis.R
new file mode 100644
index 0000000..9da4e42
--- /dev/null
+++ b/R/orthobasis.R
@@ -0,0 +1,366 @@
+## THIS CODE HAS BEEN TAKEN FROM ADE4
+## IT HAS BEEN MOVED TO ADESPATIAL
+## THIS IS MERELY A TEMPORARY FIX.
+
+## only orthobasis.listw is used.
+## renamed into .orthobasis.listw to avoid having to document it.
+
+## - Thibaut Jombart, April 2015
+
+#######################################################
+
+.orthobasis.listw <- function( listw) {
+ appel = match.call()
+ if(!inherits(listw,"listw")) stop ("object of class 'listw' expected")
+ if(listw$style!="W") stop ("object of class 'listw' with style 'W' expected")
+ n = length(listw$weights)
+ fun <- function (x) {
+ num = listw$neighbours[[x]]
+ wei = listw$weights[[x]]
+ res = rep(0,n)
+ res[num] = wei
+ return (res)
+ }
+ b0 <- matrix(unlist(lapply(1:n,fun)),n,n)
+ b0=(t(b0)+b0)/2
+ b0=bicenter.wt(b0)
+ a0 <- eigen(b0, symmetric = TRUE)
+ #barplot(a0$values)
+ a0 <- a0$vectors
+ a0 <- cbind(rep(1,n),a0)
+ a0 <- qr.Q(qr(a0))
+ a0 <- as.data.frame(a0[,-1])*sqrt(n)
+ row.names(a0) <- attr(listw,"region.id")
+ names(a0) <- paste("VP", 1:(n-1), sep = "")
+ z <- apply(a0,2,function(x) sum((t(b0*x)*x))/n)
+ attr(a0,"values") <- z
+ attr(a0,"weights") <- rep(1/n,n)
+ attr(a0,"call") <- appel
+ attr(a0,"class") <- c("orthobasis","data.frame")
+ return(a0)
+}
+
+
+
+
+## print.orthobasis <- function(x,...) {
+## if (!inherits(x,"orthobasis")) stop ("for 'orthobasis' object")
+## cat("Orthonormal basis: ")
+## n <- nrow(x)
+## p <- ncol(x)
+## if (n!=(p+1)) stop ("Non convenient dimension: author's error")
+## cat("data.frame with",n,"rows and",ncol(x),"columns\n")
+## cat("--------------------------------------\n")
+## cat("Columns are an orthonormal basis of 1n-orthogonal for\n")
+## cat("the inner product defined by the weights attribute\n")
+## cat("---------------------------------------\n")
+## w <- attributes(x)
+## if (!is.null(w$"names")) cat("names =", w$names[1],"...",w$names[p],"\n")
+## if (!is.null(w$"row.names")) cat("row.names =", w$row.names[1],"...",w$row.names[n],"\n")
+## if (!is.null(w$"weights")) cat("weights =", w$weights[1],"...",w$weights[n],"\n")
+## if (!is.null(w$"values")) cat("values =", w$values[1],"...",w$values[p],"\n")
+## if (!is.null(w$"class")) cat("class =", w$class,"\n")
+## if (!is.null(w$"call")) {
+## cat("call =")
+## print(w$"call")
+## }
+## }
+
+
+## orthobasis.mat <- function(mat, cnw=TRUE) {
+## if (!is.matrix(mat)) stop ("matrix expected")
+## if (any(mat<0)) stop ("negative value in 'mat'")
+## if (nrow(mat)!=ncol(mat)) stop ("squared matrix expected")
+## mat <- (mat+t(mat))/2
+## nlig <- nrow(mat)
+## if (is.null(dimnames(mat))) {
+## w <- paste("P",1:nrow(mat),sep="")
+## dimnames(mat) <- list(w,w)
+## }
+## labels <- dimnames(mat)[[1]]
+## if (cnw) {
+## margi <- apply(mat,1,sum)
+## margi <- max(margi)-margi
+## mat <- mat+diag(margi)
+## }
+## mat <- mat/sum(mat)
+## wt <- rep ((1/nlig),nlig)
+## # calculs extensibles a une ponderation quelconque
+## wt <- wt/sum(wt)
+## # si mat wt est la ponderation marginale associee a mat
+## # tot = sum(mat)
+## # mat = mat-matrix(wt,nlig,nlig,byrow=TRUE)*wt*tot
+## # encore plus particulier mat = mat-1/nlig/nlig
+## # en general les precedents sont des cas particuliers
+## U <- matrix(1,nlig,nlig)
+## U <- diag(1,nlig)-U*wt
+## mat <- U%*%mat%*%t(U)
+## wt <- sqrt(wt)
+## mat <- t(t(mat)/wt)
+## mat <- mat/wt
+## eig <- eigen(mat,sym=TRUE)
+## w0 <- abs(eig$values)/max(abs(eig$values))
+## tol <- 1e-07
+## w0 <- which(w0<tol)
+## if (length(w0)==0) stop ("abnormal output : no null eigenvalue")
+## else if (length(w0)==1) w0 <- (1:nlig)[-w0]
+## else if (length(w0)>1) {
+## # on ajoute le vecteur derive de 1n
+## w <- cbind(wt,eig$vectors[,w0])
+## # on orthonormalise l'ensemble
+## w <- qr.Q(qr(w))
+## # on met les valeurs propres a 0
+## eig$values[w0] <- 0
+## # on remplace les vecteurs du noyau par une base orthonormee contenant
+## # en premiere position le parasite
+## eig$vectors[,w0] <- w[,-ncol(w)]
+## # on enleve la position du parasite
+## w0 <- (1:nlig)[-w0[1]]
+## }
+## mat <- eig$vectors[,w0]/wt
+## mat <- data.frame(mat)
+## row.names(mat) <- labels
+## names(mat) <- paste("S",1:(nlig-1),sep="")
+## attr(mat,"values") <- eig$values[w0]
+## attr(mat,"weights") <- rep(1/nlig,nlig)
+## attr(mat,"call") <- match.call()
+## attr(mat,"class") <- c("orthobasis","data.frame")
+## return(mat)
+## }
+
+## "orthobasis.haar" <- function(n) {
+## # on definit deux fonctions :
+## appel = match.call()
+## a <- log(n)/log(2)
+## b <- floor(a)
+## if ((a-b)^2>1e-10) stop ("Haar is not a power of 2")
+## # la premiere est ecrite par Daniel et elle donne la demonstration (par analogie avec la fonction qui construit la base Bscores)
+## # que la base Bscores est exactement la base de Haar quand on prend une phylogenie reguliere resolue.
+## "haar.basis.1" <- function (n) {
+## pari <- matrix(c(1,n),1)
+## "div2" <- function (mat) {
+## res <- NULL
+## for (k in 1 : nrow(mat)) {
+## n1 <- mat[k,1]
+## n2 <- mat[k,2]
+## diff <- n2-n1
+## if (diff <=0) break
+## n3 <- floor((n1+n2)/2)
+## res <- rbind(res,c(n1,n3),c(n3+1,n2))
+## }
+## if (!is.null(res)) pari <<- rbind(pari,res)
+## return(res)
+## }
+## mat <- div2(pari)
+## while (!is.null(mat)) mat <- div2(mat)
+## res <- NULL
+## for (k in 1:nrow(pari)) {
+## x<-rep(0,n)
+## x[(pari[k,1]):(pari[k,2])] <- 1
+## res <-c(res,x)
+## }
+## res = matrix(res,n)
+## res <- qr.Q(qr(res))
+## res <- res[, -1] * sqrt(n)
+## res <- data.frame(res)
+## row.names(res) <- paste("u",1:n,sep="")
+## names(res) <- paste("B",1:(n-1),sep="")
+## return(res)
+## }
+
+## # la seconde exploite les potentialites de la librairie waveslim, en remarquant qu'il existe un lien etroit entre la definition des filtres et la definition
+## # des bases. Cette strategie permettra a l'avenir de definir les bases associees a d'autres famille de fonctions.
+## "haar.basis.2" <- function (n) {
+## if (!require(waveslim)) stop ("Please install waveslim")
+## J <- a #nombre de niveau
+## res <- matrix(0, nrow = n,ncol = n-1)
+## filter.seq <- "H" #filtre correspondant au niveau 1
+## h <- waveslim::wavelet.filter(wf.name = "haar", filter.seq = filter.seq) #parametre du filtre au niveau 1
+## k <- 0
+## for(i in 1:J){
+## z <- rep(h,2**(J-i))
+## x <- 1:n
+## y <- rep((n-1-k):(n-2**(J-i)-k),rep(2**i,2**(J-i)))
+## for(j in 1:n) res[x[j],y[j]] <- z[j]
+## k <- k+2**(J-i)
+## filter.seq <- paste(filter.seq, "L", sep = "")
+## h <- waveslim::wavelet.filter(wf.name = "haar", filter.seq = filter.seq)
+## }
+## res <- res*sqrt(n)
+## res <- data.frame(res)
+## row.names(res) <- paste("u", 1:n, sep = "")
+## names(res) <- paste("B", 1:(n-1), sep = "")
+## return(res)
+## }
+
+## # suivant que n est grand (n > 257) ou non, on choisit l'une des deux strategies :
+## if (n < 257)
+## res <- haar.basis.1(n)
+## else
+## res <- haar.basis.2(n)
+
+## attr(res,"values") <- NULL
+## attr(res,"weights") <- rep(1/n,n)
+## attr(res,"call") <- appel
+## attr(res,"class") <- c("orthobasis","data.frame")
+## return(res)
+## }
+
+## "orthobasis.line" <- function (n) {
+## appel <- match.call()
+## # solution de Cornillon p. 12
+## res <- NULL
+## for (k in 1:(n-1)) {
+## x <- cos(k*pi*(2*(1:n)-1)/2/n)
+## x <- sqrt(n)*x/sqrt(sum(x*x))
+## res <-c(res,x)
+## }
+## res=matrix(res,n)
+## res <- data.frame(res)
+## row.names(res) <- paste("u",1:n,sep="")
+## names(res) <- paste("B",1:(n-1),sep="")
+## w <- (1:(n-1))*pi/2/n
+## valpro <- 4*(sin(w)^2)/n
+## poivoisi <- c(1,rep(2,n-2),1)
+## poivoisi <- poivoisi/sum(poivoisi)
+## norm <- unlist(apply(res, 2, function(a) sum(a*a*poivoisi)))
+## y <- valpro*n*n/2/(n-1)
+## val <- norm - y
+## attr(res,"values") <- val
+## attr(res,"weights") <- rep(1/n,n)
+## attr(res,"call") <- appel
+## attr(res,"class") <- c("orthobasis","data.frame")
+
+## # verification locale. Ce paragraphe verifie que les vecteurs et les valeurs
+## # proposee par Cornillon p. 12 sont bien les vecteurs propres de l'operateur de voisinage
+## # rangee dans la solution analytique par variance locale croissante
+## # l'article de Meot est errone et a donne le graphe circulaire pour le graphe lineaire
+## # d0=neig2mat(neig(n.lin=n))
+## # d0 = d0/n
+## # d1=apply(d0,1,sum)
+## # d0=diag(d1)-d0
+## # fun2 <- function(x) {
+## # z <- sum(t(d0*x)*x)/n
+## # z <- z/sum(x*x)
+## # return(z)
+## # }
+## # lambda <- unlist(apply(res,2,fun2))
+## # print(lambda)
+## # print(attr(res,"values"))
+## # plot(lambda,attr(res,"values"))
+## # abline(lm(attr(res,"values")~lambda))
+## # print(coefficients(lm(attr(res,"values")~lambda)))
+
+## # verification que les valeurs derivees des valeurs propres sont exactement des indices de Moran
+## # d = neig2mat(neig(n.lin=n))
+## # d = d/sum(d) # Moran type W
+## # moran <- unlist(lapply(res,function(x) sum(t(d*x)*x)))
+## # print(moran)
+## # plot(moran,attr(res,"values"))
+## # abline(lm(attr(res,"values")~moran))
+## # print(summary(lm(attr(res,"values")~moran)))
+## return(res)
+## }
+
+## "orthobasis.circ" <- function (n) {
+## appel = match.call()
+## if (n<3) stop ("'n' too small")
+## "vecprosin" <- function(k) {
+## x <- sin(2*k*pi*(1:n)/n)
+## x <- x/sqrt(sum(x*x))
+## }
+## "vecprocos" <- function(k) {
+## x <- cos(2*k*pi*(1:n)/n)
+## x <- x/sqrt(sum(x*x))
+## }
+## "valpro" <- function(k,bis=TRUE) {
+## x <- (4/n)*((sin(k*pi/n))^2)
+## if (bis) x <- c(x,x)
+## return(x)
+## }
+
+## k <- floor(n/2)
+## if (k==n/2) {
+## #n est pair
+## w1 <- matrix(unlist(lapply(1:k,vecprocos)),n,k)
+## w2 <- matrix(unlist(lapply(1:(k-1),vecprosin)),n,k-1)
+## res <- cbind(w1,w2)
+## res[,seq(1,2*k-1,by=2)]<-w1
+## res[,seq(2,2*k-2,by=2)]<-w2
+## vp <- unlist(lapply(1:(k-1),valpro))
+## vp <- c(vp, valpro(k,FALSE))
+## } else {
+## # n est impair
+## w1 <- matrix(unlist(lapply(1:k,vecprocos)),n,k)
+## w2 <- matrix(unlist(lapply(1:k,vecprosin)),n,k)
+## res <- cbind(w1,w2)
+## res[,seq(1,2*k-1,by=2)]<-w1
+## res[,seq(2,2*k,by=2)]<-w2
+## vp <- unlist(lapply(1:k,valpro))
+## }
+## res=sqrt(n)*res
+## res <- as.data.frame(res)
+## row.names(res) <- paste("u",1:n,sep="")
+## names(res) <- paste("B",1:(n-1),sep="")
+## attr(res,"values") <- 1 - n*vp/2
+## attr(res,"weights") <- rep(1/n,n)
+## attr(res,"call") <- appel
+## attr(res,"class") <- c("orthobasis","data.frame")
+## # verification qu'on a exactement des indices de Moran a partie des valeurs propres
+## # d = neig2mat(neig(n.cir=n))
+## # d = d/sum(d) # Moran type W
+## # moran <- unlist(lapply(res,function(x) sum(t(d*x)*x)))
+## # print(moran)
+## # plot(moran,attr(res,"values"))
+## # abline(lm(attr(res,"values")~moran))
+## # print(summary(lm(attr(res,"values")~moran)))
+## return(res)
+## }
+
+## "orthobasis.neig" <- function( neig) {
+## appel = match.call()
+## if(!inherits(neig,"neig")) stop ("object of class 'neig' expected")
+## n <- length(attr(neig,"degree"))
+## m <- sum(attr(neig,"degree"))
+## poivoisi <- attr(neig,"degree")/m
+## if (is.null(names(poivoisi))) names(poivoisi) <- as.character(1:n)
+## d0 = neig2mat(neig)
+## d0 = diag(poivoisi)-d0/m
+## eig <- eigen(d0, sym = TRUE)
+## ########
+## tol <- 1e-07
+## w0 <- abs(eig$values)/max(abs(eig$values))
+## w0 <- which(w0<tol)
+## if (length(w0)==0) stop ("abnormal output : no null eigenvalue")
+## else if (length(w0)==1) w0 <- (1:n)[-w0]
+## else if (length(w0)>1) {
+## # on ajoute le vecteur derive de 1n
+## wt <- rep(1,n)
+## w <- cbind(wt,eig$vectors[,w0])
+## # on orthonormalise l'ensemble
+## w <- qr.Q(qr(w))
+## # on met les valeurs propres a 0
+## eig$values[w0] <- 0
+## # on remplace les vecteurs du noyau par une base orthonormee contenant
+## # en premiere position le parasite
+## eig$vectors[,w0] <- w[,-ncol(w)]
+## # on enleve la position du parasite
+## w0 <- (1:n)[-w0[1]]
+## }
+## w0 <- rev(w0)
+## valpro <- eig$values[w0]
+## eig <- eig$vectors[,w0]
+## eig <- as.data.frame(eig)*sqrt(n)
+## z <- apply(eig,2,function(x) sum(x*x*poivoisi))
+## z <- z - valpro*n
+## w <- rev(order(z))
+## z <- z[w]
+## eig <- eig[,w]
+## row.names(eig) <- names(poivoisi)
+## names(eig) <- paste("VP", 1:(n-1), sep = "")
+## attr(eig,"values") <- z
+## attr(eig,"weights") <- rep(1/n,n)
+## attr(eig,"call") <- appel
+## attr(eig,"class") <- c("orthobasis","data.frame")
+## return(eig)
+## }
diff --git a/R/pairDist.R b/R/pairDist.R
new file mode 100644
index 0000000..bd45928
--- /dev/null
+++ b/R/pairDist.R
@@ -0,0 +1,171 @@
+## AVOID:
+## airDistPlot.dist: no visible binding for global variable ‘groups’
+## pairDistPlot.dist: no visible binding for global variable ‘distance’
+if(getRversion() >= "2.15.1") utils::globalVariables(c("groups","distance"))
+
+
+
+##############
+## GENERICS ##
+##############
+pairDistPlot <- function (x, ...) UseMethod("pairDistPlot")
+pairDist <- function (x, ...) UseMethod("pairDistPlot")
+
+
+
+
+
+#############
+## DEFAULT ##
+#############
+pairDistPlot.default <- function(x, ...){
+ stop(paste("No method for objects of class",class(x)))
+} # end pairDistPlot.default
+
+
+pairDist.default <- function(x, grp, within=FALSE, sep="-", ...){
+ temp <- pairDistPlot(x=x, grp=grp, within=within, sep=sep,
+ data=TRUE, violin=FALSE, boxplot=FALSE, jitter=FALSE)
+ return(temp$data)
+}
+
+
+##########
+## DIST ##
+##########
+##
+## this is the basic method
+##
+pairDistPlot.dist <- function(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE,
+ jitter=TRUE, ...){
+ ## CHECKS ##
+ if(attr(x, "Size")!=length(grp)) stop("inconsistent length for grp")
+ grp <- factor(grp)
+ K <- length(levels(grp))
+ N <- length(grp)
+
+
+ ## GET DATA FOR OUTPUT AND PLOTTING ##
+ ## get groups of pairwise comparisons ##
+ allCombs <- combn(N, 2)
+ d <- as.vector(x)
+
+ ## remove within if needed ##
+ if(!within){
+ toKeep <- grp[allCombs[1,]] != grp[allCombs[2,]]
+ allCombs <- allCombs[,toKeep,drop=FALSE]
+ d <- d[toKeep]
+ }
+
+ ## get group-group ##
+ d.grp <- paste(grp[allCombs[1,]], grp[allCombs[2,]], sep=sep)
+
+
+ ## BUILD OUTPUT ##
+ out <- list()
+
+ ## data ##
+ fig.dat <- data.frame(distance=d, groups=d.grp)
+ if(data){
+ out$data <- fig.dat
+ }
+
+ ## plots ##
+ base <- ggplot(data=fig.dat)
+
+ ## violinplot
+ if(violin){
+ out$violin <- base + geom_violin(aes(x=groups, y=distance, fill=groups), alpha=.5) +
+ coord_flip() + guides(fill=FALSE) + labs(x="",y="Pairwise distances")
+ }
+
+ ## boxplot
+ if(boxplot){
+ out$boxplot <- base + geom_boxplot(aes(x=groups, y=distance, fill=groups), alpha=.5) +
+ coord_flip() + guides(fill=FALSE) + labs(x="",y="Pairwise distances")
+ }
+
+ ## jitter
+ if(jitter){
+ out$jitter <- base + geom_jitter(aes(x=groups, y=distance, colour=groups), alpha=.2) +
+ coord_flip() + guides(colour=FALSE) + labs(x="",y="Pairwise distances")
+ }
+
+
+ return(out)
+
+} # end pairDistPlot.dist
+
+
+
+
+
+
+
+############
+## MATRIX ##
+############
+pairDistPlot.matrix <- function(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE,
+ jitter=TRUE, ...){
+ ## CHECKS ##
+ if(nrow(x) != ncol(x)) stop("x is not a square matrix")
+
+ ## RETURN ##
+ out <- pairDistPlot(as.dist(x), grp=grp, within=within, sep=sep,
+ data=data, violin=violin, boxplot=boxplot, jitter=jitter, ...)
+
+ return(out)
+} # end pairDistPlot.matrix
+
+
+
+
+
+
+############
+## GENIND ##
+############
+pairDistPlot.genind <- function(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE,
+ jitter=TRUE, ...){
+ ## CHECKS ##
+ if(missing(grp)){
+ if(!is.null(pop(x))) {
+ grp <- pop(x)
+ } else {
+ stop("grp is missing with no population defined in x")
+ }
+ }
+
+
+ ## RETURN ##
+ D <- dist(x at tab)^2
+ out <- pairDistPlot(D, grp=grp, within=within, sep=sep,
+ data=data, violin=violin, boxplot=boxplot, jitter=jitter, ...)
+
+ return(out)
+} # end pairDistPlot.matrix
+
+
+
+
+
+
+############
+## DNAbin ##
+############
+pairDistPlot.DNAbin <- function(x, grp, within=FALSE, sep="-", data=TRUE, violin=TRUE, boxplot=TRUE,
+ jitter=TRUE, ...){
+
+ ## RETURN ##
+ D <- dist.dna(x, ...)
+ out <- pairDistPlot(D, grp=grp, within=within, sep=sep,
+ data=data, violin=violin, boxplot=boxplot, jitter=jitter, ...)
+
+ return(out)
+} # end pairDistPlot.matrix
+
+
+
+
+
+
diff --git a/R/propShared.R b/R/propShared.R
new file mode 100644
index 0000000..e49624b
--- /dev/null
+++ b/R/propShared.R
@@ -0,0 +1,41 @@
+## propShared computes the proportion of shared alleles
+## in a genind object
+
+
+######################
+# Function propShared
+######################
+propShared <- function(obj){
+ ## CHECK THAT THIS IS A VALID GENIND ##
+ if(!inherits(obj,"genind")) stop("obj must be a genind object.")
+ invisible(validObject(obj))
+
+
+ ## GET MATRIX OF NB OF ALLELES ##
+ x <- tab(obj)
+ x[is.na(x)] <- 0L
+
+ ## COMPUTE NB OF SHARED ALLELES ##
+ n <- nInd(obj)
+ resVec <- integer(n*(n-1)/2)
+
+ res <- .C("nb_shared_all", as.integer(x), as.integer(resVec), as.integer(n), as.integer(ncol(obj$tab)), PACKAGE="adegenet")[[2]]
+ attr(res,"Size") <- n
+ attr(res,"Diag") <- FALSE
+ attr(res,"Upper") <- FALSE
+ class(res) <- "dist"
+ res <- as.matrix(res)
+
+
+ ## COMPUTE NB OF ALLELES TYPED IN COMMON ##
+ tabNA <- propTyped(obj, by="both")
+ tabTypCom <- tabNA %*% t(tabNA) * ploidy(obj)
+
+
+ ## GET PROPORTIONS OF SHARED ALLELES ##
+ res <- res/tabTypCom
+ diag(res) <- 1L
+ colnames(res) <-rownames(res) <- indNames(obj)
+ return(res)
+}
+
diff --git a/R/propTyped.R b/R/propTyped.R
new file mode 100644
index 0000000..d21837a
--- /dev/null
+++ b/R/propTyped.R
@@ -0,0 +1,140 @@
+############
+# propTyped
+############
+setGeneric("propTyped", function(x,...){
+ standardGeneric("propTyped")
+})
+
+
+
+setMethod("propTyped","genind", function(x, by=c("ind","loc","both")){
+
+ ## checkType(x)
+ by <- match.arg(by)
+
+ ## PA case ##
+ if(x at type=="PA"){
+ temp <- as.matrix(x)
+
+ if(by=="ind"){
+ res <- apply(temp,1,function(r) mean(is.na(r)))
+ return(1-res)
+ }
+
+ if(by=="loc"){
+ res <- apply(temp,2,function(c) mean(is.na(c)))
+ return(1-res)
+ }
+
+ if(by=="both"){
+ res <- !is.na(temp)
+ return(res*1)
+ }
+ } # end PA case
+
+
+ ## codom case ##
+
+ ## auxil function f1
+ f1 <- function(vec){
+ if(any(is.na(vec))) return(0)
+ else return(1)
+ }
+
+ ## temp is a list (one component / marker)
+ ## with n values (0: not typed, 1: typed)
+ kX <- seploc(x,res.type="matrix")
+ temp <- lapply(kX, function(X) apply(X, 1, f1))
+
+ ## by individual
+ if(by=="ind"){
+ temp <- as.data.frame(temp)
+ res <- apply(temp,1,mean)
+ }
+
+ ## by locus
+ if(by=="loc"){
+ res <- unlist(lapply(temp,mean))
+ }
+
+ ## by individual and locus
+ if(by=="both"){
+ res <- as.matrix(as.data.frame(temp))
+ }
+
+ return(res)
+})
+
+
+
+
+
+setMethod("propTyped","genpop", function(x, by=c("pop","loc","both")){
+
+ ## checkType(x)
+ by <- match.arg(by)
+
+
+ ## PA case ##
+ if(x at type=="PA"){
+ temp <- as.matrix(x)
+
+ if(by=="pop"){
+ res <- apply(temp,1,function(r) mean(is.na(r)))
+ return(1-res)
+ }
+
+ if(by=="loc"){
+ res <- apply(temp,2,function(c) mean(is.na(c)))
+ return(1-res)
+ }
+
+ if(by=="both"){
+ res <- !is.na(temp)
+ return(res*1)
+ }
+ } # end PA case
+
+
+ ## codom case ##
+
+
+ ## auxil function f1
+ f1 <- function(vec){
+ if(any(is.na(vec))) return(0)
+ else return(1)
+ }
+
+ ## weighted mean
+ mean.w <- function(x,w=rep(1/length(x),length(x))){
+ x <- x[!is.na(x)]
+ w <- w[!is.na(x)]
+ w <- w/sum(w)
+ return(sum(x*w))
+ }
+
+ ## temp is a list (one component / marker)
+ ## with n values (0: not typed, 1: typed)
+ kX <- seploc(x,res.type="matrix")
+ temp <- lapply(kX, function(X) apply(X, 1, f1))
+
+ ## by individual
+ if(by=="pop"){
+ temp <- as.data.frame(temp)
+ w <- unlist(lapply(kX, sum,na.rm=TRUE))
+ res <- apply(temp,1,mean.w,w=w)
+ }
+
+ ## by locus
+ if(by=="loc"){
+ w <- apply(x at tab,1,sum,na.rm=TRUE)
+ res <- unlist(lapply(temp,mean.w,w=w))
+ }
+
+ ## by individual and locus
+ if(by=="both"){
+ res <- as.matrix(as.data.frame(temp))
+ }
+
+ return(res)
+})
diff --git a/R/scale.R b/R/scale.R
new file mode 100644
index 0000000..58a7ad6
--- /dev/null
+++ b/R/scale.R
@@ -0,0 +1,123 @@
+
+#' Compute scaled allele frequencies
+#'
+#' The generic function \code{scaleGen} is an analogue to the \code{scale}
+#' function, but is designed with further arguments giving scaling options.\cr
+#'
+#' Methods are defined for \linkS4class{genind} and \linkS4class{genpop}
+#' objects. Both return data.frames of scaled allele frequencies.
+#'
+#'
+#' @rdname scaleGen
+#' @aliases scaleGen scaleGen-methods scaleGen,genind-method
+#' scaleGen,genpop-method
+#' @docType methods
+#' @export
+#' @param x a \linkS4class{genind} and \linkS4class{genpop} object
+#' @param center a logical stating whether alleles frequencies should be
+#' centred to mean zero (default to TRUE). Alternatively, a vector of numeric
+#' values, one per allele, can be supplied: these values will be substracted
+#' from the allele frequencies.
+#' @param scale a logical stating whether alleles frequencies should be scaled
+#' (default to TRUE). Alternatively, a vector of numeric values, one per
+#' allele, can be supplied: these values will be substracted from the allele
+#' frequencies.
+#' @param truenames no longer used; kept for backward compatibility
+#' @param NA.method a method to replace NA; asis: leave NAs as is; mean: replace by the mean allele frequencies; zero: replace by zero
+#' @param ... further arguments passed to other methods.
+#' @return A matrix of scaled allele frequencies with genotypes
+#' (\linkS4class{genind}) or populations in (\linkS4class{genpop}) in rows and
+#' alleles in columns.
+#' @author Thibaut Jombart \email{t.jombart@@imperial.ac.uk}
+#' @keywords methods manip
+#' @examples
+#'
+#' \dontrun{
+#' ## load data
+#' data(microbov)
+#' obj <- genind2genpop(microbov)
+#'
+#' ## compare different scaling
+#' X1 <- scaleGen(obj)
+#' X2 <- scaleGen(obj,met="bin")
+#'
+#' ## compute PCAs
+#' pcaObj <- dudi.pca(obj,scale=FALSE,scannf=FALSE) # pca with no scaling
+#' pcaX1 <- dudi.pca(X1,scale=FALSE,scannf=FALSE,nf=100) # pca with usual scaling
+#' pcaX2 <- dudi.pca(X2,scale=FALSE,scannf=FALSE,nf=100) # pca with scaling for binomial variance
+#'
+#' ## get the loadings of alleles for the two scalings
+#' U1 <- pcaX1$c1
+#' U2 <- pcaX2$c1
+#'
+#'
+#' ## find an optimal plane to compare loadings
+#' ## use a procustean rotation of loadings tables
+#' pro1 <- procuste(U1,U2,nf=2)
+#'
+#' ## graphics
+#' par(mfrow=c(2,2))
+#' # eigenvalues
+#' barplot(pcaObj$eig,main="Eigenvalues\n no scaling")
+#' barplot(pcaX1$eig,main="Eigenvalues\n usual scaling")
+#' barplot(pcaX2$eig,main="Eigenvalues\n 'binomial' scaling")
+#' # differences between loadings of alleles
+#' s.match(pro1$scor1,pro1$scor2,clab=0,sub="usual -> binom (procustean rotation)")
+#'
+#' }
+#'
+setGeneric("scaleGen", function(x,...){standardGeneric("scaleGen")})
+
+#' @rdname scaleGen
+#' @export
+setMethod("scaleGen", "genind", function(x, center=TRUE, scale=TRUE,
+ NA.method=c("asis","mean","zero"), truenames=TRUE){
+
+ THRES <- 1e-10
+
+ ## get table of frequencies
+ out <- tab(x, NA.method=NA.method, freq=TRUE, quiet=TRUE)
+
+ ## scale output
+ out <- scale(out, center=center, scale=scale)
+
+ ## issue a warning if some variances are null
+ temp <- attr(out,"scaled:scale") < THRES
+ if(any(temp)) {
+ warning("Some scaling values are null.\n Corresponding alleles are removed.")
+ out <- out[, !temp]
+ attr(out,"scaled:center") <- attr(out,"scaled:center")[!temp]
+ attr(out,"scaled:scale") <- attr(out,"scaled:scale")[!temp]
+ }
+
+ return(out)
+})
+
+
+
+
+
+#' @rdname scaleGen
+#' @export
+setMethod("scaleGen", "genpop", function(x, center=TRUE, scale=TRUE,
+ NA.method=c("asis","mean","zero"), truenames=TRUE){
+
+ THRES <- 1e-10
+
+ ## get table of frequencies
+ out <- tab(x, NA.method=NA.method, freq=TRUE, quiet=TRUE)
+
+ ## scale output
+ out <- scale(out, center=center, scale=scale)
+ ## issue a warning if some variances are null
+ temp <- attr(out,"scaled:scale") < THRES
+ if(any(temp)) {
+ warning("Some scaling values are null.\n Corresponding alleles are removed.")
+ out <- out[, !temp]
+ attr(out,"scaled:center") <- attr(out,"scaled:center")[!temp]
+ attr(out,"scaled:scale") <- attr(out,"scaled:scale")[!temp]
+ }
+
+ return(out)
+})
+
diff --git a/R/seqTrack.R b/R/seqTrack.R
new file mode 100644
index 0000000..ffb9316
--- /dev/null
+++ b/R/seqTrack.R
@@ -0,0 +1,1145 @@
+############
+## generics
+############
+seqTrack <- function(...){
+ UseMethod("seqTrack")
+}
+
+seqTrack.default <- function(x, ...){
+ cat("\nseqTrack not implemented for object of the class", class(x),"\n")
+ return(invisible(NULL))
+}
+
+## seqTrackG <- function(...){
+## UseMethod("seqTrackG")
+## }
+
+
+## optimize.seqTrack <- function(...){
+## UseMethod("optimize.seqTrack")
+## }
+
+
+get.likelihood <- function(...){
+ UseMethod("get.likelihood")
+}
+
+
+
+
+
+########################
+## seqTrack - basic version
+########################
+##
+## - x is a matrix giving weights x[i,j] such that:
+## 'i is ancestor j'
+## - prox.mat is a directed proximity measure, so that prox.mat[i,j] is
+## the 'proximity when going from i to j'
+##
+seqTrack.matrix <- function(x, x.names, x.dates, best=c("min","max"),
+ prox.mat=NULL, mu=NULL, haplo.length=NULL, ...){
+
+ ## CHECKS ##
+ best <- match.arg(best)
+ if(best=="min"){
+ best <- min
+ which.best <- which.min
+ } else {
+ best <- max
+ which.best <- which.max
+ }
+
+ if(length(x.names) != length(x.dates)){
+ stop("inconsistent length for x.dates")
+ }
+
+ if(is.character(x.dates)){
+ msg <- paste("x.dates is a character vector; " ,
+ "please convert it as dates using 'as.POSIXct'" ,
+ "\n(making sure dates are given as 'YYYY/MM/DD' or 'YYYY-MM-DD').", sep="")
+ stop(msg)
+ }
+
+ x <- as.matrix(x)
+
+ if(!is.null(prox.mat) && !identical(dim(prox.mat),dim(x))) {
+ stop("prox.mat is provided but its dimensions are inconsistent with that of x")
+ }
+
+ N <- length(x.names)
+ id <- 1:N
+
+ x.dates <- as.POSIXct(round.POSIXt(x.dates,units="days")) # round dates to the day
+
+ temp <- as.vector(unique(x))
+ D.ARE.MUT <- all(temp-round(temp,10)<1e-14)
+
+
+ ## rename dimensions using id
+ colnames(x) <- rownames(x) <- id
+ if(!is.null(prox.mat)){
+ colnames(prox.mat) <- rownames(prox.mat) <- id
+ }
+
+ if(length(x.names) != nrow(x)){
+ stop("inconsistent dimension for x")
+ }
+
+
+ ## AUXILIARY FUNCTIONS ##
+ ## test equality in floats
+ test.equal <- function(val,vec){
+ return(abs(val-vec) < 1e-12)
+ }
+
+
+ ## return the names of optimal value(s) in a named vector
+ which.is.best <- function(vec){
+ res <- names(vec)[test.equal(best(vec), vec)]
+ return(res)
+ }
+
+
+ ## select among different possible ancestors
+ selAmongAncestors <- function(idx,ances){
+ ## Choose the most connected ancestor, given prox.mat
+ if(!is.null(prox.mat)){ # if we've got no other info
+ toKeep <- test.equal(max(prox.mat[ances,idx]), prox.mat[ances,idx])
+ ances <- ances[toKeep]
+ }
+
+ ## If several ancestors remain, take the one closest to the average generation time.
+ if(length(ances)>1){
+ if(!D.ARE.MUT | is.null(mu) | is.null(haplo.length)) { # if we don't have mutation rates / haplo length, or if dist. are not nb of mutations
+ ances <- ances[which.min(x.dates[ances])] # take the oldest ancestor
+ } else { # if distances are mutations and we've got mu and L
+ timeDiff <- as.numeric(difftime(x.dates[idx], x.dates[ances], units="day")) # days between candidates and target
+ ##nbGen <- round(timeDiff / gen.time) # number of generations
+ nbMut <- x[ances, idx]
+ prob <- dbinom(nbMut, timeDiff*haplo.length, mu)
+ ances <- ances[which.max(prob)] # take the most likely ancestor
+ }
+ }
+
+ return(ances)
+ }
+
+
+ ## findAncestor
+ findAncestor <- function(idx){ # returns the index of one seq's ancestor
+ candid <- which(x.dates < x.dates[idx])
+ if(length(candid)==0) return(list(ances=NA, weight=NA))
+ if(length(candid)==1) return(list(ances=candid, weight=x[candid, idx]))
+ ancesId <- as.numeric(which.is.best(x[candid, idx]))
+ if(length(ancesId)>1) {
+ ancesId <- selAmongAncestors(idx,ancesId) # handle several 'best' ancestors
+ }
+ return(list(ances=ancesId, weight=x[ancesId, idx])) # Id of the ancestor
+ }
+
+
+ ## BUILD THE OUTPUT ##
+ res <- sapply(id, findAncestor)
+ res <- data.frame(ances=unlist(res[1,]), weight=unlist(res[2,]))
+ ances.date <- x.dates[res[,1]]
+ res <- cbind.data.frame(id,res, date=x.dates, ances.date)
+ rownames(res) <- x.names
+
+ class(res) <- c("seqTrack","data.frame")
+
+ return(res)
+} # end seqTrack.matrix
+
+
+
+
+
+################
+## plotSeqTrack
+################
+plotSeqTrack <- function(x, xy, use.arrows=TRUE, annot=TRUE, labels=NULL,
+ col=NULL, bg="grey", add=FALSE, quiet=FALSE, date.range=NULL,
+ jitter.arrows=0, plot=TRUE,...){
+
+ ## CHECKS ##
+ if(!inherits(x,"seqTrack")) stop("x is not a seqTrack object")
+ if(ncol(xy) != 2) stop("xy does not have two columns")
+ if(nrow(xy) != nrow(x)) stop("x and xy have inconsistent dimensions")
+
+
+ ## RECYCLE COL
+ if(!is.null(col)){
+ col <- rep(col,length=nrow(x))
+ } else {
+ col <- rep("black", nrow(x))
+ }
+
+
+ ## DEFAULT LABELS
+ if(is.null(labels)){
+ if(!is.null(rownames(x))){
+ labels <- rownames(x)
+ } else {
+ labels <- 1:nrow(x)
+ }
+ }
+
+
+ ## SUBSET DATA (REMOVE NAs) ##
+ isNA <- is.na(x[,2])
+ x <- x[!isNA,,drop=FALSE]
+ xy.all <- xy # used to retrieve all coordinates
+ xy <- xy[!isNA,,drop=FALSE]
+ if(!is.null(labels)){ # subset labels
+ labels <- labels[!isNA]
+ }
+ if(!is.null(col)){ # subset colors
+ col <- col[!isNA]
+ }
+
+
+ ## FIND SEGMENTS COORDS ##
+ from <- unlist(x[,2])
+ to <- unlist(x[,1])
+
+ x.from <- xy.all[from,1]
+ y.from <- xy.all[from,2]
+ x.to <- xy.all[to,1]
+ y.to <- xy.all[to,2]
+
+
+ ## HANDLE RANGE OF DATES ##
+ if(!is.null(date.range)){
+
+ if(is.character(date.range)){
+ msg <- paste("date.range is a character vector; " ,
+ "please convert it as dates using 'as.POSIXct'" ,
+ "\n(making sure dates are given as 'YYYY/MM/DD' or 'YYYY-MM-DD').", sep="")
+ stop(msg)
+ }
+
+ if(any(is.na(date.range))){
+ stop("NA in date.range")
+ }
+
+ dates <- x$date
+ toKeep <- (dates > min(date.range)) & (dates < max(date.range))
+ if(sum(toKeep)==0) {
+ if(!quiet) cat("\nNo item in the specified date range.\n")
+ return(NULL)
+ }
+
+
+ ## SUBSETTING
+ x.from <- x.from[toKeep]
+ y.from <- y.from[toKeep]
+ x.to <- x.to[toKeep]
+ y.to <- y.to[toKeep]
+ col <- col[toKeep]
+ xy <- xy[toKeep,,drop=FALSE]
+ x <- x[toKeep,,drop=FALSE]
+ labels <- labels[toKeep]
+
+ }
+
+
+ ## DO THE PLOTTING ##
+ if(plot){
+ obg <- par("bg")
+ on.exit(par(bg=obg))
+ if(!add){
+ par(bg=bg)
+ plot(xy, type="n", ...)
+ }
+ }
+
+
+ ## PLOTTING ##
+ if(plot){
+ ## ARROWS
+ if(use.arrows){
+ ## handle segments/arrows with length 0 ##
+ nullLength <- (abs(x.from-x.to)<1e-10) & (abs(y.from-y.to)<1e-10)
+
+ ## handle random noise around coordinates
+ if(jitter.arrows>0){
+ x.from[!nullLength] <- jitter(x.from[!nullLength], jitter.arrows)
+ x.to[!nullLength] <- jitter(x.to[!nullLength], jitter.arrows)
+ y.from[!nullLength] <- jitter(y.from[!nullLength], jitter.arrows)
+ y.to[!nullLength] <- jitter(y.to[!nullLength], jitter.arrows)
+ }
+
+ arrows(x.from[!nullLength], y.from[!nullLength],
+ x.to[!nullLength], y.to[!nullLength],
+ col=col[!nullLength], angle=15, ...)
+ } else{
+ ## SEGMENTS
+ ## handle random noise around coordinates
+ if(jitter.arrows>0){
+ x.from[!nullLength] <- jitter(x.from[!nullLength], jitter.arrows)
+ x.to[!nullLength] <- jitter(x.to[!nullLength], jitter.arrows)
+ y.from[!nullLength] <- jitter(y.from[!nullLength], jitter.arrows)
+ y.to[!nullLength] <- jitter(y.to[!nullLength], jitter.arrows)
+ }
+
+ segments(x.from, y.from, x.to, y.to, col=col,...)
+ }
+
+ ## ANNOTATIONS
+ if(annot) {
+ text(xy,lab=labels, font=2)
+ }
+
+ ## SUNFLOWERS / POINTS
+ if(any(nullLength)) {
+ sunflowerplot(x.from[nullLength], y.from[nullLength], seg.lwd=2, size=1/6,
+ col=col[nullLength], seg.col=col[nullLength], add=TRUE, ...)
+ points(x.from[nullLength], y.from[nullLength], col=col[nullLength], cex=2, pch=20, ...)
+ }
+
+ }
+
+
+ ## RESULT ##
+ res <- data.frame(x.from, y.from, x.to, y.to, col=col)
+
+ return(invisible(res))
+} # end plotSeqTrack
+
+
+
+
+
+
+###########################
+## get.likelihood.seqTrack
+###########################
+get.likelihood.seqTrack <- function(x, mu, haplo.length,...){
+ if(any(na.omit(x$weight - round(x$weight)) > 1e-10)){
+ warning("Non-integer weights: number of mutations expected in x$weight.")
+ }
+
+ dates <- as.POSIXct(x$date)
+ anc.dates <- as.POSIXct(x$ances.date)
+ nb.days <- abs(as.integer(anc.dates-dates))
+ nb.mut <- x$weight
+
+ ## res <- dbinom(nb.mut, size=haplo.length*nb.days, prob=mu)
+ res <- dpois(x=nb.mut, lambda=mu*haplo.length*nb.days)
+
+ return(res)
+} # end get.likelihood.seqTrack
+
+
+
+
+
+
+######################
+## as.igraph.seqTrack
+######################
+as.igraph.seqTrack <- function(x, col.pal=redpal, ...){
+
+ ## GET DAG ##
+ from.old <- x$ances
+ to.old <- x$id
+ isNotNA <- !is.na(from.old) & !is.na(to.old)
+ vnames <- sort(unique(c(from.old,to.old)))
+ from <- match(from.old,vnames)
+ to <- match(to.old,vnames)
+ dat <- data.frame(from,to,stringsAsFactors=FALSE)[isNotNA,,drop=FALSE]
+
+ out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(names=vnames))
+
+ ## SET VARIOUS INFO ##
+ ## WEIGHTS FOR EDGES
+ E(out)$weight <- x$weight[isNotNA]
+
+ ## DATES FOR VERTICES (IN NB OF DAYS FROM EARLIEST DATE)
+ V(out)$dates <- difftime(x$date, min(x$date), units="days")
+
+ ## SET EDGE LABELS ##
+ E(out)$label <- E(out)$weight
+
+ ## SET EDGE COLORS
+ E(out)$color <- num2col(E(out)$weight, col.pal=col.pal, reverse=TRUE)
+
+ ## SET LAYOUT ##
+ ypos <- V(out)$dates
+ ypos <- abs(ypos-max(ypos))
+ attr(out, "layout") <- layout.fruchterman.reingold(out, params=list(miny=ypos, maxy=ypos))
+
+ ## RETURN OBJECT ##
+ return(out)
+
+} # end as.igraph.seqTrack
+
+
+
+
+
+
+#################
+## plot.seqTrack
+#################
+plot.seqTrack <- function(x, y=NULL, col.pal=redpal, ...){
+
+ ## get graph ##
+ g <- as.igraph(x, col.pal=col.pal)
+
+ ## make plot ##
+ plot(g, layout=attr(g,"layout"), ...)
+
+ ## return graph invisibly ##
+ return(invisible(g))
+
+} # end plot.seqTrack
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+################################################
+################################################
+######### OLD STUFF - NOT USED FOR NOW ######
+################################################
+################################################
+
+##########################
+## as("seqTrack", "graphNEL")
+##########################
+## if(require(graph)){
+## setOldClass("seqTrack")
+## setAs("seqTrack", "graphNEL", def=function(from){
+## ## if(!require(ape)) stop("package ape is required")
+## if(!require(graph)) stop("package graph is required")
+
+## ori.labels <- rownames(from)
+## from <- from[!is.na(from$ances),,drop=FALSE]
+
+
+## ## CONVERT TO GRAPH
+## res <- ftM2graphNEL(ft=cbind(ori.labels[from$ances], ori.labels[from$id]), W=from$weight, edgemode = "directed", V=ori.labels)
+## return(res)
+## })
+## }
+
+
+
+
+## #############
+## ## .dTimeSeq
+## #############
+## ##
+## ## mu0 and L are vectors, having one value per segment/chromosome
+## ## mu0 is per nucleotide and per day
+## .dTimeSeq <- function(mu, L, maxNbDays=100){
+## ##mu <- mu/365 # mutation rates / site / day
+## t <- 0:maxNbDays # in days added / substracted
+## temp <- sapply((1-mu)^L, function(x) x^t )
+## Pt <- apply(temp,1,prod)
+## t <- c(-rev(t[-1]), t)
+## Pt <- c(rev(Pt[-1]), Pt)
+## return(list(t, Pt))
+## }
+
+
+## #############
+## ## .rTimeSeq
+## #############
+## ##
+## ## mu and L are vectors, having one value per segment/chromosome
+## ##
+## ## this returns nb days
+## .rTimeSeq <- function(n, mu, L, maxNbDays=100){
+## temp <- .dTimeSeq(mu, L, maxNbDays)
+## res <- sample(temp[[1]], size=n, replace=TRUE, prob= temp[[2]]/sum(temp[[2]]))
+## return(res)
+## }
+
+
+
+## #################
+## ## .rUnifDate
+## #################
+## ##
+## ## this returns random uniform dates in a given range
+## ##
+## .rUnifDate <- function(n, dateMin, dateMax, ...){
+## rangeSize <- as.integer(difftime(dateMax,dateMin, units="days"))
+## nbDays <- round(runif(n, min=0, max=rangeSize))
+## res <- dateMin + nbDays*3600*24
+## res <- as.POSIXct(round.POSIXt(res, units="days"))
+## return(res)
+## }
+
+
+
+## #################
+## ## .rNormTimeSeq
+## #################
+## ##
+## ## this returns nb of days
+## .rNormTimeSeq <- function(n, mean, sd, ...){
+## res <- round(rnorm(n, mean=mean, sd=sd))
+## return(res)
+## }
+
+
+
+## #################
+## ## .rSampTimeSeq
+## #################
+## ##
+## ## this returns nb of days
+## .rSampTime <- function(n,...){
+## res <- round(rnorm(n*2, -2))
+## res <- res[res < 0 & res > -7][1:n]
+## return(res)
+## }
+
+
+## ##################
+## ## .pAbeforeBfast
+## ##################
+## ##
+## ## faster version, same mu and length for both sequences
+## ## already vectorised for dateA and dateB
+## .pAbeforeBfast <- function(dateA, dateB, mu, L, maxNbDays=100){
+## ## proba dist for both haplo
+## temp <- .dTimeSeq(mu, L, maxNbDays)
+## days <- temp[[1]]
+## p <- temp[[2]]/sum(temp[[2]]) # scale to proba mass function
+
+## ## days for A and B
+## nbDays <- as.integer(round(difftime(dateB,dateA,units="days"))) # dateA - dateB, in days
+
+## ## function for one comparison
+## f1 <- function(Dt,max){ # does not work for Dt < 0 (have to reverse proba after)
+## if(is.na(Dt)) return(NA)
+## if(Dt>max) return(1)
+## if(round(Dt)==0){
+## temp <- sapply(1:(max-1), function(i) p[i]*sum(p[(i+1):max]))
+## return(sum(temp))
+## }
+## term1 <- sum(p[1:Dt])
+## idx <- seq(2,by=1,length=(max-Dt))
+## temp <- sapply(idx, function(i) sum(p[i:max]))
+## term2 <- sum( p[(Dt+1):max] * temp)
+
+## return(term1+term2)
+## }
+
+## ## computations
+## distribSize <- length(days)
+## res <- sapply(nbDays, f1, max=distribSize)
+## res[nbDays<0] <- 1-res[nbDays<0] # reverse proba for negative time diff
+
+## return(res)
+## } # end .pAbeforeBfast
+
+
+
+
+## ##############
+## ## .pAbeforeB
+## ##############
+## ##
+## ## allows for different distributions for both haplo
+## .pAbeforeB <- function(dateA, dateB, muA, muB, LA, LB, maxNbDays=100){
+## ## proba dist for A
+## tempA <- .dTimeSeq(muA, LA, maxNbDays)
+## days <- tempA[[1]]
+## pA <- tempA[[2]]/sum(tempA[[2]]) # scale to proba mass function
+
+## ## proba dist for B
+## tempB <- .dTimeSeq(muB, LB, maxNbDays)
+## pB <- tempB[[2]]/sum(tempB[[2]]) # scale to proba mass function
+
+## ## days for A and B
+## nbDaysDiff <- as.integer(round(difftime(dateA,dateB,units="days"))) # dateA - dateB, in days
+## daysA <- days
+## daysB <- days - nbDaysDiff
+
+## f1 <- function(i){ # proba A before B for one day
+## idx <- daysB > daysA[i]
+## return(pA[i] * sum(pB[idx]))
+## }
+
+## res <- sapply(1:length(days), f1) # proba for all days
+## res <- sum(res) # sum
+## return(res)
+## }
+
+## .pAbeforeB <- Vectorize(.pAbeforeB,
+## vectorize.args=c("dateA","dateB", "muA", "muB", "LA", "LB")) ## end .pAbeforeB
+
+
+
+
+## ##############
+## ## seqTrackG - graph version of SeqTrack
+## ##############
+## ##
+## ## - x is a matrix giving weights x[i,j] such that:
+## ## 'i is ancestor j'; the algo looks for maximal weight branching
+## ##
+## ## - prox.mat is a directed proximity measure, so that prox.mat[i,j] is
+## ## the 'proximity when going from i to j'
+## ##
+## seqTrackG.default <- function(x, x.names, x.dates, best=c("min","max"), force.temporal.order=TRUE,
+## res.type=c("seqTrack", "graphNEL"), ...){
+
+## ## CHECKS ##
+## if(!require("graph")) stop("the graph package is not installed")
+## if(!require("RBGL")) stop("the RBGL package is not installed")
+## if(!exists("edmondsOptimumBranching")) {
+## stop("edmondsOptimumBranching does not exist; \nmake sure to use the latest Bioconductor (not CRAN) version of RBGL")
+## cat("\nWould you like to try and install latest version of RBGL (needs internet connection)\n y/n: ")
+## ans <- tolower(as.character(readLines(n = 1)))
+## if(ans=="y"){
+## source("http://bioconductor.org/biocLite.R")
+## biocLite("RBGL")
+## }
+## }
+
+## best <- match.arg(best)
+## res.type <- match.arg(res.type)
+
+## if(length(x.names) != length(x.dates)){
+## stop("inconsistent length for x.dates")
+## }
+
+## if(is.character(x.dates)){
+## msg <- paste("x.dates is a character vector; " ,
+## "please convert it as dates using 'as.POSIXct'" ,
+## "\n(making sure dates are given as 'YYYY/MM/DD' or 'YYYY-MM-DD').", sep="")
+## stop(msg)
+## }
+
+## x <- as.matrix(x)
+
+## x.dates <- as.POSIXct(round.POSIXt(x.dates,units="days")) # round dates to the day
+
+## if(length(x.names) != nrow(x)){
+## stop("inconsistent dimension for x")
+## }
+
+
+## ## HANDLE BEST==MIN ##
+## ## reverse x by a translation
+## x.old <- x
+## areZero <- x<1e-14
+## x <- (max(x)+1) - x
+## x[areZero] <- 0
+## diag(x) <- 0
+
+
+## ## BUILD THE GRAPH ##
+## ## make prox matrix with temporal consistency
+## if(force.temporal.order){
+## x[outer(myDates, myDates, ">=")] <- 0
+## }
+
+## ## tweak to get around a bug in as(...,"graphNEL") - looses edge weights
+## ## to replace with commented line once fixed in CRAN release
+## ## myGraph <- as(x, "graphNEL")
+## myGraph <- as(new("graphAM", x, edgemode="directed", values=list(weight=1)), "graphNEL")
+
+
+## ## CALL EDMONDSOPTIMUMBRANCHING ##
+## temp <- edmondsOptimumBranching(myGraph)
+
+
+## ## SHAPE OUTPUT ##
+## if(res.type=="seqTrack"){
+## ## reorder output from edmondsOptimumBranching
+## N <- length(x.names)
+## myLev <- x.names
+## ances <- as.integer(factor(temp$edgeList["from",], levels=myLev))
+## desc <- as.integer(factor(temp$edgeList["to",], levels=myLev))
+## newOrd <- order(desc)
+## desc <- 1:N
+## ances <- ances[newOrd]
+## weights <- as.numeric(temp$weights)[newOrd]
+
+## ## create the data.frame
+## res <- data.frame(id=1:N)
+## hasNoAnces <- difftime(myDates, min(myDates), units="secs") < 1 # 1 sec resolution for dates
+## res$weight <- res$ances <- 1:N
+## res$date <- x.dates
+
+## ## fill in the d.f. with correct values
+## res$ances[!hasNoAnces] <- ances
+## res$ances[hasNoAnces] <- NA
+
+## res$weight[!hasNoAnces] <- weights
+## res$weight[hasNoAnces] <- NA
+
+## res$ances.date <- x.dates[res$ances]
+
+## res[is.na(res)] <- NA # have clean NAs
+## row.names(res) <- x.names
+## class(res) <- c("seqTrack","data.frame")
+
+## ## handle best==min
+## if(best=="min"){
+## res$weight <- max(x.old)+1 - res$weight
+## }
+
+
+## }
+
+## if(res.type=="graphNEL"){
+## ## handle optim==min
+## if(best=="min"){
+## temp$weights <- max(x.old)+1 - temp$weights
+## }
+## res <- ftM2graphNEL(t(temp$edgeList), W=temp$weights, edgemode="directed")
+## }
+
+
+## ## RETURN RESULT ##
+## return(res)
+
+## } # end seqTrackG
+
+
+
+
+#####################
+## optimize.seqTrack
+#####################
+##
+## TODO:
+## 1) Change the output to retain xxx simulations | ok. -- done.
+## 2) VECTORIZE mu and seq.length, recycle if needed with a warning
+## 3) uncomment, adapt, and test code for missing data
+##
+## optimize.seqTrack.default <- function(x, x.names, x.dates, typed.chr=NULL, mu=NULL, seq.length=NULL,
+## thres=0.2, best=c("min","max"), prox.mat=NULL, nstep=10, step.size=1e3,
+## rDate=.rTimeSeq, arg.rDate=NULL, rMissDate=.rUnifDate, ...){
+
+
+## ## CHECKS ##
+## best <- match.arg(best)
+## if(best=="min"){
+## which.best <- which.min
+## } else {
+## which.best <- which.max
+## }
+
+## if(length(x.names) != length(x.dates)){
+## stop("inconsistent length for x.dates")
+## }
+
+## if(is.character(x.dates)){
+## msg <- paste("x.dates is a character vector; " ,
+## "please convert it as dates using 'as.POSIXct'" ,
+## "\n(making sure dates are given as 'YYYY/MM/DD' or 'YYYY-MM-DD').", sep="")
+## stop(msg)
+## }
+
+## isMissDate <- is.na(x.dates)
+
+## if(!identical(rDate, .rTimeSeq)){
+## if(is.null(arg.rDate)){
+## warning("Specific time distribution specified without arguments.")
+## arg.rDate <- list(n=step.size)
+## } else {
+## if(!is.list(arg.rDate)) stop("If provided, arg.rDate must be a list.")
+## if(!is.null(arg.rDate$n)) {
+## warning("arg.rDate$n is provided, but will be replaced by step.size.")
+## }
+## arg.rDate$n <- step.size
+## }
+## }
+
+
+## N <- length(x.names)
+## id <- 1:N
+## ## if(length(mu) < N) { # recycle mu
+## ## mu <- rep(mu, length=N)
+## ## }
+## ## if(length(seq.length) < N) {# recycle seq.length
+## ## seq.length <- rep(seq.length, length=N)
+## ## }
+
+
+## ## handle typed.chr, mu, seq.length
+## if(identical(rDate, .rTimeSeq)){
+## if(is.null(typed.chr)|is.null(mu)|is.null(seq.length)){
+## stop("typed.chr, mu, and seq.length must be provided if rDate is .rTimeSeq")
+## }
+
+## if(!is.list(typed.chr)) {
+## stop("typed.chr must be a list")
+## }
+## if(length(typed.chr)!=N) {
+## stop("typed.chr has an inconsistent length")
+## }
+
+## if(is.null(names(mu))) stop("mu has no names")
+## if(is.null(names(seq.length))) stop("seq.length has no names")
+## if(any(mu > 1)) stop("mu has values > 1")
+## if(any(mu < 0)) stop("mu has negative values")
+
+## if(!identical(names(mu) , names(seq.length))) stop("Names of mu and seq.length differ.")
+## if(any(!unique(unlist(typed.chr)) %in% names(mu))) {
+## stop("Some chromosomes indicated in typed.chr are not in mu.")
+## }
+
+## list.mu <- lapply(typed.chr, function(e) mu[e])
+## list.seq.length <- lapply(typed.chr, function(e) seq.length[e])
+## }
+
+## x.dates <- as.POSIXct(round.POSIXt(x.dates,units="days")) # round dates to the day
+
+## x <- as.matrix(x)
+
+## if(!is.null(prox.mat) && !identical(dim(prox.mat),dim(x))) {
+## stop("prox.mat is provided but its dimensions are inconsistent with that of x")
+## }
+
+
+## ## rename dimensions using id
+## colnames(x) <- rownames(x) <- id
+
+## if(length(x.names) != nrow(x)){
+## stop("inconsistent dimension for x")
+## }
+
+
+## ## SET THRESHOLD IF NEEDED ## ## NO LONGER USED
+## ## if(is.null(thres)){
+## ## thres <- sum(seqTrack(x.names=x.names, x.dates=x.dates, W=W,
+## ## best=best, prox.mat=prox.mat, ...)$weight, na.rm=TRUE)
+## ## }
+
+
+## ## AUXILIARY FUNCTIONS ##
+
+## ## to compare results -> returns a list of length two: logical, and the value of the res
+## val.res <- function(res){
+## return(sum(res$weight, na.rm=TRUE))
+## }
+
+
+## ## DO THE OPTIMISATION ##
+## RANGE.DATES <- as.integer(round(diff(range(x.dates, na.rm=TRUE)))) # time window of the sample, in days
+## NB.DATES.TO.SIM <- sum(!isMissDate)
+
+
+## ## for loop is not to slow for < 1e6 rep
+## ## and allows not to handle huge objects
+## ## (which would grow exponentially)
+
+## ## res.best <- res.ini # initialization
+
+
+## ## DEFINE OUTPUTS ##
+## ances <- integer(0)
+## date <- character(0)
+## ances.date <- character(0)
+## valRes <- numeric(0)
+
+
+## ## DEFAULT CASE: NO MISSING DATES
+## if(!any(isMissDate)){
+## ## dates initialisation, taken from initial prior
+## ## If dates distrib is .rTimeSeq
+## if(identical(rDate, .rTimeSeq)){
+## newDates <- sapply(1:N, function(i)
+## rDate(n=step.size, mu=list.mu[[i]], L=list.seq.length[[i]],
+## maxNbDays=RANGE.DATES))
+## } else { ## Else, any other distrib with free arguements
+## newDates <- sapply(1:N, function(i) do.call(rDate, arg.rDate))
+## }
+
+## newDates <- t(newDates)*24*3600 + x.dates
+
+## ## >> one step of 'step.size' simulations, all with same prior << ##
+## for(i in 1:nstep){
+## ## >> each step contains 'step.size' iterations << ##
+## for(j in 1:step.size){
+## myDates <- as.POSIXct(newDates[,j])
+
+## res.new <- seqTrack(x, x.names=x.names, x.dates=myDates,
+## best=best, prox.mat=prox.mat, ...)
+
+## ##ances <- cbind(ances, res.new$ances) # not needed now
+## date <- cbind(date, as.character(res.new$date))
+## ##ances.date <- cbind(ances.date, as.character(res.new$ances.date)) # not needed now
+## valRes <- c(valRes, val.res(res.new))
+## ##}
+## } # end for j
+
+## ## retain a given % (thres) of the dates ##
+## toKeep <- valRes <= quantile(valRes, thres) ## NOT WORKING FOR optim==max !!!
+## valRes <- valRes[toKeep]
+
+## date <- date[,toKeep,drop=FALSE] # retained posterior
+
+## ## DEBUGING ##
+## ## cat("\ntoKeep:\n")
+## ## print(toKeep)
+## ## cat("\nhead date (posterior):\n")
+## ## print(head(date))
+## ## END DEBUGING ##
+
+## newDates <- apply(date, 1, function(vec)
+## sample(vec, size=step.size, replace=TRUE)) # new prior
+## newDates <- t(newDates)
+
+## ## stop if all dates are fixed
+## if(all(apply(newDates, 1, function(r) length(unique(r))==1))){
+## cat("\nConvergence reached at step",i,"\n")
+## break # stop the algorithm
+## }
+
+## ## re-initialize posterior distributions
+## if(i<nstep){
+## ## ances <- integer(0) # not needed now
+## date <- character(0)
+## ## ances.date <- character(0) # not needed now
+## valRes <- numeric(0)
+## } # end if
+
+## } # end for i
+
+## ## ## dates: new prior taken from obtained posterior
+## ## if(length(valRes)==0) { # if no simul are retained
+## ## warning(paste("No simulation was retained at the given threshold at step",i))
+## ## } else {
+## ## if(optim=="min"){ # define weights for further samplings
+## ## w <- max(valRes,na.rm=TRUE) - valRes
+## ## w <- w/sum(w)
+## ## } else {
+## ## w <- valRes
+## ## w <- w/sum(w)
+## ## }
+
+## ## newDates <- apply(date, 1, function(vec) # used a weighted sampling
+## ## sample(vec, size=step.size, replace=TRUE, prob=w))
+
+
+## } # end if(!any(isMissDate))
+
+
+## ## ## OTHER CASE: HANDLE MISSING DATES
+## ## if(any(isMissDate)){
+
+## ## ## Handle distribution and its parameters ##
+## ## argList <- list(...)
+
+## ## if(is.null(argList$dateMin) & identical(rMissDate, .rUnifDate)){ # earliest date
+## ## argList$dateMin <- min(x.dates,na.rm=TRUE)
+## ## } else {
+## ## argList$dateMin[is.na(argList$dateMin)] <- min(x.dates,na.rm=TRUE)
+## ## }
+## ## if(is.null(argList$dateMax) & identical(rMissDate, .rUnifDate)){ # latest date
+## ## argList$dateMax <- max(x.dates,na.rm=TRUE)
+## ## } else {
+## ## argList$dateMax[is.na(argList$dateMax)] <- max(x.dates,na.rm=TRUE)
+## ## }
+
+## ## argList$n <- sum(isMissDate)
+
+## ## ## Make simulations ##
+## ## for(i in 1:nstep){
+## ## myDates <- x.dates
+## ## ## distribution for available dates
+## ## myDates[!isMissDate] <- myDates[!isMissDate] +
+## ## rDate(n=NB.DATES.TO.SIM, mu=mu, L=seq.length, maxNbDays=2*RANGE.DATES)
+## ## ## distribution for missing dates
+## ## myDates[isMissDate] <- do.call(rMissDate, argList)
+
+## ## res.new <- seqTrack(x.names=x.names, x.dates=myDates, W=W, optim=optim, prox.mat=prox.mat, ...)
+
+## ## valRes[i] <- sum(res.new$weight,na.rm=TRUE)
+## ## if(use.new.res(res.best, res.new)){
+## ## res.best <- res.new
+## ## }
+## ## }
+## ## }
+
+
+## ## RESULT ##
+
+## ## reconstruct the result with new dates
+## res <- lapply(1:ncol(date), function(i)
+## seqTrack(x=x, x.names=x.names, x.dates=as.POSIXct(date[,i]),
+## best=best, prox.mat=prox.mat, ...))
+## ances <- data.frame(lapply(res, function(e) e$ances))
+## ances <- matrix(as.integer(unlist(ances)), nrow=nrow(ances))
+
+## ances.date <- data.frame(lapply(res, function(e) as.character(e$ances.date)))
+## ances.date <- matrix(as.character(unlist(ances.date)), nrow=nrow(ances.date))
+
+## res <- list(ances=ances, date=date, ances.date=ances.date, valsim=valRes)
+## return(res)
+
+## } # optimize.seqTrack
+
+
+
+
+
+
+## #################
+## ## get.result.by
+## #################
+## .get.result.by <- function(x, ...){
+## dat <- list(...)
+## if(length(dat)==0) return(x)
+
+
+## ## DEFINE NEW VALUES ##
+
+## convertElem <- function(e){
+## if(class(e)=="DNAbin") {
+## e <- as.matrix(e)
+## }
+## ori.dim <- dim(e)
+## e <- as.character(e)
+## dim(e) <- ori.dim
+## return(e)
+## }
+
+
+## dat <- lapply(dat,convertElem)
+## dat <- as.matrix(data.frame(dat))
+
+## newval <- apply(dat, 1, function(vec) paste(vec, collapse=""))
+## newval <- unclass(factor(newval))
+## newlev <- levels(newval)
+
+
+## ## if x is a single output of seqTrack
+## if(is.vector(x$ances)){
+## newId <- newval # new values
+## newAnces <- newval[x$ances] # new values
+## ## make output
+## res <- x
+## res$id <- newId
+## res$ances <- newAnces
+## attr(res$ances, "levels") <- newlev
+## }
+
+
+## ## if x is an optimize.seqTrack output
+## if(is.matrix(x$ances)){
+## res <- x
+## ori.ncol <- ncol(res$ances)
+## res$ances <- matrix(newval[res$ances], ncol=ori.ncol)
+## attr(res$ances, "levels") <- newlev
+## }
+
+## ## method for haploGen
+## if(inherits(x,"haploGen")){
+## res <- x
+## ances.id <- match(x$ances, labels(x))
+## }
+
+## return(res)
+
+## } # end get.result.by
+
+
+
+
+
+
+## #################
+## ## get.consensus
+## #################
+## .get.consensus <- function(orires, listres, mode=c("majority","best")){
+## ## handle mode
+## mode <- match.arg(mode)
+
+## res <- orires
+
+## if(mode=="majority"){
+## nbDraws <- 0
+
+## ## tables of occurences of ancestors
+## temp <- apply(listres$ances, 1, table)
+
+## ## compute compromise
+## if(!is.list(temp)){
+## newances <- temp
+## ances.support <- rep(1,length(temp))
+## } else {
+## f1 <- function(tab){
+## if(length(tab)==0) return(NA)
+
+## res <- names(tab)[tab==max(tab)]
+## ## if(length(res)==1) return(res)
+## ## return(NA)
+## if(length(res)>1) {
+## nbDraws <- nbDraws+1
+## }
+## return(res[1])
+## }
+
+## newances <- sapply(temp, f1)
+## ances.support <- sapply(temp, function(e) max(e, na.rm=TRUE)/sum(e, na.rm=TRUE))
+## ances.support[is.na(newances)] <- NA
+## }
+
+## ## form the output
+## olev <- levels(orires$ances)
+## res$ances <- newances
+## levels(res$ances) <- olev
+## res$support <- ances.support
+## res$weight <- rep(1, length(res$date))
+
+## if(is.numeric(listres$ances)){
+## res$ances <- as.numeric(res$ances)
+## }
+## cat("\nThere were\n",nbDraws, "draws.\n")
+## } # end majority
+
+
+## if(mode=="best"){
+## toKeep <- which.min(listres$valsim)
+## nbDraws <- sum(listres$valsim < (min(listres$valsim) + 1e-10 )) -1
+## cat("\nThere were\n",nbDraws, "draws.\n")
+
+## res$ances <- listres$ances[,toKeep]
+## res$inf.date <- listres$date[,toKeep]
+## res$ances.date <- listres$ances.date[,toKeep]
+## res$weight <- rep(-1, length(res$date))
+## }
+
+## return(res)
+## } # end get.consensus
+
+
+
+
+
diff --git a/R/sequences.R b/R/sequences.R
new file mode 100644
index 0000000..2f6fce8
--- /dev/null
+++ b/R/sequences.R
@@ -0,0 +1,317 @@
+######################################
+##
+## The code below implements import
+## from alignement data.
+##
+######################################
+
+
+
+################
+# DNAbin2genind
+################
+DNAbin2genind <- function(x, pop=NULL, exp.char=c("a","t","g","c"), polyThres=1/100){
+
+ ## MISC CHECKS ##
+ if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
+ if(is.list(x)) {
+ x <- as.matrix(x)
+ }
+
+ if(is.null(colnames(x))) {
+ colnames(x) <- 1:ncol(x)
+ }
+
+
+ ## FUNCTION TO PROCESS ONE LOCUS ##
+ ## INPUTS:
+ ## locus is a column of a DNAbin matrix
+ ## posi is the index of this column
+ ## OUTPUTS:
+ ## returns NULL if no polymorphism
+ ## returns a disjonctive table with named columns otherwise
+ ## column names are given as [position.allele]
+ processLocus <- function(locus, posi){
+ vec <- as.character(locus)
+ vec[!vec %in% exp.char] <- NA
+ N <- sum(!is.na(vec)) # N: number of sequences
+ if(N==0 || sum(table(vec)/N >= polyThres )<2) return(NULL) # escape if untyped locus or no SNPs
+ alleles <- unique(na.omit(vec))
+ ## vec[!vec %in% alleles] <- NA # this would replace rare alleles by NAs
+ out <- sapply(alleles, function(e) 1*(vec==e))
+ colnames(out) <- paste(posi, alleles, sep=".")
+ return(out)
+ }
+
+
+ ## PROCESS ALL LOCI ##
+ ## get disjonctive matrix ##
+ ## system.time(res at tab <- Reduce(cbind, lapply(1:ncol(x), function(i) processLocus(x[,i], i)))) # works, but Reduce is real slow
+ temp <- lapply(1:ncol(x), function(i) processLocus(x[,i], i)) # process all loci, return a list
+ col.names <- unlist(sapply(temp, colnames))
+ temp <- as.matrix(data.frame(temp[!sapply(temp, is.null)])) # remove NULL slots, list -> matrix
+ if(is.null(temp) || ncol(temp)==0){
+ cat("\nNo polymorphism detected - returning NULL.\n")
+ return(NULL)
+ }
+
+ ## sort out col/row names ##
+ ## check if col.names is in matrix format and change to vector format
+ if(class(col.names)=="matrix") col.names <- as.vector(col.names)
+ colnames(temp) <- col.names # restore correct names
+ rownames(temp) <- rownames(x)
+
+ ## create genind output ##
+ res <- genind(temp, ploidy=1, pop=pop, type="codom")
+ rm(temp) # remove temp
+ gc() # collect garbage
+ res$call <- match.call()
+
+ return(res)
+} # end DNAbin2genind
+
+
+
+
+
+
+
+####################
+## alignment2genind
+####################
+alignment2genind <- function(x, pop=NULL, exp.char=c("a","t","g","c"), na.char="-", polyThres=1/100){
+
+ ## misc checks
+ ## if(!require(seqinr)) stop("The package seqinr is required.")
+ if(!inherits(x,"alignment")) stop("x is not a alignment object")
+ N <- length(x$seq)
+ if(!is.null(x$nam) && length(x$nam)!=N) stop("Inconsistent names in x (length of x$nam and x$seq do not match). ")
+
+
+ ## check that na.char does not overide specified exp.char
+ if(!is.null(na.char) && na.char %in% exp.char){
+ na.char <- na.char[!na.char %in% exp.char]
+ if(length(na.char)==0) na.char <- NULL
+ }
+
+
+ ## convert alignment to matrix of characters
+ mat <- sapply(x$seq, s2c, USE.NAMES=FALSE)
+ if(nrow(mat)!=x$nb){
+ mat <- t(mat)
+ }
+
+ rownames(mat) <- x$nam
+
+ if(is.null(colnames(x))) {
+ colnames(mat) <- 1:ncol(mat)
+ }
+
+ ## replace NAs
+ if(is.null(na.char)){
+ if(is.null(exp.char)) stop("both exp.char and na.char are NULL")
+ temp <- paste(exp.char, collapse="", sep="")
+ if(any(exp.char=="-")) {
+ temp <- paste("-",temp, sep="") # string '-' must begin the regexp
+ }
+ temp <- paste("[^", temp, "]", sep="") # anything but the expected is NA
+ mat <- gsub(temp,NA,mat)
+ } else {
+ temp <- paste(na.char, collapse="", sep="")
+ if(any(na.char=="-")) {
+ temp <- paste("-",temp, sep="") # string '-' must start the regexp
+ }
+ temp <- paste("[", temp, "]", sep="")
+ mat <- gsub(temp,NA,mat)
+ }
+
+ ## keep only columns with polymorphism (i.e., SNPs)
+ isPoly <- function(vec){
+ N <- sum(!is.na(vec)) # N: number of sequences
+ temp <- table(vec)/N
+ if(sum(temp > polyThres) >= 2) return(TRUE)
+ return(FALSE)
+ }
+
+ toKeep <- apply(mat, 2, isPoly)
+ if(sum(toKeep)==0) stop("No polymorphic site detected")
+
+ mat <- mat[,toKeep, drop=FALSE]
+
+ ## build output
+ res <- df2genind(mat, pop=pop, ploidy=1, ncode=1, type="codom")
+ res$call <- match.call()
+
+ if(!is.null(x$com)){
+ res at other$com <- x$com
+ }
+
+ return(res)
+} # end alignment2genind
+
+
+
+
+
+
+
+## #################
+## ## findMutations
+## #################
+
+## ## GENERIC
+## findMutations <- function(...){
+## UseMethod("findMutations")
+## }
+
+## ## METHOD FOR DNABIN
+## findMutations.DNAbin <- function(x, from=NULL, to=NULL, ...){
+## ## CHECKS ##
+## if(!require(ape)) stop("the ape package is needed")
+## if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
+## x <- as.matrix(x)
+
+## ## function to pull out mutations from sequence a to b ##
+## NUCL <- c('a','t','g','c')
+## f1 <- function(a,b){
+## seqa <- as.character(x[a,])
+## seqb <- as.character(x[b,])
+## temp <- which(seqa != seqb)
+## ori <- seqa[temp]
+## mut <- seqb[temp]
+## names(ori) <- names(mut) <- temp
+## toRemove <- !ori %in% NUCL | !mut %in% NUCL
+## ori <- ori[!toRemove]
+## mut <- mut[!toRemove]
+## if(all(toRemove)) return(NULL)
+## res <- data.frame(ori,mut)
+## names(res) <- rownames(x)[c(a,b)]
+## res$short <- paste(row.names(res),":",res[,1],"->",res[,2],sep="")
+## return(res)
+## }
+
+## ## GET LIST OF PAIRS TO COMPARE ##
+## ## handle NULL
+## if(is.null(from)) from <- 1:nrow(x)
+## if(is.null(to)) to <- 1:nrow(x)
+
+## ## get pairs
+## pairs <- expand.grid(from, to)
+
+## ## remove unwanted comparisons
+## pairs <- pairs[pairs[,1]!=pairs[,2],,drop=FALSE]
+
+## ## GET NUMBER OF MUTATIONS ##
+## out <- lapply(1:nrow(pairs), function(i) f1(pairs[i,1], pairs[i,2]))
+## names(out) <- paste(rownames(x)[pairs[,1]], rownames(x)[pairs[,2]],sep="->")
+
+## return(out)
+
+## } # end findMutations
+
+
+
+
+
+
+
+## ##################
+## ## graphMutations
+## ##################
+
+## ## GENERIC
+## graphMutations <- function(...){
+## UseMethod("graphMutations")
+## }
+
+## ## METHOD FOR DNABIN
+## graphMutations.DNAbin <- function(x, from=NULL, to=NULL, plot=TRUE, edge.curved=TRUE, ...){
+## if(!require(igraph)) stop("igraph is required")
+
+## ## GET MUTATIONS ##
+## x <- findMutations(x, from=from, to=to)
+
+## ## GET GRAPH ##
+## from <- gsub("->.*","",names(x))
+## to <- gsub(".*->","",names(x))
+## vnames <- sort(unique(c(from,to)))
+## dat <- data.frame(from,to,stringsAsFactors=FALSE)
+## out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(vnames, label=vnames))
+
+## ## SET ANNOTATIONS FOR THE BRANCHES ##
+## annot <- unlist(lapply(x, function(e) paste(e$short, collapse="\n")))
+## E(out)$label <- annot
+## E(out)$curved <- edge.curved
+
+## ## PLOT / RETURN ##
+## if(plot) plot(out, ...)
+
+## return(out)
+## } # end graphMutations
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+## ###############
+## ## transiProb
+## ###############
+## ##
+## ## proba/distance based on transition prob from one sequence to another
+## ## time is taken into account
+## ## output: matrix with term proba(rowIdx to colIdx)
+## ##
+## transiProb <- function(x, mu, dates, result=c("prob","dist")){
+## ## MISC CHECKS ##
+## if(!inherits(x,"DNAbin")) stop("x is not a DNAbin object")
+## if(!require(ape)) stop("The package ape is required.")
+## result <- match.arg(result)
+
+## ## COMPUTATIONS ##
+
+## ## get numbers of differing nucleotides between sequences
+## seq.length <- ncol(as.matrix(x))
+## D <- as.matrix(dist.dna(x, model="raw")) * seq.length
+## ## if(sum(D-round(D)) > 1e-10){ # make sure we've got integers there
+## ## warning("Number of nucleotides are not all integers")
+## ## }
+## D <- round(D)
+
+## ## compute matrix T (time between sequences)
+## if(inherits(dates,"POSIXct")){ # dates in POSIXct format
+## temp <- outer(dates, dates, difftime, unit="days")
+## T <- -matrix(as.numeric(temp),ncol=length(dates))
+## } else { # dates are numeric
+## T <- -outer(dates, dates, "-")
+## }
+
+## ## spot negative times
+## toSetToNull <- T < 1e-15
+
+## ## compute proba(no change @ a site) term
+## mu <- mu/365 # express mu per day
+## p1 <- exp(-T*mu) + (1-exp(-T*mu))/4
+## p1[toSetToNull] <- 0
+## res <- dbinom(D, size=seq.length, prob=(1-p1))
+
+## ## PROCESS/RETURN RESULT
+## if(result=="prob"){ # return probabilities
+## res[toSetToNull] <- 0
+## diag(res) <- 1
+## } else { # return d = -log(proba)
+## res <- -log(res)
+## res[toSetToNull] <- 1e15
+## diag(res) <- 0
+## }
+
+## return(res)
+## } # end transiProb
diff --git a/R/servers.R b/R/servers.R
new file mode 100644
index 0000000..8d353f9
--- /dev/null
+++ b/R/servers.R
@@ -0,0 +1,51 @@
+
+
+##################
+## adegenetServer
+##################
+## function starting a web-server
+## for adegenet tools
+adegenetServer <- function(what=c("DAPC")){
+ what <- match.arg(what)
+ if(what=="DAPC"){
+ .dapcServer()
+ }
+
+ return(invisible())
+}
+
+
+###############
+## .dapcServer
+###############
+## hidden function - DAPC server
+.dapcServer <- function(){
+ runApp(system.file("dapcServer",package="adegenet"))
+}
+
+
+
+#######################
+## .render.server.info
+#######################
+## INVISIBLE FUNCTION RENDERING SERVER INFO ##
+.render.server.info <- function(){
+ renderPrint(
+ {
+ cat("\n== R version ==\n")
+ print(R.version)
+
+ cat("\n== Date ==\n")
+ print(date())
+
+ cat("\n== adegenet version ==\n")
+ print(packageDescription("adegenet", fields=c("Package", "Version", "Date", "Built")))
+
+ cat("\n== shiny version ==\n")
+ print(packageDescription("adegenet", fields=c("Package", "Version", "Date", "Built")))
+
+ cat("\n== attached packages ==\n")
+ print(search())
+ }
+ ) # end renderPrint
+} # end .render.server.info
diff --git a/R/setAs.R b/R/setAs.R
new file mode 100644
index 0000000..06f3c92
--- /dev/null
+++ b/R/setAs.R
@@ -0,0 +1,105 @@
+#############
+# S4 methods
+#############
+setAs("genind", "data.frame", function(from, to) {
+ return(as.data.frame(from at tab))
+})
+
+
+
+setAs("genpop", "data.frame", function(from, to) {
+ return(as.data.frame(from at tab))
+})
+
+
+
+setAs("genind", "matrix", function(from, to) {
+ return(from at tab)
+})
+
+
+
+setAs("genpop", "matrix", function(from, to) {
+ return(from at tab)
+})
+
+
+
+setAs("genind", "genpop", function(from, to) {
+ if(!is.genind(from)) stop("object is not a valid genind")
+
+ x <- genind2genpop(from, quiet=TRUE)
+ warning("You had better use genind2genpop to specify treatment of NAs")
+
+ return(x at tab)
+})
+
+
+
+
+setOldClass("ktab")
+setAs("genind", "ktab", function(from, to) {
+ checkType(from)
+ res <- ktab.data.frame(df=as.data.frame(from), blocks=from at loc.n.all, rownames=indNames(from),
+ colnames=unlist(alleles(from)), tabnames=locNames(from))
+ return(res)
+})
+
+
+
+
+setAs("genpop", "ktab", function(from, to) {
+ checkType(from)
+ res <- ktab.data.frame(df=as.data.frame(from), blocks=from at loc.n.all, rownames=popNames(from),
+ colnames=unlist(alleles(from)), tabnames=locNames(from))
+ return(res)
+})
+
+
+
+
+##############
+# S3 versions
+##############
+as.data.frame.genind <- function(x,...){
+ return(as(x,"data.frame"))
+}
+
+
+
+as.data.frame.genpop <- function(x,...){
+ return(as(x,"data.frame"))
+}
+
+
+
+as.matrix.genind <- function(x,...){
+ return(as(x,"matrix"))
+}
+
+
+
+as.matrix.genpop <- function(x,...){
+ return(as(x,"matrix"))
+}
+
+
+
+as.genpop.genind <- function(x,...){
+ return(as(x,"genpop"))
+}
+
+
+
+
+as.ktab.genind <- function(x,...){
+ return(as(x,"ktab"))
+}
+
+
+
+
+as.ktab.genpop <- function(x,...){
+ return(as(x,"ktab"))
+}
+
diff --git a/R/simOutbreak.R b/R/simOutbreak.R
new file mode 100644
index 0000000..b8657ca
--- /dev/null
+++ b/R/simOutbreak.R
@@ -0,0 +1,367 @@
+## ###############
+## ## simOutbreak
+## ###############
+## simOutbreak <- function(R0, infec.curve, n.hosts=200, duration=50,
+## seq.length=1e4, mu.transi=1e-4, mu.transv=mu.transi/2,
+## tree=TRUE){
+
+## ## CHECKS ##
+## if(!require(ape)) stop("The ape package is required.")
+
+
+## ## HANDLE ARGUMENTS ##
+## ## normalize gen.time
+## infec.curve <- infec.curve/sum(infec.curve)
+## infec.curve <- c(infec.curve, rep(0, duration)) # make sure dates go all the way
+## t.clear <- which(diff(infec.curve<1e-10)==1) # time at which infection is cleared
+
+## ## GENETIC FUNCTIONS ##
+## NUCL <- as.DNAbin(c("a","t","c","g"))
+## TRANSISET <- list('a'=as.DNAbin('g'), 'g'=as.DNAbin('a'), 'c'=as.DNAbin('t'), 't'=as.DNAbin('c'))
+## TRANSVSET <- list('a'=as.DNAbin(c('c','t')), 'g'=as.DNAbin(c('c','t')), 'c'=as.DNAbin(c('a','g')), 't'=as.DNAbin(c('a','g')))
+
+
+## ## AUXILIARY FUNCTIONS ##
+## ## generate sequence from scratch
+## seq.gen <- function(){
+## ##res <- list(sample(NUCL, size=seq.length, replace=TRUE)) # DNAbin are no longer lists by default
+## res <- sample(NUCL, size=seq.length, replace=TRUE)
+## class(res) <- "DNAbin"
+## return(res)
+## }
+
+## ## create substitutions for defined SNPs - no longer used
+## substi <- function(snp){
+## res <- sapply(1:length(snp), function(i) sample(setdiff(NUCL,snp[i]),1)) # ! sapply does not work on DNAbin vectors directly
+## class(res) <- "DNAbin"
+## return(res)
+## }
+
+## ## create transitions for defined SNPs
+## transi <- function(snp){
+## res <- unlist(TRANSISET[as.character(snp)])
+## class(res) <- "DNAbin"
+## return(res)
+## }
+
+## ## create transversions for defined SNPs
+## transv <- function(snp){
+## res <- sapply(TRANSVSET[as.character(snp)],sample,1)
+## class(res) <- "DNAbin"
+## return(res)
+## }
+
+## ## duplicate a sequence (including possible mutations)
+## seq.dupli <- function(seq, T){ # T is the number of time units between ancestor and decendent
+## ## transitions ##
+## n.transi <- rbinom(n=1, size=seq.length*T, prob=mu.transi) # total number of transitions
+## if(n.transi>0) {
+## idx <- sample(1:seq.length, size=n.transi, replace=FALSE)
+## seq[idx] <- transi(seq[idx])
+## }
+
+## ## transversions ##
+## n.transv <- rbinom(n=1, size=seq.length*T, prob=mu.transv) # total number of transitions
+## if(n.transv>0) {
+## idx <- sample(1:seq.length, size=n.transv, replace=FALSE)
+## seq[idx] <- transv(seq[idx])
+## }
+## return(seq)
+## }
+
+
+## ## MAIN FUNCTION ##
+## ## initialize results ##
+## dynam <- data.frame(nsus=integer(duration+1), ninf=integer(duration+1), nrec=integer(duration+1))
+## rownames(dynam) <- 0:duration
+## res <- list(n=1, dna=NULL, dates=NULL, id=NULL, ances=NULL, dynam=dynam)
+## res$dynam$nsus[1] <- n.hosts-1
+## res$dynam$ninf[1] <- 1
+## res$dates[1] <- 0
+## res$ances <- NA
+## res$dna <- matrix(seq.gen(),nrow=1)
+## class(res$dna) <- "DNAbin"
+
+## ## run outbreak ##
+## for(t in 1:duration){
+## ## individual force of infection
+## indivForce <- infec.curve[t-res$dates+1]
+
+## ## global force of infection (R0 \sum_j I_t^j / N)
+## globForce <- sum(indivForce)*R0/n.hosts
+
+## ## number of new infections
+## nbNewInf <- rbinom(1, size=res$dynam$nsus[t], prob=globForce)
+
+## ## dates of new infections
+## if(nbNewInf>0){
+## res$dates <- c(res$dates, rep(t,nbNewInf))
+
+## ## ancestries of the new infections
+## temp <- as.vector(rmultinom(1, size=nbNewInf, prob=indivForce))
+## newAnces <- rep(which(temp>0), temp[which(temp>0)])
+## res$ances <- c(res$ances,newAnces)
+
+## ## dna sequences of the new infections
+## newSeq <- t(sapply(newAnces, function(i) seq.dupli(res$dna[i,], t-res$dates[i])))
+## res$dna <- rbind(res$dna, newSeq)
+## }
+
+## ## update nb of infected, recovered, etc.
+## res$dynam$nrec[t+1] <- sum(res$dates>=t.clear)
+## res$dynam$ninf[t+1] <- sum(res$dates>=0 & res$dates < t.clear)
+## res$dynam$nsus[t+1] <- res$dynam$nsus[t] - nbNewInf
+## } # end for
+
+
+## ## SHAPE AND RETURN OUTPUT ##
+## res$n <- nrow(res$dna)
+## res$id <- 1:res$n
+## res$nmut <- sapply(1:res$n, function(i) dist.dna(res$dna[c(res$id[i],res$ances[i]),], model="raw"))*ncol(res$dna)
+## res$call <- match.call()
+## if(tree){
+## res$tree <- fastme.ols(dist.dna(res$dna, model="TN93"))
+## res$tree <- root(res$tree,"1")
+## }
+## class(res) <- "simOutbreak"
+## return(res)
+
+## } # end simOutbreak
+
+
+
+
+
+
+
+
+## ##################
+## ## print.simOutbreak
+## ##################
+## print.simOutbreak <- function(x, ...){
+
+## cat("\t\n=========================")
+## cat("\t\n= simulated outbreak =")
+## cat("\t\n= (simOutbreak object) =")
+## cat("\t\n=========================\n")
+
+## cat("\nSize :", x$n,"cases (out of", x$dynam$nsus[1],"susceptible hosts)")
+## cat("\nGenome length :", ncol(x$dna),"nucleotids")
+## cat("\nDate range :", min(x$dates),"-",max(x$dates))
+
+## cat("\nContent:\n")
+## print(names(x))
+
+## return(NULL)
+## } # end print.simOutbreak
+
+
+
+
+
+
+
+## ##############
+## ## [.simOutbreak
+## ##############
+## "[.simOutbreak" <- function(x,i,j,drop=FALSE){
+## res <- x
+## res$dna <- res$dna[i,,drop=FALSE]
+## res$id <- res$id[i]
+## res$ances <- res$ances[i]
+## res$ances[!res$ances %in% res$id] <- NA
+## res$dates <- res$dates[i]
+## res$n <- nrow(res$dna)
+
+## return(res)
+## }
+
+
+
+
+
+## ##################
+## ## labels.simOutbreak
+## ##################
+## labels.simOutbreak <- function(object, ...){
+## return(object$id)
+## }
+
+
+
+
+
+
+## #########################
+## ## as.igraph.simOutbreak
+## #########################
+## as.igraph.simOutbreak <- function(x, ...){
+## if(!require(igraph)) stop("package igraph is required for this operation")
+## if(!require(ape)) stop("package ape is required for this operation")
+
+## ## GET DAG ##
+## from <- x$ances
+## to <- x$id
+## isNotNA <- !is.na(from) & !is.na(to)
+## dat <- data.frame(from,to,stringsAsFactors=FALSE)[isNotNA,,drop=FALSE]
+## vnames <- as.character(unique(unlist(dat)))
+## out <- graph.data.frame(dat, directed=TRUE, vertices=data.frame(names=vnames, dates=x$dates[vnames]))
+
+## ## SET WEIGHTS ##
+## D <- as.matrix(dist.dna(x$dna,model="raw")*ncol(x$dna))
+## temp <- mapply(function(i,j) return(D[i,j]), as.integer(from), as.integer(to))
+## E(out)$weight <- temp[isNotNA]
+
+## ## SET ARROW WIDTH ##
+## temp <- max(E(out)$weight) - E(out)$weight
+## temp <- temp/max(temp) * 4
+## E(out)$width <- round(temp)+1
+
+## return(out)
+## }
+
+
+
+
+
+
+
+## ####################
+## ## plot.simOutbreak
+## ####################
+## plot.simOutbreak <- function(x, y=NULL, cex=1, col=num2col(x$dates), label=x$id,
+## edge.col=num2col(x$nmut[-1], col.pal=seasun), lwd=1, ...){
+## if(!require(igraph)) stop("package igraph is required for this operation")
+## if(!require(ape)) stop("package ape is required for this operation")
+## plot(as.igraph(x), vertex.size=15*cex, vertex.color=col, vertex.label=label,
+## vertex.label.cex=cex, edge.color=edge.col, edge.width=lwd, ...)
+## } # end plot.simOutbreak
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+## ## #####################
+## ## ## seqTrack.simOutbreak
+## ## #####################
+## ## seqTrack.simOutbreak <- function(x, best=c("min","max"), prox.mat=NULL, ...){
+## ## myX <- dist.dna(x$dna, model="raw")
+## ## x.names <- labels(x)
+## ## x.dates <- as.POSIXct(x)
+## ## seq.length <- ncol(x$dna)
+## ## myX <- myX * seq.length
+## ## myX <- as.matrix(myX)
+## ## prevCall <- as.list(x$call)
+## ## if(is.null(prevCall$mu)){
+## ## mu0 <- 0.0001
+## ## } else {
+## ## mu0 <- eval(prevCall$mu)
+## ## }
+## ## res <- seqTrack(myX, x.names=x.names, x.dates=x.dates, best=best, prox.mat=prox.mat,...)
+## ## return(res)
+## ## }
+
+
+
+
+
+
+## ## ########################
+## ## ## as.seqTrack.simOutbreak
+## ## ########################
+## ## as.seqTrack.simOutbreak <- function(x){
+## ## ## x.ori <- x
+## ## ## x <- na.omit(x)
+## ## toSetToNA <- x$dates==min(x$dates)
+## ## res <- list()
+## ## res$id <- labels(x)
+## ## res <- as.data.frame(res)
+## ## res$ances <- x$ances
+## ## res$ances[toSetToNA] <- NA
+## ## res$weight <- 1 # ??? have to recompute that...
+## ## res$weight[toSetToNA] <- NA
+## ## res$date <- as.POSIXct(x)[labels(x)]
+## ## res$ances.date <- as.POSIXct(x)[x$ances]
+
+## ## ## set results as indices rather than labels
+## ## res$ances <- match(res$ances, res$id)
+## ## res$id <- 1:length(res$id)
+
+## ## ## SET CLASS
+## ## class(res) <- c("seqTrack", "data.frame")
+
+## ## return(res)
+## ## }
+
+
+
+
+
+
+
+
+## ## ###################
+## ## ## sample.simOutbreak
+## ## ###################
+## ## sample.simOutbreak <- function(x, n){
+## ## ##sample.simOutbreak <- function(x, n, rDate=.rTimeSeq, arg.rDate=NULL){
+## ## ## EXTRACT THE SAMPLE ##
+## ## res <- x[sample(1:nrow(x$dna), n, replace=FALSE)]
+
+
+## ## ## RETRIEVE SOME PARAMETERS FROM HAPLOSIM CALL
+## ## prevCall <- as.list(x$call)
+## ## if(!is.null(prevCall$mu)){
+## ## mu0 <- eval(prevCall$mu)
+## ## } else {
+## ## mu0 <- 1e-04
+## ## }
+
+## ## if(!is.null(prevCall$dna.length)){
+## ## L <- eval(prevCall$dna.length)
+## ## } else {
+## ## L <- 1000
+## ## }
+
+## ## ## truedates <- res$dates
+## ## ## daterange <- diff(range(res$dates,na.rm=TRUE))
+
+## ## ## if(identical(rDate,.rTimeSeq)){
+## ## ## sampdates <- .rTimeSeq(n=length(truedates), mu=mu0, L=L, maxNbDays=daterange/2)
+## ## ## } else{
+## ## ## arg.rDate$n <- n
+## ## ## sampdates <- do.call(rDate, arg.rDate)
+## ## ## }
+## ## ## sampdates <- truedates + abs(sampdates)
+
+## ## return(res)
+## ## } # end sample.simOutbreak
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/R/snpposi.R b/R/snpposi.R
new file mode 100644
index 0000000..b62dc28
--- /dev/null
+++ b/R/snpposi.R
@@ -0,0 +1,129 @@
+################
+## snpposi.test
+################
+
+## GENERIC
+snpposi.test <- function(...){
+ UseMethod("snpposi.test")
+}
+
+
+
+
+
+## METHOD FOR INTEGER - BASIC METHOD
+snpposi.test.integer <- function(x, genome.size, n.sim=999, stat=median, ...){
+ ## AUXILIARY FUNCTION ##
+ ## computes the test statistics for one vector of SNP positions
+ f1 <- function(snpposi, stat=median){
+ temp <- as.matrix(dist(snpposi))
+ diag(temp) <- 1e15
+ out <- stat(apply(temp, 1, min))
+ return(out)
+ }
+
+ ## GET OBSERVATION ##
+ obs <- f1(x, stat=stat)
+
+ ## GET SIMULATIONS ##
+ n.snps <- length(x)
+ sim <- sapply(1:n.sim, function(e) f1(sample(1:genome.size, n.snps, replace=FALSE), stat=stat))
+
+ ## MAKE RANDTEST OUTPUT ##
+ out <- as.randtest(obs=obs, sim=sim, alter="less")
+ return(out)
+} # end snpposi.test.integer
+
+
+
+
+
+## METHOD FOR NUMERIC
+snpposi.test.numeric <- function(x, ...){
+ out <- snpposi.test(as.integer(x), ...)
+ return(out)
+}
+
+
+
+
+
+## METHOD FOR DNABIN
+snpposi.test.DNAbin <- function(x, ...){
+ out <- snpposi.test(x=as.integer(seg.sites(x)),
+ genome.size=ncol(x), ...)
+ return(out)
+} # end snpposi.test.DNAbin
+
+
+
+
+
+
+
+
+
+
+
+################
+## snpposi.plot
+################
+
+## GENERIC
+snpposi.plot <- function(...){
+ UseMethod("snpposi.plot")
+}
+
+
+
+
+## METHOD FOR INTEGER - BASIC METHOD
+snpposi.plot.integer <- function(x, genome.size, smooth=0.1, col="royalblue", alpha=.2,
+ codon=TRUE, start.at=1, ...){
+ ## IF WE REPRESENT DENSITY PER CODON POSITION ##
+ if(codon){
+ ## define base positions (1/2/3) ##
+ fac <- rep(1:3, length=genome.size)
+ if(start.at==2) fac <- c(2:3,fac)[1:genome.size]
+ if(start.at==3) fac <- c(3,fac)[1:genome.size]
+ fac <- factor(fac, levels=1:3)
+ fac <- fac[x]
+
+ ## make ggplot output ##
+ out <- ggplot(data.frame(x=x, codon=fac), aes(x=x)) + xlim(0, genome.size)
+ out <- out + geom_density(adjust=smooth, aes(fill=codon, colour=codon),alpha=I(alpha)) + geom_rug(aes(colour=codon),alpha=.7)
+ out <- out + labs(x="Nucleotide position", title="Distribution of SNPs in the genome")
+ out <- out + guides(fill=guide_legend(title="Codon position"), colour=guide_legend(title="Codon position"))
+ } else {
+ ## OTHERWISE, JUST ONE DENSITY ##
+ ## make ggplot output ##
+ out <- ggplot(data.frame(x=x), aes(x=x)) + xlim(0, genome.size)
+ out <- out + geom_density(adjust=smooth, fill=transp(col,alpha=alpha), colour=col) + geom_rug(colour=col,alpha=.7)
+ out <- out + labs(x="Nucleotide position", title="Distribution of SNPs in the genome")
+ }
+
+
+ ## return ##
+ return(out)
+} # end snpposi.plot.integer
+
+
+
+
+
+## METHOD FOR NUMERIC
+snpposi.plot.numeric <- function(x, ...){
+ out <- snpposi.plot(as.integer(x), ...)
+ return(out)
+}
+
+
+
+
+## METHOD FOR DNABIN
+snpposi.plot.DNAbin <- function(x, ...){
+ out <- snpposi.plot(x=as.integer(seg.sites(x)),
+ genome.size=ncol(x), ...)
+ return(out)
+} # end snpposi.plot.DNAbin
+
diff --git a/R/snpzip.R b/R/snpzip.R
new file mode 100644
index 0000000..cc6a500
--- /dev/null
+++ b/R/snpzip.R
@@ -0,0 +1,340 @@
+
+##############
+### snpzip ###
+##############
+
+
+snpzip <- function(snps, y, plot=TRUE, xval.plot=FALSE, loading.plot=FALSE,
+ method=c("complete","single","average","centroid",
+ "mcquitty","median","ward"), ...) {
+
+ ## dapc input prompts only SNP selection function
+ if(class(y)=="dapc"){
+
+ dapc1 <- y
+ phen <- 0
+
+
+ if(xval.plot==TRUE){
+ warning("cross-validation not performed when x is a dapc object; xval.plot will not be shown")
+ xval.plot=FALSE
+ }
+ }
+
+ ## snps, phen input prompts cross-validation, DAPC, and SNP selection functions
+ else{
+
+ if(missing(y)){
+ stop("phen argument needed")
+ }
+ phen <- y
+
+ }
+
+
+ if(class(y)!="dapc"){
+
+ ################################################
+ ######## Stratified Cross-Validation ###########
+ ################################################
+
+ xvalDapc <- function(x, grp, n.pca.max = 200, n.da = NULL,
+ training.set = 0.9, result = "groupMean",
+ center = TRUE, scale = FALSE, n.pca = NULL, n.rep = 30, ...){
+
+ ## CHECKS ##
+ grp <- factor(grp)
+ n.pca <- n.pca[n.pca>0]
+ n.da <- length(levels(grp))-1
+ if(missing(training.set)){
+ training.set <- 0.9}
+ else{
+ training.set <- training.set}
+ if(missing(n.rep)){
+ n.rep<-30}
+ else{
+ n.rep<-n.rep}
+
+
+ ## GET TRAINING SET SIZE ##
+ N <- nrow(x)
+ groups <- levels(grp)
+ if(all(lapply(groups, function(e) sum(as.vector(unclass(grp==e))))>=10)==TRUE){
+ N.training <- round(N*training.set)}
+ else{
+ groups1 <- (levels(grp))[(as.vector(which.min((lapply(groups,
+ function(e) sum(as.vector(unclass(grp==e))))))))]
+ popmin <- length(which(grp%in%groups1))
+ training.set2 <- ((popmin - 1)/popmin)
+ N.training <- round(N*training.set2)}
+
+
+ ## GET FULL PCA ##
+ if(missing(n.pca.max)) n.pca.max <- min(dim(x))
+ pcaX <- dudi.pca(x, nf=n.pca.max, scannf=FALSE, center=center, scale=scale)
+ n.pca.max <- min(n.pca.max, pcaX$rank, N.training-1)
+
+ ## DETERMINE N.PCA IF NEEDED ##
+ if(n.pca.max < 10){
+ runs <- n.pca.max}
+ else{
+ runs<- 10}
+
+ if(is.null(n.pca)){
+ n.pca <- round(pretty(1:n.pca.max, runs))
+ }
+ n.pca <- n.pca[n.pca>0 & n.pca<(N.training-1)]
+
+ ## FUNCTION GETTING THE % OF ACCURATE PREDICTION FOR ONE NUMBER OF PCA PCs ##
+ ## n.pca is a number of retained PCA PCs
+ get.prop.pred <- function(n.pca){
+ f1 <- function(){
+ if(all(lapply(groups, function(e) sum(as.vector(unclass(grp==e))))>=10)==TRUE){
+ toKeep <- unlist(lapply(groups, function(e) sample(which(grp==e),
+ size=(round(training.set*sum(as.vector(unclass(grp==e))))))))}
+ else{
+ toKeep <- unlist(lapply(groups, function(e) sample(which(grp==e),
+ size=(round(training.set2*sum(as.vector(unclass(grp==e))))))))}
+ temp.pca <- pcaX
+ temp.pca$li <- temp.pca$li[toKeep,,drop=FALSE]
+ temp.dapc <- suppressWarnings(dapc(x[toKeep,,drop=FALSE], grp[toKeep],
+ n.pca=n.pca, n.da=n.da, dudi=temp.pca))
+ temp.pred <- predict.dapc(temp.dapc, newdata=x[-toKeep,,drop=FALSE])
+ if(result=="overall"){
+ out <- mean(temp.pred$assign==grp[-toKeep])
+ }
+ if(result=="groupMean"){
+ out <- mean(tapply(temp.pred$assign==grp[-toKeep], grp[-toKeep], mean), na.rm=TRUE)
+ }
+ return(out)
+ }
+ return(replicate(n.rep, f1()))
+ }
+
+
+ ## GET %SUCCESSFUL OF ACCURATE PREDICTION FOR ALL VALUES ##
+ res.all <- unlist(lapply(n.pca, get.prop.pred))
+ xval <- data.frame(n.pca=rep(n.pca, each=n.rep), success=res.all)
+
+
+ n.pcaF <- as.factor(xval$n.pca)
+ successV <- as.vector(xval$success)
+ pca.success <- tapply(successV, n.pcaF, mean)
+ n.opt <- which.max(tapply(successV, n.pcaF, mean))
+
+
+ ################################################
+ ##### MSE Calculation and n.pca Selection #####
+ ################################################
+ temp <- seq(from=1, to=length(xval$n.pca), by=n.rep)
+ orary <-c(temp+(n.rep-1))
+ index <-c(1:length(temp))
+ lins <-sapply(index, function(e) seq(from=temp[e], to=orary[e]))
+ lin <-c(1:ncol(lins))
+ col <-successV
+ cait<-sapply(lin, function(e) ((col[lins[,e]])-1)^2)
+ FTW <-sapply(lin, function(e) sum(cait[,e])/n.rep)
+ RMSE <- sqrt(FTW)
+ names(RMSE) <- xval$n.pca[temp]
+ best.n.pca <- names(which.min(RMSE))
+
+
+
+ ################################################
+ ################# DAPC #######################
+ ################################################
+ n.pcaF <- as.factor(xval$n.pca)
+ successV <- as.vector(xval$success)
+ pca.success <- tapply(successV, n.pcaF, mean)
+ n.opt <- which.max(tapply(successV, n.pcaF, mean))
+ n.pca <- as.integer(best.n.pca)
+ n.da <- nlevels(grp)-1
+ dapc1 <- dapc(x, grp, n.pca=n.pca, n.da=n.da)
+
+ answerme <- list(n.da, n.pca, dapc1, xval, successV, RMSE, best.n.pca, pca.success, n.opt)
+ return(answerme)
+ }
+
+
+ x <- snps
+ grp <- phen
+
+ XVAL <- xvalDapc(x, grp, n.da=NULL, training.set=0.9, result="groupMean",
+ center=TRUE, scale=FALSE, n.pca=NULL, ...)
+ n.da <- XVAL[[1]]
+ n.pca <- XVAL[[2]]
+ dapc1 <- XVAL[[3]]
+ xval <- XVAL[[4]]
+ successV <- XVAL[[5]]
+ RMSE <- XVAL[[6]]
+ best.n.pca <- XVAL[[7]]
+ pca.success <- XVAL[[8]]
+ n.opt <- XVAL[[9]]
+
+
+ ################################################
+ ######## Show Cross-Validation Results #########
+ ################################################
+ snps <- x
+ phen <- grp
+
+ if(xval.plot==TRUE){
+ par(ask=TRUE)
+ random <- replicate(300, mean(tapply(sample(phen)==phen, phen, mean)))
+ q.phen <- quantile(random, c(0.025,0.5,0.975))
+ smoothScatter(xval$n.pca, successV, nrpoints=Inf, pch=20, col=transp("black"),
+ ylim=c(0,1), xlab="Number of PCA axes retained",
+ ylab="Proportion of successful outcome prediction",
+ main="DAPC Cross-Validation")
+ abline(h=q.phen,lty=c(2,1,2))
+
+ xvalResults <- list(xval, q.phen, pca.success, (names(n.opt)), RMSE, best.n.pca)
+ names(xvalResults)[[1]] <- "Cross-Validation Results"
+ names(xvalResults)[[2]] <- "Median and Confidence Interval for Random Chance"
+ names(xvalResults)[[3]] <- "Mean Successful Assignment by Number of PCs of PCA"
+ names(xvalResults)[[4]] <- "Number of PCs Achieving Highest Mean Success"
+ names(xvalResults)[[5]] <- "Root Mean Squared Error by Number of PCs of PCA"
+ names(xvalResults)[[6]] <- "Number of PCs Achieving Lowest MSE"
+ print(xvalResults)
+ }
+
+ } # end of snps, phen section
+
+
+ ################################################
+ ############# Plot DAPC Results #############
+ ################################################
+
+ if(plot==TRUE){
+ myCol <- colorRampPalette(c("blue", "gold", "red"))
+ scatter(dapc1, bg="white", scree.da=FALSE, scree.pca=TRUE, posi.pca="topright",
+ col=myCol((dapc1$n.da)+1), legend=TRUE, posi.leg="topleft")
+ title("DAPC")}
+
+ ################################################
+ ###### Select Cluster of Structural SNPS #######
+ ################################################
+
+ if(missing(method)){
+ method <- "ward"
+ }
+ else{
+ method <- method}
+
+ selector <- function(dapc1, dimension){
+
+ z <- dapc1$var.contr[,dimension]
+ xTotal <- dapc1$var.contr[,dimension]
+ toto <- which(xTotal%in%tail(sort(xTotal), 2000))
+ z <- sapply(toto, function(e) xTotal[e])
+
+ D <- dist(z)
+ clust <- hclust(D,method)
+ pop <- factor(cutree(clust,k=2,h=NULL))
+ m <- which.max(tapply(z,pop,mean))
+ maximus <- which(pop==m)
+ maximus <- as.vector(unlist(sapply(maximus, function(e) toto[e])))
+ popvect <- as.vector(unclass(pop))
+ n.snp.selected <- sum(popvect==m)
+ sel.snps <- snps[,maximus]
+
+ selection <- c((ncol(snps)-ncol(snps[,-maximus])), ncol(snps[,-maximus]))
+
+ resultat <- list(selection, maximus, dimnames(sel.snps)[[2]], dapc1$var.contr[maximus, dimension])
+
+ names(resultat)[[1]] <- "Number of selected vs. unselected alleles"
+ names(resultat)[[2]] <- "List of selected alleles"
+ names(resultat)[[3]] <- "Names of selected alleles"
+ names(resultat)[[4]] <- "Contributions of selected alleles to discriminant axis"
+ gc()
+ return(resultat)
+ }
+
+ if(dapc1$n.da==1){
+ features <- selector(dapc1, dimension=1)
+ }
+ else{
+ dimensions <- c(1:dapc1$n.da)
+ features <- lapply(dimensions, function(e)
+ selector(dapc1, dimension=e))
+ }
+
+ ################################################
+ #### Calculate success in discrimination ####
+ ################################################
+
+ # overall
+ grp <- dapc1$grp
+ ass <- dapc1$assign
+ dapc.success.overall <- length(which(ass==grp)) / length(grp)
+
+ # by group
+
+ # give grp and ass numbered factor levels
+ GRP <- factor(grp, levels=levels(grp), labels=c(0:(nlevels(grp)-1)))
+ ASS <- factor(ass, levels=levels(ass), labels=c(0:(nlevels(ass)-1)))
+
+ # make each level of those factors into one element of a list
+ index <- c(0:(nlevels(grp) - 1))
+ ASSIGN <- sapply(index, function(e) which(ASS==e))
+ GROUP <- sapply(index, function(e) which(GRP==e))
+
+ index2 <- c(1:(nlevels(grp)))
+ dapc.success.byGroup <- sum(sapply(index2, function(e)
+ (length(which(ASSIGN[[e]]%in%GROUP[[e]]))) /
+ length(GROUP[[e]]))) / length(index2)
+
+ dapc.success <- c(dapc.success.overall, dapc.success.byGroup)
+
+ ################################################
+ #### Loading Plot Delineating SNP Clusters ####
+ ################################################
+
+ if(loading.plot==TRUE){
+ if(dapc1$n.da==1){
+ par(ask=TRUE)
+ maximus <- features[[2]]
+ decimus <- abs(dapc1$var.contr[maximus][(which.min(dapc1$var.contr[maximus]))])-0.000001
+ meridius <- loadingplot(dapc1$var.contr[,1], threshold=c(decimus))
+ }
+ else{
+ par(ask=TRUE)
+ # specify that you want to run the following lines for all DA (ie. from DA=1 to DA=(k-1))
+ DA <- c(1:dapc1$n.da)
+ # generate separate loading plots for each DA
+ for(i in DA){
+ title <- paste("Loading Plot for DA", i, sep=" ")
+ maximus <- features[[i]][[2]]
+ decimus <- abs(dapc1$var.contr[maximus,i][(which.min(dapc1$var.contr[maximus,i]))])-0.000001
+ meridius <- loadingplot(dapc1$var.contr[, i], threshold=decimus, main=title)
+ }
+ }
+ }
+
+ ################################################
+ ########## Return snpzip Results ##############
+ ################################################
+
+ if(class(y)=="dapc"){
+
+ answer <- list(dapc1$n.pca, features)
+ names(answer)[[1]] <- "Number of PCs of PCA retained"
+ names(answer)[[2]] <- "FS"
+ return(answer)
+ }
+
+ else{
+ answer <- list(best.n.pca, features, dapc.success, dapc1)
+ names(answer)[[1]] <- "Number of PCs of PCA retained"
+ names(answer)[[2]] <- "FS"
+ names(answer)[[3]] <- "Discrimination success overall & by group"
+ names(answer)[[4]] <- "DAPC"
+ return(answer)
+ }
+
+ par(ask=FALSE)
+} # end snpzip
+
+
+
+
diff --git a/R/spca.R b/R/spca.R
new file mode 100644
index 0000000..4d5e280
--- /dev/null
+++ b/R/spca.R
@@ -0,0 +1,442 @@
+##############################################
+#
+# spatial Principal Components Analysis
+#
+# require ade4, spdep and eventually tripack
+#
+# generic functions were derived from
+# those of multispati class (ade4)
+#
+# T. Jombart (t.jombart at imperial.ac.uk)
+# 31 may 2007
+##############################################
+
+
+################
+# spca genind
+################
+spca <- function(obj, xy=NULL, cn=NULL, matWeight=NULL,
+ scale=FALSE,
+ scannf=TRUE, nfposi=1, nfnega=1,
+ type=NULL, ask=TRUE, plot.nb=TRUE, edit.nb=FALSE,
+ truenames=TRUE, d1=NULL, d2=NULL, k=NULL, a=NULL, dmin=NULL){
+
+ ## first checks
+ if(!any(inherits(obj,c("genind","genpop")))) stop("obj must be a genind or genpop object.")
+ invisible(validObject(obj))
+ ## checkType(obj)
+
+
+ ## handle xy coordinates
+ if(is.null(xy) & (inherits(cn,"nb") & !inherits(cn,"listw")) ){
+ xy <- attr(cn,"xy") # xy can be retrieved from a nb object (not from listw)
+ }
+ if(is.null(xy) & !is.null(obj$other$xy)) {
+ xy <- obj$other$xy # xy from @other$xy if it exists
+ }
+ if(is.null(xy)) stop("xy coordinates are not provided")
+ if(is.data.frame(xy)) {
+ xy <- as.matrix(xy)
+ }
+ if(!is.matrix(xy)) stop("wrong 'xy' provided")
+ if(ncol(xy) != 2) stop("xy does not have two columns.")
+ if(nrow(xy) != nrow(obj at tab)) stop("obj at tab and xy must have the same row numbers.")
+
+
+ appel <- match.call()
+
+ ## == To find the spatial weights ==
+ resCN <- NULL
+
+ ## connection network from matWeight
+ if(!is.null(matWeight)){
+ if(!is.matrix(matWeight)) stop("matWeight is not a matrix")
+ if(!is.numeric(matWeight)) stop("matWeight is not numeric")
+ if(nrow(matWeight) != ncol(matWeight)) stop("matWeight is not square")
+ if(nrow(matWeight) != nrow(obj at tab)) stop("dimension of datWeight does not match genetic data")
+ diag(matWeight) <- 0
+ matWeight <- prop.table(matWeight, 1)
+ resCN <- mat2listw(matWeight)
+ resCN$style <- "W"
+
+ }
+
+ ## connection network from cn argument
+ if(is.null(resCN) & !is.null(cn)) {
+ if(inherits(cn,"nb")) {
+ if(!inherits(cn,"listw")){ # cn is a 'pure' nb object (i.e., nb but not listw)
+ cn <- nb2listw(cn, style="W", zero.policy=TRUE)
+ }
+ resCN <- cn
+ } else stop("cn does not have a recognized class")
+ }
+
+
+ ## connection network from xy coordinates
+ if(is.null(resCN)) {
+ resCN <- chooseCN(xy=xy, ask=ask, type=type, plot.nb=plot.nb, edit.nb=edit.nb,
+ result.type="listw", d1=d1, d2=d2, k=k, a=a, dmin=dmin)
+ }
+
+ ## == spatial weights are done ==
+
+
+ ## handle NAs warning
+ if(any(is.na(obj at tab))){
+ warning("NAs in data are automatically replaced (to mean allele frequency)")
+ }
+
+ ## handle NAs, centring and scaling
+ X <- scaleGen(obj, center=TRUE, scale=scale, NA.method="mean")
+
+ ## perform analyses
+ pcaX <- dudi.pca(X, center=FALSE, scale=FALSE, scannf=FALSE)
+
+ spcaX <- multispati(dudi=pcaX, listw=resCN, scannf=scannf, nfposi=nfposi, nfnega=nfnega)
+
+ nfposi <- spcaX$nfposi
+ nfnega <- spcaX$nfnega
+
+ spcaX$xy <- xy
+ rownames(spcaX$xy) <- rownames(spcaX$li)
+ colnames(spcaX$xy) <- c("x","y")
+
+ spcaX$lw <- resCN
+
+ spcaX$call <- appel
+
+ posaxes <- if(nfposi>0) {1:nfposi} else NULL
+ negaxes <- if(nfnega>0) {(length(spcaX$eig)-nfnega+1):length(spcaX$eig)} else NULL
+ keptaxes <- c(posaxes,negaxes)
+
+ ## set names of different components
+ colnames(spcaX$c1) <- paste("Axis",keptaxes)
+ colnames(spcaX$li) <- paste("Axis",keptaxes)
+ colnames(spcaX$ls) <- paste("Axis",keptaxes)
+ row.names(spcaX$c1) <- colnames(X)
+ colnames(spcaX$as) <- colnames(spcaX$c1)
+ temp <- row.names(spcaX$as)
+ row.names(spcaX$as) <- paste("PCA",temp)
+
+ class(spcaX) <- "spca"
+
+ return(spcaX)
+
+} # end spca
+
+
+
+
+
+######################
+# Function print.spca
+######################
+print.spca <- function(x, ...){
+ cat("\t########################################\n")
+ cat("\t# spatial Principal Component Analysis #\n")
+ cat("\t########################################\n")
+ cat("class: ")
+ cat(class(x))
+ cat("\n$call: ")
+ print(x$call)
+ cat("\n$nfposi:", x$nfposi, "axis-components saved")
+ cat("\n$nfnega:", x$nfnega, "axis-components saved")
+
+ cat("\nPositive eigenvalues: ")
+ l0 <- sum(x$eig >= 0)
+ cat(signif(x$eig, 4)[1:(min(5, l0))])
+ if (l0 > 5)
+ cat(" ...\n")
+ else cat("\n")
+ cat("Negative eigenvalues: ")
+ l0 <- sum(x$eig <= 0)
+ cat(sort(signif(x$eig, 4))[1:(min(5, l0))])
+ if (l0 > 5)
+ cat(" ...\n")
+ else cat("\n")
+ cat('\n')
+ sumry <- array("", c(1, 4), list(1, c("vector", "length",
+ "mode", "content")))
+ sumry[1, ] <- c('$eig', length(x$eig), mode(x$eig), 'eigenvalues')
+ class(sumry) <- "table"
+ print(sumry)
+ cat("\n")
+ sumry <- array("", c(4, 4), list(1:4, c("data.frame", "nrow", "ncol", "content")))
+ sumry[1, ] <- c("$c1", nrow(x$c1), ncol(x$c1), "principal axes: scaled vectors of alleles loadings")
+ sumry[2, ] <- c("$li", nrow(x$li), ncol(x$li), "principal components: coordinates of entities ('scores')")
+ sumry[3, ] <- c("$ls", nrow(x$ls), ncol(x$ls), 'lag vector of principal components')
+ sumry[4, ] <- c("$as", nrow(x$as), ncol(x$as), 'pca axes onto spca axes')
+
+ class(sumry) <- "table"
+ print(sumry)
+
+ cat("\n$xy: matrix of spatial coordinates")
+ cat("\n$lw: a list of spatial weights (class 'listw')")
+
+ cat("\n\nother elements: ")
+ if (length(names(x)) > 10)
+ cat(names(x)[11:(length(names(x)))], "\n")
+ else cat("NULL\n")
+}
+
+
+
+
+
+########################
+# Function summary.spca
+########################
+summary.spca <- function (object, ..., printres=TRUE) {
+ if (!inherits(object, "spca"))stop("to be used with 'spca' object")
+
+ #util <- function(n) { ## no longer used
+ # x <- "1"
+ # for (i in 2:n) x[i] <- paste(x[i - 1], i, sep = "+")
+ # return(x)
+ #}
+ norm.w <- function(X, w) {
+ f2 <- function(v) sum(v * v * w)/sum(w)
+ norm <- apply(X, 2, f2)
+ return(norm)
+ }
+
+ resfin <- list()
+
+ if(printres) {
+ cat("\nSpatial principal component analysis\n")
+ cat("\nCall: ")
+ print(object$call)
+ }
+
+ appel <- as.list(object$call)
+ ## compute original pca
+ # prepare data
+ obj <- eval(appel$obj)
+ if(is.null(appel$truenames)) appel$truenames <- FALSE
+
+ f1 <- function(vec){
+ m <- mean(vec,na.rm=TRUE)
+ vec[is.na(vec)] <- m
+ return(vec)
+ }
+
+ if(is.genind(obj)) { X <- obj at tab }
+ if(is.genpop(obj)) { X <- makefreq(obj, quiet=TRUE) }
+
+ X <- apply(X,2,f1)
+
+ nfposi <- object$nfposi
+ nfnega <- object$nfnega
+
+ dudi <- dudi.pca(X, center=TRUE, scale=FALSE, scannf=FALSE, nf=nfposi+nfnega)
+ ## end of pca
+
+ lw <- object$lw
+
+ # I0, Imin, Imax
+ n <- nrow(X)
+ I0 <- -1/(n-1)
+ L <- listw2mat(lw)
+ ## use 'as.numeric' to avoid possible bug with large matrices,
+ ## returning complex numbers with zero imaginary parts
+ eigL <- suppressWarnings(as.numeric(eigen(0.5*(L+t(L)))$values))
+ Imin <- min(eigL)
+ Imax <- max(eigL)
+ Ival <- data.frame(I0=I0,Imin=Imin,Imax=Imax)
+ row.names(Ival) <- ""
+ if(printres) {
+ cat("\nConnection network statistics:\n")
+ print(Ival)
+ }
+
+ Istat <- c(I0,Imin,Imax)
+ names(Istat) <- c("I0","Imin","Imax")
+ resfin$Istat <- Istat
+
+
+ # les scores de l'analyse de base
+ nf <- dudi$nf
+ eig <- dudi$eig[1:nf]
+ cum <- cumsum(dudi$eig)[1:nf]
+ ratio <- cum/sum(dudi$eig)
+ w <- apply(dudi$l1,2,lag.listw,x=lw)
+ moran <- apply(w*as.matrix(dudi$l1)*dudi$lw,2,sum)
+ res <- data.frame(var=eig,cum=cum,ratio=ratio, moran=moran)
+ row.names(res) <- paste("Axis",1:nf)
+ if(printres) {
+ cat("\nScores from the centred PCA\n")
+ print(res)
+ }
+
+ resfin$pca <- res
+
+
+ # les scores de l'analyse spatiale
+ # on recalcule l'objet en gardant tous les axes
+ eig <- object$eig
+ nfposimax <- sum(eig > 0)
+ nfnegamax <- sum(eig < 0)
+
+ ms <- multispati(dudi=dudi, listw=lw, scannf=FALSE,
+ nfposi=nfposimax, nfnega=nfnegamax)
+
+ ndim <- dudi$rank
+ nf <- nfposi + nfnega
+ agarder <- c(1:nfposi,if (nfnega>0) (ndim-nfnega+1):ndim)
+ varspa <- norm.w(ms$li,dudi$lw)
+ moran <- apply(as.matrix(ms$li)*as.matrix(ms$ls)*dudi$lw,2,sum)
+ res <- data.frame(eig=eig,var=varspa,moran=moran/varspa)
+ row.names(res) <- paste("Axis",1:length(eig))
+
+ if(printres) {
+ cat("\nsPCA eigenvalues decomposition:\n")
+ print(res[agarder,])
+ }
+
+ resfin$spca <- res
+
+ return(invisible(resfin))
+}
+
+
+
+#####################
+# Function plot.spca
+#####################
+plot.spca <- function (x, axis = 1, useLag=FALSE, ...){
+ if (!inherits(x, "spca")) stop("Use only with 'spca' objects.")
+
+ if(axis>ncol(x$li)) stop("wrong axis required.")
+
+ opar <- par(no.readonly = TRUE)
+ on.exit(par(opar))
+ par(mar = rep(.1,4), mfrow=c(3,2))
+
+ n <- nrow(x$li)
+ xy <- x$xy
+
+ ## handle useLag argument
+ if(useLag){
+ z <- x$ls[,axis]
+ } else {
+ z <- x$li[,axis]
+ } # end if useLag
+ nfposi <- x$nfposi
+ nfnega <- x$nfnega
+ ## handle neig parameter - hide cn if nore than 100 links
+ nLinks <- sum(card(x$lw$neighbours))
+ if(nLinks < 500) {
+ neig <- nb2neig(x$lw$neighbours)
+ } else {
+ neig <- NULL
+ }
+
+ sub <- paste("Score",axis)
+ csub <- 2
+
+ # 1
+ if(n<30) clab <- 1 else clab <- 0
+ s.label(xy, clabel=clab, include.origin=FALSE, addaxes=FALSE, neig=neig,
+ cneig=1, sub="Connection network", csub=2)
+
+ # 2
+ s.image(xy,z, include.origin=FALSE, grid=TRUE, kgrid=10, cgrid=1,
+ sub=sub, csub=csub, possub="bottomleft")
+ box()
+
+ # 3
+ if(n<30) {neig <- nb2neig(x$lw$neighbours)} else {neig <- NULL}
+ s.value(xy,z, include.origin=FALSE, addaxes=FALSE, clegend=0, csize=.6,
+ neig=neig, sub=sub, csub=csub, possub="bottomleft")
+
+ # 4
+ s.value(xy,z, include.origin=FALSE, addaxes=FALSE, clegend=0, csize=.6,
+ method="greylevel", neig=neig, sub=sub, csub=csub, possub="bottomleft")
+
+ # 5
+ omar <- par("mar")
+ par(mar = c(0.8, 2.8, 0.8, 0.8))
+ m <- length(x$eig)
+ col.w <- rep("white", m) # elles sont toutes blanches
+ col.w[1:nfposi] <- "grey"
+ if (nfnega>0) {col.w[m:(m-nfnega+1)] <- "grey"}
+ j <- axis
+ if (j>nfposi) {j <- j-nfposi +m -nfnega}
+ col.w[j] <- "black"
+ barplot(x$eig, col = col.w)
+ scatterutil.sub(cha ="Eigenvalues", csub = 2.5, possub = "topright")
+ par(mar=rep(.1,4))
+ box()
+ par(mar=omar)
+
+ # 6
+ par(mar=c(4,4,2,1))
+ screeplot(x,main="Eigenvalues decomposition")
+ par(mar=rep(.1,4))
+ box()
+ return(invisible(match.call()))
+}
+
+
+
+##########################
+# Function screeplot.spca
+##########################
+screeplot.spca <- function(x,...,main=NULL){
+
+ opar <- par("las")
+ on.exit(par(las=opar))
+
+ sumry <- summary(x,printres=FALSE)
+
+ labels <- lapply(1:length(x$eig),function(i) bquote(lambda[.(i)]))
+
+ par(las=1)
+
+ xmax <- sumry$pca[1,1]*1.1
+ I0 <- sumry$Istat[1]
+ Imin <- sumry$Istat[2]
+ Imax <- sumry$Istat[3]
+
+ plot(x=sumry$spca[,2],y=sumry$spca[,3],type='n',xlab='Variance',ylab="Spatial autocorrelation (I)",xlim=c(0,xmax),ylim=c(Imin*1.1,Imax*1.1),yaxt='n',...)
+ text(x=sumry$spca[,2],y=sumry$spca[,3],do.call(expression,labels))
+
+ ytick <- c(I0,round(seq(Imin,Imax,le=5),1))
+ ytlab <- as.character(round(seq(Imin,Imax,le=5),1))
+ ytlab <- c(as.character(round(I0,1)),as.character(round(Imin,1)),ytlab[2:4],as.character(round(Imax,1)))
+ axis(side=2,at=ytick,labels=ytlab)
+
+ rect(0,Imin,xmax,Imax,lty=2)
+ segments(0,I0,xmax,I0,lty=2)
+ abline(v=0)
+
+ if(is.null(main)) main <- ("Spatial and variance components of the eigenvalues")
+ title(main)
+
+ return(invisible(match.call()))
+}
+
+
+
+
+
+###################
+# colorplot method
+###################
+colorplot.spca <- function(x, axes=1:ncol(x$li), useLag=FALSE, ...){
+ ## some checks
+ if(!any(inherits(x,"spca"))) stop("x in not a spca object.")
+
+ ## get args to be passed to colorplot
+ xy <- x$xy
+
+ if(useLag) {
+ X <- as.matrix(x$ls)
+ } else {
+ X <- as.matrix(x$li)
+ }
+
+ ## call to colorplot
+ colorplot(xy, X, axes, ...)
+
+} # end colorplot.spca
diff --git a/R/spca.rtests.R b/R/spca.rtests.R
new file mode 100644
index 0000000..5766f94
--- /dev/null
+++ b/R/spca.rtests.R
@@ -0,0 +1,89 @@
+########################################
+#
+# Tests for global and local structures
+#
+# Thibaut Jombart 2007
+# t.jombart at imperial.ac.uk
+#
+########################################
+
+
+
+###############
+# global.rtest
+###############
+global.rtest <- function(X, listw, k=1, nperm=499){
+ if (!inherits(listw, "listw")) stop("object of class 'listw' expected")
+ if (listw$style != "W") stop("object of class 'listw' with style 'W' expected")
+ if(any(is.na(X))) stop("NA entries in X")
+
+ n <- nrow(X)
+ X <- scalewt(X)
+
+ # computation of U+
+ temp <- .orthobasis.listw(listw)
+ val <- attr(temp,"values")
+ U <- as.matrix(temp)
+ Upos <- U[,val > -1/(n-1)]
+
+ # test statistic
+ calcstat <- function(X,k){
+ R <- ( t(X) %*% Upos ) / n
+ R2 <- R*R
+ temp <- sort(apply(R2,2,mean),decreasing=TRUE)
+ stat <- sum(temp[1:k])
+ return(stat)
+ }
+
+ ini <- calcstat(X,k)
+
+ sim <- sapply(1:nperm, function(i) calcstat( X[sample(1:n),], k ) )
+
+ res <- as.randtest(sim=sim, obs=ini, alter="greater")
+ res$call <- match.call()
+
+ return(res)
+} #end global.rtest
+
+
+
+
+
+###############
+# local.rtest
+###############
+local.rtest <- function(X, listw, k=1, nperm=499){
+ if (!inherits(listw, "listw")) stop("object of class 'listw' expected")
+ if (listw$style != "W") stop("object of class 'listw' with style 'W' expected")
+ if(any(is.na(X))) stop("NA entries in X")
+
+ n <- nrow(X)
+ X <- scalewt(X)
+
+ # computation of U-
+ temp <- .orthobasis.listw(listw)
+ val <- attr(temp,"values")
+ U <- as.matrix(temp)
+ Uneg <- U[,val < -1/(n-1)]
+
+ X <- scalewt(X)
+
+ # test statistic
+ calcstat <- function(X,k){
+ R <- ( t(X) %*% Uneg ) / n
+ R2 <- R*R
+ temp <- sort(apply(R2,2,mean),decreasing=TRUE)
+ stat <- sum(temp[1:k])
+ return(stat)
+ }
+
+ ini <- calcstat(X,k)
+
+ sim <- sapply(1:nperm, function(i) calcstat( X[sample(1:n),], k ) )
+
+ res <- as.randtest(sim=sim, obs=ini, alter="greater")
+ res$call <- match.call()
+
+ return(res)
+} #end local.rtest
+
diff --git a/R/strataMethods.R b/R/strataMethods.R
new file mode 100644
index 0000000..d13032a
--- /dev/null
+++ b/R/strataMethods.R
@@ -0,0 +1,686 @@
+########################################################################
+# strata methods definitions.
+#
+# Zhian Kamvar, March 2015
+# kamvarz at science.oregonstate.edu
+########################################################################
+#==============================================================================#
+#==============================================================================#
+# Workhorse functions for strata methods. These avoids needless copying and
+# pasting of code to dispatch the methods to two unrelated classes
+# (genind and genlight).
+#==============================================================================#
+#==============================================================================#
+.getStrata <- function(x, formula = NULL, combine = TRUE, call = match.call()){
+ if (is.null(x at strata)) return(NULL)
+ if (is.null(formula)) return(x at strata)
+ vars <- all.vars(formula)
+ if (any(!vars %in% names(x at strata))){
+ stop(.strata_incompatible_warning(vars, x at strata), call. = FALSE)
+ }
+ if (combine){
+ strata <- .make_strata(formula, x at strata)
+ } else {
+ strata <- x at strata[all.vars(formula)]
+ }
+ invisible(return(strata))
+}
+
+.setStrata <- function(x, value, call = match.call()){
+ if (is.null(value)){
+ x at strata <- value
+ return(x)
+ }
+ if (!inherits(value, "data.frame")){
+ callval <- as.character(call["value"])
+ stop(paste(callval, "is not a data frame"), call. = FALSE)
+ }
+ if (nrow(value) != nInd(x)){
+ stop("Number of rows in data frame not equal to number of individuals in object.", call. = FALSE)
+ }
+ value <- data.frame(lapply(value, function(f) factor(f, unique(f))))
+ x at strata <- value
+ return(x)
+}
+
+.nameStrata <- function(x, value, call = match.call()){
+ if (missing(value)){
+ return(names(x at strata))
+ }
+ if (is.null(x at strata)){
+ warning("Cannot name an empty strata", call. = FALSE)
+ return(x)
+ }
+ if (is.language(value)){
+ value <- all.vars(value)
+ }
+ if (!is.vector(value) | length(value) != length(x at strata)){
+ stop(paste("nameStrata needs a vector argument of length", length(x at strata)), call. = FALSE)
+ }
+ names(x at strata) <- value
+ return(x)
+}
+
+.splitStrata <- function(x, value, sep = "_", call = match.call()){
+ if (is.null(x at strata)){
+ warning("Cannot split empty strata", call. = FALSE)
+ return(x)
+ }
+ if (is.language(value)){
+ # valterms <- attr(terms(value), "term.labels")
+ # valterms <- valterms[length(valterms)]
+ # valterms <- gsub(":", sep, valterms)
+ value <- all.vars(value)
+ } else {
+ stop("Value must be a formula.", call. = FALSE)
+ }
+ if (length(value) < 1){
+ stop("Value must have more than one level.", call. = FALSE)
+ }
+ strata <- x at strata
+ if (length(strata) > 1){
+ warning("Strata must be length 1. Taking the first column.", call. = FALSE)
+ strata <- strata[1]
+ }
+ seps <- gregexpr(sep, strata[[1]])
+ sepmatch <- vapply(seps, function(val) all(as.integer(val) > 0), logical(1))
+ seps <- vapply(seps, length, numeric(1))
+ all_seps_match <- all(sepmatch)
+ given_seps <- length(value) - 1
+ if (!all_seps_match | all(seps != given_seps)){
+ seps <- ifelse(all_seps_match, seps[1], 0) + 1
+ msg1 <- paste("\n Data has", seps, ifelse(seps == 1, "level", "levels"),
+ "of strata with the separator", sep, ".")
+ msg2 <- paste("Here is the fist column of the data:", strata[1, ])
+ stop(paste(msg1, "\n ", msg2), call. = FALSE)
+ }
+ x at strata <- colsplit(as.character(strata[[1]]), pattern = sep, value)
+ x at strata <- data.frame(lapply(x at strata, function(f) factor(f, levels = unique(f))))
+ # names(strata) <- value
+ # x at strata <- strata
+ return(x)
+}
+
+.addStrata <- function(x, value, name = "NEW", call = match.call()){
+ if (is.null(x at strata)){
+ strata <- data.frame(vector(mode = "character", length = nInd(x)))
+ wasNULL <- TRUE
+ } else {
+ strata <- x at strata
+ wasNULL <- FALSE
+ }
+
+ if ((is.vector(value) | is.factor(value)) & length(value) == nrow(strata)){
+ value <- factor(value, levels = unique(value))
+ NEW <- data.frame(value)
+ names(NEW) <- name
+ strata <- cbind(strata, NEW)
+ } else if (is.data.frame(value) && nrow(value) == nrow(strata)){
+ value <- data.frame(lapply(value, function(f) factor(f, unique(f))))
+ strata <- cbind(strata, value)
+ } else if (is.data.frame(value)){
+ callval <- as.character(call["value"])
+ msg <- .not_enough_rows_warning(callval, nrow(value), nrow(strata))
+ stop(msg, call. = FALSE)
+ } else {
+ stop("value must be a vector or data frame.", call. = FALSE)
+ }
+ if (wasNULL){
+ strata <- strata[-1, , drop = FALSE]
+ }
+ x at strata <- strata
+ return(x)
+}
+
+.setPop <- function(x, formula = NULL, call = match.call()){
+ if (is.null(x at strata)){
+ warning("Cannot set the population from an empty strata", call. = FALSE)
+ return(x)
+ }
+ if (is.null(formula) | !is.language(formula)){
+ callform <- as.character(call["formula"])
+ stop(paste(callform, "must be a valid formula object."), call. = FALSE)
+ }
+ vars <- all.vars(formula)
+ if (!all(vars %in% names(x at strata))){
+ stop(.strata_incompatible_warning(vars, x at strata), call. = FALSE)
+ }
+ pop(x) <- .make_strata(formula, x at strata)[[length(vars)]]
+ return(x)
+}
+
+#==============================================================================#
+#==============================================================================#
+# Formal methods definitions and documentation.
+#==============================================================================#
+#==============================================================================#
+
+#==============================================================================#
+#' Access and manipulate the population strata for genind or genlight objects.
+#'
+#' The following methods allow the user to quickly change the strata of a genind
+#' or genlight object.
+#'
+#' @export
+#' @rdname strata-methods
+#' @aliases strata,genind-method strata,genlight-method
+#' @param x a genind or genlight object
+#' @param formula a nested formula indicating the order of the population
+#' strata.
+#' @param combine if \code{TRUE} (default), the levels will be combined according to the
+#' formula argument. If it is \code{FALSE}, the levels will not be combined.
+#' @param value a data frame OR vector OR formula (see details).
+#' @docType methods
+#'
+#' @details \subsection{Function Specifics}{ \itemize{ \item \strong{strata()} -
+#' Use this function to view or define population stratification of a
+#' \linkS4class{genind} or \linkS4class{genlight} object. \item
+#' \strong{nameStrata()} - View or rename the different levels of strata.
+#' \item \strong{splitStrata()} - Split strata that are combined with a common
+#' separator. This function should only be used once during a workflow.
+#' \itemize{ \item \emph{Rationale:} It is often difficult to import files
+#' with several levels of strata as most data formats do not allow unlimited
+#' population levels. This is circumvented by collapsing all population strata
+#' into a single population factor with a common separator for each
+#' observation. } \item \strong{addStrata()} - Add levels to your population
+#' strata. This is ideal for adding groups defined by
+#' \code{\link{find.clusters}}. You can input a data frame or a vector, but if
+#' you put in a vector, you have the option to name it. }}
+#'
+#' \subsection{Argument Specifics}{
+#'
+#' These functions allow the user to seamlessly carry all possible population
+#' stratification with their \linkS4class{genind} or \linkS4class{genlight}
+#' object. Note that there are two ways of performing all methods: \itemize{
+#' \item modifying: \code{strata(myData) <- myStrata} \item preserving:
+#' \code{myNewData <- strata(myData, value = myStrata)} } They essentially do
+#' the same thing except that the modifying assignment method (the one with
+#' the "\code{<-}") will modify the object in place whereas the non-assignment
+#' method will preserve the original object (unless you overwrite it). Due to
+#' convention, everything right of the assignment is termed \code{value}. To
+#' avoid confusion, here is a guide to the argument \strong{\code{value}} for
+#' each function: \itemize{ \item \strong{strata()} \code{value = }a
+#' \code{\link{data.frame}} that defines the strata for each individual in the
+#' rows. \item \strong{nameStrata()} \code{value = }a \code{\link{vector}} or
+#' a \code{\link{formula}} that will define the names. \item
+#' \strong{splitStrata()} \code{value = }a \code{\link{formula}} argument with
+#' the same number of levels as the strata you wish to split. \item
+#' \strong{addStrata()} \code{value = }a \code{\link{vector}} or
+#' \code{\link{data.frame}} with the same length as the number of individuals
+#' in your data. }}
+#'
+#' \subsection{Details on Formulas}{
+#'
+#' The preferred use of these functions is with a \code{\link{formula}}
+#' object. Specifically, a hierarchical formula argument is used to assign the
+#' levels of the strata. An example of a hierarchical formula would
+#' be:\tabular{r}{ \code{~Country/City/Neighborhood}} This convention was
+#' chosen as it becomes easier to type and makes intuitive sense when defining
+#' a \code{\link{hierarchy}}. Note: it is important to use hiearchical
+#' formulas when specifying hierarchies as other types of formulas (eg.
+#' \code{~Country*City*Neighborhood}) will give incorrect results.}
+#'
+#' @seealso \code{\link{setPop}} \code{\link{genind}}
+#' \code{\link{as.genind}}
+#'
+#' @author Zhian N. Kamvar
+#' @examples
+#' # let's look at the microbov data set:
+#' data(microbov)
+#' microbov
+#'
+#' # We see that we have three vectors of different names in the 'other' slot.
+#' # ?microbov
+#' # These are Country, Breed, and Species
+#' names(other(microbov))
+#'
+#' # Let's set the strata
+#' strata(microbov) <- data.frame(other(microbov))
+#' microbov
+#'
+#' # And change the names so we know what they are
+#' nameStrata(microbov) <- ~Country/Breed/Species
+#'
+#' \dontrun{
+#' # let's see what the strata looks like by Species and Breed:
+#' head(strata(microbov, ~Breed/Species))
+#'
+#' # If we didn't want the last column combined with the first, we can set
+#' # combine = FALSE
+#' head(strata(microbov, ~Breed/Species, combine = FALSE))
+#'
+#' #### USING splitStrata ####
+#'
+#' # For the sake of example, we'll imagine that we have imported our data set
+#' # with all of the stratifications combined.
+#' setPop(microbov) <- ~Country/Breed/Species
+#' strata(microbov) <- NULL
+#'
+#' # This is what our data would look like after import.
+#' microbov
+#'
+#' # To set our strata here, we need to use the functions strata and splitStrata
+#' strata(microbov) <- data.frame(x = pop(microbov))
+#' microbov # shows us that we have "one" level of stratification
+#' head(strata(microbov)) # all strata are separated by "_"
+#'
+#' splitStrata(microbov) <- ~Country/Breed/Species
+#' microbov # Now we have all of our strata named and split
+#' head(strata(microbov)) # all strata are appropriately named and split.
+#' }
+#==============================================================================#
+strata <- function(x, formula = NULL, combine = TRUE, value){
+ standardGeneric("strata")
+}
+
+#' @export
+setGeneric("strata")
+
+setMethod(
+ f = "strata",
+ signature(x = "genind"),
+ definition = function(x, formula = NULL, combine = TRUE, value){
+ theCall <- match.call()
+ if (missing(value)){
+ .getStrata(x, formula = formula, combine = combine, theCall)
+ } else {
+ .setStrata(x, value, theCall)
+ }
+ })
+
+setMethod(
+ f = "strata",
+ signature(x = "genlight"),
+ definition = function(x, formula = NULL, combine = TRUE, value){
+ theCall <- match.call()
+ if (missing(value)){
+ .getStrata(x, formula = formula, combine = combine, theCall)
+ } else {
+ .setStrata(x, value, theCall)
+ }
+
+ })
+
+
+#==============================================================================#
+#' @export
+#' @rdname strata-methods
+#' @aliases strata<-,genind-method strata<-,genlight-method
+#' @docType methods
+#==============================================================================#
+"strata<-" <- function(x, value){
+ standardGeneric("strata<-")
+}
+
+#' @export
+setGeneric("strata<-")
+
+setMethod(
+ f = "strata<-",
+ signature(x = "genind"),
+ definition = function(x, value){
+ theCall <- match.call()
+ return(.setStrata(x, value, theCall))
+ })
+
+setMethod(
+ f = "strata<-",
+ signature(x = "genlight"),
+ definition = function(x, value){
+ theCall <- match.call()
+ return(.setStrata(x, value, theCall))
+ })
+
+#==============================================================================#
+#' @export
+#' @rdname strata-methods
+#' @aliases nameStrata,genind-method nameStrata,genlight-method
+#' @docType methods
+#==============================================================================#
+nameStrata <- function(x, value){
+ standardGeneric("nameStrata")
+}
+
+#' @export
+setGeneric("nameStrata")
+
+setMethod(
+ f = "nameStrata",
+ signature(x = "genind"),
+ definition = function(x, value){
+ .nameStrata(x, value)
+ })
+
+setMethod(
+ f = "nameStrata",
+ signature(x = "genlight"),
+ definition = function(x, value){
+ .nameStrata(x, value)
+ })
+
+#==============================================================================#
+#' @export
+#' @rdname strata-methods
+#' @aliases nameStrata<-,genind-method nameStrata<-,genlight-method
+#' @docType methods
+#==============================================================================#
+"nameStrata<-" <- function(x, value){
+ standardGeneric("nameStrata<-")
+}
+
+#' @export
+setGeneric("nameStrata<-")
+
+setMethod(
+ f = "nameStrata<-",
+ signature(x = "genind"),
+ definition = function(x, value){
+ return(nameStrata(x, value))
+ })
+
+setMethod(
+ f = "nameStrata<-",
+ signature(x = "genlight"),
+ definition = function(x, value){
+ return(nameStrata(x, value))
+ })
+#==============================================================================#
+#' @export
+#' @rdname strata-methods
+#' @aliases splitStrata,genind-method splitStrata,genlight-method
+#' @docType methods
+#' @param sep a \code{character} indicating the character used to separate
+#' hierarchical levels. This defaults to "_".
+#' @importFrom reshape2 colsplit
+#==============================================================================#
+splitStrata <- function(x, value, sep = "_"){
+ standardGeneric("splitStrata")
+}
+
+#' @export
+setGeneric("splitStrata")
+
+setMethod(
+ f = "splitStrata",
+ signature(x = "genind"),
+ definition = function(x, value, sep = "_"){
+ .splitStrata(x, value, sep = sep)
+ })
+
+setMethod(
+ f = "splitStrata",
+ signature(x = "genlight"),
+ definition = function(x, value, sep = "_"){
+ .splitStrata(x, value, sep = sep)
+ })
+
+#==============================================================================#
+#' @export
+#' @rdname strata-methods
+#' @aliases splitStrata<-,genind-method splitStrata<-,genlight-method
+#' @docType methods
+#==============================================================================#
+"splitStrata<-" <- function(x, sep = "_", value){
+ standardGeneric("splitStrata<-")
+}
+
+#' @export
+setGeneric("splitStrata<-")
+
+setMethod(
+ f = "splitStrata<-",
+ signature(x = "genind"),
+ definition = function(x, sep = "_", value){
+ return(splitStrata(x, value, sep))
+ })
+
+setMethod(
+ f = "splitStrata<-",
+ signature(x = "genlight"),
+ definition = function(x, sep = "_", value){
+ return(splitStrata(x, value, sep))
+ })
+
+#==============================================================================#
+#' @export
+#' @rdname strata-methods
+#' @aliases addStrata,genind-method addStrata,genlight-method
+#' @param name an optional name argument for use with addStrata if supplying
+#' a vector. Defaults to "NEW".
+#' @docType methods
+#==============================================================================#
+addStrata <- function(x, value, name = "NEW"){
+ standardGeneric("addStrata")
+}
+
+#' @export
+setGeneric("addStrata")
+
+setMethod(
+ f = "addStrata",
+ signature(x = "genind"),
+ definition = function(x, value, name = "NEW"){
+ theCall <- match.call()
+ .addStrata(x, value, name = name, theCall)
+ })
+
+setMethod(
+ f = "addStrata",
+ signature(x = "genlight"),
+ definition = function(x, value, name = "NEW"){
+ theCall <- match.call()
+ .addStrata(x, value, name = name, theCall)
+ })
+
+#==============================================================================#
+#' @export
+#' @rdname strata-methods
+#' @aliases addStrata<-,genind-method addStrata<-,genlight-method
+#' @docType methods
+#==============================================================================#
+"addStrata<-" <- function(x, name = "NEW", value){
+ standardGeneric("addStrata<-")
+}
+
+#' @export
+setGeneric("addStrata<-")
+
+setMethod(
+ f = "addStrata<-",
+ signature(x = "genind"),
+ definition = function(x, name = "NEW", value){
+ theCall <- match.call()
+ return(.addStrata(x, value, name = name, theCall))
+ })
+
+setMethod(
+ f = "addStrata<-",
+ signature(x = "genlight"),
+ definition = function(x, name = "NEW", value){
+ theCall <- match.call()
+ return(.addStrata(x, value, name = name, theCall))
+ })
+
+#==============================================================================#
+#' Manipulate the population factor of genind objects.
+#'
+#' The following methods allow the user to quickly change the population of a
+#' genind object.
+#'
+#' @export
+#' @rdname population-methods
+#' @param x a genind or genlight object
+#' @param formula a nested formula indicating the order of the population
+#' strata.
+#' @param value same as formula
+#' @aliases setPop,genind-method setPop,genlight-method
+#' @docType methods
+#' @author Zhian N. Kamvar
+#' @examples
+#'
+#' data(microbov)
+#'
+#' strata(microbov) <- data.frame(other(microbov))
+#'
+#' # Currently set on just
+#' head(pop(microbov))
+#'
+#' # setting the strata to both Pop and Subpop
+#' setPop(microbov) <- ~coun/breed
+#' head(pop(microbov))
+#'
+#' \dontrun{
+#'
+#' # Can be used to create objects as well.
+#' microbov.old <- setPop(microbov, ~spe)
+#' head(pop(microbov.old))
+#' }
+#==============================================================================#
+setPop <- function(x, formula = NULL) standardGeneric("setPop")
+
+#' @export
+setGeneric("setPop")
+
+setMethod(
+ f = "setPop",
+ signature(x = "genind"),
+ definition = function(x, formula = NULL){
+ .setPop(x, formula = formula)
+ })
+
+setMethod(
+ f = "setPop",
+ signature(x = "genlight"),
+ definition = function(x, formula = NULL){
+ .setPop(x, formula = formula)
+ })
+#==============================================================================#
+#' @export
+#' @rdname population-methods
+#' @aliases setPop<-,genind-method setPop<-,genlight-method
+#' @docType methods
+#==============================================================================#
+"setPop<-" <- function(x, value) standardGeneric("setPop<-")
+
+#' @export
+setGeneric("setPop<-")
+
+setMethod(
+ f = "setPop<-",
+ signature(x = "genind"),
+ definition = function(x, value){
+ return(setPop(x, value))
+ })
+
+setMethod(
+ f = "setPop<-",
+ signature(x = "genlight"),
+ definition = function(x, value){
+ return(setPop(x, value))
+ })
+
+#==============================================================================#
+#==============================================================================#
+# internal functions utilized
+#==============================================================================#
+#==============================================================================#
+
+#==============================================================================#
+# A function for creating a population strata using a formula and data frame
+#
+# hier = a nested formula such as ~ A/B/C where C is nested within B, which is
+# nested within A.
+#
+# df = a data frame containing columns corresponding to the variables in hier.
+#
+# example:
+# df <- data.frame(list(a = letters, b = LETTERS, c = 1:26))
+# newdf <- .make_strata(~ a/b/c, df)
+# df[names(newdf)] <- newdf # Add new columns.
+#
+# Public functions utilizing this function:
+#
+# # setPop, strata
+#
+# Internal functions utilizing this function:
+# # none
+#==============================================================================#
+.make_strata <- function(strata, df, expand_label = FALSE){
+ newlevs <- attr(terms(strata), "term.labels")
+ levs <- all.vars(strata)
+ if (length(levs) > 1){
+ newlevs <- gsub(":", "_", newlevs)
+ }
+ if (!all(levs %in% names(df))){
+ stop(.strata_incompatible_warning(levs, df), call. = FALSE)
+ }
+ newdf <- df[levs[1]]
+ if (!expand_label){
+ newlevs <- levs
+ }
+ lapply(1:length(levs), function(x) newdf[[newlevs[x]]] <<- as.factor(.pop_combiner(df, levs[1:x])))
+ return(newdf)
+}
+
+#==============================================================================#
+# This will be used to join heirarchical population vectors for the purposes of
+# maintaining strata.
+# Public functions utilizing this function:
+# #
+#
+# Internal functions utilizing this function:
+# # .make_strata
+#==============================================================================#
+
+.pop_combiner <- function(df, strata=c(1), sep="_"){
+ if(!is.list(df)){
+ warning("df must be a data frame or a list", call. = FALSE)
+ return(df)
+ }
+ else{
+ if(length(strata)==1){
+ return(df[[strata]])
+ }
+ else{
+ comb <- vector(length=length(df[[strata[1]]]))
+ comb <- df[[strata[1]]]
+ lapply(strata[-1], function(x) comb <<- paste(comb, df[[x]], sep=sep))
+ return(comb)
+ }
+ }
+}
+
+#==============================================================================#
+# A function that will quit the function if a level in the strata is not
+# present in the given data frame.
+#
+# Public functions utilizing this function:
+# # setPop strata poppr.amova
+#
+# Internal functions utilizing this function:
+# # .make_strata make_ade_df
+#==============================================================================#
+.strata_incompatible_warning <- function(levs, df){
+ msg <- paste("One or more levels in the given strata is not present",
+ "in the data frame.\n", paste(rep("-", 78), collapse = ""),
+ "\nstrata:\t", paste(levs, collapse = ", "), "\nData:\t",
+ paste(names(df), collapse = ", "))
+ return(msg)
+}
+
+#==============================================================================#
+# A function that will send a message if the number of rows in a data frame does
+# not match what is expected.
+#
+# Public functions utilizing this function:
+# # addStrata
+#
+# Internal functions utilizing this function:
+# # .addStrata
+#==============================================================================#
+.not_enough_rows_warning <- function(dfname, dfrow, nind){
+ msg <- paste("The data frame or vector does not have enough rows\n",
+ paste(rep("-", 78), collapse = ""),
+ "\n", dfname, ":\t", dfrow, "\nData :\t", nind)
+ return(msg)
+}
diff --git a/R/xvalDapc.R b/R/xvalDapc.R
new file mode 100644
index 0000000..42150ac
--- /dev/null
+++ b/R/xvalDapc.R
@@ -0,0 +1,257 @@
+
+##############
+## xvalDapc ##
+##############
+
+# Return randomly sampled indices from a group.
+# @param e group name
+# @param vector of group assignments per sample
+# @param training.set fraction of samples to be kept for validation
+.group_sampler <- function(e, grp, training.set){
+ group_e <- grp == e
+ N_group_e <- sum(group_e)
+ if (N_group_e < 2){
+ # If the size of the group is less than two, then leave the whole thing in
+ # the training set
+ return(which(group_e))
+ } else {
+ samp_group <- which(group_e)
+ samp_size <- round(training.set * N_group_e)
+ return(sample(samp_group, size = samp_size))
+ }
+}
+
+
+# Function to subsample the data. This is to be used as the ran.gen function
+# in the boot function. DATA is a data frame or matrix containing the samples,
+# GRP is the group identities of the samples, PCA is the result of dudi.pca
+# on the full data set, KEEP is the subset of samples based on the training
+# set (mle). Note that this function only has two inputs, dat, and mle.
+.boot_group_sampler <- function(dat = list(DATA = NULL, GRP = NULL, PCA = NULL,
+ KEEP = NULL),
+ mle = NULL){
+ to_keep <- unlist(lapply(levels(dat$GRP), .group_sampler, dat$GRP, mle))
+ dat$PCA$li <- dat$PCA$li[to_keep, , drop = FALSE]
+ dat$KEEP <- to_keep
+ return(dat)
+}
+
+
+# Function to pass to the "statistic" parameter of boot. This will subset the
+# data, calculate the DAPC, give the predictions and return the results.
+.boot_dapc_pred <- function(x, n.pca = n.pca, n.da = n.da, result = "overall"){
+ if (length(x$KEEP) == nrow(x$DATA)){
+ out <- 1
+ } else {
+ new_dat <- x$DATA[-x$KEEP, ,drop = FALSE]
+ train_dat <- x$DATA[x$KEEP, ,drop = FALSE]
+
+ new_grp <- x$GRP[-x$KEEP]
+ train_grp <- x$GRP[x$KEEP]
+
+ temp.dapc <- suppressWarnings(dapc(train_dat, train_grp, dudi = x$PCA,
+ n.pca = n.pca, n.da = n.da))
+ temp.pred <- predict.dapc(temp.dapc, newdata = new_dat)
+ if (result=="overall"){
+ out <- mean(temp.pred$assign == new_grp)
+ }
+ if (result=="groupMean"){
+ out <- mean(tapply(temp.pred$assign == new_grp, new_grp, mean), na.rm = TRUE)
+ }
+ }
+ return(out)
+}
+
+
+# Function that will actually do the bootstrapping. It will return a numeric
+# vector with the successes ratios. Note that the ellipses are used to pass
+# parameters to boot. When implemented in the xvalDapc function, this will allow
+# the user to implement this in parallel.
+# @param n.pca number of pcs
+# @param x data frame/matrix with samples in rows
+# @param n.da number of das
+# @param groups the names of each of the populations
+# @param grp factor of group assignments per sample
+# @param training.set fraction of samples used for training
+# @param training.set2 NULL or largest possible fraction that can be obtained
+# @param pcaX principal componenets
+# @param result user's choice of result type
+# @param reps the number of replicates per number of retained PCs
+# @param ... methods to be passed on to boot such as parallel and ncores
+####################
+## .get.prop.pred ##
+####################
+.get.prop.pred <- function(n.pca, x, n.da, groups, grp, training.set,
+ pcaX, result = "overall", reps = 100,
+ ...){
+
+ bootlist <- list(DATA = x, GRP = grp, PCA = pcaX, KEEP = 1:nrow(x))
+
+ out <- boot::boot(bootlist, .boot_dapc_pred, sim = "parametric", R = reps,
+ ran.gen = .boot_group_sampler, mle = training.set,
+ n.pca = n.pca, n.da = n.da, result = result, ...)$t
+ # }
+ return(as.vector(out))
+} # end .get.prop.pred
+
+
+
+
+##############
+## xvalDapc ##
+##############
+xvalDapc <- function(x, grp, n.pca.max = 300, n.da = NULL, training.set = 0.9,
+ result = c("groupMean", "overall"), center = TRUE, scale = FALSE,
+ n.pca = NULL, n.rep = 30, xval.plot = TRUE, ...){
+
+ ## CHECKS ##
+ grp <- factor(grp)
+ n.pca <- n.pca[n.pca > 0]
+ if(!is.null(n.da)){
+ n.da <- n.da
+ }else{
+ n.da <- length(levels(grp))-1}
+ # if(missing(n.da)){
+ # n.da <- length(levels(grp))-1}
+ # if(is.null(n.da)){
+ # n.da <- length(levels(grp))-1} # want to fix this to make interactive n.da selection an option!
+ # else{
+ # n.da <- n.da}
+ if(missing(training.set)){
+ training.set <- 0.9
+ }else{
+ training.set <- training.set}
+ if(missing(n.rep)){
+ n.rep <- 30
+ }else{
+ n.rep <- n.rep}
+
+ if(missing(result)){
+ result <- "groupMean"
+ }else{
+ if(length(result) > 1) result <- result[1]
+ result <- result}
+
+
+ ## GET TRAINING SET SIZE ##
+ N <- nrow(x)
+ groups <- levels(grp)
+ ## identify the sizes of groups
+ group.n <- as.vector(table(grp))
+ ## identify the smallest group size
+ popmin <- min(group.n)
+
+ ## check if any groups are of length 1:
+ if(popmin == 1){
+ singles <- which(group.n == 1)
+ counter <- length(singles)
+
+ ## get msg to print
+ if(counter == 1){
+ msg <- "1 group has only 1 member so it cannot be represented in both training and validation sets."
+ }else{
+ msg <- paste(counter, "groups have only 1 member: these groups cannot be represented in both training and validation sets.")
+ }
+ warning(msg)
+
+ ## exclude groups of length 1
+ popmin <- min(group.n[-which(group.n==1)])
+ } # end if popmin ==1
+
+ ## get training.set2
+ ## (ie. the max proportion we can use as training.set | smallest group)
+ ## to be used as argument to .get.prop.pred
+ training.set2 <- (popmin - 1)/popmin
+ ## update training.set if needs reduction to accommodate small groups
+ if(training.set2 < training.set) training.set <- training.set2
+
+ ## get N.training | training.set
+ N.training <- round(N*training.set)
+
+
+
+ ## GET FULL PCA ##
+ if(missing(n.pca.max)) n.pca.max <- min(dim(x))
+ pcaX <- dudi.pca(x, nf=n.pca.max, scannf=FALSE, center=center, scale=scale)
+ n.pca.max <- min(n.pca.max, pcaX$rank, N.training-1) # re-defines n.pca.max (so user's input may not be the value used...)
+
+ ## DETERMINE N.PCA IF NEEDED ##
+ if(n.pca.max < 10){
+ runs <- n.pca.max
+ }else{
+ runs <- 10}
+
+ if(is.null(n.pca)){
+ n.pca <- round(pretty(1:n.pca.max, runs))
+ }
+
+ n.pca <- n.pca[n.pca>0 & n.pca<(N.training-1) & n.pca<n.pca.max]
+
+
+ ## GET %SUCCESSFUL OF ACCURATE PREDICTION FOR ALL VALUES ##
+ res.all <- unlist(lapply(n.pca, .get.prop.pred, x, n.da, groups, grp,
+ training.set, pcaX, result,
+ n.rep, ...))
+ xval <- data.frame(n.pca=rep(n.pca, each=n.rep), success=res.all)
+
+
+ n.pcaF <- as.factor(xval$n.pca)
+ successV <- as.vector(xval$success)
+ pca.success <- tapply(successV, n.pcaF, mean)
+ n.opt <- which.max(tapply(successV, n.pcaF, mean))
+
+
+ ###### MSE-BASED OPTIMAL n.pca SELECTION:
+ temp <- seq(from=1, to=length(xval$n.pca), by=n.rep)
+ orary <-c(temp+(n.rep-1))
+ index <-c(1:length(temp))
+ lins <-sapply(index, function(e) seq(from=temp[e], to=orary[e]))
+ lin <-c(1:ncol(lins))
+ col <-successV
+ cait<-sapply(lin, function(e) ((col[lins[,e]])-1)^2)
+ FTW <-sapply(lin, function(e) sum(cait[,e])/n.rep)
+ RMSE <- sqrt(FTW)
+ names(RMSE) <- xval$n.pca[temp]
+ ## if more than one n.pc give highest success, choose the largest one
+ best.n.pca <- names(which(RMSE == min(RMSE)))
+ if(length(best.n.pca) > 1) best.n.pca <- best.n.pca[length(best.n.pca)]
+
+ # DAPC
+ n.pca <- as.integer(best.n.pca)
+ n.da <- nlevels(grp)-1
+ dapc1 <- suppressWarnings(dapc(x, grp, n.pca=n.pca, n.da=n.da))
+
+ # PLOT CROSS-VALIDATION RESULTS
+ snps <- x
+ phen <- grp
+ random <- replicate(300, mean(tapply(sample(phen)==phen, phen, mean)))
+ q.phen <- quantile(random, c(0.025,0.5,0.975))
+
+ if(xval.plot==TRUE){
+ smoothScatter(xval$n.pca, successV, nrpoints=Inf, pch=20, col=transp("black"),
+ ylim=c(0,1), xlab="Number of PCA axes retained",
+ ylab="Proportion of successful outcome prediction",
+ main="DAPC Cross-Validation")
+ abline(h=q.phen, lty=c(2,1,2))
+ }
+
+
+ # RESULTS
+ xvalResults <- list(xval, q.phen, pca.success, (names(n.opt)), RMSE, best.n.pca, dapc1)
+ names(xvalResults)[[1]] <- "Cross-Validation Results"
+ names(xvalResults)[[2]] <- "Median and Confidence Interval for Random Chance"
+ names(xvalResults)[[3]] <- "Mean Successful Assignment by Number of PCs of PCA"
+ names(xvalResults)[[4]] <- "Number of PCs Achieving Highest Mean Success"
+ names(xvalResults)[[5]] <- "Root Mean Squared Error by Number of PCs of PCA"
+ names(xvalResults)[[6]] <- "Number of PCs Achieving Lowest MSE"
+ names(xvalResults)[[7]] <- "DAPC"
+
+
+ return(xvalResults)
+
+} # end xvalDapc.data.frame
+
+
+xvalDapc.data.frame <- xvalDapc
+xvalDapc.matrix <- xvalDapc.data.frame
+
diff --git a/R/zzz.R b/R/zzz.R
new file mode 100644
index 0000000..7f07db2
--- /dev/null
+++ b/R/zzz.R
@@ -0,0 +1,10 @@
+.onAttach <- function(libname, pkgname){
+ pkg.version <- packageDescription("adegenet", fields = "Version")
+
+ startup.txt <- paste("\n /// adegenet ", pkg.version, " is loaded ////////////",
+ "\n\n > overview: '?adegenet'",
+ "\n > tutorials/doc/questions: 'adegenetWeb()' ",
+ "\n > bug reports/feature requests: adegenetIssues()\n\n", sep="")
+
+ packageStartupMessage(startup.txt)
+}
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..c30fce0
--- /dev/null
+++ b/README.md
@@ -0,0 +1,18 @@
+[](https://travis-ci.org/thibautjombart/adegenet)
+
+adegenet
+========
+*adegenet*: a R Package for the Multivariate Analysis of Genetic Markers
+
+This wiki is dedicated to the development of *adegenet*.
+It is relevant for developers of the package, developers of other packages depending on *adegenet*, and for users who want to be using the latest features as well.
+
+The *adegenet website* is available at http://adegenet.r-forge.r-project.org/.
+
+The following sections are available:
+- [Installing adegenet devel](https://github.com/thibautjombart/adegenet/wiki/Installing-adegenet-devel)
+- [Tutorials](https://github.com/thibautjombart/adegenet/wiki/Tutorials)
+- [Ask a question](https://github.com/thibautjombart/adegenet/wiki/Questions)
+- [Features request / bug report](https://github.com/thibautjombart/adegenet/issues)
+- [Branches](https://github.com/thibautjombart/adegenet/wiki/Branches)
+- [Contributors](https://github.com/thibautjombart/adegenet/wiki/Contributors)
diff --git a/data/H3N2.rda b/data/H3N2.rda
new file mode 100644
index 0000000..a41f656
Binary files /dev/null and b/data/H3N2.rda differ
diff --git a/data/dapcIllus.rda b/data/dapcIllus.rda
new file mode 100644
index 0000000..f11e84a
Binary files /dev/null and b/data/dapcIllus.rda differ
diff --git a/data/datalist b/data/datalist
new file mode 100644
index 0000000..fcf4fb0
--- /dev/null
+++ b/data/datalist
@@ -0,0 +1,8 @@
+H3N2
+dapcIllus
+eHGDP
+microbov
+nancycats
+rupica
+sim2pop
+spcaIllus
diff --git a/data/eHGDP.rda b/data/eHGDP.rda
new file mode 100644
index 0000000..239e172
Binary files /dev/null and b/data/eHGDP.rda differ
diff --git a/data/microbov.rda b/data/microbov.rda
new file mode 100644
index 0000000..d890314
Binary files /dev/null and b/data/microbov.rda differ
diff --git a/data/nancycats.rda b/data/nancycats.rda
new file mode 100644
index 0000000..330e044
Binary files /dev/null and b/data/nancycats.rda differ
diff --git a/data/rupica.rda b/data/rupica.rda
new file mode 100644
index 0000000..a93c6c9
Binary files /dev/null and b/data/rupica.rda differ
diff --git a/data/sim2pop.rda b/data/sim2pop.rda
new file mode 100644
index 0000000..cf6afa2
Binary files /dev/null and b/data/sim2pop.rda differ
diff --git a/data/spcaIllus.rda b/data/spcaIllus.rda
new file mode 100644
index 0000000..8b10b1d
Binary files /dev/null and b/data/spcaIllus.rda differ
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 0cda4e2..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,66 +0,0 @@
-Explanation for binary files inside source package according to
- http://lists.debian.org/debian-devel/2013/09/msg00332.html
-
-Files: data/H3N2.rda
-Documentation: man/H3N2.Rd
- Seasonal influenza (H3N2) HA segment data
- These data were gathered from DNA sequences available from
- Genbank (http://www.ncbi.nlm.nih.gov/Genbank/)
-
-Files: data/dapcIllus.rda
-Documentation: man/dapcIllus.Rd
- Simulated data illustrating the DAPC
- Jombart, T., Devillard, S. and Balloux, F.: "Discriminant analysis of
- principal components: a new method for the analysis of genetically
- structured populations.", BMC genetics
-
-Files: data/eHGDP.rda
-Documentation: man/eHGDP.Rd
- Extended HGDP-CEPH dataset
- Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, et al.
- "Genetic Variation and Population Structure in Native Americans"
- PLoS Genetics, 2007 3: e185.
- .
- This copy of the dataset was prepared by Francois Balloux.
-
-Files: data/microbov.rda
-Documentation: man/microbov.Rd
- Microsatellites genotypes of 15 cattle breeds
- Data prepared by Katayoun Moazami-Goudarzi and Denis Laloë (INRA,
- Jouy-en-Josas, France)
-
-Files: data/nancycats.rda
-Documentation: man/nancycats.Rd
- Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
- Dominique Pontier (UMR CNRS 5558, University Lyon1, France)
-
-Files: data/rupica.rda
-Documentation: man/rupica.Rd
- Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the
- Bauges mountains (France)
- Daniel Maillard, 'Office National de la Chasse et de la Faune
- Sauvage' (ONCFS), France.
-
-Files: data/sim2pop.rda
-Documentation: man/sim2pop.Rd
- Simulated genotypes of two georeferenced populations
- Easypop version 2.0.1 was run with the following parameters:
- - two diploid populations, one sex, random mating
- - 1000 individuals per population
- - proportion of migration: 0.002
- - 20 loci
- - mutation rate: 0.0001 (KAM model)
- - maximum of 50 allelic states
- - 1000 generations (last one taken)
-
-Files: data/spcaIllus.rda
-Documentation: man/spcaIllus.Rd
- Simulated data illustrating the sPCA
- Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D.
- Revealing cryptic spatial patterns in genetic variability by a new
- multivariate method.
- Heredity, 101, 92-103
-
- -- Andreas Tille <tille at debian.org> Tue, 28 Jun 2016 14:57:24 +0200
-
-
diff --git a/debian/README.test b/debian/README.test
deleted file mode 100644
index 53fb4d7..0000000
--- a/debian/README.test
+++ /dev/null
@@ -1,8 +0,0 @@
-Notes on how this package can be tested.
-────────────────────────────────────────
-
-This package can be tested by running the provided test:
-
- sh ./run-unit-test
-
-in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index c555899..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-r-cran-adegenet (2.0.1-1) unstable; urgency=low
-
- * Initial release (Closes: #828844)
-
- -- Andreas Tille <tille at debian.org> Tue, 28 Jun 2016 15:27:35 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 4deca78..0000000
--- a/debian/control
+++ /dev/null
@@ -1,52 +0,0 @@
-Source: r-cran-adegenet
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Section: gnu-r
-Priority: optional
-Build-Depends: debhelper (>= 9),
- cdbs,
- r-base-dev,
- r-cran-ade4,
- r-cran-mass,
- r-cran-igraph,
- r-cran-ape,
- r-cran-ggplot2,
- r-cran-seqinr,
- r-cran-boot,
- r-cran-reshape2,
- r-cran-vegan,
- r-cran-shiny,
- r-cran-dplyr,
- r-cran-spdep
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-adegenet/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-adegenet/trunk/
-Homepage: https://cran.r-project.org/web/packages/adegenet/
-
-Package: r-cran-adegenet
-Architecture: any
-Depends: ${misc:Depends},
- ${shlibs:Depends},
- ${R:Depends},
- r-cran-ade4,
- r-cran-mass,
- r-cran-igraph,
- r-cran-ape,
- r-cran-ggplot2,
- r-cran-seqinr,
- r-cran-boot,
- r-cran-reshape2,
- r-cran-vegan,
- r-cran-shiny,
- r-cran-dplyr,
- r-cran-spdep
-Description: GNU R exploratory analysis of genetic and genomic data
- Toolset for the exploration of genetic and genomic data. Adegenet
- provides formal (S4) classes for storing and handling various genetic
- data, including genetic markers with varying ploidy and hierarchical
- population structure ('genind' class), alleles counts by populations
- ('genpop'), and genome-wide SNP data ('genlight'). It also implements
- original multivariate methods (DAPC, sPCA), graphics, statistical tests,
- simulation tools, distance and similarity measures, and several spatial
- methods. A range of both empirical and simulated datasets is also
- provided to illustrate various methods.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 03b237f..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,47 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Contact: Thibaut Jombart <thibautjombart at gmail.com>
-Source: https://cran.r-project.org/web/packages/adegenet/
-
-Files: *
-Copyright: 2013-2016 Thibaut Jombart <thibautjombart at gmail.com>,
- Zhian N. Kamvar, Roman Lustrik, Caitlin Collins,
- Marie-Pauline Beugin, Brian Knaus, Peter Solymos,
- Klaus Schliep, Ismail Ahmed, Anne Cori, Federico Calboli
-License: GPL-2+
-
-Files: src/monmonier-utils.c
-Comment: A part of this code (intersection between segments) is based on
- Joseph O'Rourke code to identify intersection between two segments (originaly
- called 'segseg.c').
- .
- The original code was modified in order to handle double coordinates instead
- of integer. A part of the code is new and devoted to some monmonier algorithm
- computations
-Copyright: 2006 Thibaut Jombart <t.jombart at imperial.ac.uk>
- 1997-1998 Joseph O'Rourke <orourke at cs.smith.edu>
-License: keep_copyright
- It may be freely
- redistributed in its entirety provided that this copyright notice is
- not removed.
-
-Files: debian/*
-Copyright: 2016 Andreas Tille <tille at debian.org>
-License: GPL-2+
-
-License: GPL-2+
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- .
- On Debian systems, the complete text of the GNU General Public
- License can be found in `/usr/share/common-licenses/GPL-2'.
diff --git a/debian/docs b/debian/docs
deleted file mode 100644
index 960011c..0000000
--- a/debian/docs
+++ /dev/null
@@ -1,3 +0,0 @@
-tests
-debian/README.test
-debian/tests/run-unit-test
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 087b288..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/make -f
-
-include /usr/share/R/debian/r-cran.mk
-
-install/$(package)::
- chmod -x $(debRlib)/$(cranName)/files/nancycats.*
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
deleted file mode 100644
index b044b0c..0000000
--- a/debian/tests/control
+++ /dev/null
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @, r-cran-testthat
-Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
deleted file mode 100644
index b1aa7d1..0000000
--- a/debian/tests/run-unit-test
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/sh -e
-
-oname=adegenet
-pkg=r-cran-`echo $oname | tr [A-Z] [a-z]`
-
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
-fi
-cd $ADTTMP
-cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
-LC_ALL=C R --no-save < testthat.R
-rm -fr $ADTTMP/*
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index 7b81bb9..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,12 +0,0 @@
-Reference:
- Author: Thibaut Jombart
- Title: "adegenet: a R package for the multivariate analysis of genetic markers"
- Journal: Bioinformatics
- Year: 2008
- Volume: 24
- Number: 11
- Pages: 1403-5
- DOI: 10.1093/bioinformatics/btn129
- PMID: 18397895
- URL: http://bioinformatics.oxfordjournals.org/content/24/11/1403
- eprint: http://bioinformatics.oxfordjournals.org/content/24/11/1403.full.pdf+html
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index e57c72a..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=3
-http://cran.r-project.org/src/contrib/adegenet_([-0-9\.]*).tar.gz
-
diff --git a/inst/CITATION b/inst/CITATION
new file mode 100644
index 0000000..55baadc
--- /dev/null
+++ b/inst/CITATION
@@ -0,0 +1,26 @@
+citHeader("To cite the adegenet package:")
+
+citEntry(
+entry="Article",
+title = "adegenet: a R package for the multivariate analysis of genetic markers",
+journal= "Bioinformatics",
+year = "2008",
+author = "T. Jombart",
+volume = "24",
+pages = "1403-1405",
+doi = "10.1093/bioinformatics/btn129",
+textVersion = "Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405. doi: 10.1093/bioinformatics/btn129"
+)
+
+
+citEntry(
+entry="Article",
+title = "adegenet 1.3-1: new tools for the analysis of genome-wide SNP data",
+journal= "Bioinformatics",
+year = "2011",
+author = "T. Jombart and I. Ahmed",
+volume = "",
+pages = "",
+doi = "10.1093/bioinformatics/btr521",
+textVersion = "Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi: 10.1093/bioinformatics/btr521"
+)
diff --git a/inst/dapcServer/server.R b/inst/dapcServer/server.R
new file mode 100644
index 0000000..0fd6f55
--- /dev/null
+++ b/inst/dapcServer/server.R
@@ -0,0 +1,436 @@
+library(shiny)
+library(adegenet)
+
+
+## DEFINE THE SERVER SIDE OF THE APPLICATION
+shinyServer(function(input, output) {
+
+ ## GET DYNAMIC ANNOTATION
+ graphTitle <- reactive({
+ paste(input$dataset, ": DAPC scatterplot, axes ", input$xax,"-", input$yax, sep="")
+ })
+
+ ## DEFINE CAPTION
+ output$caption <- renderText({
+ graphTitle()
+ })
+
+
+ ## GET DATA ##
+ getData <- reactive({
+ out <- NULL
+
+ if(input$datatype=="expl"){
+ if(input$dataset=="microbov") data("microbov", package="adegenet", envir=environment())
+ if(input$dataset=="sim2pop") data("sim2pop", package="adegenet", envir=environment())
+ if(input$dataset=="nancycats") data("nancycats", package="adegenet", envir=environment())
+ out <- get(input$dataset)
+ }
+
+ if(input$datatype=="file" && !is.null(input$datafile)){
+ ## need to rename input file
+ oldName <- input$datafile$datapath
+ extension <- .readExt(input$datafile$name)
+ newName <- paste(input$datafile$datapath, extension, sep=".")
+ file.rename(oldName, newName)
+
+ ## treat different types of input
+ if(extension %in% c("gtx","gen","dat","GTX","GEN","DAT")){
+ out <- import2genind(newName)
+ }
+
+ if(extension %in% c("RData","Rdata","Rda","rda")){
+ out <- get(load(newName))
+ }
+
+ if(extension %in% c("fasta","fa","fas","aln","FASTA","FA","FAS","ALN")){
+ out <- DNAbin2genind(fasta2DNAbin(newName))
+ }
+ }
+ return(out)
+ })
+
+
+
+
+ ## DYNAMIC UI COMPONENTS ##
+ ## SELECTION OF PCA AXES
+ output$npca <- renderUI({
+ if(!is.null(x <- getData())) {
+ nmax <- min(dim(x at tab))
+ def <- min(10, nmax)
+
+ if(input$useoptimnpca){
+ xval1 <- xvaldapc()
+ npca <- as.integer(xval1[[6]])
+ def <- npca}
+
+ } else {
+ nmax <- 1000
+ def <- 1
+ }
+ sliderInput("npca", "Number of PCA axes retained:", min=1, max=nmax, value=def,step=1)
+ })
+
+ ## SELECTION OF DA AXES
+ output$nda <- renderUI({
+ if(!is.null(x <- getData())) {
+ nmax <- max(length(levels(pop(x)))-1,2)
+ def <- length(levels(pop(x)))-1
+ } else {
+ nmax <- 100
+ def <- 1
+ }
+ sliderInput("nda", "Number of DA axes retained:", min=1, max=nmax, value=def,step=1)
+ })
+
+ ## SELECTION OF PLOTTED AXES
+ output$xax <- renderUI({
+ if(!is.null(x <- getData())) {
+ nmax <- min(dim(x at tab))
+ } else {
+ nmax <- 1000
+ }
+ numericInput("xax", "Indicate the x axis", value=1, min=1, max=nmax)
+ })
+
+ output$yax <- renderUI({
+ def <- 1
+ nda <- 1
+ if(!is.null(input$nda)) nda <- input$nda
+ if(!is.null(x <- getData())) {
+ nmax <- min(dim(x at tab))
+ if(nda>1 && length(levels(pop(x)))>1) def <- 2
+ } else {
+ nmax <- 1000
+ }
+
+ numericInput("yax", "Indicate the y axis", value=def, min=1, max=nmax)
+ })
+
+ ## CROSS-VALIDATION
+ ## DYNAMIC TICKBOX (TICKED IF OPTIMNPCA CHOSEN)
+ output$doxval <- renderUI({
+ checkboxInput("doxval", "Perform cross validation (computer intensive)?", input$doxval)
+ })
+
+ ## DYNAMIC SLIDER FOR MAX NPCA SELECTION
+ output$npcaMax <- renderUI({
+ if(!is.null(x <- getData())) {
+ nmax <- min(dim(x at tab))
+ def <- nmax
+ } else {
+ nmax <- 1000
+ def <- 1
+ }
+ sliderInput("npcaMax", "Maximum number of PCs:", min=1, max=nmax, value=def,step=1)
+ })
+
+
+ ## CROSS-VALIDATION FUNCTION
+ xvaldapc <- reactive({
+ doxval <- FALSE
+ if(!is.null(input$doxval)) doxval <- input$doxval
+ if(input$useoptimnpca || doxval){
+ x <- getData()
+ mat <- tab(x, NA.method="mean")
+ grp <- pop(x)
+ result <- input$result
+ n.rep <- input$nrep
+ nda <- 1
+ if(!is.null(input$nda)) nda <- input$nda
+ training.set <- input$trainingset
+ npcaMax <- 1
+ if(!is.null(input$npcaMax)) npcaMax <- input$npcaMax
+ out <- xvalDapc(mat, grp, n.pca.max=npcaMax,
+ result=result, n.rep=n.rep, n.da=nda, training.set=training.set,
+ xval.plot=FALSE)
+ }
+ else{
+ out <- NULL
+ }
+ return(out)
+ })
+
+
+ ## XVALPLOT
+ output$xvalPlot <- renderPlot({
+ xval1 <- xvaldapc()
+ if(!is.null(xval1)){
+ x <- getData()
+ mat <- tab(x, NA.method="mean")
+ grp <- pop(x)
+ xval2 <- xval1[[1]]
+ successV <-as.vector(xval2$success)
+ random <- replicate(300, mean(tapply(sample(grp)==grp, grp, mean)))
+ q.GRP <- quantile(random, c(0.025,0.5,0.975))
+ smoothScatter(xval2$n.pca, successV, nrpoints=Inf, pch=20, col=transp("black"),
+ ylim=c(0,1), xlab="Number of PCA axes retained",
+ ylab="Proportion of successful outcome prediction",
+ main="DAPC Cross-Validation")
+ print(abline(h=q.GRP, lty=c(2,1,2)))
+ }
+ })
+
+ ## XVAL OUTPUT
+ output$xvalResults1 <-renderPrint({
+ xval1 <- xvaldapc()
+ if(!is.null(xval1)){
+ print(xval1[[1]])
+ }
+
+ })
+ output$xvalResults2 <-renderPrint({
+ xval1 <- xvaldapc()
+ if(!is.null(xval1)){
+ print(xval1[[2]])
+ }
+
+ })
+ output$xvalResults3 <-renderPrint({
+ xval1 <- xvaldapc()
+ if(!is.null(xval1)){
+ print(xval1[[3]])
+ }
+ })
+ output$xvalResults4 <-renderPrint({
+ xval1 <- xvaldapc()
+ if(!is.null(xval1)){
+ print(xval1[[4]])
+ }
+
+ })
+ output$xvalResults5 <-renderPrint({
+ xval1 <- xvaldapc()
+ if(!is.null(xval1)){
+ print(xval1[[5]])
+ }
+
+ })
+ output$xvalResults6 <-renderPrint({
+ xval1 <- xvaldapc()
+ if(!is.null(xval1)){
+ print(xval1[[6]])
+ }
+
+ })
+
+
+ ## PERFORM THE DAPC ##
+ getDapc <- reactive({
+ out <- NULL
+ x <- getData()
+ npca <- nda <- 1
+
+ ## n.pca determined by xval or slider?
+ if(input$useoptimnpca){
+ xval1 <- xvaldapc()
+ npca <- as.integer(xval1[[6]])
+ } else {
+ if(!is.null(input$npca)) npca <- input$npca
+ }
+ if(!is.null(input$nda)) nda <- input$nda
+
+ if(!is.null(x)) out <- dapc(x, n.pca=npca, n.da=nda, parallel=FALSE)
+ return(out)
+ })
+
+
+ ## GET PLOT PARAM ##
+ getPlotParam <- reactive({
+ col.pal <- get(input$col.pal)
+ return(list(col.pal=col.pal))
+ })
+
+
+ ## MAKE OUTPUT PLOT ##
+ output$scatterplot <- renderPlot({
+ dapc1 <- getDapc()
+ if(!is.null(dapc1)){
+
+ ## get colors
+ K <- length(levels(dapc1$grp))
+ myCol <- get(input$col.pal)(K)
+
+ ## get screeplot info
+ scree.pca <- ifelse(input$screepca=="none", FALSE, TRUE)
+ scree.da <- ifelse(input$screeda=="none", FALSE, TRUE)
+ cellipse <- ifelse(input$ellipses, 1.5, 0)
+ cstar <- ifelse(input$stars, 1, 0)
+ scatter(dapc1, xax=input$xax, yax=input$yax, col=myCol,
+ scree.pca=scree.pca, scree.da=scree.da,
+ posi.pca=input$screepca, posi.da=input$screeda,
+ cellipse=cellipse, cstar=cstar, mstree=input$mstree,
+ cex=input$pointsize, clabel=input$labelsize, solid=1-input$alpha)
+ } else {
+ NULL
+ }
+ })
+
+
+ ## MAKE SUMMARY PLOT ##
+ output$summary <- renderPrint({
+ dapc1 <- getDapc()
+ if(!is.null(dapc1)){
+ summary(dapc1)
+ }
+ })
+
+ ## MAKE COMPOPLOT ##
+ output$compoplot <- renderPlot({
+ dapc1 <- getDapc()
+ if(!is.null(dapc1)){
+ ## get colors
+ K <- length(levels(dapc1$grp))
+ myCol <- get(input$col.pal)(K)
+ ##myCol <- transp(myCol, 1-input$alpha)
+ compoplot(dapc1, col=myCol, lab=input$compo.lab, legend=input$compo.legend)
+
+ }
+ })
+
+
+ ## DYNAMIC SELECTION OF DISCRIMINANT AXIS FOR LOADING PLOT
+ output$LPax <- renderUI({
+ def <- 1
+ nda <- 1
+ nmax <- 2
+ if(!is.null(x <- getData())) {
+ if(!is.null(input$nda)) nda <- input$nda
+ nmax <- nda
+ if(!is.null(input$LPax)) def <- input$LPax
+ }
+
+ numericInput("LPax", "Select discriminant axis", value=def, min=1, max=nmax)
+ })
+
+
+
+ # REACTIVE THRESHOLD/SNP SELECTION FUNCTION if using snpzip-like method
+ selector <- reactive({
+
+ dimension <- 1
+
+ dapc1 <- getDapc()
+ if(!is.null(dapc1)){
+ if(!is.null(input$thresholdMethod)) method <- input$thresholdMethod
+ if(!is.null(input$LPaxis)) dimension <- input$LPaxis
+ x <- getData()
+ mat <- tab(x, NA.method="mean")
+ }
+
+ if(method=="quartile"){
+ x <- dapc1$var.contr[,dimension]
+ thresh <- quantile(x,0.75)
+ maximus <- which(x > thresh)
+ n.snp.selected <- length(maximus)
+ sel.snps <- mat[,maximus]
+ }
+ else{
+ z <- dapc1$var.contr[,dimension]
+ xTotal <- dapc1$var.contr[,dimension]
+ toto <- which(xTotal%in%tail(sort(xTotal), 2000))
+ z <- sapply(toto, function(e) xTotal[e])
+
+ D <- dist(z)
+ clust <- hclust(D,method)
+ pop <- factor(cutree(clust,k=2,h=NULL))
+ m <- which.max(tapply(z,pop,mean))
+ maximus <- which(pop==m)
+ maximus <- as.vector(unlist(sapply(maximus, function(e) toto[e])))
+ popvect <- as.vector(unclass(pop))
+ n.snp.selected <- sum(popvect==m)
+ sel.snps <- mat[,maximus]
+ }
+
+ selection <- c((ncol(mat)-ncol(mat[,-maximus])), ncol(mat[,-maximus]))
+ resultat <- list(selection, maximus, dimnames(sel.snps)[[2]], dapc1$var.contr[maximus, dimension])
+ return(resultat)
+ })
+
+
+
+ ## MAKE LOADINGPLOT ##
+ output$loadingplot <- renderPlot({
+ dapc1 <- getDapc()
+ LPaxis <- 1
+ if(!is.null(dapc1)){
+ ## get loadings for LP axis
+ LPaxis <- 1
+ if(!is.null(input$LPax)) LPaxis <- input$LPax
+ if(input$threshold){
+ # if threshold is by quantile
+ if(input$thresholdMethod=="quartile"){
+ x <- dapc1$var.contr[,LPaxis]
+ def <- quantile(x,0.75)
+ }else{
+ # if threshold is by clustering
+ select <- selector()
+ thresh <- select[[2]]
+ def <- abs(dapc1$var.contr[thresh][(which.min(dapc1$var.contr[thresh]))])-0.000001}
+ }
+ else{
+ def <- NULL}
+ loadingplot(dapc1$var.contr[,LPaxis], threshold=def)
+ }
+ })
+
+
+ ## FEATURE SELECTION OUTPUT
+ output$FS1 <-renderPrint({
+ if(input$FS){
+ fs1 <- selector()
+ if(!is.null(fs1)){
+ print(fs1[[1]])
+ }
+ }
+ })
+
+ output$FS2 <-renderPrint({
+ if(input$FS){
+ fs1 <- selector()
+ if(!is.null(fs1)){
+ print(fs1[[2]])
+ }
+ }
+ })
+
+ output$FS3 <-renderPrint({
+ if(input$FS){
+ fs1 <- selector()
+ if(!is.null(fs1)){
+ print(fs1[[3]])
+ }
+ }
+ })
+
+ output$FS4 <-renderPrint({
+ if(input$FS){
+ fs1 <- selector()
+ if(!is.null(fs1)){
+ print(fs1[[4]])
+ }
+ }
+ })
+
+ ## RENDER SYSTEM INFO ##
+ output$systeminfo <- renderPrint({
+ cat("\n== R version ==\n")
+ print(R.version)
+
+ cat("\n== Date ==\n")
+ print(date())
+
+ cat("\n== adegenet version ==\n")
+ print(packageDescription("adegenet", fields=c("Package", "Version", "Date", "Built")))
+
+ cat("\n== shiny version ==\n")
+ print(packageDescription("adegenet", fields=c("Package", "Version", "Date", "Built")))
+
+ cat("\n== attached packages ==\n")
+ print(search())
+ }) # end renderPrint
+
+# .render.server.info()
+
+}) # end shinyServer
diff --git a/inst/dapcServer/ui.R b/inst/dapcServer/ui.R
new file mode 100644
index 0000000..5742795
--- /dev/null
+++ b/inst/dapcServer/ui.R
@@ -0,0 +1,501 @@
+library(shiny)
+##library(adegenet)
+
+## DEFINE UI ##
+shinyUI(
+ pageWithSidebar(
+ ## TITLE
+ headerPanel("DAPC web server"),
+
+ ## SIDE PANEL CONTENT
+ sidebarPanel(
+ ## define the type of input
+ conditionalPanel(
+ ## condition
+ condition = "$('li.active a').first().html()!='Help'",
+ radioButtons("datatype", "What data source to use?",
+ list("Example from adegenet"="expl","Input file"="file"))),
+
+ ## choice of dataset if source is an example
+ conditionalPanel(condition = "input.datatype=='expl'&& $('li.active a').first().html()!= 'Help'",
+ selectInput("dataset", "Select an example dataset:",
+ choices=c("microbov","sim2pop","nancycats"))
+ ),
+
+ ## choice of dataset if source is a file
+ conditionalPanel(condition = "input.datatype=='file'&& $('li.active a').first().html()!= 'Help'",
+ fileInput('datafile', 'Choose input file',
+ accept=c('gtx/gen/dat/GTX/GEN/DAT/RData/Rdata/Rda/rda', 'GENETIX/genepop/Fstat/R data')),
+ tags$hr()
+ ),
+
+
+
+ ## CROSS-VALIDATION
+ # n.pca.max slider
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Cross-Validation'",
+ h3("Cross-validation"),
+ uiOutput("doxval"),
+ uiOutput("npcaMax")
+ ),
+
+
+ ## Select Output variable:
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()!='Cross-Validation'&& $('li.active a').first().html()!= 'Help'",
+ checkboxInput("useoptimnpca", "Use suggested number of PCA components?", FALSE)
+ ),
+
+
+ ##sliderInput("npca", "Number of PCA axes retained:", min=1, max=1000, value=10),
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()!='Cross-Validation'&& $('li.active a').first().html()!= 'Help'",
+ uiOutput("npca")
+ ),
+
+ ## select number of DA axes
+ ##sliderInput("nda", "Number of discriminant functions retained:", min=1, max=100, value=1),
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()!= 'Help'",
+ uiOutput("nda")),
+
+ ## nrep slider
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Cross-Validation'",
+ sliderInput("nrep",
+ "Number of replicates:",
+ min = 1,
+ max = 100,
+ value = 3)
+ ),
+
+ ## trainingset slider
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Cross-Validation'",
+ sliderInput("trainingset",
+ "Training set size:",
+ min = 0.1,
+ max = 0.95,
+ value = 0.9,
+ step = 0.01)
+ ),
+
+
+ ## result type
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Cross-Validation'",
+ radioButtons("result", "Assess by:",
+ list("Group" = "groupMean",
+ "Overall" = "overall"))
+ ),
+
+
+
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Scatterplot'",
+ h3("Graphical parameters")
+ ),
+
+
+
+ ## inputs specific of scatterplot tab
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Scatterplot'",
+
+ ## select first axis to plot
+ ##numericInput("xax", "Indicate the x axis", value=1, min=1),
+ uiOutput("xax"),
+
+ ## select second axis to plot
+ ##numericInput("yax", "Indicate the y axis", value=1, min=1),
+ uiOutput("yax")
+ ),
+
+
+
+ conditionalPanel(
+ ## condition
+ condition = "$('li.active a').first().html()=='Scatterplot'",
+ h3("Aesthetics")
+ ),
+
+ conditionalPanel(
+ ## condition
+ condition = "$('li.active a').first().html()=='Compoplot'",
+ h3("Aesthetics")
+ ),
+
+
+
+ ## select color palette
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Scatterplot'",
+ selectInput("col.pal", "Indicate a color palette to be used",
+ choices=c("funky","spectral","seasun","azur","wasp"))
+ ),
+
+ ## select color palette
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Compoplot'",
+ selectInput("col.pal", "Indicate a color palette to be used",
+ choices=c("funky","spectral","seasun","azur","wasp"))
+ ),
+
+
+
+ ## select transparency
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Scatterplot'",
+ sliderInput("alpha", "Choose transparency", min=0, max=1, step=0.05, value=0.5)
+ ),
+
+
+
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()==='Scatterplot'",
+ ## symbol size
+ sliderInput("pointsize", "Size of the points", value=1, min=0, max=10, step=0.2),
+
+ ## label size
+ sliderInput("labelsize", "Size of the labels", value=1, min=0, max=10, step=0.2),
+
+ ## add screeplot of PCA?
+ selectInput("screepca", "Position of the PCA screeplot:",
+ choices=c("None" = "none",
+ "Bottom right" = "bottomright",
+ "Bottom left" = "bottomleft",
+ "Top right" = "topright",
+ "Top left" = "topleft")),
+
+ ## add screeplot of DA?
+ selectInput("screeda", "Position of the DA screeplot:",
+ choices=c("None" = "none",
+ "Bottom right" = "bottomright",
+ "Bottom left" = "bottomleft",
+ "Top right" = "topright",
+ "Top left" = "topleft")),
+
+ ## plot ellipses?
+ checkboxInput("ellipses", "Show inertia ellipses?", value=TRUE),
+
+ ## plot stars?
+ checkboxInput("stars", "Link points to their centre?", value=TRUE),
+
+ ## plot minimum spanning tree?
+ checkboxInput("mstree", "Show minimum spanning tree?", value=FALSE)
+
+ ),
+
+ ## input specific of compoplot tab
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()==='Compoplot'",
+
+ ## add legend?
+ checkboxInput("compo.legend", "Add a legend?", TRUE),
+
+ ## add labels?
+ checkboxInput("compo.lab", "Display labels?", FALSE)
+ ),
+
+ ## inputs specific of loadingplot tab
+ conditionalPanel(
+ ## condition
+ "$('li.active a').first().html()=='Loading Plot'",
+
+ h3("Graphical parameters"),
+
+ ## select axis to plot
+ uiOutput("LPax"),
+
+ checkboxInput("threshold", "Display threshold?", TRUE),
+
+ selectInput("thresholdMethod", "Method for selecting threshold:",
+ choices=c("Third quartile" = "quartile",
+ "Complete linkage clustering" = "complete",
+ "Single linkage clustering" = "single",
+ "Average linkage clustering" = "average",
+ "Centroid clustering" = "centroid",
+ "McQuitty's similarity analysis" = "mcquitty",
+ "Median clustering" = "median",
+ "Ward's minimum variance method" = "ward")),
+
+ checkboxInput("FS", "Select and describe features above threshold", FALSE))
+
+
+ ), # end sidebarPanel
+
+ ## MAIN PANEL
+ mainPanel(
+ tabsetPanel(
+
+ tabPanel("Scatterplot",plotOutput("scatterplot")),
+
+ tabPanel("Summary", verbatimTextOutput("summary")),
+
+ tabPanel("Compoplot", plotOutput("compoplot")),
+
+ tabPanel("Loading Plot", plotOutput("loadingplot"),
+ conditionalPanel(condition = "input.FS==1",
+ h3("Number of selected vs. unselected alleles"),
+ verbatimTextOutput("FS1"),
+ h3("List of selected alleles"),
+ verbatimTextOutput("FS2"),
+ h3("Names of selected alleles"),
+ verbatimTextOutput("FS3"),
+ h3("Contributions of selected alleles to discriminant axis"),
+ verbatimTextOutput("FS4"))),
+
+ tabPanel("Cross-Validation", plotOutput("xvalPlot"),
+ h3("Mean success by number of PCs"),
+ verbatimTextOutput("xvalResults3"),
+ h3("Number of PCs with highest mean"),
+ verbatimTextOutput("xvalResults4"),
+ h3("RMSE by number of PCs"),
+ verbatimTextOutput("xvalResults5"),
+ h3("Number of PCs with lowest RMSE"),
+ verbatimTextOutput("xvalResults6"),
+ h3("Cross-validation results"),
+ verbatimTextOutput("xvalResults1"),
+ h3("Median and CI for random chance"),
+ verbatimTextOutput("xvalResults2")),
+
+
+
+
+
+######################
+#### HELP SECTION ####
+######################
+
+ tabPanel("Help",
+
+ ## OVERVIEW ##
+
+ h3("Overview"),
+ p("Welcome to the DAPC Server Help Section. Under each section heading below you can find a brief description and useful information
+ about the content of each tab on the Server. If you want to know more about a specific item or are seeking the definition of a term,
+ you may be more interested in the Glossary on the adjacent tab."),
+
+ p("The DAPC Server aims to provide a user-friendly interactive application of some of the functions contained in the R package adegenet.
+ More information about adegenet can be found on the adegenet website:"),
+
+ a("http://adegenet.r-forge.r-project.org/", href="http://adegenet.r-forge.r-project.org/", target="_blank"),
+
+ p(br(),"On the DAPC Server, users can explore the Discriminant Analysis of Principal Components (DAPC) method.
+ DAPC is a multivariate method that uses genetic data to describe the differences between pre-defined biological populations.
+ DAPC is a dimension reduction approach that generates synthetic variables composed of weighted combinations of the original variables
+ in a dataset to optimally capture between-group variation. DAPC uses Principal Components Analysis (PCA) as a prior step
+ to Discriminant Analysis (DA) to identify up to (K - 1) linearly uncorrelated discriminant axes that can optimally discriminate between
+ K groups of individuals. Unlike DA alone, DAPC is able to perform this procedure when the number of variables (alleles) greatly
+ exceeds the number of individuals, and also in the presence of correlations between variables."),
+
+ p("DAPC is a supervised method, which means that the clusters of individuals to be analysed must be pre-defined by the user.
+ In cases where individuals are not classified into groups, procedures (like that of the find.clusters function in R) can be
+ used to identify clusters so that a DAPC analysis can be carried out. These procedures are not included in the present version of the
+ DAPC Server, however, which requires all data to be imported with inherently defined populations."),
+
+ p("For any dataset containing a set of genetic variables for any number of individuals and a population grouping factor,
+ DAPC can be used to explore between-population differentiation,
+ estimate the probabilities of individual assignment to all possible groups,
+ and to examine the contribution of individual alleles to population structuring."),
+
+ p("Acceptable file types for input datasets include 'gtx/gen/dat/GTX/GEN/DAT/RData/Rdata/Rda/rda' and 'GENETIX/genepop/Fstat/R data'."),
+
+
+ ## EMAIL ##
+ h3(br(),"Ask your questions on the adegenet forum"),
+ p("Use the adegenet forum to ask all non-confidential questions: ", a("send an email", href="mailto:adegenet-forum at lists.r-forge.r-project.org", target="_top")),
+ p("Make sure to describe your problem clearly and to provide, whenever possible, a reproducible example for any reported error. Please also give your session info (copy and paste the content of the serverInfo tab at the end of your email)"),
+
+ p("Note that this mailing list is moderated, and if not subscribed your post may be differed by a day or two. To subscribe to the mailing list, go to", a("this page", href="http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum", target="_blank")),
+
+
+ ## CITATION ##
+
+ h3(br(),"Citing the DAPC Server"),
+ h5("Citation for adegenet:"),
+ p("Jombart T.(2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405. doi:10.1093/bioinformatics/btn129", a("[link to paper]", href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btn129?ijkey=6sqx5BTXCdYtBZz&keytype=ref", target="_blank")),
+ p("Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi: 10.1093/bioinformatics/btr521"),
+
+ h5("Citation for the DAPC:"),
+ p("Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11:94. doi:10.1186/1471-2156-11-94", a("[link to paper]", href="http://www.biomedcentral.com/1471-2156/11/94", target="_blank")),
+
+
+ ## SCATTER PLOT ##
+
+ h3(br(),"Scatter Plot"),
+ p("The Scatter Plot page provides a visual assessment of between-population differentiation.
+ Generated by applying the R function scatterplot to a dapc object, the output generated will appear in one of two forms.
+ If only one DA is retained (always the case if there are only 2 groups),
+ or both the x-axis and y-axis of the scatterplot are set to the same value, the output will display the
+ densities of individuals on the given discriminant function.
+ If more than one DA is retained and selected, the output will display individuals as dots and
+ groups as inertia ellipses, and will represent the relative position of each along the two
+ selected axes."),
+
+ p("The number of axes retained in both the PCA and DA steps of DAPC will have an impact on the
+ analysis and affect the scatter plot. By default, the number of DA axes retained is set at
+ the maximum of (K - 1) axes, where K is the number of groups. The default value of the number of
+ PCA axes is more arbitrarily defined, however, the 'Use suggested number of PCA components?'
+ tickbox provides the user with the option to use cross-validation to identify and select an optimal number
+ of PCs, where one exists. For more on this, see the section on cross-validation."),
+
+ p("There are a wide variety of graphical parameters for the DAPC scatterplot that can be customised
+ by the user. Those parameters that lack intuitive definition are described further in the Glossary."),
+
+
+ ## SUMMARY ##
+
+ h3(br(),"Summary"),
+ p("This page provides a summary of the dapc object."),
+ p("$n.dim' indicates the number of retained DAPC axes, which is affected by both the number of PCA
+ axes and DA axes retained."),
+ p("'$n.pop' indicates the number of groups or populations, which is defined by the dataset."),
+ p("'$assign.prop' indicates the proportion of overall correct assignment"),
+ p("'$assign.per.pop' indicates the proportions of successful reassignment (based on the discriminant
+ functions) of individuals to their original clusters. Large values indicate clear-cut clusters, while low
+ values suggest admixed groups."),
+ p("'$prior.grp.size' indicates prior group sizes."),
+ p("'$post.grp.size' indicates posterior group sizes."),
+
+
+
+
+ ## COMPOPLOT ##
+
+ h3(br(),"Compoplot"),
+ p("This page displays a compoplot, which is a bar plot showing the probabilities of assignment of
+ individuals to the different clusters. Individuals are plotted along the x-axis and membership probabilities are
+ plotted along the y-axis.From the compoplot, one can draw inferences about potential
+ admixture, and about the way in which the selection of PCA axes affects the stability of membership probabilities."),
+
+
+ ## LOADING PLOT ##
+
+ h3(br(), "Loading Plot"),
+ p("The Loading Plot page allows the user to examine how the original variables contribute to the
+ discriminant functions created by DAPC. Variables are plotted along the x-axis, and the contribution
+ of those variables to the DAPC is plotted in the y-axis."),
+ p("The side panel on the Loading Plot page provides the option of selecting a threshold above which variables are identified.
+ This can be useful simply for clarifying the image; hence, by default, only variables above the third quartile threshold are labelled.
+ A drop-down menu contains a variety of clustering methods that can also be used to set this threshold.
+ If desired, the user can choose to 'Select and describe features above the threshold'"),
+
+
+ ## CROSS-VALIDATION ##
+
+ h3(br(),"Cross-validation"),
+ p("When the 'Perform cross-validation?' box is ticked, this optimisation procedure will be carried
+ out on the Cross-validation page."),
+ p("Cross-validation is an optimisation procedure that is used in the context of DAPC to identify the number of principal components
+ that gives rise to the model with the highest predictive capacity. In cross-validation for DAPC, the data is divided into a training
+ set and a validation set (by default, comprising 90% and 10% of the data, respectively). The analysis is run on the training set with
+ variable numbers of PCs retained, and the degree to which the analysis is able to accurately predict the group membership of
+ excluded individuals (those in the validation set) is used to select the optimal number of PCs to retain. This procedure is replicated
+ with different random sub-samples a number of times specified by a slider on the side panel. In the interest of computational time,
+ only 3 replicates are performed by default, though more replicates are recommended to achieve greater optimisation.
+ Success is calculated either by group (the default) or measured as overall success."),
+
+ p("A scatterplot of the results is displayed, showing the number of PCs retained on the x-axis and
+ success on the y-axis. Individual replicates appear as dots, and the density of points is displayed
+ in blue."),
+ p("Ideally, the data should fall in an arc, indicating an optimal point at its maximum where
+ the number of PCs retained leads to better predictive success than numbers of PCs either
+ above or below."),
+ p("Below the plot, a variety of summary statistics are provided.
+ Ultimately, it is the number of PCs associated with the lowest RMSE (root mean squared error,
+ see Glossary) which is selected if 'Use suggested number of PCA components?' is ticked.",br(),br(),br())
+
+
+
+ ), # end Help section
+
+
+
+
+ ## GLOSSARY ##
+
+ tabPanel("Glossary",
+ h3("Compoplot"),
+ p("A compoplot is a bar plot showing the probabilities of assignment of individuals to the different clusters."),
+ h3("Cross-validation"),
+ p("Cross-validation is an optimisation procedure that is used in the context of DAPC to identify the number of principal components
+ that gives rise to the model with the highest predictive capacity. In cross-validation for DAPC, the data is divided into a training
+ set and a validation set (by default, comprising 90% and 10% of the data, respectively). The analysis is run on the training set with
+ variable numbers of PCs retained, and the degree to which the analysis is able to accurately predict the group membership of
+ excluded individuals (those in the validation set) is used to select the optimal number of PCs to retain."),
+ p("Note: Performing cross-validation can substantially improve the results of DAPC; however, the amount of computational time
+ required increases with the size of the dataset in question and the number of replicates carried out."),
+ h3("DA"),
+ p("Discriminant Analysis (DA) is a procedure for optimally describing the differences between groups of individuals.
+ DAPC uses DA subsequent to Principal Component Analysis to maximise discrimination between groups in conditions
+ where DA alone would be inappropriate."),
+ h3("DA axis"),
+ p("DAPC uses Discriminant Analysis (DA) to describe the differences between K groups of individuals along
+ a maximum of (K - 1) Discriminant Analysis axes (DA axes)."),
+ h3("DAPC"),
+ p("Discriminant Analysis of Principal Components (DAPC) is a multivariate method that uses genetic data to describe the
+ differences between pre-defined biological populations. DAPC uses Principal Component Analysis as a prior step to
+ Discriminant Analysis to identify weighted linear combinations of the original variables which give rise to optimal
+ between-group discrimination."),
+ p("For more, see: Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the
+ analysis of genetically structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94."),
+ h3("Inertia ellipse"),
+ p("The inertia ellipses displayed optionally on the DAPC scatter plot provide graphical summaries of a cloud of points.
+ They are meant to give shape to groups of individuals, and do not necessarily represent a 95% confidence
+ interval on the position of the centroid of a cluster."),
+ h3("Loading"),
+ p("Loadings provide a measure of the contribution of each original variable to the discrimination between groups along a given
+ discriminant axis. A loading plot is used to visualise these loadings so that one can, for example, assess the weight of each
+ variable and identify those variables whose contributions exceed a threshold of interest."),
+ h3("Minimum spanning tree"),
+ p("A minimum spanning tree is a graph theoretical phenomenon in which all of the vertices (in our case, cluster centroids) of
+ a graph are connected into the tree that contains the shortest set of possible paths between vertices."),
+ h3("PCA"),
+ p("Principal Component Analysis (PCA) is a multivariate statistical method that generates linearly
+ uncorrelated principal components (PCs) composed of weighted linear combinations of the original variables
+ to represent overall variation in the data in a reduced space."),
+ h3("PC, PCA axis"),
+ p("Principal components (PCs, or PCA axes) are sets of linearly uncorrelated synthetic variables composed of
+ weighted linear combinations of original variables. PCs are used to describe multivariate phenomenon in a smaller (or equal)
+ number of dimensions. The 'optimal' number of PCs depends on the data. In DAPC, retaining too few PCs will cause useful
+ information to be excluded from the analysis (and hence discriminative power to be lost), while retaining too many PCs
+ may lead to problems of overfitting and uninterpretability."),
+ h3("RMSE"),
+ p("The root mean squared error (RMSE) is a measure of the error of an estimator. On the DAPC Server, RMSE is used in
+ cross-validation to assess the ability of the model, with variable numbers of principal components retained, to achieve
+ perfect prediction of individuals into the correct group."),
+ p("RMSE = sqrt((1/n)*sum(i=1 to n)(Yhat.i - Yi)^2), where Yhat is a vector of n predictions,
+ and Y is the vector of the true values."),
+ h3("Screeplot"),
+ p("A graphical representation of the variance, or cumulative variance, contained in the set of principal components
+ or discriminant functions. Components shaded in black represent those that have been retained in the analysis."),
+ h3("Training set"),
+ p("The training set, in cross-validation, is the set of individuals retained in the analysis.
+ The complement of the training set is the 'validation set', which contains the remaining individuals excluded from the analysis
+ who are used to test the performance of the model which varies as a function of the number of PCs retained.",br(),br(),br())
+ ), # end Glossary
+
+
+ ## SERVER INFO ##
+
+ tabPanel("System info", verbatimTextOutput("systeminfo"))
+ ) # end tabsetPanel
+ ) # end mainPanel
+ ) # end pageWithSidebar
+ ) # end shinyUI
diff --git a/inst/files/AFLP.txt b/inst/files/AFLP.txt
new file mode 100644
index 0000000..1c27fdb
--- /dev/null
+++ b/inst/files/AFLP.txt
@@ -0,0 +1,8 @@
+ loc1 loc2 loc3 loc4
+indA 1 0 1 1
+indB 0 1 1 1
+indC 1 1 0 1
+indD 0 NA 1 NA
+indE 1 1 0 0
+indF 1 0 1 1
+indG 0 1 1 0
diff --git a/inst/files/exampleSnpDat.snp b/inst/files/exampleSnpDat.snp
new file mode 100644
index 0000000..9877fa9
--- /dev/null
+++ b/inst/files/exampleSnpDat.snp
@@ -0,0 +1,55 @@
+>>>> begin comments - do not remove this line <<<<
+Here is a description of the format.
+Any information is stored on two lines, the first for the type of information, the second for the content.
+
+
+=== Lines starting with ">>" ===
+They store generic information about the loci or the individuals.
+They are all optional.
+Character strings following the ">>" can match:
+- "position": the following line contains integers giving the position of the SNPs on the sequence
+- "allele": the following line contains a vector of two alleles separated by "/"
+- "population": population, or more generally a grouping factor for the individuals
+- "ploidy": the ploidy of each individual given as an integer; alternatively, one single integer if
+all individuals have the same ploidy
+- "chromosome": the chromosome where the SNP are located
+
+Elements are separated by a space, and their length must match exactly the number of loci
+(position, allele, chromosome) or individuals (population, ploidy). Therefore, no space is allowed
+for the names of these items (especially chromosomes or populations).
+
+
+=== Lines starting with ">" ===
+They store individual genotypes.
+The character string following the sign ">" is the label of the individual. Spaces before and after
+are ignored.
+The following line contains integers without separators, each representing the number of copies of
+the second allele.
+Missing values are to be coded by a single non-integer character (by default, "-").
+
+For instance, in the following toy dataset:
+- foo ("1020") is "at" at position 1, "gg" at position 8, "cc" at position 11, and "tt" at position
+43.
+- bar ("0012") is "aa", "gg", "ac" and "aa"
+- toto ("10-0") is "at", "gg", not typed (NA) and "tt"
+
+
+>>>> end comments - do not remove this line <<<<
+>> position
+1 8 11 43
+>> allele
+a/t g/c a/c t/a
+>> population
+Brit Brit Fren monster NA
+>> ploidy
+2
+> foo
+1020
+> bar
+0012
+> toto
+10-0
+> Nyarlathotep
+0120
+> an even longer label but OK since on a single line
+1100
diff --git a/inst/files/mondata1.rda b/inst/files/mondata1.rda
new file mode 100644
index 0000000..bd16b6f
Binary files /dev/null and b/inst/files/mondata1.rda differ
diff --git a/inst/files/mondata2.rda b/inst/files/mondata2.rda
new file mode 100644
index 0000000..698c29e
Binary files /dev/null and b/inst/files/mondata2.rda differ
diff --git a/inst/files/nancycats.dat b/inst/files/nancycats.dat
new file mode 100755
index 0000000..4b666ec
--- /dev/null
+++ b/inst/files/nancycats.dat
@@ -0,0 +1,247 @@
+17 9 18 2
+fca8
+fca23
+fca43
+fca45
+fca77
+fca78
+fca90
+fca96
+fca37
+ 1 0000 0409 0404 0103 0909 0306 0909 0808 1010
+ 1 0000 0909 0407 0305 0909 0306 0209 0808 1010
+ 1 0913 0409 0505 0101 0709 0303 0808 0808 1111
+ 1 0809 0505 0405 0105 0606 0306 0909 0104 1010
+ 1 0809 0609 0507 0505 0707 0306 0609 0808 1010
+ 1 0913 0409 0709 0305 0609 0606 0607 0108 1010
+ 1 0909 0409 0407 0105 0707 0306 0909 0408 1010
+ 1 0913 0409 0209 0305 0810 0306 0608 0101 1012
+ 1 1013 0409 0404 0105 0611 0303 0808 0408 1012
+ 1 0909 0303 0507 0305 0609 0606 0808 0104 1010
+ 2 1012 0204 0307 0606 0707 0307 0609 0101 0101
+ 2 0608 0204 0207 0506 0306 0202 0609 0108 0110
+ 2 0608 0202 0207 0607 0709 0303 0609 0101 1010
+ 2 0808 0204 0202 0607 0909 0303 0909 0101 0109
+ 2 0709 0404 0303 0507 0707 0203 0909 0101 1010
+ 2 0609 0409 0202 0607 0303 0303 0609 0101 0104
+ 2 0608 0208 0101 0505 0303 0202 0505 0101 0104
+ 2 0609 0505 0202 0305 0410 0206 0509 0108 0101
+ 2 0909 0408 0207 0505 0409 0207 0205 0101 0101
+ 2 0709 0204 0203 0305 0710 0307 0509 0212 1010
+ 2 0608 0404 0207 0607 0410 0303 0609 0108 0109
+ 2 0709 0404 0207 0606 0410 0206 0609 0808 0110
+ 2 0809 0202 0307 0606 0511 0303 0609 0101 1010
+ 2 0708 0409 0202 0507 0305 0303 0505 0808 0104
+ 2 0709 0404 0207 0606 0303 0202 0609 0808 0105
+ 2 0909 0404 0207 0306 0309 0202 0211 0108 0105
+ 2 0610 0409 0707 0305 0505 0303 0509 0506 1010
+ 2 0707 0204 0207 0206 0309 0202 0909 0108 0110
+ 2 0606 0404 0303 0505 0608 0306 0909 0101 0110
+ 2 0709 0209 0203 0307 0707 0306 0609 0101 1013
+ 2 0607 0204 0101 0708 0208 0202 0609 0101 1010
+ 2 0909 0404 0207 0506 0303 0206 0808 0808 0110
+ 3 1010 0308 0404 0508 0808 0306 0609 0105 1010
+ 3 1010 0308 0305 0505 0208 0307 0808 0105 1010
+ 3 1010 0304 0304 0105 0208 0707 0609 0105 0909
+ 3 1012 0202 0507 0306 0208 0408 0608 0808 1010
+ 3 1212 0909 0303 0305 0206 0306 0707 0505 0210
+ 3 1214 0909 0204 0505 0505 0306 0707 0508 0210
+ 3 0410 0407 0409 0305 0508 0303 0607 0108 1010
+ 3 0410 0606 0404 0303 0508 0303 0708 0808 1010
+ 3 0412 0202 0207 0506 0608 0206 0607 0508 1010
+ 3 0410 0104 0404 0303 0707 0303 0209 0508 1010
+ 3 0911 0404 0204 0306 0207 0303 0608 0509 1010
+ 3 1314 0309 0204 0505 0608 0307 0709 0105 0709
+ 4 1111 0404 0207 0305 0404 0306 0208 0606 1013
+ 4 1011 0304 0707 0305 0405 0303 0208 0608 0609
+ 4 1015 0307 0404 0405 0505 0303 0208 0808 1010
+ 4 0410 0304 0304 0405 0202 0507 0609 0808 1016
+ 4 1010 0102 0304 0505 0202 0303 0909 0105 1010
+ 4 0916 0207 0404 0505 0509 0505 0609 0108 1010
+ 4 0815 0404 0407 0505 0204 0305 0608 0108 1013
+ 4 0409 0707 0407 0505 0205 0303 0606 0101 1010
+ 4 0914 0406 0709 0505 0202 0204 0206 0108 1113
+ 4 1212 0708 0204 0203 0505 0305 0208 0106 1010
+ 4 1212 0909 0207 0208 0508 0305 0609 0106 1013
+ 4 1012 0406 0204 0305 0508 0307 0206 0808 1010
+ 4 1414 0809 0407 0608 0509 0305 0707 0810 1315
+ 4 0412 0409 0204 0205 0508 0404 0609 0808 1010
+ 4 1010 0204 0404 0305 0506 0407 0911 0308 1010
+ 4 0912 0409 0404 0103 0510 0404 0610 0109 1010
+ 4 1010 0404 0404 0205 0808 0407 0608 0101 0110
+ 4 1010 0206 0204 0303 0508 0307 0211 0808 1010
+ 4 0909 0409 0307 0305 0509 0406 0606 0108 1013
+ 4 1010 0304 0405 0305 0606 0606 0808 0308 1010
+ 4 1010 0303 0205 0405 0606 0606 0211 0308 0910
+ 4 1012 0404 0407 0405 0209 0305 0202 0308 0910
+ 4 0913 0404 0205 0406 0509 0405 0303 0303 0909
+ 5 1113 0406 0507 0306 0205 0307 0909 0808 0110
+ 5 1315 0404 0307 0507 0209 0303 0606 0808 1010
+ 5 1314 0409 0509 0507 0509 0404 0608 0108 0709
+ 5 0913 0409 0507 0505 0909 0303 0607 0909 1010
+ 5 0914 0404 0505 0606 0505 0303 0308 0808 1010
+ 5 0410 0608 0409 0507 0505 0303 0608 0108 1010
+ 5 0909 0404 0305 0103 0509 0307 0909 0108 1010
+ 5 1013 0410 0304 0607 0607 0303 0608 0101 1010
+ 5 1212 0410 0409 0505 0508 0303 0808 0105 1010
+ 5 1010 0707 0409 0507 0206 0303 0608 0108 1010
+ 5 1010 0709 0509 0107 0507 0303 0808 0108 1010
+ 5 1010 0406 0509 0303 0306 0303 0808 0208 1010
+ 5 0913 0409 0709 0707 0909 0307 0608 0109 1010
+ 5 0910 0404 0304 0105 0505 0707 0808 0808 1010
+ 5 0910 0409 0304 0305 0509 0303 0608 0108 1010
+ 6 1111 0609 0204 0606 0808 0307 0309 0105 0310
+ 6 0310 0409 0204 0505 0808 0205 0308 0305 1018
+ 6 1012 0609 0204 0505 0308 0306 0808 0102 0710
+ 6 1111 0608 0404 0608 0308 0303 0305 0408 0107
+ 6 1214 0404 0205 0305 0808 0303 0609 0107 1014
+ 6 0410 0409 0407 0505 0505 0303 0606 0102 0110
+ 6 1111 0409 0204 0505 0707 0303 0306 0105 0610
+ 6 1111 0408 0404 0505 0909 0202 0808 0102 0918
+ 6 0409 0609 0507 0505 0407 0307 0609 0508 1010
+ 6 1011 0404 0404 0305 0306 0405 0608 0102 1010
+ 6 0409 0707 0505 0608 0507 0303 0707 0101 1112
+ 7 0410 0606 0207 0505 0709 0507 0608 0808 0110
+ 7 0909 0405 0202 0103 0709 0306 0608 0108 0909
+ 7 0410 0505 0204 0105 0707 0306 0606 0108 0109
+ 7 0809 0608 0407 0108 0909 0306 0209 0108 0101
+ 7 0809 0606 0204 0105 0707 0303 0608 0808 1010
+ 7 0809 0608 0202 0105 0909 0304 0608 0708 0110
+ 7 0909 0406 0204 0505 0709 0303 0608 0708 0110
+ 7 1212 0409 0208 0305 0707 0506 0909 0710 1010
+ 7 1616 0509 0404 0305 0909 0202 0609 0808 1010
+ 7 0000 0505 0405 0505 0909 0404 0606 0108 1010
+ 7 0000 0409 0204 0505 0711 0404 0609 0707 1010
+ 7 0000 0606 0202 0505 0707 0303 0609 0808 0110
+ 7 0000 0707 0202 0505 0711 0303 0609 0810 0110
+ 7 0000 0509 0202 0505 0609 0303 0609 0101 0109
+ 8 0409 0209 0507 0305 0205 0202 0606 0101 1010
+ 8 0913 0206 0506 0709 0309 0307 0206 0811 0109
+ 8 1010 0909 0202 0305 0909 0306 0205 0405 1212
+ 8 1010 0611 0404 0505 0909 0204 0609 0101 1010
+ 8 1012 0609 0205 0507 0709 0101 0609 0410 0309
+ 8 0909 0409 0204 0303 0909 0406 0206 0108 1013
+ 8 0910 0409 0205 0203 0606 0303 0205 0808 1313
+ 8 0909 0409 0309 0305 0606 0406 0509 0508 1014
+ 8 0810 0409 0202 0305 0308 0303 0606 0104 1010
+ 8 0909 0204 0204 0303 0909 0505 0606 0108 1010
+ 9 0309 0406 0404 0606 0608 0307 0309 0308 1010
+ 9 1010 0406 0707 0305 0606 0307 0909 0203 0101
+ 9 0909 0304 0407 0405 0609 0307 0309 0208 0110
+ 9 0309 0304 0407 0406 0608 0307 0309 0308 0110
+ 9 0909 0304 0407 0406 0610 0307 0609 0308 1010
+ 9 1010 0406 0407 0305 0306 0307 0309 0309 0110
+ 9 0909 0509 0404 0408 1010 0303 0210 0108 1013
+ 9 0310 0304 0507 0407 0606 0307 0609 0303 0109
+ 9 0410 0407 0404 0102 1010 0306 0909 0102 1013
+ 10 1313 0209 0606 0507 0310 0306 0909 0110 1010
+ 10 0909 0209 0407 0309 0309 0307 0309 0108 1010
+ 10 1313 0202 0204 0309 0309 0307 0608 0101 1010
+ 10 0913 0209 0207 0109 0309 0307 0808 0108 0310
+ 10 0913 0202 0510 0103 0310 0307 0608 0108 0310
+ 10 0909 0204 0505 0305 0307 0307 0609 0103 0117
+ 10 0411 0204 0505 0505 0808 0303 0909 0101 1010
+ 10 0913 0909 0202 0101 0909 0307 0909 0108 1017
+ 10 1313 0209 0102 0103 0909 0303 0909 0101 0110
+ 10 0909 0609 0205 0607 0808 0306 0909 0811 1010
+ 10 0409 0409 0404 0406 0206 0307 0305 0308 0101
+ 11 0911 0309 0407 0305 0512 0303 0209 0408 0909
+ 11 0911 0204 0508 0505 0303 0307 0609 0108 1010
+ 11 0914 0304 0508 0509 0509 0307 0209 0408 1010
+ 11 0911 0409 0507 0206 0512 0303 0909 0808 1010
+ 11 1313 0404 0404 0408 0707 0407 0608 0408 1010
+ 11 0413 0309 0404 0406 0509 0307 0909 0808 1016
+ 11 1313 0404 0404 0407 0707 0303 0608 0108 1010
+ 11 0913 0404 0505 0606 0505 0307 0909 0408 1010
+ 11 0913 0606 0404 0303 0707 0303 0912 0108 1016
+ 11 0412 0410 0205 0303 0808 0308 0909 0911 1010
+ 11 1212 0610 0209 0406 0205 0303 0303 0809 0810
+ 11 0409 0408 0205 0406 0608 0306 0205 0108 0913
+ 11 1212 0609 0404 0000 0808 0406 0308 0709 0210
+ 11 0412 0609 0204 0000 0108 0406 0309 0107 0208
+ 11 0412 0609 0203 0000 0708 0406 0305 0101 0909
+ 11 0404 0609 0204 0000 0809 0404 0308 0109 0210
+ 11 0000 0511 0204 0000 0808 0406 0508 0107 0108
+ 11 1012 0909 0404 0000 0306 0303 0208 0506 1010
+ 11 0000 0304 0707 0000 0608 0407 0508 0508 1010
+ 11 0000 0104 0407 0000 0808 0306 0410 0000 0910
+ 12 0909 0709 0407 0505 0609 0303 0209 0108 1010
+ 12 0614 0206 0303 0105 1010 0306 0609 0808 1010
+ 12 0612 0404 0707 0505 0306 0303 0606 0808 0114
+ 12 1012 0409 0606 0505 1010 0606 0409 0808 0114
+ 12 0609 0409 0305 0505 0306 0303 0609 0810 0110
+ 12 0610 0407 0303 0505 0611 0303 0607 0808 1014
+ 12 0612 0404 0407 0305 0311 0307 0606 0808 0101
+ 12 0000 0409 0407 0508 0909 0307 0609 0808 1010
+ 12 1616 0409 0407 0508 0909 0303 0909 0308 1010
+ 12 0000 0404 0407 0508 0909 0707 0909 0308 1010
+ 12 1616 0909 0405 0505 0310 0303 0607 0808 1313
+ 12 0000 0409 0405 0506 0309 0307 0606 0808 0913
+ 12 0413 0211 0407 0405 0608 0307 0505 0308 0916
+ 12 0410 0608 0404 0405 0606 0306 0606 0808 1015
+ 13 0909 0409 0207 0505 0610 0303 0411 0101 0110
+ 13 0709 0909 0207 0506 1010 0303 0204 0808 0909
+ 13 0707 0509 0404 0305 0911 0306 0408 0108 1010
+ 13 1010 0707 0709 0505 0911 0308 0404 1010 1010
+ 13 0707 0409 0407 0506 0911 0306 0208 0109 0110
+ 13 0710 0409 0209 0205 0611 0303 0208 1010 1010
+ 13 0707 0808 0207 0305 0611 0303 0808 0104 0909
+ 13 0606 0409 0709 0305 0610 0308 0408 0110 1010
+ 13 0607 0909 0407 0508 0909 0306 0408 0110 1013
+ 13 0708 0404 0606 0508 0909 0303 0408 0110 1010
+ 13 0607 0509 0709 0103 0608 0308 0408 0110 1013
+ 13 0607 0509 0407 0508 0911 0306 0408 0109 0110
+ 13 0708 0509 0407 0508 1010 0308 0505 0110 0210
+ 14 0508 0409 0404 0103 0306 0406 0808 0309 0210
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+ 14 0000 0404 0407 0303 0506 0707 0709 0308 0202
+ 14 0108 0409 0101 0305 0306 0204 0707 0808 0210
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+ 14 0000 0909 0404 0509 0306 0306 0507 0101 0202
+ 14 0000 0409 0204 0509 0306 0407 0808 0808 0210
+ 14 0000 0404 0202 0309 0306 0204 0707 0707 1010
+ 14 0000 0404 0407 0507 0306 0707 0808 0909 0208
+ 14 0314 0306 0507 0103 0609 0307 0909 0308 0810
+ 14 1012 0404 0207 0105 0306 0207 0609 0610 0810
+ 14 0000 0304 0305 0305 0509 0307 0206 0308 1010
+ 14 0909 0409 0407 0507 0610 0307 0206 0103 1010
+ 14 0310 0306 0307 0307 0707 0307 0207 0609 0202
+ 14 0412 0409 0303 0305 0307 0206 0607 0410 0210
+ 14 1010 0309 0205 0507 0309 0407 0808 0309 0210
+ 14 1113 0505 0303 0305 1010 0307 0608 0101 1010
+ 15 0909 0111 0405 0509 0309 0307 0606 0909 0910
+ 15 0809 0211 0207 0308 0306 0306 0207 0101 1010
+ 15 0810 0211 0207 0303 0609 0306 0102 0108 0910
+ 15 1013 0202 0407 0308 0610 0306 0809 0106 0910
+ 15 0910 0411 0407 0305 0606 0306 0109 0108 1010
+ 15 1013 0204 0204 0306 1012 0306 0909 0106 1111
+ 15 1010 0211 0407 0305 0606 0607 0808 0108 1010
+ 15 0909 0211 0207 0305 0609 0808 0608 0606 1010
+ 15 0913 0204 0204 0505 0610 0307 0609 0101 1014
+ 15 1013 0204 0204 0506 0610 0307 0909 0707 1014
+ 15 0813 0104 0404 0506 0912 0307 0609 0104 1010
+ 16 1013 0404 0204 0406 0207 0308 0909 0103 0910
+ 16 1011 0606 0707 0506 0207 0307 0609 0103 0910
+ 16 0913 0609 0707 0405 0208 0707 0606 0308 0910
+ 16 0913 0109 0409 0406 0609 0205 0506 0608 1011
+ 16 0913 0404 0405 0406 0309 0303 0508 0101 0909
+ 16 1111 0406 0409 0505 0306 0707 0509 0101 1011
+ 16 1011 0404 0409 0405 0208 0303 0508 0101 1011
+ 16 1011 0406 0407 0405 0307 0307 0508 0103 1010
+ 16 1013 0406 0709 0505 0707 0303 0508 1010 0910
+ 16 0911 0404 0709 0405 0707 0707 0509 0310 1111
+ 16 1113 0404 0707 0405 0709 0303 0508 0103 1010
+ 16 0911 0406 0909 0305 0707 0307 0506 0303 1010
+ 17 0809 0405 0204 0000 0609 0307 0509 0808 1010
+ 17 0809 0404 0204 0000 0409 0303 0909 0808 0101
+ 17 0812 0404 0204 0000 0609 0307 0808 0808 0110
+ 17 0812 0209 0505 0000 0509 0307 0509 0000 1010
+ 17 0408 0505 0507 0000 0509 0303 0508 0000 1010
+ 17 0408 0505 0404 0000 0609 0303 0809 0000 1010
+ 17 0812 0409 0404 0000 0606 0306 0808 0000 1010
+ 17 0812 0204 0407 0000 0710 0303 0509 0000 1010
+ 17 0812 0409 0407 0000 0610 0306 0909 0000 1016
+ 17 0813 0202 0207 0000 0509 0303 0808 0000 1010
+ 17 0912 0408 0606 0000 0306 0307 0508 0810 1010
+ 17 1013 0204 0207 0000 0606 0303 0609 0810 1010
+ 17 0912 0209 0204 0000 0609 0307 0808 0000 1010
\ No newline at end of file
diff --git a/inst/files/nancycats.gen b/inst/files/nancycats.gen
new file mode 100755
index 0000000..78fbe21
--- /dev/null
+++ b/inst/files/nancycats.gen
@@ -0,0 +1,264 @@
+Genotypes of cats from 17 colonies of Nancy (France)
+fca8
+fca23
+fca43
+fca45
+fca77
+fca78
+fca90
+fca96
+fca37
+Pop
+1, 0000 0409 0404 0103 0909 0306 0909 0808 1010
+1, 0000 0909 0407 0305 0909 0306 0209 0808 1010
+1, 0913 0409 0505 0101 0709 0303 0808 0808 1111
+1, 0809 0505 0405 0105 0606 0306 0909 0104 1010
+1, 0809 0609 0507 0505 0707 0306 0609 0808 1010
+1, 0913 0409 0709 0305 0609 0606 0607 0108 1010
+1, 0909 0409 0407 0105 0707 0306 0909 0408 1010
+1, 0913 0409 0209 0305 0810 0306 0608 0101 1012
+1, 1013 0409 0404 0105 0611 0303 0808 0408 1012
+1, 0909 0303 0507 0305 0609 0606 0808 0104 1010
+Pop
+2, 1012 0204 0307 0606 0707 0307 0609 0101 0101
+2, 0608 0204 0207 0506 0306 0202 0609 0108 0110
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\ No newline at end of file
diff --git a/inst/files/nancycats.gtx b/inst/files/nancycats.gtx
new file mode 100755
index 0000000..e133965
--- /dev/null
+++ b/inst/files/nancycats.gtx
@@ -0,0 +1,293 @@
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\ No newline at end of file
diff --git a/inst/files/nancycats.str b/inst/files/nancycats.str
new file mode 100644
index 0000000..8c056db
--- /dev/null
+++ b/inst/files/nancycats.str
@@ -0,0 +1,475 @@
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+N132 11 1 143 136 141 128 148 150 199 113 208
+N133 11 1 135 140 139 120 152 142 199 91 208
+N133 11 1 143 140 139 120 152 142 205 113 220
+N246 11 1 123 136 135 120 154 142 199 115 208
+N246 11 1 141 148 141 120 154 152 199 119 208
+N247 11 1 141 140 135 122 142 142 187 113 204
+N247 11 1 141 148 149 128 148 142 187 115 208
+N271 11 1 123 136 135 122 150 142 185 91 206
+N271 11 1 135 144 141 128 154 148 191 113 214
+N298 11 1 141 140 139 -9 154 144 187 111 184
+N298 11 1 141 146 139 -9 154 148 197 115 208
+N299 11 1 123 140 135 -9 132 144 187 91 184
+N299 11 1 141 146 139 -9 154 148 199 111 204
+N300 11 1 123 140 135 -9 152 144 187 91 206
+N300 11 1 141 146 137 -9 154 148 191 91 206
+N301 11 1 123 140 135 -9 154 144 187 91 184
+N301 11 1 123 146 139 -9 156 144 197 115 208
+N302 11 1 -9 138 135 -9 154 144 191 91 182
+N302 11 1 -9 150 139 -9 154 148 197 111 204
+N303 11 1 137 146 139 -9 144 142 185 107 208
+N303 11 1 141 146 139 -9 150 142 197 109 208
+N304 11 1 -9 132 145 -9 150 144 191 107 208
+N304 11 1 -9 136 145 -9 154 150 197 113 208
+N310 11 1 -9 128 139 -9 154 142 189 -9 206
+N310 11 1 -9 136 145 -9 154 148 201 -9 208
+N134 12 1 135 142 139 126 150 142 185 91 208
+N134 12 1 135 146 145 126 156 142 199 113 208
+N135 12 1 129 130 137 116 158 142 193 113 208
+N135 12 1 145 140 137 126 158 148 199 113 208
+N136 12 1 129 136 145 126 144 142 193 113 182
+N136 12 1 141 136 145 126 150 142 193 113 216
+N137 12 1 137 136 143 126 158 148 189 113 182
+N137 12 1 141 146 143 126 158 148 199 113 216
+N138 12 1 129 136 137 126 144 142 193 113 182
+N138 12 1 135 146 141 126 150 142 199 117 208
+N139 12 1 129 136 137 126 150 142 193 113 208
+N139 12 1 137 142 137 126 160 142 195 113 216
+N140 12 1 129 136 139 120 144 142 193 113 182
+N140 12 1 141 136 145 126 160 150 193 113 182
+N164 13 1 135 136 135 126 150 142 189 91 182
+N164 13 1 135 146 145 126 158 142 203 91 208
+N165 13 1 131 146 135 126 158 142 185 113 206
+N165 13 1 135 146 145 128 158 142 189 113 206
+N166 13 1 131 138 139 120 156 142 189 91 208
+N166 13 1 131 146 139 126 160 148 197 113 208
+N167 13 1 137 142 145 126 156 142 189 117 208
+N167 13 1 137 142 149 126 160 152 189 117 208
+N168 13 1 131 136 139 126 156 142 185 91 182
+N168 13 1 131 146 145 128 160 148 197 115 208
+N169 13 1 131 136 135 118 150 142 185 117 208
+N169 13 1 137 146 149 126 160 142 197 117 208
+N170 13 1 131 144 135 120 150 142 197 91 206
+N170 13 1 131 144 145 126 160 142 197 105 206
+N171 13 1 129 136 145 120 150 142 189 91 208
+N171 13 1 129 146 149 126 158 152 197 117 208
+N172 13 1 129 146 139 126 156 142 189 91 208
+N172 13 1 131 146 145 132 156 148 197 117 214
+N173 13 1 131 136 143 126 156 142 189 91 208
+N173 13 1 133 136 143 132 156 142 197 117 208
+N174 13 1 129 138 145 116 150 142 189 91 208
+N174 13 1 131 146 149 120 154 152 197 117 214
+N175 13 1 129 138 139 126 156 142 189 91 182
+N175 13 1 131 146 145 132 160 148 197 115 208
+N176 13 1 131 138 139 126 158 142 191 91 184
+N176 13 1 133 146 145 132 158 152 191 117 208
+N193 14 1 127 136 139 116 144 144 197 103 184
+N193 14 1 133 146 139 120 150 148 197 115 208
+N194 14 1 119 146 139 120 144 146 195 107 184
+N194 14 1 133 146 139 126 150 146 195 113 208
+N195 14 1 -9 136 139 120 148 150 195 103 184
+N195 14 1 -9 136 145 120 150 150 199 113 184
+N196 14 1 117 136 133 120 144 140 195 113 184
+N196 14 1 133 146 133 126 150 144 195 113 208
+N197 14 1 -9 142 139 130 150 142 185 91 208
+N197 14 1 -9 142 149 130 156 142 203 113 208
+N198 14 1 -9 146 139 126 144 142 191 91 184
+N198 14 1 -9 146 139 134 150 148 195 91 184
+N199 14 1 -9 136 135 126 144 144 197 113 184
+N199 14 1 -9 146 139 134 150 150 197 113 208
+N200 14 1 -9 136 135 120 144 140 195 111 208
+N200 14 1 -9 136 135 134 150 144 195 111 208
+N201 14 1 -9 136 139 126 144 150 197 115 184
+N201 14 1 -9 136 145 130 150 150 197 115 204
+N202 14 1 121 132 141 116 150 142 199 103 204
+N202 14 1 145 140 145 120 156 150 199 113 208
+N203 14 1 137 136 135 116 144 140 193 109 204
+N203 14 1 141 136 145 126 150 150 199 117 208
+N206 14 1 -9 132 137 120 148 142 185 103 208
+N206 14 1 -9 136 141 126 156 150 193 113 208
+N207 14 1 135 136 139 126 150 142 185 91 208
+N207 14 1 135 146 145 130 158 150 193 103 208
+N209 14 1 121 132 137 120 152 142 185 109 184
+N209 14 1 137 140 145 130 152 150 195 115 184
+N210 14 1 123 136 137 120 144 140 193 105 184
+N210 14 1 141 146 137 126 152 148 195 117 208
+N211 14 1 137 132 135 126 144 144 197 103 184
+N211 14 1 137 146 141 130 156 150 197 115 208
+N212 14 1 139 138 137 120 158 142 193 91 208
+N212 14 1 143 138 137 126 158 150 197 91 208
+N204 15 1 135 128 139 126 144 142 193 115 206
+N204 15 1 135 150 141 134 156 150 193 115 208
+N227 15 1 133 130 135 120 144 142 185 91 208
+N227 15 1 135 150 145 132 150 148 195 91 208
+N228 15 1 133 130 135 120 150 142 181 91 206
+N228 15 1 137 150 145 120 156 148 185 113 208
+N229 15 1 137 130 139 120 150 142 197 91 206
+N229 15 1 143 130 145 132 158 148 199 109 208
+N230 15 1 135 136 139 120 150 142 181 91 208
+N230 15 1 137 150 145 126 150 148 199 113 208
+N231 15 1 137 130 135 120 158 142 199 91 210
+N231 15 1 143 136 139 128 162 148 199 109 210
+N232 15 1 137 130 139 120 150 148 197 91 208
+N232 15 1 137 150 145 126 150 150 197 113 208
+N233 15 1 135 130 135 120 150 152 193 109 208
+N233 15 1 135 150 145 126 156 152 197 109 208
+N234 15 1 135 130 135 126 150 142 193 91 208
+N234 15 1 143 136 139 126 158 150 199 91 216
+N235 15 1 137 130 135 126 150 142 199 111 208
+N235 15 1 143 136 139 128 158 150 199 111 216
+N236 15 1 133 128 139 126 156 142 193 91 208
+N236 15 1 143 136 139 128 162 150 199 105 208
+N251 16 1 137 136 135 122 142 142 199 91 206
+N251 16 1 143 136 139 128 152 152 199 103 208
+N252 16 1 137 140 145 126 142 142 193 91 206
+N252 16 1 139 140 145 128 152 150 199 103 208
+N253 16 1 135 140 145 122 142 150 193 103 206
+N253 16 1 143 146 145 126 154 150 193 113 208
+N254 16 1 135 128 139 122 150 140 191 109 208
+N254 16 1 143 146 149 128 156 146 193 113 210
+N255 16 1 135 136 139 122 144 142 191 91 206
+N255 16 1 143 136 141 128 156 142 197 91 206
+N256 16 1 139 136 139 126 144 150 191 91 208
+N256 16 1 139 140 149 126 150 150 199 91 210
+N257 16 1 137 136 139 122 142 142 191 91 208
+N257 16 1 139 136 149 126 154 142 197 91 210
+N258 16 1 137 136 139 122 144 142 191 91 208
+N258 16 1 139 140 145 126 152 150 197 103 208
+N259 16 1 137 136 145 126 152 142 191 117 206
+N259 16 1 143 140 149 126 152 142 197 117 208
+N260 16 1 135 136 145 122 152 150 191 103 210
+N260 16 1 139 136 149 126 152 150 199 117 210
+N261 16 1 139 136 145 122 152 142 191 91 208
+N261 16 1 143 136 145 126 156 142 197 103 208
+N262 16 1 135 136 149 120 152 142 191 103 208
+N262 16 1 139 140 149 126 152 150 193 103 208
+N182 12 1 -9 136 139 126 156 142 193 113 208
+N182 12 1 -9 146 145 132 156 150 199 113 208
+N183 12 1 149 136 139 126 156 142 199 103 208
+N183 12 1 149 146 145 132 156 142 199 113 208
+N184 12 1 -9 136 139 126 156 150 199 103 208
+N184 12 1 -9 136 145 132 156 150 199 113 208
+N185 12 1 149 146 139 126 144 142 193 113 214
+N185 12 1 149 146 141 126 158 142 195 113 214
+N186 12 1 -9 136 139 126 144 142 193 113 206
+N186 12 1 -9 146 141 128 156 150 193 113 214
+N269 12 1 123 130 139 122 150 142 191 103 206
+N269 12 1 143 150 145 126 154 150 191 113 220
+N270 12 1 123 140 139 122 150 142 193 113 208
+N270 12 1 137 144 139 126 150 148 193 113 218
+N282 17 1 133 136 135 -9 150 142 191 113 208
+N282 17 1 135 138 139 -9 156 150 199 113 208
+N283 17 1 133 136 135 -9 146 142 199 113 182
+N283 17 1 135 136 139 -9 156 142 199 113 182
+N288 17 1 133 136 135 -9 150 142 197 113 182
+N288 17 1 141 136 139 -9 156 150 197 113 208
+N291 17 1 133 130 141 -9 148 142 191 -9 208
+N291 17 1 141 146 141 -9 156 150 199 -9 208
+N292 17 1 123 138 141 -9 148 142 191 -9 208
+N292 17 1 133 138 145 -9 156 142 197 -9 208
+N293 17 1 123 138 139 -9 150 142 197 -9 208
+N293 17 1 133 138 139 -9 156 142 199 -9 208
+N294 17 1 133 136 139 -9 150 142 197 -9 208
+N294 17 1 141 146 139 -9 150 148 197 -9 208
+N295 17 1 133 130 139 -9 152 142 191 -9 208
+N295 17 1 141 136 145 -9 158 142 199 -9 208
+N296 17 1 133 136 139 -9 150 142 199 -9 208
+N296 17 1 141 146 145 -9 158 148 199 -9 220
+N297 17 1 133 130 135 -9 148 142 197 -9 208
+N297 17 1 143 130 145 -9 156 142 197 -9 208
+N281 17 1 135 136 143 -9 144 142 191 113 208
+N281 17 1 141 144 143 -9 150 150 197 117 208
+N289 17 1 137 130 135 -9 150 142 193 113 208
+N289 17 1 143 136 145 -9 150 142 199 117 208
+N290 17 1 135 130 135 -9 150 142 197 -9 208
+N290 17 1 141 146 139 -9 156 150 197 -9 208
+
diff --git a/inst/files/pdH1N1-HA.fasta b/inst/files/pdH1N1-HA.fasta
new file mode 100644
index 0000000..e67a91c
--- /dev/null
+++ b/inst/files/pdH1N1-HA.fasta
@@ -0,0 +1,12557 @@
+> GQ243757
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaaaat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160611
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ243751
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaaaat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ243761
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ243755
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgacacgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ247724
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ356787
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaaaccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ368667
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ368665
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagcttg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ998207
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctggg tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt gttgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ998209
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465673
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gttctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465679
+caatactagt aattatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402200
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cakaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatrtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaca agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402201
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402202
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cakaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaca agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402203
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaca agaatagaga
+atttaaacaa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402204
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cakaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttaccac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402205
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402206
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cakaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaca agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402187
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cakaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaca agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465674
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctggg tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt gttgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465675
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctggg tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt gttgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465676
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctggg tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt gttgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465678
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465677
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465680
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402194
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402195
+caatactagt agttctgcta tatacatttg caaccgcaaa tacagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402199
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402196
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465681
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactctgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402197
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgatgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactctgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465682
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactctgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465683
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactctgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402198
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactctgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ465672
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cakaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaca agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ385300
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgattcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtc aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ411897
+caatactagt agttctgcta tatacatttg caaccgcaaa tgccgacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232085
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaggttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ250161
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattctat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ223435
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaggttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ225365
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctaccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ225349
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcatagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ166223
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt agtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ225357
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ253492
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ253498
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ200287
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaca agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ225381
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagc tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232093
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgttgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ183617
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ223440
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg ataaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ293077
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccacg gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggggctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ259909
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttct tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ288372
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctaccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457519
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggaa caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtgaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ411907
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ411908
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acgacagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt gaaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ455032
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ290106
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagc tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044147
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa agatttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagtaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacaattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgatctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ982430
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043334
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa tttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043342
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattt gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041983
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtggga tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc catgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga agttggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043102
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtggga tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc catgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga agttggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043110
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtggga tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc catgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga agttggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041960
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtggga tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc catgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga agttggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ183633
+caatactagt ggttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat cgagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ283488
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaaaccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ283493
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ249333
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggaa caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ249337
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ214138
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagagggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagaraaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ214156
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ214144
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ214151
+caatactaat agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctacg
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagagggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccaaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgcgatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ329100
+caatactagt aattatgcta tacacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ329082
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtgccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg gggatggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tgatagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ329106
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc tctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ329088
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggtct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tgaaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ329070
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ166213
+caatactagt agttctgcta tatacattta caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ166212
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365666
+caatactagt agttctgcta tatacattta caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365658
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaagaaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagaac cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365674
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ283484
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ421201
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acgacagcat gtcctcacgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa caagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ421203
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaaa agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggaa caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctgtt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt canaaatgga acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ392029
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ351290
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ351319
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ219575
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ219576
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ219578
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctaatt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ219579
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttatca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ219580
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ219581
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ165814
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ287619
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atacatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaaaccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ287625
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtata acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taaggcccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc caggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ287621
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ287623
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ287627
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ334330
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atacatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaaaccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ334338
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atacatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaaaccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365410
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365418
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtccct tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatgga gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365426
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365428
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgta tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043078
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaaa ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> AB514227
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> AB514226
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaac
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttgaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365436
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atacatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaaaccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365446
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggaa caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa gataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaaa
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa aggactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgcaagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ334346
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ334355
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggga attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactaatg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ365455
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggga attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactaatg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FN423713
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162194
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc acyctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgaggggt caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tgattctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggagca atcagtttct ggatgtgctc taatgggtct ct
+> GQ149689
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tgattctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggagca atcagtttct ggatgtgctc taatgggtct ct
+> GQ149692
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162182
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162172
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+atagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcgaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ149671
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ149623
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgttccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca ggaatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162197
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162174
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162191
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ149630
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ149634
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162200
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaaa aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ162204
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040888
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgca acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ998208
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044163
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgca acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402189
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacactc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402190
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402192
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402193
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ402191
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaaaat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcaggggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY039527
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ205434
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ150338
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaatcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ150335
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaracaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044155
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ202695
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040880
+caatactagt agttttgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ243753
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ243749
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagag gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ255897
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtggga tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc catgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga agttggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ255901
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ219586
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ247726
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctaatagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ330645
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagt aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ392022
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ131023
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ227545
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+aatgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataatattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ360060
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ359765
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctag ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttatcca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaggttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044204
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044228
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctaatagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044196
+caatactagt agttctgcta tatacatttg cagccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044212
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgattcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagcttg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ169382
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcgtttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatggaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY039986
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcgtttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatggaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ166661
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117067
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117079
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttgacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ221805
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ221809
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actaaaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgaggrat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232037
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggaa
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ966082
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atacatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ966952
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ966960
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattaa
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ981613
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377052
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160579
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160606
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtt cacgattgca atacaacttg tcagacaccc aaaggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160607
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232038
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttta tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117040
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117119
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca ggaatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ221820
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca ggaatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160594
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160541
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ221823
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat cragaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232057
+caatactagt agttctgcta tatacatttg caaccgcaar tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232023
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160526
+caatactagt agttctgcta tatacattta caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcaat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ221826
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca ggaatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232028
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117097
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctc ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtata acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ168642
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacctaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattga acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117059
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117062
+caatactagt agttctgcta tatacattta caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcatatcc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232009
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+gcaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232067
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+aatgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232033
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160565
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117043
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117103
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117112
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ231987
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagaac cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgttgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232070
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgagtgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160599
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160582
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ168851
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ168650
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat cragaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ168886
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984375
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984347
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984337
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggyagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117116
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ221814
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984355
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ969509
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117082
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ200250
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117024
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984364
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcattta ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160601
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232049
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat cragaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984360
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ231999
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat cragaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160567
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaagggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160543
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160527
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaayctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160602
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160586
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt gagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232060
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984397
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ231993
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232052
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040637
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041122
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca rttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232044
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacgccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117056
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgagtgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ231981
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtmtctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgagtgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ231990
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca ggaatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232054
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgagtgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160531
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggaactaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taaggcccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctggt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ966959
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ984385
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> FJ966982
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117091
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtac tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg agggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggttttc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ168671
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232002
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggrt caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232076
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgaggggt caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ122097
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcaatgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttaaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232019
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta atattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtc aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat cgagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160574
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160550
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tgggaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232014
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtac tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg agggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ117051
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232007
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160591
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160578
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232073
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag gaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ232035
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ200237
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgaggggt caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160534
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggaa caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ160538
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041130
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041482
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tagttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040838
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aatyggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040862
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040693
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040717
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040457
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacaattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040822
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040629
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040854
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041114
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041170
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040645
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040830
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040007
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatactgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041522
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041605
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040701
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041613
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041186
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041058
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041066
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041597
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041178
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041194
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041506
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041530
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaat ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagcttg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041589
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041514
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041106
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041146
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041162
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040042
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041090
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041498
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg gataaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040023
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041082
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040015
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040709
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041565
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041098
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041581
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041645
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041050
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY039901
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041637
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actttccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcaatgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041490
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041074
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041202
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg gataaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041549
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041573
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY039999
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY040031
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacatgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041621
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY039893
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041541
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041557
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041154
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323486
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tgrtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323495
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323560
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agattggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323443
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaatga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323530
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323470
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagcttat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323473
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+aatgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323446
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323520
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtata acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatataat atggttagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323451
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323455
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323576
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtac tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg agggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ323509
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377101
+caatactagy agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377085
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacaattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457517
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaraaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctggtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgmta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatgatag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338394
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtaa
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338355
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgatag agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgcg atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338358
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338416
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338339
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338364
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtac tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg agggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457511
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377043
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457482
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338372
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457497
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377103
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgar caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338405
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338335
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggagaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377069
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttcr tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338368
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338378
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagcct gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377087
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338402
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca cctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atacatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcaaacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatatcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338400
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacatt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338381
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaagta ctcaaaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044235
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044243
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacatga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044251
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgaaatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaaactgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc tggtatgttt ct
+> CY044187
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaaaccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377045
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa amtcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377061
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta atattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtc aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat cragaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457501
+caatactagt agttctgcta catacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtac tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg agggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaacgctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtgc
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338375
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtac tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg agggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagcttct ggatgtgctc taatgggtct ct
+> GQ338409
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta atattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtc aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377047
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377107
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagcctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgc
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457465
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ396732
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ457470
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377064
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+gcaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338391
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ377075
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338414
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> GQ338361
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044171
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggggta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta tcactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattgggaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043118
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta tcactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattgggaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043086
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtt cacgattgca atacaacttg tcagacaccc aaaggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043094
+caatactagt agttatgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044179
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc tcatatggtc ct
+> CY043267
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043219
+caatactagt agttctgcta tatacattta caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041758
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041726
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043283
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041750
+caatactagt agttctgcta tatacattta caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043195
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041734
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041798
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041830
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041782
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cttggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043227
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043131
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041766
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044096
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaaattgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043211
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044080
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaggttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043275
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaattatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041822
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043235
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactaatg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043243
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043259
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041814
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gataagttca tggcccaatc
+atgactcgaa cagaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcatc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043147
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041790
+caacactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044104
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041806
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044128
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044112
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc caactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044056
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctggg tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY041774
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggga attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043203
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043171
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta atattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043299
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043187
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044072
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaggttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044088
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043155
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044136
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043139
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043291
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043251
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044120
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacagcttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043307
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044048
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gctgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043179
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY044064
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg acatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctggg tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043163
+caatactagt agttctgcta tatacattta caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cagaatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ctaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
+> CY043123
+caatactagt agttctgcta tatacatttg caaccgcaaa tgcagacaca ttatgtatag
+gttatcatgc gaacaattca acagacactg tagacacagt actagaaaag aatgtaacag
+taacacactc tgttaacctt ctagaagaca agcataacgg gaaactatgc aaactaagag
+gggtagcccc attgcatttg ggtaaatgta acattgctgg ctggatcctg ggaaatccag
+agtgtgaatc actctccaca gcaagctcat ggtcctacat tgtggaaaca tctagttcag
+acaatggaac gtgttaccca ggagatttca tcgattatga ggagctaaga gagcaattga
+gctcagtgtc atcatttgaa aggtttgaga tattccccaa gacaagttca tggcccaatc
+atgactcgaa caaaggtgta acggcagcat gtcctcatgc tggagcaaaa agcttctaca
+aaaatttaat atggctagtt aaaaaaggaa attcataccc aaagctcagc aaatcctaca
+ttaatgataa agggaaagaa gtcctcgtgc tatggggcat tcaccatcca tctactagtg
+ctgaccaaca aagtctctat cagaatgcag atgcatatgt ttttgtgggg tcatcaagat
+acagcaagaa gttcaagccg gaaatagcaa taagacccaa agtgagggat caagaaggga
+gaatgaacta ttactggaca ctagtagagc cgggagacaa aataacattc gaagcaactg
+gaaatctagt ggtaccgaga tatgcattcg caatggaaag aaatgctgga tctggtatta
+tcatttcaga tacaccagtc cacgattgca atacaacttg tcagacaccc aagggtgcta
+taaacaccag cctcccattt cataatatac atccgatcac aattggaaaa tgtccaaaat
+atgtaaaaag cacaaaattg agactggcca caggattgag gaatgtcccg tctattcaat
+ctagaggcct atttggggcc attgccggtt tcattgaagg ggggtggaca gggatggtag
+atggatggta cggttatcac catcaaaatg agcaggggtc aggatatgca gccgacctga
+agagcacaca gaatgccatt gacgagatta ctaacaaagt aaattctgtt attgaaaaga
+tgaatacaca gttcacagca gtaggtaaag agttcaacca cctggaaaaa agaatagaga
+atttaaataa aaaagttgat gatggtttcc tggacatttg gacttacaat gccgaactgt
+tggttctatt ggaaaatgaa agaactttgg actaccacga ttcaaatgtg aagaacttat
+atgaaaaggt aagaagccag ttaaaaaaca atgccaagga aattggaaac ggctgctttg
+aattttacca caaatgcgat aacacgtgca tggaaagtgt caaaaatggg acttatgact
+acccaaaata ctcagaggaa gcaaaattaa acagagaaga aatagatggg gtaaagctgg
+aatcaacaag gatttaccag attttggcga tctattcaac tgtcgccagt tcattggtac
+tggtagtctc cctgggggca atcagtttct ggatgtgctc taatgggtct ct
diff --git a/inst/files/pdH1N1-NA.fasta b/inst/files/pdH1N1-NA.fasta
new file mode 100644
index 0000000..7b1165c
--- /dev/null
+++ b/inst/files/pdH1N1-NA.fasta
@@ -0,0 +1,10392 @@
+> GQ243758
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160610
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ243752
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttacgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ243762
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca acatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ243756
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataaga gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+gatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ368663
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatctcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ367490
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ368668
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ368666
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ998213
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ998215
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465697
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465702
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402240
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402241
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggctccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tggtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402242
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgagatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402243
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402244
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402245
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggctccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tggtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402246
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402227
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataagg
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465698
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465699
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465707
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465701
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465700
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465703
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402234
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402235
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttgggg atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatgaaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gggcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataagtgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402239
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgaa tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402236
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tggtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465704
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcctgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402237
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagccctta tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcctgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465705
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcctgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465706
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcctgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402238
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcctgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ465696
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccacttaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc agttggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ385302
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataaga gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+acatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ411899
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tggtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ232087
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ250162
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ223436
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ225367
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt accctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ225351
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ166224
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcaatggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgctc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcttt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ225359
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ253495
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ253504
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ200288
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ225383
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ232095
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataaga gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ183619
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataaga gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ223445
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ293078
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ433898
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct attgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ288374
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt accctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ463958
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac atgatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtat
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ411905
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgtcct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ340060
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ455034
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcaatggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcttt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ290107
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044149
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaaccaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaaccttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ982431
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043336
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043344
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041985
+cggtctgtat gacaattgga atggccaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043104
+cggtctgtat gacaattgga atggccaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043112
+cggtctgtat gacaattgga atggccaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041962
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ183634
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ283487
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ283492
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ254710
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacctta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ254714
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ214140
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ222423
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ214146
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ214152
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggagcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggg tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ329102
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ329084
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ329108
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ329090
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ329072
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ166217
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+catggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag cgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ166216
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365668
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag cgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365660
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365676
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ283481
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ421202
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgt tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ421204
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttccggtcca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtat
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ392031
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc ttcactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttaagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ351292
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ351320
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ220731
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaaaagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ220732
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ220734
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ220735
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ220736
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ220737
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ166204
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataaga gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+acatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ287620
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gagccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ287626
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ287622
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ287624
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ287628
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ334332
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ334340
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365412
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365420
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365427
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365430
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043080
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag gatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> AB514228
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> AB514229
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataaga gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365438
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365448
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtat
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ334348
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ334357
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ365457
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FN423714
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ162193
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ149650
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ149691
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ162181
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ162171
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ149670
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagata
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ149664
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ162196
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ162173
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+cgtacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ397116
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatctcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ149681
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag trtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatctcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ149631
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttagaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ397117
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtrat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatctcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ397120
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040890
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggccagt ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccatgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ998214
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044165
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccatgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402229
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402230
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402232
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402233
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ402231
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agtgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY039528
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagagtc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcagggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg ctacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttrttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ205435
+cggtctgtat gacaattgga atggctaact taatattaca gattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ150336
+cggtctgtat gacaattgga atggctaact taatattaca gattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ150333
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044157
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt aatgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040874
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040882
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ243754
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcaatggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcttt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ243750
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ255898
+cggtctgtat gacaattgga atggccaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac catgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct agattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ375286
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ219585
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtggca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ247727
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ330646
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggga agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ392023
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacag tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ132185
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggaataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc cgtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ227546
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ360062
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ359766
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044206
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044230
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca acatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044198
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044214
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ169381
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ctgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY039988
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ctgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat gaacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ166659
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117064
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaactt
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117077
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtga tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ221806
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ221810
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323554
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ966084
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ966956
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ971075
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377078
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcataca
+aatatggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377050
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ221819
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377092
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccatgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggactgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323523
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcaggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323555
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacaa tcagtggttt ccgtgaaatt agcaggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaacgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117036
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117118
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ221821
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160593
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160540
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ221824
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323568
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323545
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160524
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttc ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ221827
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga arttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ232025
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117094
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttataaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggagcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ396740
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc ttttaaycag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117058
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtagttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323478
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323515
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taactgacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323570
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatagac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323547
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg gataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323521
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117042
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117102
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117108
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccatgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338330
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323571
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323566
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160581
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984340
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ168648
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323565
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984371
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984344
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggcy atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984335
+cggtctgtat gacaattgga atggctaact taatattacr aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatggrct atatacagta aagacaacag cataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117114
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ221815
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatmgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg gracagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984350
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984390
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ969541
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ200251
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117022
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984362
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ168669
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ396745
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984357
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338348
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323481
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323460
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgcacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323482
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323525
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160585
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttacygtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323569
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gctaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ969534
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323459
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323556
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040639
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041124
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ232041
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117053
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ231980
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggcc atatacagca aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323458
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323557
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160529
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataaga gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323512
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984383
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ981614
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323542
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcaaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117028
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtagttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttaccataa tgaccgatgg acccagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323513
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggtca gacggtgctg agt
+> GQ323573
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggtca gacggtgctg agt
+> GQ122096
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttctcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323526
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160571
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtagttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160547
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323524
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcaaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagca tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117048
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ232005
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160589
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323543
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323572
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323548
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ200238
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160533
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtat
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ160536
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg ctacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041132
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041484
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040840
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040864
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040695
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040719
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gtgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccaaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040458
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040824
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040631
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040856
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041116
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041172
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040647
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040832
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040009
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041524
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041607
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040703
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041615
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccaaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041188
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041060
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041068
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041599
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga accaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041180
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041196
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041508
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041532
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041591
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041516
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041108
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041148
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041164
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040044
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041092
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041500
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccaaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040025
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041084
+cggtctgtat gtcaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040017
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040711
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041567
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041100
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041583
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041647
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041052
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccaaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY039903
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat ctttagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041639
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041492
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041076
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041204
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccaaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041551
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041575
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040001
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY040033
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041623
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat ctttagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY039895
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041543
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041559
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041156
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323488
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+gaagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323493
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcaatggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcttt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323559
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggacta ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323442
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323529
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcaatggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcttt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323468
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323472
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatagac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323445
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323519
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttataaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctcttt
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323450
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323456
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtgcttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323575
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac atagtctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcaaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323507
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377100
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377084
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ457516
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccatgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggactgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338396
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338357
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338360
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338418
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcaatggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccmagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcttt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338341
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atggatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg gataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ117071
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa caacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ457510
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377040
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ457481
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338374
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtga tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> FJ984378
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377102
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338406
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338336
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377067
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338370
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338380
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtat
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377086
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338404
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaaggg ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338401
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcaatggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcttt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338384
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaat aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044237
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggtca gacggtgctg agt
+> CY044245
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044253
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggtca gacggtgctg agt
+> CY044189
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377044
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag ygtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg artaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377060
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ323553
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctcttt
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgagg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa attaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338377
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338411
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377046
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377105
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ457464
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaaacaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ396731
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ457469
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377063
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taactgacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338393
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ377074
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccggaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338415
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> GQ338362
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgt agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044173
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga ggacgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043120
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043088
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043096
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcaggcaat tcctctctct
+gccctgttgg tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc cctcttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044181
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043269
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043221
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041760
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaaaat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041728
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043285
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041752
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043197
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041736
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041800
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagattgg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041832
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041784
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043229
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043133
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041768
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044098
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043213
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044082
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacat tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043277
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc cttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtatc agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041824
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043237
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043245
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043261
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041816
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgataaatg ataaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaaycgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043149
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagattgg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041792
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044106
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaagtca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041808
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044130
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044114
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044058
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actgatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY041776
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043205
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043173
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043301
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043189
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044074
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgtccag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044090
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043157
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044138
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043141
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043293
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagattgg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043253
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044122
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043309
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044050
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043181
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY044066
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043165
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tgtaagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtaat ggacaggcct
+catacaagat cttcagaata gaaaagggaa aaatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
+> CY043125
+cggtctgtat gacaattgga atggctaact taatattaca aattggaaac ataatctcaa
+tatggattag ccactcaatt caacttggga atcaaaatca gattgaaaca tgcaatcaaa
+gcgtcattac ttatgaaaac aacacttggg taaatcagac atatgttaac atcagcaaca
+ccaactttgc tgctggacag tcagtggttt ccgtgaaatt agcgggcaat tcctctctct
+gccctgttag tggatgggct atatacagta aagacaacag tataagaatc ggttccaagg
+gggatgtgtt tgtcataagg gaaccattca tatcatgctc ccccttggaa tgcagaacct
+tcttcttgac tcaaggggcc ttgctaaatg acaaacattc caatggaacc attaaagaca
+ggagcccata tcgaacccta atgagctgtc ctattggtga agttccctct ccatacaact
+caagatttga gtcagtcgct tggtcagcaa gtgcttgtca tgatggcatc aattggctaa
+caattggaat ttctggccca gacaatgggg cagtggctgt gttaaagtac aacggcataa
+taacagacac tatcaagagt tggagaaaca atatattgag aacacaagag tctgaatgtg
+catgtgtaaa tggttcttgc tttactgtaa tgaccgatgg accaagtgat ggacaggcct
+catacaagat cttcagaata gaaaagggaa agatagtcaa atcagtcgaa atgaatgccc
+ctaattatca ctatgaggaa tgctcctgtt atcctgattc tagtgaaatc acatgtgtgt
+gcagggataa ctggcatggc tcgaatcgac cgtgggtgtc tttcaaccag aatctggaat
+atcagatagg atacatatgc agtgggattt tcggagacaa tccacgccct aatgataaga
+caggcagttg tggtccagta tcgtctaatg gagcaaatgg agtaaaagga ttttcattca
+aatacggcaa tggtgtttgg atagggagaa ctaaaagcat tagttcaaga aacggttttg
+agatgatttg ggatccgaac ggatggactg ggacagacaa taacttctca ataaagcaag
+atatcgtagg aataaatgag tggtcaggat atagcgggag ttttgttcag catccagaac
+taacagggct ggattgtata agaccttgct tctgggttga actaatcaga gggcgaccca
+aagagaacac aatctggact agcgggagca gcatatcctt ttgtggtgta aacagtgaca
+ctgtgggttg gtcttggcca gacggtgctg agt
diff --git a/inst/files/pdH1N1-data.csv b/inst/files/pdH1N1-data.csv
new file mode 100644
index 0000000..d9ef48f
--- /dev/null
+++ b/inst/files/pdH1N1-data.csv
@@ -0,0 +1,434 @@
+,"HA-acc-nb","NA-acc-nb","longitude","latitude","date"
+"1","GQ243757","GQ243758",130.83,-12.45,"2009-05-29"
+"2","GQ160611","GQ160610",153.03,-27.47,"2009-05-07"
+"3","GQ243751","GQ243752",144.96,-37.81,"2009-05-19"
+"4","GQ243761","GQ243762",144.96,-37.81,"2009-05-21"
+"5","GQ243755","GQ243756",115.86,-31.95,"2009-05-26"
+"6","GQ247724","GQ368663",-46.63,-23.55,"2009-04-29"
+"7","GQ356787","GQ367490",-46.63,-23.55,"2009-06-01"
+"8","GQ368667","GQ368668",-47.92,-15.83,"2009-06-05"
+"9","GQ368665","GQ368666",-37.76,-6.51,"2009-05-28"
+"10","FJ998207","FJ998213",-63.2,44.85,"2009-04-24"
+"11","FJ998209","FJ998215",-79.38,43.65,"2009-04-24"
+"12","GQ465673","GQ465697",-114.06,51.05,"2009-04-28"
+"13","GQ465679","GQ465702",-114.06,51.05,"2009-05-01"
+"14","GQ402200","GQ402240",-98.81,53.76,"2009-05-20"
+"15","GQ402201","GQ402241",-98.81,53.76,"2009-05-24"
+"16","GQ402202","GQ402242",-98.81,53.76,"2009-05-22"
+"17","GQ402203","GQ402243",-98.81,53.76,"2009-05-21"
+"18","GQ402204","GQ402244",-98.81,53.76,"2009-05-28"
+"19","GQ402205","GQ402245",-98.81,53.76,"2009-05-29"
+"20","GQ402206","GQ402246",-98.81,53.76,"2009-05-30"
+"21","GQ402187","GQ402227",-98.81,53.76,"2009-05-24"
+"22","GQ465674","GQ465698",-63.2,44.85,"2009-04-29"
+"23","GQ465675","GQ465699",-63.2,44.85,"2009-04-29"
+"24","GQ465676","GQ465707",-63.2,44.85,"2009-04-30"
+"25","GQ465678","GQ465701",-79.38,43.65,"2009-04-27"
+"26","GQ465677","GQ465700",-73.55,52.94,"2009-04-26"
+"27","GQ465680","GQ465703",-73.55,52.94,"2009-05-08"
+"28","GQ402194","GQ402234",-73.55,52.94,"2009-04-16"
+"29","GQ402195","GQ402235",-73.55,52.94,"2009-05-07"
+"30","GQ402199","GQ402239",-73.55,52.94,"2009-05-17"
+"31","GQ402196","GQ402236",-106.45,52.94,"2009-05-04"
+"32","GQ465681","GQ465704",-106.45,52.94,"2009-04-30"
+"33","GQ402197","GQ402237",-106.45,52.94,"2009-05-08"
+"34","GQ465682","GQ465705",-106.45,52.94,"2009-05-07"
+"35","GQ465683","GQ465706",-106.45,52.94,"2009-05-07"
+"36","GQ402198","GQ402238",-106.45,52.94,"2009-05-06"
+"37","GQ465672","GQ465696",-106.45,52.94,"2009-07-01"
+"38","GQ385300","GQ385302",-79.38,43.65,"2009-05-26"
+"39","GQ411897","GQ411899",-79.38,43.65,"2009-06-03"
+"40","GQ232085","GQ232087",113.5,23.33,"2009-05-27"
+"41","GQ250161","GQ250162",113.5,23.33,"2009-05-29"
+"42","GQ223435","GQ223436",113.5,23.33,"2009-05-29"
+"43","GQ225365","GQ225367",117.85,26.55,"2009-05-22"
+"44","GQ225349","GQ225351",120,29,"2009-05-23"
+"45","GQ166223","GQ166224",104.07,30.66,"2009-05-10"
+"46","GQ225357","GQ225359",121.5,31.2,"2009-05-23"
+"47","GQ253492","GQ253495",121.5,31.2,"2009-05-24"
+"48","GQ253498","GQ253504",121.5,31.2,"2009-05-31"
+"49","GQ200287","GQ200288",120.33,36.08,"2009-05-10"
+"50","GQ225381","GQ225383",116.39,39.91,"2009-05-23"
+"51","GQ232093","GQ232095",116.39,39.91,"2009-05-23"
+"52","GQ183617","GQ183619",116.39,39.91,"2009-05-15"
+"53","GQ223440","GQ223445",113.5,23.33,"2009-05-17"
+"54","GQ293077","GQ293078",120,29,"2009-05-31"
+"55","GQ259909","GQ433898",120,33,"2009-06-13"
+"56","GQ288372","GQ288374",117.85,26.55,"2009-05-28"
+"57","GQ457519","GQ463958",112.94,28.23,"2009-06-29"
+"58","GQ411907","GQ411905",121.5,31.2,"2009-06-06"
+"59","GQ411908","GQ340060",121.5,31.2,"2009-05-28"
+"60","GQ455032","GQ455034",118.77,32.05,"2009-06-17"
+"61","GQ290106","GQ290107",116.39,39.91,"2009-05-20"
+"62","CY044147","CY044149",-74.08,4.61,"2009-06-25"
+"63","FJ982430","FJ982431",12.57,55.72,"2009-04-29"
+"64","CY043334","CY043336",12.57,55.72,"2009-06-04"
+"65","CY043342","CY043344",12.57,55.72,"2009-06-04"
+"66","CY041983","CY041985",-69.89,18.48,"2009-05-24"
+"67","CY043102","CY043104",-69.89,18.48,"2009-05-26"
+"68","CY043110","CY043112",-69.89,18.48,"2009-05-26"
+"69","CY041960","CY041962",-69.89,18.48,"2009-05-24"
+"70","GQ183633","GQ183634",24.94,60.17,"2009-05-10"
+"71","GQ283488","GQ283487",24.94,60.17,"2009-05-26"
+"72","GQ283493","GQ283492",24.94,60.17,"2009-05-28"
+"73","GQ249333","GQ254710",2.35,48.86,"2009-05-01"
+"74","GQ249337","GQ254714",2.35,48.86,"2009-05-11"
+"75","GQ214138","GQ214140",2.35,48.86,"2009-04-30"
+"76","GQ214156","GQ222423",2.35,48.86,"2009-05-01"
+"77","GQ214144","GQ214146",2.35,48.86,"2009-04-30"
+"78","GQ214151","GQ214152",2.35,48.86,"2009-04-29"
+"79","GQ329100","GQ329102",2.35,48.86,"2009-05-17"
+"80","GQ329082","GQ329084",2.35,48.86,"2009-05-22"
+"81","GQ329106","GQ329108",7.44,48.32,"2009-05-06"
+"82","GQ329088","GQ329090",7.44,48.32,"2009-05-05"
+"83","GQ329070","GQ329072",-0.52,48.88,"2009-06-02"
+"84","GQ166213","GQ166217",9.99,53.55,"2009-04-28"
+"85","GQ166212","GQ166216",11.57,48.14,"2009-04-27"
+"86","GQ365666","GQ365668",12.56,52.41,"2009-05-02"
+"87","GQ365658","GQ365660",11.57,48.14,"2009-04-29"
+"88","GQ365674","GQ365676",12.56,52.41,"2009-05-04"
+"89","GQ283484","GQ283481",12.5,41.9,"2009-05-27"
+"90","GQ421201","GQ421202",13.52,43.62,"2009-07-01"
+"91","GQ421203","GQ421204",13.52,43.62,"2009-07-12"
+"92","GQ392029","GQ392031",12.5,41.9,"2009-06-17"
+"93","GQ351290","GQ351292",12.5,41.9,"2009-06-14"
+"94","GQ351319","GQ351320",11.26,43.77,"2009-06-06"
+"95","GQ219575","GQ220731",135.2,34.68,"2009-05-17"
+"96","GQ219576","GQ220732",135.2,34.68,"2009-05-17"
+"97","GQ219578","GQ220734",135.5,34.69,"2009-05-16"
+"98","GQ219579","GQ220735",135.5,34.69,"2009-05-16"
+"99","GQ219580","GQ220736",135.5,34.69,"2009-05-16"
+"100","GQ219581","GQ220737",135.5,34.69,"2009-05-17"
+"101","GQ165814","GQ166204",140.32,35.78,"2009-05-08"
+"102","GQ287619","GQ287620",130.4,33.58,"2009-06-07"
+"103","GQ287625","GQ287626",134.55,34.07,"2009-06-02"
+"104","GQ287621","GQ287622",136.07,35.12,"2009-05-19"
+"105","GQ287623","GQ287624",136.07,35.12,"2009-06-06"
+"106","GQ287627","GQ287628",139.63,35.45,"2009-06-09"
+"107","GQ334330","GQ334332",130.4,33.58,"2009-06-07"
+"108","GQ334338","GQ334340",130.4,33.58,"2009-06-07"
+"109","GQ365410","GQ365412",140.1,39.72,"2009-06-11"
+"110","GQ365418","GQ365420",140.47,37.76,"2009-06-23"
+"111","GQ365426","GQ365427",141.15,39.7,"2009-06-09"
+"112","GQ365428","GQ365430",141.15,39.7,"2009-06-18"
+"113","CY043078","CY043080",138.25,36.2,"2009-06-29"
+"114","AB514227","AB514228",139.65,35.86,"2009-05-21"
+"115","AB514226","AB514229",139.65,35.86,"2009-06-03"
+"116","GQ365436","GQ365438",130.56,31.6,"2009-06-13"
+"117","GQ365446","GQ365448",141.35,43.06,"2009-06-11"
+"118","GQ334346","GQ334348",138.38,34.98,"2009-06-02"
+"119","GQ334355","GQ334357",139.88,36.56,"2009-06-16"
+"120","GQ365455","GQ365457",139.88,36.56,"2009-06-16"
+"121","FN423713","FN423714",6.13,49.82,"2009-06-01"
+"122","GQ162194","GQ162193",-99.13,19.43,"2009-04-02"
+"123","GQ149689","GQ149650",-99.13,19.43,"2009-04-03"
+"124","GQ149692","GQ149691",-99.13,19.43,"2009-04-07"
+"125","GQ162182","GQ162181",-99.13,19.43,"2009-04-13"
+"126","GQ162172","GQ162171",-99.13,19.43,"2009-04-15"
+"127","GQ149671","GQ149670",-99.13,19.43,"2009-04-14"
+"128","GQ149623","GQ149664",-99.13,19.43,"2009-04-14"
+"129","GQ162197","GQ162196",-99.13,19.43,"2009-04-20"
+"130","GQ162174","GQ162173",-99.13,19.43,"2009-04-20"
+"131","GQ162191","GQ397116",-99.13,19.43,"2009-04-20"
+"132","GQ149630","GQ149681",-99.13,19.43,"2009-04-19"
+"133","GQ149634","GQ149631",-99.13,19.43,"2009-04-19"
+"134","GQ162200","GQ397117",-99.13,19.43,"2009-04-20"
+"135","GQ162204","GQ397120",-99.13,19.43,"2009-04-20"
+"136","CY040888","CY040890",-99.13,19.43,"2009-04-25"
+"137","FJ998208","FJ998214",-99.13,19.43,"2009-04-14"
+"138","CY044163","CY044165",-99.13,19.43,"2009-04-25"
+"139","GQ402189","GQ402229",-99.13,19.43,"2009-04-29"
+"140","GQ402190","GQ402230",-99.13,19.43,"2009-04-29"
+"141","GQ402192","GQ402232",-99.13,19.43,"2009-04-28"
+"142","GQ402193","GQ402233",-99.13,19.43,"2009-04-29"
+"143","GQ402191","GQ402231",-99.13,19.43,"2009-04-27"
+"144","CY039527","CY039528",4.48,51.93,"2009-04-29"
+"145","GQ205434","GQ205435",174.78,-36.85,"2009-04-25"
+"146","GQ150338","GQ150336",174.78,-36.85,"2009-04-25"
+"147","GQ150335","GQ150333",172.62,-43.53,"2009-04-29"
+"148","CY044155","CY044157",-86.3,12.37,"2009-06-26"
+"149","GQ202695","CY040874",10.76,59.95,"2009-05-07"
+"150","CY040880","CY040882",8.5,59.33,"2009-05-08"
+"151","GQ243753","GQ243754",120.97,14.58,"2009-05-20"
+"152","GQ243749","GQ243750",120.97,14.58,"2009-05-23"
+"153","GQ255897","GQ255898",36.28,54.55,"2009-05-22"
+"154","GQ255901","GQ375286",37.62,55.75,"2009-06-04"
+"155","GQ219586","GQ219585",37.62,55.75,"2009-05-21"
+"156","GQ247726","GQ247727",37.62,55.75,"2009-05-26"
+"157","GQ330645","GQ330646",37.62,55.75,"2009-06-03"
+"158","GQ392022","GQ392023",37.62,55.75,"2009-07-09"
+"159","GQ131023","GQ132185",126.98,37.55,"2009-05-02"
+"160","GQ227545","GQ227546",17.97,59.37,"2009-05-08"
+"161","GQ360060","GQ360062",17.97,59.37,"2009-05-30"
+"162","GQ359765","GQ359766",17.97,59.37,"2009-05-29"
+"163","CY044204","CY044206",121.56,25.09,"2009-05-22"
+"164","CY044228","CY044230",121.56,25.09,"2009-05-30"
+"165","CY044196","CY044198",121.3,24.99,"2009-05-19"
+"166","CY044212","CY044214",121.56,25.09,"2009-05-22"
+"167","GQ169382","GQ169381",100.48,13.75,"2009-05-06"
+"168","CY039986","CY039988",100.48,13.75,"2009-05-06"
+"169","GQ166661","GQ166659",-0.13,51.51,"2009-04-28"
+"170","GQ117067","GQ117064",-112.07,33.45,"2009-04-22"
+"171","GQ117079","GQ117077",-112.07,33.45,"2009-04-26"
+"172","GQ221805","GQ221806",-112.07,33.45,"2009-04-26"
+"173","GQ221809","GQ221810",-112.07,33.45,"2009-04-27"
+"174","GQ232037","GQ323554",-112.07,33.45,"2009-04-28"
+"175","FJ966082","FJ966084",-116.89,33.04,"2009-04-01"
+"176","FJ966952","FJ966956",-115.49,32.78,"2009-03-30"
+"177","FJ966960","FJ971075",-115.53,32.84,"2009-04-16"
+"178","FJ981613","GQ377078",-116.76,33.28,"2009-04-09"
+"179","GQ377052","GQ377050",-116.76,33.28,"2009-04-09"
+"180","GQ160579","GQ221819",-117.89,33.84,"2009-04-24"
+"181","GQ160606","GQ377092",-118.25,34.05,"2009-04-22"
+"182","GQ160607","GQ323523",-118.25,34.05,"2009-04-21"
+"183","GQ232038","GQ323555",-118.25,34.05,"2009-04-25"
+"184","GQ117040","GQ117036",-119.18,34.19,"2009-04-25"
+"185","GQ117119","GQ117118",-104.98,39.74,"2009-04-27"
+"186","GQ221820","GQ221821",-104.98,39.74,"2009-04-26"
+"187","GQ160594","GQ160593",-75.55,39.75,"2009-04-28"
+"188","GQ160541","GQ160540",-75.55,39.75,"2009-04-28"
+"189","GQ221823","GQ221824",-75.55,39.75,"2009-04-28"
+"190","GQ232057","GQ323568",-75.55,39.75,"2009-04-28"
+"191","GQ232023","GQ323545",-77.04,38.9,"2009-04-27"
+"192","GQ160526","GQ160524",-80.15,25.99,"2009-04-27"
+"193","GQ221826","GQ221827",-116.2,43.61,"2009-04-28"
+"194","GQ232028","GQ232025",-87.62,41.89,"2009-04-24"
+"195","GQ117097","GQ117094",-86.16,39.77,"2009-04-22"
+"196","GQ168642","GQ396740",-91.12,40.81,"2009-04-24"
+"197","GQ117059","GQ117058",-97.22,38.92,"2009-04-24"
+"198","GQ117062","GQ323478",-97.22,38.92,"2009-04-24"
+"199","GQ232009","GQ323515",-85.76,38.25,"2009-04-30"
+"200","GQ232067","GQ323570",-90.07,29.96,"2009-05-01"
+"201","GQ232033","GQ323547",-90.07,29.96,"2009-04-30"
+"202","GQ160565","GQ323521",-76.62,39.28,"2009-04-29"
+"203","GQ117043","GQ117042",-71.06,42.36,"2009-04-26"
+"204","GQ117103","GQ117102",-71.06,42.36,"2009-04-25"
+"205","GQ117112","GQ117108",-83.05,42.33,"2009-04-26"
+"206","GQ231987","GQ338330",-90.2,38.63,"2009-05-01"
+"207","GQ232070","GQ323571",-90.2,38.63,"2009-05-04"
+"208","GQ160599","GQ323566",-96,41.25,"2009-04-27"
+"209","GQ160582","GQ160581",-71.46,42.99,"2009-04-28"
+"210","GQ168851","FJ984340",-74,40.72,"2009-04-25"
+"211","GQ168650","GQ168648",-74,40.72,"2009-04-25"
+"212","GQ168886","GQ323565",-74,40.72,"2009-04-25"
+"213","FJ984375","FJ984371",-74,40.72,"2009-04-25"
+"214","FJ984347","FJ984344",-74,40.72,"2009-04-25"
+"215","FJ984337","FJ984335",-74,40.72,"2009-04-25"
+"216","GQ117116","GQ117114",-74,40.72,"2009-04-25"
+"217","GQ221814","GQ221815",-74,40.72,"2009-04-24"
+"218","FJ984355","FJ984350",-74,40.72,"2009-04-25"
+"219","FJ969509","FJ984390",-74,40.72,"2009-04-25"
+"220","GQ117082","FJ969541",-74,40.72,"2009-04-25"
+"221","GQ200250","GQ200251",-74,40.72,"2009-04-24"
+"222","GQ117024","GQ117022",-74,40.72,"2009-04-24"
+"223","FJ984364","FJ984362",-74,40.72,"2009-04-24"
+"224","GQ160601","GQ168669",-74,40.72,"2009-04-24"
+"225","GQ232049","GQ396745",-74,40.72,"2009-04-24"
+"226","FJ984360","FJ984357",-74,40.72,"2009-04-24"
+"227","GQ231999","GQ338348",-74,40.72,"2009-04-25"
+"228","GQ160567","GQ323481",-74,40.72,"2009-04-25"
+"229","GQ160543","GQ323460",-74,40.72,"2009-04-25"
+"230","GQ160527","GQ323482",-74,40.72,"2009-04-25"
+"231","GQ160602","GQ323525",-74,40.72,"2009-04-25"
+"232","GQ160586","GQ160585",-80.84,35.23,"2009-04-28"
+"233","GQ232060","GQ323569",-96.79,46.88,"2009-05-11"
+"234","FJ984397","FJ969534",-82.98,39.98,"2009-04-24"
+"235","GQ231993","GQ323459",-82.98,39.98,"2009-05-05"
+"236","GQ232052","GQ323556",-82.98,39.98,"2009-04-30"
+"237","CY040637","CY040639",-73.92,40.7,"2009-04-25"
+"238","CY041122","CY041124",-73.92,40.7,"2009-04-25"
+"239","GQ232044","GQ232041",-71.5,41.7,"2009-04-28"
+"240","GQ117056","GQ117053",-81.04,34,"2009-04-26"
+"241","GQ231981","GQ231980",-81.04,34,"2009-04-26"
+"242","GQ231990","GQ323458",-96.73,43.54,"2009-05-05"
+"243","GQ232054","GQ323557",-96.73,43.54,"2009-04-30"
+"244","GQ160531","GQ160529",-97.68,30.65,"2009-04-28"
+"245","FJ966959","GQ323512",-98.27,29.53,"2009-04-15"
+"246","FJ984385","FJ984383",-98.27,29.53,"2009-04-23"
+"247","FJ966982","FJ981614",-95.38,29.76,"2009-04-14"
+"248","GQ117091","GQ323542",-95.38,29.76,"2009-04-25"
+"249","GQ168671","GQ117028",-95.38,29.76,"2009-04-25"
+"250","GQ232002","GQ323513",-95.38,29.76,"2009-04-23"
+"251","GQ232076","GQ323573",-95.38,29.76,"2009-04-23"
+"252","GQ122097","GQ122096",-95.38,29.76,"2009-04-15"
+"253","GQ232019","GQ323526",-95.38,29.76,"2009-04-24"
+"254","GQ160574","GQ160571",-95.38,29.76,"2009-04-26"
+"255","GQ160550","GQ160547",-95.38,29.76,"2009-04-27"
+"256","GQ232014","GQ323524",-95.38,29.76,"2009-04-29"
+"257","GQ117051","GQ117048",-96.72,32.97,"2009-04-24"
+"258","GQ232007","GQ232005",-73.15,44.47,"2009-05-04"
+"259","GQ160591","GQ160589",-77.5,37.38,"2009-04-27"
+"260","GQ160578","GQ323543",-122.2,47.49,"2009-04-28"
+"261","GQ232073","GQ323572",-87.96,43.05,"2009-05-04"
+"262","GQ232035","GQ323548",-87.96,43.05,"2009-05-04"
+"263","GQ200237","GQ200238",-84.39,33.76,"2009-04-27"
+"264","GQ160534","GQ160533",-74.57,40.68,"2009-04-25"
+"265","GQ160538","GQ160536",-106.74,34.81,"2009-04-26"
+"266","CY041130","CY041132",-73.92,40.7,"2009-04-25"
+"267","CY041482","CY041484",-73.21,40.82,"2009-04-29"
+"268","CY040838","CY040840",-73.92,40.7,"2009-04-27"
+"269","CY040862","CY040864",-74,40.72,"2009-04-29"
+"270","CY040693","CY040695",-74,40.72,"2009-04-30"
+"271","CY040717","CY040719",-73.92,40.7,"2009-04-28"
+"272","CY040457","CY040458",-89.97,35.12,"2009-05-01"
+"273","CY040822","CY040824",-74,40.72,"2009-04-27"
+"274","CY040629","CY040631",-74,40.72,"2009-04-28"
+"275","CY040854","CY040856",-74,40.72,"2009-04-29"
+"276","CY041114","CY041116",-73.92,40.7,"2009-04-28"
+"277","CY041170","CY041172",-74,40.72,"2009-04-26"
+"278","CY040645","CY040647",-74,40.72,"2009-04-30"
+"279","CY040830","CY040832",-74,40.72,"2009-04-29"
+"280","CY040007","CY040009",-74.02,41.52,"2009-04-27"
+"281","CY041522","CY041524",-73.92,40.7,"2009-04-27"
+"282","CY041605","CY041607",-73.92,40.7,"2009-04-26"
+"283","CY040701","CY040703",-73.92,40.7,"2009-04-28"
+"284","CY041613","CY041615",-73.59,40.73,"2009-04-25"
+"285","CY041186","CY041188",-74,40.72,"2009-04-28"
+"286","CY041058","CY041060",-73.92,40.7,"2009-04-26"
+"287","CY041066","CY041068",-73.92,40.7,"2009-04-26"
+"288","CY041597","CY041599",-74,40.72,"2009-05-02"
+"289","CY041178","CY041180",-74,40.72,"2009-05-01"
+"290","CY041194","CY041196",-74,40.72,"2009-04-29"
+"291","CY041506","CY041508",-74,40.72,"2009-04-28"
+"292","CY041530","CY041532",-73.92,40.7,"2009-04-26"
+"293","CY041589","CY041591",-73.92,40.7,"2009-04-28"
+"294","CY041514","CY041516",-73.21,40.82,"2009-04-27"
+"295","CY041106","CY041108",-74,40.72,"2009-04-28"
+"296","CY041146","CY041148",-74,40.72,"2009-04-28"
+"297","CY041162","CY041164",-74,40.72,"2009-04-29"
+"298","CY040042","CY040044",-77.61,43.17,"2009-04-27"
+"299","CY041090","CY041092",-73.92,40.7,"2009-04-28"
+"300","CY041498","CY041500",-73.59,40.73,"2009-04-28"
+"301","CY040023","CY040025",-74.02,41.52,"2009-04-27"
+"302","CY041082","CY041084",-75.04,42.63,"2009-04-27"
+"303","CY040015","CY040017",-79.24,42.1,"2009-04-27"
+"304","CY040709","CY040711",-73.92,40.7,"2009-04-28"
+"305","CY041565","CY041567",-73.59,40.73,"2009-04-27"
+"306","CY041098","CY041100",-74,40.72,"2009-04-26"
+"307","CY041581","CY041583",-74,40.72,"2009-04-28"
+"308","CY041645","CY041647",-76.2,43.01,"2009-05-04"
+"309","CY041050","CY041052",-73.92,40.7,"2009-04-26"
+"310","CY039901","CY039903",-73.21,40.82,"2009-04-27"
+"311","CY041637","CY041639",-73.89,40.84,"2009-05-01"
+"312","CY041490","CY041492",-74,40.72,"2009-04-28"
+"313","CY041074","CY041076",-73.92,40.7,"2009-05-02"
+"314","CY041202","CY041204",-73.92,40.7,"2009-04-28"
+"315","CY041549","CY041551",-73.92,40.7,"2009-04-24"
+"316","CY041573","CY041575",-73.92,40.7,"2009-04-28"
+"317","CY039999","CY040001",-73.21,40.82,"2009-04-27"
+"318","CY040031","CY040033",-73.21,40.82,"2009-04-29"
+"319","CY041621","CY041623",-73.21,40.82,"2009-04-30"
+"320","CY039893","CY039895",-74.02,41.52,"2009-04-26"
+"321","CY041541","CY041543",-73.92,40.7,"2009-04-25"
+"322","CY041557","CY041559",-73.92,40.7,"2009-04-28"
+"323","CY041154","CY041156",-74,40.72,"2009-04-28"
+"324","GQ323486","GQ323488",-112.07,33.45,"2009-05-19"
+"325","GQ323495","GQ323493",-92.2,34.8,"2009-05-07"
+"326","GQ323560","GQ323559",-80.15,25.99,"2009-05-01"
+"327","GQ323443","GQ323442",-80.15,25.99,"2009-04-30"
+"328","GQ323530","GQ323529",-87.62,41.89,"2009-05-23"
+"329","GQ323470","GQ323468",-85.76,38.25,"2009-05-04"
+"330","GQ323473","GQ323472",-90.07,29.96,"2009-05-01"
+"331","GQ323446","GQ323445",-69,45.5,"2009-05-09"
+"332","GQ323520","GQ323519",-83.05,42.33,"2009-05-05"
+"333","GQ323451","GQ323450",-71.5,41.7,"2009-04-30"
+"334","GQ323455","GQ323456",-95.38,29.76,"2009-05-11"
+"335","GQ323576","GQ323575",-95.38,29.76,"2009-05-12"
+"336","GQ323509","GQ323507",-122.2,47.49,"2009-05-07"
+"337","GQ377101","GQ377100",-118.25,34.05,"2009-04-30"
+"338","GQ377085","GQ377084",-118.25,34.05,"2009-05-01"
+"339","GQ457517","GQ457516",-118.25,34.05,"2009-05-01"
+"340","GQ338394","GQ338396",-75.55,39.75,"2009-04-28"
+"341","GQ338355","GQ338357",-75.55,39.75,"2009-04-28"
+"342","GQ338358","GQ338360",-157.8,21.31,"2009-04-30"
+"343","GQ338416","GQ338418",-86.16,39.77,"2009-04-29"
+"344","GQ338339","GQ338341",-90.07,29.96,"2009-04-29"
+"345","GQ338364","GQ117071",-83.05,42.33,"2009-04-27"
+"346","GQ457511","GQ457510",-108.54,45.79,"2009-05-05"
+"347","GQ377043","GQ377040",-108.54,45.79,"2009-05-04"
+"348","GQ457482","GQ457481",-115.14,36.18,"2009-04-26"
+"349","GQ338372","GQ338374",-115.14,36.18,"2009-04-29"
+"350","GQ457497","FJ984378",-74,40.72,"2009-04-25"
+"351","GQ377103","GQ377102",-74,40.72,"2009-04-24"
+"352","GQ338405","GQ338406",-74,40.72,"2009-05-08"
+"353","GQ338335","GQ338336",-74,40.72,"2009-05-23"
+"354","GQ377069","GQ377067",-74,40.72,"2009-05-18"
+"355","GQ338368","GQ338370",-82.98,39.98,"2009-04-27"
+"356","GQ338378","GQ338380",-97.47,35.66,"2009-05-01"
+"357","GQ377087","GQ377086",-122.68,45.52,"2009-04-29"
+"358","GQ338402","GQ338404",-75.17,39.95,"2009-04-30"
+"359","GQ338400","GQ338401",-75.17,39.95,"2009-04-28"
+"360","GQ338381","GQ338384",-71.5,41.7,"2009-06-01"
+"361","CY044235","CY044237",-98.47,29.53,"2009-04-14"
+"362","CY044243","CY044245",-98.47,29.53,"2009-04-15"
+"363","CY044251","CY044253",-98.47,29.53,"2009-04-23"
+"364","CY044187","CY044189",-77.02,39,"2009-06-18"
+"365","GQ377045","GQ377044",-97.68,30.65,"2009-04-30"
+"366","GQ377061","GQ377060",-97.7,26.19,"2009-04-24"
+"367","GQ457501","GQ323553",-95.38,29.76,"2009-05-05"
+"368","GQ338375","GQ338377",-95.38,29.76,"2009-04-29"
+"369","GQ338409","GQ338411",-95.38,29.76,"2009-04-26"
+"370","GQ377047","GQ377046",-95.38,29.76,"2009-05-22"
+"371","GQ377107","GQ377105",-111.88,40.75,"2009-05-31"
+"372","GQ457465","GQ457464",-111.88,40.75,"2009-06-14"
+"373","GQ396732","GQ396731",-111.88,40.75,"2009-06-05"
+"374","GQ457470","GQ457469",-111.88,40.75,"2009-06-14"
+"375","GQ377064","GQ377063",-77.5,37.38,"2009-05-06"
+"376","GQ338391","GQ338393",-122.33,47.61,"2009-04-27"
+"377","GQ377075","GQ377074",-122.33,47.61,"2009-04-30"
+"378","GQ338414","GQ338415",-87.96,43.05,"2009-04-27"
+"379","GQ338361","GQ338362",-87.96,43.05,"2009-05-07"
+"380","CY044171","CY044173",-77.12,38.99,"2009-06-16"
+"381","CY043118","CY043120",-77.12,38.99,"2009-06-18"
+"382","CY043086","CY043088",-115.53,32.98,"2009-04-22"
+"383","CY043094","CY043096",-115.53,32.98,"2009-04-21"
+"384","CY044179","CY044181",-77.02,39,"2009-06-18"
+"385","CY043267","CY043269",-73.21,40.82,"2009-05-19"
+"386","CY043219","CY043221",-78.75,42.7,"2009-05-11"
+"387","CY041758","CY041760",-73.21,40.82,"2009-05-11"
+"388","CY041726","CY041728",-74,40.72,"2009-04-29"
+"389","CY043283","CY043285",-73.78,41.04,"2009-05-13"
+"390","CY041750","CY041752",-78.75,42.7,"2009-05-06"
+"391","CY043195","CY043197",-73.37,43.25,"2009-05-06"
+"392","CY041734","CY041736",-73.92,40.7,"2009-04-26"
+"393","CY041798","CY041800",-74,41.15,"2009-05-17"
+"394","CY041830","CY041832",-73.89,40.84,"2009-04-28"
+"395","CY041782","CY041784",-73.59,40.73,"2009-05-04"
+"396","CY043227","CY043229",-73.59,40.73,"2009-05-17"
+"397","CY043131","CY043133",-73.59,40.73,"2009-05-14"
+"398","CY041766","CY041768",-76.2,43.01,"2009-05-08"
+"399","CY044096","CY044098",-73.21,40.82,"2009-06-03"
+"400","CY043211","CY043213",-73.6,44.79,"2009-05-13"
+"401","CY044080","CY044082",-73.75,41.78,"2009-05-29"
+"402","CY043275","CY043277",-75.91,43.98,"2009-05-25"
+"403","CY041822","CY041824",-73.95,40.62,"2009-05-06"
+"404","CY043235","CY043237",-73.59,40.73,"2009-05-16"
+"405","CY043243","CY043245",-73.59,40.73,"2009-05-16"
+"406","CY043259","CY043261",-76.2,43.01,"2009-05-20"
+"407","CY041814","CY041816",-73.92,40.7,"2009-05-06"
+"408","CY043147","CY043149",-74,41.15,"2009-05-20"
+"409","CY041790","CY041792",-74.69,41.65,"2009-05-14"
+"410","CY044104","CY044106",-74.69,41.65,"2009-06-05"
+"411","CY041806","CY041808",-73.78,41.04,"2009-05-02"
+"412","CY044128","CY044130",-73.94,42.58,"2009-05-17"
+"413","CY044112","CY044114",-76.55,42.77,"2009-06-10"
+"414","CY044056","CY044058",-73.75,41.78,"2009-05-20"
+"415","CY041774","CY041776",-74.12,42.3,"2009-05-16"
+"416","CY043203","CY043205",-73.59,40.73,"2009-05-04"
+"417","CY043171","CY043173",-73.59,40.73,"2009-05-04"
+"418","CY043299","CY043301",-73.59,40.73,"2009-05-12"
+"419","CY043187","CY043189",-73.59,40.73,"2009-05-16"
+"420","CY044072","CY044074",-74,40.72,"2009-05-26"
+"421","CY044088","CY044090",-74,40.72,"2009-05-18"
+"422","CY043155","CY043157",-76.2,43.01,"2009-05-12"
+"423","CY044136","CY044138",-76.2,43.01,"2009-05-19"
+"424","CY043139","CY043141",-76.2,43.01,"2009-05-19"
+"425","CY043291","CY043293",-74,41.15,"2009-05-16"
+"426","CY043251","CY043253",-74,41.15,"2009-05-16"
+"427","CY044120","CY044122",-73.85,43.01,"2009-06-17"
+"428","CY043307","CY043309",-73.21,40.82,"2009-05-17"
+"429","CY044048","CY044050",-73.21,40.82,"2009-05-20"
+"430","CY043179","CY043181",-73.78,41.04,"2009-05-12"
+"431","CY044064","CY044066",-73.75,41.78,"2009-05-19"
+"432","CY043163","CY043165",-78.75,42.7,"2009-05-11"
+"433","CY043123","CY043125",-73.21,40.82,"2009-05-08"
diff --git a/inst/files/usflu.fasta b/inst/files/usflu.fasta
new file mode 100644
index 0000000..b373486
--- /dev/null
+++ b/inst/files/usflu.fasta
@@ -0,0 +1,2400 @@
+> CY013200
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcagcaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaaccgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY013781
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttccgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagaagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012128
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacatcatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggggaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaatcagaatacaaatacccagcgctg
+aacgtgtctatgccaaacaatggcaaatttaacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaaccccgaatatcgggtctagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcacctgcagttttgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY013613
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctaggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttccgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012160
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctagagtttatcaatgaagac
+ttcaattggactggagtagctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012272
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgaaaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY010988
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacggcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggctgcataaattagaatacaaatatccagcgctg
+aacgtgaccatgccaaacaatggaaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gtcgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012288
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaattgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcgacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012568
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcgaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggctgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gtcgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY013016
+atgaagactatcattgctttgagctacatttcatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcggtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcatcgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttatcaatgaagac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcgagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtttagaccctgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacggaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggggcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcaccatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012480
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttccccaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaagaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaacgaaaac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgtccgagcatcagggaaagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccggatatcgggtatagaccatgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcagaattctgagggcacaggacaagct
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+gtcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaat
+gcggagcttcttgttgctctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactatttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgcttgggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY010748
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacatcatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaatgaaggc
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaactgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtccagaccctgggtgagg
+ggcatctccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattgacaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgatcaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtggaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaatcaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcagcatttgcatttga
+> CY011528
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttccccaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaagaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaacgaaaac
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagactacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgtccgagcatcagggaaagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccggatatcgggtatagaccatgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgccccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcagaattctgagggcacaggacaagct
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+gtcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaat
+gcggagcttcttgttgctctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactatttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgttttgttttgcttgggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY017291
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttccccaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaagaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaacgaaaac
+ttcaattggactggagtcgctcaggatgggaaaagctattcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcgctg
+aacgtgactatgccaaacaatggcaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgtccgagcatcagggaaagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccggatatcgggtatagaccatgggtaagg
+ggtctgtccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcagttctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatgggacc
+tgccccagatatgttaagcaaaacacactgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcagaattctgagggcacaggacaagct
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaaactgaataggtta
+gtcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaat
+gcggagcttcttgttgctctggagaatcaacatacaattgatctaactgactcagaaatg
+aacaaactatttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgcttgggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY012504
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacagcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgatcaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaccaaggaaggc
+ttcaattggactggagtcgctcaggatgggaaaagctatgcttgcaaaaggggatctgtt
+aacagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagcacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtatctccagtagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaaatgggaaa
+agctcaataatgaggtcagatgcacccattggcaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaagttggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcgaccaaatcaacgggaagctgaataggtta
+atcgagaaaacgaacgaaaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY009476
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaccaaagaaggc
+ttcaattggaccggagtcgctcaggatggaacaagctatgcttgcaaaaggggatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcggatgcacccattgacaactgcaattctgaatgcattactcca
+aatggaagcatttccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgaaggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaagaaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcattatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY010028
+atgaagactattattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgcccagaatggaacaagctatgcttgcaaaaggagatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcaggataagcatatattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtggaaaa
+agctcaataatgaggtcagatgcacccattgacaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY011128
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaccaaagaaggc
+ttcaattggactggagtcgctcaggatggaacaagctatgcttgcaaaaggggatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcggatgcacccattgacaactgcaattctgaatgcattactcca
+aatggaagcatttccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgaaggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaagaaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcattatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY010036
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttcaaaaataaggaatgg
+gacctttttgttgaacgcagcacagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaccaatgaaggc
+ttcaattggactggagtcgctcaggatggaacaagctatgcttgcaaaaggggatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcgggtctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattgacaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccttttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctaaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcttacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaagaaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatatatcacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgc
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY011424
+atgaagactattattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+ggttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggaaaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcttacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatcaggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgcccagaatggaacaagctatgcttgcaaaaggagatctgtt
+aaaagtttctttagtagattgaattggttgcacaaattagaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgttcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatatattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattgacaactgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacggaaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaatcgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaagacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006259
+atgaagactatcattgctttgagctacatttcatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcactctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006243
+atgaagactatcattgctttgagctacatttcatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcactctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacattagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006267
+atgaagactatcattgctttgagctacatttcatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcactctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006235
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgattgatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacaccctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagaccttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatgtcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006627
+atgaagactatcattgctttgagctacatttcatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcactctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaattgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006787
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgattgatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaataagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacaccctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagaccttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatgtcatgt
+tttttgttttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006563
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaaattccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaagccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggtttcagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY002384
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctaat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctggaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY008964
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaaattccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcagagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactaagggaaaatgctgaggatatgggcaat
+ggttgcttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006595
+atgaagactatcattgctttgagctacatttcatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcactctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctatgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgttggaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001453
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+gtaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccacattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttacaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcataataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcaaatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggaa
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacaaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001413
+atgaagactatcattgctttgagctacattttatgtctggtttttgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgagtgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctttgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtttccagcagaataagcatctattggacaatagtgaaaccgggagacatacttctg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatggcaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattcacagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccacatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001704
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctaat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001616
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgagtgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccgaatccttgatggagaaaactgc
+acactgatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcaccctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctttgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgacaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaaccagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtttccagcagaataagcatctattggacaatagtgaaaccgggagacatacttctg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaagtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcaggtttcatagaaaatggttgggag
+ggaatggtagacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattcacagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgtctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccacatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY003785
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+gtaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaacacattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttactttaaaatacgaagtgggaaa
+agctcaataatgaggtcaaatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacaaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaagtataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000737
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+gtaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccacattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctttgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatctggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttactttaaaatacgaagtgggaaa
+agctcaataatgaggtcaaatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacaaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001365
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+gtaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccacattgaagtgactaatgccactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaagataaggaatgg
+gacctttttgttgaacgcagcacagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttactttaaaatacgaagtgggaaa
+agctcaataatgaggtcaaatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaccactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacaaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY003272
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+gtaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccacattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcccacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttactttaaaatacgaagtgggaaa
+agctcaataatgaggtcaaatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacaaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000705
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+gtaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccacattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcaggaagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttactttaaaatacgaagtgggaaa
+agctcaataatgaggtcaaatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacaaacgagaagttccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000657
+atgaagactatcattgctttgagctacattttatgtatggttttcgctcaaaaacttccc
+gtaaatgacaacagcacggcaacgctgtgcctgggacaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccacattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcacagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctatt
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgaccatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgagtacggacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcaaatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggcgcaatcgcgggtttcatagaaaatggttgggaa
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacaaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaggaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY002816
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctaat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctggaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtgcca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000584
+atgaagactatcattgctttgagctacattttatgcctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtaactaatgctactgagctggttcag
+agttcctcaacaagtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaagagaagccaacaaactgtaatcccgaatatcggatctggaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtccgatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001720
+atgaagactatcattgctttgagctacattttatgcctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtaactaatgctactgagctggttcag
+agttcctcaacaagtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000185
+atgaagactatcattgctttgagctacattttatgcctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtaactaatgctactgagctggttcag
+agttcctcaacaagtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctggaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaagctagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY002328
+atgaagactatcattgctttgagctacattttatgcctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtaactaatgctactgagctggttcag
+agttcctcaacaagtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaagagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtccgatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000297
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcatggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctaat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccggatacagacagtaaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccaaatatcggatctggaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatactttta
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtgcca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgaaggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactaaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacacacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY003096
+atgaagactatcattgctttgagctacattttatgcctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtaactaatgctactgagctggttcag
+agttcctcaacaagtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctggggaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcacacaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgaaaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000545
+atgaagactatcattgctttgagctacattttatgcctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtaactaatgctactgagctggttcag
+agttcctcaacaagtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctggaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtacca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000289
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcttatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatgggccc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtgcca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001152
+atgaaggctatcattgctttgagctacattttatgcctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcatcatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtaactaatgctactgagctggttcag
+agttcctcaacaggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctctgcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctggaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtgcca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccaaatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000105
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggtacag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcgattggactggagtcactcagaatggaacaagctctgcttgcaaaaggagatctaat
+aaaagtttctttagtagattgaattggttgacccacttaaaatacaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacagtgaccaaatcagcctatatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtgatcccgaatatcggatctagacccagggtaagg
+gatgtctccagccgaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattccgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactttgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggcttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaaactgaataggtta
+atcgggaaaacaaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaactaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtgtacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY002104
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggtacag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactagagtttaacaatgaaagc
+ttcgattggactggagtcactcagaatggaacaagctctgcttgcaaaaggagatctaat
+aaaagtttctttagtagattgaattggttgacccacttaaaatacaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacagtgaccaaatcagcctatatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatgtctccagccgaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatattaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaaactgaataggtta
+atcgggaaaacaaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggacatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtgtacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY001648
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggtacag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactagagtttaacaatgaaagc
+ttcgattggactggagtcactcagaatggaacaagctctgcttgcaaaaggagatctaat
+aaaagtttctttagtagattgaattggttgacccacttaaaatacaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacagtgaccaaatcagcctatatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatctccagccgaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaatagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatattaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaaactgaataggtta
+atcgggaaaacaaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtgtacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY000353
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcagaatggaacaagctctgcttgcgaaaggagatctaat
+aaaagtttctttagtagattgaattggttgacccacttaaaatacaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacagtgaccaaatcagcctatatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatgtctccagccgaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggattacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggacggttggtacggtttcaggcatcaaaattctgagggcacaggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaaactgaataggtta
+atcgggaaaacaaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtgtacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcgacatttgcatttga
+> CY001552
+atgaagactatcattgctttgagctacattttatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctggggcaccatgcagtgccaaacggaacg
+ctagtgaaaacaatcacgaatgaccaaattgaagtgactaatgctactgagctggttcag
+agttcctcaataggtagaatatgcgacagtcctcaccaaatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcattgtgatggcttccaaaataaggaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgtctcccttaggtcactagttgcctcatcaggcacgctggagtttaacaatgaaagc
+ttcaattggactggagtcgctcagaatggaacaagctcttcttgcaaaaggagatctgat
+aaaagtttctttagtagattgaattggttgcaccaattaaaatacaaatatccagcactg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacagacagtgaccaaatcagcctatatgctcaagcatcagggagagtcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaacatcggatctagaccctgggtaagg
+ggtgtctccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgaggtcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatgggccc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcggaatgtgcca
+gagaaacaaactagaggcatattcggtgcaatcgcgggcttcatagaaaatggttgggag
+ggaatgatggacggttggtacggtttcaggcatcaaaattctgagggcacagggcaagca
+gcagatcttaaaagcactcaagcagcaatcaaccagatcaacgggaaactgaataggtta
+atcgagaaaacgaacgagaaattccatcaaattgaaaaagaattctcagaagtagaaggg
+agaatccaggacctcgagaaatatgttgaggacactaaaatagatctctggtcgtacaat
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagacgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtattgttttgctggggttcatcatgtgggcctgccaaaaaggcaacatt
+agatgcaacatttgcatttga
+> CY019245
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcatgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaattagcctatatgctcaagcttcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY021989
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcatgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaattagcctatatgctcaagcttcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY003336
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttattgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggaatttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggagttcaccac
+ccgggtacggacaatgaccaaatcagcctatatgctcaagcttcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaggcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY003664
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgaccatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcagcctatatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaatagggcaagca
+gcagatctcaaaagcactcaagcagcaataaaccaaatcaatgggaagctgaataggttg
+atcggaaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY002432
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaaattccc
+ggaaatgacaacagcacggcaacgctgtgcgttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaattagcctatatgctcaagcttcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY003640
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaagaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggacaggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaaccagcctatatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggttttaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcggaaaaaccaacgaaaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgttcgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagttaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY019301
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaattagcctatatgctcaagcttcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY019285
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccaggtacggacaatgaccaaattagcctatatgctcaagcttcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY006155
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttattgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggaatttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcagcctatatgctcaagcttcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagggtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctcggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaaccaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcatagggtcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattgaacaaccggttccagatcaaaggt
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY034116
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacgatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctcttcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccaattaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccggttacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagaataagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EF554795
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagactgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacctagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacagaatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgagaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY019859
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgagaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagccctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaaggagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU100713
+------------------------------------------------caaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtggaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgccctawtgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatctggcacactggagtttaacaatgaaagc
+ttcaattggacgggagtcactcaaaatggaacaagctcttcttgcaaaaggggatctgat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattgacaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcagaacaccctgaaattggcaacaggaatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagagaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatacctgcataggatcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggc
+gttgagctgaagtcaggctacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttaa
+> CY019843
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagactgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcttgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatccagacctagagtaagg
+ratatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacagaatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgagaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgttttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY014159
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaacagcacggcaacgctgtgcctcgggcaccatgcagtaccaaacggaacg
+atagtgagaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagccctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgagagc
+ttcaattggactggagtcactcaaaatggaacaagctctgcttgcaaaaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaaggagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccatttcaaaatgtaaacaggatcacatatggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcaatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtagaaggg
+agaattcaggacctcgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaagaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccatgatgtatacagagatgaagcattaaacaaccggttccagatcaaaggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU199369
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcmastgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aaaagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+gatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaagggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU199254
+------------------------------------------------------------
+---------------------------------------catgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaagtcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaagggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> CY031555
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaagtcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaagggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU516036
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttccc
+ggaaatgacaaaagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatctggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaactctgaatgcatcactcca
+aacggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaagggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU516212
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaaaaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaattccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactttgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggaa
+ggaatggtggatggttggtacggtttcaggcatcaaaattmtgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+aggattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaagggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> FJ549055
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccactcaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaagaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatggaaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+aggattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaagggc
+gttgagctgaaatcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU779498
+atgaagactatcattgctttgagctacattctatgtctggtttccgctcaaaaatttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaatcgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatctggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagactgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaagaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccccagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaataggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaataggttg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactatttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaagggc
+gttgagctgaagtcaggatacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU779500
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaacaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+gatatccctagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaagaggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaatagattg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacactaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagggatgaagcattaaacaaccggttccagatcaaggga
+gttgagctgaagtcagggtacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+agatgcaacatttgcatttga
+> CY035190
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatccggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctgcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaacaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccctagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gataaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaagaggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaatagattg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagagaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaaggga
+gttgagctgaagtcagggtacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
+> EU852005
+atgaagactatcattgctttgagctacattctatgtctggttttcgctcaaaaacttcct
+ggaaatgacaacagcacggcaacgctgtgccttgggcaccatgcagtaccaaacggaacg
+atagtgaaaacaatcacgaatgaccaaattgaagttactaatgctactgagctggttcag
+agttcctcaacaggtgaaatatgcgacagtcctcatcagatccttgatggagaaaactgc
+acactaatagatgctctattgggagaccctcagtgtgatggcttccaaaataagaaatgg
+gacctttttgttgaacgcagcaaagcctacagcaactgttacccttatgatgtgccggat
+tatgcctcccttaggtcactagttgcctcatctggcacactggagtttaacaatgaaagc
+ttcaattggactggagtcactcaaaacggaacaagctctkcttgcataaggagatctaat
+aacagtttctttagtagattgaattggttgacccacttaaaattcaaatacccagcattg
+aacgtgactatgccaaacaatgaacaatttgacaaattgtacatttggggggttcaccac
+ccgggtacggacaatgaccaaatcttcctgtatgctcaagcatcaggaagaatcacagtc
+tctaccaaaagaagccaacaaactgtaatcccgaatatcggatctagacccagagtaagg
+aatatccctagcagaataagcatctattggacaatagtaaaaccgggagacatacttttg
+attaacagcacagggaatctaattgctcctaggggttacttcaaaatacgaagtgggaaa
+agctcaataatgagatcagatgcacccattggcaaatgcaattctgaatgcatcactcca
+aatggaagcattcccaatgacaaaccattccaaaatgtaaacaggatcacatacggggcc
+tgtcccagatatgttaagcaaaacactctgaaattggcaacagggatgcgaaatgtacca
+gagaaacaaactagaggcatatttggcgcaatcgcgggtttcatagaaaatggttgggag
+ggaatggtggatggttggtacggtttcaggcatcaaaattctgagggaagaggacaagca
+gcagatctcaaaagcactcaagcagcaatcgatcaaatcaatgggaagctgaatagattg
+atcgggaaaaccaacgagaaattccatcagattgaaaaagaattctcagaagtcgaaggg
+agaattcaggaccttgagaaatatgttgaggacaccaaaatagatctctggtcatacaac
+gcggagcttcttgttgccctggagaaccaacatacaattgatctaactgactcagaaatg
+aacaaactgtttgaaaaaacaaagaagcaactgagggaaaatgctgaggatatgggcaat
+ggttgtttcaaaatataccacaaatgtgacaatgcctgcataggatcaatcagaaatgga
+acttatgaccacgatgtatacagagatgaagcattaaacaaccggttccagatcaaggga
+gttgagctgaagtcagggtacaaagattggatcctatggatttcctttgccatatcatgt
+tttttgctttgtgttgctttgttggggttcatcatgtgggcctgccaaaaaggcaacatt
+aggtgcaacatttgcatttga
diff --git a/man/H3N2.Rd b/man/H3N2.Rd
new file mode 100644
index 0000000..b2fdcd7
--- /dev/null
+++ b/man/H3N2.Rd
@@ -0,0 +1,88 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\name{H3N2}
+\alias{H3N2}
+\alias{USflu}
+\alias{USflu.fasta}
+\alias{usflu}
+\alias{usflu.fasta}
+\title{Seasonal influenza (H3N2) HA segment data}
+\format{\code{H3N2} is a genind object with several data frame as
+supplementary components (\code{H3N2 at other) slort}, which contains the
+following items: \describe{ \item{x}{a \code{data.frame} containing
+miscellaneous annotations of the sequences.} \item{xy}{a matrix with two
+columns indicating the geographic coordinates of the strains, as longitudes
+and latitudes.} \item{epid}{a character vector indicating the epidemic of
+the strains.} }}
+\source{
+This dataset was prepared by Thibaut Jombart
+(t.jombart at imperia.ac.uk), from annotated sequences available on Genbank
+(http://www.ncbi.nlm.nih.gov/Genbank/).
+}
+\description{
+The dataset \code{H3N2} consists of 1903 strains of seasonal influenza
+(H3N2) distributed worldwide, and typed at 125 SNPs located in the
+hemagglutinin (HA) segment. It is stored as an R object with class
+\linkS4class{genind} and can be accessed as usual using \code{data(H3N2)}
+(see example). These data were gathered from DNA sequences available from
+Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).
+}
+\details{
+The data file \code{usflu.fasta} is a toy dataset also gathered from
+Genbank, consisting of the aligned sequences of 80 seasonal influenza
+isolates (HA segment) sampled in the US, in \code{fasta} format. This file
+is installed alongside the package; the path to this file is automatically
+determined by R using \code{system.file} (see example in this manpage and in
+?fasta2genlight) as well.
+}
+\examples{
+
+\dontrun{
+#### H3N2 ####
+## LOAD DATA
+data(H3N2)
+H3N2
+
+## set population to yearly epidemics
+pop(H3N2) <- factor(H3N2$other$epid)
+
+
+
+## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
+## to reproduce exactly analyses from the paper, use "n.pca=1000"
+dapc1 <- dapc(H3N2, all.contrib=TRUE, scale=FALSE, n.pca=150, n.da=5)
+dapc1
+
+## (see ?dapc for details about the output)
+
+
+## SCREEPLOT OF EIGENVALUES
+barplot(dapc1$eig, main="H3N2 - DAPC eigenvalues")
+
+
+## SCATTERPLOT (axes 1-2)
+scatter(dapc1, posi.da="topleft", cstar=FALSE, cex=2, pch=17:22,
+solid=.5, bg="white")
+
+
+
+
+#### usflu.fasta ####
+myPath <- system.file("files/usflu.fasta",package="adegenet")
+myPath
+
+## extract SNPs from alignments using fasta2genlight
+## see ?fasta2genlight for more details
+obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time
+obj
+}
+
+}
+\references{
+Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis
+of principal components: a new method for the analysis of genetically
+structured populations. Submitted to \emph{BMC genetics}.
+}
+\keyword{datasets}
+
diff --git a/man/HWE.Rd b/man/HWE.Rd
new file mode 100644
index 0000000..a86d5f6
--- /dev/null
+++ b/man/HWE.Rd
@@ -0,0 +1,70 @@
+\encoding{UTF-8}
+\name{HWE.test.genind}
+\alias{HWE.test.genind}
+
+\title{Hardy-Weinberg Equilibrium test for multilocus data}
+\description{The function \code{HWE.test} is a generic function to
+ perform Hardy-Weinberg Equilibrium tests defined by the
+ \code{genetics} package. adegenet proposes a method for \code{genind}
+ objects.\cr
+
+ The output can be of two forms:\cr
+ - a list of tests (class \code{htest}) for each locus-population
+ combinaison \cr
+ - a population x locus matrix containing p-values of the tests
+}
+\usage{
+\method{HWE.test}{genind}(x,pop=NULL,permut=FALSE,nsim=1999,hide.NA=TRUE,res.type=c("full","matrix"))
+}
+\arguments{
+ \item{x}{an object of class \code{genind}.}
+ \item{pop}{a factor giving the population of each individual. If NULL,
+ pop is seeked from x\$pop.}
+ \item{permut}{a logical passed to \code{HWE.test} stating whether
+ Monte Carlo version (TRUE) should be used or not (FALSE, default).}
+ \item{nsim}{number of simulations if Monte Carlo is used (passed to \code{HWE.test}).}
+ \item{hide.NA}{a logical stating whether non-tested loci (e.g., when
+ an allele is fixed) should be hidden in the results (TRUE, default)
+ or not (FALSE).}
+ \item{res.type}{a character or a character vector whose only first
+ argument is considered giving the type of result to display. If
+ "full", then a list of complete tests is returned. If "matrix",
+ then a matrix of p-values is returned.}
+}
+\details{Monte Carlo procedure is quiet computer-intensive when large
+ datasets are involved. For more precision on the performed test, read
+ \code{HWE.test} documentation (\code{genetics} package).
+}
+\value{Returns either a list of tests or a matrix of p-values. In the
+ first case, each test is designated by locus first and then by
+ population. For instance if \code{res} is the "full" output of the
+ function, then the test for population "PopA" at locus "Myloc" is
+ given by res$Myloc$PopA. If \code{res} is a matrix of p-values,
+ populations are in rows and loci in columns. P-values are given for
+ the upper-tail: they correspond to the probability that an oberved
+ chi-square statistic as high as or higher than the one observed
+ occured under H0 (HWE).\cr
+
+ In all cases, NA values are likely to appear in fixed loci, or
+ entirely non-typed loci.
+}
+\seealso{\code{HWE.test} in the \code{genetics} package, \code{\link[stats]{chisq.test}}
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+data(nancycats)
+obj <- nancycats
+if(require(genetics)){
+obj.test <- HWE.test(obj)
+
+# pvalues matrix to have a preview
+HWE.test(obj,res.type="matrix")
+
+#more precise view to...
+obj.test$fca90$P10
+}
+}
+}
+\keyword{manip}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/Hs.Rd b/man/Hs.Rd
new file mode 100644
index 0000000..108068d
--- /dev/null
+++ b/man/Hs.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Hs.R
+\name{Hs}
+\alias{Hs}
+\title{Expected heterozygosity (Hs)}
+\usage{
+Hs(x, pop = NULL)
+}
+\arguments{
+\item{x}{a \linkS4class{genind} or \linkS4class{genpop} object.}
+
+\item{pop}{only used if x is a \linkS4class{genind}; an optional factor to be used as population; if not provided, pop(x) is used.}
+}
+\value{
+a vector of Hs values (one value per population)
+}
+\description{
+This function computes the expected heterozygosity (Hs) within
+populations of a \linkS4class{genpop} object. This function is
+available for codominant markers (\code{@type="codom"}) only. Hs is
+commonly used for measuring within population genetic diversity (and
+as such, it still has sense when computed from haploid data).
+}
+\details{
+Let \emph{m(k)} be the number of alleles of locus \emph{k}, with a
+total of \emph{K} loci. We note \eqn{f_i} the allele frequency of
+allele \emph{i} in a given population. Then, \eqn{Hs} is given for a
+given population by:\cr
+
+\eqn{\frac{1}{K} \sum_{k=1}^K (1 - \sum_{i=1}^{m(k)} f_i^2)}
+}
+\examples{
+\dontrun{
+data(nancycats)
+Hs(genind2genpop(nancycats))
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{Hs.test}} to test differences in Hs between two groups
+}
+
diff --git a/man/Hs.test.Rd b/man/Hs.test.Rd
new file mode 100644
index 0000000..f21d8f8
--- /dev/null
+++ b/man/Hs.test.Rd
@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Hs.R
+\name{Hs.test}
+\alias{Hs.test}
+\title{Test differences in expected heterozygosity (Hs)}
+\usage{
+Hs.test(x, y, n.sim = 999, alter = c("two-sided", "greater", "less"))
+}
+\arguments{
+\item{x}{a \linkS4class{genind} object.}
+
+\item{y}{a \linkS4class{genind} object.}
+
+\item{n.sim}{the number of permutations to be used to generate the reference distribution.}
+
+\item{alter}{a character string indicating the alternative hypothesis}
+}
+\value{
+an object of the class randtest
+}
+\description{
+This procedure permits to test if two groups have
+significant differences in expected heterozygosity (Hs).
+The test statistic used is simply the difference in Hs
+between the two groups 'x' and 'y':
+}
+\details{
+\eqn{Hs(x) - Hs(y)}
+
+Individuals are randomly permuted between groups to obtain
+a reference distribution of the test statistics.
+}
+\examples{
+\dontrun{
+data(microbov)
+Hs(microbov)
+test <- Hs.test(microbov[pop="Borgou"],
+ microbov[pop="Lagunaire"],
+ n.sim=499)
+test
+plot(test)
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{Hs}} to compute Hs for different populations;
+\code{\link[ade4]{as.randtest}} for the class of Monte Carlo tests.
+}
+
diff --git a/man/SNPbin.Rd b/man/SNPbin.Rd
new file mode 100644
index 0000000..3dab5ec
--- /dev/null
+++ b/man/SNPbin.Rd
@@ -0,0 +1,164 @@
+\name{SNPbin-class}
+\docType{class}
+\alias{SNPbin}
+\alias{SNPbin-class}
+\alias{[,SNPbin-method}
+\alias{[,SNPbin,ANY,ANY-method}
+\alias{[,SNPbin,ANY,ANY,ANY-method}
+\alias{initialize,SNPbin-method}
+\alias{show,SNPbin-method}
+\alias{nLoc,SNPbin-method}
+\alias{$,SNPbin-method}
+\alias{$<-,SNPbin-method}
+\alias{names,SNPbin-method}
+\alias{ploidy,SNPbin-method}
+\alias{ploidy<-,SNPbin-method}
+\alias{coerce,SNPbin,integer-method}
+\alias{as.integer.SNPbin}
+\alias{NA.posi,SNPbin-method}
+\alias{cbind.SNPbin}
+\alias{c.SNPbin}
+\alias{as,integer,SNPbin-method}
+\alias{as,numeric,SNPbin-method}
+
+
+% \alias{,SNPbin-method}
+% \alias{,SNPbin-method}
+% \alias{,SNPbin-method}
+% \alias{,SNPbin-method}
+%%%%
+\title{Formal class "SNPbin"}
+\description{
+ The class \code{SNPbin} is a formal (S4) class for storing a genotype
+ of binary SNPs in a compact way, using a bit-level coding scheme.
+ This storage is most efficient with haploid data, where the memory
+ taken to represent data can reduced more than 50 times. However,
+ \code{SNPbin} can be used for any level of ploidy, and still remain an
+ efficient storage mode.
+
+ A \code{SNPbin} object can be constructed from
+ a vector of integers giving the number of the second allele for each
+ locus.
+
+ \code{SNPbin} stores a single genotype. To store multiple genotypes,
+ use the \linkS4class{genlight} class.
+}
+\section{Objects from the class SNPbin}{
+ \code{SNPbin} objects can be created by calls to \code{new("SNPbin",
+ ...)}, where '...' can be the following arguments:
+
+ \describe{
+ \item{\code{snp}}{a vector of integers or numeric giving numbers of
+ copies of the second alleles for each locus. If only one unnamed
+ argument is provided to 'new', it is considered as this one.}
+ \item{\code{ploidy}}{an integer indicating the ploidy of the
+ genotype; if not provided, will be guessed from the data (as the
+ maximum from the 'snp' input vector).}
+ \item{\code{label}}{an optional character string serving as a label
+ for the genotype.}
+ }
+}
+\section{Slots}{
+ The following slots are the content of instances of the class
+ \code{SNPbin}; note that in most cases, it is better to retrieve
+ information via accessors (see below), rather than by accessing the
+ slots manually.
+ \describe{
+ \item{\code{snp}:}{a list of vectors with the class \code{raw}.}
+ \item{\code{n.loc}:}{an integer indicating the number of SNPs of the
+ genotype.}
+ \item{\code{NA.posi}:}{a vector of integer giving the position of
+ missing data.}
+ \item{\code{label}:}{an optional character string serving as a label
+ for the genotype..}
+ \item{\code{ploidy}:}{an integer indicating the ploidy of the genotype.}
+ }
+}
+\section{Methods}{
+ Here is a list of methods available for \code{SNPbin} objects. Most of
+ these methods are accessors, that is, functions which are used to
+ retrieve the content of the object. Specific manpages can exist for
+ accessors with more than one argument. These are indicated by a '*'
+ symbol next to the method's name. This list also contains methods
+ for conversion from \code{SNPbin} to other classes.
+ \describe{
+ \item{[}{\code{signature(x = "SNPbin")}: usual method to subset
+ objects in R. The argument indicates how SNPs are to be
+ subsetted. It can be a vector of signed integers or of logicals.}
+ \item{show}{\code{signature(x = "SNPbin")}: printing of the
+ object.}
+ \item{$}{\code{signature(x = "SNPbin")}: similar to the @ operator;
+ used to access the content of slots of the object.}
+ \item{$<-}{\code{signature(x = "SNPbin")}: similar to the @ operator;
+ used to replace the content of slots of the object.}
+ \item{nLoc}{\code{signature(x = "SNPbin")}: returns the number of
+ SNPs in the object.}
+ \item{names}{\code{signature(x = "SNPbin")}: returns the names of
+ the slots of the object.}
+ \item{ploidy}{\code{signature(x = "SNPbin")}: returns the ploidy of
+ the genotype.}
+ \item{as.integer}{\code{signature(x = "SNPbin")}: converts a
+ \code{SNPbin} object to a vector of integers. The S4 method 'as' can
+ be used as well (e.g. as(x, "integer")).}
+ \item{cbind}{\code{signature(x = "SNPbin")}: merges genotyping of
+ the same individual at different SNPs (all stored as
+ \linkS4class{SNPbin} objects) into a single \linkS4class{SNPbin}.}
+ \item{c}{\code{signature(x = "SNPbin")}: same as cbind.SNPbin.}
+ }
+}
+\author{Thibaut Jombart (\email{t.jombart at imperial.ac.uk})}
+\seealso{
+ Related class:\cr
+ - \code{\linkS4class{genlight}}, for storing multiple binary SNP
+ genotypes. \cr
+ - \code{\linkS4class{genind}}, for storing other types of genetic markers. \cr
+}
+\examples{
+\dontrun{
+#### HAPLOID EXAMPLE ####
+## create a genotype of 100,000 SNPs
+dat <- sample(c(0,1,NA), 1e5, prob=c(.495, .495, .01), replace=TRUE)
+dat[1:10]
+x <- new("SNPbin", dat)
+x
+x[1:10] # subsetting
+as.integer(x[1:10])
+
+## try a few accessors
+ploidy(x)
+nLoc(x)
+head(x$snp[[1]]) # internal bit-level coding
+
+## check that conversion is OK
+identical(as(x, "integer"),as.integer(dat)) # SHOULD BE TRUE
+
+## compare the size of the objects
+print(object.size(dat), unit="auto")
+print(object.size(x), unit="auto")
+object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
+
+
+#### TETRAPLOID EXAMPLE ####
+## create a genotype of 100,000 SNPs
+dat <- sample(c(0:4,NA), 1e5, prob=c(rep(.995/5,5), 0.005), replace=TRUE)
+x <- new("SNPbin", dat)
+identical(as(x, "integer"),as.integer(dat)) # MUST BE TRUE
+
+## compare the size of the objects
+print(object.size(dat), unit="auto")
+print(object.size(x), unit="auto")
+object.size(dat)/object.size(x) # EFFICIENCY OF CONVERSION
+
+
+#### c, cbind ####
+a <- new("SNPbin", c(1,1,1,1,1))
+b <- new("SNPbin", c(0,0,0,0,0))
+a
+b
+ab <- c(a,b)
+ab
+identical(c(a,b),cbind(a,b))
+as.integer(ab)
+}
+}
+\keyword{classes}
diff --git a/man/accessors.Rd b/man/accessors.Rd
new file mode 100644
index 0000000..3f3ff94
--- /dev/null
+++ b/man/accessors.Rd
@@ -0,0 +1,243 @@
+\encoding{UTF-8}
+\docType{methods}
+\name{Accessors}
+\alias{$,genind-method}
+\alias{$,genpop-method}
+\alias{$<-,genind-method}
+\alias{$<-,genpop-method}
+\alias{[,genind-method}
+\alias{[,genind,ANY,ANY,ANY-method}
+\alias{[,genpop-method}
+\alias{[,genpop,ANY,ANY,ANY-method}
+\alias{nLoc}
+\alias{nLoc,gen-method}
+\alias{nLoc,genind-method}
+\alias{nLoc,genpop-method}
+\alias{locFac}
+\alias{locFac,gen-method}
+\alias{locFac,genind-method}
+\alias{locFac,genpop-method}
+\alias{nAll}
+\alias{nAll,gen-method}
+\alias{nAll,genind-method}
+\alias{nAll,genpop-method}
+\alias{nPop}
+\alias{nPop,genind-method}
+\alias{nPop,genpop-method}
+\alias{nInd}
+\alias{nInd,genind-method}
+\alias{pop}
+\alias{pop<-}
+\alias{pop,genind-method}
+\alias{pop<-,gen-method}
+\alias{pop<-,genind-method}
+\alias{locNames}
+\alias{locNames,gen-method}
+\alias{locNames,genind-method}
+\alias{locNames,genpop-method}
+\alias{locNames<-}
+\alias{locNames<-,gen-method}
+\alias{locNames<-,genind-method}
+\alias{locNames<-,genpop-method}
+\alias{popNames}
+\alias{popNames,genind-method}
+\alias{popNames,genpop-method}
+\alias{popNames<-}
+\alias{popNames<-,genind-method}
+\alias{popNames<-,genpop-method}
+\alias{indNames}
+\alias{indNames,genind-method}
+\alias{indNames<-}
+\alias{indNames<-,genind-method}
+\alias{ploidy}
+\alias{ploidy,genind-method}
+\alias{ploidy,genpop-method}
+\alias{ploidy<-}
+\alias{ploidy<-,genind-method}
+\alias{ploidy<-,genpop-method}
+\alias{alleles}
+\alias{alleles,gen-method}
+\alias{alleles,genind-method}
+\alias{alleles,genpop-method}
+\alias{alleles<-}
+\alias{alleles<-,gen-method}
+\alias{alleles<-,genind-method}
+\alias{alleles<-,genpop-method}
+\alias{other}
+\alias{other,gen-method}
+\alias{other,genind-method}
+\alias{other,genpop-method}
+\alias{other<-}
+\alias{other<-,gen-method}
+\alias{other<-,genind-method}
+\alias{other<-,genpop-method}
+
+\title{Accessors for adegenet objects}
+\description{
+ An accessor is a function that allows to interact with slots of an
+ object in a convenient way. Several accessors are available for \linkS4class{genind} or
+ \linkS4class{genpop} objects. The operator "\$" and "\$<-" are used to
+ access the slots, being equivalent to "@" and "@<-".\cr
+
+ The operator "[" is a flexible way to subset data by individuals,
+ populations, alleles, and loci. When using a matrix-like syntax,
+ subsetting will apply to the dimensios of the @tab slot. In addition,
+ specific arguments \code{loc} and \code{pop} can be used to indicate
+ subsets of loci and populations. The argument \code{drop} is a logical
+ indicating if alleles becoming non-polymorphic in a new dataset should
+ be removed (default: FALSE). Examples:\cr
+ \itemize{
+ \item "obj[i,j]" returns "obj" with a subset 'i' of individuals and 'j' of
+ alleles.\cr
+
+ \item "obj[1:10,]" returns an object with only the first 10 genotypes (if
+ "obj" is a \linkS4class{genind}) or the first 10 populations (if
+ "obj" is a \linkS4class{genpop}) \cr
+
+ \item "obj[1:10, 5:10]" returns an object keeping the first 10 entities and
+ the alleles 5 to 10.\cr
+
+ \item "obj[loc=c(1,3)]" returns an object keeping only the 1st and 3rd
+ loci, using \code{locNames(obj)} as reference; logicals, or named loci
+ also work; this overrides other subsetting of alleles.\cr
+
+ \item "obj[pop=2:4]" returns an object keeping only individuals from the
+ populations 2, 3 and 4, using \code{popNames(obj)} as reference;
+ logicals, or named populations also work; this overrides other
+ subsetting of individuals.\cr
+
+ \item "obj[i=1:2, drop=TRUE]" returns an object keeping only the first
+ two individuals (or populations), dropping the alleles no longer
+ present in the data.\cr
+}
+ The argument \code{treatOther} handles the treatment of objects in the
+ \code{@other} slot (see details). The argument \code{drop} can be set
+ to TRUE to drop alleles that are no longer represented in the subset.
+}
+\section{Methods}{
+ \describe{
+ \item{nInd}{returns the number of individuals in the \code{genind} object}
+ \item{nLoc}{returns the number of loci}
+ \item{nAll}{returns the number of alleles in each locus}
+ \item{nPop}{returns the number of populations}
+ \item{pop}{returns a factor assigning individuals to populations.}
+ \item{pop<-}{replacement method for the \code{@pop} slot of an
+ object.}
+ \item{popNames}{returns the names of populations.}
+ \item{popNames<-}{sets the names of populations using a vector of
+ length \code{nPop(x)}.}
+ \item{indNames}{returns the names of individuals.}
+ \item{indNames<-}{sets the names of individuals using a vector of
+ length \code{nInd(x)}.}
+ \item{locNames}{returns the names of markers and/or alleles.}
+ \item{locNames<-}{sets the names of markers using a vector of
+ length \code{nLoc(x)}.}
+ \item{locFac}{returns a factor that defines which locus each column of the \code{@tab} slot belongs to}
+ \item{ploidy}{returns the ploidy of the data.}
+ \item{ploidy<-}{sets the ploidy of the data using an integer.}
+ \item{alleles}{returns the alleles of each locus.}
+ \item{alleles<-}{sets the alleles of each locus using a list with
+ one character vector for each locus.}
+ \item{other}{returns the content of the \code{@other} slot
+ (misc. information); returns \code{NULL} if the slot is empty or of
+ length zero.}
+ \item{other<-}{sets the content of the \code{@other} slot
+ (misc. information); the provided value needs to be a list; it
+ not, provided value will be stored within a list.}
+ }
+}
+\usage{
+nInd(x, \dots)
+nLoc(x, \dots)
+nPop(x, \dots)
+pop(x)
+indNames(x, \dots)
+\S4method{indNames}{genind}(x, \dots)
+locNames(x, \dots)
+\S4method{locNames}{genind}(x, withAlleles=FALSE, \dots)
+\S4method{locNames}{genpop}(x, withAlleles=FALSE, \dots)
+popNames(x, \dots)
+\S4method{popNames}{genind}(x, \dots)
+popNames(x, \dots)
+\S4method{popNames}{genpop}(x, \dots)
+ploidy(x, \dots)
+\S4method{ploidy}{genind}(x, \dots)
+\S4method{ploidy}{genpop}(x, \dots)
+\S4method{other}{genind}(x, \dots)
+\S4method{other}{genpop}(x, \dots)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} or a \linkS4class{genpop} object.}
+ \item{withAlleles}{a logical indicating whether the result should be
+ of the form [locus name].[allele name], instead of [locus name].}
+ \item{\dots}{further arguments to be passed to other methods
+ (currently not used).}
+}
+\value{
+ A \linkS4class{genind} or \linkS4class{genpop} object.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\details{
+ The "[" operator can treat elements in the \code{@other} slot as
+ well. For instance, if \code{obj at other$xy} contains spatial
+ coordinates, the \code{obj[1:3, ]@other$xy} will contain the spatial
+ coordinates of the genotypes (or population) 1,2 and 3. This is
+ handled through the argument \code{treatOther}, a logical defaulting
+ to TRUE. If set to FALSE, the \code{@other} returned unmodified.\cr
+
+ Note that only matrix-like, vector-like and lists can be proceeded in
+ \code{@other}. Other kind of objects will issue a warning an be
+ returned as they are, unless the argument \code{quiet} is left to
+ TRUE, its default value.\cr
+
+ The \code{drop} argument can be set to TRUE to retain only alleles
+ that are present in the subset. To achieve better control of
+ polymorphism of the data, see \code{\link{isPoly}}.
+}
+\examples{
+data(nancycats)
+nancycats
+pop(nancycats) # get the populations
+indNames(nancycats) # get the labels of individuals
+locNames(nancycats) # get the labels of the loci
+alleles(nancycats) # get the alleles
+
+head(tab(nancycats)) # get allele counts
+
+# get allele frequencies, replace NAs
+head(tab(nancycats, freq = TRUE, NA.method = "mean"))
+
+# let's isolate populations 4 and 8
+popNames(nancycats)
+obj <- nancycats[pop=c(4,8)]
+obj
+popNames(obj)
+pop(obj)
+
+# let's isolate two markers, fca23 and fca90
+locNames(nancycats)
+obj <- nancycats[loc=c("fca23","fca90")]
+obj
+locNames(obj)
+
+# illustrate pop
+obj <- nancycats[sample(1:100, 10)]
+pop(obj)
+pop(obj) <- rep(c('b', 'a'), each = 5)
+pop(obj)
+
+# illustrate locNames
+locNames(obj)
+locNames(obj, withAlleles = TRUE)
+locNames(obj)[1] <- "newLocus"
+locNames(obj)
+locNames(obj, withAlleles=TRUE)
+
+# illustrate how 'other' slot is handled
+data(sim2pop)
+nInd(sim2pop)
+other(sim2pop[1:6]) # xy is subsetted automatically
+other(sim2pop[1:6, treatOther=FALSE]) # xy is left as is
+
+}
+\keyword{manip}
diff --git a/man/adegenet.package.Rd b/man/adegenet.package.Rd
new file mode 100644
index 0000000..63bc2bb
--- /dev/null
+++ b/man/adegenet.package.Rd
@@ -0,0 +1,210 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/adegenet.package.R
+\docType{package}
+\encoding{utf-8}
+\name{adegenet.package}
+\alias{adegenet}
+\alias{adegenet.package}
+\alias{adegenet.package-package}
+\title{The adegenet package}
+\description{
+This package is devoted to the multivariate analysis of genetic markers
+data. These data can be codominant markers (e.g. microsatellites) or
+presence/absence data (e.g. AFLP), and have any level of ploidy. 'adegenet'
+defines three formal (S4) classes:\cr - \linkS4class{genind}: a class for
+data of individuals ("genind" stands for genotypes-individuals).\cr -
+\linkS4class{genpop}: a class for data of groups of individuals ("genpop"
+stands for genotypes-populations)\cr - \linkS4class{genlight}: a class for
+genome-wide SNP data\cr
+}
+\details{
+For more information about these classes, type "class ? genind", "class ?
+genpop", or "?genlight".\cr
+
+Essential functionalities of the package are presented througout 4
+tutorials, accessible using \code{adegenetTutorial(which="name-below")}:\cr
+- \code{basics}: introduction to the package.\cr - \code{spca}: multivariate
+analysis of spatial genetic patterns.\cr - \code{dapc}: population structure
+and group assignment using DAPC.\cr - \code{genomics}: introduction to the
+class \linkS4class{genlight} for the handling and analysis of genome-wide
+SNP data.\cr
+
+Note: In older versions of adegenet, these tutorials were avilable as
+vignettes, accessible through the function \code{vignette("name-below",
+package="adegenet")}:\cr - \code{adegenet-basics}.\cr -
+\code{adegenet-spca}.\cr - \code{adegenet-dapc}.\cr -
+\code{adegenet-genomics}.\cr
+
+Important functions are also summarized below.\cr
+
+=== IMPORTING DATA ===\cr = TO GENIND OBJECTS = \cr \code{adegenet} imports
+data to \linkS4class{genind} object from the following softwares:\cr -
+STRUCTURE: see \code{\link{read.structure}}\cr - GENETIX: see
+\code{\link{read.genetix}}\cr - FSTAT: see \code{\link{read.fstat}}\cr -
+Genepop: see \code{\link{read.genepop}}\cr To import data from any of these
+formats, you can also use the general function
+\code{\link{import2genind}}.\cr
+
+In addition, it can extract polymorphic sites from nucleotide and amino-acid
+alignments:\cr - DNA files: use \code{\link[ape]{read.dna}} from the ape
+package, and then extract SNPs from DNA alignments using
+\code{\link{DNAbin2genind}}. \cr
+
+- protein sequences alignments: polymorphic sites can be extracted from
+protein sequences alignments in \code{alignment} format (package
+\code{seqinr}, see \code{\link[seqinr]{as.alignment}}) using the function
+\code{\link{alignment2genind}}. \cr
+
+The function \code{\link{fasta2DNAbin}} allows for reading fasta files into
+DNAbin object with minimum RAM requirements.\cr
+
+It is also possible to read genotypes coded by character strings from a
+data.frame in which genotypes are in rows, markers in columns. For this, use
+\code{\link{df2genind}}. Note that \code{\link{df2genind}} can be used for
+any level of ploidy.\cr
+
+= TO GENLIGHT OBJECTS = \cr SNP data can be read from the following
+formats:\cr - PLINK: see function \code{\link{read.PLINK}}\cr - .snp
+(adegenet's own format): see function \code{\link{read.snp}}\cr
+
+SNP can also be extracted from aligned DNA sequences with the fasta format,
+using \code{\link{fasta2genlight}}\cr
+
+=== EXPORTING DATA ===\cr \code{adegenet} exports data from
+
+Genotypes can also be recoded from a \linkS4class{genind} object into a
+data.frame of character strings, using any separator between alleles. This
+covers formats from many softwares like GENETIX or STRUCTURE. For this, see
+\code{\link{genind2df}}.\cr
+
+Also note that the \code{pegas} package imports \linkS4class{genind} objects
+using the function \code{as.loci}.
+
+=== MANIPULATING DATA ===\cr Several functions allow one to manipulate
+\linkS4class{genind} or \linkS4class{genpop} objects\cr -
+\code{\link{genind2genpop}}: convert a \linkS4class{genind} object to a
+\linkS4class{genpop} \cr - \code{\link{seploc}}: creates one object per
+marker; for \linkS4class{genlight} objects, creates blocks of SNPs.\cr -
+\code{\link{seppop}}: creates one object per population \cr -
+- \code{\link{tab}}: access the allele data (counts or frequencies) of an object
+(\linkS4class{genind} and \linkS4class{genpop}) \cr -
+x[i,j]: create a new object keeping only genotypes (or populations) indexed
+by 'i' and the alleles indexed by 'j'.\cr - \code{\link{makefreq}}: returns
+a table of allelic frequencies from a \linkS4class{genpop} object.\cr -
+\code{\link{repool}} merges genoptypes from different gene pools into one
+single \linkS4class{genind} object.\cr - \code{\link{propTyped}} returns the
+proportion of available (typed) data, by individual, population, and/or
+locus.\cr - \code{\link{selPopSize}} subsets data, retaining only genotypes
+from a population whose sample size is above a given level.\cr -
+\code{\link{pop}} sets the population of a set of genotypes.\cr
+
+=== ANALYZING DATA ===\cr Several functions allow to use usual, and less
+usual analyses:\cr - \code{\link{HWE.test.genind}}: performs HWE test for
+all populations and loci combinations \cr - \code{\link{dist.genpop}}: computes 5 genetic distances among populations.
+\cr - \code{\link{monmonier}}: implementation of the Monmonier algorithm,
+used to seek genetic boundaries among individuals or populations. Optimized
+boundaries can be obtained using \code{\link{optimize.monmonier}}. Object of
+the class \code{monmonier} can be plotted and printed using the
+corresponding methods. \cr - \code{\link{spca}}: implements Jombart et al.
+(2008) spatial Principal Component Analysis \cr -
+\code{\link{global.rtest}}: implements Jombart et al. (2008) test for global
+spatial structures \cr - \code{\link{local.rtest}}: implements Jombart et
+al. (2008) test for local spatial structures \cr - \code{\link{propShared}}:
+computes the proportion of shared alleles in a set of genotypes (i.e. from a
+genind object)\cr - \code{\link{propTyped}}: function to investigate missing
+data in several ways \cr - \code{\link{scaleGen}}: generic method to scale
+\linkS4class{genind} or \linkS4class{genpop} before a principal component
+analysis \cr - \code{\link{Hs}}: computes the average expected
+heterozygosity by population in a \linkS4class{genpop}. Classically Used as
+a measure of genetic diversity.\cr - \code{\link{find.clusters}} and
+\code{\link{dapc}}: implement the Discriminant Analysis of Principal
+Component (DAPC, Jombart et al., 2010).\cr - \code{\link{seqTrack}}:
+implements the SeqTrack algorithm for recontructing transmission trees of
+pathogens (Jombart et al., 2010) .\cr \code{\link{glPca}}: implements PCA
+for \linkS4class{genlight} objects.\cr - \code{\link{gengraph}}: implements
+some simple graph-based clustering using genetic data. -
+\code{\link{snpposi.plot}} and \code{\link{snpposi.test}}: visualize the
+distribution of SNPs on a genetic sequence and test their randomness. -
+\code{\link{adegenetServer}}: opens up a web interface for some
+functionalities of the package (DAPC with cross validation and feature
+selection).\cr
+
+=== GRAPHICS ===\cr - \code{\link{colorplot}}: plots points with associated
+values for up to three variables represented by colors using the RGB system;
+useful for spatial mapping of principal components.\cr -
+\code{\link{loadingplot}}: plots loadings of variables. Useful for
+representing the contribution of alleles to a given principal component in a
+multivariate method. \cr - \code{\link{scatter.dapc}}: scatterplots for DAPC
+results.\cr - \code{\link{compoplot}}: plots membership probabilities from a
+DAPC object. \cr
+
+=== SIMULATING DATA ===\cr - \code{\link{hybridize}}: implements
+hybridization between two populations. \cr - \code{\link{haploGen}}:
+simulates genealogies of haplotypes, storing full genomes. \cr
+\code{\link{glSim}}: simulates simple \linkS4class{genlight} objects.\cr
+
+=== DATASETS ===\cr - \code{\link{H3N2}}: Seasonal influenza (H3N2) HA
+segment data. \cr - \code{\link{dapcIllus}}: Simulated data illustrating the
+DAPC. \cr - \code{\link{eHGDP}}: Extended HGDP-CEPH dataset. \cr -
+\code{\link{microbov}}: Microsatellites genotypes of 15 cattle breeds. \cr -
+\code{\link{nancycats}}: Microsatellites genotypes of 237 cats from 17
+colonies of Nancy (France). \cr - \code{\link{rupica}}: Microsatellites
+genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains
+(France).\cr - \code{\link{sim2pop}}: Simulated genotypes of two
+georeferenced populations.\cr - \code{\link{spcaIllus}}: Simulated data
+illustrating the sPCA. \cr
+
+For more information, visit the adegenet website using the function
+\code{\link{adegenetWeb}}.\cr
+
+Tutorials are available via the command \code{adegenetTutorial}.\cr
+
+To cite adegenet, please use the reference given by
+\code{citation("adegenet")} (or see references below).
+}
+\author{
+Thibaut Jombart <t.jombart at imperial.ac.uk>\cr
+Developers: Zhian N. Kamvar <zkamvar at gmail.com>,
+Caitlin Collins <caitiecollins17 at gmail.com>,
+Ismail Ahmed <ismail.ahmed at inserm.fr>,
+Federico Calboli, Tobias Erik Reiners, Peter
+Solymos, Anne Cori, \cr Contributed datasets from: Katayoun
+Moazami-Goudarzi, Denis Laloë, Dominique Pontier, Daniel Maillard, Francois
+Balloux.
+}
+\references{
+Jombart T. (2008) adegenet: a R package for the multivariate
+analysis of genetic markers \emph{Bioinformatics} 24: 1403-1405. doi:
+10.1093/bioinformatics/btn129\cr
+
+Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of
+genome-wide SNP data. \emph{Bioinformatics}. doi:
+10.1093/bioinformatics/btr521
+
+Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+principal components: a new method for the analysis of genetically
+structured populations. BMC Genetics 11:94. doi:10.1186/1471-2156-11-94\cr
+
+Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease outbreaks
+from genetic data: a graph approach. \emph{Heredity}. doi:
+10.1038/hdy.2010.78.\cr
+
+Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. (2008) Revealing
+cryptic spatial patterns in genetic variability by a new multivariate
+method. \emph{Heredity}, \bold{101}, 92--103.\cr
+
+See adegenet website: \url{http://adegenet.r-forge.r-project.org/}\cr
+
+Please post your questions on 'the adegenet forum':
+adegenet-forum at lists.r-forge.r-project.org
+}
+\seealso{
+adegenet is related to several packages, in particular:\cr -
+\code{ade4} for multivariate analysis\cr - \code{pegas} for population
+genetics tools\cr - \code{ape} for phylogenetics and DNA data handling\cr -
+\code{seqinr} for handling nucleic and proteic sequences\cr - \code{shiny}
+for R-based web interfaces\cr
+}
+\keyword{manip}
+\keyword{multivariate}
+
diff --git a/man/as-methods.Rd b/man/as-methods.Rd
new file mode 100644
index 0000000..e2aae08
--- /dev/null
+++ b/man/as-methods.Rd
@@ -0,0 +1,75 @@
+\name{as methods in adegenet}
+\docType{methods}
+\alias{as-method}
+\alias{as,genind,data.frame-method}
+\alias{as,genpop,data.frame-method}
+\alias{as,genind,matrix-method}
+\alias{as,genpop,matrix-method}
+\alias{as,genind,genpop-method}
+\alias{ktab-class}
+\alias{as,genind,ktab-method}
+\alias{as,genpop,ktab-method}
+\alias{coerce,genind,data.frame-method}
+\alias{coerce,genpop,data.frame-method}
+\alias{coerce,genind,matrix-method}
+\alias{coerce,genpop,matrix-method}
+\alias{coerce,genind,genpop-method}
+\alias{coerce,genind,ktab-method}
+\alias{coerce,genpop,ktab-method}
+\alias{as.data.frame.genind}
+\alias{as.data.frame.genpop}
+\alias{as.matrix.genind}
+\alias{as.matrix.genpop}
+\alias{as.genpop.genind}
+\alias{as.ktab.genind}
+\alias{as.ktab.genpop}
+\title{Converting genind/genpop objects to other classes}
+\description{
+ These S3 and S4 methods are used to coerce \linkS4class{genind} and
+ \linkS4class{genpop} objects to matrix-like objects. In most cases,
+ this is equivalent to calling the \code{@tab} slot. An exception to
+ this is the convertion to \code{\link[ade4]{ktab}} objects used in the
+ ade4 package as inputs for K-tables methods (e.g. Multiple Coinertia
+ Analysis).\cr
+}
+\section{Usage}{
+\code{as(object, Class)}
+}
+\section{Arguments}{
+\describe{
+ \item{\code{object}}{a \linkS4class{genind} or a \linkS4class{genpop} object.}
+ \item{\code{Class}}{the name of the class to which the object should
+ be coerced, for instance \code{"data.frame"} or \code{"matrix"}.}
+}
+}
+\section{Methods}{
+\describe{
+ \item{coerce}{from one object class to another using
+ \code{as(object,"Class")}, where the \code{object} is of the old
+ class and the returned object is of the new class \code{"Class"}.}
+}
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
+\examples{
+\dontrun{
+data(microbov)
+x <- tab(microbov,NA.method="mean")
+as(x[1:3],"data.frame")
+
+## dudi functions attempt to convert their first argument
+## to a data.frame; so they can be used on genind/genpop objects.
+## perform a PCA
+pca1 <- dudi.pca(x, scale=FALSE, scannf=FALSE)
+pca1
+
+x <- genind2genpop(microbov,miss="chi2")
+x <- as(x,"ktab")
+class(x)
+## perform a STATIS analysis
+statis1 <- statis(x, scannf=FALSE)
+statis1
+plot(statis1)
+
+}
+}
+\keyword{methods}
\ No newline at end of file
diff --git a/man/as.SNPbin.Rd b/man/as.SNPbin.Rd
new file mode 100644
index 0000000..d7e72b8
--- /dev/null
+++ b/man/as.SNPbin.Rd
@@ -0,0 +1,56 @@
+\name{as.SNPbin}
+\alias{as,SNPbin,integer-method}
+\alias{as,SNPbin,numeric-method}
+\alias{as.SNPbin}
+\alias{as.SNPbin,integer-method}
+\alias{as.SNPbin,numeric-method}
+\alias{coerce,integer,SNPbin-method}
+\alias{coerce,numeric,SNPbin-method}
+
+% \alias{,SNPbin-method}
+% \alias{,SNPbin-method}
+% \alias{,SNPbin-method}
+% \alias{,SNPbin-method}
+%%%%
+\title{Conversion to class "SNPbin"}
+\description{
+ The class \linkS4class{SNPbin} is a formal (S4) class for storing a genotype
+ of binary SNPs in a compact way, using a bit-level coding scheme. New
+ instances of this class are best created using \code{new}; see the
+ manpage of \linkS4class{SNPbin} for more information on this point.
+
+ As a shortcut, conversion methods can be used to convert various
+ objects into a \linkS4class{SNPbin} object. Conversions can be
+ achieved using S3-style (\code{as.SNPbin(x)}) or S4-style
+ (\code{as(x,"SNPbin"}) procedures. All of them call upon the
+ constructor (\code{new}) of \linkS4class{SNPbin} objects.
+
+ Conversion is currently available from the following objects:
+ - integer vectors
+ - numeric vectors
+}
+\author{Thibaut Jombart (\email{t.jombart at imperial.ac.uk})}
+\seealso{
+ Related class:\cr
+ - \code{\linkS4class{SNPbin}}
+ - \code{\linkS4class{genlight}}, for storing multiple binary SNP
+ genotypes. \cr
+}
+\examples{
+\dontrun{
+## data to be converted
+dat <- c(1,0,0,2,1,1,1,2,2,1,1,0,0,1)
+
+## using the constructor
+x1 <- new("SNPbin", dat)
+x1
+
+## using 'as' methods
+x2 <- as.SNPbin(dat)
+x3 <- as(dat, "SNPbin")
+
+identical(x1,x2)
+identical(x1,x3)
+}
+}
+\keyword{classes}
diff --git a/man/as.genlight.Rd b/man/as.genlight.Rd
new file mode 100644
index 0000000..00a4d98
--- /dev/null
+++ b/man/as.genlight.Rd
@@ -0,0 +1,65 @@
+\name{as.genlight}
+\alias{as,genlight,matrix-method}
+\alias{as,genlight,data.frame-method}
+\alias{as,genlight,list-method}
+% \alias{as,genlight,snp.matrix-method}
+\alias{as.genlight}
+\alias{as.genlight,matrix-method}
+\alias{as.genlight,data.frame-method}
+\alias{as.genlight,list-method}
+% \alias{as.genlight,snp.matrix-method}
+\alias{coerce,genlight,matrix-method}
+\alias{coerce,genlight,data.frame-method}
+\alias{coerce,genlight,list-method}
+% \alias{coerce,genlight,snp.matrix-method}
+
+% \alias{,genlight-method}
+% \alias{,genlight-method}
+% \alias{,genlight-method}
+% \alias{,genlight-method}
+%%%%
+\title{Conversion to class "genlight"}
+\description{
+ The class \code{genlight} is a formal (S4) class for storing a genotypes
+ of binary SNPs in a compact way, using a bit-level coding scheme. New
+ instances of this class are best created using \code{new}; see the
+ manpage of \linkS4class{genlight} for more information on this point.
+
+ As a shortcut, conversion methods can be used to convert various
+ objects into a \linkS4class{genlight} object. Conversions can be
+ achieved using S3-style (\code{as.genlight(x)}) or S4-style
+ (\code{as(x,"genlight"}) procedures. All of them call upon the
+ constructor (\code{new}) of \linkS4class{genlight} objects.
+
+ Conversion is currently available from the following objects:
+ - matrix of type integer/numeric
+ - data.frame with integer/numeric data
+ - list of vectors of integer/numeric type
+}
+\author{Thibaut Jombart (\email{t.jombart at imperial.ac.uk})}
+\seealso{
+ Related class:\cr
+ - \code{\linkS4class{SNPbin}}, for storing individual genotypes of
+ binary SNPs\cr
+
+ - \code{\linkS4class{genind}}
+}
+\examples{
+\dontrun{
+## data to be converted
+dat <- list(toto=c(1,1,0,0,2,2,1,2,NA), titi=c(NA,1,1,0,1,1,1,0,0), tata=c(NA,0,3, NA,1,1,1,0,0))
+
+## using the constructor
+x1 <- new("genlight", dat)
+x1
+
+## using 'as' methods
+x2 <- as.genlight(dat)
+x3 <- as(dat, "genlight")
+
+identical(x1,x2)
+identical(x1,x3)
+}
+
+}
+\keyword{classes}
diff --git a/man/ascore.Rd b/man/ascore.Rd
new file mode 100644
index 0000000..6c6920b
--- /dev/null
+++ b/man/ascore.Rd
@@ -0,0 +1,94 @@
+\encoding{UTF-8}
+\name{a-score}
+\alias{a.score}
+\alias{optim.a.score}
+\title{Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)}
+\description{
+ These functions are under development. Please email the author before
+ using them for published results.
+}
+\usage{
+a.score(x, n.sim=10, \ldots)
+
+optim.a.score(x, n.pca=1:ncol(x$tab), smart=TRUE, n=10, plot=TRUE,
+ n.sim=10, n.da=length(levels(x$grp)), \ldots)
+}
+\arguments{
+\item{x}{a \code{dapc} object.}
+\item{n.pca}{a vector of \code{integers} indicating the number of axes retained in the
+ Principal Component Analysis (PCA) steps of DAPC. \code{nsim} DAPC
+ will be run for each value in \code{n.pca}, unless the smart approach
+ is used (see details).}
+\item{smart}{a \code{logical} indicating whether a smart, less
+ computer-intensive approach should be used (TRUE, default) or not
+ (FALSE). See details section.}
+\item{n}{an \code{integer} indicating the numbers of values spanning the
+ range of \code{n.pca} to be used in the smart approach.}
+\item{plot}{a \code{logical} indicating whether the results should be
+ displayed graphically (TRUE, default) or not (FALSE).}
+\item{n.sim}{an \code{integer} indicating the number of simulations to
+ be performed for each number of retained PC.}
+\item{n.da}{an \code{integer} indicating the number of axes retained in the
+ Discriminant Analysis step.}
+\item{\ldots}{further arguments passed to other methods; currently unused..}
+}
+\details{
+ The Discriminant Analysis of Principal Components seeks a reduced
+ space inside which observations are best discriminated into
+ pre-defined groups. One way to assess the quality of the
+ discrimination is looking at re-assignment of individuals to their
+ prior group, successful re-assignment being a sign of strong discrimination.
+
+ However, when the original space is very large, ad hoc solutions can
+ be found, which discriminate very well the sampled individuals but
+ would perform poorly on new samples. In such a case, DAPC
+ re-assignment would be high even for randomly chosen clusters.
+ The a-score measures this bias. It is computed as (Pt-Pr), where Pt is
+ the reassignment probability using the true cluster, and Pr is the
+ reassignment probability for randomly permuted clusters. A a-score
+ close to one is a sign that the DAPC solution is both strongly
+ discriminating and stable, while low values (toward 0 or lower)
+ indicate either weak discrimination or instability of the results.
+
+ The a-score can serve as a criterion for choosing the optimal number of
+ PCs in the PCA step of DAPC, i.e. the number of PC maximizing the
+ a-score. Two procedures are implemented in \code{optim.a.score}. The
+ smart procedure selects evenly distributed number of PCs in a
+ pre-defined range, compute the a-score for each, and then interpolate
+ the results using splines, predicting an approximate optimal number of
+ PCs. The other procedure (when \code{smart} is FALSE) performs the
+ computations for all number of PCs request by the user. The 'optimal'
+ number is then the one giving the highest mean a-score (computed over
+ the groups).
+}
+\value{
+ === a.score ===\cr
+ \code{a.score} returns a list with the following components:\cr
+ \item{tab}{a matrix of a-scores with groups in columns and simulations in row.}
+ \item{pop.score}{a vector giving the mean a-score for each population.}
+ \item{mean}{the overall mean a-score.}\cr
+
+ === optim.a.score ===\cr
+ \code{optima.score} returns a list with the following components:\cr
+ \item{pop.score}{a list giving the mean a-score of the populations
+ for each number of retained PC (each element of the list corresponds
+ to a number of retained PCs).}
+ \item{mean}{a vector giving the overall mean a-score for each number
+ of retained PCs.}
+ \item{pred}{(only when \code{smart} is TRUE) the predictions of the
+ spline, given in x and y coordinates.}
+ \item{best}{the optimal number of PCs to be retained.}
+}
+\references{
+ Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+ principal components: a new method for the analysis of genetically
+ structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
+}
+\seealso{
+ - \code{\link{find.clusters}}: to identify clusters without prior.
+
+ - \code{\link{dapc}}: the Discriminant Analysis of Principal
+ Components (DAPC)
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/auxil.Rd b/man/auxil.Rd
new file mode 100644
index 0000000..2d07dd1
--- /dev/null
+++ b/man/auxil.Rd
@@ -0,0 +1,151 @@
+\encoding{UTF-8}
+\docType{methods}
+\name{Auxiliary functions}
+\alias{checkType}
+\alias{.rmspaces}
+\alias{.genlab}
+\alias{.readExt}
+\alias{corner}
+\alias{num2col}
+\alias{fac2col}
+\alias{any2col}
+\alias{transp}
+\alias{bluepal}
+\alias{redpal}
+\alias{greenpal}
+\alias{greypal}
+\alias{flame}
+\alias{azur}
+\alias{seasun}
+\alias{lightseasun}
+\alias{deepseasun}
+\alias{spectral}
+\alias{wasp}
+\alias{funky}
+
+\title{ Auxiliary functions for adegenet}
+\description{
+ adegenet implements a number of auxiliary procedures that might be of
+ interest for users. These include graphical tools to translate
+ variables (numeric or factors) onto a color scale, adding transparency
+ to existing colors, pre-defined color palettes, extra functions to
+ access documentation, and low-level treatment of character vectors.
+
+ These functions are mostly auxiliary procedures used internally in
+ adegenet.\cr
+
+ These items include:
+ \itemize{
+ \item \code{num2col}: translates a numeric vector into colors.
+ \item \code{fac2col}: translates a factor into colors.
+ \item \code{any2col}: translates a vector of type numeric, character
+ or factor into colors.
+ \item \code{transp}: adds transparency to a vector of colors. Note that
+ transparent colors are not supported on some graphical devices.
+ \item \code{corner}: adds text to a corner of a figure.
+ \item \code{checkType}: checks the type of markers being used in a
+ function and issues an error if appropriate.
+ \item \code{.rmspaces}: remove peripheric spaces in a character string.
+ \item \code{.genlab}: generate labels in a correct alphanumeric ordering.
+ \item \code{.readExt}: read the extension of a given file.
+ }
+
+ Color palettes include:
+ \itemize{
+ \item \code{bluepal}: white -> dark blue
+ \item \code{redpal}: white -> dark red
+ \item \code{greenpal}: white -> dark green
+ \item \code{greypal}: white -> dark grey
+ \item \code{flame}: gold -> red
+ \item \code{azur}: gold -> blue
+ \item \code{seasun}: blue -> gold -> red
+ \item \code{lightseasun}: blue -> gold -> red (light variant)
+ \item \code{deepseasun}: blue -> gold -> red (deep variant)
+ \item \code{spectral}: red -> yellow -> blue (RColorBrewer variant)
+ \item \code{wasp}: gold -> brown -> black
+ \item \code{funky}: many colors
+ }
+}
+\seealso{
+ The R package RColorBrewer, proposing a nice selection of color palettes.
+}
+\usage{
+.genlab(base, n)
+corner(text, posi="topleft", inset=0.1, \dots)
+num2col(x, col.pal=heat.colors, reverse=FALSE,
+ x.min=min(x,na.rm=TRUE), x.max=max(x,na.rm=TRUE),
+ na.col="transparent")
+fac2col(x, col.pal=funky, na.col="transparent", seed=NULL)
+any2col(x, col.pal=seasun, na.col="transparent")
+transp(col, alpha=.5)
+}
+\arguments{
+ \item{base}{a character string forming the base of the labels}
+ \item{n}{the number of labels to generate}
+ \item{text}{a character string to be added to the plot}
+ \item{posi}{a character matching any combinations of "top/bottom" and
+ "left/right".}
+ \item{inset}{a vector of two numeric values (recycled if needed)
+ indicating the inset, as a fraction of the plotting region.}
+ \item{\dots}{further arguments to be passed to \code{\link{text}}}
+ \item{x}{a numeric vector (for \code{num2col}) or a vector converted
+ to a factor (for \code{fac2col}).}
+ \item{col.pal}{a function generating colors according to a given palette.}
+ \item{reverse}{a logical stating whether the palette should be
+ inverted (TRUE), or not (FALSE, default).}
+ \item{x.min}{the minimal value from which to start the color scale}
+ \item{x.max}{the maximal value from which to start the color scale}
+ \item{na.col}{the color to be used for missing values (NAs)}
+ \item{seed}{a seed for R's random number generated, used to fix the
+ random permutation of colors in the palette used; if NULL, no
+ randomization is used and the colors are taken from the palette
+ according to the ordering of the levels.}
+ \item{col}{a vector of colors}
+ \item{alpha}{a numeric value between 0 and 1 representing the alpha
+ coefficient; 0: total transparency; 1: no transparency.}
+}
+\value{
+ For \code{.genlab}, a character vector of size "n".
+ \code{num2col} and \code{fac2col} return a vector of
+ colors. \code{any2col} returns a list with the following components:
+ \code{$col} (a vector of colors), \code{$leg.col} (colors for the
+ legend), and \code{$leg.txt} (text for the legend).
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+
+.genlab("Locus-",11)
+
+## transparent colors using "transp"
+plot(rnorm(1000), rnorm(1000), col=transp("blue",.3), pch=20, cex=4)
+
+
+## numeric values to color using num2col
+plot(1:100, col=num2col(1:100), pch=20, cex=4)
+plot(1:100, col=num2col(1:100, col.pal=bluepal), pch=20, cex=4)
+plot(1:100, col=num2col(1:100, col.pal=flame), pch=20, cex=4)
+plot(1:100, col=num2col(1:100, col.pal=wasp), pch=20, cex=4)
+plot(1:100, col=num2col(1:100, col.pal=azur,rev=TRUE), pch=20, cex=4)
+plot(1:100, col=num2col(1:100, col.pal=spectral), pch=20, cex=4)
+
+## factor as colors using fac2col
+dat <- cbind(c(rnorm(50,8), rnorm(100), rnorm(150,3),
+rnorm(50,10)),c(rnorm(50,1),rnorm(100),rnorm(150,3), rnorm(50,5)))
+fac <- rep(letters[1:4], c(50,100,150,50))
+plot(dat, col=fac2col(fac), pch=19, cex=4)
+plot(dat, col=transp(fac2col(fac)), pch=19, cex=4)
+plot(dat, col=transp(fac2col(fac,seed=2)), pch=19, cex=4)
+
+## use of any2col
+x <- factor(1:10)
+col.info <- any2col(x, col.pal=funky)
+plot(x, col=col.info$col, main="Use of any2col on a factor")
+legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white")
+
+x <- 100:1
+col.info <- any2col(x, col.pal=wasp)
+barplot(x, col=col.info$col, main="Use of any2col on a numeric")
+legend("bottomleft", fill=col.info$leg.col, legend=col.info$leg.txt, bg="white")
+
+}
+\keyword{manip}
\ No newline at end of file
diff --git a/man/chooseCN.Rd b/man/chooseCN.Rd
new file mode 100644
index 0000000..481ea14
--- /dev/null
+++ b/man/chooseCN.Rd
@@ -0,0 +1,96 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/chooseCN.R
+\name{chooseCN}
+\alias{chooseCN}
+\title{Function to choose a connection network}
+\usage{
+chooseCN(xy, ask = TRUE, type = NULL, result.type = "nb", d1 = NULL,
+ d2 = NULL, k = NULL, a = NULL, dmin = NULL, plot.nb = TRUE,
+ edit.nb = FALSE)
+}
+\arguments{
+\item{xy}{an matrix or data.frame with two columns for x and y coordinates.}
+
+\item{ask}{a logical stating whether graph should be chosen interactively
+(TRUE,default) or not (FALSE). Set to FALSE if \code{type} is provided.}
+
+\item{type}{an integer giving the type of graph (see details).}
+
+\item{result.type}{a character giving the class of the returned object.
+Either "nb" (default) or "listw", both from \code{spdep} package. See
+details.}
+
+\item{d1}{the minimum distance between any two neighbours. Used if
+\code{type=5.}}
+
+\item{d2}{the maximum distance between any two neighbours. Used if
+\code{type=5}. Can also be a character: "dmin" for the minimum distance so
+that each site has at least one connection, or "dmax" to have all sites
+connected (despite the later has no sense).}
+
+\item{k}{the number of neighbours per point. Used if \code{type=6}.}
+
+\item{a}{the exponent of the inverse distance matrix. Used if \code{type=7}.}
+
+\item{dmin}{the minimum distance between any two distinct points. Used to
+avoid infinite spatial proximities (defined as the inversed spatial
+distances). Used if \code{type=7}.}
+
+\item{plot.nb}{a logical stating whether the resulting graph should be
+plotted (TRUE, default) or not (FALSE).}
+
+\item{edit.nb}{a logical stating whether the resulting graph should be
+edited manually for corrections (TRUE) or not (FALSE, default).}
+}
+\value{
+Returns a connection network having the class \code{nb} or
+\code{listw}. The xy coordinates are passed as attribute to the created
+object.
+}
+\description{
+The function \code{chooseCN} is a simple interface to build a connection
+network (CN) from xy coordinates. The user chooses from 6 types of graph and
+one additional weighting scheme. \code{chooseCN} calls functions from
+appropriate packages, handles non-unique coordinates and returns a
+connection network either with classe \code{nb} or \code{listw}. For graph
+types 1-4, duplicated locations are not accepted and will issue an error.
+}
+\details{
+There are 7 kinds of graphs proposed: \cr Delaunay triangulation (type 1)\cr
+Gabriel graph (type 2)\cr Relative neighbours (type 3)\cr Minimum spanning
+tree (type 4)\cr Neighbourhood by distance (type 5)\cr K nearests neighbours
+(type 6)\cr Inverse distances (type 7)\cr
+
+The last option (type=7) is not a true neighbouring graph: all sites are
+neighbours, but the spatial weights are directly proportional to the
+inversed spatial distances.\cr Also not that in this case, the output of the
+function is always a \code{listw} object, even if \code{nb} was
+requested.\cr
+
+The choice of the connection network has been discuted on the adegenet
+forum. Please search the archives from adegenet website (section 'contact')
+using 'graph' as keyword.
+}
+\examples{
+
+\dontrun{
+data(nancycats)
+
+par(mfrow=c(2,2))
+cn1 <- chooseCN(nancycats at other$xy,ask=FALSE,type=1)
+cn2 <- chooseCN(nancycats at other$xy,ask=FALSE,type=2)
+cn3 <- chooseCN(nancycats at other$xy,ask=FALSE,type=3)
+cn4 <- chooseCN(nancycats at other$xy,ask=FALSE,type=4)
+par(mfrow=c(1,1))
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{spca}}
+}
+\keyword{spatial}
+\keyword{utilities}
+
diff --git a/man/colorplot.Rd b/man/colorplot.Rd
new file mode 100644
index 0000000..3cde74f
--- /dev/null
+++ b/man/colorplot.Rd
@@ -0,0 +1,65 @@
+\name{colorplot}
+\alias{colorplot}
+\alias{colorplot.default}
+\title{Represents a cloud of points with colors}
+\description{
+ The \code{colorplot} function represents a cloud of points with colors
+ corresponding to a combination of 1,2 or 3 quantitative variables,
+ assigned to RGB (Red, Green, Blue) channels. For instance, this can be useful to
+ represent up to 3 principal components in space. Note that the
+ property of such representation to convey multidimensional information
+ has not been investigated.\cr
+
+ \code{colorplot} is a S3 generic function. Methods are defined for
+ particular objects, like \code{\link{spca}} objects.
+
+}
+\usage{
+colorplot(\dots)
+
+\method{colorplot}{default}(xy, X, axes=NULL, add.plot=FALSE, defaultLevel=0, transp=FALSE, alpha=.5, \dots)
+}
+\arguments{
+ \item{xy}{a numeric matrix with two columns (e.g. a matrix of spatial coordinates.}
+ \item{X}{a matrix-like containing numeric values that are translated
+ into the RGB system. Variables are considered to be in columns.}
+ \item{axes}{the index of the columns of X to be represented. Up to
+ three axes can be chosen. If null, up to the first three columns of
+ X are used.}
+ \item{add.plot}{a logical stating whether the colorplot should be
+ added to the existing plot (defaults to FALSE).}
+ \item{defaultLevel}{a numeric value between 0 and 1, giving the
+ default level in a color for which values are not specified. Used
+ whenever less than three axes are specified.}
+ \item{transp}{a logical stating whether the produced colors should be
+ transparent (TRUE) or not (FALSE, default).}
+ \item{alpha}{the alpha level for transparency, between 0 (fully
+ transparent) and 1 (not transparent); see \code{?rgb} for more details.}
+ \item{\dots}{further arguments to be passed to other methods. In
+ \code{colorplot.default}, these arguments are passed to plot/points
+ functions. See \code{?plot.default} and \code{?points}.}
+}
+\value{
+ Invisibly returns a vector of colours used in the plot.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
+\examples{
+# a toy example
+xy <- expand.grid(1:10,1:10)
+df <- data.frame(x=1:100, y=100:1, z=runif(100,0,100))
+colorplot(xy,df,cex=10,main="colorplot: toy example")
+
+\dontrun{
+# a genetic example using a sPCA
+if(require(spdep)){
+data(spcaIllus)
+dat3 <- spcaIllus$dat3
+spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
+colorplot(spca3, cex=4, main="colorplot: a sPCA example")
+text(spca3$xy[,1], spca3$xy[,2], dat3$pop)
+mtext("P1-P2 in cline\tP3 random \tP4 local repulsion")
+}
+}
+}
+\keyword{multivariate}
+\keyword{hplot}
diff --git a/man/coords.monmonier.Rd b/man/coords.monmonier.Rd
new file mode 100644
index 0000000..77e3e64
--- /dev/null
+++ b/man/coords.monmonier.Rd
@@ -0,0 +1,49 @@
+\name{coords.monmonier}
+\alias{coords.monmonier}
+\title{Returns original points in results paths of an object of class 'monmonier'}
+\description{
+ The original implementation of \code{monmonier} in package
+ \bold{adegenet} returns path coordinates, \code{coords.monmonier}
+ additionally displays identities of the original points of the network,
+ based on original coordinates.
+}
+\usage{
+coords.monmonier(x)
+}
+\arguments{
+ \item{x}{an object of class \code{\link{monmonier}}.}
+}
+\value{
+ Returns a list with elements according to the \code{x$nrun} result of the \code{\link{monmonier}} object.
+ Corresponding path points are in the same order as in the original object.
+
+ run1 (run2, ...): for each run, a list containing a matrix giving the
+ original points in the network (\code{first} and \code{second},
+ indicating pairs of neighbours). Path coordinates are stored in
+ columns \code{x.hw} and \code{y.hw}. \code{first} and \code{second}
+ are integers referring to the row numbers in the \code{x$xy} matrix of
+ the original \code{\link{monmonier}} object.
+}
+\author{Peter Solymos, \email{Solymos.Peter at aotk.szie.hu}}
+\seealso{
+ \code{\link{monmonier}}
+}
+\examples{
+
+\dontrun{
+if(require(spdep)){
+
+load(system.file("files/mondata1.rda",package="adegenet"))
+cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE)
+mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2,nrun=3)
+
+mon1$run1
+mon1$run2
+mon1$run3
+path.coords <- coords.monmonier(mon1)
+path.coords
+}
+}
+}
+\keyword{methods}
+\keyword{manip}
diff --git a/man/dapc.Rd b/man/dapc.Rd
new file mode 100644
index 0000000..63044f1
--- /dev/null
+++ b/man/dapc.Rd
@@ -0,0 +1,332 @@
+\encoding{UTF-8}
+\name{dapc}
+\alias{dapc}
+\alias{dapc.data.frame}
+\alias{dapc.matrix}
+\alias{dapc.genind}
+\alias{dapc.dudi}
+\alias{dapc.genlight}
+\alias{print.dapc}
+\alias{summary.dapc}
+\alias{predict.dapc}
+\alias{as.lda}
+\alias{as.lda.dapc}
+\title{Discriminant Analysis of Principal Components (DAPC)}
+\description{
+ These functions implement the Discriminant Analysis of Principal
+ Components (DAPC, Jombart et al. 2010). This method descibes the
+ diversity between pre-defined groups. When groups are unknown, use
+ \code{find.clusters} to infer genetic clusters. See 'details' section
+ for a succint description of the method, and
+ \code{vignette("adegenet-dapc")} for a tutorial. Graphical methods for
+ DAPC are documented in \code{\link{scatter.dapc}} (see
+ \code{?scatter.dapc}).
+
+ \code{dapc} is a generic function performing the DAPC on the following
+ types of objects:\cr
+ - \code{data.frame} (only numeric data)\cr
+ - \code{matrix} (only numeric data)\cr
+ - \code{\linkS4class{genind}} objects (genetic markers)\cr
+ - \code{\linkS4class{genlight}} objects (genome-wide SNPs)
+
+ These methods all return an object with class \code{dapc}.
+
+ Functions that can be applied to these objects are (the ".dapc" can be
+ ommitted):
+
+ - \code{print.dapc}: prints the content of a \code{dapc} object.\cr
+ - \code{summary.dapc}: extracts useful information from a \code{dapc}
+ object.\cr
+ - \code{predict.dapc}: predicts group memberships based on DAPC results.\cr
+ - \code{xvalDapc}: performs cross-validation of DAPC using varying
+ numbers of PCs (and keeping the number of discriminant functions
+ fixed); it currently has methods for \code{data.frame} and \code{matrix}.\cr
+
+
+
+ DAPC implementation calls upon \code{\link[ade4]{dudi.pca}} from the
+ \code{ade4} package (except for \linkS4class{genlight} objects)
+ and \code{\link[MASS]{lda}} from the \code{MASS} package. The
+ \code{predict} procedure uses \code{\link[MASS]{predict.lda}} from the
+ \code{MASS} package.
+
+ \code{as.lda} is a generic with a method for \code{dapc} object which
+ converts these objects into outputs similar to that of
+ \code{lda.default}.
+}
+\usage{
+\method{dapc}{data.frame}(x, grp, n.pca=NULL, n.da=NULL, center=TRUE,
+ scale=FALSE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE,
+ pca.select=c("nbEig","percVar"), perc.pca=NULL, \ldots, dudi=NULL)
+
+\method{dapc}{matrix}(x, \ldots)
+
+\method{dapc}{genind}(x, pop=NULL, n.pca=NULL, n.da=NULL, scale=FALSE,
+ truenames=TRUE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE,
+ pca.select=c("nbEig","percVar"), perc.pca=NULL, \ldots)
+
+\method{dapc}{genlight}(x, pop=NULL, n.pca=NULL, n.da=NULL,
+ scale=FALSE, var.contrib=TRUE, var.loadings=FALSE, pca.info=TRUE,
+ pca.select=c("nbEig", "percVar"), perc.pca=NULL, glPca=NULL, \ldots)
+
+\method{dapc}{dudi}(x, grp, \ldots)
+
+\method{print}{dapc}(x, \dots)
+
+\method{summary}{dapc}(object, \dots)
+
+\method{predict}{dapc}(object, newdata, prior = object$prior, dimen,
+ method = c("plug-in", "predictive", "debiased"), ...)
+}
+\arguments{
+ \item{x}{\code{a data.frame}, \code{matrix}, or \code{\linkS4class{genind}}
+ object. For the \code{data.frame} and \code{matrix} arguments, only
+ quantitative variables should be provided.}
+ \item{grp,pop}{a \code{factor} indicating the group membership of
+ individuals; for \code{scatter}, an optional grouping of individuals.}
+ \item{n.pca}{an \code{integer} indicating the number of axes retained in the
+ Principal Component Analysis (PCA) step. If \code{NULL}, interactive selection is triggered.}
+ \item{n.da}{an \code{integer} indicating the number of axes retained in the
+ Discriminant Analysis step. If \code{NULL}, interactive selection is triggered.}
+ \item{center}{a \code{logical} indicating whether variables should be centred to
+ mean 0 (TRUE, default) or not (FALSE). Always TRUE for \linkS4class{genind} objects.}
+ \item{scale}{a \code{logical} indicating whether variables should be scaled
+ (TRUE) or not (FALSE, default). Scaling consists in dividing variables by their
+ (estimated) standard deviation to account for trivial differences in
+ variances.}
+ \item{var.contrib}{a \code{logical} indicating whether the
+ contribution of original variables (alleles, for \linkS4class{genind} objects)
+ should be provided (TRUE, default) or not (FALSE). Such output can be useful,
+ but can also create huge matrices when there is a lot of variables.}
+ \item{var.loadings}{a \code{logical} indicating whether the
+ loadings of original variables (alleles, for \linkS4class{genind} objects)
+ should be provided (TRUE) or not (FALSE, default). Such output can be useful,
+ but can also create huge matrices when there is a lot of variables.}
+ \item{pca.info}{a \code{logical} indicating whether information about
+ the prior PCA should be stored (TRUE, default) or not (FALSE). This
+ information is required to predict group membership of new
+ individuals using \code{predict}, but makes the object slightly bigger.}
+ \item{pca.select}{a \code{character} indicating the mode of selection of PCA
+ axes, matching either "nbEig" or "percVar". For "nbEig", the user
+ has to specify the number of axes retained (interactively, or via
+ \code{n.pca}). For "percVar", the user has to specify the minimum amount of
+ the total variance to be preserved by the retained axes, expressed as a
+ percentage (interactively, or via \code{perc.pca}). }
+ \item{perc.pca}{a \code{numeric} value between 0 and 100 indicating the
+ minimal percentage of the total variance of the data to be expressed by the
+ retained axes of PCA.}
+ \item{\ldots}{further arguments to be passed to other functions. For
+ \code{dapc.matrix}, arguments are to match those of
+ \code{dapc.data.frame}; for \code{dapc.genlight}, arguments passed
+ to \code{\link{glPca}}}
+ \item{glPca}{an optional \code{\link{glPca}} object; if provided,
+ dimension reduction is not performed (saving computational time) but
+ taken directly from this object.}
+ \item{object}{a \code{dapc} object.}
+ \item{truenames}{a \code{logical} indicating whether true (i.e., user-specified)
+ labels should be used in object outputs (TRUE, default) or not (FALSE).}
+ \item{dudi}{optionally, a multivariate analysis with the class
+ \code{dudi} (from the ade4 package). If provided, prior PCA will be
+ ignored, and this object will be used as a prior step for variable
+ orthogonalisation.}
+ \item{newdata}{an optional dataset of individuals whose membership is
+ seeked; can be a data.frame, a matrix, a \linkS4class{genind} or a
+ \linkS4class{genlight} object, but object class must match the
+ original ('training') data. In particular, variables must be exactly
+ the same as in the original data. For \linkS4class{genind}
+ objects, see \code{\link{repool}} to ensure matching of alleles.}
+ \item{prior,dimen,method}{see \code{?predict.lda}.}
+}
+\details{
+ The Discriminant Analysis of Principal Components (DAPC) is designed
+ to investigate the genetic structure of biological populations. This
+ multivariate method consists in a two-steps procedure. First, genetic
+ data are transformed (centred, possibly scaled) and submitted to a
+ Principal Component Analysis (PCA). Second, principal components of
+ PCA are submitted to a Linear Discriminant Analysis (LDA). A trivial
+ matrix operation allows to express discriminant functions as linear
+ combination of alleles, therefore allowing one to compute allele
+ contributions. More details about the computation of DAPC are to be
+ found in the indicated reference.
+
+ DAPC does not infer genetic clusters ex nihilo; for this, see the
+ \code{\link{find.clusters}} function.
+}
+\value{
+ === dapc objects ===\cr
+ The class \code{dapc} is a list with the following
+ components:\cr
+ \item{call}{the matched call.}
+ \item{n.pca}{number of PCA axes retained}
+ \item{n.da}{number of DA axes retained}
+ \item{var}{proportion of variance conserved by PCA principal components}
+ \item{eig}{a numeric vector of eigenvalues.}
+ \item{grp}{a factor giving prior group assignment}
+ \item{prior}{a numeric vector giving prior group probabilities}
+ \item{assign}{a factor giving posterior group assignment}
+ \item{tab}{matrix of retained principal components of PCA}
+ \item{loadings}{principal axes of DAPC, giving coefficients of the linear
+ combination of retained PCA axes.}
+ \item{ind.coord}{principal components of DAPC, giving the coordinates
+ of individuals onto principal axes of DAPC; also called the
+ discriminant functions.}
+ \item{grp.coord}{coordinates of the groups onto the principal axes of DAPC.}
+ \item{posterior}{a data.frame giving posterior membership probabilities for
+ all individuals and all clusters.}
+ \item{var.contr}{(optional) a data.frame giving the contributions of original
+ variables (alleles in the case of genetic data) to the principal components
+ of DAPC.}
+ \item{var.load}{(optional) a data.frame giving the loadings of original
+ variables (alleles in the case of genetic data) to the principal components
+ of DAPC.}
+ \item{match.prp}{a list, where each item is the proportion of individuals
+ correctly matched to their original population in cross-validation.}
+
+
+ === other outputs ===\cr
+ Other functions have different outputs:\cr
+ - \code{summary.dapc} returns a list with 6 components: \code{n.dim} (number
+ of retained DAPC axes), \code{n.pop} (number of groups/populations),
+ \code{assign.prop} (proportion of overall correct assignment),
+ \code{assign.per.pop} (proportion of correct assignment per group),
+ \code{prior.grp.size} (prior group sizes), and \code{post.grp.size} (posterior
+ group sizes), \code{xval.dapc}, \code{xval.genind} and \code{xval}
+ (all return a list of four lists, each one with as many items as
+ cross-validation runs. The first item is a list of \code{assign}
+ components, the secon is a list of \code{posterior} components, the
+ thirs is a list of \code{ind.score} components and the fourth is a
+ list of \code{match.prp} items, i.e. the prortion of the validation
+ set correctly matched to its original population)
+}
+\references{
+ Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+ principal components: a new method for the analysis of genetically
+ structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
+}
+\seealso{
+ \itemize{
+ \item \code{\link{xvalDapc}}: selection of the optimal numbers of PCA axes
+ retained in DAPC using cross-validation.
+
+ \item \code{\link{scatter.dapc}}, \code{\link{assignplot}},
+ \code{\link{compoplot}}: graphics for DAPC.
+
+ \item \code{\link{find.clusters}}: to identify clusters without prior.
+
+ \item \code{\link{dapcIllus}}: a set of simulated data illustrating
+ the DAPC
+
+ \item \code{\link{eHGDP}}, \code{\link{H3N2}}: empirical datasets
+ illustrating DAPC
+ }
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+## data(dapcIllus), data(eHGDP), and data(H3N2) illustrate the dapc
+## see ?dapcIllus, ?eHGDP, ?H3N2
+##
+\dontrun{
+example(dapcIllus)
+example(eHGDP)
+example(H3N2)
+}
+
+## H3N2 EXAMPLE ##
+data(H3N2)
+pop(H3N2) <- factor(H3N2$other$epid)
+dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)
+
+## remove internal segments and ellipses, different pch, add MStree
+scatter(dapc1, cell=0, pch=18:23, cstar=0, mstree=TRUE, lwd=2, lty=2)
+
+## label individuals at the periphery
+# air = 2 is a measure of how much space each label needs
+# pch = NA suppresses plotting of points
+scatter(dapc1, label.inds = list(air = 2, pch = NA))
+
+## only ellipse, custom labels
+scatter(dapc1, cell=2, pch="", cstar=0, posi.da="top",
+ label=paste("year\n",2001:2006), axesel=FALSE, col=terrain.colors(10))
+
+
+## SHOW COMPOPLOT ON MICROBOV DATA ##
+data(microbov)
+dapc1 <- dapc(microbov, n.pca=20, n.da=15)
+compoplot(dapc1, lab="")
+
+
+
+
+\dontrun{
+## EXAMPLE USING GENLIGHT OBJECTS ##
+## simulate data
+x <- glSim(50,4e3-50, 50, ploidy=2)
+x
+plot(x)
+
+## perform DAPC
+dapc1 <- dapc(x, n.pca=10, n.da=1)
+dapc1
+
+## plot results
+scatter(dapc1, scree.da=FALSE)
+
+## SNP contributions
+loadingplot(dapc1$var.contr)
+loadingplot(tail(dapc1$var.contr, 100), main="Loading plot - last 100 SNPs")
+
+
+
+## USE "PREDICT" TO PREDICT GROUPS OF NEW INDIVIDUALS ##
+## load data
+data(sim2pop)
+
+## we make a dataset of:
+## 30 individuals from pop A
+## 30 individuals from pop B
+## 30 hybrids
+
+## separate populations and make F1
+temp <- seppop(sim2pop)
+temp <- lapply(temp, function(e) hybridize(e,e,n=30)) # force equal popsizes
+
+## make hybrids
+hyb <- hybridize(temp[[1]], temp[[2]], n=30)
+
+## repool data - needed to ensure allele matching
+newdat <- repool(temp[[1]], temp[[2]], hyb)
+pop(newdat) <- rep(c("pop A", "popB", "hyb AB"), c(30,30,30))
+
+## perform the DAPC on the first 2 pop (60 first indiv)
+dapc1 <- dapc(newdat[1:60],n.pca=5,n.da=1)
+
+## plot results
+scatter(dapc1, scree.da=FALSE)
+
+## make prediction for the 30 hybrids
+hyb.pred <- predict(dapc1, newdat[61:90])
+hyb.pred
+
+## plot the inferred coordinates (circles are hybrids)
+points(hyb.pred$ind.scores, rep(.1, 30))
+
+## look at assignment using assignplot
+assignplot(dapc1, new.pred=hyb.pred)
+title("30 indiv popA, 30 indiv pop B, 30 hybrids")
+
+## image using compoplot
+compoplot(dapc1, new.pred=hyb.pred, ncol=2)
+title("30 indiv popA, 30 indiv pop B, 30 hybrids")
+
+## CROSS-VALIDATION ##
+data(sim2pop)
+xval <- xvalDapc(sim2pop at tab, pop(sim2pop), n.pca.max=100, n.rep=3)
+xval
+boxplot(xval$success~xval$n.pca, xlab="Number of PCA components",
+ylab="Classification succes", main="DAPC - cross-validation")
+
+}
+
+
+}
+\keyword{multivariate}
diff --git a/man/dapcGraphics.Rd b/man/dapcGraphics.Rd
new file mode 100644
index 0000000..72bdb0f
--- /dev/null
+++ b/man/dapcGraphics.Rd
@@ -0,0 +1,204 @@
+\encoding{UTF-8}
+\name{dapc graphics}
+\alias{scatter.dapc}
+\alias{assignplot}
+\alias{compoplot}
+\title{Graphics for Discriminant Analysis of Principal Components (DAPC)}
+\description{
+ These functions provide graphic outputs for Discriminant Analysis of
+ Principal Components (DAPC, Jombart et al. 2010). See \code{?dapc} for
+ details about this method. DAPC graphics are detailed in the DAPC tutorial
+ accessible using \code{vignette("adegenet-dapc")}.
+
+ These functions all require an object of class \code{dapc}
+ (the ".dapc" can be ommitted when calling the functions):\cr
+ - \code{scatter.dapc}: produces scatterplots of principal components (or
+ 'discriminant functions'), with a screeplot of eigenvalues as inset.\cr
+ - \code{assignplot}: plot showing the probabilities of assignment of
+ individuals to the different clusters.\cr
+ - \code{compoplot}: barplot showing the probabilities of assignment of
+ individuals to the different clusters.\cr
+
+}
+\usage{
+\method{scatter}{dapc}(x, xax=1, yax=2, grp=x$grp, col=seasun(length(levels(grp))),
+ pch=20, bg="white", solid=.7, scree.da=TRUE,
+ scree.pca=FALSE, posi.da="bottomright",
+ posi.pca="bottomleft", bg.inset="white", ratio.da=.25,
+ ratio.pca=.25, inset.da=0.02, inset.pca=0.02,
+ inset.solid=.5, onedim.filled=TRUE, mstree=FALSE, lwd=1,
+ lty=1, segcol="black", legend=FALSE, posi.leg="topright",
+ cleg=1, txt.leg=levels(grp), cstar = 1, cellipse = 1.5,
+ axesell = FALSE, label = levels(grp), clabel = 1, xlim =
+ NULL, ylim = NULL, grid = FALSE, addaxes = TRUE, origin =
+ c(0,0), include.origin = TRUE, sub = "", csub = 1, possub =
+ "bottomleft", cgrid = 1, pixmap = NULL, contour = NULL, area
+ = NULL, label.inds = NULL, \ldots)
+
+assignplot(x, only.grp=NULL, subset=NULL, new.pred=NULL, cex.lab=.75,pch=3)
+
+compoplot(x, only.grp=NULL, subset=NULL, new.pred=NULL, col=NULL, lab=NULL,
+ legend=TRUE, txt.leg=NULL, ncol=4, posi=NULL, cleg=.8, bg=transp("white"), ...)
+}
+\arguments{
+ \item{x}{a \code{dapc} object.}
+ \item{xax,yax}{\code{integers} specifying which principal components of DAPC
+ should be shown in x and y axes. }
+ \item{grp}{a factor defining group membership for the individuals. The scatterplot
+ is optimal only for the default group, i.e. the one used in the
+ DAPC analysis.}
+ \item{col}{a suitable color to be used for groups. The specified vector
+ should match the number of groups, not the number of individuals.}
+ \item{pch}{a \code{numeric} indicating the type of point to be used to indicate
+ the prior group of individuals (see \code{\link{points}} documentation for
+ more details); one value is expected for each group; recycled if necessary.}
+ \item{bg}{the color used for the background of the scatterplot.}
+ \item{solid}{a value between 0 and 1 indicating the alpha level for the colors of
+ the plot; 0=full transparency, 1=solid colours.}
+ \item{scree.da}{a logical indicating whether a screeplot of Discriminant Analysis
+ eigenvalues should be displayed in inset (TRUE) or not (FALSE).}
+ \item{scree.pca}{a logical indicating whether a screeplot of Principal Component Analysis
+ eigenvalues should be displayed in inset (TRUE) or not (FALSE); retained axes are
+ displayed in black.}
+ \item{posi.da}{the position of the inset of DA eigenvalues; can match any
+ combination of "top/bottom" and "left/right".}
+ \item{posi.pca}{the position of the inset of PCA eigenvalues; can match any
+ combination of "top/bottom" and "left/right".}
+ \item{bg.inset}{the color to be used as background for the inset plots.}
+ \item{ratio.da}{the size of the inset of DA eigenvalues as a proportion of the
+ current plotting region.}
+ \item{ratio.pca}{the size of the inset of PCA eigenvalues as a proportion of the
+ current plotting region.}
+ \item{inset.da}{a vector with two numeric values (recycled if needed) indicating
+ the inset to be used for the screeplot of DA eigenvalues as a proportion of the
+ current plotting region; see \code{?add.scatter} for more details.}
+ \item{inset.pca}{a vector with two numeric values (recycled if needed) indicating
+ the inset to be used for the screeplot of PCA eigenvalues as a proportion of the
+ current plotting region; see \code{?add.scatter} for more details.}
+ \item{inset.solid}{a value between 0 and 1 indicating the alpha level for the colors of
+ the inset plots; 0=full transparency, 1=solid colours.}
+ \item{onedim.filled}{a logical indicating whether curves should be filled when
+ plotting a single discriminant function (TRUE), or not (FALSE).}
+ \item{mstree}{a logical indicating whether a minimum spanning tree linking the
+ groups and based on the squared distances between the groups inside the entire
+ space should added to the plot (TRUE), or not (FALSE).}
+ \item{lwd,lty,segcol}{the line width, line type, and segment colour to be used for
+ the minimum spanning tree.}
+ \item{legend}{a logical indicating whether a legend for group colours should added
+ to the plot (TRUE), or not (FALSE).}
+ \item{posi.leg}{the position of the legend for group colours; can match any
+ combination of "top/bottom" and "left/right", or a set of x/y coordinates stored
+ as a list (\code{locator} can be used).}
+ \item{cleg}{a size factor used for the legend.}
+ \item{cstar,cellipse,axesell,label,clabel,xlim,ylim,grid,addaxes,origin,include.origin,sub,csub,possub,cgrid,pixmap,contour,area}{arguments
+ passed to \code{\link[ade4]{s.class}}; see \code{?s.class} for more informations}
+ \item{only.grp}{a \code{character} vector indicating which groups should be
+ displayed. Values should match values of \code{x$grp}. If \code{NULL}, all
+ results are displayed}
+ \item{subset}{\code{integer} or \code{logical} vector indicating which
+ individuals should be displayed. If \code{NULL}, all
+ results are displayed}
+ \item{new.pred}{an optional list, as returned by the \code{predict} method for
+ \code{dapc} objects; if provided, the individuals with unknown groups are added
+ at the bottom of the plot. To visualize these individuals only, specify
+ \code{only.grp="unknown"}.}
+ \item{cex.lab}{a \code{numeric} indicating the size of labels.}
+ \item{lab}{a vector of characters (recycled if necessary) of labels
+ for the individuals; if left to NULL, the row names of \code{x$tab}
+ are used.}
+ \item{txt.leg}{a character vector indicating the text to be used in
+ the legend; if not provided, group names stored in \code{x$grp} are
+ used.}
+ \item{ncol}{an integer indicating the number of columns of the legend,
+ defaulting to 4.}
+ \item{posi}{a characther string indicating the position of the legend; can match
+ any combination of "top/bottom" and "left/right". See \code{?legend}.}
+ \item{label.inds}{Named list of arguments passed to the
+ \code{\link[vegan]{orditorp}} function. This will label individual points
+ witout overlapping. Arguments \code{x} and \code{display} are hardcoded and
+ should not be specified by user.}
+ \item{\ldots}{further arguments to be passed to other functions. For
+ \code{scatter}, arguments passed to \code{points}; for \code{compoplot},
+ arguments passed to \code{barplot}.}
+}
+\details{
+ See the documentation of \code{\link{dapc}} for more information about the method.
+}
+\value{
+ All functions return the matched call.\cr
+}
+\references{
+ Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+ principal components: a new method for the analysis of genetically
+ structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
+}
+\seealso{
+ - \code{\link{dapc}}: implements the DAPC.
+
+ - \code{\link{find.clusters}}: to identify clusters without prior.
+
+ - \code{\link{dapcIllus}}: a set of simulated data illustrating the DAPC
+
+ - \code{\link{eHGDP}}, \code{\link{H3N2}}: empirical datasets illustrating
+ DAPC
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+data(H3N2)
+dapc1 <- dapc(H3N2, pop=H3N2$other$epid, n.pca=30,n.da=6)
+
+## defautl plot ##
+scatter(dapc1)
+
+## label individuals at the periphery
+# air = 2 is a measure of how much space each label needs
+# pch = NA suppresses plotting of points
+scatter(dapc1, label.inds = list(air = 2, pch = NA))
+
+## showing different scatter options ##
+## remove internal segments and ellipses, different pch, add MStree
+scatter(dapc1, pch=18:23, cstar=0, mstree=TRUE, lwd=2, lty=2, posi.da="topleft")
+
+## only ellipse, custom labels, use insets
+scatter(dapc1, cell=2, pch="", cstar=0, posi.pca="topleft", posi.da="topleft", scree.pca=TRUE,
+inset.pca=c(.01,.3), label=paste("year\n",2001:2006), axesel=FALSE, col=terrain.colors(10))
+
+## without ellipses, use legend for groups
+scatter(dapc1, cell=0, cstar=0, scree.da=FALSE, clab=0, cex=3,
+solid=.4, bg="white", leg=TRUE, posi.leg="topleft")
+
+## only one axis
+scatter(dapc1,1,1,scree.da=FALSE, legend=TRUE, solid=.4,bg="white")
+
+
+
+## example using genlight objects ##
+## simulate data
+x <- glSim(50,4e3-50, 50, ploidy=2)
+x
+plot(x)
+
+## perform DAPC
+dapc2 <- dapc(x, n.pca=10, n.da=1)
+dapc2
+
+## plot results
+scatter(dapc2, scree.da=FALSE, leg=TRUE, txt.leg=paste("group",
+c('A','B')), col=c("red","blue"))
+
+## SNP contributions
+loadingplot(dapc2$var.contr)
+loadingplot(tail(dapc2$var.contr, 100), main="Loading plot - last 100 SNPs")
+
+
+
+## assignplot / compoplot ##
+assignplot(dapc1, only.grp=2006)
+
+data(microbov)
+dapc3 <- dapc(microbov, n.pca=20, n.da=15)
+compoplot(dapc3, lab="")
+}
+}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/dapcIllus.Rd b/man/dapcIllus.Rd
new file mode 100644
index 0000000..53ebeae
--- /dev/null
+++ b/man/dapcIllus.Rd
@@ -0,0 +1,91 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\name{dapcIllus}
+\alias{dapcIllus}
+\title{Simulated data illustrating the DAPC}
+\format{\code{dapcIllus} is list of 4 components being all genind objects.}
+\source{
+Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of
+principal components: a new method for the analysis of genetically
+structured populations. Submitted to \emph{BMC genetics}.
+}
+\description{
+Datasets illustrating the Discriminant Analysis of Principal Components
+(DAPC, Jombart et al. submitted).\cr
+}
+\details{
+These data were simulated using various models using Easypop (2.0.1). The
+\code{dapcIllus} is a list containing the following \linkS4class{genind}
+objects:\cr - "a": island model with 6 populations \cr - "b": hierarchical
+island model with 6 populations (3,2,1) \cr - "c": one-dimensional stepping
+stone with 2x6 populations, and a boundary between the two sets of 6
+populations\cr - "d": one-dimensional stepping stone with 24 populations\cr
+
+See "source" for a reference providing simulation details.
+}
+\examples{
+
+\dontrun{
+
+data(dapcIllus)
+attach(dapcIllus)
+a # this is a genind object, like b, c, and d.
+
+
+## FINS CLUSTERS EX NIHILO
+clust.a <- find.clusters(a, n.pca=100, n.clust=6)
+clust.b <- find.clusters(b, n.pca=100, n.clust=6)
+clust.c <- find.clusters(c, n.pca=100, n.clust=12)
+clust.d <- find.clusters(d, n.pca=100, n.clust=24)
+
+## examin outputs
+names(clust.a)
+lapply(clust.a, head)
+
+
+## PERFORM DAPCs
+dapc.a <- dapc(a, pop=clust.a$grp, n.pca=100, n.da=5)
+dapc.b <- dapc(b, pop=clust.b$grp, n.pca=100, n.da=5)
+dapc.c <- dapc(c, pop=clust.c$grp, n.pca=100, n.da=11)
+dapc.d <- dapc(d, pop=clust.d$grp, n.pca=100, n.da=23)
+
+
+## LOOK AT ONE RESULT
+dapc.a
+summary(dapc.a)
+
+## FORM A LIST OF RESULTS FOR THE 4 DATASETS
+lres <- list(dapc.a, dapc.b, dapc.c, dapc.d)
+
+
+## DRAW 4 SCATTERPLOTS
+par(mfrow=c(2,2))
+lapply(lres, scatter)
+
+
+# detach data
+detach(dapcIllus)
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Jombart, T., Devillard, S. and Balloux, F. Discriminant
+analysis of principal components: a new method for the analysis of
+genetically structured populations. Submitted to \emph{Genetics}.
+}
+\seealso{
+- \code{\link{dapc}}: implements the DAPC.
+
+- \code{\link{eHGDP}}: dataset illustrating the DAPC and
+\code{find.clusters}.
+
+- \code{\link{H3N2}}: dataset illustrating the DAPC.
+
+- \code{\link{find.clusters}}: to identify clusters without prior.
+}
+\keyword{datasets}
+
diff --git a/man/df2genind.Rd b/man/df2genind.Rd
new file mode 100644
index 0000000..7374acb
--- /dev/null
+++ b/man/df2genind.Rd
@@ -0,0 +1,94 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{df2genind}
+\alias{df2genind}
+\title{Convert a data.frame of allele data to a genind object.}
+\usage{
+df2genind(X, sep = NULL, ncode = NULL, ind.names = NULL,
+ loc.names = NULL, pop = NULL, NA.char = "", ploidy = 2,
+ type = c("codom", "PA"), strata = NULL, hierarchy = NULL)
+}
+\arguments{
+\item{X}{a matrix or a data.frame containing allelle data only (see
+decription)}
+
+\item{sep}{a character string separating alleles. See details.}
+
+\item{ncode}{an optional integer giving the number of characters used for
+coding one genotype at one locus. If not provided, this is determined from
+data.}
+
+\item{ind.names}{optinal, a vector giving the individuals names; if NULL, taken
+from rownames of X. If factor or numeric, vector is converted to character.}
+
+\item{loc.names}{an optional character vector giving the markers names; if
+NULL, taken from colnames of X.}
+
+\item{pop}{an optional factor giving the population of each individual.}
+
+\item{NA.char}{a character string corresponding to missing allele (to be treated as NA)}
+
+\item{ploidy}{an integer indicating the degree of ploidy of the genotypes.}
+
+\item{type}{a character string indicating the type of marker: 'codom' stands
+for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for
+'presence/absence' markers (e.g. AFLP, RAPD).}
+
+\item{strata}{an optional data frame that defines population stratifications
+for your samples. This is especially useful if you have a hierarchical or
+factorial sampling design.}
+
+\item{hierarchy}{a hierarchical formula that explicitely defines hierarchical
+levels in your strata. see \code{\link{hierarchy}} for details.}
+}
+\value{
+an object of the class \linkS4class{genind} for \code{df2genind}; a
+matrix of biallelic genotypes for \code{genind2df}
+}
+\description{
+The function \code{df2genind} converts a data.frame (or a matrix) into a
+\linkS4class{genind} object. The data.frame must meet the following
+requirements:\cr
+- genotypes are in row (one row per genotype)\cr
+- markers/loci are in columns\cr
+- each element is a string of characters coding alleles, ideally separated by a character string (argument \code{sep});
+if no separator is used, the number of characters coding alleles must be indicated (argument \code{ncode}).\cr
+}
+\details{
+See \code{\link{genind2df}} to convert \linkS4class{genind} objects back to such a
+data.frame.
+
+=== Details for the \code{sep} argument ===\cr this character is directly
+used in reguar expressions like \code{gsub}, and thus require some
+characters to be preceeded by double backslashes. For instance, "/" works
+but "|" must be coded as "\\|".
+}
+\examples{
+
+## simple example
+df <- data.frame(locusA=c("11","11","12","32"),
+locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22"))
+row.names(df) <- .genlab("genotype",4)
+df
+
+obj <- df2genind(df, ploidy=2, ncode=1)
+obj
+tab(obj)
+
+
+## converting a genind as data.frame
+genind2df(obj)
+genind2df(obj, sep="/")
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}, Zhian N. Kamvar
+ \email{kamvarz at science.oregonstate.edu}
+}
+\seealso{
+\code{\link{genind2df}}, \code{\link{import2genind}},
+ \code{\link{read.genetix}}, \code{\link{read.fstat}},
+ \code{\link{read.structure}}
+}
+\keyword{manip}
+
diff --git a/man/dist.genpop.Rd b/man/dist.genpop.Rd
new file mode 100644
index 0000000..e662ea9
--- /dev/null
+++ b/man/dist.genpop.Rd
@@ -0,0 +1,121 @@
+\encoding{UTF-8}
+\name{dist.genpop}
+\alias{dist.genpop}
+\title{ Genetic distances between populations }
+\description{
+ This function computes measures of genetic distances
+ between populations using a \code{genpop} object. \cr
+ Currently, five distances are available, some of which are euclidian
+ (see details).\cr
+
+ A non-euclidian distance can be transformed into an Euclidean one
+ using \code{\link[ade4]{cailliez}} in order to perform a
+ Principal Coordinate Analysis \code{\link[ade4]{dudi.pco}} (both
+ functions in \code{ade4}). \cr
+
+ The function \code{dist.genpop} is based on former \code{dist.genet}
+ function of \code{ade4} package.
+}
+\usage{
+dist.genpop(x, method = 1, diag = FALSE, upper = FALSE)
+}
+\arguments{
+ \item{x}{ a list of class \code{genpop} }
+ \item{method}{ an integer between 1 and 5. See details }
+ \item{diag}{ a logical value indicating whether the diagonal of the distance matrix should be printed by \code{print.dist} }
+ \item{upper}{ a logical value indicating whether the upper triangle of the distance matrix should be printed by \code{print.dist} }
+}
+\details{
+Let \bold{A} a table containing allelic frequencies with \emph{t} populations (rows) and \emph{m} alleles (columns).\cr
+Let \eqn{\nu} the number of loci. The locus \emph{j} gets \emph{m(j)} alleles.
+\eqn{m=\sum_{j=1}^{\nu} m(j)}\cr
+
+For the row \emph{i} and the modality \emph{k} of the variable \emph{j}, notice the value \eqn{a_{ij}^k} (\eqn{1 \leq i \leq t}, \eqn{1 \leq j \leq \nu},
+\eqn{1 \leq k \leq m(j)}) the value of the initial table.\cr
+
+\eqn{a_{ij}^+=\sum_{k=1}^{m(j)}a_{ij}^k} and \eqn{p_{ij}^k=\frac{a_{ij}^k}{a_{ij}^+}}\cr
+
+Let \bold{P} the table of general term \eqn{p_{ij}^k}\cr
+\eqn{p_{ij}^+=\sum_{k=1}^{m(j)}p_{ij}^k=1}, \eqn{p_{i+}^+=\sum_{j=1}^{\nu}p_{ij}^+=\nu}, \eqn{p_{++}^+=\sum_{j=1}^{\nu}p_{i+}^+=t\nu}\cr
+
+The option \code{method} computes the distance matrices between populations using the frequencies \eqn{p_{ij}^k}. \cr
+
+1. Nei's distance (not Euclidean): \cr
+\eqn{D_1(a,b)=- \ln(\frac{\sum_{k=1}^{\nu} \sum_{j=1}^{m(k)}
+p_{aj}^k p_{bj}^k}{\sqrt{\sum_{k=1}^{\nu} \sum_{j=1}^{m(k)}
+{(p_{aj}^k) }^2}\sqrt{\sum_{k=1}^{\nu} \sum_{j=1}^{m(k)}
+{(p_{bj}^k)}^2}})}\cr
+
+2. Angular distance or Edwards' distance (Euclidean):\cr
+\eqn{D_2(a,b)=\sqrt{1-\frac{1}{\nu} \sum_{k=1}^{\nu}
+\sum_{j=1}^{m(k)} \sqrt{p_{aj}^k p_{bj}^k}}}\cr
+
+3. Coancestrality coefficient or Reynolds' distance (Eucledian):\cr
+\eqn{D_3(a,b)=\sqrt{\frac{\sum_{k=1}^{\nu}
+\sum_{j=1}^{m(k)}{(p_{aj}^k - p_{bj}^k)}^2}{2 \sum_{k=1}^{\nu} (1-
+\sum_{j=1}^{m(k)}p_{aj}^k p_{bj}^k)}}}\cr
+
+4. Classical Euclidean distance or Rogers' distance (Eucledian):\cr
+\eqn{D_4(a,b)=\frac{1}{\nu} \sum_{k=1}^{\nu} \sqrt{\frac{1}{2}
+\sum_{j=1}^{m(k)}{(p_{aj}^k - p_{bj}^k)}^2}}\cr
+
+5. Absolute genetics distance or Provesti 's distance (not Euclidean):\cr
+\eqn{D_5(a,b)=\frac{1}{2{\nu}} \sum_{k=1}^{\nu} \sum_{j=1}^{m(k)}
+|p_{aj}^k - p_{bj}^k|}
+}
+\value{
+returns a distance matrix of class \code{dist} between the rows of the data frame
+}
+\references{
+To complete informations about distances:\cr
+
+Distance 1:\cr
+Nei, M. (1972) Genetic distances between populations. \emph{American Naturalist}, \bold{106}, 283--292. \cr
+Nei M. (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. \emph{Genetics}, \bold{23}, 341--369. \cr
+Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.
+
+Distance 2:\cr
+Edwards, A.W.F. (1971) Distance between populations on the basis of gene frequencies. \emph{Biometrics}, \bold{27}, 873--881. \cr
+Cavalli-Sforza L.L. and Edwards A.W.F. (1967) Phylogenetic analysis: models and estimation procedures. \emph{Evolution}, \bold{32}, 550--570. \cr
+Hartl, D.L. and Clark, A.G. (1989) Principles of population genetics. Sinauer Associates, Sunderland, Massachussetts (p. 303).
+
+Distance 3:\cr
+Reynolds, J. B., B. S. Weir, and C. C. Cockerham. (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. \emph{Genetics}, \bold{105}, 767--779.
+
+Distance 4:\cr
+Rogers, J.S. (1972) Measures of genetic similarity and genetic distances. \emph{Studies in Genetics}, Univ. Texas Publ., \bold{7213}, 145--153. \cr
+Avise, J. C. (1994) Molecular markers, natural history and evolution. Chapman & Hall, London.
+
+Distance 5:\cr
+Prevosti A. (1974) La distancia genetica entre poblaciones. \emph{Miscellanea Alcobe}, \bold{68}, 109--118. \cr
+Prevosti A., Oca\~na J. and Alonso G. (1975) Distances between populations of Drosophila subobscura, based on chromosome arrangements frequencies. \emph{Theoretical and Applied Genetics}, \bold{45}, 231--241. \cr
+
+For more information on dissimilarity indexes:\cr
+Gower J. and Legendre P. (1986) Metric and Euclidean properties of
+dissimilarity coefficients. \emph{Journal of Classification}, \bold{3},
+5--48 \cr
+
+Legendre P. and Legendre L. (1998) \emph{Numerical Ecology}, Elsevier
+Science B.V. 20, pp274--288.\cr
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}\cr
+Former dist.genet code by Daniel Chessel \email{chessel at biomserv.univ-lyon1.fr}\cr
+and documentation by Anne B. Dufour \email{dufour at biomserv.univ-lyon1.fr}
+}
+\seealso{ \code{\link[ade4]{cailliez}},\code{\link[ade4]{dudi.pco}}
+}
+\examples{
+\dontrun{
+data(microsatt)
+obj <- as.genpop(microsatt$tab)
+
+listDist <- lapply(1:5, function(i) cailliez(dist.genpop(obj,met=i)))
+for(i in 1:5) {attr(listDist[[i]],"Labels") <- popNames(obj)}
+listPco <- lapply(listDist, dudi.pco,scannf=FALSE)
+
+par(mfrow=c(2,3))
+for(i in 1:5) {scatter(listPco[[i]],sub=paste("Dist:", i))}
+
+}
+}
+\keyword{multivariate}
diff --git a/man/eHGDP.Rd b/man/eHGDP.Rd
new file mode 100644
index 0000000..a8a5111
--- /dev/null
+++ b/man/eHGDP.Rd
@@ -0,0 +1,148 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\name{eHGDP}
+\alias{eHGDP}
+\title{Extended HGDP-CEPH dataset}
+\format{\code{eHGDP} is a genind object with a data frame named
+\code{popInfo} as supplementary component (\code{eHGDP at other$popInfo}),
+which contains the following variables: \describe{ \item{Population: }{a
+character vector indicating populations.} \item{Region: }{a character vector
+indicating the geographic region of each population.} \item{Label: }{a
+character vector indicating the correspondence with population labels used
+in the genind object (i.e., as output by \code{pop(eHGDP)}).}
+\item{Latitude,Longitude: }{geographic coordinates of the populations,
+indicated as north and east degrees.} }}
+\source{
+Original panel by Human Genome Diversity Project (HGDP) and Centre
+d'Etude du Polymorphisme Humain (CEPH). See reference [4] for Native
+American populations.
+
+This copy of the dataset was prepared by Francois Balloux.
+}
+\description{
+This dataset consists of 1350 individuals from native Human populations
+distributed worldwide typed at 678 microsatellite loci. The original
+HGDP-CEPH panel [1-3] has been extended by several native American
+populations [4]. This dataset was used to illustrate the Discriminant
+Analysis of Principal Components (DAPC, [5]).
+}
+\examples{
+
+\dontrun{
+## LOAD DATA
+data(eHGDP)
+eHGDP
+
+
+## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
+## to reproduce exactly analyses from the paper, use "n.pca=1000"
+dapc1 <- dapc(eHGDP, all.contrib=TRUE, scale=FALSE,
+n.pca=200, n.da=80) # takes 2 minutes
+dapc1
+
+## (see ?dapc for details about the output)
+
+
+
+## SCREEPLOT OF EIGENVALUES
+barplot(dapc1$eig, main="eHGDP - DAPC eigenvalues",
+col=c("red","green","blue", rep("grey", 1000)))
+
+
+
+## SCATTERPLOTS
+## (!) Note: colors may be inverted with respect to [5]
+## as signs of principal components are arbitrary
+## and change from one computer to another
+##
+## axes 1-2
+s.label(dapc1$grp.coord[,1:2], clab=0, sub="Axes 1-2")
+par(xpd=T)
+colorplot(dapc1$grp.coord[,1:2], dapc1$grp.coord, cex=3, add=TRUE)
+add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25)
+
+## axes 2-3
+s.label(dapc1$grp.coord[,2:3], clab=0, sub="Axes 2-3")
+par(xpd=T)
+colorplot(dapc1$grp.coord[,2:3], dapc1$grp.coord, cex=3, add=TRUE)
+add.scatter.eig(dapc1$eig,10,1,2, posi="bottomright", ratio=.3, csub=1.25)
+
+
+
+## MAP DAPC1 RESULTS
+if(require(maps)){
+
+xy <- cbind(eHGDP$other$popInfo$Longitude, eHGDP$other$popInfo$Latitude)
+
+par(mar=rep(.1,4))
+map(fill=TRUE, col="lightgrey")
+colorplot(xy, -dapc1$grp.coord, cex=3, add=TRUE, trans=FALSE)
+}
+
+
+
+## LOOK FOR OTHER CLUSTERS
+## to reproduce results of the reference paper, use :
+## grp <- find.clusters(eHGDP, max.n=50, n.pca=200, scale=FALSE)
+## and then
+## plot(grp$Kstat, type="b", col="blue")
+
+grp <- find.clusters(eHGDP, max.n=30, n.pca=200,
+scale=FALSE, n.clust=4) # takes about 2 minutes
+names(grp)
+
+## (see ?find.clusters for details about the output)
+
+
+
+## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
+## to reproduce exactly analyses from the paper, use "n.pca=1000"
+dapc2 <- dapc(eHGDP, pop=grp$grp, all.contrib=TRUE,
+scale=FALSE, n.pca=200, n.da=80) # takes around a 1 minute
+dapc2
+
+
+## PRODUCE SCATTERPLOT
+scatter(dapc2) # axes 1-2
+scatter(dapc2,2,3) # axes 2-3
+
+
+## MAP DAPC2 RESULTS
+if(require(maps)){
+xy <- cbind(eHGDP$other$popInfo$Longitude,
+eHGDP$other$popInfo$Latitude)
+
+myCoords <- apply(dapc2$ind.coord, 2, tapply, pop(eHGDP), mean)
+
+par(mar=rep(.1,4))
+map(fill=TRUE, col="lightgrey")
+colorplot(xy, myCoords, cex=3, add=TRUE, trans=FALSE)
+}
+
+}
+
+}
+\references{
+[1] Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, et
+al. (2002) Genetic structure of human populations. \emph{Science} 298:
+2381-2385.
+
+[2] Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, et
+al. (2005) Support from the relationship of genetic and geographic distance
+in human populations for a serial founder effect originating in Africa.
+\emph{Proc Natl Acad Sci U S A} 102: 15942-15947.
+
+[3] Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, et al. (2002) A human
+genome diversity cell line panel. \emph{Science} 296: 261-262.
+
+[4] Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, et al. (2007)
+Genetic Variation and Population Structure in Native Americans. \emph{PLoS
+Genetics} 3: e185.
+
+[5] Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of
+principal components: a new method for the analysis of genetically
+structured populations. Submitted to \emph{BMC genetics}.
+}
+\keyword{datasets}
+
diff --git a/man/fasta2DNAbin.Rd b/man/fasta2DNAbin.Rd
new file mode 100644
index 0000000..ecd0330
--- /dev/null
+++ b/man/fasta2DNAbin.Rd
@@ -0,0 +1,61 @@
+\encoding{UTF-8}
+\name{fasta2DNAbin}
+\alias{fasta2DNAbin}
+\title{ Read large DNA alignments into R}
+\description{
+ The function \code{fasta2DNAbin} reads alignments with the fasta
+ format (extensions ".fasta", ".fas", or ".fa"), and outputs a
+ \code{\link[ape]{DNAbin}} object (the efficient DNA representation from the
+ ape package). The output contains either the full alignments, or only
+ SNPs. This implementation is designed for memory-efficiency,
+ and can read in larger datasets than Ape's \code{\link[ape]{read.dna}}.
+
+ The function reads data by chunks of a few genomes (minimum 1, no
+ maximum) at a time, which allows one to read massive datasets with
+ negligible RAM requirements (albeit at a cost of computational
+ time). The argument \code{chunkSize} indicates the number of genomes
+ read at a time. Increasing this value decreases the computational time
+ required to read data in, while increasing memory requirements.
+
+}
+\usage{
+fasta2DNAbin(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE)
+}
+\arguments{
+ \item{file}{ a character string giving the path to the file to
+ convert, with the extension ".fa", ".fas", or ".fasta".}
+ \item{quiet}{a logical stating whether a conversion messages should be
+ printed (FALSE, default) or not (TRUE).}
+ \item{chunkSize}{an integer indicating the number of genomes to be
+ read at a time; larger values require more RAM but decrease the time
+ needed to read the data.}
+ \item{snpOnly}{a logical indicating whether SNPs only should be returned.}
+}
+\value{an object of the class \code{\link[ape]{DNAbin}}}
+\seealso{
+ - \code{?DNAbin} for a description of the class \code{\link[ape]{DNAbin}}.
+
+ - \code{\link{read.snp}}: read SNPs in adegenet's '.snp' format.
+
+ - \code{\link{read.PLINK}}: read SNPs in PLINK's '.raw' format.
+
+ - \code{\link{df2genind}}: convert any multiallelic markers into
+ adegenet \linkS4class{genind}.
+
+ - \code{\link{import2genind}}: read multiallelic markers from various
+ software into adegenet.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+## show the example file ##
+## this is the path to the file:
+myPath <- system.file("files/usflu.fasta",package="adegenet")
+myPath
+
+## read the file
+obj <- fasta2DNAbin(myPath, chunk=10) # process 10 sequences at a time
+obj
+}
+}
+\keyword{manip}
diff --git a/man/fasta2genlight.Rd b/man/fasta2genlight.Rd
new file mode 100644
index 0000000..1702c6f
--- /dev/null
+++ b/man/fasta2genlight.Rd
@@ -0,0 +1,96 @@
+\encoding{UTF-8}
+\name{fasta2genlight}
+\alias{fasta2genlight}
+\title{ Extract Single Nucleotide Polymorphism (SNPs) from alignments}
+\description{
+ The function \code{fasta2genlight} reads alignments with the fasta
+ format (extensions ".fasta", ".fas", or ".fa"), extracts the binary
+ SNPs, and converts the output into a \linkS4class{genlight} object.
+
+ The function reads data by chunks of a few genomes (minimum 1, no
+ maximum) at a time, which allows one to read massive datasets with
+ negligible RAM requirements (albeit at a cost of computational
+ time). The argument \code{chunkSize} indicates the number of genomes
+ read at a time. Increasing this value decreases the computational time
+ required to read data in, while increasing memory requirements.
+
+ Multiple cores can be used to decrease the overall computational time
+ on parallel architectures (needs the package \code{parallel}).
+}
+\usage{
+fasta2genlight(file, quiet=FALSE, chunkSize = 1000, saveNbAlleles=FALSE,
+ parallel = require("parallel"), n.cores = NULL, \dots)
+}
+\arguments{
+ \item{file}{ a character string giving the path to the file to
+ convert, with the extension ".fa", ".fas", or ".fasta".}
+ \item{quiet}{ logical stating whether a conversion messages should be
+ printed (FALSE,default) or not (TRUE).}
+ \item{chunkSize}{an integer indicating the number of genomes to be
+ read at a time; larger values require more RAM but decrease the time
+ needed to read the data.}
+ \item{saveNbAlleles}{a logical indicating whether the number of
+ alleles for each loci in the original alignment should be saved in the
+ \code{other} slot (TRUE), or not (FALSE, default). In large genomes,
+ this takes some space but allows for tracking SNPs with more than 2
+ alleles, lost during the conversion.}
+ \item{parallel}{a logical indicating whether multiple cores -if
+ available- should be used for the computations (TRUE, default), or
+ not (FALSE); requires the package \code{parallel} to be installed
+ (see details).}
+ \item{n.cores}{if \code{parallel} is TRUE, the number of cores to be
+ used in the computations; if NULL, then the maximum number of cores
+ available on the computer is used.}
+ \item{\dots}{other arguments to be passed to other functions -
+ currently not used.}
+}
+\details{
+
+ === Using multiple cores ===
+
+ Most recent machines have one or several processors with multiple
+ cores. R processes usually use one single core. The package
+ \code{parallel} allows for parallelizing some computations on
+ multiple cores, which decreases drastically computational time.
+
+ To use this functionality, you need to have the last version of the
+ \code{parallel} package installed.
+}
+\value{an object of the class \linkS4class{genlight}}
+\seealso{
+ - \code{?genlight} for a description of the class \linkS4class{genlight}.
+
+ - \code{\link{read.snp}}: read SNPs in adegenet's '.snp' format.
+
+ - \code{\link{read.PLINK}}: read SNPs in PLINK's '.raw' format.
+
+ - \code{\link{df2genind}}: convert any multiallelic markers into
+ adegenet \linkS4class{genind}.
+
+ - \code{\link{import2genind}}: read multiallelic markers from various
+ software into adegenet.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+## show the example file ##
+## this is the path to the file:
+myPath <- system.file("files/usflu.fasta",package="adegenet")
+myPath
+
+## read the file
+obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time
+obj
+
+## look at extracted information
+position(obj)
+alleles(obj)
+locNames(obj)
+
+## plot positions of polymorphic sites
+temp <- density(position(obj), bw=10)
+plot(temp, xlab="Position in the alignment", lwd=2, main="Location of the SNPs")
+points(position(obj), rep(0, nLoc(obj)), pch="|", col="red")
+}
+}
+\keyword{manip}
diff --git a/man/find.clusters.Rd b/man/find.clusters.Rd
new file mode 100644
index 0000000..5b2f7dc
--- /dev/null
+++ b/man/find.clusters.Rd
@@ -0,0 +1,280 @@
+\encoding{UTF-8}
+\name{find.clusters}
+\alias{find.clusters}
+\alias{find.clusters.data.frame}
+\alias{find.clusters.matrix}
+\alias{find.clusters.genind}
+\alias{find.clusters.genlight}
+\alias{.find.sub.clusters}
+\title{find.cluster: cluster identification using successive K-means}
+\description{
+ These functions implement the clustering procedure used in
+ Discriminant Analysis of Principal Components (DAPC, Jombart et
+ al. 2010). This procedure consists in running successive K-means with
+ an increasing number of clusters (\code{k}), after transforming data
+ using a principal component analysis (PCA). For each model, a
+ statistical measure of goodness of fit (by default, BIC) is computed,
+ which allows to choose the optimal \code{k}. See \code{details} for a
+ description of how to select the optimal \code{k} and
+ \code{vignette("adegenet-dapc")} for a tutorial.
+
+ Optionally, hierarchical clustering can be sought by providing a prior
+ clustering of individuals (argument \code{clust}). In such case, clusters will
+ be sought within each prior group.
+
+ The K-means procedure used in \code{find.clusters} is \code{\link[stats]{kmeans}} function
+ from the \code{stats} package. The PCA function is \code{\link[ade4]{dudi.pca}} from the
+ \code{ade4} package, except for \linkS4class{genlight} objects which
+ use the \code{\link{glPca}} procedure from adegenet.
+
+ \code{find.clusters} is a generic function with methods for the
+ following types of objects:\cr
+ - \code{data.frame} (only numeric data)\cr
+ - \code{matrix} (only numeric data)\cr
+ - \code{\linkS4class{genind}} objects (genetic markers)\cr
+ - \code{\linkS4class{genlight}} objects (genome-wide SNPs)
+
+}
+\usage{
+\method{find.clusters}{data.frame}(x, clust=NULL, n.pca=NULL,
+ n.clust=NULL, stat=c("BIC","AIC", "WSS"),
+ choose.n.clust=TRUE,criterion=c("diffNgroup",
+ "min","goesup", "smoothNgoesup", "goodfit"),
+ max.n.clust=round(nrow(x)/10), n.iter=1e5, n.start=10,
+ center=TRUE, scale=TRUE, pca.select=c("nbEig","percVar"),
+ perc.pca=NULL, \ldots, dudi=NULL)
+
+\method{find.clusters}{matrix}(x, \ldots)
+
+\method{find.clusters}{genind}(x, clust=NULL, n.pca=NULL, n.clust=NULL,
+ stat=c("BIC","AIC", "WSS"), choose.n.clust=TRUE,
+ criterion=c("diffNgroup", "min","goesup", "smoothNgoesup",
+ "goodfit"), max.n.clust=round(nrow(x at tab)/10), n.iter=1e5,
+ n.start=10, scale=FALSE, truenames=TRUE, \ldots)
+
+\method{find.clusters}{genlight}(x, clust=NULL, n.pca=NULL,
+ n.clust=NULL, stat=c("BIC", "AIC",
+ "WSS"),choose.n.clust=TRUE, criterion=c("diffNgroup",
+ "min","goesup","smoothNgoesup", "goodfit"),
+ max.n.clust=round(nInd(x)/10), n.iter=1e5,n.start=10,
+ scale=FALSE, pca.select=c("nbEig","percVar"),
+ perc.pca=NULL,glPca=NULL, \ldots)
+}
+\arguments{
+ \item{x}{\code{a data.frame}, \code{matrix}, or \code{\linkS4class{genind}}
+ object. For the \code{data.frame} and \code{matrix} arguments, only
+ quantitative variables should be provided.}
+ \item{clust}{an optional \code{factor} indicating a prior group membership of
+ individuals. If provided, sub-clusters will be sought within each prior
+ group.}
+ \item{n.pca}{an \code{integer} indicating the number of axes retained in the
+ Principal Component Analysis (PCA) step. If \code{NULL}, interactive selection
+ is triggered.}
+ \item{n.clust}{ an optinal \code{integer} indicating the number of clusters to
+ be sought. If provided, the function will only run K-means once, for this
+ number of clusters. If left as \code{NULL}, several K-means are run for a
+ range of k (number of clusters) values.}
+ \item{stat}{ a \code{character} string matching 'BIC', 'AIC', or 'WSS', which
+ indicates the statistic to be computed for each model (i.e., for each value of
+ \code{k}). BIC: Bayesian Information Criterion. AIC: Aikaike's Information
+ Criterion. WSS: within-groups sum of squares, that is, residual variance.}
+ \item{choose.n.clust}{ a \code{logical} indicating whether the number of
+ clusters should be chosen by the user (TRUE, default), or automatically,
+ based on a given criterion (argument \code{criterion}). It is HIGHLY
+ RECOMMENDED to choose the number of clusters INTERACTIVELY, since
+ i) the decrease of the summary statistics (BIC by default) is
+ informative, and ii) no criteria for automatic selection is
+ appropriate to all cases (see details).}
+ \item{criterion}{ a \code{character} string matching "diffNgroup",
+ "min","goesup", "smoothNgoesup", or "goodfit", indicating the criterion for automatic
+ selection of the optimal number of clusters. See \code{details} for
+ an explanation of these procedures.}
+ \item{max.n.clust}{ an \code{integer} indicating the maximum number of
+ clusters to be tried. Values of 'k' will be picked up between 1 and \code{max.n.clust}}
+ \item{n.iter}{ an \code{integer} indicating the number of iterations to be used
+ in each run of K-means algorithm. Corresponds to \code{iter.max} of
+ \code{kmeans} function.}
+ \item{n.start}{ an \code{integer} indicating the number of randomly
+ chosen starting centroids to be used in each run of the K-means
+ algorithm. Using more starting points ensures convergence of the
+ algorithm. Corresponds to \code{nstart} of \code{kmeans} function.}
+ \item{center}{a \code{logical} indicating whether variables should be centred to
+ mean 0 (TRUE, default) or not (FALSE). Always TRUE for \linkS4class{genind}
+ objects.}
+ \item{scale}{a \code{logical} indicating whether variables should be
+ scaled (TRUE) or not (FALSE, default). Scaling consists in dividing
+ variables by their (estimated) standard deviation to account for
+ trivial differences in variances. In allele frequencies, it comes with
+ the risk of giving uninformative alleles more importance while
+ downweighting informative alleles. Further scaling options are
+ available for \linkS4class{genind} objects (see argument
+ \code{scale.method}).}
+ \item{pca.select}{a \code{character} indicating the mode of selection of PCA
+ axes, matching either "nbEig" or "percVar". For "nbEig", the user
+ has to specify the number of axes retained (interactively, or via
+ \code{n.pca}). For "percVar", the user has to specify the minimum amount of
+ the total variance to be preserved by the retained axes, expressed as a
+ percentage (interactively, or via \code{perc.pca}). }
+ \item{perc.pca}{a \code{numeric} value between 0 and 100 indicating the
+ minimal percentage of the total variance of the data to be expressed by the
+ retained axes of PCA.}
+ \item{truenames}{a \code{logical} indicating whether true (i.e., user-specified)
+ labels should be used in object outputs (TRUE, default) or not
+ (FALSE), in which case generic labels are used.}
+ \item{\ldots}{further arguments to be passed to other functions. For
+ \code{find.clusters.matrix}, arguments are to match those of the
+ \code{data.frame} method.}
+ \item{dudi}{optionally, a multivariate analysis with the class
+ \code{dudi} (from the ade4 package). If provided, prior PCA will be
+ ignored, and this object will be used as a prior step for variable
+ orthogonalisation.}
+ \item{glPca}{an optional \code{\link{glPca}} object; if provided,
+ dimension reduction is not performed (saving computational time) but
+ taken directly from this object.}
+}
+\details{
+ === ON THE SELECTION OF K ===\cr
+ (where K is the 'optimal' number of clusters)
+
+ So far, the analysis of data simulated under various population
+ genetics models (see reference) suggested an ad hoc rule for the
+ selection of the optimal number of clusters. First important result is
+ that BIC seems for efficient than AIC and WSS to select the
+ appropriate number of clusters (see example). The rule of thumb
+ consists in increasing K until it no longer leads to an appreciable
+ improvement of fit (i.e., to a decrease of BIC). In the most simple
+ models (island models), BIC decreases until it reaches the optimal K,
+ and then increases. In these cases, our rule amounts to choosing the
+ lowest K. In other models such as stepping stones, the decrease of BIC
+ often continues after the optimal K, but is much less steep.
+
+
+ An alternative approach is the automatic selection based on a fixed
+ criterion. Note that, in any case, it is highly recommended to look at
+ the graph of the BIC for different numbers of clusters as displayed
+ during the interactive cluster selection.
+ To use automated selection, set \code{choose.n.clust} to FALSE and specify
+ the \code{criterion} you want to use, from the following values:
+
+ - "diffNgroup": differences between successive values of the summary
+ statistics (by default, BIC) are splitted into two groups using a
+ Ward's clustering method (see \code{?hclust}), to differentiate sharp
+ decrease from mild decreases or increases. The retained K is the one
+ before the first group switch. Appears to work well for
+ island/hierarchical models, and decently for isolation by distance
+ models, albeit with some unstability. Can be impacted by an initial,
+ very sharp decrease of the test statistics. IF UNSURE ABOUT THE
+ CRITERION TO USE, USE THIS ONE.
+
+ - "min": the model with the minimum summary statistics (as specified
+ by \code{stat} argument, BIC by default) is retained. Is likely to
+ work for simple island model, using BIC. It is likely to fail in
+ models relating to stepping stones, where the BIC always decreases
+ (albeit by a small amount) as K increases. In general, this approach
+ tends to over-estimate the number of clusters.
+
+ - "goesup": the selected model is the K after which increasing the
+ number of clusters leads to increasing the summary statistics. Suffers
+ from inaccuracy, since i) a steep decrease might follow a small 'bump'
+ of increase of the statistics, and ii) increase might never happen, or
+ happen after negligible decreases. Is likely to work only for
+ clear-cut island models.
+
+ - "smoothNgoesup": a variant of "goesup", in which the summary
+ statistics is first smoothed using a lowess approach. Is meant to be
+ more accurate than "goesup" as it is less prone to stopping to small
+ 'bumps' in the decrease of the statistics.
+
+ - "goodfit": another criterion seeking a good fit with a minimum
+ number of clusters. This approach does not rely on differences between
+ successive statistics, but on absolute fit. It selects the model with
+ the smallest K so that the overall fit is above a given threshold.
+}
+\value{
+ The class \code{find.clusters} is a list with the following
+ components:\cr
+ \item{Kstat}{a \code{numeric} vector giving the values of the summary
+ statistics for the different values of K. Is NULL if \code{n.clust} was specified.}
+ \item{stat}{a \code{numeric} value giving the value of the summary statistics
+ for the retained model}
+ \item{grp}{a \code{factor} giving group membership for each individual.}
+ \item{size}{an \code{integer} vector giving the size of the different clusters.}
+}
+\references{
+ Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+ principal components: a new method for the analysis of genetically
+ structured populations. BMC Genetics 11:94. doi:10.1186/1471-2156-11-94
+}
+\seealso{
+ - \code{\link{dapc}}: implements the DAPC.
+
+ - \code{\link{scatter.dapc}}: graphics for DAPC.
+
+ - \code{\link{dapcIllus}}: dataset illustrating the DAPC and \code{find.clusters}.
+
+ - \code{\link{eHGDP}}: dataset illustrating the DAPC and \code{find.clusters}.
+
+ - \code{\link[stats]{kmeans}}: implementation of K-means in the stat package.
+
+ - \code{\link[ade4]{dudi.pca}}: implementation of PCA in the ade4 package.
+
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+## THIS ONE TAKES A FEW MINUTES TO RUN ##
+data(eHGDP)
+
+## here, n.clust is specified, so that only on K value is used
+grp <- find.clusters(eHGDP, max.n=30, n.pca=200, scale=FALSE,
+n.clust=4) # takes about 2 minutes
+names(grp)
+grp$Kstat
+grp$stat
+
+
+## to try different values of k (interactive)
+grp <- find.clusters(eHGDP, max.n=50, n.pca=200, scale=FALSE)
+
+## and then, to plot BIC values:
+plot(grp$Kstat, type="b", col="blue")
+
+
+
+## ANOTHER SIMPLE EXAMPLE ##
+data(sim2pop) # this actually contains 2 pop
+
+## DETECTION WITH BIC (clear result)
+foo.BIC <- find.clusters(sim2pop, n.pca=100, choose=FALSE)
+plot(foo.BIC$Kstat, type="o", xlab="number of clusters (K)", ylab="BIC",
+col="blue", main="Detection based on BIC")
+points(2, foo.BIC$Kstat[2], pch="x", cex=3)
+mtext(3, tex="'X' indicates the actual number of clusters")
+
+
+## DETECTION WITH AIC (less clear-cut)
+foo.AIC <- find.clusters(sim2pop, n.pca=100, choose=FALSE, stat="AIC")
+plot(foo.AIC$Kstat, type="o", xlab="number of clusters (K)",
+ylab="AIC", col="purple", main="Detection based on AIC")
+points(2, foo.AIC$Kstat[2], pch="x", cex=3)
+mtext(3, tex="'X' indicates the actual number of clusters")
+
+
+## DETECTION WITH WSS (less clear-cut)
+foo.WSS <- find.clusters(sim2pop, n.pca=100, choose=FALSE, stat="WSS")
+plot(foo.WSS$Kstat, type="o", xlab="number of clusters (K)", ylab="WSS
+(residual variance)", col="red", main="Detection based on WSS")
+points(2, foo.WSS$Kstat[2], pch="x", cex=3)
+mtext(3, tex="'X' indicates the actual number of clusters")
+
+
+## TOY EXAMPLE FOR GENLIGHT OBJECTS ##
+x <- glSim(100,500,500)
+x
+plot(x)
+grp <- find.clusters(x, n.pca=100, choose=FALSE, stat="BIC")
+plot(grp$Kstat, type="o", xlab="number of clusters (K)",
+ylab="BIC",main="find.clusters on a genlight object\n(two groups)")
+}
+}
+\keyword{multivariate}
diff --git a/man/gengraph.Rd b/man/gengraph.Rd
new file mode 100644
index 0000000..47a2b8d
--- /dev/null
+++ b/man/gengraph.Rd
@@ -0,0 +1,118 @@
+\encoding{UTF-8}
+\name{gengraph}
+\alias{gengraph}
+\alias{gengraph.default}
+\alias{gengraph.matrix}
+\alias{gengraph.dist}
+\alias{gengraph.genind}
+\alias{gengraph.genpop}
+\alias{gengraph.DNAbin}
+\title{Genetic transitive graphs}
+\description{
+ These functions are under development. Please email the author before
+ using them for published work.\cr
+
+ The function \code{gengraph} generates graphs based on genetic
+ distances, so that pairs of entities (individuals or populations) are
+ connected if and only if they are distant by less than a given
+ threshold distance. Graph algorithms and classes from the
+ \code{\link[igraph]{igraph}} package are used.\cr
+
+ \code{gengraph} is a generic function with methods for the
+ following types of objects:\cr
+ - \code{matrix} (only numeric data)\cr
+ - \code{dist} \cr
+ - \code{\linkS4class{genind}} objects (genetic markers, individuals)\cr
+ - \code{\linkS4class{genpop}} objects (genetic markers, populations)\cr
+ - \code{\link[ape]{DNAbin}} objects (DNA sequences)
+}
+\usage{
+gengraph(x, \dots)
+
+\method{gengraph}{matrix}(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
+ plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
+ nbreaks=10, \dots)
+
+\method{gengraph}{dist}(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
+ plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
+ nbreaks=10, \dots)
+
+\method{gengraph}{genind}(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
+ plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
+ nbreaks=10, \dots)
+
+\method{gengraph}{genpop}(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
+ plot=TRUE, show.graph=TRUE, col.pal=funky, method=1,
+ truenames=TRUE, nbreaks=10, \dots)
+
+\method{gengraph}{DNAbin}(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
+ plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
+ nbreaks=10, \dots)
+
+}
+\arguments{
+ \item{x}{a \code{matrix}, \code{dist}, \code{\linkS4class{genind}},
+ \code{\linkS4class{genpop}}, or \code{DNAbin} object. For
+ \code{matrix} and \code{dist}, the object represents pairwise
+ (by default, Hamming) distances between considered individuals.}
+
+ \item{cutoff}{a \code{numeric} value indicating the cutoff point,
+ i.e. the distance at which two entities are no longer connected in
+ the garph produced by the method.}
+
+ \item{ngrp}{an \code{integer} indicating the number of groups to be
+ looked for. A message is issued if this exact number could not be found.}
+
+ \item{computeAll}{a \code{logical} stating whether to investigate
+ solutions for every (integer) cutoff point; defaults to FALSE.}
+
+ \item{plot}{a \code{logical} indicating whether plots should be drawn;
+ defaults to TRUE; this operation can take time for large, highly-connected graphs.}
+
+ \item{show.graph}{a \code{logical} indicating whether the found graph
+ should be drawn, only used in the interactive mode; this operation
+ can take time for large, highly-connected graphs; defaults to FALSE.}
+
+ \item{col.pal}{a color palette used to define group colors.}
+
+ \item{method}{an \code{integer} ranging from 1 to 6 indicating the
+ type of method to be used to derive a matrix of pairwise distances
+ between populations; values from 1 to 5 are passed to the function
+ \code{dist.genpop}; other values are not supported.}
+
+ \item{truenames}{a logical indicating whether original labels should
+ be used for plotting (TRUE), as opposed to indices of sequences
+ (FALSE).}
+
+ \item{nbreaks}{an integer indicating the number of breaks used by the
+ heuristic when seeking an exact number of groups.}
+
+ \item{\dots}{further arguments to be used by other functions;
+ currently not used.}
+}
+\value{
+ The class \code{gengraph} is a list with the following
+ components:\cr
+ \item{graph}{a graph of class \code{\link[igraph]{igraph}}.}
+ \item{clust}{a list containing group information: \code{$membership}:
+ an integer giving group membership; \code{$csize}: the size of each
+ cluster; \code{$no}: the number of clusters}
+ \item{cutoff}{the value used as a cutoff point}
+ \item{col}{the color used to plot each group.}
+}
+\seealso{
+ The \code{\link[igraph]{igraph}} package.
+}
+\author{
+ Original idea by Anne Cori and Christophe Fraser.
+ Implementation by Thibaut Jombart \email{t.jombart at imperial.ac.uk}.
+ }
+\examples{
+if(require(ape)){
+ data(woodmouse)
+ g <- gengraph(woodmouse, cutoff=5)
+ g
+ plot(g$graph)
+
+}
+}
diff --git a/man/genind.Rd b/man/genind.Rd
new file mode 100644
index 0000000..16d5d8a
--- /dev/null
+++ b/man/genind.Rd
@@ -0,0 +1,104 @@
+\encoding{UTF-8}
+\name{genind class}
+\alias{genind-class}
+\alias{print,genind-method}
+\alias{show,genind-method}
+\alias{names,genind-method}
+\alias{summary,genind-method}
+\alias{print,genindSummary-method}
+\alias{print.genindSummary}
+\alias{is.genind}
+\alias{.valid.genind}
+\title{adegenet formal class (S4) for individual genotypes}
+\description{The S4 class \code{genind} is used to store individual genotypes.\cr
+ It contains several components described in the 'slots' section).\cr
+ The \code{summary} of a \code{genind} object invisibly returns a list of component.
+ The function \code{.valid.genind} is for internal use.
+ The function \code{genind} creates a genind object from a valid table
+ of alleles corresponding to the \code{@tab} slot.
+ Note that as in other S4 classes, slots are accessed using @ instead
+ of \$.
+}
+\section{Slots}{
+ \describe{
+ \item{\code{tab}:}{
+ matrix integers containing genotypes data for
+ individuals (in rows) for all alleles (in columns). The table
+ differs depending on the \code{@type} slot:\cr
+ - 'codom': values
+ are numbers of alleles, summing up to the
+ individuals' ploidies.\cr
+ - 'PA': values are presence/absence of alleles.\cr
+ In all cases, rows and columns are given generic names.}
+ \item{\code{loc.fac}:}{locus factor for the columns of \code{tab}}
+ \item{\code{loc.n.all}:}{integer vector giving the number of alleles per locus}
+ \item{\code{all.names}:}{list having one component per locus, each containing a character vector of alleles names}
+ \item{\code{ploidy}:}{ an integer indicating the degree of ploidy of
+ the genotypes. Beware: 2 is not an integer, but as.integer(2) is.}
+ \item{\code{type}:}{ a character string indicating the type of
+ marker: 'codom' stands for 'codominant' (e.g. microstallites,
+ allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP).}
+ \item{\code{call}:}{the matched call}
+ \item{\code{strata}:}{(optional) data frame giving levels of population stratification for each individual}
+ \item{\code{hierarchy}:}{(optional) a hierarchical \code{\link{formula}} defining the hierarchical levels in the \code{@@strata} slot.}
+ \item{\code{pop}:}{(optional) factor giving the population of each individual}
+ \item{\code{other}:}{(optional) a list containing other information}
+ }
+}
+
+\section{Extends}{
+Class \code{"\linkS4class{gen}"}, directly.
+Class \code{"\linkS4class{indInfo}"}, directly.
+}
+\section{Methods}{
+ \describe{
+ \item{names}{\code{signature(x = "genind")}: give the names of the
+ components of a genind object}
+ \item{print}{\code{signature(x = "genind")}: prints a genind object}
+ \item{show}{\code{signature(object = "genind")}: shows a genind
+ object (same as print)}
+ \item{summary}{\code{signature(object = "genind")}: summarizes a
+ genind object, invisibly returning its content or suppress printing of auxiliary information by specifying \code{verbose = FALSE}}
+ }
+}
+\seealso{\code{\link{as.genind}}, \code{\link{genind2genpop}},
+ \code{\link{genpop}}, \code{\link{import2genind}},
+ \code{\link{read.genetix}}, \code{\link{read.genepop}},
+ \code{\link{read.fstat}}\cr
+
+ Related classes:\cr
+ - \linkS4class{genpop} for storing data per populations\cr
+
+ - \linkS4class{genlight} for an efficient storage of binary SNPs genotypes\cr
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+showClass("genind")
+
+obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"))
+obj
+validObject(obj)
+summary(obj)
+
+\dontrun{
+# test inter-colonies structuration
+if(require(hierfstat)){
+gtest <- gstat.randtest(obj,nsim=99)
+gtest
+plot(gtest)
+}
+
+# perform a between-class PCA
+pca1 <- dudi.pca(scaleGen(obj, NA.method="mean"),scannf=FALSE,scale=FALSE)
+pcabet1 <- between(pca1,obj at pop,scannf=FALSE)
+pcabet1
+
+s.class(pcabet1$ls,obj at pop,sub="Inter-class PCA",possub="topleft",csub=2)
+add.scatter.eig(pcabet1$eig,2,xax=1,yax=2)
+
+}
+}
+\keyword{classes}
+\keyword{manip}
+\keyword{multivariate}
+
diff --git a/man/genind2df.Rd b/man/genind2df.Rd
new file mode 100644
index 0000000..8496a80
--- /dev/null
+++ b/man/genind2df.Rd
@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/export.R
+\name{genind2df}
+\alias{genind2df}
+\title{Convert a genind object to a data.frame.}
+\usage{
+genind2df(x, pop = NULL, sep = "", usepop = TRUE, oneColPerAll = FALSE)
+}
+\arguments{
+\item{x}{a \linkS4class{genind} object}
+
+\item{pop}{an optional factor giving the population of each individual.}
+
+\item{sep}{a character string separating alleles. See details.}
+
+\item{usepop}{a logical stating whether the population (argument \code{pop}
+or \code{x at pop} should be used (TRUE, default) or not (FALSE)).}
+
+\item{oneColPerAll}{a logical stating whether or not alleles should be split
+into columns (defaults to \code{FALSE}). This will only work with data with
+consistent ploidies.}
+}
+\value{
+a data.frame of raw allelic data, with individuals in rows and loci in column
+}
+\description{
+The function \code{genind2df} converts a \linkS4class{genind} back to a
+data.frame of raw allelic data.
+}
+\examples{
+
+## simple example
+df <- data.frame(locusA=c("11","11","12","32"),
+locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22"))
+row.names(df) <- .genlab("genotype",4)
+df
+
+obj <- df2genind(df, ploidy=2, ncode=1)
+obj
+obj at tab
+
+
+## converting a genind as data.frame
+genind2df(obj)
+genind2df(obj, sep="/")
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{df2genind}}, \code{\link{import2genind}}, \code{\link{read.genetix}},
+\code{\link{read.fstat}}, \code{\link{read.structure}}
+}
+\keyword{manip}
+
diff --git a/man/genind2genpop.Rd b/man/genind2genpop.Rd
new file mode 100644
index 0000000..02e2404
--- /dev/null
+++ b/man/genind2genpop.Rd
@@ -0,0 +1,102 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genind2genpop.R
+\name{genind2genpop}
+\alias{genind2genpop}
+\title{Conversion from a genind to a genpop object}
+\usage{
+genind2genpop(x, pop = NULL, quiet = FALSE, process.other = FALSE,
+ other.action = mean)
+}
+\arguments{
+\item{x}{an object of class \code{genind}.}
+
+\item{pop}{a factor giving the population of each genotype in 'x' OR a
+formula specifying which strata are to be used when converting to a genpop
+object. If none provided, population factors are sought in x at pop, but if
+given, the argument prevails on x at pop.}
+
+\item{quiet}{logical stating whether a conversion message must be printed
+(TRUE,default) or not (FALSE).}
+
+\item{process.other}{a logical indicating whether the \code{@other} slot
+should be processed (see details).}
+
+\item{other.action}{a function to be used when processing the \code{@other}
+slot. By default, 'mean' is used.}
+}
+\value{
+A genpop object. The component @other in 'x' is passed to the
+ created genpop object.
+}
+\description{
+The function \code{genind2genpop} converts genotypes data (genind) into
+alleles counts per population (genpop).
+}
+\details{
+=== 'missing' argument ===\cr The values of the 'missing' argument in
+\code{genind2genpop} have the following effects:\cr - "NA": if all genotypes
+of a population for a given allele are missing, count value will be NA\cr
+
+- "0": if all genotypes of a population for a given allele are missing, count
+value will be 0\cr
+
+- "chi2": if all genotypes of a population for a given allele are missing,
+count value will be that of a theoretical count in of a Chi-squared test.
+This is obtained by the product of the margins sums divided by the total
+number of alleles.\cr
+
+=== processing the \code{@other} slot ===\cr Essentially,
+\code{genind2genpop} is about aggregating data per population. The function
+can do the same for all numeric items in the \code{@other} slot provided
+they have the same length (for vectors) or the same number of rows
+(matrix-like objects) as the number of genotypes. When the case is
+encountered and if \code{process.other} is TRUE, then these objects are
+processed using the function defined in \code{other.action} per population.
+For instance, spatial coordinates of genotypes would be averaged to obtain
+population coordinates.
+}
+\examples{
+
+## simple conversion
+data(nancycats)
+nancycats
+catpop <- genind2genpop(nancycats)
+catpop
+summary(catpop)
+
+## processing the @other slot
+data(sim2pop)
+sim2pop$other$foo <- letters
+sim2pop
+dim(sim2pop$other$xy) # matches the number of genotypes
+sim2pop$other$foo # does not match the number of genotypes
+
+obj <- genind2genpop(sim2pop, process.other=TRUE)
+obj$other # the new xy is the populations' centre
+
+pch <- as.numeric(pop(sim2pop))
+col <- pop(sim2pop)
+levels(col) <- c("blue","red")
+col <- as.character(col)
+plot(sim2pop$other$xy, pch=pch, col=col)
+text(obj$other$xy, lab=row.names(obj$other$xy), col=c("blue","red"), cex=2, font=2)
+\dontrun{
+data(microbov)
+strata(microbov) <- data.frame(other(microbov))
+summary(genind2genpop(microbov)) # Conversion based on population factor
+summary(genind2genpop(microbov, ~coun)) # Conversion based on country
+summary(genind2genpop(microbov, ~coun/spe)) # Conversion based on country and species
+
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\linkS4class{genind}, \linkS4class{genpop}
+}
+\keyword{classes}
+\keyword{manip}
+\keyword{multivariate}
+
diff --git a/man/genlight.Rd b/man/genlight.Rd
new file mode 100644
index 0000000..41552c4
--- /dev/null
+++ b/man/genlight.Rd
@@ -0,0 +1,348 @@
+\name{genlight-class}
+\docType{class}
+\alias{genlight}
+\alias{genlight-class}
+\alias{[,genlight-method}
+\alias{[,genlight,ANY,ANY-method}
+\alias{[,genlight,ANY,ANY,ANY-method}
+\alias{initialize,genlight-method}
+\alias{show,genlight-method}
+\alias{nLoc,genlight-method}
+\alias{nInd,genlight-method}
+\alias{dim,genlight-method}
+\alias{nPop,genlight-method}
+\alias{$,genlight-method}
+\alias{$<-,genlight-method}
+\alias{names,genlight-method}
+\alias{ploidy,genlight-method}
+\alias{ploidy<-,genlight-method}
+\alias{locNames,genlight-method}
+\alias{locNames<-,genlight-method}
+\alias{indNames,genlight-method}
+\alias{indNames<-,genlight-method}
+\alias{popNames,genlight-method}
+\alias{popNames<-,genlight-method}
+\alias{alleles,genlight-method}
+\alias{alleles<-,genlight-method}
+\alias{chromosome}
+\alias{chromosome<-}
+\alias{chromosome,genlight-method}
+\alias{chromosome<-,genlight-method}
+\alias{chr}
+\alias{chr<-}
+\alias{chr,genlight-method}
+\alias{chr<-,genlight-method}
+\alias{position}
+\alias{position<-}
+\alias{position,genlight-method}
+\alias{position<-,genlight-method}
+\alias{pop,genlight-method}
+\alias{pop<-,genlight-method}
+\alias{NA.posi}
+\alias{NA.posi,genlight-method}
+\alias{other,genlight-method}
+\alias{other<-,genlight-method}
+\alias{as.matrix.genlight}
+\alias{as.data.frame.genlight}
+\alias{as,matrix,genlight-method}
+\alias{as,data.frame,genlight-method}
+\alias{as,list,genlight-method}
+\alias{coerce,matrix,genlight-method}
+\alias{coerce,data.frame,genlight-method}
+\alias{coerce,list,genlight-method}
+\alias{as.list.genlight}
+\alias{cbind.genlight}
+\alias{rbind.genlight}
+% \alias{,genlight-method}
+% \alias{,genlight-method}
+% \alias{,genlight-method}
+% \alias{,genlight-method}
+%%%%
+\title{Formal class "genlight"}
+\description{
+ The class \code{genlight} is a formal (S4) class for storing a genotypes
+ of binary SNPs in a compact way, using a bit-level coding scheme.
+ This storage is most efficient with haploid data, where the memory
+ taken to represent data can be reduced more than 50 times. However,
+ \code{genlight} can be used for any level of ploidy, and still remain an
+ efficient storage mode.
+
+ A \code{genlight} object can be constructed from vectors of integers
+ giving the number of the second allele for each locus and each
+ individual (see 'Objects of the class genlight' below).
+
+ \code{genlight} stores multiple genotypes. Each genotype is stored
+ as a \linkS4class{SNPbin} object.
+}
+\section{Objects from the class genlight}{
+ \code{genlight} objects can be created by calls to \code{new("genlight",
+ ...)}, where '...' can be the following arguments:
+ \describe{
+ \item{\code{gen}}{input genotypes, where each genotype is coded as a
+ vector of numbers of the second allele. If a list, each slot of the
+ list correspond to an individual; if a matrix or a data.frame, rows
+ correspond to individuals and columns to SNPs. If individuals or
+ loci are named in the input, these names will we stored in the
+ produced object. All individuals are expected to have the same
+ number of SNPs. Shorter genotypes are completed with NAs, issuing a
+ warning.}
+ \item{\code{ploidy}}{an optional vector of integers indicating the ploidy of the
+ genotypes. Genotypes can therefore have different ploidy. If not
+ provided, ploidy will be guessed from the data (as the
+ maximum number of second alleles in each individual).}
+ \item{\code{ind.names}}{an optional vector of characters giving the labels
+ of the genotypes.}
+ \item{\code{loc.names}}{an optional vector of characters giving the labels
+ of the SNPs.}
+ \item{\code{loc.all}}{an optional vector of characters indicating
+ the alleles of each SNP; for each SNP, alleles must be coded by two
+ letters separated by '/', e.g. 'a/t' is valid, but 'a t' or 'a |t'
+ are not.}
+ \item{\code{chromosome}}{an optional factor indicating the
+ chromosome to which each SNP belongs.}
+ \item{\code{position}}{an optional vector of integers indicating the
+ position of the SNPs.}
+ \item{\code{other}}{an optional list storing miscellaneous information.}
+ }
+}
+\section{Slots}{
+ The following slots are the content of instances of the class
+ \code{genlight}; note that in most cases, it is better to retrieve
+ information via accessors (see below), rather than by accessing the
+ slots manually.
+ \describe{
+ \item{\code{gen}:}{a list of genotypes stored as \linkS4class{SNPbin} objects.}
+ \item{\code{n.loc}:}{an integer indicating the number of SNPs of the
+ genotype.}
+ \item{\code{ind.names}:}{a vector of characters indicating the names of
+ genotypes.}
+ \item{\code{loc.names}:}{a vector of characters indicating the names of
+ SNPs.}
+ \item{\code{loc.all}:}{a vector of characters indicating the alleles
+ of each SNP.}
+ \item{\code{chromosome}:}{an optional factor indicating the
+ chromosome to which each SNP belongs.}
+ \item{\code{position}:}{an optional vector of integers indicating the
+ position of the SNPs.}
+ \item{\code{ploidy}:}{a vector of integers indicating the ploidy of each individual.}
+ \item{\code{pop}:}{a factor indicating the population of each individual.}
+ \item{\code{strata}:}{a data frame containing different levels of population definition. (For methods, see \code{\link{addStrata}} and \code{\link{setPop}})}
+ \item{\code{hierarchy}:}{a hierarchical \code{\link{formula}} defining the hierarchical levels in the \code{@@strata} slot.}
+ \item{\code{other}:}{a list containing other miscellaneous information.}
+ }
+}
+\section{Methods}{
+ Here is a list of methods available for \code{genlight} objects. Most of
+ these methods are accessors, that is, functions which are used to
+ retrieve the content of the object. Specific manpages can exist for
+ accessors with more than one argument. These are indicated by a '*'
+ symbol next to the method's name. This list also contains methods
+ for conversion from \code{genlight} to other classes.
+ \describe{
+ \item{[}{\code{signature(x = "genlight")}: usual method to subset
+ objects in R. Is to be applied as if the object was a matrix where
+ genotypes were rows and SNPs were columns. Indexing can be done via
+ vectors of signed integers or of logicals. See details for extra
+ supported arguments.}
+ \item{show}{\code{signature(x = "genlight")}: printing of the
+ object.}
+
+ \item{$}{\code{signature(x = "genlight")}: similar to the @ operator;
+ used to access the content of slots of the object.}
+ \item{$<-}{\code{signature(x = "genlight")}: similar to the @ operator;
+ used to replace the content of slots of the object.}
+
+ \item{nInd}{\code{signature(x = "genlight")}: returns the number of
+ individuals in the object.}
+ \item{nPop}{\code{signature(x = "genlight")}: returns the number of
+ populations in the object.}
+ \item{nLoc}{\code{signature(x = "genlight")}: returns the number of
+ SNPs in the object.}
+ \item{dim}{\code{signature(x = "genlight")}: returns the number of
+ individuals and SNPs in the object, respectively.}
+
+ \item{names}{\code{signature(x = "genlight")}: returns the names of
+ the slots of the object.}
+
+ \item{indNames}{\code{signature(x = "genlight")}: returns the names of
+ the individuals, if provided when the object was constructed.}
+ \item{indNames<-}{\code{signature(x = "genlight")}: sets the names of
+ the individuals using a character vector of length
+ \code{nInd(x)}.}
+ \item{popNames}{\code{signature(x = "genlight")}: returns the names of
+ the populations, if provided when the object was constructed.}
+ \item{popNames<-}{\code{signature(x = "genlight")}: sets the names of
+ the populations using a character vector of length
+ \code{nPop(x)}.}
+
+ \item{locNames}{\code{signature(x = "genlight")}: returns the names of
+ the loci, if provided when the object was constructed.}
+ \item{locNames<-}{\code{signature(x = "genlight")}: sets the names of
+ the SNPs using a character vector of length \code{nLoc(x)}.}
+
+ \item{ploidy}{\code{signature(x = "genlight")}: returns the ploidy of
+ the genotypes.}
+ \item{ploidy<-}{\code{signature(x = "genlight")}: sets the ploidy of
+ the individuals using a vector of integers of size \code{nInd(x)};
+ if a single value is provided, the same ploidy is assumed for all
+ individuals.}
+
+ \item{NA.posi}{\code{signature(x = "genlight")}: returns the indices
+ of missing values (NAs) as a list with one vector of integer for each individual.}
+
+ \item{alleles}{\code{signature(x = "genlight")}: returns the names
+ of the alleles of each SNPs, if provided when the object was
+ constructed.}
+ \item{alleles<-}{\code{signature(x = "genlight")}: sets the names
+ of the alleles of each SNPs using a character vector of length
+ \code{nLoc(x)}; for each SNP, two alleles must be provided,
+ separated by a "/", e.g. 'a/t', 'c/a', etc.}
+
+ \item{chromosome}{\code{signature(x = "genlight")}: returns a factor
+ indicating the chromosome of each SNPs, or NULL if the information
+ is missing.}
+ \item{chromosome<-}{\code{signature(x = "genlight")}: sets the
+ chromosome to which SNPs belong using a factor of length
+ \code{nLoc(x)}.}
+
+ \item{chr}{\code{signature(x = "genlight")}: shortcut for
+ \code{chromosome}.}
+ \item{chr<-}{\code{signature(x = "genlight")}: shortcut for
+ \code{chromosome<-}.}
+
+ \item{position}{\code{signature(x = "genlight")}: returns an integer
+ vector indicating the position of each SNPs, or NULL if the
+ information is missing.}
+ \item{position<-}{\code{signature(x = "genlight")}: sets the
+ positions of the SNPs using an integer vector of length
+ \code{nLoc(x)}.}
+
+ \item{pop}{\code{signature(x = "genlight")}: returns a factor
+ indicating the population of each individual, if provided when the
+ object was constructed.}
+ \item{pop<-}{\code{signature(x = "genlight")}: sets the population
+ of each individual using a factor of length \code{nInd(x)}.}
+ \item{other}{\code{signature(x = "genlight")}: returns the content of
+ the slot \code{@other}.}
+ \item{other<-}{\code{signature(x = "genlight")}: sets the content of
+ the slot \code{@other}.}
+
+ \item{as.matrix}{\code{signature(x = "genlight")}: converts a
+ \code{genlight} object into a matrix of integers, with individuals
+ in rows and SNPs in columns. The S4 method 'as' can be used as
+ well (e.g. as(x, "matrix")).}
+ \item{as.data.frame}{\code{signature(x = "genlight")}: same as \code{as.matrix}.}
+ \item{as.list}{\code{signature(x = "genlight")}: converts a
+ \code{genlight} object into a list of genotypes coded as vector of
+ integers (numbers of second allele). The S4 method 'as' can be
+ used as well (e.g. as(x, "list")).}
+
+ \item{cbind}{\code{signature(x = "genlight")}: merges several
+ \linkS4class{genlight} objects by column, i.e. regroups data of
+ identical individuals genotyped for different SNPs.}
+ \item{rbind}{\code{signature(x = "genlight")}: merges several
+ \linkS4class{genlight} objects by row, i.e. regroups data of
+ different individuals genotyped for the same SNPs.}
+ }
+}
+\details{
+ === On the subsetting using \code{[} ===
+
+ The function \code{[} accepts the following extra arguments:
+ \describe{
+ \item{treatOther}{a logical stating whether elements of the
+ \code{@other} slot should be treated as well (TRUE), or not
+ (FALSE). If treated, elements of the list are examined for a
+ possible match of length (vectors, lists) or number of rows
+ (matrices, data frames) with the number of individuals. Those who
+ match are subsetted accordingly. Others are left as is, issuing a
+ warning unless the argument \code{quiet} is set to TRUE.}
+ \item{quiet}{a logical indicating whether warnings should be issued
+ when trying to subset components of the \code{@other} slot which
+ do not match the number of individuals (TRUE), or not (FALSE,
+ default). }
+ \item{\dots}{further arguments passed to the genlight constructor.}
+ }
+}
+\author{Thibaut Jombart (\email{t.jombart at imperial.ac.uk})\cr
+Zhian N. Kamvar (\email{kamvarz at science.oregonstate.edu})}
+\seealso{
+ Related class:\cr
+ - \code{\linkS4class{SNPbin}}, for storing individual genotypes of
+ binary SNPs\cr
+
+ - \code{\linkS4class{genind}}, for storing other types of genetic markers. \cr
+}
+\examples{
+\dontrun{
+## TOY EXAMPLE ##
+## create and convert data
+dat <- list(toto=c(1,1,0,0), titi=c(NA,1,1,0), tata=c(NA,0,3, NA))
+x <- new("genlight", dat)
+x
+
+## examine the content of the object
+names(x)
+x at gen
+x at gen[[1]]@snp # bit-level coding for first individual
+
+## conversions
+as.list(x)
+as.matrix(x)
+
+## round trips - must return TRUE
+identical(x, new("genlight", as.list(x))) # list
+identical(x, new("genlight", as.matrix(x))) # matrix
+identical(x, new("genlight", as.data.frame(x))) # data.frame
+
+## test subsetting
+x[c(1,3)] # keep individuals 1 and 3
+as.list(x[c(1,3)])
+x[c(1,3), 1:2] # keep individuals 1 and 3, loci 1 and 2
+as.list(x[c(1,3), 1:2])
+x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)] # same, using logicals
+as.list(x[c(TRUE,FALSE), c(TRUE,TRUE,FALSE,FALSE)])
+
+
+## REAL-SIZE EXAMPLE ##
+## 50 genotypes of 1,000,000 SNPs
+dat <- lapply(1:50, function(i) sample(c(0,1,NA), 1e6, prob=c(.5, .49, .01), replace=TRUE))
+names(dat) <- paste("indiv", 1:length(dat))
+print(object.size(dat), unit="aut") # size of the original data
+
+x <- new("genlight", dat) # conversion
+x
+print(object.size(x), unit="au") # size of the genlight object
+object.size(dat)/object.size(x) # conversion efficiency
+
+
+
+#### cbind, rbind ####
+a <- new("genlight", list(toto=rep(1,10), tata=rep(c(0,1), each=5), titi=c(NA, rep(1,9)) ))
+
+ara <- rbind(a,a)
+ara
+as.matrix(ara)
+
+aca <- cbind(a,a)
+aca
+as.matrix(aca)
+
+
+#### subsetting @other ####
+x <- new("genlight", list(a=1,b=0,c=1), other=list(1:3, letters,data.frame(2:4)))
+x
+other(x)
+x[2:3]
+other(x[2:3])
+other(x[2:3, treatOther=FALSE])
+
+
+#### seppop ####
+pop(x) # no population info
+pop(x) <- c("pop1","pop1", "pop2") # set population memberships
+pop(x)
+seppop(x)
+}
+}
+\keyword{classes}
diff --git a/man/genpop.Rd b/man/genpop.Rd
new file mode 100644
index 0000000..ab0af2b
--- /dev/null
+++ b/man/genpop.Rd
@@ -0,0 +1,84 @@
+\encoding{UTF-8}
+\name{genpop class}
+\alias{genpop-class}
+\alias{dist,genpop,ANY,ANY,ANY,missing-method}
+\alias{names,genpop-method}
+\alias{show,genpop-method}
+\alias{summary,genpop-method}
+\alias{print,genpopSummary-method}
+\alias{print.genpopSummary}
+\alias{is.genpop}
+\title{adegenet formal class (S4) for allele counts in populations}
+\description{An object of class \code{genpop} contain alleles counts
+ for several loci.\cr
+ It contains several components (see 'slots' section).\cr
+ Such object is obtained using \code{genind2genpop} which converts
+ individuals genotypes of known population into a \code{genpop} object.
+ Note that the function \code{summary} of a \code{genpop} object
+ returns a list of components.
+ Note that as in other S4 classes, slots are accessed using @ instead
+ of \$.
+}
+\section{Slots}{
+ \describe{
+ \item{\code{tab}:}{matrix of alleles counts for each combinaison of population
+ (in rows) and alleles (in columns).}
+ \item{\code{loc.fac}:}{locus factor for the columns of \code{tab}}
+ \item{\code{loc.n.all}:}{integer vector giving the number of alleles per locus}
+ \item{\code{all.names}:}{list having one component per locus, each containing a character vector of alleles names}
+ \item{\code{call}:}{the matched call}
+ \item{\code{ploidy}:}{ an integer indicating the degree of ploidy of
+ the genotypes. Beware: 2 is not an integer, but as.integer(2) is.}
+ \item{\code{type}:}{ a character string indicating the type of
+ marker: 'codom' stands for 'codominant' (e.g. microstallites,
+ allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP).}
+ \item{\code{other}:}{(optional) a list containing other information}
+ }
+}
+\section{Extends}{
+Class \code{"\linkS4class{gen}"}, directly.
+Class \code{"\linkS4class{popInfo}"}, directly.
+}
+\section{Methods}{
+ \describe{
+ \item{names}{\code{signature(x = "genpop")}: give the names of the
+ components of a genpop object}
+ \item{print}{\code{signature(x = "genpop")}: prints a genpop object}
+ \item{show}{\code{signature(object = "genpop")}: shows a genpop
+ object (same as print)}
+ \item{summary}{\code{signature(object = "genpop")}: summarizes a
+ genpop object, invisibly returning its content or suppress printing of auxiliary information by specifying \code{verbose = FALSE}}
+ }
+}
+\seealso{\code{\link{as.genpop}}, \code{\link{is.genpop}},\code{\link{makefreq}}, \code{\link{genind}}, \code{\link{import2genind}}, \code{\link{read.genetix}}, \code{\link{read.genepop}}, \code{\link{read.fstat}}
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+obj1 <- import2genind(system.file("files/nancycats.gen",
+package="adegenet"))
+obj1
+
+
+obj2 <- genind2genpop(obj1)
+obj2
+
+\dontrun{
+data(microsatt)
+# use as.genpop to convert convenient count tab to genpop
+obj3 <- as.genpop(microsatt$tab)
+obj3
+
+all(obj3 at tab==microsatt$tab)
+
+# perform a correspondance analysis
+obj4 <- genind2genpop(obj1,missing="chi2")
+ca1 <- dudi.coa(as.data.frame(obj4 at tab),scannf=FALSE)
+s.label(ca1$li,sub="Correspondance Analysis",csub=2)
+add.scatter.eig(ca1$eig,2,xax=1,yax=2,posi="top")
+
+}
+}
+\keyword{classes}
+\keyword{manip}
+\keyword{multivariate}
+
diff --git a/man/glAux.Rd b/man/glAux.Rd
new file mode 100644
index 0000000..6958492
--- /dev/null
+++ b/man/glAux.Rd
@@ -0,0 +1,122 @@
+\encoding{UTF-8}
+\name{genlight auxiliary functions}
+\alias{glSum}
+\alias{glNA}
+\alias{glMean}
+\alias{glVar}
+\alias{glDotProd}
+\title{Auxiliary functions for genlight objects}
+\description{
+ These functions provide facilities for usual computations using
+ \linkS4class{genlight} objects. When ploidy varies across individuals,
+ the outputs of these functions depend on whether the information
+ units are individuals, or alleles within individuals (see details).
+
+ These functions are:
+
+ - \code{glSum}: computes the sum of the number of second allele in each SNP.
+
+ - \code{glNA}: computes the number of missing values in each SNP.
+
+ - \code{glMean}: computes the mean number of second allele in each SNP.
+
+ - \code{glVar}: computes the variance of the number of second allele in each SNP.
+
+ - \code{glDotProd}: computes dot products between (possibly
+ centred/scaled) vectors of individuals - uses compiled C code - used
+ by glPca.
+}
+\usage{
+glSum(x, alleleAsUnit = TRUE, useC = FALSE)
+glNA(x, alleleAsUnit = TRUE)
+glMean(x, alleleAsUnit = TRUE)
+glVar(x, alleleAsUnit = TRUE)
+glDotProd(x, center = FALSE, scale = FALSE, alleleAsUnit = FALSE,
+ parallel = require("parallel"), n.cores = NULL)
+}
+\arguments{
+ \item{x}{a \linkS4class{genlight} object}
+ \item{alleleAsUnit}{a logical indicating whether alleles are
+ considered as units (i.e., a diploid genotype equals two samples, a
+ triploid, three, etc.) or whether individuals are considered as
+ units of information.}
+ \item{center}{a logical indicating whether SNPs should be centred to
+ mean zero.}
+ \item{scale}{a logical indicating whether SNPs should be scaled to
+ unit variance.}
+ \item{useC}{a logical indicating whether compiled C code should be
+ used (TRUE) or not (FALSE, default).}
+ \item{parallel}{a logical indicating whether multiple cores -if
+ available- should be used for the computations (TRUE, default), or
+ not (FALSE); requires the package \code{parallel} to be installed
+ (see details); this option cannot be used alongside useCoption.}
+ \item{n.cores}{if \code{parallel} is TRUE, the number of cores to
+ be used in the computations; if NULL, then the maximum number of
+ cores available on the computer is used.}
+}
+\details{
+ === On the unit of information ===
+
+ In the cases where individuals can have different ploidy, computation
+ of sums, means, etc. of allelic data depends on what we consider as a
+ unit of information.
+
+ To estimate e.g. allele frequencies, unit of information can be
+ considered as the allele, so that a diploid genotype contains two
+ samples, a triploid individual, three samples, etc. In such a case,
+ all computations are done directly on the number of alleles. This
+ corresponds to \code{alleleAsUnit = TRUE}.
+
+ However, when the focus is put on studying differences/similarities
+ between individuals, the unit of information is the individual, and
+ all genotypes possess the same information no matter what their ploidy
+ is. In this case, computations are made after standardizing
+ individual genotypes to relative allele frequencies. This
+ corresponds to \code{alleleAsUnit = FALSE}.
+
+ Note that when all individuals have the same ploidy, this distinction
+ does not hold any more.
+}
+\value{
+ A numeric vector containing the requested information.
+}
+
+\seealso{
+ - \code{\linkS4class{genlight}}: class of object for storing massive binary
+ SNP data.
+
+ - \code{\link{dapc}}: Discriminant Analysis of Principal Components.
+
+ - \code{\link{glPca}}: PCA for \linkS4class{genlight} objects.
+
+ - \code{\link{glSim}}: a simple simulator for \linkS4class{genlight} objects.
+
+ - \code{\link{glPlot}}: plotting \linkS4class{genlight} objects.
+
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+x <- new("genlight", list(c(0,0,1,1,0), c(1,1,1,0,0,1), c(2,1,1,1,1,NA)))
+x
+as.matrix(x)
+ploidy(x)
+
+## compute statistics - allele as unit ##
+glNA(x)
+glSum(x)
+glMean(x)
+
+## compute statistics - individual as unit ##
+glNA(x, FALSE)
+glSum(x, FALSE)
+glMean(x, FALSE)
+
+## explanation: data are taken as relative frequencies
+temp <- as.matrix(x)/ploidy(x)
+apply(temp,2, function(e) sum(is.na(e))) # NAs
+apply(temp,2,sum, na.rm=TRUE) # sum
+apply(temp,2,mean, na.rm=TRUE) # mean
+}
+}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/glPca.Rd b/man/glPca.Rd
new file mode 100644
index 0000000..c5983d0
--- /dev/null
+++ b/man/glPca.Rd
@@ -0,0 +1,184 @@
+\encoding{UTF-8}
+\name{glPca}
+\alias{glPca}
+\alias{print.glPca}
+\alias{scatter.glPca}
+\alias{loadingplot.glPca}
+\title{Principal Component Analysis for genlight objects}
+\description{
+ These functions implement Principal Component Analysis (PCA) for
+ massive SNP datasets stored as \linkS4class{genlight} object. This
+ implementation has the advantage of never representing to complete data
+ matrix, therefore making huge economies in terms of rapid access
+ memory (RAM). When the \code{parallel} package is available,
+ \code{glPca} uses multiple-core ressources for more efficient
+ computations. \code{glPca} returns lists with the class \code{glPca}
+ (see 'value').
+
+ Other functions are defined for objects of this class:
+
+ - \code{print}: prints the content of a \code{glPca} object.
+
+ - \code{scatter}: produces scatterplots of principal components,
+ with a screeplot of eigenvalues as inset.
+
+ - \code{loadingplot}: plots the loadings of the analysis for one given
+ axis, using an adapted version of the generic function \code{loadingplot}.
+}
+\usage{
+glPca(x, center = TRUE, scale = FALSE, nf = NULL, loadings = TRUE,
+ alleleAsUnit = FALSE, useC = TRUE, parallel = require("parallel"),
+ n.cores = NULL, returnDotProd=FALSE, matDotProd=NULL)
+
+\method{print}{glPca}(x, \dots)
+
+\method{scatter}{glPca}(x, xax = 1, yax = 2, posi = "bottomleft", bg = "white",
+ ratio = 0.3, label = rownames(x$scores), clabel = 1, xlim = NULL,
+ ylim = NULL, grid = TRUE, addaxes = TRUE, origin = c(0, 0),
+ include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft",
+ cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, \dots)
+
+\method{loadingplot}{glPca}(x, at=NULL, threshold=NULL, axis=1,
+ fac=NULL, byfac=FALSE, lab=rownames(x$loadings), cex.lab=0.7, cex.fac=1,
+ lab.jitter=0, main="Loading plot", xlab="SNP positions",
+ ylab="Contributions", srt = 90, adj = c(0, 0.5), \dots)
+
+}
+\arguments{
+ \item{x}{for \code{glPca}, a \linkS4class{genlight} object; for
+ \code{print}, \code{scatter}, and \code{loadingplot}, a \code{glPca}
+ object.}
+ \item{center}{a logical indicating whether the numbers of alleles
+ should be centered; defaults to TRUE}
+ \item{scale}{a logical indicating whether the numbers of alleles
+ should be scaled; defaults to FALSE}
+ \item{nf}{an integer indicating the number of principal components to
+ be retained; if NULL, a screeplot of eigenvalues will be displayed
+ and the user will be asked for a number of retained axes.}
+ \item{loadings}{a logical indicating whether loadings of the alleles
+ should be computed (TRUE, default), or not (FALSE). Vectors of
+ loadings are not always useful, and can take a large amount of
+ RAM when millions of SNPs are considered.}
+ \item{alleleAsUnit}{a logical indicating whether alleles are
+ considered as units (i.e., a diploid genotype equals two samples, a
+ triploid, three, etc.) or whether individuals are considered as
+ units of information.}
+ \item{useC}{a logical indicating whether compiled C code should be
+ used for faster computations; this option cannot be used alongside
+ parallel option.}
+ \item{parallel}{a logical indicating whether multiple cores -if
+ available- should be used for the computations (TRUE, default), or
+ not (FALSE); requires the package \code{parallel} to be installed
+ (see details); this option cannot be used alongside useCoption.}
+ \item{n.cores}{if \code{parallel} is TRUE, the number of cores to be
+ used in the computations; if NULL, then the maximum number of cores
+ available on the computer is used.}
+ \item{returnDotProd}{a logical indicating whether the matrix of dot
+ products between individuals should be returned (TRUE) or not
+ (FALSE, default).}
+ \item{matDotProd}{an optional matrix of dot products between
+ individuals, NULL by default. This option is used internally to
+ speed up computation time when re-running the same PCA several
+ times. Leave this argument as NULL unless you really know what you
+ are doing.}
+ \item{\dots}{further arguments to be passed to other functions.}
+
+ \item{xax,yax}{\code{integers} specifying which principal components
+ should be shown in x and y axes. }
+ \item{posi,bg,ratio}{arguments used to customize the inset in scatterplots
+ of \code{glPca} results. See \code{\link[ade4]{add.scatter}} documentation in the
+ ade4 package for more details.}
+ \item{label,clabel,xlim,ylim,grid,addaxes,origin,include.origin,sub,csub,possub,cgrid,pixmap,contour,area}{
+ arguments passed to \code{\link[ade4]{s.class}}; see \code{?s.label} for more information}
+ \item{at}{an optional numeric vector giving the abscissa at which
+ loadings are plotted. Useful when variates are SNPs with a known
+ position in an alignement.}
+ \item{threshold}{a threshold value above which values of x are
+ identified. By default, this is the third quartile of x.}
+ \item{axis}{an integer indicating the column of x to be plotted; used
+ only if x is a matrix-like object.}
+ \item{fac}{a factor defining groups of SNPs.}
+ \item{byfac}{a logical stating whether loadings should be averaged by
+ groups of SNPs, as defined by \code{fac}.}
+ \item{lab}{a character vector giving the labels used to annotate
+ values above the threshold.}
+ \item{cex.lab}{a numeric value indicating the size of annotations.}
+ \item{cex.fac}{a numeric value indicating the size of annotations for
+ groups of observations.}
+ \item{lab.jitter}{a numeric value indicating the factor of
+ randomisation for the position of annotations. Set to 0 (by default)
+ implies no randomisation.}
+ \item{main}{the main title of the figure.}
+ \item{xlab}{the title of the x axis.}
+ \item{ylab}{the title of the y axis.}
+ \item{srt}{rotation of the labels; see ?text.}
+ \item{adj}{adjustment of the labels; see ?text.}
+}
+\details{
+ === Using multiple cores ===
+
+ Most recent machines have one or several processors with multiple
+ cores. R processes usually use one single core. The package
+ \code{parallel} allows for parallelizing some computations on
+ multiple cores, which can decrease drastically computational time.
+
+ Lastly, note that using compiled C code (\code{useC=TRUE})is an
+ alternative for speeding up computations, but cannot be used together
+ with the parallel option.
+}
+\value{
+ === glPca objects ===
+
+ The class \code{glPca} is a list with the following
+ components:\cr
+ \item{call}{the matched call.}
+ \item{eig}{a numeric vector of eigenvalues.}
+ \item{scores}{a matrix of principal components, containing the
+ coordinates of each individual (in row) on each principal axis (in column).}
+ \item{loadings}{(optional) a matrix of loadings, containing the loadings of each
+ SNP (in row) for each principal axis (in column).}
+
+ -
+
+ === other outputs ===
+
+ Other functions have different outputs:\cr
+ - \code{scatter} return the matched call.\cr
+ - \code{loadingplot} returns information about the most contributing
+ SNPs (see \code{\link{loadingplot.default}})
+}
+
+\seealso{
+ - \code{\linkS4class{genlight}}: class of object for storing massive binary
+ SNP data.
+
+ - \code{\link{glSim}}: a simple simulator for \linkS4class{genlight} objects.
+
+ - \code{\link{glPlot}}: plotting \linkS4class{genlight} objects.
+
+ - \code{\link{dapc}}: Discriminant Analysis of Principal Components.
+
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+## simulate a toy dataset
+x <- glSim(50,4e3, 50, ploidy=2)
+x
+plot(x)
+
+## perform PCA
+pca1 <- glPca(x, nf=2)
+
+## plot eigenvalues
+barplot(pca1$eig, main="eigenvalues", col=heat.colors(length(pca1$eig)))
+
+## basic plot
+scatter(pca1, ratio=.2)
+
+## plot showing groups
+s.class(pca1$scores, pop(x), col=colors()[c(131,134)])
+add.scatter.eig(pca1$eig,2,1,2)
+}
+}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/glPlot.Rd b/man/glPlot.Rd
new file mode 100644
index 0000000..20e2165
--- /dev/null
+++ b/man/glPlot.Rd
@@ -0,0 +1,65 @@
+\encoding{UTF-8}
+\name{glPlot}
+\alias{glPlot}
+\alias{plot.genlight}
+\alias{plot,genlight-method}
+\alias{plot,genlight,ANY-method}
+\title{Plotting genlight objects}
+\description{
+ \linkS4class{genlight} object can be plotted using the function
+ \code{glPlot}, which is also used as the dedicated \code{plot}
+ method. These functions relie on \code{\link{image}} to represent SNPs
+ data. More specifically, colors are used to represent the number of
+ second allele for each locus and individual.
+}
+\usage{
+glPlot(x, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),\dots)
+
+\S4method{plot}{genlight}(x, y=NULL, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),\dots)
+
+}
+\arguments{
+ \item{x}{a \linkS4class{genlight} object.}
+ \item{col}{an optional color vector; the first value corresponds to 0
+ alleles, the last value corresponds to the ploidy level of the
+ data. Therefore, the vector should have a length of (\code{ploidy(x)+1}).}
+ \item{legend}{a logical indicating whether a legend should be added to
+ the plot.}
+ \item{posi}{a character string indicating where the legend should be
+ positioned. Can be any concatenation of "bottom"/"top" and "left"/"right".}
+ \item{bg}{a color used as a background for the legend; by default,
+ transparent white is used; this may not be supported on some
+ devices, and therefore background should be specified
+ (e.g. \code{bg="white"}).}
+ \item{\dots}{further arguments to be passed to \code{\link{image}}.}
+ \item{y}{ununsed argument, present for compatibility with the
+ \code{plot} generic.}
+}
+\seealso{
+ - \code{\link{genlight}}: class of object for storing massive binary
+ SNP data.
+
+ - \code{\link{glSim}}: a simple simulator for \linkS4class{genlight}
+ objects.
+
+ - \code{\link{glPca}}: PCA for \linkS4class{genlight} objects.
+
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+## simulate data
+x <- glSim(100, 1e3, n.snp.struc=100, ploid=2)
+
+## default plot
+glPlot(x)
+plot(x) # identical plot
+
+## disable legend
+plot(x, leg=FALSE)
+
+## use other colors
+plot(x, col=heat.colors(3), bg="white")
+}
+}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/glSim.Rd b/man/glSim.Rd
new file mode 100644
index 0000000..dc50fc8
--- /dev/null
+++ b/man/glSim.Rd
@@ -0,0 +1,130 @@
+\encoding{UTF-8}
+\name{glSim}
+\alias{glSim}
+\title{Simulation of simple genlight objects}
+\description{
+ The function \code{glSim} simulates simple SNP data with the
+ possibility of contrasted structures between two groups
+ as well as background ancestral population structure.
+ Returned objects are instances of the class \linkS4class{genlight}.
+}
+\usage{
+glSim(n.ind, n.snp.nonstruc, n.snp.struc = 0, grp.size = c(0.5, 0.5), k = NULL,
+ pop.freq = NULL, ploidy = 1, alpha = 0, parallel = FALSE,
+ LD = TRUE, block.minsize = 10, block.maxsize = 1000, theta = NULL,
+ sort.pop = FALSE, \dots)
+}
+\arguments{
+ \item{n.ind}{an integer indicating the number of individuals to be simulated.}
+ \item{n.snp.nonstruc}{an integer indicating the number of
+ non-structured SNPs to be simulated; for these SNPs, all individuals
+ are drawn from the same binomial distribution.}
+ \item{n.snp.struc}{an integer indicating the number of
+ structured SNPs to be simulated; for these SNPs, different
+ binomial distributions are used for the two simulated groups;
+ frequencies of the derived alleles in groups A and B are built to
+ differ (see details).}
+ \item{grp.size}{a vector of length 2 specifying the proportions of the two
+ phenotypic groups (must sum to 1). By default, both groups have the same
+ size.}
+ \item{k}{an integer specifying the number of ancestral populations to be
+ generated.}
+ \item{pop.freq}{a vector of length \code{k} specifying the proportions of the
+ k ancestral populations (must sum to 1). If, as by default, \code{pop.freq}
+ is null, and \code{k} is non-null, \code{pop.freq} will be the result of
+ random sampling into k population groups.}
+ \item{ploidy}{an integer indicating the ploidy of the simulated
+ genotypes.}
+ \item{alpha}{asymmetry parameter: a numeric value between 0 and 0.5,
+ used to enforce allelic differences between the groups. Differences
+ between groups are strongest when alpha = 0.5 and weakest when
+ alpha = 0 (see details).}
+ \item{parallel}{a logical indicating whether multiple cores should be used in
+ generating the simulated data (TRUE). This option can reduce the amount of
+ computational time required to simulate the data, but is not supported on
+ Windows.}
+ \item{LD}{a logical indicating whether loci should be displaying
+ linkage disequilibrium (TRUE) or be generated independently
+ (FALSE, default). When set to TRUE, data are generated by blocks of
+ correlated SNPs (see details).}
+ \item{block.minsize}{an optional integer indicating the minimum number of
+ SNPs to be handled at a time during the simulation of linked SNPs (when
+ \code{LD=TRUE}. Increasing the minimum block size will increase
+ the RAM requirement but decrease the amount of computational time
+ required to simulate the genotypes.}
+ \item{block.maxsize}{an optional integer indicating the maximum number of SNPs
+ to be handled at a time during the simulation of linked SNPs. Note: if LD
+ blocks of equal size are desired, set block.minsize = block.maxsize.}
+ \item{theta}{an optional numeric value between 0 and 0.5 specifying
+ the extent to which linkage should be diluted.
+ Linkage is strongest when theta = 0 and weakest when theta = 0.5.}
+ \item{sort.pop}{a logical specifying whether individuals should be ordered by
+ ancestral population (\code{sort.pop=TRUE}) or phenotypic population
+ (\code{sort.pop=FALSE}).}
+ \item{\dots}{arguments to be passed to the genlight constructor.}
+}
+\details{
+ === Allele frequencies in contrasted groups ===
+
+ When \code{n.snp.struc} is greater than 0, some SNPs are simulated in
+ order to differ between groups (noted 'A' and 'B'). Different patterns
+ between groups are achieved by using different
+ frequencies of the second allele for A and B, denoted \eqn{p_A} and
+ \eqn{p_B}. For a given SNP, \eqn{p_A} is drawn from a uniform
+ distribution between 0 and (0.5 - alpha). \eqn{p_B} is then computed
+ as 1 - \eqn{p_A}. Therefore, differences between groups are mild for
+ alpha=0, and total for alpha = 0.5.
+
+
+ === Linked or independent loci ===
+
+ Independent loci (\code{LD=FALSE}) are simulated using the standard
+ binomial distribution, with randomly generated allele
+ frequencies. Linked loci (\code{LD=FALSE}) are trickier towe need to
+ simulate discrete variables with pre-defined correlation structure.
+
+ Here, we first generate deviates from multivariate normal
+ distributions with randomly generated correlation structures. These
+ variables are then discretized using the quantiles of the
+ distribution. Further improvement of the procedure will aim at i)
+ specifying the strength of the correlations between blocks of alleles
+ and ii) enforce contrasted structures between groups.
+}
+\value{
+ A \linkS4class{genlight} object.
+}
+
+\seealso{
+ - \code{\linkS4class{genlight}}: class of object for storing massive binary
+ SNP data.
+
+ - \code{\link{glPlot}}: plotting \linkS4class{genlight} objects.
+
+ - \code{\link{glPca}}: PCA for \linkS4class{genlight} objects.
+}
+\author{ Caitlin Collins \email{caitlin.collins12 at imperial.ac.uk},
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
+\examples{
+\dontrun{
+## no structure
+x <- glSim(100, 1e3, ploid=2)
+plot(x)
+
+## 1,000 non structured SNPs, 100 structured SNPs
+x <- glSim(100, 1e3, n.snp.struc=100, ploid=2)
+plot(x)
+
+## 1,000 non structured SNPs, 100 structured SNPs, ploidy=4
+x <- glSim(100, 1e3, n.snp.struc=100, ploid=4)
+plot(x)
+
+## same thing, stronger differences between groups
+x <- glSim(100, 1e3, n.snp.struc=100, ploid=2, alpha=0.4)
+plot(x)
+
+## same thing, loci with LD structures
+x <- glSim(100, 1e3, n.snp.struc=100, ploid=2, alpha=0.4, LD=TRUE, block.minsize=100)
+plot(x)
+}
+}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/haploGen.Rd b/man/haploGen.Rd
new file mode 100644
index 0000000..062ecf4
--- /dev/null
+++ b/man/haploGen.Rd
@@ -0,0 +1,194 @@
+\name{haploGen}
+\alias{haploGen}
+\alias{print.haploGen}
+\alias{[.haploGen}
+\alias{labels.haploGen}
+\alias{as.POSIXct.haploGen}
+\alias{seqTrack.haploGen}
+\alias{haploGen-class}
+\alias{as.seqTrack.haploGen}
+\alias{as.igraph.haploGen}
+\alias{plot.haploGen}
+\alias{plotHaploGen}
+\alias{sample.haploGen}
+\title{Simulation of genealogies of haplotypes}
+\description{
+ The function \code{haploGen} implements simulations of genealogies of
+ haplotypes. This forward-time, individual-based simulation tool allows
+ haplotypes to replicate and mutate according to specified parameters,
+ and keeps track of their genealogy.
+
+ Simulations can be spatially explicit or not (see \code{geo.sim}
+ argument). In the first case, haplotypes are assigned to locations on
+ a regular grip. New haplotypes disperse from their ancestor's location
+ according to a random Poisson diffusion, or alternatively according to
+ a pre-specified migration scheme. This tool does not allow for
+ simulating selection or linkage disequilibrium.
+
+ Produced objects are lists with the class \code{haploGen}; see 'value'
+ section for more information on this class. Other functions are
+ available to print, plot, subset, sample or convert \code{haploGen}
+ objects. A seqTrack method is also provided for analysing
+ \code{haploGen} objects.
+
+ Note that for simulation of outbreaks, the new tool \code{simOutbreak}
+ in the \code{outbreaker} package should be used.
+}
+\usage{
+haploGen(seq.length=1e4, mu.transi=1e-4, mu.transv=mu.transi/2, t.max=20,
+ gen.time=function(){1+rpois(1,0.5)},
+ repro=function(){rpois(1,1.5)}, max.nb.haplo=200,
+ geo.sim=FALSE, grid.size=10, lambda.xy=0.5,
+ mat.connect=NULL,
+ ini.n=1, ini.xy=NULL)
+\method{print}{haploGen}(x, \dots)
+\method{as.igraph}{haploGen}(x, col.pal=redpal, \dots)
+\method{plot}{haploGen}(x, y=NULL, col.pal=redpal, \dots)
+\method{[}{haploGen}(x, i, j, drop=FALSE)
+\method{labels}{haploGen}(object, \dots)
+\method{as.POSIXct}{haploGen}(x, tz="", origin=as.POSIXct("2000/01/01"), \dots)
+\method{seqTrack}{haploGen}(x, best=c("min","max"), prox.mat=NULL, \dots)
+as.seqTrack.haploGen(x)
+plotHaploGen(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", add=FALSE, \dots)
+sample.haploGen(x, n)
+%\S4method{coerce}{haploGen,graphNEL}(from, to, strict=TRUE)
+}
+\arguments{
+ \item{seq.length}{an integer indicating the length of the simulated
+ haplotypes, in number of nucleotides.}
+ \item{mu.transi}{the rate of transitions, in number of mutation per site and per
+ time unit.}
+ \item{mu.transv}{the rate of transversions, in number of mutation per site and per
+ time unit.}
+ \item{t.max}{an integer indicating the maximum number of time units to
+ run the simulation for.}
+ \item{gen.time}{an integer indicating the generation time, in number
+ of time units. Can be a (fixed) number or a function returning a number
+ (then called for each reproduction event).}
+ \item{repro}{an integer indicating the number of descendents per
+ haplotype. Can be a (fixed) number or a function returning a number
+ (then called for each reproduction event).}
+ \item{max.nb.haplo}{an integer indicating the maximum number of
+ haplotypes handled at any time of the simulation, used to control the
+ size of the produced object. Larger number will lead to slower
+ simulations. If this number is exceeded, the genealogy is prunded to as
+ to keep this number of haplotypes.}
+ \item{geo.sim}{a logical stating whether simulations should be
+ spatially explicit (TRUE) or not (FALSE, default). Spatially-explicit
+ simulations are slightly slower than their non-spatial counterpart.}
+ \item{grid.size}{the size of the square grid of possible locations for
+ spatial simulations. The total number of locations will be this number
+ squared.}
+ \item{lambda.xy}{the parameter of the Poisson distribution used to
+ determine dispersion in x and y axes.}
+ \item{mat.connect}{a matrix of connectivity describing migration
+ amongts all pairs of locations. \code{mat.connect[i,j]} indicates the
+ probability, being in 'i', to migrate to 'j'. The rows of this matrix
+ thus sum to 1. It has as many rows and columns as there are locations,
+ with row 'i' / column 'j' corresponding to locations number 'i' and 'j'.
+ Locations are numbered as in a matrix in which rows and columns are
+ respectively x and y coordinates. For instance, in a 5x5 grid, locations
+ are numbered as in \code{matrix(1:25,5,5)}.}
+ \item{ini.n}{an integer specifying the number of (identical)
+ haplotypes to initiate the simulation}
+ \item{ini.xy}{a vector of two integers giving the x/y coordinates of the initial haplotype.}
+ \item{x,object}{\code{haploGen} objects.}
+ \item{y}{unused argument, for compatibility with 'plot'.}
+ \item{col.pal}{a color palette to be used to represent weights using
+ colors on the edges of the graph. See \code{?num2col}. Note that the
+ palette is inversed by default.}
+ \item{i,j, drop}{\code{i} is a vector used for subsetting the object. For
+ instance, \code{i=1:3} will retain only the first three haplotypes of the
+ genealogy. \code{j} and \code{drop} are only provided for compatibility,
+ but not used.}
+ \item{best, prox.mat}{arguments to be passed to the
+ \code{\link{seqTrack}} function. See documentation of
+ \code{\link{seqTrack}} for more information.}
+ \item{annot,date.range,col,bg,add}{arguments to be passed to \code{\link{plotSeqTrack}}.}
+ \item{n}{an integer indicating the number of haplotypes to be retained
+ in the sample}
+ % \item{from, to}{arguments of the conversion function, for converting a
+ % \code{haploGen} object into a \code{graphNEL-class}.}
+ \item{tz, origin}{ aguments to be passed to \code{\link{as.POSIXct}}
+ (see ?as.POSIXct)}
+ \item{\dots}{further arguments to be passed to other methods; for
+ 'plot', arguments are passed to \code{plot.igraph}.}
+ % \item{strict}{a logical used for compatibility with \code{as} generic
+ % function, but not used in the conversion. See \code{\link{setAs}} for
+ % more information.}
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
+\references{
+ Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
+ outbreaks from genetic data: a graph approach. Heredity. doi:
+ 10.1038/hdy.2010.78.
+}
+\value{
+ === haploGen class ===\cr
+ \code{haploGen} objects are lists containing the following slots:\cr
+ - seq: DNA sequences in the DNAbin matrix format\cr
+ - dates: dates of appearance of the haplotypes\cr
+ - ances: a vector of integers giving the index of each haplotype's
+ ancestor\cr
+ - id: a vector of integers giving the index of each haplotype\cr
+ - xy: (optional) a matrix of spatial coordinates of haplotypes\cr
+ - call: the matched call
+
+
+ === misc functions ===\cr
+ - as.POSIXct: returns a vector of dates with POSIXct format\cr
+ - labels: returns the labels of the haplotypes\cr
+ - as.seqTrack: returns a seqTrack object. Note that this object is not a
+ proper seqTrack analysis, but just a format conversion convenient for
+ plotting \code{haploGen} objects.
+}
+\details{
+ === Dependencies with other packages ===\cr
+ - ape package is required as it implements efficient handling of DNA
+ sequences used in \code{haploGen} objects. To install this package,
+ simply type:\cr
+ \code{install.packages("ape")}
+
+ - for various purposes including plotting, converting genealogies to
+ graphs can be useful. From adegenet version 1.3-5 onwards, this is
+ achieved using the package \code{igraph}. See below.
+
+ === Converting haploGen objects to graphs ===\cr
+ \code{haploGen} objects can be converted to \code{igraph}
+ objects (package \code{igraph}), which can in turn be plotted and manipulated using classical
+ graph tools. Simply use 'as.igraph(x)' where 'x' is a
+ \code{haploGen} object. This functionality requires the \code{igraph}
+ package. Graphs are time oriented (top=old, bottom=recent).
+}
+\seealso{
+ \code{simOutbreak} in the package 'outbreaker' for simulating disease
+ outbreaks under a realistic epidemiological model.
+}
+\examples{
+\dontrun{
+if(require(ape) && require(igraph)){
+## PERFORM SIMULATIONS
+x <- haploGen(geo.sim=TRUE)
+x
+
+## PLOT DATA
+plot(x)
+
+## PLOT SPATIAL SPREAD
+plotHaploGen(x, bg="white")
+title("Spatial dispersion")
+
+
+## USE SEQTRACK RECONSTRUCTION
+x.recons <- seqTrack(x)
+mean(x.recons$ances==x$ances, na.rm=TRUE) # proportion of correct reconstructions
+
+g <- as.igraph(x)
+g
+plot(g)
+plot(g, vertex.size=0)
+
+
+}
+}
+}
diff --git a/man/hierarchy-methods.Rd b/man/hierarchy-methods.Rd
new file mode 100644
index 0000000..1fb7c67
--- /dev/null
+++ b/man/hierarchy-methods.Rd
@@ -0,0 +1,80 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/hierarchyMethods.R
+\docType{methods}
+\name{hier}
+\alias{hier}
+\alias{hier,genind-method}
+\alias{hier,genlight-method}
+\alias{hier<-}
+\alias{hier<-,genind-method}
+\alias{hier<-,genlight-method}
+\title{Access and manipulate the population hierarchy for genind or genlight objects.}
+\usage{
+hier(x, formula = NULL, combine = TRUE, value)
+
+hier(x) <- value
+}
+\arguments{
+\item{x}{a genind or genlight object}
+
+\item{formula}{a nested formula indicating the order of the population
+hierarchy to be returned.}
+
+\item{combine}{if \code{TRUE} (default), the levels will be combined
+according to the formula argument. If it is \code{FALSE}, the levels will
+not be combined.}
+
+\item{value}{a formula specifying the full hierarchy of columns in the strata
+slot. \strong{(See Details below)}}
+}
+\description{
+The following methods allow the user to quickly change the hierarchy or
+population of a genind or genlight object.
+}
+\details{
+You must first specify your strata before you can specify your
+ hierarchies. Hierarchies are special cases of strata in that the levels
+ must be nested within each other. An error will occur if you specify a
+ hierarchy that is not truly hierarchical.
+
+ \subsection{Details on Formulas}{
+
+ The preferred use of these functions is with a \code{\link{formula}}
+ object. Specifically, a hierarchical formula argument is used to name which
+ strata are hierarchical. An example of a hierarchical formula would
+ be:\tabular{r}{ \code{~Country/City/Neighborhood}} This convention was
+ chosen as it becomes easier to type and makes intuitive sense when defining
+ a hierarchy. Note: it is important to use hierarchical formulas when
+ specifying hierarchies as other types of formulas (eg.
+ \code{~Country*City*Neighborhood}) will give incorrect results.}
+}
+\examples{
+# let's look at the microbov data set:
+data(microbov)
+microbov
+
+# We see that we have three vectors of different names in the 'other' slot.
+?microbov
+# These are Country, Breed, and Species
+names(other(microbov))
+
+# Let's set the hierarchy
+strata(microbov) <- data.frame(other(microbov))
+microbov
+
+# And change the names so we know what they are
+nameStrata(microbov) <- ~Country/Breed/Species
+
+# let's see what the hierarchy looks like by Species and Breed:
+hier(microbov) <- ~Species/Breed
+head(hier(microbov, ~Species/Breed))
+
+}
+\author{
+Zhian N. Kamvar
+}
+\seealso{
+\code{\link{strata}} \code{\link{genind}}
+ \code{\link{as.genind}}
+}
+
diff --git a/man/hybridize.Rd b/man/hybridize.Rd
new file mode 100644
index 0000000..eddb1d7
--- /dev/null
+++ b/man/hybridize.Rd
@@ -0,0 +1,104 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/hybridize.R
+\name{hybridize}
+\alias{hybridize}
+\title{Function hybridize takes two genind in inputs
+and generates hybrids individuals having one parent
+in both objects.}
+\usage{
+hybridize(x1, x2, n, pop = "hybrid", res.type = c("genind", "df",
+ "STRUCTURE"), file = NULL, quiet = FALSE, sep = "/", hyb.label = "h")
+}
+\arguments{
+\item{x1}{a \linkS4class{genind} object}
+
+\item{x2}{a \linkS4class{genind} object}
+
+\item{n}{an integer giving the number of hybrids requested}
+
+\item{pop}{a character string giving naming the population of the
+created hybrids.}
+
+\item{res.type}{a character giving the type of output requested. Must
+be "genind" (default), "df" (i.e. data.frame like in
+\code{\link{genind2df}}), or "STRUCTURE" to generate a .str file
+readable by STRUCTURE (in which case the 'file' must be supplied). See
+'details' for STRUCTURE output.}
+
+\item{file}{a character giving the name of the file to be written
+when 'res.type' is "STRUCTURE"; if NULL, a the created file is of the
+form "hybrids\_[the current date].str".}
+
+\item{quiet}{a logical specifying whether the writing to a file (when
+'res.type' is "STRUCTURE") should be announced (FALSE, default) or
+not (TRUE).}
+
+\item{sep}{a character used to separate two alleles}
+
+\item{hyb.label}{a character string used to construct the hybrids
+labels; by default, "h", which gives labels: "h01", "h02", "h03",...}
+}
+\value{
+A \linkS4class{genind} object (by default), or a data.frame of alleles
+(res.type="df"). No R output if res.type="STRUCTURE" (results written
+to the specified file).
+}
+\description{
+The function \code{hybridize} performs hybridization between two set
+of genotypes stored in \linkS4class{genind} objects (referred as the "2
+populations"). Allelic frequencies are derived for each population,
+and then gametes are sampled following a multinomial distribution. \cr
+}
+\details{
+The result consists in a set of 'n' genotypes, with different possible
+outputs (see 'res.type' argument).
+
+
+ If the output is a STRUCTURE file, this file will have the following
+ caracteristics:\cr
+ - file contains the genotypes of the parents, and then the genotypes
+ of hybrids\cr
+ - the first column identifies genotypes\cr
+ - the second column identifies the population (1 and 2 for parents x1 and x2;
+ 3 for hybrids)\cr
+ - the first line contains the names of the markers\cr
+ - one row = one genotype (onerowperind will be true)\cr
+ - missing values coded by "-9" (the software's default)\cr
+}
+\examples{
+\dontrun{
+## Let's make some cattle hybrids
+data(microbov)
+
+## first, isolate each breed
+temp <- seppop(microbov)
+names(temp)
+salers <- temp$Salers
+zebu <- temp$Zebu
+
+## let's make some... Zeblers
+zebler <- hybridize(salers, zebu, n=40,
+ pop="Zebler")
+
+
+## now let's merge all data into a single genind
+newDat <- repool(microbov, zebler)
+
+## make a correspondance analysis
+## and see where hybrids are placed
+X <- genind2genpop(newDat, quiet=TRUE)
+coa1 <- dudi.coa(tab(X),scannf=FALSE,nf=3)
+s.label(coa1$li)
+add.scatter.eig(coa1$eig,2,1,2)
+
+}
+
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{seploc}}, \code{\link{seppop}}, \code{\link{repool}}
+}
+
diff --git a/man/import2genind.Rd b/man/import2genind.Rd
new file mode 100644
index 0000000..6944ba0
--- /dev/null
+++ b/man/import2genind.Rd
@@ -0,0 +1,85 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{import2genind}
+\alias{import2genind}
+\title{Importing data from several softwares to a genind object}
+\usage{
+import2genind(file, quiet = FALSE, ...)
+}
+\arguments{
+\item{file}{a character string giving the path to the file to convert, with
+the appropriate extension.}
+
+\item{quiet}{logical stating whether a conversion message must be printed
+(TRUE,default) or not (FALSE).}
+
+\item{\dots}{other arguments passed to the appropriate 'read' function
+(currently passed to \code{read.structure})}
+}
+\value{
+an object of the class \code{genind}
+}
+\description{
+Their are several ways to import genotype data to a \linkS4class{genind}
+object: i) from a data.frame with a given format (see
+\code{\link{df2genind}}), ii) from a file with a recognized extension, or
+iii) from an alignement of sequences (see \code{\link{DNAbin2genind}}).\cr
+}
+\details{
+The function \code{import2genind} detects the extension of the file given in
+argument and seeks for an appropriate import function to create a
+\code{genind} object.\cr Current recognized formats are :\cr - GENETIX files
+(.gtx) \cr - Genepop files (.gen) \cr - Fstat files (.dat) \cr - STRUCTURE
+files (.str or .stru) \cr
+
+Beware: same data in different formats are not expected to produce exactly
+the same \code{genind} objects.\cr For instance, conversions made by GENETIX
+to Fstat may change the the sorting of the genotypes; GENETIX stores
+individual names whereas Fstat does not; Genepop chooses a sample's name
+from the name of its last genotype; etc.
+}
+\examples{
+
+import2genind(system.file("files/nancycats.gtx",
+package="adegenet"))
+
+import2genind(system.file("files/nancycats.dat",
+package="adegenet"))
+
+import2genind(system.file("files/nancycats.gen",
+package="adegenet"))
+
+import2genind(system.file("files/nancycats.str",
+package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F.
+(1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la genetique des
+populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000,
+Universite de Montpellier II, Montpellier (France). \cr
+
+Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of population
+structure using multilocus genotype data. \emph{Genetics}, \bold{155}:
+945-959
+
+Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population genetics
+software for exact tests and ecumenicism. \emph{J. Heredity},
+\bold{86}:248-249 \cr
+
+Fstat (version 2.9.3). Software by Jerome Goudet.
+http://www2.unil.ch/popgen/softwares/fstat.htm\cr
+
+Excoffier L. & Heckel G.(2006) Computer programs for population genetics
+data analysis: a survival guide \emph{Nature}, \bold{7}: 745-758
+}
+\seealso{
+\code{\link{import2genind}}, \code{\link{read.genetix}},
+\code{\link{read.fstat}}, \code{\link{read.structure}},
+\code{\link{read.genepop}}
+}
+\keyword{manip}
+
diff --git a/man/inbreeding.Rd b/man/inbreeding.Rd
new file mode 100644
index 0000000..5b2f418
--- /dev/null
+++ b/man/inbreeding.Rd
@@ -0,0 +1,113 @@
+\encoding{UTF-8}
+\name{Inbreeding estimation}
+\alias{inbreeding}
+\title{Likelihood-based estimation of inbreeding}
+\description{
+ The function \code{inbreeding} estimates the inbreeding coefficient
+ of an individuals (F) by computing its likelihood function. It can
+ return either the density of probability of F, or a sample of F values
+ from this distribution. This operation is performed for all the
+ individuals of a \linkS4class{genind} object. Any ploidy greater than
+ 1 is acceptable.
+}
+\usage{
+inbreeding(x, pop = NULL, truenames = TRUE,
+ res.type = c("sample", "function", "estimate"), N = 200, M = N * 10)
+}
+\arguments{
+ \item{x}{an object of class \linkS4class{genind}.}
+ \item{pop}{a factor giving the 'population' of each individual. If NULL,
+ pop is seeked from \code{pop(x)}. Note that the term population refers in
+ fact to any grouping of individuals'.}
+ \item{truenames}{a logical indicating whether true names should be
+ used (TRUE, default) instead of generic labels (FALSE); used if
+ res.type is "matrix".}
+ \item{res.type}{a character string matching "sample", "function", or "estimate"
+ specifying whether the output should be a function giving the density
+ of probability of F values ("function"), the maximum likelihood estimate
+ of F from this distribution ("estimate"), or a sample of F values taken
+ from this distribution ("sample", default).}
+ \item{N}{an integer indicating the size of the sample to be taken from
+ the distribution of F values.}
+ \item{M}{an integer indicating the number of different F values to be
+ used to generate the sample. Values larger than N are recommended to
+ avoid poor sampling of the distribution.}
+}
+\value{
+ A named list with one component for each individual, each of which is
+ a function or a vector of sampled F values (see \code{res.type} argument).
+}
+\seealso{
+ \code{\link{Hs}}: computation of expected heterozygosity.
+}
+\details{
+ Let \eqn{F} denote the inbreeding coefficient, defined as the
+ probability for an individual to inherit two identical alleles from a
+ single ancestor.
+
+ Let \eqn{p_i} refer to the frequency of allele \eqn{i} in the
+ population. Let \eqn{h} be an variable which equates 1 if the
+ individual is homozygote, and 0 otherwise. For one locus, the
+ probability of being homozygote is computed as:
+
+ \eqn{ F + (1-F) \sum_i p_i^2}
+
+ The probability of being heterozygote is:
+ \eqn{1 - (F + (1-F) \sum_i p_i^2)}
+
+ The likelihood of a genotype is defined as the probability of being
+ the observed state (homozygote or heterozygote). In the case of
+ multilocus genotypes, log-likelihood are summed over the loci.
+}
+\author{
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}\cr
+ Zhian N. Kamvar\cr
+}
+\examples{
+\dontrun{
+## cattle breed microsatellite data
+data(microbov)
+
+## isolate Lagunaire breed
+lagun <- seppop(microbov)$Lagunaire
+
+## estimate inbreeding - return sample of F values
+Fsamp <- inbreeding(lagun, N=30)
+
+## plot the first 10 results
+invisible(sapply(Fsamp[1:10], function(e) plot(density(e), xlab="F",
+xlim=c(0,1), main="Density of the sampled F values")))
+
+## compute means for all individuals
+Fmean=sapply(Fsamp, mean)
+hist(Fmean, col="orange", xlab="mean value of F",
+main="Distribution of mean F across individuals")
+
+## estimate inbreeding - return proba density functions
+Fdens <- inbreeding(lagun, res.type="function")
+
+## view function for the first individual
+Fdens[[1]]
+
+## plot the first 10 functions
+invisible(sapply(Fdens[1:10], plot, ylab="Density",
+main="Density of probability of F values"))
+
+## estimate inbreeding - return maximum likelihood estimates
+Fest <- inbreeding(lagun, res.type = "estimate")
+mostInbred <- which.max(Fest)
+plot(Fdens[[mostInbred]], ylab = "Density", xlab = "F",
+ main = paste("Probability density of F values\nfor", names(mostInbred)))
+abline(v = Fest[mostInbred], col = "red", lty = 2)
+legend("topright", legend = "MLE", col = "red", lty = 2)
+
+## note that estimates and average samples are likely to be different.
+plot(Fest, ylab = "F", col = "blue",
+ main = "comparison of MLE and average sample estimates of F")
+points(Fmean, pch = 2, col = "red")
+arrows(x0 = 1:length(Fest), y0 = Fest,
+ y1 = Fmean, x1 = 1:length(Fest), length = 0.125)
+legend("topleft", legend = c("estimate", "sample"), col = c("blue", "red"),
+ pch = c(1, 2), title = "res.type")
+}
+}
\ No newline at end of file
diff --git a/man/isPoly.Rd b/man/isPoly.Rd
new file mode 100644
index 0000000..0845c05
--- /dev/null
+++ b/man/isPoly.Rd
@@ -0,0 +1,37 @@
+\name{isPoly-methods}
+\docType{methods}
+\alias{isPoly}
+\alias{isPoly-methods}
+\alias{isPoly,genind-method}
+\alias{isPoly,genpop-method}
+\title{ Assess polymorphism in genind/genpop objects }
+\description{
+ The simple function \code{isPoly} can be used to check which loci are
+ polymorphic, or alternatively to check which alleles give rise to polymorphism.
+}
+\usage{
+\S4method{isPoly}{genind}(x, by=c("locus","allele"), thres=1/100)
+\S4method{isPoly}{genpop}(x, by=c("locus","allele"), thres=1/100)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} and \linkS4class{genpop} object}
+ \item{by}{a character being "locus" or "allele", indicating whether
+ results should indicate polymorphic loci ("locus"), or alleles giving
+ rise to polymorphism ("allele").}
+ \item{thres}{a numeric value giving the minimum frequency of an allele
+ giving rise to polymorphism (defaults to 0.01).}
+ }
+ \value{
+ A vector of logicals.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+data(nancycats)
+isPoly(nancycats,by="loc", thres=0.1)
+isPoly(nancycats[1:3],by="loc", thres=0.1)
+genind2df(nancycats[1:3])
+}
+}
+\keyword{methods}
+\keyword{manip}
diff --git a/man/loadingplot.Rd b/man/loadingplot.Rd
new file mode 100644
index 0000000..0943270
--- /dev/null
+++ b/man/loadingplot.Rd
@@ -0,0 +1,71 @@
+\name{loadingplot}
+\alias{loadingplot}
+\alias{loadingplot.default}
+\title{Represents a cloud of points with colors}
+\description{
+ The \code{loadingplot} function represents positive values of a vector
+ and identifies the values above a given threshold. It can also
+ indicate groups of observations provided as a factor. \cr
+
+ Such graphics can be used, for instance, to assess the weight of each
+ variable (loadings) in a given analysis.
+}
+\usage{
+loadingplot(x, \dots)
+
+\method{loadingplot}{default}(x, at=NULL, threshold=quantile(x,0.75),
+ axis=1, fac=NULL, byfac=FALSE,
+ lab=NULL, cex.lab=0.7, cex.fac=1, lab.jitter=0,
+ main="Loading plot", xlab="Variables", ylab="Loadings",
+ srt = 0, adj = NULL, \dots)
+}
+\arguments{
+ \item{x}{either a vector with numeric values to be plotted, or a
+ matrix-like object containing numeric values. In such case, the
+ \code{x[,axis]} is used as vector of values to be plotted.}
+ \item{at}{an optional numeric vector giving the abscissa at which
+ loadings are plotted. Useful when variates are SNPs with a known
+ position in an alignement.}
+ \item{threshold}{a threshold value above which values of x are
+ identified. By default, this is the third quartile of x.}
+ \item{axis}{an integer indicating the column of x to be plotted; used
+ only if x is a matrix-like object.}
+ \item{fac}{a factor defining groups of observations.}
+ \item{byfac}{a logical stating whether loadings should be averaged by
+ groups of observations, as defined by \code{fac}.}
+ \item{lab}{a character vector giving the labels used to annotate
+ values above the threshold; if NULL, names are taken from the object.}
+ \item{cex.lab}{a numeric value indicating the size of annotations.}
+ \item{cex.fac}{a numeric value indicating the size of annotations for
+ groups of observations.}
+ \item{lab.jitter}{a numeric value indicating the factor of
+ randomisation for the position of annotations. Set to 0 (by default)
+ implies no randomisation.}
+ \item{main}{the main title of the figure.}
+ \item{xlab}{the title of the x axis.}
+ \item{ylab}{the title of the y axis.}
+ \item{srt}{rotation of the labels; see ?text.}
+ \item{adj}{adjustment of the labels; see ?text.}
+ \item{\dots}{further arguments to be passed to the plot function.}
+}
+ \value{
+ Invisibly returns a list with the following components:\cr
+ - threshold: the threshold used\cr
+ - var.names: the names of observations above the threshold\cr
+ - var.idx: the indices of observations above the threshold\cr
+ - var.values: the values above the threshold\cr
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
+\examples{
+x <- runif(20)
+names(x) <- letters[1:20]
+grp <- factor(paste("group", rep(1:4,each=5)))
+
+## basic plot
+loadingplot(x)
+
+## adding groups
+loadingplot(x,fac=grp,main="My title",cex.lab=1)
+}
+\keyword{multivariate}
+\keyword{hplot}
diff --git a/man/makefreq.Rd b/man/makefreq.Rd
new file mode 100644
index 0000000..9aeb140
--- /dev/null
+++ b/man/makefreq.Rd
@@ -0,0 +1,82 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/makefreq.R
+\docType{methods}
+\name{makefreq}
+\alias{makefreq}
+\alias{makefreq,genind-method}
+\alias{makefreq,genind-methods}
+\alias{makefreq,genpop-method}
+\alias{makefreq,genpop-methods}
+\title{Compute allelic frequencies}
+\usage{
+makefreq(x, ...)
+
+\S4method{makefreq}{genind}(x, quiet = FALSE, missing = NA,
+ truenames = TRUE, ...)
+
+\S4method{makefreq}{genpop}(x, quiet = FALSE, missing = NA,
+ truenames = TRUE, ...)
+}
+\arguments{
+\item{x}{a \linkS4class{genind} or \linkS4class{genpop} object.}
+
+\item{...}{further arguments (curently unused)}
+
+\item{quiet}{logical stating whether a conversion message must be printed
+(TRUE,default) or not (FALSE).}
+
+\item{missing}{treatment for missing values. Can be NA, 0 or "mean" (see
+details)}
+
+\item{truenames}{deprecated; there for backward compatibility}
+}
+\value{
+Returns a list with the following components: \item{tab}{matrix of
+allelic frequencies (rows: populations; columns: alleles).}
+\item{nobs}{number of observations (i.e. alleles) for each population x
+locus combinaison.} \item{call}{the matched call}
+}
+\description{
+The function \code{makefreq} is a generic to compute allele frequencies.
+These can be derived for \linkS4class{genind} or \linkS4class{genpop} objects.
+In the case of \linkS4class{genind} objects, data are kept at the individual level, but standardised so that allele frequencies sum up to 1.
+}
+\details{
+There are 3 treatments for missing values: \cr - NA: kept as NA.\cr - 0:
+missing values are considered as zero. Recommended for a PCA on
+compositionnal data.\cr - "mean": missing values are given the mean
+frequency of the corresponding allele. Recommended for a centred PCA.
+
+Note that this function is now a simple wrapper for the accessor \code{\link{tab}}.
+}
+\examples{
+
+\dontrun{
+data(microbov)
+obj1 <- microbov
+obj2 <- genind2genpop(obj1)
+
+# perform a correspondance analysis on counts data
+Xcount <- tab(obj2, NA.method="zero")
+ca1 <- dudi.coa(Xcount,scannf=FALSE)
+s.label(ca1$li,sub="Correspondance Analysis",csub=1.2)
+add.scatter.eig(ca1$eig,nf=2,xax=1,yax=2,posi="topleft")
+
+# perform a principal component analysis on frequency data
+Xfreq <- makefreq(obj2, missing="mean")
+Xfreq <- tab(obj2, NA.method="mean") # equivalent to line above
+pca1 <- dudi.pca(Xfreq,scale=FALSE,scannf=FALSE)
+s.label(pca1$li,sub="Principal Component Analysis",csub=1.2)
+add.scatter.eig(pca1$eig,nf=2,xax=1,yax=2,posi="top")
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{genpop}}
+}
+\keyword{manip}
+\keyword{multivariate}
+
diff --git a/man/microbov.Rd b/man/microbov.Rd
new file mode 100644
index 0000000..69f265c
--- /dev/null
+++ b/man/microbov.Rd
@@ -0,0 +1,103 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\name{microbov}
+\alias{microbov}
+\title{Microsatellites genotypes of 15 cattle breeds}
+\format{\code{microbov} is a genind object with 3 supplementary components:
+\describe{ \item{coun}{a factor giving the country of each individual (AF:
+Afric; FR: France).} \item{breed}{a factor giving the breed of each
+individual.} \item{spe}{is a factor giving the species of each individual
+(BT: Bos taurus; BI: Bos indicus).} }}
+\source{
+Data prepared by Katayoun Moazami-Goudarzi and Denis Lalo\"e (INRA,
+Jouy-en-Josas, France)
+}
+\description{
+This data set gives the genotypes of 704 cattle individuals for 30
+microsatellites recommended by the FAO. The individuals are divided into two
+countries (Afric, France), two species (Bos taurus, Bos indicus) and 15
+breeds. Individuals were chosen in order to avoid pseudoreplication
+according to their exact genealogy.
+}
+\examples{
+
+\dontrun{
+data(microbov)
+microbov
+summary(microbov)
+
+# make Y, a genpop object
+Y <- genind2genpop(microbov)
+
+# make allelic frequency table
+temp <- makefreq(Y,missing="mean")
+X <- temp$tab
+nsamp <- temp$nobs
+
+# perform 1 PCA per marker
+
+kX <- ktab.data.frame(data.frame(X),Y at loc.n.all)
+
+kpca <- list()
+for(i in 1:30) {kpca[[i]] <- dudi.pca(kX[[i]],scannf=FALSE,nf=2,center=TRUE,scale=FALSE)}
+
+
+sel <- sample(1:30,4)
+col = rep('red',15)
+col[c(2,10)] = 'darkred'
+col[c(4,12,14)] = 'deepskyblue4'
+col[c(8,15)] = 'darkblue'
+
+# display \%PCA
+par(mfrow=c(2,2))
+for(i in sel) {
+s.multinom(kpca[[i]]$c1,kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i])
+add.scatter.eig(kpca[[i]]$eig,3,xax=1,yax=2,posi="top")
+}
+
+# perform a Multiple Coinertia Analysis
+kXcent <- kX
+for(i in 1:30) kXcent[[i]] <- as.data.frame(scalewt(kX[[i]],center=TRUE,scale=FALSE))
+mcoa1 <- mcoa(kXcent,scannf=FALSE,nf=3, option="uniform")
+
+# coordinated \%PCA
+mcoa.axes <- split(mcoa1$axis, Y at loc.fac)
+mcoa.coord <- split(mcoa1$Tli,mcoa1$TL[,1])
+var.coord <- lapply(mcoa.coord,function(e) apply(e,2,var))
+
+par(mfrow=c(2,2))
+for(i in sel) {
+s.multinom(mcoa.axes[[i]][,1:2],kX[[i]],n.sample=nsamp[,i],coulrow=col,sub=locNames(Y)[i])
+add.scatter.eig(var.coord[[i]],2,xax=1,yax=2,posi="top")
+}
+
+# reference typology
+par(mfrow=c(1,1))
+s.label(mcoa1$SynVar,lab=popNames(microbov),sub="Reference typology",csub=1.5)
+add.scatter.eig(mcoa1$pseudoeig,nf=3,xax=1,yax=2,posi="top")
+
+# typologial values
+tv <- mcoa1$cov2
+tv <- apply(tv,2,function(c) c/sum(c))*100
+rownames(tv) <- locNames(Y)
+tv <- tv[order(locNames(Y)),]
+
+par(mfrow=c(3,1),mar=c(5,3,3,4),las=3)
+for(i in 1:3){
+barplot(round(tv[,i],3),ylim=c(0,12),yaxt="n",main=paste("Typological value -
+structure",i))
+axis(side=2,at=seq(0,12,by=2),labels=paste(seq(0,12,by=2),"\%"),cex=3)
+abline(h=seq(0,12,by=2),col="grey",lty=2)
+}
+}
+
+}
+\references{
+Lalo\"e D., Jombart T., Dufour A.-B. and Moazami-Goudarzi K.
+(2007) Consensus genetic structuring and typological value of markers using
+Multiple Co-Inertia Analysis. \emph{Genetics Selection Evolution}.
+\bold{39}: 545--567.
+}
+\keyword{datasets}
+
diff --git a/man/minorAllele.Rd b/man/minorAllele.Rd
new file mode 100644
index 0000000..08dbb45
--- /dev/null
+++ b/man/minorAllele.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/minorAllele.R
+\name{minorAllele}
+\alias{minorAllele}
+\title{Compute minor allele frequency}
+\usage{
+minorAllele(x)
+}
+\arguments{
+\item{x}{a \linkS4class{genind} object}
+}
+\description{
+This function computes the minor allele frequency for each locus in a \linkS4class{genind} object. To test if loci are polymorphic, see the function \code{\link{isPoly}}.
+}
+\examples{
+\dontrun{
+
+## LOAD DATA
+data(nancycats)
+
+## COMPUTE ALLELE FREQUENCIES
+x <- nancycats
+apply(tab(x, freq=TRUE),2,mean, na.rm=TRUE)
+
+## GET MINOR ALLELE FREQUENCY
+m.freq <- minorAllele(x)
+m.freq
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{isPoly}}
+}
+
diff --git a/man/monmonier.Rd b/man/monmonier.Rd
new file mode 100644
index 0000000..8bb4ae4
--- /dev/null
+++ b/man/monmonier.Rd
@@ -0,0 +1,199 @@
+\encoding{UTF-8}
+\name{monmonier}
+\alias{monmonier}
+\alias{optimize.monmonier}
+\alias{plot.monmonier}
+\alias{print.monmonier}
+
+\title{Boundary detection using Monmonier algorithm}
+\description{
+ The Monmonier's algorithm detects boundaries among vertices of a
+ valuated graph. This is achieved by finding the path
+ exhibiting the largest distances between connected vertices.\cr
+
+ The highest distance between two connected vertices (i.e. neighbours) is
+ found, giving the starting point of the path. Then, the algorithm
+ seeks the highest distance between immediate neighbours, and so on
+ until a threshold value is attained.
+ This threshold can be chosen from the plot of sorted distances between
+ connected vertices: a boundary will likely result in an abrupt decrease
+ of these values.\cr
+
+ When several paths are looked for, the previous paths are taken into
+ account, and cannot be either crossed or redrawn. Monmonier's
+ algorithm can be used to assess the boundaries between patches of
+ homogeneous observations.\cr
+
+ Although Monmonier algorithm was initially designed for Voronoi
+ tesselation, this implementation generalizes this algorithm to different
+ connection networks. The \code{optimize.monmonier} function produces a
+ \code{monmonier} object by trying several starting points, and
+ returning the best boundary (i.e. largest sum of local distances). This
+ is designed to avoid the algorithm to be trapped by a single strong
+ local difference inside an homogeneous patch.
+}
+
+\usage{
+monmonier(xy, dist, cn, threshold=NULL, bd.length=NULL, nrun=1,
+skip.local.diff=rep(0,nrun),scanthres=is.null(threshold), allowLoop=TRUE)
+
+optimize.monmonier(xy, dist, cn, ntry=10, bd.length=NULL, return.best=TRUE,
+display.graph=TRUE, threshold=NULL, scanthres=is.null(threshold), allowLoop=TRUE)
+
+\method{plot}{monmonier}(x, variable=NULL,
+displayed.runs=1:x$nrun, add.arrows=TRUE,
+col='blue', lty=1, bwd=4, clegend=1, csize=0.7,
+method=c('squaresize','greylevel'), sub='', csub=1, possub='topleft',
+cneig=1, pixmap=NULL, contour=NULL, area=NULL, add.plot=FALSE, \dots)
+
+\method{print}{monmonier}(x, \dots)
+}
+\arguments{
+ \item{xy}{a matrix yielding the spatial coordinates of the objects, with two columns respectively giving X and Y}
+ \item{dist}{an object of class \code{dist}, giving the distances between the objects}
+ \item{cn}{a connection network of class \code{nb} (package \code{spdep})}
+ \item{threshold}{a number giving the minimal distance between two
+ neighbours crossed by the path; by default, this is the third quartile of all the distances between neighbours}
+ \item{bd.length}{an optional integer giving the requested length of
+ the boundaries (in number of local differences)}
+ \item{nrun}{is a integer giving the number of runs of the algorithm, that is, the number of paths to search, being one by default}
+ \item{skip.local.diff}{is a vector of integers, whose length is the number of paths (\code{nrun}); each integer gives the number of starting point to skip, to avoid being stuck in a local difference between two neighbours into an homogeneous patch; none are skipped by default}
+ \item{scanthres}{a logical stating whether the threshold sould be
+ chosen from the barplot of sorted distances between neighbours}
+ \item{allowLoop}{a logical specifying whether the boundary can loop
+ (TRUE, default) or not (FALSE)}
+ \item{ntry}{an integer giving the number of different starting points
+ tried.}
+ \item{return.best}{a logical stating whether the best monmonier object
+ should be returned (TRUE, default) or not (FALSE)}
+ \item{display.graph}{a logical whether the scores of each try should
+ be plotted (TRUE, default) or not}
+ \item{x}{a monmonier object}
+ \item{variable}{a variable to be plotted using \code{s.value} (package
+ \code{ade4})}
+ \item{displayed.runs}{an integer vector giving the rank of the paths to represent}
+ \item{add.arrows}{a logical, stating whether arrows should indicate the direction of the path (TRUE) or not (FALSE, used by default)}
+ \item{col}{a characters vector giving the colors to be used for each boundary; recycled is needed; 'blue' is used by default}
+ \item{lty}{a characters vector giving the type of line to be used for each boundary; 1 is used by default}
+ \item{bwd}{a number giving the boundary width factor, applying to every segments of the paths; 4 is used by default}
+ \item{clegend}{like in \code{s.value}, the size factor of the legend if a variable is represented}
+ \item{csize}{like in \code{s.value}, the size factor of the squares used to represent a variable}
+ \item{method}{like in \code{s.value}, a character giving the method to be used to represent the variable, either 'squaresize' (by default) or 'greylevel'}
+ \item{sub}{a string of characters giving the subtitle of the plot}
+ \item{csub}{the size factor of the subtitle}
+ \item{possub}{the position of the subtitle; available choices are 'topleft' (by default), 'topright', 'bottomleft', and 'bottomright'}
+ \item{cneig}{the size factor of the connection network}
+ \item{pixmap}{an object of the class \code{pixmap} displayed in the map background}
+ \item{contour}{ a data frame with 4 columns to plot the contour of the map: each row gives a segment (x1,y1,x2,y2)}
+ \item{area}{a data frame of class 'area' to plot a set of surface units in contour}
+ \item{add.plot}{a logical stating whether the plot should be added to the current one (TRUE), or displayed in a new window (FALSE, by default)}
+ \item{\dots}{further arguments passed to other methods}
+}
+\details{
+The function \code{monmonier} returns a list of the class \code{monmonier}, which contains the general informations about the algorithm, and about each run.
+When displayed, the width of the boundaries reflects their 'strength'.
+Let a segment MN be part of the path, M being the middle of AB, N of CD.
+Then the boundary width for MN is proportionnal to (d(AB)+d(CD))/2.\cr
+
+As there is no perfect method to display graphically a quantitative
+variable (see for instance the differences between the two methods of
+\code{s.value}), the boundaries provided by this algorithm seem
+sometimes more reliable than the boundaries our eyes perceive (or miss).\cr
+
+}
+
+\value{
+Returns an object of class \code{monmonier}, which contains the following elements :
+ \item{run1 (run2, \dots)}{for each run, a list containing a dataframe giving the path coordinates, and a vector of the distances between neighbours of the path}
+ \item{nrun}{the number of runs performed, i.e. the number of boundaries in the monmonier object}
+ \item{threshold}{the threshold value, minimal distance between
+ neighbours accounted for by the algorithm}
+ \item{xy}{the matrix of spatial coordinates}
+ \item{cn}{the connection network of class \code{nb}}
+ \item{call}{the call of the function}
+}
+\references{
+Monmonier, M. (1973) Maximum-difference barriers: an alternative numerical regionalization method. \emph{Geographic Analysis}, \bold{3}, 245--261.
+
+Manni, F., Guerard, E. and Heyer, E. (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by "Monmonier's algorithm". \emph{Human Biology}, \bold{76}, 173--190
+}
+
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
+
+\seealso{\code{\link{spca}},\code{\link[spdep]{edit.nb}}}
+
+\examples{
+if(require(spdep)){
+
+### non-interactive example
+
+# est-west separation
+load(system.file("files/mondata1.rda",package="adegenet"))
+cn1 <- chooseCN(mondata1$xy,type=2,ask=FALSE)
+mon1 <- monmonier(mondata1$xy,dist(mondata1$x1),cn1,threshold=2)
+plot(mon1,mondata1$x1)
+plot(mon1,mondata1$x1,met="greylevel",add.arr=FALSE,col="red",bwd=6,lty=2)
+
+# square in the middle
+load(system.file("files/mondata2.rda",package="adegenet"))
+cn2 <- chooseCN(mondata2$xy,type=1,ask=FALSE)
+mon2 <- monmonier(mondata2$xy,dist(mondata2$x2),cn2,threshold=2)
+plot(mon2,mondata2$x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5)
+
+### genetic data example
+\dontrun{
+data(sim2pop)
+
+if(require(hierfstat)){
+## try and find the Fst
+fstat(sim2pop,fst=TRUE)
+# Fst = 0.038
+}
+
+## run monmonier algorithm
+
+# build connection network
+gab <- chooseCN(sim2pop at other$xy,ask=FALSE,type=2)
+
+# filter random noise
+pca1 <- dudi.pca(sim2pop at tab,scale=FALSE, scannf=FALSE, nf=1)
+
+# run the algorithm
+mon1 <- monmonier(sim2pop at other$xy,dist(pca1$l1[,1]),gab,scanthres=FALSE)
+
+# graphical display
+plot(mon1,var=pca1$l1[,1])
+temp <- sim2pop at pop
+levels(temp) <- c(17,19)
+temp <- as.numeric(as.character(temp))
+plot(mon1)
+points(sim2pop at other$xy,pch=temp,cex=2)
+legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19))
+
+
+### interactive example
+
+# north-south separation
+xy <- matrix(runif(120,0,10), ncol=2)
+x1 <- rnorm(60)
+x1[xy[,2] > 5] <- x1[xy[,2] > 5]+3
+cn1 <- chooseCN(xy,type=1,ask=FALSE)
+mon1 <- optimize.monmonier(xy,dist(x1)^2,cn1,ntry=10)
+
+# graphics
+plot(mon1,x1,met="greylevel",csize=.6)
+
+# island in the middle
+x2 <- rnorm(60)
+sel <- (xy[,1]>3.5 & xy[,2]>3.5 & xy[,1]<6.5 & xy[,2]<6.5)
+x2[sel] <- x2[sel]+4
+cn2 <- chooseCN(xy,type=1,ask=FALSE)
+mon2 <- optimize.monmonier(xy,dist(x2)^2,cn2,ntry=10)
+
+# graphics
+plot(mon2,x2,method="greylevel",add.arr=FALSE,bwd=6,col="red",csize=.5)
+}
+}
+}
+\keyword{multivariate}
+\keyword{spatial}
diff --git a/man/mutations.Rd b/man/mutations.Rd
new file mode 100644
index 0000000..0fcfdee
--- /dev/null
+++ b/man/mutations.Rd
@@ -0,0 +1,82 @@
+\encoding{UTF-8}
+\name{findMutations}
+\alias{findMutations}
+\alias{findMutations.DNAbin}
+\alias{graphMutations}
+\alias{graphMutations.DNAbin}
+\title{Identify mutations between DNA sequences}
+\description{
+ The function \code{findMutations} identifies mutations (position and
+ nature) of pairs of aligned DNA sequences. The function
+ \code{graphMutations} does the same thing but plotting mutations on a
+ directed graph.\cr
+
+ Both functions are generics, but the only methods implemented in
+ adegenet so far is for \code{\link[ape]{DNAbin}} objects.
+}
+\usage{
+findMutations(\dots)
+
+\method{findMutations}{DNAbin}(x, from=NULL, to=NULL, allcomb=TRUE, \dots)
+
+graphMutations(\dots)
+
+\method{graphMutations}{DNAbin}(x, from=NULL, to=NULL, allcomb=TRUE, plot=TRUE,
+ curved.edges=TRUE, \dots)
+
+}
+\arguments{
+ \item{x}{a \code{DNAbin} object containing aligned sequences, as a matrix.}
+ \item{from}{a vector indicating the DNA sequences from which mutations
+ should be found. If \code{NULL}, all sequences are considered (i.e.,
+ \code{1:nrow(x)}).}
+ \item{to}{a vector indicating the DNA sequences to which mutations
+ should be found. If \code{NULL}, all sequences are considered (i.e.,
+ \code{1:nrow(x)}).}
+ \item{allcomb}{a logical indicating whether all combinations of
+ sequences (from and to) should be considered (TRUE, default), or not
+ (FALSE).}
+ \item{plot}{a logical indicating whether the graph should be plotted.}
+ \item{curved.edges}{a logical indicating whether the edges of the
+ graph should be curved.}
+ \item{\dots}{further arguments to be passed to other methods. Used in
+ \code{graphMutations} where it is passed to the plot method for
+ \code{igraph} objects.}
+}
+\value{
+ For \code{findMutations}, a named list indicating the mutations from
+ one sequence to another. For each comparison, a three-column matrix is
+ provided, corresponding to the nucleotides in first and second
+ sequence, and a summary of the mutation provided as:
+ [position]:[nucleotide in first sequence]->[nucleotide in second
+ sequence].
+
+ For \code{graphMutations}, a graph with the class \code{igraph}.
+}
+\seealso{
+ The \code{\link{fasta2DNAbin}} to read fasta alignments with minimum
+ RAM use.
+}
+\author{
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}.
+ }
+\examples{
+\dontrun{
+data(woodmouse)
+
+## mutations between first 3 sequences
+findMutations(woodmouse[1:3,])
+
+## mutations from the first to sequences 2 and 3
+findMutations(woodmouse[1:3,], from=1)
+
+## same, graphical display
+g <- graphMutations(woodmouse[1:3,], from=1)
+
+## some manual checks
+as.character(woodmouse)[1:3,35]
+as.character(woodmouse)[1:3,36]
+as.character(woodmouse)[1:3,106]
+
+}
+}
diff --git a/man/nancycats.Rd b/man/nancycats.Rd
new file mode 100644
index 0000000..da2cdd2
--- /dev/null
+++ b/man/nancycats.Rd
@@ -0,0 +1,59 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\name{nancycats}
+\alias{nancycats}
+\title{Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)}
+\format{\code{nancycats} is a genind object with spatial coordinates of the
+colonies as a supplementary components (@xy).}
+\source{
+Dominique Pontier (UMR CNRS 5558, University Lyon1, France)
+}
+\description{
+This data set gives the genotypes of 237 cats (\emph{Felis catus} L.) for 9
+microsatellites markers. The individuals are divided into 17 colonies whose
+spatial coordinates are also provided.
+}
+\examples{
+
+\dontrun{
+data(nancycats)
+nancycats
+
+# summary's results are stored in x
+x <- summary(nancycats)
+
+# some useful graphics
+barplot(x$loc.n.all,ylab="Alleles numbers",main="Alleles numbers
+per locus")
+
+plot(x$pop.eff,x$pop.nall,type="n",xlab="Sample size",ylab="Number of alleles")
+text(x$pop.eff,y=x$pop.nall,lab=names(x$pop.nall))
+
+par(las=3)
+barplot(table(nancycats at pop),ylab="Number of genotypes",main="Number of genotypes per colony")
+
+# are cats structured among colonies ?
+if(require(hierfstat)){
+
+gtest <- gstat.randtest(nancycats,nsim=99)
+gtest
+plot(gtest)
+
+
+dat <- genind2hierfstat(nancycats)
+
+Fstat <- varcomp.glob(dat$pop,dat[,-1])
+Fstat
+}
+}
+
+}
+\references{
+Devillard, S.; Jombart, T. & Pontier, D. Disentangling spatial
+and genetic structure of stray cat (\emph{Felis catus} L.) colonies in urban
+habitat using: not all colonies are equal. submitted to \emph{Molecular
+Ecology}
+}
+\keyword{datasets}
+
diff --git a/man/new.genind.Rd b/man/new.genind.Rd
new file mode 100644
index 0000000..20fa4a1
--- /dev/null
+++ b/man/new.genind.Rd
@@ -0,0 +1,62 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/constructors.R
+\docType{methods}
+\name{initialize,genind-method}
+\alias{as.genind}
+\alias{genind}
+\alias{initialize,genind-method}
+\alias{initialize,genind-methods}
+\title{genind constructor}
+\usage{
+\S4method{initialize}{genind}(.Object, tab, pop = NULL, prevcall = NULL,
+ ploidy = 2L, type = c("codom", "PA"), strata = NULL, hierarchy = NULL,
+ ...)
+
+genind(...)
+
+as.genind(...)
+}
+\arguments{
+\item{.Object}{prototyped object (generated automatically when calling 'new')}
+
+\item{tab}{A matrix of integers corresponding to the @tab slot of a genind
+object, with individuals in rows and alleles in columns, and containing
+either allele counts (if type="codom") or allele presence/absence (if
+type="PA")}
+
+\item{pop}{an optional factor with one value per row in \code{tab} indicating
+the population of each individual}
+
+\item{prevcall}{an optional call to be stored in the object}
+
+\item{ploidy}{an integer vector indicating the ploidy of the individual; each
+individual can have a different value; if only one value is provided, it is
+recycled to generate a vector of the right length.}
+
+\item{type}{a character string indicating the type of marker: codominant
+("codom") or presence/absence ("PA")}
+
+\item{strata}{a data frame containing population hierarchies or
+stratifications in columns. This must be the same length as the number of
+individuals in the data set.}
+
+\item{hierarchy}{a hierarchical formula defining the columns of the strata
+slot that are hierarchical. Defaults to NULL.}
+
+\item{...}{further arguments passed to other methods (currently not used)}
+}
+\value{
+a \linkS4class{genind} object
+}
+\description{
+The function \code{new} has a method for building \linkS4class{genind} objects.
+See the class description of \linkS4class{genind} for more information on this data structure.
+The functions \code{genind} and \code{as.genind} are aliases for \code{new("genind", ...)}.
+}
+\details{
+Most users do not need using the constructor, but merely to convert raw allele data using \code{\link{df2genind}} and related functions.
+}
+\seealso{
+the description of the \linkS4class{genind} class; \code{\link{df2genind}}
+}
+
diff --git a/man/new.genpop.Rd b/man/new.genpop.Rd
new file mode 100644
index 0000000..98337b7
--- /dev/null
+++ b/man/new.genpop.Rd
@@ -0,0 +1,45 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/constructors.R
+\docType{methods}
+\name{initialize,genpop-method}
+\alias{as.genpop}
+\alias{genpop}
+\alias{initialize,genpop-method}
+\alias{initialize,genpop-methods}
+\title{genpop constructor}
+\usage{
+\S4method{initialize}{genpop}(.Object, tab, prevcall = NULL, ploidy = 2L,
+ type = c("codom", "PA"), ...)
+
+genpop(...)
+
+as.genpop(...)
+}
+\arguments{
+\item{.Object}{prototyped object (generated automatically when calling 'new')}
+
+\item{tab}{A matrix of integers corresponding to the @tab slot of a genpop object, with individuals in rows and alleles in columns, and containing either allele counts}
+
+\item{prevcall}{an optional call to be stored in the object}
+
+\item{ploidy}{an integer vector indicating the ploidy of the individual; each individual can have a different value; if only one value is provided, it is recycled to generate a vector of the right length.}
+
+\item{type}{a character string indicating the type of marker: codominant ("codom") or presence/absence ("PA")}
+
+\item{...}{further arguments passed to other methods (currently not used)}
+}
+\value{
+a \linkS4class{genpop} object
+}
+\description{
+The function \code{new} has a method for building \linkS4class{genpop} objects.
+See the class description of \linkS4class{genpop} for more information on this data structure.
+The functions \code{genpop} and \code{as.genpop} are aliases for \code{new("genpop", ...)}.
+}
+\details{
+Most users do not need using the constructor, but merely to convert raw allele data using \code{\link{genind2genpop}}.
+}
+\seealso{
+the description of the \linkS4class{genpop} class; \code{\link{df2genind}} and related functions for reading raw allele data
+}
+
diff --git a/man/old2new.Rd b/man/old2new.Rd
new file mode 100644
index 0000000..c3d3966
--- /dev/null
+++ b/man/old2new.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/old2new.R
+\name{old2new_genind}
+\alias{old2new}
+\alias{old2new_genind}
+\alias{old2new_genlight}
+\alias{old2new_genpop}
+\title{Convert objects with obsolete classes into new objects}
+\usage{
+old2new_genind(object, donor = new("genind"))
+
+old2new_genlight(object, donor = new("genlight"))
+
+old2new_genpop(object, donor = new("genpop"))
+}
+\arguments{
+\item{object}{a genind or genlight object from version 1.4 or earlier.}
+
+\item{donor}{a new object to place all the data into.}
+}
+\description{
+The genind and genlight objects have changed in Adegenet version 2.0. They
+have each gained strata and hierarchy slots. What's more is that the genind
+objects have been optimized for storage and now store the tab slot as
+integers instead of numerics. This function will convert old genind or
+genlight objects to new ones seamlessly.
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}\cr
+Zhian N. Kamvar \email{kamvarz at science.oregonstate.edu}
+}
+\keyword{manip}
+
diff --git a/man/pairDist.Rd b/man/pairDist.Rd
new file mode 100644
index 0000000..1d21177
--- /dev/null
+++ b/man/pairDist.Rd
@@ -0,0 +1,99 @@
+\encoding{UTF-8}
+\name{pairDistPlot}
+\alias{pairDist}
+\alias{pairDist.default}
+\alias{pairDistPlot}
+\alias{pairDistPlot.default}
+\alias{pairDistPlot.dist}
+\alias{pairDistPlot.matrix}
+\alias{pairDistPlot.genind}
+\alias{pairDistPlot.DNAbin}
+\title{Pairwise distance plots}
+\description{
+ The function \code{pairDistPlot} extracts and plots pairwise distances
+ between different groups (graphs use ggplot2). The function
+ \code{pairDistPlot} does the same, without the graphs.
+
+ \code{pairDistPlot} is a generic function with methods for the
+ following types of objects:\cr
+ - \code{dist} \cr
+ - \code{matrix} (only numeric data)\cr
+ - \code{\linkS4class{genind}} objects (genetic markers, individuals)\cr
+ - \code{\link[ape]{DNAbin}} objects (DNA sequences)
+}
+\usage{
+pairDist(x, \dots)
+
+pairDistPlot(x, \dots)
+
+\method{pairDistPlot}{dist}(x, grp, within=FALSE, sep="-", data=TRUE,
+ violin=TRUE, boxplot=TRUE, jitter=TRUE, \dots)
+
+\method{pairDistPlot}{matrix}(x, grp, within=FALSE, sep="-", data=TRUE,
+ violin=TRUE, boxplot=TRUE, jitter=TRUE, \dots)
+
+\method{pairDistPlot}{genind}(x, grp, within=FALSE, sep="-", data=TRUE,
+ violin=TRUE, boxplot=TRUE, jitter=TRUE, \dots)
+
+\method{pairDistPlot}{DNAbin}(x, grp, within=FALSE, sep="-", data=TRUE,
+ violin=TRUE, boxplot=TRUE, jitter=TRUE, \dots)
+
+}
+\arguments{
+ \item{x}{pairwise distances provided as a \code{dist} or a symmetric
+ \code{matrix}, or \code{\linkS4class{genind}} or \code{DNAbin}
+ object. For \code{\linkS4class{genind}} objects, pairwise squared
+ Euclidean distances are computed from the allele data. For
+ \code{DNAbin} objects, distances are computed uing
+ \code{\link{dist.dna}}, and '...' is used to pass arguments to the
+ function. }
+
+ \item{grp}{a factor defining a grouping of individuals.}
+
+ \item{within}{a logical indicating whether to keep within-group
+ comparisons.}
+
+ \item{sep}{a character used as separator between group names}
+
+ \item{data}{a logical indicating whether data of the plot should be returned.}
+
+ \item{violin}{a logical indicating whether a violinplot should be generated.}
+
+ \item{boxplot}{a logical indicating whether a boxplot should be generated.}
+
+ \item{jitter}{a logical indicating whether a jitter-plot should be generated.}
+
+ \item{\dots}{further arguments to be used by other functions; used for
+ \code{DNAbin} object to pass argumetns to \code{dist.dna}.}
+}
+\value{
+ A list with different components, depending on the values of the
+ arguments. Plots are returned as \code{ggplot2} objects.
+}
+\seealso{
+ \code{\link{gengraph}} to identify connectivity based on distances.
+}
+\author{
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}.
+ }
+\examples{
+\dontrun{
+
+## use a subset of influenza data
+data(H3N2)
+set.seed(1)
+dat <- H3N2[sample(1:nInd(H3N2), 100)]
+
+## get pairwise distances
+temp <- pairDistPlot(dat, other(dat)$epid)
+
+## see raw data
+head(temp$data)
+
+## see plots
+temp$boxplot
+temp$violin
+temp$jitter
+
+}
+}
diff --git a/man/population-methods.Rd b/man/population-methods.Rd
new file mode 100644
index 0000000..5d2be70
--- /dev/null
+++ b/man/population-methods.Rd
@@ -0,0 +1,52 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/strataMethods.R
+\docType{methods}
+\name{setPop}
+\alias{setPop}
+\alias{setPop,genind-method}
+\alias{setPop,genlight-method}
+\alias{setPop<-}
+\alias{setPop<-,genind-method}
+\alias{setPop<-,genlight-method}
+\title{Manipulate the population factor of genind objects.}
+\usage{
+setPop(x, formula = NULL)
+
+setPop(x) <- value
+}
+\arguments{
+\item{x}{a genind or genlight object}
+
+\item{formula}{a nested formula indicating the order of the population
+strata.}
+
+\item{value}{same as formula}
+}
+\description{
+The following methods allow the user to quickly change the population of a
+genind object.
+}
+\examples{
+
+data(microbov)
+
+strata(microbov) <- data.frame(other(microbov))
+
+# Currently set on just
+head(pop(microbov))
+
+# setting the strata to both Pop and Subpop
+setPop(microbov) <- ~coun/breed
+head(pop(microbov))
+
+\dontrun{
+
+# Can be used to create objects as well.
+microbov.old <- setPop(microbov, ~spe)
+head(pop(microbov.old))
+}
+}
+\author{
+Zhian N. Kamvar
+}
+
diff --git a/man/propShared.Rd b/man/propShared.Rd
new file mode 100644
index 0000000..3da5943
--- /dev/null
+++ b/man/propShared.Rd
@@ -0,0 +1,49 @@
+\encoding{UTF-8}
+\name{propShared}
+\alias{propShared}
+\title{Compute proportion of shared alleles}
+\description{The function \code{propShared} computes the proportion of
+ shared alleles in a set of genotypes (i.e. from a \linkS4class{genind}
+ object). Current implementation works for any level of ploidy.
+}
+\usage{
+propShared(obj)
+}
+\arguments{
+ \item{obj}{a \linkS4class{genind} object.}
+ }
+ \details{
+ Computations of the numbers of shared alleles are done in C.
+ Proportions are computed from all available data, i.e. proportion can
+ be computed as far as there is at least one typed locus in common
+ between two genotypes.
+}
+\value{Returns a matrix of proportions}
+\seealso{\code{\link{dist.genpop}}
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+
+\dontrun{
+## make a small object
+data(microbov)
+obj <- microbov[1:5, loc = locNames(microbov)[1:2]]
+
+## verify results
+propShared(obj)
+genind2df(obj,sep="|")
+
+## Use this similarity measure inside a PCoA
+## ! This is for illustration only !
+## the distance should be rendered Euclidean before
+## (e.g. using cailliez from package ade4).
+matSimil <- propShared(microbov)
+matDist <- exp(-matSimil)
+D <- cailliez(as.dist(matDist))
+pcoa1 <- dudi.pco(D,scannf=FALSE,nf=3)
+s.class(pcoa1$li,microbov$pop,lab=popNames(microbov))
+
+}
+}
+\keyword{manip}
+\keyword{multivariate}
diff --git a/man/propTyped.Rd b/man/propTyped.Rd
new file mode 100644
index 0000000..07a0662
--- /dev/null
+++ b/man/propTyped.Rd
@@ -0,0 +1,48 @@
+\name{propTyped-methods}
+\docType{methods}
+\alias{propTyped}
+\alias{propTyped-methods}
+\alias{propTyped,genind-method}
+\alias{propTyped,genpop-method}
+\title{ Compute the proportion of typed elements }
+\description{
+ The generic function \code{propTyped} is devoted to investigating the
+ structure of missing data in adegenet objects.\cr
+
+ Methods are defined for \linkS4class{genind} and \linkS4class{genpop}
+ objects. They can return the proportion of available
+ (i.e. non-missing) data per individual/population, locus, or the
+ combination of both in with case the matrix indicates which entity
+ (individual or population) was typed on which locus.
+}
+\usage{
+\S4method{propTyped}{genind}(x, by=c("ind","loc","both"))
+\S4method{propTyped}{genpop}(x, by=c("pop","loc","both"))
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} and \linkS4class{genpop} object}
+ \item{by}{a character being "ind","loc", or "both" for
+ \linkS4class{genind} object and "pop","loc", or "both" for
+ \linkS4class{genpop} object. It specifies whether proportion of typed
+ data are provided by entity ("ind"/"pop"), by locus ("loc") or both
+ ("both"). See details.}
+ }
+ \value{
+ A vector of proportion (when \code{by} equals "ind", "pop", or
+ "loc"), or a matrix of binary data (when \code{by} equals "both")
+}
+\details{
+ When \code{by} is set to "both", the result is a matrix of binary data
+ with entities in rows (individuals or populations) and markers in
+ columns. The values of the matrix are 1 for typed data, and 0 for NA.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+data(nancycats)
+propTyped(nancycats,by="loc")
+propTyped(genind2genpop(nancycats),by="both")
+}
+}
+\keyword{methods}
+\keyword{manip}
diff --git a/man/read.PLINK.Rd b/man/read.PLINK.Rd
new file mode 100644
index 0000000..df40cc5
--- /dev/null
+++ b/man/read.PLINK.Rd
@@ -0,0 +1,104 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{extract.PLINKmap}
+\alias{extract.PLINKmap}
+\alias{read.PLINK}
+\alias{read.plink}
+\title{Reading PLINK Single Nucleotide Polymorphism data}
+\usage{
+extract.PLINKmap(file, x = NULL)
+
+read.PLINK(file, map.file = NULL, quiet = FALSE, chunkSize = 1000,
+ parallel = require("parallel"), n.cores = NULL, ...)
+}
+\arguments{
+\item{file}{for \code{read.PLINK} a character string giving the path to the
+file to convert, with the extension ".raw"; for \code{extract.PLINKmap}, a
+character string giving the path to a file with extension ".map".}
+
+\item{x}{an optional object of the class \code{"\linkS4class{genlight}"}, in which
+the information read is stored; if provided, information is matched against
+the names of the loci in \code{x}, as returned by \code{locNames(x)}; if not
+provided, a list of two components is returned, containing chromosome and
+position information.}
+
+\item{map.file}{an optional character string indicating the path to a ".map"
+file, which contains information about the SNPs (chromosome, position). If
+provided, this information is processed by \code{extract.PLINKmap} and
+stored in the \code{@other} slot.}
+
+\item{quiet}{logical stating whether a conversion messages should be printed
+(TRUE,default) or not (FALSE).}
+
+\item{chunkSize}{an integer indicating the number of genomes to be read at a
+time; larger values require more RAM but decrease the time needed to read
+the data.}
+
+\item{parallel}{a logical indicating whether multiple cores -if available-
+should be used for the computations (TRUE, default), or not (FALSE);
+requires the package \code{parallel} to be installed (see details).}
+
+\item{n.cores}{if \code{parallel} is TRUE, the number of cores to be used in
+the computations; if NULL, then the maximum number of cores available on the
+computer is used.}
+
+\item{\dots}{other arguments to be passed to other functions - currently not
+used.}
+}
+\value{
+- read.PLINK: an object of the class \code{"\linkS4class{genlight}"}
+
+- extract.PLINKmap: if a \code{"\linkS4class{genlight}"} is provided as argument
+\code{x}, this object incorporating the new information about SNPs in the
+\code{@other} slot (with new components 'chromosome' and 'position');
+otherwise, a list with two components containing chromosome and position
+information.
+}
+\description{
+The function \code{read.PLINK} reads a data file exported by the PLINK
+software with extension '.raw' and converts it into a \code{"\linkS4class{genlight}"}
+object. Optionally, information about SNPs can be read from a ".map" file,
+either by specifying the argument \code{map.file} in \code{read.PLINK}, or
+using \code{extract.PLINKmap} to add information to an existing
+\code{"\linkS4class{genlight}"} object.
+}
+\details{
+The function reads data by chunks of several genomes (minimum 1, no maximum)
+at a time, which allows one to read massive datasets with negligible RAM
+requirements (albeit at a cost of computational time). The argument
+\code{chunkSize} indicates the number of genomes read at a time. Increasing
+this value decreases the computational time required to read data in, while
+increasing memory requirements.
+
+See details for the documentation about how to export data using PLINK to
+the '.raw' format.
+
+=== Exporting data from PLINK ===
+
+Data need to be exported from PLINK using the option "--recodeA" (and NOT
+"--recodeAD"). The PLINK command should therefore look like: \code{plink
+--file data --recodeA}. For more information on this topic, please look at
+this webpage: \url{http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml}
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+- \code{?genlight} for a description of the class
+\code{"\linkS4class{genlight}"}.
+
+- \code{\link{read.snp}}: read SNPs in adegenet's '.snp' format.
+
+- \code{\link{fasta2genlight}}: extract SNPs from alignments with fasta
+format.
+
+- other import function in adegenet: \code{\link{import2genind}},
+\code{\link{df2genind}}, \code{\link{read.genetix}}
+\code{\link{read.fstat}}, \code{\link{read.structure}},
+\code{\link{read.genepop}}.
+
+- another function \code{read.plink} is available in the package
+\code{snpMatrix}.
+}
+\keyword{manip}
+
diff --git a/man/read.fstat.Rd b/man/read.fstat.Rd
new file mode 100644
index 0000000..9cb0f95
--- /dev/null
+++ b/man/read.fstat.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{read.fstat}
+\alias{read.fstat}
+\title{Reading data from Fstat}
+\usage{
+read.fstat(file, quiet = FALSE)
+}
+\arguments{
+\item{file}{a character string giving the path to the file to convert, with
+the appropriate extension.}
+
+\item{quiet}{logical stating whether a conversion message must be printed
+(TRUE,default) or not (FALSE).}
+}
+\value{
+an object of the class \code{genind}
+}
+\description{
+The function \code{read.fstat} reads Fstat data files (.dat) and convert
+them into a \linkS4class{genind} object.
+}
+\details{
+Note: \code{read.fstat} is meant for DIPLOID DATA ONLY. Haploid data with
+the Hierfstat format can be read into R using \code{read.table} or
+\code{read.csv} after removing headers and 'POP' lines, and then converted
+using \code{\link{df2genind}}.
+}
+\examples{
+
+obj <- read.fstat(system.file("files/nancycats.dat",package="adegenet"))
+obj
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Fstat (version 2.9.3). Software by Jerome Goudet.
+http://www2.unil.ch/popgen/softwares/fstat.htm\cr
+}
+\seealso{
+\code{\link{import2genind}}, \code{\link{df2genind}},
+\code{\link{read.genetix}}, \code{\link{read.structure}},
+\code{\link{read.genepop}}
+}
+\keyword{manip}
+
diff --git a/man/read.genepop.Rd b/man/read.genepop.Rd
new file mode 100644
index 0000000..7018c2b
--- /dev/null
+++ b/man/read.genepop.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{read.genepop}
+\alias{read.genepop}
+\title{Reading data from Genepop}
+\usage{
+read.genepop(file, ncode = 2L, quiet = FALSE)
+}
+\arguments{
+\item{file}{a character string giving the path to the file to convert, with
+the appropriate extension.}
+
+\item{ncode}{an integer indicating the number of characters used to code an allele.}
+
+\item{quiet}{logical stating whether a conversion message must be printed
+(TRUE,default) or not (FALSE).}
+}
+\value{
+an object of the class \code{genind}
+}
+\description{
+The function \code{read.genepop} reads Genepop data files (.gen) and convert
+them into a \linkS4class{genind} object.
+}
+\details{
+Note: \code{read.genepop} is meant for DIPLOID DATA ONLY. Haploid data with
+the Genepop format can be read into R using \code{read.table} or
+\code{read.csv} after removing headers and 'POP' lines, and then converted
+using \code{\link{df2genind}}.
+}
+\examples{
+
+obj <- read.genepop(system.file("files/nancycats.gen",package="adegenet"))
+obj
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Raymond M. & Rousset F, (1995). GENEPOP (version 1.2):
+population genetics software for exact tests and ecumenicism. \emph{J.
+Heredity}, \bold{86}:248-249 \cr
+}
+\seealso{
+\code{\link{import2genind}}, \code{\link{df2genind}},
+\code{\link{read.fstat}}, \code{\link{read.structure}},
+\code{\link{read.genetix}}
+}
+\keyword{manip}
+
diff --git a/man/read.genetix.Rd b/man/read.genetix.Rd
new file mode 100644
index 0000000..e5bf2e9
--- /dev/null
+++ b/man/read.genetix.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{read.genetix}
+\alias{read.genetix}
+\title{Reading data from GENETIX}
+\usage{
+read.genetix(file = NULL, quiet = FALSE)
+}
+\arguments{
+\item{file}{a character string giving the path to the file to convert, with
+the appropriate extension.}
+
+\item{quiet}{logical stating whether a conversion message must be printed
+(TRUE,default) or not (FALSE).}
+}
+\value{
+an object of the class \code{genind}
+}
+\description{
+The function \code{read.genetix} reads GENETIX data files (.gtx) and convert
+them into a \linkS4class{genind} object.
+}
+\details{
+Note: \code{read.genetix} is meant for DIPLOID DATA ONLY. Haploid data with
+the GENETIX format can be read into R using \code{read.table} or
+\code{read.csv} after removing headers and 'POP' lines, and then converted
+using \code{\link{df2genind}}.
+}
+\examples{
+
+obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"))
+obj
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F.
+(1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la genetique des
+populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000,
+Universite de Montpellier II, Montpellier (France). \cr
+}
+\seealso{
+\code{\link{import2genind}}, \code{\link{df2genind}},
+\code{\link{read.fstat}}, \code{\link{read.structure}},
+\code{\link{read.genepop}}
+}
+\keyword{manip}
+
diff --git a/man/read.snp.Rd b/man/read.snp.Rd
new file mode 100644
index 0000000..a5c4062
--- /dev/null
+++ b/man/read.snp.Rd
@@ -0,0 +1,99 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{read.snp}
+\alias{read.snp}
+\title{Reading Single Nucleotide Polymorphism data}
+\usage{
+read.snp(file, quiet = FALSE, chunkSize = 1000,
+ parallel = require("parallel"), n.cores = NULL, ...)
+}
+\arguments{
+\item{file}{a character string giving the path to the file to convert, with
+the extension ".snp".}
+
+\item{quiet}{logical stating whether a conversion messages should be printed
+(TRUE,default) or not (FALSE).}
+
+\item{chunkSize}{an integer indicating the number of genomes to be read at a
+time; larger values require more RAM but decrease the time needed to read
+the data.}
+
+\item{parallel}{a logical indicating whether multiple cores -if available-
+should be used for the computations (TRUE, default), or not (FALSE);
+requires the package \code{parallel} to be installed (see details).}
+
+\item{n.cores}{if \code{parallel} is TRUE, the number of cores to be used in
+the computations; if NULL, then the maximum number of cores available on the
+computer is used.}
+
+\item{\dots}{other arguments to be passed to other functions - currently not
+used.}
+}
+\value{
+an object of the class \code{"\linkS4class{genlight}"}
+}
+\description{
+The function \code{read.snp} reads a SNP data file with extension '.snp' and
+converts it into a \linkS4class{genlight} object. This format is devoted to
+handle biallelic SNP only, but can accommodate massive datasets such as
+complete genomes with considerably less memory than other formats.
+}
+\details{
+The function reads data by chunks of a few genomes (minimum 1, no maximum)
+at a time, which allows one to read massive datasets with negligible RAM
+requirements (albeit at a cost of computational time). The argument
+\code{chunkSize} indicates the number of genomes read at a time. Increasing
+this value decreases the computational time required to read data in, while
+increasing memory requirements.
+
+A description of the .snp format is provided in an example file distributed
+with adegenet (see example below).
+
+=== The .snp format ===
+
+Details of the .snp format can be found in the example file distributed with
+adegenet (see below), or on the adegenet website (type \code{adegenetWeb()}
+in R).
+}
+\examples{
+
+\dontrun{
+## show the example file ##
+## this is the path to the file:
+system.file("files/exampleSnpDat.snp",package="adegenet")
+
+## show its content:
+file.show(system.file("files/exampleSnpDat.snp",package="adegenet"))
+
+
+## read the file
+obj <-
+read.snp(system.file("files/exampleSnpDat.snp",package="adegenet"), chunk=2)
+obj
+as.matrix(obj)
+ploidy(obj)
+alleles(obj)
+locNames(obj)
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+- \code{?genlight} for a description of the class
+\code{"\linkS4class{genlight}"}.
+
+- \code{\link{read.PLINK}}: read SNPs in PLINK's '.raw' format.
+
+- \code{\link{fasta2genlight}}: extract SNPs from alignments with fasta
+format.
+
+- \code{\link{df2genind}}: convert any multiallelic markers into adegenet
+\code{"\linkS4class{genlight}"}.
+
+- \code{\link{import2genind}}: read multiallelic markers from various
+software into adegenet.\cr
+}
+\keyword{manip}
+
diff --git a/man/read.structure.Rd b/man/read.structure.Rd
new file mode 100644
index 0000000..4099186
--- /dev/null
+++ b/man/read.structure.Rd
@@ -0,0 +1,90 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import.R
+\name{read.structure}
+\alias{read.structure}
+\title{Reading data from STRUCTURE}
+\usage{
+read.structure(file, n.ind = NULL, n.loc = NULL, onerowperind = NULL,
+ col.lab = NULL, col.pop = NULL, col.others = NULL,
+ row.marknames = NULL, NA.char = "-9", pop = NULL, sep = NULL,
+ ask = TRUE, quiet = FALSE)
+}
+\arguments{
+\item{file}{a character string giving the path to the file to convert, with
+the appropriate extension.}
+
+\item{n.ind}{an integer giving the number of genotypes (or 'individuals') in
+the dataset}
+
+\item{n.loc}{an integer giving the number of markers in the dataset}
+
+\item{onerowperind}{a STRUCTURE coding option: are genotypes coded on a
+single row (TRUE), or on two rows (FALSE, default)}
+
+\item{col.lab}{an integer giving the index of the column containing labels
+of genotypes. '0' if absent.}
+
+\item{col.pop}{an integer giving the index of the column containing
+population to which genotypes belong. '0' if absent.}
+
+\item{col.others}{an vector of integers giving the indexes of the columns
+containing other informations to be read. Will be available in @other of the
+created object.}
+
+\item{row.marknames}{an integer giving the index of the row containing the
+names of the markers. '0' if absent.}
+
+\item{NA.char}{the character string coding missing data. "-9" by default.
+Note that in any case, series of zero (like "000") are interpreted as NA
+too.}
+
+\item{pop}{an optional factor giving the population of each individual.}
+
+\item{sep}{a character string used as separator between alleles.}
+
+\item{ask}{a logical specifying if the function should ask for optional
+informations about the dataset (TRUE, default), or try to be as quiet as
+possible (FALSE).}
+
+\item{quiet}{logical stating whether a conversion message must be printed
+(TRUE,default) or not (FALSE).}
+}
+\value{
+an object of the class \code{genind}
+}
+\description{
+The function \code{read.structure} reads STRUCTURE data files (.str ou
+.stru) and convert them into a \linkS4class{genind} object. By default, this
+function is interactive and asks a few questions about data content. This
+can be disabled (for optional questions) by turning the 'ask' argument to
+FALSE. However, one has to know the number of genotypes, of markers and if
+genotypes are coded on a single or on two rows before importing data.
+}
+\details{
+Note: \code{read.structure} is meant for DIPLOID DATA ONLY. Haploid data
+with the STRUCTURE format can easily be read into R using \code{read.table}
+or \code{read.csv} and then converted using \code{\link{df2genind}}.
+}
+\examples{
+
+obj <- read.structure(system.file("files/nancycats.str",package="adegenet"),
+ onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)
+
+obj
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of
+population structure using multilocus genotype data. \emph{Genetics},
+\bold{155}: 945-959
+}
+\seealso{
+\code{\link{import2genind}}, \code{\link{df2genind}},
+\code{\link{read.fstat}}, \code{\link{read.genetix}},
+\code{\link{read.genepop}}
+}
+\keyword{manip}
+
diff --git a/man/repool.Rd b/man/repool.Rd
new file mode 100644
index 0000000..1e330c4
--- /dev/null
+++ b/man/repool.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/handling.R
+\name{repool}
+\alias{repool}
+\title{Pool several genotypes into a single dataset}
+\usage{
+repool(..., list = FALSE)
+}
+\arguments{
+\item{...}{a list of \linkS4class{genind} objects, or a series of \linkS4class{genind} objects separated by commas}
+
+\item{list}{a logical indicating whether a list of objects with matched alleles shall be returned (TRUE), or a single \linkS4class{genind} object (FALSE, default).}
+}
+\description{
+The function \code{repool} allows to merge genotypes from different
+ \linkS4class{genind} objects into a single 'pool' (i.e. a new \linkS4class{genind}).
+ The markers have to be the same for all objects to be merged, but
+ there is no constraint on alleles.\cr
+}
+\details{
+This function can be useful, for instance, when hybrids are created
+ using \code{\link{hybridize}}, to merge hybrids with their parent
+ population for further analyses. Note that \code{repool} can also
+ reverse the action of \code{\link{seppop}}.
+}
+\examples{
+\dontrun{
+## use the cattle breeds dataset
+data(microbov)
+temp <- seppop(microbov)
+names(temp)
+## hybridize salers and zebu -- nasty cattle
+zebler <- hybridize(temp$Salers, temp$Zebu, n=40)
+zebler
+## now merge zebler with other cattle breeds
+nastyCattle <- repool(microbov, zebler)
+nastyCattle
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\seealso{
+\code{\link{seploc}}, \code{\link{seppop}}
+}
+
diff --git a/man/rupica.Rd b/man/rupica.Rd
new file mode 100644
index 0000000..eba1d1c
--- /dev/null
+++ b/man/rupica.Rd
@@ -0,0 +1,80 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\encoding{utf-8}
+\name{rupica}
+\alias{rupica}
+\title{Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the
+Bauges mountains (France)}
+\format{\code{rupica} is a genind object with 3 supplementary components
+inside the \code{@other} slot: \describe{ \item{xy}{a matrix containing the
+spatial coordinates of the genotypes.} \item{mnt}{a raster map of elevation,
+with the \code{asc} format from the \code{adehabitat} package.}
+\item{showBauges}{a function to display the map of elevation with an
+appropriate legend (use \code{showBauges()}).} }}
+\source{
+Daniel Maillard, 'Office National de la Chasse et de la Faune
+Sauvage' (ONCFS), France.
+}
+\description{
+This data set contains the genotypes of 335 chamois (\emph{Rupicapra
+rupicapra}) from the Bauges mountains, in France. No prior clustering about
+individuals is known. Each genotype is georeferenced. These data also
+contain a raster map of elevation of the sampling area.
+}
+\examples{
+
+
+data(rupica)
+rupica
+
+
+\dontrun{
+if(require(adehabitat)){
+
+## see the sampling area
+showBauges <- rupica$other$showBauges
+showBauges()
+points(rupica$other$xy,col="red")
+
+## perform a sPCA
+spca1 <- spca(rupica,type=5,d1=0,d2=2300,plot=FALSE,scannf=FALSE,nfposi=2,nfnega=0)
+barplot(spca1$eig,col=rep(c("black","grey"),c(2,100)),main="sPCA eigenvalues")
+screeplot(spca1,main="sPCA eigenvalues: decomposition")
+
+## data visualization
+showBauges(,labcex=1)
+s.value(spca1$xy,spca1$ls[,1],add.p=TRUE,csize=.5)
+add.scatter.eig(spca1$eig,1,1,1,posi="topleft",sub="Eigenvalues")
+
+showBauges(,labcex=1)
+s.value(spca1$xy,spca1$ls[,2],add.p=TRUE,csize=.5)
+add.scatter.eig(spca1$eig,2,2,2,posi="topleft",sub="Eigenvalues")
+
+rupica$other$showBauges()
+colorplot(spca1$xy,spca1$li,cex=1.5,add.plot=TRUE)
+
+## global and local tests
+Gtest <- global.rtest(rupica at tab,spca1$lw,nperm=999)
+Gtest
+plot(Gtest)
+Ltest <- local.rtest(rupica at tab,spca1$lw,nperm=999)
+Ltest
+plot(Ltest)
+}
+}
+
+}
+\references{
+Cassar S (2008) Organisation spatiale de la variabilité
+génétique et phénotypique a l'échelle du paysage: le cas du chamois et du
+chevreuil, en milieu de montagne. PhD Thesis. University Claude Bernard -
+Lyon 1, France. \cr
+
+Cassar S, Jombart T, Loison A, Pontier D, Dufour A-B, Jullien J-M, Chevrier
+T, Maillard D. Spatial genetic structure of Alpine chamois (\emph{Rupicapra
+rupicapra}): a consequence of landscape features and social factors?
+submitted to \emph{Molecular Ecology}.
+}
+\keyword{datasets}
+
diff --git a/man/scaleGen.Rd b/man/scaleGen.Rd
new file mode 100644
index 0000000..cdb06e9
--- /dev/null
+++ b/man/scaleGen.Rd
@@ -0,0 +1,93 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/scale.R
+\docType{methods}
+\name{scaleGen}
+\alias{scaleGen}
+\alias{scaleGen,genind-method}
+\alias{scaleGen,genpop-method}
+\alias{scaleGen-methods}
+\title{Compute scaled allele frequencies}
+\usage{
+scaleGen(x, ...)
+
+\S4method{scaleGen}{genind}(x, center = TRUE, scale = TRUE,
+ NA.method = c("asis", "mean", "zero"), truenames = TRUE)
+
+\S4method{scaleGen}{genpop}(x, center = TRUE, scale = TRUE,
+ NA.method = c("asis", "mean", "zero"), truenames = TRUE)
+}
+\arguments{
+\item{x}{a \linkS4class{genind} and \linkS4class{genpop} object}
+
+\item{...}{further arguments passed to other methods.}
+
+\item{center}{a logical stating whether alleles frequencies should be
+centred to mean zero (default to TRUE). Alternatively, a vector of numeric
+values, one per allele, can be supplied: these values will be substracted
+from the allele frequencies.}
+
+\item{scale}{a logical stating whether alleles frequencies should be scaled
+(default to TRUE). Alternatively, a vector of numeric values, one per
+allele, can be supplied: these values will be substracted from the allele
+frequencies.}
+
+\item{NA.method}{a method to replace NA; asis: leave NAs as is; mean: replace by the mean allele frequencies; zero: replace by zero}
+
+\item{truenames}{no longer used; kept for backward compatibility}
+}
+\value{
+A matrix of scaled allele frequencies with genotypes
+(\linkS4class{genind}) or populations in (\linkS4class{genpop}) in rows and
+alleles in columns.
+}
+\description{
+The generic function \code{scaleGen} is an analogue to the \code{scale}
+function, but is designed with further arguments giving scaling options.\cr
+}
+\details{
+Methods are defined for \linkS4class{genind} and \linkS4class{genpop}
+objects. Both return data.frames of scaled allele frequencies.
+}
+\examples{
+
+\dontrun{
+## load data
+data(microbov)
+obj <- genind2genpop(microbov)
+
+## compare different scaling
+X1 <- scaleGen(obj)
+X2 <- scaleGen(obj,met="bin")
+
+## compute PCAs
+pcaObj <- dudi.pca(obj,scale=FALSE,scannf=FALSE) # pca with no scaling
+pcaX1 <- dudi.pca(X1,scale=FALSE,scannf=FALSE,nf=100) # pca with usual scaling
+pcaX2 <- dudi.pca(X2,scale=FALSE,scannf=FALSE,nf=100) # pca with scaling for binomial variance
+
+## get the loadings of alleles for the two scalings
+U1 <- pcaX1$c1
+U2 <- pcaX2$c1
+
+
+## find an optimal plane to compare loadings
+## use a procustean rotation of loadings tables
+pro1 <- procuste(U1,U2,nf=2)
+
+## graphics
+par(mfrow=c(2,2))
+# eigenvalues
+barplot(pcaObj$eig,main="Eigenvalues\\n no scaling")
+barplot(pcaX1$eig,main="Eigenvalues\\n usual scaling")
+barplot(pcaX2$eig,main="Eigenvalues\\n 'binomial' scaling")
+# differences between loadings of alleles
+s.match(pro1$scor1,pro1$scor2,clab=0,sub="usual -> binom (procustean rotation)")
+
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\keyword{manip}
+\keyword{methods}
+
diff --git a/man/selpopsize.Rd b/man/selpopsize.Rd
new file mode 100644
index 0000000..96df54d
--- /dev/null
+++ b/man/selpopsize.Rd
@@ -0,0 +1,41 @@
+\encoding{UTF-8}
+\docType{methods}
+\name{selPopSize}
+\alias{selPopSize}
+\alias{selPopSize-methods}
+\alias{selPopSize,ANY-method}
+\alias{selPopSize,genind-method}
+\title{ Select genotypes of well-represented populations}
+\description{
+ The function \code{selPopSize} checks the sample size of each population in
+ a \linkS4class{genind} object and keeps only genotypes of populations
+ having a given minimum size.
+}
+\usage{
+\S4method{selPopSize}{genind}(x,pop=NULL,nMin=10)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} object}
+ \item{pop}{a vector of characters or a factor giving the population of
+ each genotype in 'x'. If not provided, seeked from x\$pop.}
+ \item{nMin}{the minimum sample size for a population to be
+ retained. Samples sizes strictly less than \code{nMin} will be
+ discarded, those equal to or greater than \code{nMin} are kept.}
+}
+\value{
+ A \linkS4class{genind} object.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\seealso{\code{\link{seploc}}, \code{\link{repool}}}
+\examples{
+\dontrun{
+data(microbov)
+
+table(pop(microbov))
+obj <- selPopSize(microbov, n=50)
+
+obj
+table(pop(obj))
+}
+}
+\keyword{manip}
\ No newline at end of file
diff --git a/man/seploc.Rd b/man/seploc.Rd
new file mode 100644
index 0000000..ee516f6
--- /dev/null
+++ b/man/seploc.Rd
@@ -0,0 +1,78 @@
+\encoding{UTF-8}
+\docType{methods}
+\name{seploc}
+\alias{seploc}
+\alias{seploc-methods}
+\alias{seploc,ANY-method}
+\alias{seploc,genind-method}
+\alias{seploc,genpop-method}
+\alias{seploc,genlight-method}
+\title{ Separate data per locus}
+\description{
+ The function \code{seploc} splits an object (\linkS4class{genind},
+ \linkS4class{genpop} or \linkS4class{genlight}) by marker. For
+ \linkS4class{genind} and \linkS4class{genpop} objects, the method
+ returns a list of objects whose components each correspond to a
+ marker. For \linkS4class{genlight} objects, the methods returns blocks
+ of SNPs.
+}
+\usage{
+\S4method{seploc}{genind}(x,truenames=TRUE,res.type=c("genind","matrix"))
+\S4method{seploc}{genpop}(x,truenames=TRUE,res.type=c("genpop","matrix"))
+\S4method{seploc}{genlight}(x, n.block=NULL, block.size=NULL, random=FALSE,
+ parallel=require(parallel), n.cores=NULL)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} or a \linkS4class{genpop} object.}
+ \item{truenames}{a logical indicating whether true names should be
+ used (TRUE, default) instead of generic labels (FALSE).}
+ \item{res.type}{a character indicating the type of returned results,
+ a genind or genpop object (default) or a matrix of data
+ corresponding to the 'tab' slot.}
+ \item{n.block}{an integer indicating the number of blocks of SNPs to
+ be returned.}
+ \item{block.size}{an integer indicating the size (in number of SNPs)
+ of the blocks to be returned.}
+ \item{random}{should blocks be formed of contiguous SNPs, or should
+ they be made or randomly chosen SNPs.}
+ \item{parallel}{a logical indicating whether multiple cores -if
+ available- should be used for the computations (TRUE, default), or
+ not (FALSE); requires the package \code{parallel} to be installed.}
+ \item{n.cores}{if \code{parallel} is TRUE, the number of cores to be
+ used in the computations; if NULL, then the maximum number of cores
+ available on the computer is used.}
+}
+\value{The function \code{seploc} returns an list of objects of the
+ same class as the initial object, or a list of matrices similar to
+ x\$tab.\cr
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\seealso{\code{\link{seppop}}, \code{\link{repool}}}
+\examples{
+\dontrun{
+## example on genind objects
+data(microbov)
+
+# separate all markers
+obj <- seploc(microbov)
+names(obj)
+
+obj$INRA5
+
+
+## example on genlight objects
+x <- glSim(100, 1000, 0, ploidy=2) # simulate data
+x <- x[,order(glSum(x))] # reorder loci by frequency of 2nd allele
+glPlot(x, main="All data") # plot data
+foo <- seploc(x, n.block=3) # form 3 blocks
+foo
+glPlot(foo[[1]], main="1st block") # plot 1st block
+glPlot(foo[[2]], main="2nd block") # plot 2nd block
+glPlot(foo[[3]], main="3rd block") # plot 3rd block
+
+foo <- seploc(x, block.size=600, random=TRUE) # split data, randomize loci
+foo # note the different block sizes
+glPlot(foo[[1]])
+}
+}
+\keyword{manip}
\ No newline at end of file
diff --git a/man/seppop.Rd b/man/seppop.Rd
new file mode 100644
index 0000000..a75b55b
--- /dev/null
+++ b/man/seppop.Rd
@@ -0,0 +1,83 @@
+\encoding{UTF-8}
+\docType{methods}
+\name{seppop}
+\alias{seppop}
+\alias{seppop-methods}
+\alias{seppop,ANY-method}
+\alias{seppop,genind-method}
+\alias{seppop,genlight-method}
+\title{ Separate genotypes per population}
+\description{
+ The function \code{seppop} splits a \linkS4class{genind} or a
+ \linkS4class{genlight} object by population, returning a list of
+ objects whose components each correspond to a population.\cr
+
+ For \linkS4class{genind} objects, the output can either be a list of
+ \linkS4class{genind} (default), or a list of matrices corresponding to
+ the \code{@tab} slot.
+}
+\usage{
+\S4method{seppop}{genind}(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"),
+ drop=FALSE, treatOther=TRUE, quiet=TRUE)
+
+\S4method{seppop}{genlight}(x,pop=NULL, treatOther=TRUE, quiet=TRUE, \dots)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} object}
+ \item{pop}{a factor giving the population of each genotype in 'x' OR a
+ formula specifying which strata are to be used when converting to a genpop
+ object. If none provided, population factors are sought in x at pop, but if
+ given, the argument prevails on x at pop.}
+ \item{truenames}{a logical indicating whether true names should be
+ used (TRUE, default) instead of generic labels (FALSE); used if
+ res.type is "matrix".}
+ \item{res.type}{a character indicating the type of returned results,
+ a list of \linkS4class{genind} object (default) or a matrix of data
+ corresponding to the 'tab' slots.}
+ \item{drop}{a logical stating whether alleles that are no longer
+ present in a subset of data should be discarded (TRUE) or kept anyway
+ (FALSE, default).}
+ \item{treatOther}{a logical stating whether elements of the
+ \code{@other} slot should be treated as well (TRUE), or not
+ (FALSE). See details in accessor documentations
+ (\code{\link{pop}}).}
+ \item{quiet}{a logical indicating whether warnings should be issued
+ when trying to subset components of the \code{@other} slot (TRUE),
+ or not (FALSE, default). }
+ \item{\dots}{further arguments passed to the genlight constructor.}
+}
+\value{
+ According to 'res.type': a list of \linkS4class{genind} object
+ (default) or a matrix of data corresponding to the 'tab' slots.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\seealso{\code{\link{seploc}}, \code{\link{repool}}}
+\examples{
+\dontrun{
+data(microbov)
+strata(microbov) <- data.frame(other(microbov))
+
+obj <- seppop(microbov)
+names(obj)
+
+obj$Salers
+
+### example using strata
+obj2 <- seppop(microbov, ~coun/spe)
+names(obj2)
+
+obj2$AF_BI
+
+#### example for genlight objects ####
+x <- new("genlight", list(a=rep(1,1e3),b=rep(0,1e3),c=rep(1, 1e3)))
+x
+
+pop(x) # no population info
+pop(x) <- c("pop1","pop2", "pop1") # set population memberships
+pop(x)
+seppop(x)
+as.matrix(seppop(x)$pop1)[,1:20]
+as.matrix(seppop(x)$pop2)[,1:20,drop=FALSE]
+}
+}
+\keyword{manip}
\ No newline at end of file
diff --git a/man/seqTrack.Rd b/man/seqTrack.Rd
new file mode 100644
index 0000000..25d6071
--- /dev/null
+++ b/man/seqTrack.Rd
@@ -0,0 +1,270 @@
+\name{seqTrack}
+\alias{seqTrack}
+\alias{seqTrack.default}
+\alias{seqTrack.matrix}
+\alias{plotSeqTrack}
+\alias{get.likelihood}
+\alias{get.likelihood.seqTrack}
+\alias{seqTrack-class}
+\alias{as.igraph.seqTrack}
+\alias{plot.seqTrack}
+%\alias{as,seqTrack,graphNEL-method}
+%\alias{coerce,seqTrack,graphNEL-method}
+\title{SeqTrack algorithm for reconstructing genealogies}
+\description{
+ The SeqTrack algorithm [1] aims at reconstructing genealogies of sampled
+ haplotypes or genotypes for which a collection date is
+ available. Contrary to phylogenetic methods which aims at reconstructing
+ hypothetical ancestors for observed sequences, SeqTrack
+ considers that ancestors and descendents are sampled together, and
+ therefore infers ancestry relationships among the sampled sequences.
+
+ This approach proved more efficient than phylogenetic approaches for
+ reconstructing transmission trees in densely sampled disease outbreaks
+ [1]. This implementation defines a generic function \code{seqTrack}
+ with methods for specific object classes.
+
+}
+\usage{
+seqTrack(\ldots)
+
+\method{seqTrack}{matrix}(x, x.names, x.dates, best = c("min", "max"),
+ prox.mat = NULL, mu = NULL, haplo.length = NULL, \dots)
+
+\method{as.igraph}{seqTrack}(x, col.pal=redpal, \dots)
+
+\method{plot}{seqTrack}(x, y=NULL, col.pal=redpal, \dots)
+
+plotSeqTrack(x, xy, use.arrows=TRUE, annot=TRUE, labels=NULL, col=NULL,
+ bg="grey", add=FALSE, quiet=FALSE,
+ date.range=NULL, jitter.arrows=0, plot=TRUE, \dots)
+
+get.likelihood(\ldots)
+
+\method{get.likelihood}{seqTrack}(x, mu, haplo.length, \ldots)
+}
+\arguments{
+ \item{x}{for seqTrack, a matrix giving weights to pairs of ancestries
+ such that x[i,j] is the weight of 'i ancestor of j'. For
+ plotSeqTrack and get.likelihood. seqTrack, a \code{seqTrack}
+ object.}
+ \item{x.names}{a character vector giving the labels of the haplotypes/genotypes}
+ \item{x.dates}{a vector of collection dates for the sampled
+ haplotypes/genotypes. Dates must have the POSIXct format. See
+ \code{details} or \code{?as.POSIXct} for more information.}
+ \item{best}{a character string matching 'min' or 'max', indicating
+ whether genealogies should minimize or maximize the sum of weights
+ of ancestries.}
+ \item{prox.mat}{an optional matrix of proximities between
+ haplotypes/genotypes used to resolve ties in the choice of
+ ancestors, by picking up the 'closest' ancestor amongst possible
+ ancestors, in the sense of \code{prox.mat}. \code{prox.mat[i,j]}
+ must indicate a proximity for the relationship 'i ancestor to
+ j'. For instance, if \code{prox.mat} contains spatial proximities,
+ then \code{prox.mat[i,j]} gives a measure of how easy it is to
+ migrate from location 'i' to 'j'.
+ }
+ \item{mu}{(optional) a mutation rate, per site and per day. When 'x'
+ contains numbers of mutations, used to resolve ties using a maximum
+ likelihood approach (requires \code{haplo.length} to be provided).}
+ \item{haplo.length}{(optional) the length of analysed sequences in
+ number of nucleotides. When 'x' contains numbers of mutations, used
+ to resolve ties using a maximum likelihood approach (requires
+ \code{mu} to be provided).}
+ \item{y}{unused argument, for compatibility with 'plot'.}
+ \item{col.pal}{a color palette to be used to represent weights using
+ colors on the edges of the graph. See \code{?num2col}. Note that the
+ palette is inversed by default.}
+ \item{xy}{spatial coordinates of the sampled haplotypes/genotypes.}
+ \item{use.arrows}{a logical indicating whether arrows should be used to
+ represented ancestries (pointing from ancestor to descendent, TRUE),
+ or whether segments shall be used (FALSE).}
+ \item{annot}{a logical indicating whether arrows or segments
+ representing ancestries should be annotated (TRUE) or not (FALSE).}
+ \item{labels}{a character vector containing annotations of the
+ ancestries. If left empty, ancestries are annotated by the descendent.}
+ \item{col}{a vector of colors to be used for plotting ancestries.}
+ \item{bg}{a color to be used as background.}
+ \item{add}{a logical stating whether the plot should be added to
+ current figure (TRUE), or drawn as a new plot (FALSE, default).}
+ \item{quiet}{a logical stating whether messages other than errors
+ should be displayed (FALSE, default), or hidden (TRUE).}
+ \item{date.range}{a vector of length two with POSIXct format indicating
+ the time window for which ancestries should be displayed.}
+ \item{jitter.arrows}{a positive number indicating the amount of noise
+ to be added to coordinates of arrows; useful when several arrows
+ overlap. See \code{\link{jitter}}.}
+ \item{plot}{a logical stating whether a plot should be drawn (TRUE,
+ default), or not (FALSE). In all cases, the
+ function invisibly returns plotting information.}
+ \item{\ldots}{further arguments to be passed to other methods}
+}
+\author{
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+ Jombart T, Eggo R, Dodd P, Balloux F (2010) Reconstructing disease
+ outbreaks from genetic data: a graph approach. Heredity. doi:
+ 10.1038/hdy.2010.78.
+}
+\value{
+ === output of seqTrack ===\cr
+ seqTrack function returns data.frame with the class \code{seqTrack},
+ in which each row is an inferred ancestry described by the following columns:
+ - id: indices identifying haplotypes/genotypes\cr
+ - ances: index of the inferred ancestor\cr
+ - weight: weight of the inferred ancestries\cr
+ - date: date of the haplotype/genotype\cr
+ - ances.date: date of the ancestor
+
+ === output of plotSeqTrack ===\cr
+ This graphical function invisibly returns the coordinates of the
+ arrows/segments drawn and their colors, as a data.frame.
+}
+\details{
+ === Maximum parsimony genealogies ===\cr
+ Maximum parsimony genealogies can be obtained easily using this
+ implementation of seqTrack. One has to provide in \code{x} a matrix of
+ genetic distances. The most straightforward distance is the number of
+ differing nucleotides. See \code{\link[ape]{dist.dna}} in the ape
+ package for a wide range of genetic distances between aligned
+ sequences. The argument \code{best} should be set to "min" (its
+ default value), so that the identified genealogy minimizes the total
+ number of mutations. If \code{x} contains number of mutations, then
+ \code{mu} and \code{haplo.length} should also be provided for
+ resolving ties in equally parsimonious ancestors using maximum
+ likelihood.
+
+ === Likelihood of observed genetic differentiation ===\cr
+ The probability of oberving a given number of mutations between a
+ sequence and its ancestor can be computed using
+ \code{get.likelihood.seqTrack}. Note that this is only possible
+ if \code{x} contained number of mutations.
+
+
+ === Plotting/converting seqTrack objects to graphs ===\cr
+ seqTrack objects are best plotted as graphs. From adegenet_1.3-5
+ onwards, seqTrack objects can be converted to \code{igraph} objects (from the
+ package \code{igraph}), which can in turn be plotted and manipulated
+ using classical graph tools. The plot method does this operation
+ automatically, using colors to represent edge weights, and using
+ time-ordering of the data from top (ancient) to bottom (recent).
+}
+\seealso{
+ \code{\link[ape]{dist.dna}} in the ape package to compute pairwise
+ genetic distances in aligned sequences.
+}
+\examples{
+\dontrun{
+if(require(ape && require(igraph))){
+## ANALYSIS OF SIMULATED DATA ##
+## SIMULATE A GENEALOGY
+dat <- haploGen(seq.l=1e4, repro=function(){sample(1:4,1)}, gen.time=1, t.max=3)
+plot(dat, main="Simulated data")
+
+## SEQTRACK ANALYSIS
+res <- seqTrack(dat, mu=0.0001, haplo.length=1e4)
+plot(res, main="seqTrack reconstruction")
+
+## PROPORTION OF CORRECT RECONSTRUCTION
+mean(dat$ances==res$ances,na.rm=TRUE)
+
+
+## ANALYSIS OF PANDEMIC A/H1N1 INFLUENZA DATA ##
+## note:
+## this is for reproduction purpose only
+## seqTrack is best kept for the analysis
+## of densely sampled outbreaks, which
+## is not the case of this dataset.
+##
+dat <- read.csv(system.file("files/pdH1N1-data.csv",package="adegenet"))
+ha <- read.dna(system.file("files/pdH1N1-HA.fasta",package="adegenet"), format="fa")
+na <- read.dna(system.file("files/pdH1N1-NA.fasta",package="adegenet"), format="fa")
+
+
+## COMPUTE NUCLEOTIDIC DISTANCES
+nbNucl <- ncol(as.matrix(ha)) + ncol(as.matrix(na))
+D <- dist.dna(ha,model="raw")*ncol(as.matrix(ha)) +
+dist.dna(na,model="raw")*ncol(as.matrix(na))
+D <- round(as.matrix(D))
+
+
+## MATRIX OF SPATIAL CONNECTIVITY
+## (to promote local transmissions)
+xy <- cbind(dat$lon, dat$lat)
+temp <- as.matrix(dist(xy))
+M <- 1* (temp < 1e-10)
+
+
+## SEQTRACK ANALYSIS
+dat$date <- as.POSIXct(dat$date)
+res <- seqTrack(D, rownames(dat), dat$date, prox.mat=M, mu=.00502/365, haplo.le=nbNucl)
+
+
+## COMPUTE GENETIC LIKELIHOOD
+p <- get.likelihood(res, mu=.00502/365, haplo.length=nbNucl)
+# (these could be shown as colors when plotting results)
+# (but mutations will be used instead)
+
+
+## EXAMINE RESULTS
+head(res)
+tail(res)
+range(res$weight, na.rm=TRUE)
+barplot(table(res$weight)/sum(!is.na(res$weight)), ylab="Frequency",
+xlab="Mutations between inferred ancestor and descendent", col="orange")
+
+
+## DISPLAY SPATIO-TEMPORAL DYNAMICS
+if(require(maps)){
+myDates <- as.integer(difftime(dat$date, as.POSIXct("2009-01-21"), unit="day"))
+myMonth <- as.POSIXct(
+c("2009-02-01", "2009-03-01","2009-04-01","2009-05-01","2009-06-01","2009-07-01"))
+x.month <- as.integer(difftime(myMonth, as.POSIXct("2009-01-21"), unit="day"))
+
+
+## FIRST STAGE:
+## SPREAD TO THE USA AND CANADA
+curRange <- as.POSIXct(c("2009-03-29","2009-04-25"))
+par(bg="deepskyblue")
+map("world", fill=TRUE, col="grey")
+opal <- palette()
+palette(rev(heat.colors(10)))
+plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2,date.range=curRange,
+col=res$weight+1)
+title(paste(curRange, collapse=" to "))
+legend("bottom", lty=1, leg=0:8, title="number of mutations", col=1:9,
+lwd=2, horiz=TRUE)
+
+
+## SECOND STAGE:
+## SPREAD WITHIN AMERICA, FIRST SEEDING OUTSIDE AMERICA
+curRange <- as.POSIXct(c("2009-04-30","2009-05-07"))
+par(bg="deepskyblue")
+map("world", fill=TRUE, col="grey")
+opal <- palette()
+palette(rev(heat.colors(10)))
+plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2,
+date.range=curRange, col=res$weight+1)
+title(paste(curRange, collapse=" to "))
+legend("bottom", lty=1, leg=0:8, title="number of mutations",
+col=1:9,lwd=2, horiz=TRUE)
+
+
+## THIRD STAGE:
+## PANDEMIC
+curRange <- as.POSIXct(c("2009-05-15","2009-05-25"))
+par(bg="deepskyblue")
+map("world", fill=TRUE, col="grey")
+opal <- palette()
+palette(rev(heat.colors(10)))
+plotSeqTrack(res, round(xy), add=TRUE,annot=FALSE,lwd=2, date.range=curRange,
+col=res$weight+1)
+title(paste(curRange, collapse=" to "))
+legend("bottom", lty=1, leg=0:8, title="number of mutations",
+col=1:9,lwd=2, horiz=TRUE)
+
+}
+}
+}
+}
\ No newline at end of file
diff --git a/man/sequences.Rd b/man/sequences.Rd
new file mode 100644
index 0000000..9ab75f5
--- /dev/null
+++ b/man/sequences.Rd
@@ -0,0 +1,69 @@
+\encoding{UTF-8}
+\name{SequencesToGenind}
+\alias{DNAbin2genind}
+\alias{alignment2genind}
+\title{ Importing data from an alignement of sequences to a genind object}
+\description{
+ These functions take an alignement of sequences and translate SNPs
+ into a \linkS4class{genind} object. Note that only polymorphic loci
+ are retained.\cr
+
+ Currently, accepted sequence formats are:\cr
+ - DNAbin (ape package): function DNAbin2genind\cr
+ - alignment (seqinr package): function alignment2genind\cr
+}
+\usage{
+DNAbin2genind(x, pop=NULL, exp.char=c("a","t","g","c"), polyThres=1/100)
+
+alignment2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char="-",
+ polyThres=1/100)
+
+}
+\arguments{
+ \item{x}{an object containing aligned sequences.}
+ \item{pop}{an optional factor giving the population to which each sequence belongs.}
+ \item{exp.char}{a vector of single character providing expected values;
+ all other characters will be turned to NA.}
+ \item{na.char}{a vector of single characters providing values that should be
+ considered as NA. If not NULL, this is used instead of \code{exp.char}.}
+ \item{polyThres}{the minimum frequency of a minor allele for a locus to
+ be considered as polymorphic (defaults to 0.01).}
+}
+
+\value{an object of the class \linkS4class{genind}}
+
+\seealso{\code{\link{import2genind}}, \code{\link{read.genetix}},
+ \code{\link{read.fstat}}, \code{\link{read.structure}},
+ \code{\link{read.genepop}}, \code{\link[ape]{DNAbin}},
+ \code{\link[seqinr]{as.alignment}}.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+\dontrun{
+data(woodmouse)
+x <- DNAbin2genind(woodmouse)
+x
+genind2df(x)
+}
+
+if(require(seqinr)){
+mase.res <- read.alignment(file=system.file("sequences/test.mase",package="seqinr"),
+format = "mase")
+mase.res
+x <- alignment2genind(mase.res)
+x
+locNames(x) # list of polymorphic sites
+genind2df(x)
+
+## look at Euclidean distances
+D <- dist(tab(x))
+D
+
+## summarise with a PCoA
+pco1 <- dudi.pco(D, scannf=FALSE,nf=2)
+scatter(pco1, posi="bottomright")
+title("Principal Coordinate Analysis\n-based on proteic distances-")
+
+}
+}
+\keyword{manip}
diff --git a/man/servers.Rd b/man/servers.Rd
new file mode 100644
index 0000000..008f3bf
--- /dev/null
+++ b/man/servers.Rd
@@ -0,0 +1,39 @@
+\encoding{UTF-8}
+\name{Adegenet servers}
+\alias{adegenetServer}
+\title{ Web servers for adegenet }
+\description{
+ The function \code{adegenetServer} opens up a web page providing a
+ simple user interface for some of the functionalities implemented in
+ adegenet. These servers have been developed using the package
+ \code{shiny}.\cr
+
+ Currently available servers include:
+ \itemize{
+ \item \code{DAPC}: a server for the Discriminant Analysis of
+ Principal Components (see ?dapc)
+ }
+}
+\seealso{
+ \link{dapc}
+}
+\usage{
+adegenetServer(what=c("DAPC"))
+}
+\arguments{
+ \item{what}{a character string indicating which server to start;
+ currently accepted values are: "DAPC"}
+}
+\value{
+ The function invisibly returns NULL.
+}
+\author{
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+ Caitlin Collins
+}
+\examples{
+\dontrun{
+## this opens a web page for DAPC
+adegenetServer()
+}
+}
diff --git a/man/sim2pop.Rd b/man/sim2pop.Rd
new file mode 100644
index 0000000..fe2c9b5
--- /dev/null
+++ b/man/sim2pop.Rd
@@ -0,0 +1,65 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\name{sim2pop}
+\alias{sim2pop}
+\title{Simulated genotypes of two georeferenced populations}
+\format{\code{sim2pop} is a genind object with a matrix of xy coordinates as
+supplementary component.}
+\source{
+Easypop version 2.0.1 was run with the following parameters:\cr -
+two diploid populations, one sex, random mating\cr - 1000 individuals per
+population\cr - proportion of migration: 0.002\cr - 20 loci\cr - mutation
+rate: 0.0001 (KAM model)\cr - maximum of 50 allelic states\cr - 1000
+generations (last one taken)\cr
+}
+\description{
+This simple data set was obtained by sampling two populations evolving in a
+island model, simulated using Easypop (2.0.1). See \code{source} for
+simulation details. Sample sizes were respectively 100 and 30 genotypes. The
+genotypes were given spatial coordinates so that both populations were
+spatially differentiated.
+}
+\examples{
+
+\dontrun{
+data(sim2pop)
+
+if(require(hierfstat)){
+## try and find the Fst
+temp <- genind2hierfstat(sim2pop)
+varcomp.glob(temp[,1],temp[,-1])
+# Fst = 0.038
+}
+
+## run monmonier algorithm
+
+# build connection network
+gab <- chooseCN(sim2pop at other$xy,ask=FALSE,type=2)
+
+# filter random noise
+pca1 <- dudi.pca(sim2pop at tab,scale=FALSE, scannf=FALSE, nf=1)
+
+# run the algorithm
+mon1 <- monmonier(sim2pop at other$xy,dist(pca1$l1[,1]),gab, scanthres=FALSE)
+
+# graphical display
+temp <- sim2pop at pop
+levels(temp) <- c(17,19)
+temp <- as.numeric(as.character(temp))
+plot(mon1)
+points(sim2pop at other$xy,pch=temp,cex=2)
+legend("topright",leg=c("Pop A", "Pop B"),pch=c(17,19))
+}
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Balloux F (2001) Easypop (version 1.7): a computer program for
+oppulation genetics simulations \emph{Journal of Heredity}, \bold{92}:
+301-302
+}
+\keyword{datasets}
+
diff --git a/man/snpposi.Rd b/man/snpposi.Rd
new file mode 100644
index 0000000..bbc9590
--- /dev/null
+++ b/man/snpposi.Rd
@@ -0,0 +1,107 @@
+\encoding{UTF-8}
+\name{snpposi}
+
+\alias{snpposi.plot}
+\alias{snpposi.plot.integer}
+\alias{snpposi.plot.numeric}
+\alias{snpposi.plot.DNAbin}
+
+\alias{snpposi.test}
+\alias{snpposi.test.integer}
+\alias{snpposi.test.numeric}
+\alias{snpposi.test.DNAbin}
+
+\title{Analyse the position of polymorphic sites}
+\description{
+ These functions are used to describe the distribution of polymorphic
+ sites (SNPs) in an alignment.
+
+ The function \code{snpposi.plot} plots the positions and density of
+ SNPs in the alignment.
+
+ The function \code{snpposi.test} tests whether SNPs are randomly
+ distributed in the genome, the alternative hypothesis being that they
+ are clustered. This test is based on the distances of each SNP to the
+ closest SNP. This provides one measure of clustering for each SNP.
+ Different statistics can be used to summarise these values (argument
+ \code{stat}), but by default the statistics used is the median.
+
+ \code{snpposi.plot} and \code{snpposi.test} are generic functions with
+ methods for vectors of integers or numeric (indicating SNP position),
+ and for \code{\link[ape]{DNAbin}} objects.
+}
+\usage{
+snpposi.plot(\dots)
+
+\method{snpposi.plot}{integer}(x, genome.size, smooth=0.1,
+ col="royalblue", alpha=.2, codon=TRUE, start.at=1, \dots)
+
+\method{snpposi.plot}{numeric}(x, \dots)
+
+\method{snpposi.plot}{DNAbin}(x, \dots)
+
+
+snpposi.test(\dots)
+
+\method{snpposi.test}{integer}(x, genome.size, n.sim=999, stat=median, \dots)
+
+\method{snpposi.test}{numeric}(x, \dots)
+
+\method{snpposi.test}{DNAbin}(x, \dots)
+
+
+
+}
+\arguments{
+ \item{x}{a vector of integers or numerics containing SNP positions, or
+ a set of aligned sequences in a \code{DNAbin} object.}
+
+ \item{genome.size}{an integer indicating the length of genomes.}
+
+ \item{smooth}{a smoothing parameter for the density estimation;
+ smaller values will give more local peaks; values have to be
+ positive but can be less than 1.}
+
+ \item{col}{the color to be used for the plot; ignored if codon
+ positions are represented.}
+
+ \item{alpha}{the alpha level to be used for transparency (density curve).}
+
+ \item{codon}{a logical indicating if codon position should be
+ indicated (TRUE, default) or not.}
+
+ \item{start.at}{an integer indicating at which base of a codon the
+ alignment starts (defaults to 1); values other than 1, 2 and 3 will
+ be ignored.}
+
+ \item{n.sim}{an integer indicating the number of randomizations to be
+ used in the Monte Carlo test.}
+
+ \item{stat}{a function used to summarize the measure of physical
+ proximity between SNPs; by default, the median is used.}
+ \item{\dots}{further arguments to be passed to the \code{integer}
+ method.}
+}
+\value{
+ A Monte Carlo test of the class \code{randtest}.
+}
+\seealso{
+ The \code{\link{fasta2DNAbin}} to read fasta alignments with minimum
+ RAM use.
+}
+\author{
+ Thibaut Jombart \email{t.jombart at imperial.ac.uk}.
+}
+\examples{
+if(require(ape)){
+data(woodmouse)
+snpposi.plot(woodmouse, codon=FALSE)
+snpposi.plot(woodmouse)
+
+\dontrun{
+snpposi.test(c(1,3,4,5), 100)
+snpposi.test(woodmouse)
+}
+}
+}
+
diff --git a/man/snpzip.rd b/man/snpzip.rd
new file mode 100644
index 0000000..91d14a8
--- /dev/null
+++ b/man/snpzip.rd
@@ -0,0 +1,109 @@
+\encoding{UTF-8}
+\name{snpzip}
+\alias{snpzip}
+\title{Identification of structural SNPs}
+\description{
+ The function \code{snpzip} identifies the set of alleles which contribute most
+ significantly to phenotypic structure.
+
+ This procedure uses Discriminant Analysis of Principal Components (DAPC)
+ to quantify the contribution of individual alleles to between-population
+ structure. Then, defining contribution to DAPC as the measure of distance
+ between alleles, hierarchical clustering is used to identify two groups
+ of alleles: structural SNPs and non-structural SNPs.
+}
+\usage{
+ snpzip(snps, y, plot = TRUE, xval.plot = FALSE, loading.plot = FALSE,
+ method = c("complete", "single", "average", "centroid",
+ "mcquitty", "median", "ward"), \dots)
+}
+\arguments{
+ \item{snps}{a snps \code{matrix} used as input of DAPC.}
+ \item{y}{either a \code{factor} indicating the group membership of individuals,
+ or a dapc object.}
+ \item{plot}{a \code{logical} indicating whether a graphical representation of the
+ DAPC results should be displayed.}
+ \item{xval.plot}{a \code{logical} indicating whether the results of the
+ cross-validation step should be displayed (iff \code{y} is a factor).}
+ \item{loading.plot}{a \code{logical} indicating whether a loading.plot displaying
+ the SNP selection threshold should be displayed.}
+ \item{method}{the clustering method to be used. This should be
+ (an unambiguous abbreviation of) one of \code{"complete", "single", "average",
+ "centroid", "mcquitty", "median",} or \code{"ward"}.}
+ \item{\dots}{further arguments.}
+
+}
+
+\details{
+ \code{snpzip} provides an objective procedure to delineate between structural
+ and non-structural SNPs identified by Discriminant Analysis of Principal Components
+ (DAPC, Jombart et al. 2010).
+ \code{snpzip} precedes the multivariate analysis with a cross-validation step
+ to ensure that the subsequent DAPC is performed optimally.
+ The contributions of alleles to the DAPC are then submitted to \code{hclust},
+ where they define a distance matrix upon which hierarchical clustering is carried out.
+ To complete the procedure, \code{snpzip} uses \code{cutree} to automatically
+ subdivide the set of SNPs fed into the analysis into two groups:
+ those which contribute significantly to the phenotypic structure of interest,
+ and those which do not.
+}
+
+\value{
+ A \code{list} with four items if \code{y} is a factor, or two items if
+ \code{y} is a dapc object:
+ The first cites the number of principal components (PCs) of PCA retained in the DAPC.
+
+ The second item is an embedded list which
+ first indicates the number of structural and non-structural SNPs identified by
+ \code{snpzip}, second provides a list of the structuring alleles, third
+ gives the names of the selected alleles, and fourth details the
+ contributions of these structuring alleles to the DAPC.
+
+ The optional third item provides measures of discrimination success both overall
+ and by group.
+
+ The optional fourth item contains the dapc object generated if \code{y} was a factor.
+
+
+ If \code{plot=TRUE}, a scatter plot will provide a visualization of the DAPC results.
+
+ If \code{xval.plot=TRUE}, the results of the cross-validation step will be displayed
+ as an \code{array} of the format generated by xvalDapc, and a scatter plot of
+ the results of cross-validation will be provided.
+
+ If \code{loading.plot=TRUE}, a loading plot will be generated to show the
+ contributions of alleles to the DAPC, and the SNP selection threshold will be indicated.
+ If the number of Discriminant Axes (\code{n.da}) in the DAPC is greater than 1,
+ \code{loading.plot=TRUE} will generate one loading plot for each discriminant axis.
+}
+
+\references{
+ Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal
+ components: a new method for the analysis of genetically structured populations.
+ BMC Genetics11:94. doi:10.1186/1471-2156-11-94
+}
+
+\author{ Caitlin Collins \email{caitlin.collins12 at imperial.ac.uk} }
+\examples{
+ \dontrun{
+ simpop <- glSim(100, 10000, n.snp.struc = 10, grp.size = c(0.3,0.7),
+ LD = FALSE, alpha = 0.4, k = 4)
+ snps <- as.matrix(simpop)
+ phen <- simpop at pop
+
+ outcome <- snpzip(snps, phen, method = "centroid")
+ outcome
+ }
+ \dontrun{
+ simpop <- glSim(100, 10000, n.snp.struc = 10, grp.size = c(0.3,0.7),
+ LD = FALSE, alpha = 0.4, k = 4)
+ snps <- as.matrix(simpop)
+ phen <- simpop at pop
+
+ dapc1 <- dapc(snps, phen, n.da = 1, n.pca = 30)
+
+ features <- snpzip(dapc1, loading.plot = TRUE, method = "average")
+ features
+ }
+}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/spca.Rd b/man/spca.Rd
new file mode 100644
index 0000000..45de115
--- /dev/null
+++ b/man/spca.Rd
@@ -0,0 +1,189 @@
+\encoding{UTF-8}
+\name{spca}
+\alias{spca}
+\alias{print.spca}
+\alias{summary.spca}
+\alias{plot.spca}
+\alias{screeplot.spca}
+\alias{colorplot.spca}
+\title{Spatial principal component analysis}
+\description{These functions are designed to perform a spatial principal
+ component analysis and to display the results. They call upon
+ \code{multispati} from the \code{ade4} package.
+
+ \code{spca} performs the spatial component analysis. Other
+ functions are:\cr
+
+ - \code{print.spca}: prints the spca content\cr
+
+ - \code{summary.spca}: gives variance and autocorrelation\cr
+ statistics
+
+ - \code{plot.spca}: usefull graphics (connection network, 3 different
+ representations of map of scores, eigenvalues barplot and
+ decomposition)\cr
+
+ - \code{screeplot.spca}: decomposes spca eigenvalues into variance and
+ autocorrelation\cr
+
+ - \code{colorplot.spca}: represents principal components of sPCA in
+ space using the RGB system.\cr
+
+ A tutorial describes how to perform a sPCA: see
+ \url{http://adegenet.r-forge.r-project.org/files/tutorial-spca.pdf} or
+ type \code{adegenetTutorial(which="spca")}.
+}
+\usage{
+spca(obj, xy=NULL, cn=NULL, matWeight=NULL,
+ scale=FALSE, scannf=TRUE, nfposi=1, nfnega=1,
+ type=NULL, ask=TRUE, plot.nb=TRUE, edit.nb=FALSE,
+ truenames=TRUE, d1=NULL, d2=NULL, k=NULL, a=NULL, dmin=NULL)
+
+\method{print}{spca}(x, \dots)
+
+\method{summary}{spca}(object, \dots, printres=TRUE)
+
+\method{plot}{spca}(x, axis = 1, useLag=FALSE, \dots)
+
+\method{screeplot}{spca}(x, \dots, main=NULL)
+
+\method{colorplot}{spca}(x, axes=1:ncol(x$li), useLag=FALSE, \dots)
+}
+\arguments{
+ \item{obj}{a \code{genind} or \code{genpop} object.}
+ \item{xy}{a matrix or data.frame with two columns for x and y
+ coordinates. Seeked from obj\$other\$xy if it exists when xy is not
+ provided. Can be NULL if a \code{nb} object is provided in
+ \code{cn}.\cr
+ Longitude/latitude coordinates should be converted first by a given
+ projection (see 'See Also' section).}
+ \item{cn}{a connection network of the class 'nb' (package spdep). Can
+ be NULL if xy is provided. Can be easily obtained using the function
+ chooseCN (see details).}
+ \item{matWeight}{a square matrix of spatial weights, indicating the
+ spatial proximities between entities. If provided, this argument
+ prevails over \code{cn} (see details).}
+ \item{scale}{a logical indicating whether alleles should be scaled to
+ unit variance (TRUE) or not (FALSE, default).}
+ \item{scannf}{a logical stating whether eigenvalues should be chosen
+ interactively (TRUE, default) or not (FALSE).}
+ \item{nfposi}{an integer giving the number of positive eigenvalues retained
+ ('global structures').}
+ \item{nfnega}{an integer giving the number of negative eigenvalues retained
+ ('local structures').}
+ \item{type}{an integer giving the type of graph (see details in
+ \code{chooseCN} help page). If provided, \code{ask} is set to FALSE.}
+ \item{ask}{a logical stating whether graph should be chosen
+ interactively (TRUE,default) or not (FALSE).}
+ \item{plot.nb}{a logical stating whether the resulting graph should be
+ plotted (TRUE, default) or not (FALSE).}
+ \item{edit.nb}{a logical stating whether the resulting graph should be
+ edited manually for corrections (TRUE) or not (FALSE, default).}
+ \item{truenames}{a logical stating whether true names should be used
+ for 'obj' (TRUE, default) instead of generic labels (FALSE)}
+ \item{d1}{the minimum distance between any two neighbours. Used if
+ \code{type=5.}}
+ \item{d2}{the maximum distance between any two neighbours. Used if
+ \code{type=5}.}
+ \item{k}{the number of neighbours per point. Used if
+ \code{type=6}.}
+ \item{a}{the exponent of the inverse distance matrix. Used if
+ \code{type=7}.}
+ \item{dmin}{the minimum distance between any two distinct points. Used
+ to avoid infinite spatial proximities (defined as the inversed
+ spatial distances). Used if \code{type=7}.}
+ \item{x}{a \code{spca} object.}
+ \item{object}{a \code{spca} object.}
+ \item{printres}{a logical stating whether results should be printed on
+ the screen (TRUE, default) or not (FALSE).}
+ \item{axis}{an integer between 1 and (nfposi+nfnega) indicating which
+ axis should be plotted.}
+ \item{main}{a title for the screeplot; if NULL, a default one is
+ used.}
+ \item{\dots}{further arguments passed to other methods.}
+ \item{axes}{the index of the columns of X to be represented. Up to
+ three axes can be chosen.}
+ \item{useLag}{a logical stating whether the lagged components
+ (\code{x\$ls}) should be used instead of the components (\code{x\$li}).}
+}
+\details{
+ The spatial principal component analysis (sPCA) is designed to
+ investigate spatial patterns in the genetic variability. Given
+ multilocus genotypes (individual level) or allelic frequency
+ (population level) and spatial coordinates, it finds individuals (or
+ population) scores maximizing the product of variance and spatial
+ autocorrelation (Moran's I). Large positive and negative eigenvalues
+ correspond to global and local structures.\cr
+
+ Spatial weights can be obtained in several ways, depending how the
+ arguments \code{xy}, \code{cn}, and \code{matWeight} are set.\cr
+ When several acceptable ways are used at the same time, priority is as
+ follows:\cr
+ \code{matWeight} > \code{cn} > \code{xy} \cr
+}
+\value{The class \code{spca} are given to lists with the following
+ components:\cr
+ \item{eig}{a numeric vector of eigenvalues.}
+ \item{nfposi}{an integer giving the number of global structures
+ retained.}
+ \item{nfnega}{an integer giving the number of local structures retained.}
+ \item{c1}{a data.frame of alleles loadings for each axis.}
+ \item{li}{a data.frame of row (individuals or populations) coordinates
+ onto the sPCA axes.}
+ \item{ls}{a data.frame of lag vectors of the row coordinates; useful
+ to clarify maps of global scores .}
+ \item{as}{a data.frame giving the coordinates of the PCA axes onto the
+ sPCA axes.}
+ \item{call}{the matched call.}
+ \item{xy}{a matrix of spatial coordinates.}
+ \item{lw}{a list of spatial weights of class \code{listw}.}
+
+ Other functions have different outputs:\cr
+ - \code{summary.spca} returns a list with 3 components: \code{Istat}
+ giving the null, minimum and maximum Moran's I values; \code{pca}
+ gives variance and I statistics for the principal component analysis;
+ \code{spca} gives variance and I statistics for the sPCA.\cr
+
+ - \code{plot.spca} returns the matched call.\cr
+
+ - \code{screeplot.spca} returns the matched call.
+}
+\references{
+Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D.
+Revealing cryptic spatial patterns in genetic variability by a new
+multivariate method. \emph{Heredity}, \bold{101}, 92--103.
+
+Wartenberg, D. E. (1985) Multivariate spatial correlation: a method for
+exploratory geographical analysis. \emph{Geographical Analysis},
+\bold{17}, 263--283.
+
+Moran, P.A.P. (1948) The interpretation of statistical
+maps. \emph{Journal of the Royal Statistical Society, B}
+\bold{10}, 243--251.
+
+Moran, P.A.P. (1950) Notes on continuous stochastic
+phenomena. \emph{Biometrika}, \bold{37}, 17--23.
+
+de Jong, P. and Sprenger, C. and van Veen, F. (1984) On extreme values
+of Moran's I and Geary's c. \emph{Geographical Analysis}, \bold{16}, 17--24.
+
+}
+\seealso{\code{\link{spcaIllus}} and \code{\link{rupica}} for datasets illustrating the sPCA \cr
+ \code{\link{global.rtest}} and \code{\link{local.rtest}} \cr
+ \code{\link{chooseCN}}, \code{\link[ade4]{multispati}},
+ \code{\link[ade4]{multispati.randtest}}\cr
+ \code{convUL}, from the package 'PBSmapping' to convert longitude/latitude to
+ UTM coordinates.
+}
+\author{ Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+## data(spcaIllus) illustrates the sPCA
+## see ?spcaIllus
+##
+\dontrun{
+example(spcaIllus)
+example(rupica)
+}
+}
+\keyword{spatial}
+\keyword{multivariate}
\ No newline at end of file
diff --git a/man/spca.rtests.Rd b/man/spca.rtests.Rd
new file mode 100644
index 0000000..41627db
--- /dev/null
+++ b/man/spca.rtests.Rd
@@ -0,0 +1,65 @@
+\name{global.rtest}
+\alias{global.rtest}
+\alias{local.rtest}
+\title{Global and local tests}
+\description{
+ These two Monte Carlo tests are used to assess the existence of global
+ and local spatial structures. They can be used as an aid to interprete
+ global and local components of spatial Principal Component Analysis
+ (sPCA).\cr
+
+ They rely on the decomposition of a data matrix X into global and local
+ components using multiple regression on Moran's Eigenvector Maps (MEMs).
+ They require a data matrix (X) and a list of weights derived from a
+ connection network. X is regressed onto global MEMs (U+) in the global
+ test and on local ones (U-) in the local test. One mean \eqn{R^2}{R^2}
+ is obtained for each MEM, the k highest being summed to form the test
+ statistic.
+
+ The reference distribution of these statistics are obtained by
+ randomly permuting the rows of X.
+}
+\usage{
+global.rtest(X, listw, k = 1, nperm = 499)
+local.rtest(X, listw, k = 1, nperm = 499)
+
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+ \item{X}{a data matrix, with variables in columns}
+ \item{listw}{a list of weights of class \code{listw}. Can be obtained
+ easily using the function \code{chooseCN}.}
+ \item{k}{integer: the number of highest \eqn{R^2}{R^2} summed to form the test statistics}
+ \item{nperm}{integer: the number of randomisations to be performed.}
+}
+\details{
+ This test is purely R code. A C or C++ version will be developped soon.
+}
+\value{
+An object of class \code{randtest}.
+}
+\references{
+ Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D.
+ Revealing cryptic spatial patterns in genetic variability by a new
+ multivariate method. \emph{Heredity}, \bold{101}, 92--103.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
+\seealso{ \code{\link{chooseCN}}, \code{\link{spca}}, \code{\link{monmonier}}}
+\examples{
+\dontrun{
+ data(sim2pop)
+if(require(spdep)){
+cn <- chooseCN(sim2pop at other$xy,ask=FALSE,type=1,plot=FALSE,res="listw")
+
+# global test
+Gtest <- global.rtest(sim2pop at tab,cn)
+Gtest
+
+# local test
+Ltest <- local.rtest(sim2pop at tab,cn)
+Ltest
+}
+}
+}
+\keyword{multivariate}
+\keyword{spatial}
diff --git a/man/spcaIllus.Rd b/man/spcaIllus.Rd
new file mode 100644
index 0000000..9c8a428
--- /dev/null
+++ b/man/spcaIllus.Rd
@@ -0,0 +1,130 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/datasets.R
+\docType{data}
+\name{spcaIllus}
+\alias{spcaIllus}
+\title{Simulated data illustrating the sPCA}
+\format{\code{spcaIllus} is list of 5 components being either genind or
+genpop objects.}
+\source{
+Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing
+cryptic spatial patterns in genetic variability by a new multivariate
+method. \emph{Heredity}, \bold{101}, 92--103.
+}
+\description{
+Datasets illustrating the spatial Principal Component Analysis (Jombart et
+al. 2009). These data were simulated using various models using Easypop
+(2.0.1). Spatial coordinates were defined so that different spatial
+patterns existed in the data. The \code{spca-illus} is a list containing the
+following \linkS4class{genind} or \linkS4class{genpop} objects:\cr - dat2A:
+2 patches \cr - dat2B: cline between two pop \cr - dat2C: repulsion among
+individuals from the same gene pool \cr - dat3: cline and repulsion \cr -
+dat4: patches and local alternance \cr
+}
+\details{
+See "source" for a reference providing simulation details.
+}
+\examples{
+
+data(spcaIllus)
+attach(spcaIllus)
+opar <- par(no.readonly=TRUE)
+## comparison PCA vs sPCA
+
+# PCA
+pca2A <- dudi.pca(dat2A$tab,center=TRUE,scale=FALSE,scannf=FALSE)
+pca2B <- dudi.pca(dat2B$tab,center=TRUE,scale=FALSE,scannf=FALSE)
+pca2C <- dudi.pca(dat2C$tab,center=TRUE,scale=FALSE,scannf=FALSE)
+pca3 <- dudi.pca(dat3$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)
+pca4 <- dudi.pca(dat4$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)
+
+# sPCA
+spca2A <-spca(dat2A,xy=dat2A$other$xy,ask=FALSE,type=1,
+plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)
+
+spca2B <- spca(dat2B,xy=dat2B$other$xy,ask=FALSE,type=1,
+plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)
+
+spca2C <- spca(dat2C,xy=dat2C$other$xy,ask=FALSE,
+type=1,plot=FALSE,scannf=FALSE,nfposi=0,nfnega=1)
+
+spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,
+type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
+
+spca4 <- spca(dat4,xy=dat4$other$xy,ask=FALSE,
+type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
+
+# an auxiliary function for graphics
+plotaux <- function(x,analysis,axis=1,lab=NULL,...){
+neig <- NULL
+if(inherits(analysis,"spca")) neig <- nb2neig(analysis$lw$neighbours)
+xrange <- range(x$other$xy[,1])
+xlim <- xrange + c(-diff(xrange)*.1 , diff(xrange)*.45)
+yrange <- range(x$other$xy[,2])
+ylim <- yrange + c(-diff(yrange)*.45 , diff(yrange)*.1)
+
+s.value(x$other$xy,analysis$li[,axis],include.ori=FALSE,addaxes=FALSE,
+cgrid=0,grid=FALSE,neig=neig,cleg=0,xlim=xlim,ylim=ylim,...)
+
+par(mar=rep(.1,4))
+if(is.null(lab)) lab = gsub("[P]","",x$pop)
+text(x$other$xy, lab=lab, col="blue", cex=1.2, font=2)
+add.scatter({barplot(analysis$eig,col="grey");box();
+title("Eigenvalues",line=-1)},posi="bottomright",ratio=.3)
+}
+
+# plots
+plotaux(dat2A,pca2A,sub="dat2A - PCA",pos="bottomleft",csub=2)
+plotaux(dat2A,spca2A,sub="dat2A - sPCA glob1",pos="bottomleft",csub=2)
+
+plotaux(dat2B,pca2B,sub="dat2B - PCA",pos="bottomleft",csub=2)
+plotaux(dat2B,spca2B,sub="dat2B - sPCA glob1",pos="bottomleft",csub=2)
+
+plotaux(dat2C,pca2C,sub="dat2C - PCA",pos="bottomleft",csub=2)
+plotaux(dat2C,spca2C,sub="dat2C - sPCA loc1",pos="bottomleft",csub=2,axis=2)
+
+par(mfrow=c(2,2))
+plotaux(dat3,pca3,sub="dat3 - PCA axis1",pos="bottomleft",csub=2)
+plotaux(dat3,spca3,sub="dat3 - sPCA glob1",pos="bottomleft",csub=2)
+plotaux(dat3,pca3,sub="dat3 - PCA axis2",pos="bottomleft",csub=2,axis=2)
+plotaux(dat3,spca3,sub="dat3 - sPCA loc1",pos="bottomleft",csub=2,axis=2)
+
+plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis1",
+pos="bottomleft",csub=2)
+plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA glob1",
+pos="bottomleft",csub=2)
+plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis2",
+pos="bottomleft",csub=2,axis=2)
+plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA loc1",
+pos="bottomleft",csub=2,axis=2)
+
+# color plot
+par(opar)
+colorplot(spca3, cex=4, main="colorplot sPCA dat3")
+text(spca3$xy[,1], spca3$xy[,2], dat3$pop)
+
+colorplot(spca4, cex=4, main="colorplot sPCA dat4")
+text(spca4$xy[,1], spca4$xy[,2], dat4$other$sup.pop)
+
+# detach data
+detach(spcaIllus)
+
+
+}
+\author{
+Thibaut Jombart \email{t.jombart at imperial.ac.uk}
+}
+\references{
+Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D.
+Revealing cryptic spatial patterns in genetic variability by a new
+multivariate method. \emph{Heredity}, \bold{101}, 92--103.
+
+Balloux F (2001) Easypop (version 1.7): a computer program for oppulation
+genetics simulations \emph{Journal of Heredity}, \bold{92}: 301-302
+}
+\seealso{
+\code{\link{spca}}
+}
+\keyword{datasets}
+\keyword{spatial}
+
diff --git a/man/strata-methods.Rd b/man/strata-methods.Rd
new file mode 100644
index 0000000..190bbfb
--- /dev/null
+++ b/man/strata-methods.Rd
@@ -0,0 +1,169 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/strataMethods.R
+\docType{methods}
+\name{strata}
+\alias{addStrata}
+\alias{addStrata,genind-method}
+\alias{addStrata,genlight-method}
+\alias{addStrata<-}
+\alias{addStrata<-,genind-method}
+\alias{addStrata<-,genlight-method}
+\alias{nameStrata}
+\alias{nameStrata,genind-method}
+\alias{nameStrata,genlight-method}
+\alias{nameStrata<-}
+\alias{nameStrata<-,genind-method}
+\alias{nameStrata<-,genlight-method}
+\alias{splitStrata}
+\alias{splitStrata,genind-method}
+\alias{splitStrata,genlight-method}
+\alias{splitStrata<-}
+\alias{splitStrata<-,genind-method}
+\alias{splitStrata<-,genlight-method}
+\alias{strata}
+\alias{strata,genind-method}
+\alias{strata,genlight-method}
+\alias{strata<-}
+\alias{strata<-,genind-method}
+\alias{strata<-,genlight-method}
+\title{Access and manipulate the population strata for genind or genlight objects.}
+\usage{
+strata(x, formula = NULL, combine = TRUE, value)
+
+strata(x) <- value
+
+nameStrata(x, value)
+
+nameStrata(x) <- value
+
+splitStrata(x, value, sep = "_")
+
+splitStrata(x, sep = "_") <- value
+
+addStrata(x, value, name = "NEW")
+
+addStrata(x, name = "NEW") <- value
+}
+\arguments{
+\item{x}{a genind or genlight object}
+
+\item{formula}{a nested formula indicating the order of the population
+strata.}
+
+\item{combine}{if \code{TRUE} (default), the levels will be combined according to the
+formula argument. If it is \code{FALSE}, the levels will not be combined.}
+
+\item{value}{a data frame OR vector OR formula (see details).}
+
+\item{sep}{a \code{character} indicating the character used to separate
+hierarchical levels. This defaults to "_".}
+
+\item{name}{an optional name argument for use with addStrata if supplying
+a vector. Defaults to "NEW".}
+}
+\description{
+The following methods allow the user to quickly change the strata of a genind
+or genlight object.
+}
+\details{
+\subsection{Function Specifics}{ \itemize{ \item \strong{strata()} -
+ Use this function to view or define population stratification of a
+ \linkS4class{genind} or \linkS4class{genlight} object. \item
+ \strong{nameStrata()} - View or rename the different levels of strata.
+ \item \strong{splitStrata()} - Split strata that are combined with a common
+ separator. This function should only be used once during a workflow.
+ \itemize{ \item \emph{Rationale:} It is often difficult to import files
+ with several levels of strata as most data formats do not allow unlimited
+ population levels. This is circumvented by collapsing all population strata
+ into a single population factor with a common separator for each
+ observation. } \item \strong{addStrata()} - Add levels to your population
+ strata. This is ideal for adding groups defined by
+ \code{\link{find.clusters}}. You can input a data frame or a vector, but if
+ you put in a vector, you have the option to name it. }}
+
+ \subsection{Argument Specifics}{
+
+ These functions allow the user to seamlessly carry all possible population
+ stratification with their \linkS4class{genind} or \linkS4class{genlight}
+ object. Note that there are two ways of performing all methods: \itemize{
+ \item modifying: \code{strata(myData) <- myStrata} \item preserving:
+ \code{myNewData <- strata(myData, value = myStrata)} } They essentially do
+ the same thing except that the modifying assignment method (the one with
+ the "\code{<-}") will modify the object in place whereas the non-assignment
+ method will preserve the original object (unless you overwrite it). Due to
+ convention, everything right of the assignment is termed \code{value}. To
+ avoid confusion, here is a guide to the argument \strong{\code{value}} for
+ each function: \itemize{ \item \strong{strata()} \code{value = }a
+ \code{\link{data.frame}} that defines the strata for each individual in the
+ rows. \item \strong{nameStrata()} \code{value = }a \code{\link{vector}} or
+ a \code{\link{formula}} that will define the names. \item
+ \strong{splitStrata()} \code{value = }a \code{\link{formula}} argument with
+ the same number of levels as the strata you wish to split. \item
+ \strong{addStrata()} \code{value = }a \code{\link{vector}} or
+ \code{\link{data.frame}} with the same length as the number of individuals
+ in your data. }}
+
+ \subsection{Details on Formulas}{
+
+ The preferred use of these functions is with a \code{\link{formula}}
+ object. Specifically, a hierarchical formula argument is used to assign the
+ levels of the strata. An example of a hierarchical formula would
+ be:\tabular{r}{ \code{~Country/City/Neighborhood}} This convention was
+ chosen as it becomes easier to type and makes intuitive sense when defining
+ a \code{\link{hierarchy}}. Note: it is important to use hiearchical
+ formulas when specifying hierarchies as other types of formulas (eg.
+ \code{~Country*City*Neighborhood}) will give incorrect results.}
+}
+\examples{
+# let's look at the microbov data set:
+data(microbov)
+microbov
+
+# We see that we have three vectors of different names in the 'other' slot.
+# ?microbov
+# These are Country, Breed, and Species
+names(other(microbov))
+
+# Let's set the strata
+strata(microbov) <- data.frame(other(microbov))
+microbov
+
+# And change the names so we know what they are
+nameStrata(microbov) <- ~Country/Breed/Species
+
+\dontrun{
+# let's see what the strata looks like by Species and Breed:
+head(strata(microbov, ~Breed/Species))
+
+# If we didn't want the last column combined with the first, we can set
+# combine = FALSE
+head(strata(microbov, ~Breed/Species, combine = FALSE))
+
+#### USING splitStrata ####
+
+# For the sake of example, we'll imagine that we have imported our data set
+# with all of the stratifications combined.
+setPop(microbov) <- ~Country/Breed/Species
+strata(microbov) <- NULL
+
+# This is what our data would look like after import.
+microbov
+
+# To set our strata here, we need to use the functions strata and splitStrata
+strata(microbov) <- data.frame(x = pop(microbov))
+microbov # shows us that we have "one" level of stratification
+head(strata(microbov)) # all strata are separated by "_"
+
+splitStrata(microbov) <- ~Country/Breed/Species
+microbov # Now we have all of our strata named and split
+head(strata(microbov)) # all strata are appropriately named and split.
+}
+}
+\author{
+Zhian N. Kamvar
+}
+\seealso{
+\code{\link{setPop}} \code{\link{genind}}
+ \code{\link{as.genind}}
+}
+
diff --git a/man/tab.Rd b/man/tab.Rd
new file mode 100644
index 0000000..2fcc40e
--- /dev/null
+++ b/man/tab.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/handling.R
+\docType{methods}
+\name{tab}
+\alias{tab}
+\alias{tab,genind-method}
+\alias{tab,genind-methods}
+\alias{tab,genpop-method}
+\alias{tab,genpop-methods}
+\title{Access allele counts or frequencies}
+\usage{
+tab(x, ...)
+
+\S4method{tab}{genind}(x, freq = FALSE, NA.method = c("asis", "mean",
+ "zero"), ...)
+
+\S4method{tab}{genpop}(x, freq = FALSE, NA.method = c("asis", "mean",
+ "zero"), ...)
+}
+\arguments{
+\item{x}{a \linkS4class{genind} or \linkS4class{genpop} object.}
+
+\item{...}{further arguments passed to other methods.}
+
+\item{freq}{a logical indicating if data should be transformed into relative frequencies (TRUE); defaults to FALSE.}
+
+\item{NA.method}{a method to replace NA; asis: leave NAs as is; mean: replace by the mean allele frequencies; zero: replace by zero}
+}
+\value{
+a matrix of integers or numeric
+}
+\description{
+This accessor is used to retrieve a matrix of allele data.
+By default, a matrix of integers representing allele counts is returned.
+If \code{freq} is TRUE, then data are standardised as frequencies, so that for any individual and any locus the data sum to 1.
+The argument \code{NA.method} allows to replace missing data (NAs).
+This accessor replaces the previous function \code{truenames} as well as the function \code{makefreq}.
+}
+\examples{
+
+data(microbov)
+head(tab(microbov))
+head(tab(microbov,freq=TRUE))
+
+
+}
+
diff --git a/man/truenames.Rd b/man/truenames.Rd
new file mode 100644
index 0000000..15f0d9f
--- /dev/null
+++ b/man/truenames.Rd
@@ -0,0 +1,36 @@
+\encoding{UTF-8}
+\docType{methods}
+\name{truenames}
+\alias{truenames}
+\alias{truenames-methods}
+\alias{truenames,ANY-method}
+\alias{truenames,genind-method}
+\alias{truenames,genpop-method}
+\title{ Restore true labels of an object}
+\description{
+ The function \code{truenames} returns some elements of an object
+ (\linkS4class{genind} or \linkS4class{genpop}) using true names
+ (as opposed to generic labels) for individuals, markers, alleles, and
+ population.\cr
+
+ Important: as of adegenet_2.0-0, these functions are deprecated as
+ true labels are used whenever possible. Please use the function
+ \code{\link{tab}} instead.
+}
+\usage{
+\S4method{truenames}{genind}(x)
+\S4method{truenames}{genpop}(x)
+}
+\arguments{
+ \item{x}{a \linkS4class{genind} or a \linkS4class{genpop} object}
+}
+\value{
+ If x\$pop is empty (NULL), a matrix similar to the x\$tab slot but
+ with true labels.
+
+ If x\$pop exists, a list with this matrix (\$tab) and a population
+ vector with true names (\$pop).\cr
+
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\seealso{\code{\link{tab}}}
\ No newline at end of file
diff --git a/man/virClasses.Rd b/man/virClasses.Rd
new file mode 100644
index 0000000..4b1dfb4
--- /dev/null
+++ b/man/virClasses.Rd
@@ -0,0 +1,18 @@
+\name{virtualClasses}
+\docType{class}
+\alias{indInfo-class}
+\alias{popInfo-class}
+\alias{gen-class}
+\alias{callOrNULL-class}
+\alias{charOrNULL-class}
+\alias{factorOrNULL-class}
+\alias{intOrNum-class}
+\alias{listOrNULL-class}
+\alias{intOrNULL-class}
+\alias{dfOrNULL-class}
+\alias{formOrNULL-class}
+\title{Virtual classes for adegenet}
+\description{These virtual classes are only for internal use in adegenet}
+\section{Objects from the Class}{A virtual Class: No objects may be created from it.}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\keyword{classes}
diff --git a/man/web.Rd b/man/web.Rd
new file mode 100644
index 0000000..6186b7e
--- /dev/null
+++ b/man/web.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/auxil.R
+\name{adegenetWeb}
+\alias{adegenetIssues}
+\alias{adegenetTutorial}
+\alias{adegenetWeb}
+\title{Functions to access online resources for adegenet}
+\usage{
+adegenetWeb()
+
+adegenetTutorial(which = c("basics", "spca", "dapc", "genomics", "strata"))
+
+adegenetIssues()
+}
+\arguments{
+\item{which}{a character string indicating which tutorial to open (see details)}
+}
+\description{
+These functions simply open websites or documents
+available online providing resources for adegenet.
+}
+\details{
+\itemize{
+\item adegenetWeb opens adegenet's website
+\item adegenetTutorial opens adegenet tutorials
+\item adegenetIssues opens the issue page on github;
+this is used to report a bug or post a feature request.
+}
+
+
+
+Available tutorials are:
+\itemize{
+\item 'basics': general introduction to adegenet; covers basic data structures, import/export, handling, and a number of population genetics methods
+\item 'spca': spatial genetic structures using the spatial Principal Component Analysis
+\item 'dapc': population structure using the Discriminant Analysis of Principal Components
+\item 'genomics': handling large genome-wide SNP data using adegenet
+\item 'strata': introduction to hierarchical population structure in adegenet
+}
+}
+
diff --git a/man/xvalDapc.Rd b/man/xvalDapc.Rd
new file mode 100644
index 0000000..bf23b11
--- /dev/null
+++ b/man/xvalDapc.Rd
@@ -0,0 +1,132 @@
+\encoding{UTF-8}
+\name{DAPC cross-validation}
+\alias{xvalDapc}
+\alias{xvalDapc.data.frame}
+\alias{xvalDapc.matrix}
+\title{Cross-validation for Discriminant Analysis of Principal Components (DAPC)}
+\description{
+ The function \code{xvalDapc} performs stratified cross-validation of DAPC
+ using varying numbers of PCs (and keeping the number of discriminant
+ functions fixed); \code{xvalDapc} is a generic with methods for
+ \code{data.frame} and \code{matrix}.\cr
+}
+\usage{
+xvalDapc(x, grp, n.pca.max = 300, n.da = NULL,
+ training.set = 0.9, result = c("groupMean", "overall"),
+ center = TRUE, scale = FALSE,
+ n.pca=NULL, n.rep = 30, xval.plot = TRUE, \dots)
+
+
+\method{xvalDapc}{data.frame}(x, grp, n.pca.max = 300, n.da = NULL,
+ training.set = 0.9, result = c("groupMean", "overall"),
+ center = TRUE, scale = FALSE,
+ n.pca=NULL, n.rep = 30, xval.plot = TRUE, \dots)
+
+\method{xvalDapc}{matrix}(x, grp, n.pca.max = 300, n.da = NULL,
+ training.set = 0.9, result = c("groupMean", "overall"),
+ center = TRUE, scale = FALSE,
+ n.pca=NULL, n.rep = 30, xval.plot = TRUE, \dots)
+}
+\arguments{
+ \item{x}{\code{a data.frame} or a \code{matrix} used as input of DAPC.}
+ \item{grp}{a \code{factor} indicating the group membership of
+ individuals.}
+ \item{n.pca.max}{maximum number of PCA components to retain.}
+ \item{n.da}{an \code{integer} indicating the number of axes retained in the
+ Discriminant Analysis step. If \code{NULL}, n.da defaults to 1 less than
+ the number of groups.}
+ \item{training.set}{the proportion of data (individuals) to be used
+ for the training set; defaults to 0.9 if all groups have >= 10 members; otherwise,
+ training.set scales automatically to the largest proportion that still
+ ensures all groups will be present in both training and validation sets.}
+ \item{result}{a character string; "groupMean" for group-wise assignment
+ sucess, or "overall" for an overall mean assignment success; see details.}
+ \item{center}{a \code{logical} indicating whether variables should be centred to
+ mean 0 (TRUE, default) or not (FALSE). Always TRUE for \linkS4class{genind} objects.}
+ \item{scale}{a \code{logical} indicating whether variables should be scaled
+ (TRUE) or not (FALSE, default). Scaling consists in dividing variables by their
+ (estimated) standard deviation to account for trivial differences in
+ variances.}
+ \item{n.pca}{an \code{integer} vector indicating the number of
+ different number of PCA axes to be retained for the cross
+ validation; if \code{NULL}, this will be dertermined automatically.}
+ \item{n.rep}{the number of replicates to be carried out at each level of
+ PC retention; defaults to 30.}
+ \item{xval.plot}{a logical indicating whether a plot of the cross-validation
+ results should be generated.}
+ \item{\dots}{further arguments to be passed to \code{\link[boot]{boot}}.
+ \strong{see Details.}} }
+\details{ The Discriminant Analysis of Principal Components (DAPC) relies on
+ dimension reduction of the data using PCA followed by a linear discriminant
+ analysis. How many PCA axes to retain is often a non-trivial question. Cross
+ validation provides an objective way to decide how many axes to retain:
+ different numbers are tried and the quality of the corresponding DAPC is
+ assessed by cross- validation: DAPC is performed on a training set, typically
+ made of 90\% of the observations (comprising 90\% of the observations in each
+ subpopulation) , and then used to predict the groups of the 10\% of remaining
+ observations. The current method uses the average prediction success per group
+ (result="groupMean"), or the overall prediction success (result="overall").
+ The number of PCs associated with the lowest Mean Squared Error is then
+ retained in the DAPC.
+ \subsection{Parallel Computing}{
+ The permutation of the data for cross-validation is performed in part by the
+ function\code{\link[boot]{boot}}. If you have a modern computer, it is
+ likely that you have multiple cores on your system. R by default utilizes
+ only one of these cores unless you tell it otherwise. For details, please
+ see the documentation of \code{\link[boot]{boot}}. Basically, if you want to
+ use multiple cores, you need two arguments:
+ \enumerate{
+ \item \code{parallel} - what R parallel system to use (see below)
+ \item \code{ncpus} - number of cores you want to use
+ }
+ If you are on a unix system (Linux or OSX), you will want to specify
+ \code{parallel = "multicore"}. If you are on Windows, you will want to
+ specify \code{parallel = "snow"}.
+ }
+}
+\value{
+ A \code{list} containing seven items, and a \code{plot} of the results. The
+ first is a \code{data.frame} with two columns, the first giving the number of
+ PCs of PCA retained in the corresponding DAPC, and the second giving the
+ proportion of successful group assignment for each replicate. The second item
+ gives the mean and confidence interval for random chance. The third gives the
+ mean successful assignment at each level of PC retention. The fourth indicates
+ which number of PCs is associated with the highest mean success. The fifth
+ gives the Root Mean Squared Error at each level of PC retention. The sixth
+ indicates which number of PCs is associated with the lowest MSE. The seventh
+ item contains the DAPC carried out with the optimal number of PCs, determined
+ with reference to MSE.
+
+ If \code{xval.plot=TRUE} a scatterplot of the results of cross-validation
+ will be displayed.
+
+}
+\references{
+ Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of
+ principal components: a new method for the analysis of genetically
+ structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
+}
+\seealso{
+ \code{\link{dapc}}
+}
+\author{ Caitlin Collins \email{caitlin.collins12 at imperial.ac.uk},
+Thibaut Jombart \email{t.jombart at imperial.ac.uk},
+Zhian N. Kamvar \email{kamvarz at science.oregonstate.edu} }
+\examples{
+\dontrun{
+## CROSS-VALIDATION ##
+data(sim2pop)
+xval <- xvalDapc(sim2pop at tab, pop(sim2pop), n.pca.max=100, n.rep=3)
+xval
+
+## 100 replicates ##
+
+# Serial version (SLOW!)
+system.time(xval <- xvalDapc(sim2pop at tab, pop(sim2pop), n.pca.max=100, n.rep=100))
+
+# Parallel version (faster!)
+system.time(xval <- xvalDapc(sim2pop at tab, pop(sim2pop), n.pca.max=100, n.rep=100,
+ parallel = "multicore", ncpus = 2))
+}
+}
+\keyword{multivariate}
diff --git a/src/GLfunctions.c b/src/GLfunctions.c
new file mode 100644
index 0000000..fa9ceac
--- /dev/null
+++ b/src/GLfunctions.c
@@ -0,0 +1,236 @@
+/*
+ Coded by Thibaut Jombart (tjombart at imperial.ac.uk), December 2010.
+ Distributed with the adephylo package for the R software.
+ Licence: GPL >=2.
+
+ Functions based on snpbin and genlightC classes, which mirror the R classes SNPbin and genlight on the C side.
+*/
+
+
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <R_ext/Print.h>
+
+#include "snpbin.h"
+
+
+/* Function to compute all dot products between individuals */
+/* centring and scaling is always used */
+/* but need to pass vectors of 0 and 1*/
+void GLdotProd(unsigned char *gen, int *nbvecperind, int *byteveclength, int *nbnaperind, int *naposi, int *nind, int *nloc, int *ploidy, double *mean, double *sd, bool *freq, double *res){
+ struct genlightC dat;
+ int i, j, k=0;
+
+ /* Check variance vector: do not divide by 0 */
+ for(i=0;i< *nloc;i++){
+ if(sd[i] < NEARZERO){
+ sd[i] = 1;
+ }
+ }
+
+ dat = genlightTogenlightC(gen, nbvecperind, byteveclength, nbnaperind, naposi, nind, nloc, ploidy);
+
+ if(*freq){
+ /* === working on frequencies === */
+ /* Lower triangle - without the diagonal */
+ for(i=0; i< (*nind-1); i++){
+ for(j=i+1; j< *nind; j++){
+ /* printf("\n == pair %i-%i ==\n", i+1,j+1); */
+ res[k] = snpbin_dotprod_freq(&dat.x[i], &dat.x[j], mean, sd);
+ ++k;
+ }
+ }
+
+ /* add the diagonal to the end of the array */
+ for(i=0; i< *nind; i++){
+ /* printf("\n == pair %i-%i == \n", i+1,i+1); */
+ res[k] = snpbin_dotprod_freq(&dat.x[i], &dat.x[i], mean, sd);
+ ++k;
+ }
+ } else {
+ /* === working on frequencies === */
+ /* Lower triangle - without the diagonal */
+ for(i=0; i< (*nind-1); i++){
+ for(j=i+1; j< *nind; j++){
+ /* printf("\n == pair %i-%i ==\n", i+1,j+1); */
+ res[k] = snpbin_dotprod_int(&dat.x[i], &dat.x[j], mean, sd);
+ ++k;
+ }
+ }
+
+ /* add the diagonal to the end of the array */
+ for(i=0; i< *nind; i++){
+ /* printf("\n == pair %i-%i == \n", i+1,i+1); */
+ res[k] = snpbin_dotprod_int(&dat.x[i], &dat.x[i], mean, sd);
+ ++k;
+ }
+ }
+}
+
+
+
+
+
+
+
+
+
+void GLsumInt(unsigned char *gen, int *nbvecperind, int *byteveclength, int *nbnaperind, int *naposi, int *nind, int *nloc, int *ploidy, int *res){
+ struct genlightC dat;
+ int i, j;
+ int *vecIntTemp;
+ vecIntTemp = (int *) calloc(*nloc, sizeof(int));
+
+ /* set res to zeros */
+ /* for(j=0;j< *nloc;j++){ */
+ /* res[j] = 0; */
+ /* } */
+
+ /* Internal C representation of the genlight object */
+ dat = genlightTogenlightC(gen, nbvecperind, byteveclength, nbnaperind, naposi, nind, nloc, ploidy);
+
+
+ /* === working on frequencies === */
+ /* Lower triangle - without the diagonal */
+ for(i=0; i < (*nind); i++){ /* for all individuals*/
+ /* conversion to integers of current indiv */
+ snpbin2intvec(&(dat.x[i]), vecIntTemp);
+
+ for(j=0; j < *nloc; j++){ /* for all loci */
+ if(!snpbin_isna(&(dat.x[i]), j)) res[j] += vecIntTemp[j];
+ }
+ }
+}
+
+
+
+
+
+void GLsumFreq(unsigned char *gen, int *nbvecperind, int *byteveclength, int *nbnaperind, int *naposi, int *nind, int *nloc, int *ploidy, double *res){
+ struct genlightC dat;
+ int i, j;
+ double *vecFreqTemp;
+ vecFreqTemp = (double *) calloc(*nloc, sizeof(double));
+
+ /* set res to zeros */
+ /* for(j=0;j< *nloc;j++){ */
+ /* res[j] = 0.0; */
+ /* } */
+
+ /* Internal C representation of the genlight object */
+ dat = genlightTogenlightC(gen, nbvecperind, byteveclength, nbnaperind, naposi, nind, nloc, ploidy);
+
+ /* === working on frequencies === */
+ /* Lower triangle - without the diagonal */
+ for(i=0; i < (*nind); i++){ /* for all individuals*/
+ /* conversion to frequencies of current indiv */
+ snpbin2freq(&(dat.x[i]), vecFreqTemp);
+
+ for(j=0; j < *nloc; j++){ /* for all loci */
+ if(!snpbin_isna(&(dat.x[i]), j)) res[j] += vecFreqTemp[j];
+ }
+ }
+}
+
+
+
+
+/* TESTING in R */
+
+/*
+
+## === DOT PRODUCTS ALLELE COUNTS === ##
+
+library(adegenet)
+dat <- rbind("a"=c(1,0,0), "b"=c(1,2,1), "c"=c(1,0,1))
+x <- new("genlight",dat)
+
+
+## RANDOM DATA
+dat <- matrix(sample(0:1, 5*1000, replace=TRUE), nrow=5)
+x <- new("genlight",dat)
+res1 <- glDotProd(x, alle=TRUE)
+res2 <- as.matrix(x) %*% t(as.matrix(x))
+all(res1==res2)
+
+
+## CENTRED, NOT SCALED
+res1 <- glDotProd(x, cent=TRUE, alle=TRUE)
+temp <- as.matrix(x) / ploidy(x)
+temp <- scalewt(temp, cent=TRUE, scale=FALSE)
+res2 <- temp %*% t(temp)
+res2
+all(abs(res1-res2)<1e-10)
+
+
+## CENTRED, SCALED
+res1 <- glDotProd(x, cent=TRUE, scale=TRUE, alle=TRUE)
+temp <- as.matrix(x) / ploidy(x)
+temp <- scalewt(temp, cent=TRUE, scale=TRUE)
+res2 <- temp %*% t(temp)
+res2
+all(abs(res1-res2)<1e-10)
+
+
+## TEST WITH NAs
+library(adegenet)
+dat <- list(a=c(1,NA,0,0,2), b=c(1,2,3,4,0), c=c(NA,0,1,NA,2))
+x <- new("genlight", dat) # conversion
+x
+res1 <- glDotProd(x, alle=TRUE)
+t(data.frame(dat))
+res1
+
+
+
+
+
+
+
+## === DOT PRODUCTS ALLELE FREQUENCIES === ##
+
+library(adegenet)
+
+
+## RANDOM DATA
+dat <- rbind(matrix(sample(0:1, 3*1000, replace=TRUE), nrow=3),
+ matrix(sample(0:2, 2*1000, replace=TRUE), nrow=2))
+x <- new("genlight",dat)
+res1 <- glDotProd(x)
+temp <- as.matrix(x) / ploidy(x)
+res2 <- temp %*% t(temp)
+all(res1==res2)
+
+
+## CENTRED, NOT SCALED
+res1 <- glDotProd(x, cent=TRUE, alle=FALSE)
+temp <- scalewt(temp, cent=TRUE, scale=FALSE)
+res2 <- temp %*% t(temp)
+res2
+all(abs(res1-res2)<1e-10)
+
+
+## CENTRED, SCALED
+res1 <- glDotProd(x, cent=TRUE, scale=TRUE, alle=FALSE)
+temp <- as.matrix(x) / ploidy(x)
+temp <- scalewt(temp, cent=TRUE, scale=TRUE)
+res2 <- temp %*% t(temp)
+res2
+all(abs(res1-res2)<1e-10)
+
+
+## TEST WITH NAs
+library(adegenet)
+dat <- list(a=c(1,NA,0,0,2), b=c(1,2,3,4,0), c=c(NA,0,1,NA,2))
+x <- new("genlight", dat) # conversion
+x
+res1 <- glDotProd(x, alle=FALSE)
+temp <- as.matrix(x)/ploidy(x)
+temp
+res1
+
+*/
+
diff --git a/src/GLfunctions.h b/src/GLfunctions.h
new file mode 100644
index 0000000..28db0d9
--- /dev/null
+++ b/src/GLfunctions.h
@@ -0,0 +1,5 @@
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
diff --git a/src/adesub.c b/src/adesub.c
new file mode 100644
index 0000000..8ac100b
--- /dev/null
+++ b/src/adesub.c
@@ -0,0 +1,1152 @@
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+#include "adesub.h"
+#include <R.h>
+
+/***********************************************************************/
+double traceXtdLXq (double **X, double **L, double *d, double *q)
+/* Produit matriciel XtDLXQ avec LX comme lag.matrix */
+{
+ /* Declarations de variables C locales */
+ int j, i, lig, col;
+ double **auxi, **A, trace;
+
+
+
+ /* Allocation memoire pour les variables C locales */
+ lig = X[0][0];
+ col = X[1][0];
+ taballoc(&auxi, lig, col);
+ taballoc(&A, col, col);
+
+
+ /* Calcul de LX */
+ prodmatABC(L, X, auxi);
+
+ /* Calcul de DLX */
+ for (i=1;i<=lig;i++) {
+ for (j=1;j<=col;j++) {
+ auxi[i][j] = auxi[i][j] * d[i];
+ }
+ }
+
+ /* Calcul de XtDLX */
+ prodmatAtBC(X,auxi,A);
+
+ /* Calcul de trace(XtDLXQ) */
+ trace=0;
+ for (i=1;i<=col;i++) {
+ trace = trace + A[i][i] * q[i];
+ }
+
+ /* Lib�ration des r�servations locales */
+ freetab (auxi);
+ freetab (A);
+ return(trace);
+}
+
+/***********************************************************************/
+void tabintalloc (int ***tab, int l1, int c1)
+/*--------------------------------------------------
+* Allocation de memoire dynamique pour un tableau
+* d'entiers (l1, c1)
+--------------------------------------------------*/
+{
+ int i, j;
+
+ *tab = (int **) calloc(l1+1, sizeof(int *));
+
+ if ( *tab != NULL) {
+ for (i=0;i<=l1;i++) {
+
+ *(*tab+i)=(int *) calloc(c1+1, sizeof(int));
+ if ( *(*tab+i) == NULL ) {
+ for (j=0;j<i;j++) {
+ free(*(*tab+j));
+ }
+ return;
+ }
+ }
+ } else return;
+ **(*tab) = l1;
+ **(*tab+1) = c1;
+ for (i=1;i<=l1;i++) {
+ for (j=1;j<=c1;j++) {
+ (*tab)[i][j] = 0;
+ }
+ }
+}
+
+/***********************************************************************/
+void freeinttab (int **tab)
+/*--------------------------------------------------
+* Allocation de memoire dynamique pour un tableau
+--------------------------------------------------*/
+{
+ int i, n;
+
+ n = *(*(tab));
+
+ for (i=0;i<=n;i++) {
+ free((char *) *(tab+i) );
+ }
+
+ free((char *) tab);
+}
+
+
+/*********************/
+int dtodelta (double **data, double *pl)
+{
+ /* la matrice de distances d2ij dans data est associee aux poids pl
+ Elle est transformee par aij - ai. -a.j + a..
+ aij = -d2ij/2);*/
+
+ int lig, i, j;
+ double *moy, a0, moytot;
+
+ lig=data[0][0];
+ vecalloc(&moy, lig);
+
+ for (i=1; i<=lig; i++) {
+ for (j=1; j<=lig; j++) data[i][j] = 0.0 - data[i][j] * data[i][j] / 2.0;
+ }
+
+ for (i=1; i<=lig; i++) {
+ a0=0;
+ for (j=1; j<=lig; j++) a0 = a0 + pl[j]*data[i][j];
+ moy[i] = a0;
+ }
+ moytot=0;
+ for (i=1; i<=lig; i++) {
+ moytot = moytot+pl[i]*moy[i];
+ }
+ for (i=1; i<=lig; i++) {
+ for (j=1; j<=lig; j++) data[i][j] = data[i][j] - moy[i] - moy[j] + moytot;
+ }
+ freevec (moy);
+ return 1;
+}
+/***************************/
+void initvec (double *v1, double r)
+/*--------------------------------------------------
+* Initialisation des elements d'un vecteur
+--------------------------------------------------*/
+{
+ int i, c1;
+
+ c1 = v1[0];
+ for (i=1;i<=c1;i++) {
+ v1[i] = r;
+ }
+}
+/**************************/
+double alea (void)
+{
+ double w;
+ GetRNGstate();
+ /* w = ((double) rand())/ (double)RAND_MAX; */
+ w = unif_rand();
+ PutRNGstate();
+ return (w);
+}
+/*************************/
+void aleapermutmat (double **a)
+{
+ /* permute au hasard les lignes du tableau a
+ Manly p. 42 le tableau est modifi� */
+ int lig, i,j, col, n, k;
+ double z;
+
+ lig = a[0][0];
+ col = a[1][0];
+ for (i=1; i<=lig-1; i++) {
+ j=lig-i+1;
+ k = (int) (j*alea ()+1);
+ /*k = (int) (j*genrand()+1);*/
+ if (k>j) k=j;
+ for (n=1; n<=col; n++) {
+ z = a[j][n];
+ a[j][n]=a[k][n];
+ a[k][n] = z;
+ }
+ }
+}
+/*************************/
+void aleapermutvec (double *a)
+{
+ /* permute au hasard les �l�ments du vecteur a
+ Manly p. 42 Le vecteur est modifi�
+ from Knuth 1981 p. 139*/
+ int lig, i,j, k;
+ double z;
+
+ lig = a[0];
+ for (i=1; i<=lig-1; i++) {
+ j=lig-i+1;
+ k = (int) (j*alea()+1);
+ /*k = (int) (j*genrand()+1);*/
+ if (k>j) k=j;
+ z = a[j];
+ a[j]=a[k];
+ a[k] = z;
+ }
+}
+/***********************************************************************/
+void DiagobgComp (int n0, double **w, double *d, int *rang)
+/*--------------------------------------------------
+* Diagonalisation
+* T. FOUCART Analyse factorielle de tableaux multiples,
+* Masson, Paris 1984,185p., p. 62. D'apr?s VPROP et TRIDI,
+* de LEBART et coll.
+--------------------------------------------------*/
+{
+ double *s, epsilon;
+ double a, b, c, x, xp, q, bp, ab, ep, h, t, u , v;
+ double dble;
+ int ni, i, i2, j, k, jk, ijk, ij, l, ix, m, m1, isnou;
+
+ vecalloc(&s, n0);
+ a = 0.000000001;
+ epsilon = 0.0000001;
+ ni = 100;
+ if (n0 == 1) {
+ d[1] = w[1][1];
+ w[1][1] = 1.0;
+ *rang = 1;
+ freevec (s);
+ return;
+ }
+
+ for (i2=2;i2<=n0;i2++) {
+
+ b=0.0;
+ c=0.0;
+ i=n0-i2+2;
+ k=i-1;
+ if (k < 2) goto Et1;
+ for (l=1;l<=k;l++) {
+ c = c + fabs((double) w[i][l]);
+ }
+ if (c != 0.0) goto Et2;
+
+Et1: s[i] = w[i][k];
+ goto Etc;
+
+Et2: for (l=1;l<=k;l++) {
+ x = w[i][l] / c;
+ w[i][l] = x;
+ b = b + x * x;
+ }
+ xp = w[i][k];
+ ix = 1;
+ if (xp < 0.0) ix = -1;
+
+/* q = -sqrt(b) * ix; */
+ dble = b;
+ dble = -sqrt(dble);
+ q = dble * ix;
+
+ s[i] = c * q;
+ b = b - xp * q;
+ w[i][k] = xp - q;
+ xp = 0;
+ for (m=1;m<=k;m++) {
+ w[m][i] = w[i][m] / b / c;
+ q = 0;
+ for (l=1;l<=m;l++) {
+ q = q + w[m][l] * w[i][l];
+ }
+ m1 = m + 1;
+ if (k < m1) goto Et3;
+ for (l=m1;l<=k;l++) {
+ q = q + w[l][m] * w[i][l];
+ }
+
+Et3: s[m] = q / b;
+ xp = xp + s[m] * w[i][m];
+ }
+ bp = xp * 0.5 / b;
+ for (m=1;m<=k;m++) {
+ xp = w[i][m];
+ q = s[m] - bp * xp;
+ s[m] = q;
+ for (l=1;l<=m;l++) {
+ w[m][l] = w[m][l] - xp * s[l] - q * w[i][l];
+ }
+ }
+ for (l=1;l<=k;l++) {
+ w[i][l] = c * w[i][l];
+ }
+
+Etc: d[i] = b;
+ } /* for (i2=2;i2<n0;i2++) */
+
+ s[1] = 0.0;
+ d[1] = 0.0;
+
+ for (i=1;i<=n0;i++) {
+
+ k = i - 1;
+ if (d[i] == 0.0) goto Et4;
+ for (m=1;m<=k;m++) {
+ q = 0.0;
+ for (l=1;l<=k;l++) {
+ q = q + w[i][l] * w[l][m];
+ }
+ for (l=1;l<=k;l++) {
+ w[l][m] = w[l][m] - q * w[l][i];
+ }
+ }
+
+Et4: d[i] = w[i][i];
+ w[i][i] = 1.0;
+ if (k < 1) goto Et5;
+ for (m=1;m<=k;m++) {
+ w[i][m] = 0.0;
+ w[m][i] = 0.0;
+ }
+
+Et5:;
+ }
+
+ for (i=2;i<=n0;i++) {
+ s[i-1] = s[i];
+ }
+ s[n0] = 0.0;
+
+ for (k=1;k<=n0;k++) {
+
+ m = 0;
+
+Et6: for (j=k;j<=n0;j++) {
+ if (j == n0) goto Et7;
+ ab = fabs((double) s[j]);
+ ep = a * (fabs((double) d[j]) + fabs((double) d[j+1]));
+ if (ab < ep) goto Et7;
+ }
+
+Et7: isnou = 1;
+ h = d[k];
+ if (j == k) goto Eta;
+ if (m < ni) goto Etd;
+
+ /*err_message("Error: can't compute matrix eigenvalues");*/
+
+Etd: m = m + 1;
+ q = (d[k+1]-h) * 0.5 / s[k];
+
+/* t = sqrt(q * q + 1.0); */
+ dble = q * q + 1.0;
+ dble = sqrt(dble);
+ t = dble;
+
+ if (q < 0.0) isnou = -1;
+ q = d[j] - h + s[k] / (q + t * isnou);
+ u = 1.0;
+ v = 1.0;
+ h = 0.0;
+ jk = j-k;
+ for (ijk=1;ijk<=jk;ijk++) {
+ i = j - ijk;
+ xp = u * s[i];
+ b = v * s[i];
+ if (fabs((double) xp) < fabs((double) q)) goto Et8;
+ u = xp / q;
+
+/* t = sqrt(u * u + 1); */
+ dble = u * u + 1.0;
+ dble = sqrt(dble);
+ t = dble;
+
+ s[i+1] = q * t;
+ v = 1 / t;
+ u = u * v;
+ goto Et9;
+
+Et8: v = q / xp;
+
+/* t = sqrt(1 + v * v); */
+ dble = 1.0 + v * v;
+ dble = sqrt(dble);
+ t = dble;
+
+ s[i+1] = t * xp;
+ u = 1 / t;
+ v = v * u;
+
+Et9:
+ q = d[i+1] - h;
+ t = (d[i] - q) * u + 2.0 * v * b;
+ h = u * t;
+ d[i+1] = q + h;
+ q = v * t - b;
+ for (l=1;l<=n0;l++) {
+ xp = w[l][i+1];
+ w[l][i+1] = u * w[l][i] + v * xp;
+ w[l][i] = v * w[l][i] - u * xp;
+ }
+ }
+ d[k] = d[k] - h;
+ s[k] = q;
+ s[j] = 0.0;
+
+ goto Et6;
+
+Eta:;
+ } /* for (k=1;k<=n0;k++) */
+
+ for (ij=2;ij<=n0;ij++) {
+
+ i = ij - 1;
+ l = i;
+ h = d[i];
+ for (m=ij;m<=n0;m++) {
+ if (d[m] >= h) {
+ l = m;
+ h = d[m];
+ }
+ }
+ if (l == i) {
+ goto Etb;
+ } else {
+ d[l] = d[i];
+ d[i] = h;
+ }
+ for (m=1;m<=n0;m++) {
+ h = w[m][i];
+ w[m][i] = w[m][l];
+ w[m][l] = h;
+ }
+
+Etb:;
+ } /* for (ij=2;ij<=n0;ij++) */
+
+ *rang = 0;
+ for (i=1;i<=n0;i++) {
+ if (d[i] / d[1] < epsilon) d[i] = 0.0;
+ if (d[i] != 0.0) *rang = *rang + 1;
+ }
+ freevec(s);
+} /* DiagoCompbg */
+/***********************************************************************/
+void freeintvec (int *vec)
+/*--------------------------------------------------
+* liberation de memoire pour un vecteur
+--------------------------------------------------*/
+{
+
+ free((char *) vec);
+
+}
+/***********************************************************************/
+void freetab (double **tab)
+/*--------------------------------------------------
+* Allocation de memoire dynamique pour un tableau (l1, c1)
+--------------------------------------------------*/
+{
+ int i, n;
+
+ n = *(*(tab));
+ for (i=0;i<=n;i++) {
+ free((char *) *(tab+i) );
+ }
+ free((char *) tab);
+}
+/***********************************************************************/
+void freevec (double *vec)
+/*--------------------------------------------------
+* liberation de memoire pour un vecteur
+--------------------------------------------------*/
+{
+ free((char *) vec);
+}
+/***********************************************************************/
+void getpermutation (int *numero, int repet)
+/*----------------------
+* affectation d'une permutation al�atoire des n premiers entiers
+* dans dans un vecteur d'entiers de dimension n
+* vecintalloc pr�alable exig�
+* *numero est un vecteur d'entier
+* repet est un entier qui peut prendre une valeur arbitraire
+* utilise dans le germe du generateur de nb pseudo-aleatoires
+* si on l'incremente dans des appels repetes (e.g. simulation) garantit
+* que deux appels donnent deux resultats distincts (seed=clock+repet)
+------------------------*/
+{
+ int i, n, seed;
+ int *alea;
+
+ n=numero[0];
+ vecintalloc (&alea,n);
+
+ /*-------------
+ * numerotation dans numero
+ -----------*/
+ for (i=1;i<=n;i++) {
+ numero[i]=i;
+ }
+
+ /*-------------
+ * affectation de nombres aleatoires dans alea
+ ----------------*/
+ /* seed = clock(); */
+ /* seed = seed + repet; */
+ /* srand(seed); */
+ GetRNGstate();
+ for (i=1;i<=n;i++) {
+ alea[i]=unif_rand();
+ }
+ PutRNGstate();
+ trirapideint (alea , numero, 1, n);
+ freeintvec (alea);
+}
+/***********************************************************************/
+void matcentrage (double **A, double *poili, char *typ)
+{
+
+ if (strcmp (typ,"nc") == 0) {
+ return;
+ } else if (strcmp (typ,"cm") == 0) {
+ matmodifcm (A, poili);
+ return;
+ } else if (strcmp (typ,"cn") == 0) {
+ matmodifcn (A, poili);
+ return;
+ } else if (strcmp (typ,"cp") == 0) {
+ matmodifcp (A, poili);
+ return;
+ } else if (strcmp (typ,"cs") == 0) {
+ matmodifcs (A, poili);
+ return;
+ } else if (strcmp (typ,"fc") == 0) {
+ matmodiffc (A, poili);
+ return;
+ } else if (strcmp (typ,"fl") == 0) {
+ matmodifcm (A, poili);
+ return;
+ }
+}
+/***********************************************************************/
+void matmodifcm (double **tab, double *poili)
+/*--------------------------------------------------
+* tab est un tableau n lignes, m colonnes
+* disjonctif complet
+* poili est un vecteur n composantes
+* la procedure retourne tab centre par colonne
+* pour la ponderation poili (somme=1)
+* centrage type correspondances multiples
+--------------------------------------------------*/
+{
+ double poid;
+ int i, j, l1, m1;
+ double *poimoda;
+ double x, z;
+
+ l1 = tab[0][0];
+ m1 = tab[1][0];
+ vecalloc(&poimoda, m1);
+
+
+ for (i=1;i<=l1;i++) {
+ poid = poili[i];
+ for (j=1;j<=m1;j++) {
+ poimoda[j] = poimoda[j] + tab[i][j] * poid;
+ }
+ }
+
+ for (j=1;j<=m1;j++) {
+ x = poimoda[j];
+ if (x==0) {
+ for (i=1;i<=l1;i++) tab[i][j] = 0;
+ } else {
+
+ for (i=1;i<=l1;i++) {
+ z = tab[i][j]/x - 1.0;
+ tab[i][j] = z;
+ }
+ }
+ }
+ freevec (poimoda);
+}
+/***********************************************************************/
+void matmodifcn (double **tab, double *poili)
+/*--------------------------------------------------
+* tab est un tableau n lignes, p colonnes
+* poili est un vecteur n composantes
+* la procedure retourne tab norme par colonne
+* pour la ponderation poili (somme=1)
+--------------------------------------------------*/
+{
+ double poid, x, z, y, v2;
+ int i, j, l1, c1;
+ double *moy, *var;
+
+ l1 = tab[0][0];
+ c1 = tab[1][0];
+
+ vecalloc(&moy, c1);
+ vecalloc(&var, c1);
+
+
+/*--------------------------------------------------
+* calcul du tableau centre/norme
+--------------------------------------------------*/
+
+ for (i=1;i<=l1;i++) {
+ poid = poili[i];
+ for (j=1;j<=c1;j++) {
+ moy[j] = moy[j] + tab[i][j] * poid;
+ }
+ }
+
+ for (i=1;i<=l1;i++) {
+ poid=poili[i];
+ for (j=1;j<=c1;j++) {
+ x = tab[i][j] - moy[j];
+ var[j] = var[j] + poid * x * x;
+ }
+ }
+
+ for (j=1;j<=c1;j++) {
+ v2 = var[j];
+ if (v2<=0) v2 = 1;
+ v2 = sqrt(v2);
+ var[j] = v2;
+ }
+
+ for (i=1;i<=c1;i++) {
+ x = moy[i];
+ y = var[i];
+ for (j=1;j<=l1;j++) {
+ z = tab[j][i] - x;
+ z = z / y;
+ tab[j][i] = z;
+ }
+ }
+
+ freevec(moy);
+ freevec(var);
+
+}
+/***********************************************************************/
+void matmodifcs (double **tab, double *poili)
+/*--------------------------------------------------
+* tab est un tableau n lignes, p colonnes
+* poili est un vecteur n composantes
+* la procedure retourne tab standardise par colonne
+* pour la ponderation poili (somme=1)
+--------------------------------------------------*/
+{
+ double poid, x, z, y, v2;
+ int i, j, l1, c1;
+ double *var;
+
+ l1 = tab[0][0];
+ c1 = tab[1][0];
+
+ vecalloc(&var, c1);
+
+
+/*--------------------------------------------------
+* calcul du tableau standardise
+--------------------------------------------------*/
+
+ for (i=1;i<=l1;i++) {
+ poid=poili[i];
+ for (j=1;j<=c1;j++) {
+ x = tab[i][j];
+ var[j] = var[j] + poid * x * x;
+ }
+ }
+
+ for (j=1;j<=c1;j++) {
+ v2 = var[j];
+ if (v2<=0) v2 = 1;
+ v2 = sqrt(v2);
+ var[j] = v2;
+ }
+
+ for (i=1;i<=c1;i++) {
+ y = var[i];
+ for (j=1;j<=l1;j++) {
+ z = tab[j][i];
+ z = z / y;
+ tab[j][i] = z;
+ }
+ }
+ freevec(var);
+}
+/***********************************************************************/
+void matmodifcp (double **tab, double *poili)
+/*--------------------------------------------------
+* tab est un tableau n lignes, p colonnes
+* poili est un vecteur n composantes
+* la procedure retourne tab centre par colonne
+* pour la ponderation poili (somme=1)
+--------------------------------------------------*/
+{
+ double poid;
+ int i, j, l1, c1;
+ double *moy, x, z;
+
+ l1 = tab[0][0];
+ c1 = tab[1][0];
+ vecalloc(&moy, c1);
+
+
+/*--------------------------------------------------
+* calcul du tableau centre
+--------------------------------------------------*/
+
+ for (i=1;i<=l1;i++) {
+ poid = poili[i];
+ for (j=1;j<=c1;j++) {
+ moy[j] = moy[j] + tab[i][j] * poid;
+ }
+ }
+
+
+ for (i=1;i<=c1;i++) {
+ x = moy[i];
+ for (j=1;j<=l1;j++) {
+ z = tab[j][i] - x;
+ tab[j][i] = z;
+ }
+ }
+ freevec(moy);
+}
+/***********************************************************************/
+void matmodiffc (double **tab, double *poili)
+/*--------------------------------------------------
+* tab est un tableau n lignes, m colonnes
+* de nombres positifs ou nuls
+* poili est un vecteur n composantes
+* la procedure retourne tab centre doublement
+* pour la ponderation poili (somme=1)
+* centrage type correspondances simples
+--------------------------------------------------*/
+{
+ double poid;
+ int i, j, l1, m1;
+ double *poimoda;
+ double x, z;
+
+ l1 = tab[0][0];
+ m1 = tab[1][0];
+ vecalloc(&poimoda, m1);
+
+
+ for (i=1;i<=l1;i++) {
+ x = 0;
+ for (j=1;j<=m1;j++) {
+ x = x + tab[i][j];
+ }
+ if (x!=0) {
+ for (j=1;j<=m1;j++) {
+ tab[i][j] = tab[i][j]/x;
+ }
+ }
+ }
+
+ for (i=1;i<=l1;i++) {
+ poid = poili[i];
+ for (j=1;j<=m1;j++) {
+ poimoda[j] = poimoda[j] + tab[i][j] * poid;
+ }
+ }
+
+ for (j=1;j<=m1;j++) {
+ x = poimoda[j];
+ if (x==0) {
+ /*err_message("column has a nul weight (matmodiffc)");*/
+ }
+
+ for (i=1;i<=l1;i++) {
+ z = tab[i][j]/x - 1.0;
+ tab[i][j] = z;
+ }
+ }
+ freevec (poimoda);
+}
+/***********************************************************************/
+void matpermut (double **A, int *num, double **B)
+{
+/*---------------------------------------
+* A est une matrice n-p
+* B est une matrice n-p
+* num est une permutation al�atoire des n premiers entiers
+* B contient en sortie les lignes de A permut�es
+* ---------------------------------------*/
+
+ int lig, col,lig1, col1, lig2, i, j, k;
+
+ lig = A[0][0];
+ col = A[1][0];
+ lig1 = B[0][0];
+ col1 = B[1][0];
+ lig2 = num[0];
+
+
+ if ( (lig!=lig1) || (col!=col1) || (lig!=lig2) ) {
+ return;
+ }
+
+ for (i=1; i<=lig; i++) {
+ k=num[i];
+ for (j=1; j<=col; j++) {
+ B[i][j] = A[k][j];
+ }
+ }
+}
+/***********************************************************************/
+void prodmatABC (double **a, double **b, double **c)
+/*--------------------------------------------------
+* Produit matriciel AB
+--------------------------------------------------*/
+{
+ int j, k, i, lig, col, col2;
+ double s;
+
+ lig = a[0][0];
+ col = a[1][0];
+
+ col2 = b[1][0];
+
+ for (i=1;i<=lig;i++) {
+ for (k=1;k<=col2;k++) {
+ s = 0;
+ for (j=1;j<=col;j++) {
+ s = s + a[i][j] * b[j][k];
+ }
+ c[i][k] = s;
+ }
+ }
+}
+
+/***********************************************************************/
+void prodmatAtAB (double **a, double **b)
+/*--------------------------------------------------
+* Produit matriciel AtA
+--------------------------------------------------*/
+{
+ int j, k, i, lig, col;
+ double s;
+
+ lig = a[0][0];
+ col = a[1][0];
+
+ for (j=1;j<=col;j++) {
+ for (k=j;k<=col;k++) {
+ s = 0;
+ for (i=1;i<=lig;i++) {
+ s = s + a[i][k] * a[i][j];
+ }
+ b[j][k] = s;
+ b[k][j] = s;
+ }
+ }
+}
+/***********************************************************************/
+void prodmatAtBC (double **a, double **b, double **c)
+/*--------------------------------------------------
+* Produit matriciel AtB
+--------------------------------------------------*/
+{
+ int j, k, i, lig, col, col2;
+ double s;
+
+ lig = a[0][0];
+ col = a[1][0];
+
+ col2 = b[1][0];
+
+ for (j=1;j<=col;j++) {
+ for (k=1;k<=col2;k++) {
+ s = 0;
+ for (i=1;i<=lig;i++) {
+ s = s + a[i][j] * b[i][k];
+ }
+ c[j][k] = s;
+ }
+ }
+}
+/***********************************************************************/
+double maxvec (double *vec)
+/*--------------------------------------------------
+* calcul le max d'un vecteur
+--------------------------------------------------*/
+{
+ int i, len;
+ double x;
+
+ x = vec[1];
+ len = vec[0];
+ for (i=1;i<=len;i++) {
+ if (vec[i] > x) x = vec[i];
+ }
+ return(x);
+}
+/***********************************************************************/
+void prodmatAAtB (double **a, double **b)
+/*--------------------------------------------------
+* Produit matriciel B = AAt
+--------------------------------------------------*/
+{
+ int j, k, i, lig, col;
+ double s;
+
+ lig = a[0][0];
+ col = a[1][0];
+
+ for (j=1;j<=lig;j++) {
+ for (k=j;k<=lig;k++) {
+ s = 0;
+ for (i=1;i<=col;i++) {
+ s = s + a[j][i] * a[k][i];
+ }
+ b[j][k] = s;
+ b[k][j] = s;
+ }
+ }
+}
+/***********************************************************************/
+void prodmatAtBrandomC (double **a, double **b, double **c, int*permut)
+/*--------------------------------------------------
+* Produit matriciel AtB
+* les lignes de B sont permut�es par la permutation permut
+--------------------------------------------------*/
+{
+ int j, k, i, i0, lig, col, col2;
+ double s;
+
+ lig = a[0][0];
+ col = a[1][0];
+
+ col2 = b[1][0];
+
+ for (j=1;j<=col;j++) {
+ for (k=1;k<=col2;k++) {
+ s = 0;
+ for (i=1;i<=lig;i++) {
+ i0 = permut[i];
+ s = s + a[i][j] * b[i0][k];
+ }
+ c[j][k] = s;
+ }
+ }
+}
+/***********************************************************************/
+void sqrvec (double *v1)
+/*--------------------------------------------------
+* Racine carree des elements d'un vecteur
+--------------------------------------------------*/
+{
+ int i, c1;
+ double v2;
+
+ c1 = v1[0];
+
+ for (i=1;i<=c1;i++) {
+ v2 = v1[i];
+ /* if (v2 < 0.0) err_message("Error: Square root of negative number (sqrvec)");*/
+ v2 = sqrt(v2);
+ v1[i] = v2;
+ }
+}
+/***********************************************************************/
+void taballoc (double ***tab, int l1, int c1)
+/*--------------------------------------------------
+* Allocation de memoire dynamique pour un tableau (l1, c1)
+--------------------------------------------------*/
+{
+ int i, j;
+
+ if ( (*tab = (double **) calloc(l1+1, sizeof(double *))) != 0) {
+ for (i=0;i<=l1;i++) {
+ if ( (*(*tab+i)=(double *) calloc(c1+1, sizeof(double))) == 0 ) {
+ return;
+ for (j=0;j<i;j++) {
+ free(*(*tab+j));
+ }
+ }
+ }
+ }
+
+ **(*tab) = l1;
+ **(*tab+1) = c1;
+}
+/***********************************************************************/
+void trild (double *x , int *num, int gauche, int droite)
+/*--------------------------------------------------
+* Tri d'un tableau de double avec conservation du rang
+* dans un tableau entier.
+--------------------------------------------------*/
+{
+ int j, dernier, milieu;
+ double t;
+
+
+ if ( (droite-gauche)<=0) return;
+ milieu = (gauche+droite)/2;
+ trildswap (x, gauche, milieu);
+
+ trildintswap (num, gauche, milieu);
+ t=x[gauche];
+ dernier=gauche;
+ for (j = gauche+1; j<=droite; j++) {
+ if (x[j] > t) {
+ dernier = dernier + 1;
+ trildswap (x, dernier, j);
+ trildintswap (num, dernier, j);
+ }
+ }
+ trildswap (x, gauche, dernier);
+ trildintswap (num, gauche, dernier);
+ trild (x, num, gauche, dernier-1);
+ trild (x, num, dernier+1, droite);
+}
+/**************************/
+void trildintswap (int *v, int i, int j)
+{
+ int provi;
+
+ provi=v[i];
+ v[i]=v[j];
+ v[j]=provi;
+}
+/***********************************************************************/
+void trildswap (double *v, int i, int j)
+/*--------------------------------------------------
+* Echange les valeurs de deux double
+--------------------------------------------------*/
+{
+ double provi;
+
+ provi=v[i];
+ v[i]=v[j];
+ v[j]=provi;
+}
+
+/***********************************************************************/
+void trirap (double *x , int *num)
+/*--------------------------------------------------
+* Tri d'un tableau de double par ordre croissant
+* avec conservation du rang dans un tableau entier.
+--------------------------------------------------*/
+{
+ int i, n, *num2, gauche, droite;
+ double *x2;
+
+ n = x[0];
+ gauche = 1;
+ droite = n;
+ vecalloc(&x2, n);
+ vecintalloc(&num2, n);
+ for (i=1;i<=n;i++) num[i] = i;
+ trild(x, num, gauche, droite);
+ for (i=1;i<=n;i++) {
+ x2[i] = x[n - i + 1];
+ num2[i] = num[n - i + 1];
+ }
+ for (i=1;i<=n;i++) {
+ x[i] = x2[i];
+ num[i] = num2[i];
+ }
+ freevec(x2);
+ freeintvec(num2);
+}
+/***********************************************************************/
+void trirapideint (int *x , int *num, int gauche, int droite)
+{
+ int j, dernier, milieu, t;
+
+ if ( (droite-gauche)<=0) return;
+
+ milieu = (gauche+droite)/2;
+ trirapideintswap (x, gauche, milieu);
+ trirapideintswap (num, gauche, milieu);
+
+ t=x[gauche];
+ dernier=gauche;
+ for (j = gauche+1; j<=droite; j++) {
+ if (x[j] < t) {
+ dernier = dernier + 1;
+ trirapideintswap (x, dernier, j);
+ trirapideintswap (num, dernier, j);
+ }
+ }
+ trirapideintswap (x, gauche, dernier);
+ trirapideintswap (num, gauche, dernier);
+
+ trirapideint (x, num, gauche, dernier-1);
+ trirapideint (x, num, dernier+1, droite);
+
+}
+/***********************************************************************/
+void trirapideintswap (int *v, int i, int j)
+{
+ int provi;
+
+ provi=v[i];
+ v[i]=v[j];
+ v[j]=provi;
+}
+/***********************************************************************/
+void vecalloc (double **vec, int n)
+/*--------------------------------------------------
+* Allocation de memoire pour un vecteur de longueur n
+--------------------------------------------------*/
+{
+ if ( (*vec = (double *) calloc(n+1, sizeof(double))) != 0) {
+ **vec = n;
+ return;
+ } else {
+ return;
+ }
+}
+/***********************************************************************/
+void vecintalloc (int **vec, int n)
+/*--------------------------------------------------
+* Allocation de memoire pour un vecteur d'entiers de longueur n
+--------------------------------------------------*/
+{
+ if ( (*vec = (int *) calloc(n+1, sizeof(int))) != NULL) {
+ **vec = n;
+ return;
+ } else {
+ return;
+ }
+}
+
+
+
+/***********************************************************************/
+void vecpermut (double *A, int *num, double *B)
+{
+/*---------------------------------------
+* A est un vecteur n elements
+* B est une vecteur n elements
+* num est une permutation al�atoire des n premiers entiers
+* B contient en sortie les elements de A permut�es
+* ---------------------------------------*/
+
+ int lig, lig1, lig2, i, k;
+
+ lig = A[0];
+ lig1 = B[0];
+ lig2 = num[0];
+
+
+ if ( (lig!=lig1) || (lig!=lig2) ) {
+ /*err_message ("Illegal parameters (vecpermut)");
+ closelisting();*/
+ }
+
+ for (i=1; i<=lig; i++) {
+ k=num[i];
+ B[i] = A[k];
+ }
+}
diff --git a/src/adesub.h b/src/adesub.h
new file mode 100644
index 0000000..6f66837
--- /dev/null
+++ b/src/adesub.h
@@ -0,0 +1,44 @@
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+
+int dtodelta (double **data, double *pl);
+void initvec (double *v1, double r);
+double alea (void);
+void aleapermutvec (double *a);
+void aleapermutmat (double **a);
+void aleapermutmat (double **a);
+void aleapermutvec (double *a);
+void DiagobgComp (int n0, double **w, double *d, int *rang);
+void freeinttab (int **tab);
+void freeintvec (int *vec);
+void freetab (double **tab);
+void freevec (double *vec);
+void getpermutation (int *numero, int repet);
+void matcentrage (double **A, double *poili, char *typ);
+void matmodifcm (double **tab, double *poili);
+void matmodifcn (double **tab, double *poili);
+void matmodifcp (double **tab, double *poili);
+void matmodifcs (double **tab, double *poili);
+void matmodiffc (double **tab, double *poili);
+void matpermut (double **A, int *num, double **B);
+double maxvec (double *vec);
+void prodmatAAtB (double **a, double **b);
+void prodmatABC (double **a, double **b, double **c);
+void prodmatAtAB (double **a, double **b);
+void prodmatAtBC (double **a, double **b, double **c);
+void prodmatAtBrandomC (double **a, double **b, double **c, int*permut);
+double traceXtdLXq (double **X, double **L, double *d, double *q);
+void sqrvec (double *v1);
+void taballoc (double ***tab, int l1, int c1);
+void tabintalloc (int ***tab, int l1, int c1);
+void trild (double *x , int *num, int gauche, int droite);
+void trildintswap (int *v, int i, int j);
+void trildswap (double *v, int i, int j);
+void trirap (double *x , int *num);
+void trirapideint (int *x , int *num, int gauche, int droite);
+void trirapideintswap (int *v, int i, int j);
+void vecalloc (double **vec, int n);
+void vecintalloc (int **vec, int n);
+void vecpermut (double *A, int *num, double *B);
diff --git a/src/monmonier-utils.c b/src/monmonier-utils.c
new file mode 100644
index 0000000..7a88a74
--- /dev/null
+++ b/src/monmonier-utils.c
@@ -0,0 +1,267 @@
+/*
+A part of this code (intersection between segments) is based on Joseph O'Rourke code to identify intersection between two segments (originaly called 'segseg.c').
+The original code was modified in order to handle double coordinates instead of integer.
+A part of the code is new and devoted to some monmonier algorithm computations
+To compile : R CMD SHLIB monmonier-utils.c
+
+Thibaut Jombart (t.jombart at imperial.ac.uk), 2006, to fit his egocentric needs.
+
+The original copyright follows.
+*/
+
+
+/*
+This code is described in "Computational Geometry in C" (Second Edition),
+Chapter 7. It is not written to be comprehensible without the
+explanation in that book.
+
+Written by Joseph O'Rourke.
+Last modified: November 1997
+Questions to orourke at cs.smith.edu.
+--------------------------------------------------------------------
+This code is Copyright 1998 by Joseph O'Rourke. It may be freely
+redistributed in its entirety provided that this copyright notice is
+not removed.
+--------------------------------------------------------------------
+*/
+
+#include <stdio.h>
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+#include "adesub.h"
+
+
+
+#define EXIT_FAILURE 1
+#define X 0
+#define Y 1
+typedef enum { FALSE, TRUE } bool;
+
+#define DIM 2 /* Dimension of points */
+
+typedef double tPointd[DIM]; /* Type double point */
+const double NEARZERO=10e-15; /* THRESHOLD for zero. */
+/*---------------------------------------------------------------------
+Function prototypes.
+---------------------------------------------------------------------*/
+int SegSeg( tPointd a, tPointd b, tPointd c, tPointd d);
+int Parallel( tPointd a, tPointd b, tPointd c, tPointd d, tPointd p );
+bool Between( tPointd a, tPointd b, tPointd c );
+void Assignpx( tPointd p, tPointd a );
+int Collinear( tPointd a, tPointd b, tPointd c );
+int AreaSign( tPointd a, tPointd b, tPointd c );
+void CheckAllSeg(int *nrow, int *ncol, double *tab, tPointd a, tPointd b, int *answer);
+double dAbs(double a);
+int dEqual(double a, double b);
+/*-------------------------------------------------------------------*/
+
+/* dAbs returns the absolute value of a double */
+double dAbs(double a)
+{
+ if(a>=0.0) return a;
+ else return -a;
+}
+
+/* dEqual returns 1 if two doubles are equal, and 0 otherwise */
+int dEqual(double a, double b)
+{
+ if(dAbs(a-b) < NEARZERO) return 1;
+ else return 0;
+}
+
+
+/*-------------------------------------------------------------------
+CheckAllSeg: performs the intersection test of a segment with
+a given set of segments. Calls SegSeg to perform 2-segments tests.
+answer is returned back to R, and is:
+0: no intersection
+1: at least one intersection
+-------------------------------------------------------------------*/
+void CheckAllSeg(int *nrow, int *ncol, double *tab, tPointd a, tPointd b, int *answer)
+{
+/* Declarations de variables C locales */
+/* X est le tableau des segments ; chaque ligne est un segment (xP,yP,xQ,yQ) */
+int i,j,n,p,k,temp;
+double **mat;
+tPointd c,d;
+
+
+/* Memory allocation for local C variables */
+n = *nrow;
+p = *ncol;
+
+ taballoc(&mat, n, p); /* function from ade4 */
+
+/* Reconstruction of the matrix of segments */
+k = 0;
+for (j=1; j<=p; j++) {
+ for (i=1; i<=n; i++) {
+ mat[i][j] = tab[k];
+ k = k + 1;
+ }
+}
+
+/* The segment of interest (ab) is checked for crossing against all other segments (cd)
+We stop as soon as one segment is crossed */
+ temp = 0;
+ i = 1;
+ while(temp ==0 && i<=n){
+ c[X] = mat[i][1];
+ c[Y] = mat[i][2];
+ d[X] = mat[i][3];
+ d[Y] = mat[i][4];
+ temp = SegSeg(a,b,c,d);
+ i++;
+ }
+ *answer = temp;
+
+ /* Free allocated memory */
+ freetab(mat);
+}
+
+
+/*---------------------------------------------------------------------
+SegSeg: Tests an intersection between two closed
+segments ab and cd. Returned values :
+ 3 : The segments collinearly overlap, sharing at least a point.
+ 2 : An endpoint (vertex) of one segment is on the other segment,
+ but segments aren't collinear.
+ 1 : The segments intersect properly (i.e. not case 2 or 3)
+ 0 : The segments do not intersect.
+ 10 : initial value, i.e. failure.
+---------------------------------------------------------------------*/
+/* int SegSeg( tPointd a, tPointd b, tPointd c, tPointd d, tPointd p) */
+int SegSeg( tPointd a, tPointd b, tPointd c, tPointd d)
+{
+ double s, t; /* The two parameters of the parametric eqns. */
+ double num, denom; /* Numerator and denoninator of equations. */
+ int code = 10; /* returned value, default 10 is a failure */
+
+ /* For debugging */
+ /*printf("\n!!! SegSeg: code initialized at %d\n",code);*/
+
+ /* Initialization of the intersection point 'p' */
+ tPointd p;
+
+ p[X] = -1;
+ p[Y] = -1;
+
+ denom = a[X] * (double)( d[Y] - c[Y] ) +
+ b[X] * (double)( c[Y] - d[Y] ) +
+ d[X] * (double)( b[Y] - a[Y] ) +
+ c[X] * (double)( a[Y] - b[Y] );
+ /* If denom is zero, then segments are parallel: handle separately.
+ Beware to avoid ... == 0 with doubles,
+ as well as ...==... */
+ if (dAbs(denom) < NEARZERO) {
+ code = Parallel(a, b, c, d, p);
+ /* For debugging */
+ /*printf("\n!!! SegSeg: call to Parallel (denom=%f)\n",denom);*/
+ }
+ else{
+ num = a[X] * (double)( d[Y] - c[Y] ) +
+ c[X] * (double)( a[Y] - d[Y] ) +
+ d[X] * (double)( c[Y] - a[Y] );
+ /* code 2 handled here */
+ /*if ( ((num < NEARZERO) && (num > -NEARZERO)) || (num == denom) ) code = 2;*/
+ if ( (dAbs(num) < NEARZERO) || (dEqual(num,denom)) ) code = 2;
+
+ /* Debugging step 1*/
+ /*printf("\n!!! SegSeg step1: dAbs(num)=%f, dEqual(num,denom)=%d), code=%d\n",dAbs(num),dEqual(num,denom),code);
+ printf("\nNEARZERO=%f\n",NEARZERO);*/
+
+ s = num / denom;
+
+ num = -( a[X] * (double)( c[Y] - b[Y] ) +
+ b[X] * (double)( a[Y] - c[Y] ) +
+ c[X] * (double)( b[Y] - a[Y] ) );
+
+ t = num / denom;
+
+ /* if ( ((num < NEARZERO) && (num > -NEARZERO)) || (num == denom) ) code = 2;*/
+ if ( (dAbs(num) < NEARZERO) || (dEqual(num,denom)) ) code = 2;
+ /* Debugging step 2*/
+ /*printf("\n!!! SegSeg step2: dAbs(num)=%f, dEqual(num,denom)=%d), code=%d\n",dAbs(num),dEqual(num,denom),code);
+ printf("\nNEARZERO=%f\n",NEARZERO);*/
+
+ if ( (NEARZERO < s) && (s < 1.0) &&
+ (NEARZERO < t) && (t < 1.0) )
+ code = 1;
+ else if ( (-NEARZERO > s) || (s > 1.0) ||
+ (-NEARZERO > t) || (t > 1.0) )
+ code = 0;
+
+ p[X] = a[X] + s * ( b[X] - a[X] );
+ p[Y] = a[Y] + s * ( b[Y] - a[Y] );
+ }
+
+ /* Debugging step 3*/
+ /*printf("\n!!! SegSeg step3: final value of code=%d\n",code);*/
+ return code;
+}
+
+int Parallel( tPointd a, tPointd b, tPointd c, tPointd d, tPointd p )
+{
+/* Avoid to consider segments as parallel whenever two points are the same. */
+/*if ( (a[X]==b[X] && a[Y]==b[Y]) || (c[X]==d[X] && c[Y]==d[Y]) ) return 0;*/
+if ( (dEqual(a[X],b[X]) && dEqual(a[Y],b[Y])) || (dEqual(c[X],d[X]) && dEqual(c[Y],d[Y])) ) return 0;
+if ( Collinear( a, b, c)==0 ) return 0;
+
+ if ( Between( a, b, c ) ) {
+ Assignpx( p, c );
+ return 3;
+ }
+ if ( Between( a, b, d ) ) {
+ Assignpx( p, d );
+ return 3;
+ }
+ if ( Between( c, d, a ) ) {
+ Assignpx( p, a );
+ return 3;
+ }
+ if ( Between( c, d, b ) ) {
+ Assignpx( p, b );
+ return 3;
+ }
+ return 0;
+}
+void Assignpx( tPointd p, tPointd a )
+{
+ int i;
+ for ( i = 0; i < DIM; i++ )
+ p[i] = a[i];
+}
+/*---------------------------------------------------------------------
+Returns TRUE iff point c lies on the closed segement ab.
+Assumes it is already known that abc are collinear.
+---------------------------------------------------------------------*/
+bool Between( tPointd a, tPointd b, tPointd c )
+{
+ /* If ab not vertical, check betweenness on x; else on y. */
+ if ( a[X] != b[X] )
+ return ((a[X] <= c[X]) && (c[X] <= b[X])) ||
+ ((a[X] >= c[X]) && (c[X] >= b[X]));
+ else
+ return ((a[Y] <= c[Y]) && (c[Y] <= b[Y])) ||
+ ((a[Y] >= c[Y]) && (c[Y] >= b[Y]));
+}
+
+int Collinear( tPointd a, tPointd b, tPointd c )
+{
+ if (AreaSign(a, b, c) ==0) return 1;
+ else return 0;
+}
+int AreaSign( tPointd a, tPointd b, tPointd c )
+{
+ double area2;
+
+ area2 = ( b[X] - a[X] ) * (double)( c[Y] - a[Y] ) -
+ ( c[X] - a[X] ) * (double)( b[Y] - a[Y] );
+
+ /* The area is not an integer. */
+ if ( area2 > NEARZERO ) return 1;
+ else if ( area2 < -NEARZERO ) return -1;
+ else return 0;
+}
diff --git a/src/sharedAll.c b/src/sharedAll.c
new file mode 100644
index 0000000..1430a39
--- /dev/null
+++ b/src/sharedAll.c
@@ -0,0 +1,159 @@
+/*
+*** THIS CODE IS PART OF THE *adegenet* PACKAGE FOR R. ***
+
+Code used to compute the proportion of alleles shared among a set of individuals.
+The arguments are:
+- matAll a matrix containing alleles coded by integers, with genotypes in rows and loci in columns. Results from the binding by columns of A1 and A2, where A1 stores the one allele and A2 the other allele.
+- nRow: the number of rows of matAll, i.e. number of genotypes
+- nCol: the number of columns of matAll, i.e. twice the number of loci
+- resVec: a vector of length (n(n-1)/2) storing the proportion of shared alleles for each couple of genotypes.
+
+Thibaut Jombart (t.jombart at imperial.ac.uk), 2008.
+*/
+
+#include <stdio.h>
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+#include <R_ext/Print.h>
+
+#include "adesub.h"
+
+
+/* THIS FUNCTION IS DEPRECATED */
+void sharedAll(int *matAll, int *nRow, int *nCol, double *resVec)
+{
+ /* Declare local C variables */
+ int i, i1, i2, j, k, n, p, nbAll, **mat;
+ n = *nRow;
+ p = *nCol;
+
+ int nLoc=p/2;
+
+ /* Memory allocation for local C variables */
+
+ tabintalloc(&mat, n, p); /* function from ade4 */
+
+ /* Local reconstruction of the matrix of alleles
+ ! beware: this matrix is to be used from 1 to n and 1 to p included,
+ and not from zero to n and p excluded as it is common in C */
+ k = 0;
+ for (j=1; j<=p; j++) {
+ for (i=1; i<=n; i++) {
+ mat[i][j] = matAll[k];
+ k = k + 1;
+ }
+ }
+
+ /* == Main Computations: ==
+ - i1, i2: indices of genotypes
+ - j: index of allele
+ - n: number of genotypes
+ - p number of columns in mat (i.e. twice the number of loci)
+ - each term in mat codes an allele (NAs are coded by 0)
+ */
+
+ k=0; /* counter used to browse resVec */
+ for(i1=1; i1<=(n-1); i1++){
+ for(i2=(i1+1); i2<=n; i2++){
+ /* Used for debugging
+ printf("\n\n debug: ## %d-%d ##",i1,i2);
+ */
+
+ resVec[k] = 0.0; /* Initialization of the result */
+ nbAll = 0; /* counts the number of types alleles */
+ for(j=1; j<=nLoc; j++){
+ /* Used for debugging
+ printf("\n debug: j=%d",j);
+ printf("\n debug: mat[i1,j]=%d",mat[i1][j]);
+ printf("\n debug: mat[i1,j]=%d",mat[i1][j+nLoc]);
+ printf("\n debug: mat[i2,j]=%d",mat[i2][j]);
+ printf("\n debug: mat[i2,j+nLoc]=%d",mat[i2][j+nLoc]);
+ */
+ if(mat[i1][j] != 0 && mat[i1][j+nLoc] != 0 &&
+ mat[i2][j] != 0 && mat[i2][j+nLoc] != 0){
+ /* Used for debugging
+ printf("\n debug: alleles are typed");
+ */
+ nbAll+=2;
+ /* Used for debugging
+ printf("\n debug: nbAll=%d", nbAll);
+ */
+ /* Compare alleles:
+ -> either both alleles are in common,
+ -> or no allele are common,
+ -> or there is one common allele */
+ /* both alleles common */
+ if((mat[i1][j] == mat[i2][j]
+ && mat[i1][j+nLoc] == mat[i2][j+nLoc])
+ || (mat[i1][j] == mat[i2][j+nLoc]
+ && mat[i1][j+nLoc] == mat[i2][j])){
+ resVec[k] += 2.0;
+ } else if(!( /* if not 'all alleles differe' */
+ mat[i1][j] != mat[i2][j]
+ && mat[i1][j] != mat[i2][j+nLoc]
+ && mat[i1][j+nLoc] != mat[i2][j]
+ && mat[i1][j+nLoc] != mat[i2][j+nLoc])
+ ) resVec[k]++;
+
+ } /* end if */
+ } /* end for j in 1:(nLoc) */
+
+ /* Divide the number of shared alleles by the number of typed alleles */
+ if(nbAll > 0) resVec[k] = resVec[k]/nbAll;
+ /*printf("\n debug: resVec[i1,i2]/nbAll (%d,%d)=# %f #", i1,i2,resVec[k]);*/
+ k++;
+
+ } /* end for i2 */
+ } /* end for i1*/
+
+ /* Free allocated memory */
+ freeinttab(mat);
+
+} /* end sharedAll */
+
+
+
+/* SMALL FUNCTION TO RETURN THE SMALLEST OF 2 INTEGERS */
+int min_int(int a, int b){
+ if(a<b) return a;
+ return b;
+}
+
+
+
+
+/* THIS IS THE FUNCTION TO USE */
+void nb_shared_all(int *in, int *out, int *nind, int *ncol){
+ int i, j, k, counter=0, **mat, n = *nind, p = *ncol;
+
+ /* allocate memory for table of allele nb */
+ tabintalloc(&mat, n, p);
+
+
+ /* reconstruct table of allele nb */
+ for(j=1;j<=p;j++){
+ for(i=1;i<=n;i++){
+ mat[i][j] = in[counter++];
+ }
+ }
+
+
+ /* perform computations */
+ counter = 0;
+ for(i=1;i<=(n-1);i++){
+ for(j=i+1;j<=n;j++){
+ out[counter] = 0; /* initialize result to zero */
+ for(k=1;k<=p;k++){
+ out[counter] = out[counter] + min_int(mat[i][k], mat[j][k]);
+ }
+ counter++;
+ }
+ }
+
+
+ /* Free allocated memory */
+ freeinttab(mat);
+
+} /* end nb_shared_all */
diff --git a/src/snpbin.c b/src/snpbin.c
new file mode 100644
index 0000000..bcd61e4
--- /dev/null
+++ b/src/snpbin.c
@@ -0,0 +1,564 @@
+/*
+ Coded by Thibaut Jombart (tjombart at imperial.ac.uk), December 2010.
+ Distributed with the adephylo package for the R software.
+ Licence: GPL >=2.
+
+ These functions are designed to recode genotypes given as binary integers into new integers which
+ map them to unique bytes. One genotype of 8 binary SNPs is mapped uniquely (bijectively) to a
+ value between 0 and 255. This is achieved by considering the genotype 'x' in the basis 2^0
+ ... 2^7, and summing the values of the vector in this basis. That is, we use the function:
+
+ {0,1}^8 |-> {0,...,255}
+ x -> x_1 * 2^0 + ... + x_8 * 2^7 = \sum_i x_i * 2^(i-1)
+
+
+ # Function named as 'SNPbin...' or 'GL...' are to be called directly from R.
+ # The structure 'snpbin' is a C representation of the class 'SNPbin'.
+ # Function named as 'snpbin...' are made to be called internally.
+*/
+
+
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <R_ext/Print.h>
+
+#include "adesub.h"
+#include "snpbin.h"
+
+/* #define NEARZERO 0.0000000001 */
+/* #define TRUE 1 */
+/* #define FALSE 0 */
+
+/* typedef short bool; */
+
+/* /\* */
+/* ========================= */
+/* === CLASS DEFINITIONS === */
+/* ========================= */
+/* *\/ */
+
+/* /\* 'bytevecnb' arrays of bytes concatenated into a single array *\/ */
+/* /\* of dim 'byteveclength' x 'bytevecnb' *\/ */
+/* /\* nloc is the number of SNPs - used for recoding to integers *\/ */
+/* /\* naposi indicates the positions of NAs *\/ */
+/* /\* nanb is the length of naposi *\/ */
+
+/* struct snpbin{ */
+/* unsigned char *bytevec; */
+/* int *byteveclength, *bytevecnb, *nloc, *nanb, *naposi, *ploidy; /\* all but naposi have length 1 *\/ */
+/* }; */
+
+
+
+
+/* struct genlightC{ */
+/* struct snpbin *x; */
+/* int *nind; */
+/* }; */
+
+
+
+
+
+/*
+ ===========================
+ === AUXILIARY FUNCTIONS ===
+ ===========================
+*/
+
+
+struct snpbin makesnpbin(unsigned char *bytevec, int *byteveclength, int *bytevecnb, int *nloc, int *nanb, int *naposi, int *ploidy) {
+ struct snpbin out;
+ int i;
+
+ out.bytevec = bytevec;
+ out.byteveclength = byteveclength;
+ out.bytevecnb = bytevecnb;
+ out.nloc = nloc;
+ out.nanb = nanb;
+ /* need to decrease the indices of NAs by 1, e.g. [1-10]->[0-9] */
+ out.naposi = naposi;
+ if(*nanb > 0){
+ for(i=0;i< *nanb; i++){
+ out.naposi[i] = out.naposi[i] - 1;
+ }
+ }
+ out.ploidy = ploidy;
+ return out;
+}
+
+
+/* Maps one byte from 0-255 to sequences of 8 (binary) integers values */
+void byteToBinInt(unsigned char in, int *out){
+ short int rest, i, temp;
+
+ rest = (int)in;
+
+ /* initialize all values to 0*/
+ for(i=0;i<=7;i++)
+ out[i]=0;
+
+ for(i=7;i>=0;i--){
+ temp = pow(2, i);
+ if(rest >= temp) {
+ out[i] = 1;
+ rest = rest- temp;
+ if(rest == 0) break;
+ }
+ }
+}
+
+
+
+
+/* Maps one byte from 0-255 to sequences of 8 (binary) double values */
+void byteToBinDouble(unsigned char in, double *out){
+ short rest, i, temp;
+
+ rest = (int) in;
+
+ /* initialize all values to 0*/
+ for(i=0;i<=7;i++)
+ out[i]=0.0;
+
+ for(i=7;i>=0;i--){
+ temp = pow(2, i);
+ if(rest >= temp) {
+ out[i] = 1.0;
+ rest = rest- temp;
+ if(rest == 0) break;
+ }
+ }
+}
+
+
+
+
+
+/* Maps an array of values from 0-255 to sequences of 8 binary values */
+/* Input are unsigned char (hexadecimal), outputs are integers */
+void bytesToBinInt(unsigned char *vecbytes, int *vecsize, int *vecres){
+ int i, j, idres=0, *temp; /* idres: index in vecres*/
+
+ temp = (int *) calloc(8, sizeof(int));
+
+ for(i=0;i<*vecsize;i++){
+ byteToBinInt(vecbytes[i], temp);
+ for(j=0;j<=7;j++){
+ vecres[j+idres] = temp[j];
+ }
+ idres = idres + 8;
+ }
+
+ free(temp);
+} /* end binIntToBytes*/
+
+
+
+
+
+
+
+
+
+
+/*
+ ===============================
+ === MAIN EXTERNAL FUNCTIONS ===
+ ===============================
+*/
+
+
+
+/* Maps an array of values from 0-255 to integers representing counts of alleles */
+/* This is done by adding arrays of 0-1 for indiv with ploidy > 1*/
+/* Input are unsigned char (hexadecimal), outputs are integers */
+/* veclength is the length of one vector of bytes */
+/* nbvec is the nb of input vectors*/
+/* input 'vecbytes' is actually concatenated, ie of size veclength * nbvec */
+void bytesToInt(unsigned char *vecbytes, int *veclength, int *nbvec, int *vecres, int *reslength){
+ int i, j, k, idres=0, *temp; /* idres: index in vecres*/
+
+ temp = (int *) calloc(8, sizeof(int));
+
+ /* initialize result vector to 0 */
+ for(i=0; i < *reslength; i++){
+ vecres[i]=0;
+ }
+
+ /* build output */
+ for(k=0;k<*nbvec;k++){ /* for all input vector */
+ idres = 0;
+ for(i=0;i<*veclength;i++){ /* for one input vector */
+ byteToBinInt(vecbytes[i+ k* *veclength], temp); /* byte -> 8 int (0/1)*/
+ for(j=0;j<=7;j++){ /* fill in the result*/
+ vecres[j+idres] += temp[j];
+ }
+ idres = idres + 8;
+ }
+ }
+ free(temp);
+} /* end bytesToInt */
+
+
+
+
+
+void bytesToDouble(unsigned char *vecbytes, int *veclength, int *nbvec, double *vecres, int *reslength){
+ int i, j, k, idres=0; /* idres: index in vecres*/
+ double *temp;
+ temp = (double *) calloc(8, sizeof(double));
+
+ /* initialize result vector to 0 */
+ for(i=0; i < *reslength; i++){
+ vecres[i]=0.0;
+ }
+
+ for(k=0;k<*nbvec;k++){ /* for all input vector */
+ idres = 0;
+ for(i=0;i<*veclength;i++){ /* for one input vector */
+ byteToBinDouble(vecbytes[i+ k* *veclength], temp); /* byte -> 8 double (0/1)*/
+ for(j=0;j<=7;j++){ /* fill in the result*/
+ vecres[j+idres] += temp[j];
+ }
+ idres = idres + 8;
+ }
+ }
+ free(temp);
+} /* end bytesToInt */
+
+
+
+
+
+/*
+ === MAP BINARY SNPS TO 1->256 SCALE ===
+ - vecsnp: vector of integers (0/1)
+ - vesize: length of vecsnp
+ - res: vector of integers valued on 0:255
+ - ressize: length of res
+*/
+void binIntToBytes(int *vecsnp, int *vecsize, unsigned char *vecres, int *ressize){
+ /* declarations */
+ int i, j, idres, *binBasis; /* must use dynamic allocation */
+
+ /* allocate memory for local variables */
+ vecintalloc(&binBasis, 8);
+
+ /* define binary basis */
+ for(i=1; i<=8; i++){
+ binBasis[i] = pow(2, i-1);
+ }
+
+ /* set all values of vecres to 0 */
+ for(i=0;i < *ressize;i++){
+ vecres[i] = 0x00;
+ }
+
+
+
+ /* INDICES */
+ /* i: idx of snp */
+ /* j: idx of binBasis (1:8) */
+ /* idres: idx in vector of results */
+
+ idres = 0;
+ j = 1;
+ for(i=0;i< *vecsize;i++){
+ vecres[idres] = vecres[idres] + (unsigned char)(binBasis[j] * vecsnp[i]);
+ if(j == 8){
+ idres++;
+ j = 1;
+ } else {
+ j++;
+ }
+ }
+
+
+ /* free memory */
+ freeintvec(binBasis);
+
+} /* end binIntToBytes */
+
+
+
+
+
+
+
+
+/*
+ =====================
+ === CLASS METHODS ===
+ =====================
+*/
+
+int nLoc(struct snpbin *x){
+ return *(x->nloc);
+}
+
+
+int ploidy(struct snpbin *x){
+ return *(x->ploidy);
+}
+
+
+
+
+
+/* transform a snpbin into a vector of integers */
+void snpbin2intvec(struct snpbin *x, int *out){
+ int *temp;
+ temp= (int *) calloc(1, sizeof(int));
+ *temp=nLoc(x);
+ bytesToInt(x->bytevec, x->byteveclength, x->bytevecnb, out, temp);
+ free(temp);
+/*reminders:
+ - void bytesToInt(unsigned char *vecbytes, int *veclength, int *nbvec, int *vecres, int reslength){
+ - snpbin: unsigned char *bytevec; int *byteveclength, *bytevecnb, *nloc, *nanb, *naposi; */
+}
+
+
+
+/* transform a snpbin into a vector of frequencies (double) */
+void snpbin2freq(struct snpbin *x, double *out){
+ double ploid = (double) ploidy(x);
+ int *temp;
+ temp= (int *) calloc(1, sizeof(int));
+ *temp=nLoc(x);
+ bytesToDouble(x->bytevec, x->byteveclength, x->bytevecnb, out, temp);
+ int i;
+
+ for(i=0; i < nLoc(x); i++){
+ out[i] = out[i] / ploid;
+ }
+ free(temp);
+/*reminders:
+ - void bytesToInt(unsigned char *vecbytes, int *veclength, int *nbvec, int *vecres, int reslength){
+ - snpbin: unsigned char *bytevec; int *byteveclength, *bytevecnb, *nloc, *nanb, *naposi; */
+}
+
+
+
+/* print a snpbin object - used for debugging */
+void printsnpbin(struct snpbin *x){
+ int i, *temp;
+ temp = (int *) calloc(nLoc(x), sizeof(int));
+ snpbin2intvec(x, temp);
+
+
+ for(i=0;i< *(x->byteveclength);i++){
+ Rprintf("%i ", (int) (x->bytevec)[i]);
+ /* printf("%i ", (int) (x->bytevec)[i]); */
+ }
+ Rprintf(" ");
+ for(i=0;i<nLoc(x);i++){
+ Rprintf("%i ", temp[i]);
+ /* printf("%i ", temp[i]); */
+ }
+
+ Rprintf("NA posi: ");
+ for(i=0;i< *(x->nanb);i++){
+ Rprintf("%i ", (x->naposi)[i]);
+ /* printf("%i ", (x->naposi)[i]); */
+ }
+
+ free(temp);
+}
+
+
+
+short int snpbin_isna(struct snpbin *x, int i){
+ int j = 0;
+ if(*(x->nanb) < 1 || i > nLoc(x)) return 0;
+
+ while(j < *(x->nanb)){
+ if( i == (x->naposi)[j]) return 1;
+ j++;
+ }
+
+ return 0;
+}
+
+
+
+
+
+/* Function to compute one dot products between two individuals */
+/* centring and scaling is always used */
+/* but need to pass vectors of 0 and 1*/
+double snpbin_dotprod_int(struct snpbin *x, struct snpbin *y, double *mean, double *sd){
+ /* define variables, allocate memory */
+ int P = nLoc(x), i;
+ double res = 0.0;
+ int *vecx, *vecy;
+ vecx = (int *) calloc(P, sizeof(int));
+ vecy = (int *) calloc(P, sizeof(int));
+
+ /* conversion to integers */
+ snpbin2intvec(x, (int *) vecx);
+ snpbin2intvec(y, (int *) vecy);
+
+
+ /* printf("\nvector x: \n"); */
+ /* for(i=0;i<P;i++){ */
+ /* printf("%i", vecx[i]); */
+ /* } */
+
+ /* printf("\nvector y: \n"); */
+ /* for(i=0;i<P;i++){ */
+ /* printf("%i", vecy[i]); */
+ /* } */
+
+ /* compute dot product */
+ for(i=0;i<P;i++){
+ if(snpbin_isna(x,i) == 0 && snpbin_isna(y,i) == 0){
+ /* res += ((vecx[i]-mean[i])/sd[i]) * ((vecy[i]-mean[i])/sd[i]); */
+ res += ((vecx[i]-mean[i])/sd[i]) * ((vecy[i]-mean[i])/sd[i]);
+ /* printf("\ntemp value of increment: %f", ((vecx[i]-mean[i])/sd[i]) * ((vecy[i]-mean[i])/sd[i])); */
+ /* printf("\ntemp value of result: %f", res); */
+ }
+ }
+
+ /* free memory */
+ free(vecx);
+ free(vecy);
+
+ return res;
+}
+
+
+
+
+
+
+double snpbin_dotprod_freq(struct snpbin *x, struct snpbin *y, double *mean, double *sd){
+ /* define variables, allocate memory */
+ int P = nLoc(x), i;
+ double res = 0.0;
+ double *vecx, *vecy;
+ vecx = (double *) calloc(P, sizeof(double));
+ vecy = (double *) calloc(P, sizeof(double));
+
+ /* conversion to integers or frequencies*/
+ snpbin2freq(x, vecx);
+ snpbin2freq(y, vecy);
+
+
+ /* printf("\nvector x: \n"); */
+ /* for(i=0;i<P;i++){ */
+ /* printf("%i", vecx[i]); */
+ /* } */
+
+ /* printf("\nvector y: \n"); */
+ /* for(i=0;i<P;i++){ */
+ /* printf("%i", vecy[i]); */
+ /* } */
+
+ /* compute dot product */
+ for(i=0;i<P;i++){
+ if(snpbin_isna(x,i) == 0 && snpbin_isna(y,i) == 0){
+ /* res += ((vecx[i]-mean[i])/sd[i]) * ((vecy[i]-mean[i])/sd[i]); */
+ res += ((vecx[i]-mean[i])/sd[i]) * ((vecy[i]-mean[i])/sd[i]);
+ /* printf("\ntemp value of increment: %f", ((vecx[i]-mean[i])/sd[i]) * ((vecy[i]-mean[i])/sd[i])); */
+ /* printf("\ntemp value of result: %f", res); */
+ }
+ }
+
+ /* free memory */
+ free(vecx);
+ free(vecy);
+
+ return res;
+}
+
+
+
+
+
+
+/* Function to convert a 'genlight' object (R side) into an array of 'snpbin' (C side) */
+/* Each component of the genlight is concatenated into a single vector */
+/* and then used to create different 'snpbin' on the C side */
+struct genlightC genlightTogenlightC(unsigned char *gen, int *nbvecperind, int *byteveclength, int *nbnaperind, int *naposi, int *nind, int *nloc, int *ploidy){
+ /* declare variables and allocate memory */
+ int i, idxByteVec=0, idxNAVec=0;
+ struct genlightC out;
+ out.x = (struct snpbin *) calloc(*nind, sizeof(struct snpbin));
+
+ /* create the list of snpbin */
+ /* printf("\n nind: %d\n", *nind); */
+ for(i=0; i < *nind; i++){
+ out.x[i] = makesnpbin(&gen[idxByteVec], byteveclength, &nbvecperind[i], nloc, &nbnaperind[i], &naposi[idxNAVec], &ploidy[i]);
+ idxByteVec += *byteveclength * nbvecperind[i]; /* update index in byte array */
+ idxNAVec += nbnaperind[i]; /* update index in byte array */
+ /* printf("\nimported genotype %i: ", i+1); */
+ /* printsnpbin(&out.x[i]); */
+ }
+
+ /* printf("step 3"); */
+
+ out.nind = nind;
+
+ /* printf("step 4"); */
+ return out;
+}
+
+
+
+
+
+
+
+/*
+ =========================
+ === TESTING FUNCTIONS ===
+ =========================
+*/
+
+/* Simple test function */
+/* Test: increases for a raw (unsigned char) vector */
+void testRaw(unsigned char *a, int *n){
+ int i;
+ for(i=0; i< *n; i++){
+ a[i] = (unsigned char)(i);
+ }
+}
+
+
+
+/* Test: increases for a raw (unsigned char) vector */
+void testSizePointer(int *sizePointer, int *sizeFirstElement, int *nbElements){
+ double *a;
+ a = (double *) calloc(5, sizeof(double));
+ *sizePointer = sizeof(a);
+ *sizeFirstElement = sizeof(a[0]);
+ *nbElements = sizeof(a) / sizeof(a[0]);
+ free(a);
+}
+
+
+/* TESTING in R */
+
+/*
+ ## test raw conversion
+ .C("testRaw", raw(256), 256L, PACKAGE="adegenet")
+ .C("testSizePointer", integer(1), integer(1), integer(1), PACKAGE="adegenet")
+
+ ## test raw->int conversion
+ x <- sample(0:1,800,replace=TRUE)
+ toto <- .bin2raw(x)$snp
+ all(.C("bytesToBinInt", toto, length(toto), integer(length(toto)*8))[[3]]==x)
+
+ ## test raw vec -> binary integers
+ .C("bytesToBinInt",as.raw(c(12,11)), 2L, integer(16), PACKAGE="adegenet")
+
+ ## test several raw vec -> int (allele counts, any ploidy)
+ .C("bytesToInt",as.raw(c(12,11)), 1L, 2L, integer(8), integer(16), PACKAGE="adegenet")
+
+
+*/
+
diff --git a/src/snpbin.h b/src/snpbin.h
new file mode 100644
index 0000000..1124c6d
--- /dev/null
+++ b/src/snpbin.h
@@ -0,0 +1,102 @@
+#include <math.h>
+#include <time.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+
+
+#define NEARZERO 0.0000000001
+#define TRUE 1
+#define FALSE 0
+
+typedef short bool;
+
+
+
+/*
+ =========================
+ === CLASS DEFINITIONS ===
+ =========================
+*/
+
+/* 'bytevecnb' arrays of bytes concatenated into a single array */
+/* of dim 'byteveclength' x 'bytevecnb' */
+/* nloc is the number of SNPs - used for recoding to integers */
+/* naposi indicates the positions of NAs */
+/* nanb is the length of naposi */
+struct snpbin{
+ unsigned char *bytevec;
+ int *byteveclength, *bytevecnb, *nloc, *nanb, *naposi, *ploidy; /* all but naposi have length 1 */
+};
+
+
+
+struct genlightC{
+ struct snpbin *x;
+ int *nind;
+};
+
+
+
+/*
+ ===========================
+ === AUXILIARY FUNCTIONS ===
+ ===========================
+*/
+
+
+void byteToBinInt(unsigned char in, int *out);
+void byteToBinDouble(unsigned char in, double *out);
+void bytesToBinInt(unsigned char *vecbytes, int *vecsize, int *vecres);
+struct snpbin makesnpbin(unsigned char *bytevec, int *byteveclength, int *bytevecnb, int *nloc, int *nanb, int *naposi, int *ploidy);
+
+
+
+
+
+/*
+ ===============================
+ === MAIN EXTERNAL FUNCTIONS ===
+ ===============================
+*/
+
+void bytesToInt(unsigned char *vecbytes, int *veclength, int *nbvec, int *vecres, int *reslength);
+void bytesToDouble(unsigned char *vecbytes, int *veclength, int *nbvec, double *vecres, int *reslength);
+void binIntToBytes(int *vecsnp, int *vecsize, unsigned char *vecres, int *ressize);
+
+
+
+
+
+/*
+ =====================
+ === CLASS METHODS ===
+ =====================
+*/
+
+int nLoc(struct snpbin *x);
+int ploidy(struct snpbin *x);
+void snpbin2intvec(struct snpbin *x, int *out);
+void snpbin2freq(struct snpbin *x, double *out);
+void printsnpbin(struct snpbin *x);
+short int snpbin_isna(struct snpbin *x, int i);
+double snpbin_dotprod_int(struct snpbin *x, struct snpbin *y, double *mean, double *sd);
+double snpbin_dotprod_freq(struct snpbin *x, struct snpbin *y, double *mean, double *sd);
+struct genlightC genlightTogenlightC(unsigned char *gen, int *nbvecperind, int *byteveclength, int *nbnaperind, int *naposi, int *nind, int *nloc, int *ploidy);
+
+
+
+
+
+
+
+
+/*
+ =========================
+ === TESTING FUNCTIONS ===
+ =========================
+*/
+
+
+void testRaw(unsigned char *a, int *n);
+void testSizePointer(int *sizePointer, int *sizeFirstElement, int *nbElements);
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..736181e
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,3 @@
+library(testthat)
+suppressPackageStartupMessages(library(adegenet))
+test_check("adegenet")
diff --git a/tests/testthat/test-prop.R b/tests/testthat/test-prop.R
new file mode 100644
index 0000000..3a3e6f5
--- /dev/null
+++ b/tests/testthat/test-prop.R
@@ -0,0 +1,18 @@
+context("Test PropShared")
+
+data("microbov", package = "adegenet")
+obj <- microbov[1:5, loc = locNames(microbov)[1:2]]
+psh <- propShared(obj)
+expected_values <- structure(c(1, 0.5, 0.5, 0.75, 0.5, 0.5, 1, 0.75, 0.75, 0.75,
+ 0.5, 0.75, 1, 0.75, 1, 0.75, 0.75, 0.75, 1, 0.75, 0.5, 0.75, 1,
+ 0.75, 1), .Dim = c(5L, 5L), .Dimnames = list(c("AFBIBOR9503",
+ "AFBIBOR9504", "AFBIBOR9505", "AFBIBOR9506", "AFBIBOR9507"),
+ c("AFBIBOR9503", "AFBIBOR9504", "AFBIBOR9505", "AFBIBOR9506",
+ "AFBIBOR9507")))
+test_that("propShared produces expected results", {
+ skip_on_cran()
+ expect_that(psh, equals(expected_values))
+ expect_true(all(psh <= 1))
+ expect_that(ncol(psh), equals(nrow(psh)))
+ expect_that(ncol(psh), equals(nInd(obj)))
+})
\ No newline at end of file
diff --git a/tests/testthat/test-seppop.R b/tests/testthat/test-seppop.R
new file mode 100644
index 0000000..3603223
--- /dev/null
+++ b/tests/testthat/test-seppop.R
@@ -0,0 +1,63 @@
+context("Test seppop")
+
+data(microbov)
+
+test_that("seppop will use the internal population factor by default", {
+ skip_on_cran()
+ blist <- seppop(microbov)
+ expect_is(blist, "list")
+ expect_equal(length(blist), nPop(microbov))
+ expect_equivalent(names(blist), popNames(microbov))
+})
+
+test_that("seppop will use the external population factor", {
+ skip_on_cran()
+ coun <- other(microbov)$coun
+ clist <- seppop(microbov, pop = coun)
+ expect_is(clist, "list")
+ expect_equal(length(clist), nlevels(coun))
+ expect_equivalent(names(clist), levels(coun))
+})
+
+test_that("seppop will use formula input", {
+ skip_on_cran()
+ strata(microbov) <- data.frame(other(microbov))
+ slist <- seppop(microbov, pop = ~spe)
+ setPop(microbov) <- ~spe
+ expect_is(slist, "list")
+ expect_equal(length(slist), nPop(microbov))
+ expect_equivalent(names(slist), popNames(microbov))
+})
+
+
+
+x <- new("genlight", list(a=rep(1,1e3),b=rep(0,1e3),c=rep(1, 1e3)), parallel = FALSE)
+pop(x) <- c("pop1","pop2", "pop1")
+
+test_that("seppop will work for genlight objects", {
+ skip_on_cran()
+ plist <- seppop(x)
+ expect_is(plist, "list")
+ expect_equal(length(plist), nPop(x))
+ expect_equivalent(names(plist), popNames(x))
+})
+
+test_that("seppop will work for genlight objects with external factor", {
+ skip_on_cran()
+ uniqpop <- rev(LETTERS)[1:3]
+ ulist <- seppop(x, pop = uniqpop)
+ expect_is(ulist, "list")
+ expect_equal(length(ulist), length(uniqpop))
+ expect_equivalent(names(ulist), sort(uniqpop))
+})
+
+test_that("seppop will work for genlight objects with formula", {
+ skip_on_cran()
+ uniqpop <- rev(LETTERS)[1:3]
+ strata(x) <- data.frame(pop = pop(x), uni = uniqpop, all = rep("A", 3))
+ setPop(x) <- ~all
+ alist <- seppop(x, pop = ~all)
+ expect_is(alist, "list")
+ expect_equal(length(alist), nPop(x))
+ expect_equivalent(names(alist), popNames(x))
+})
\ No newline at end of file
diff --git a/tests/testthat/test_accessors.R b/tests/testthat/test_accessors.R
new file mode 100644
index 0000000..8bf08b2
--- /dev/null
+++ b/tests/testthat/test_accessors.R
@@ -0,0 +1,149 @@
+context("Accessor tests")
+
+data("microbov")
+strata(microbov) <- data.frame(other(microbov))
+
+test_that("individual accessors work as expected", {
+ skip_on_cran()
+ expect_that(nInd(microbov), equals(704))
+ indNames(microbov)[1] <- "replacement"
+ expect_that(indNames(microbov)[1], equals("replacement"))
+})
+
+test_that("population accessors work for genind objects", {
+ skip_on_cran()
+ expect_that(nPop(microbov), equals(15))
+ expect_that(popNames(microbov), is_equivalent_to(levels(pop(microbov))))
+ popNames(microbov)[1] <- "replacement"
+ expect_that(popNames(microbov)[1], equals("replacement"))
+ expect_that(unique(head(pop(microbov))), is_equivalent_to(factor("replacement")))
+})
+
+test_that("population accessors work for genpop objects", {
+ skip_on_cran()
+ micpop <- genind2genpop(microbov, quiet = TRUE)
+ expect_that(nPop(micpop), equals(15))
+ expect_that(popNames(micpop), is_equivalent_to(rownames(micpop at tab)))
+ popNames(micpop)[1] <- "replacement"
+ expect_that(popNames(micpop)[1], equals("replacement"))
+ expect_that(rownames(micpop at tab)[1], equals("replacement"))
+})
+
+test_that("locus accessors work for genind objects", {
+ skip_on_cran()
+ expect_that(nLoc(microbov), equals(30))
+ locNames(microbov)[1] <- "replacement"
+ expect_that(locNames(microbov)[1], equals("replacement"))
+})
+
+test_that("locus accessors work for genpop objects", {
+ skip_on_cran()
+ micpop <- genind2genpop(microbov, quiet = TRUE)
+ expect_that(nLoc(micpop), equals(30))
+ locNames(micpop)[1] <- "replacement"
+ expect_that(locNames(micpop)[1], equals("replacement"))
+})
+
+test_that("'[' method works for genind objects", {
+ skip_on_cran()
+ two_random_loci <- sample(locNames(microbov), 2)
+ ten_random_samples <- sample(nInd(microbov), 10)
+# cat("\nLoci:", dput(two_random_loci), "\nSamples:",
+# dput(ten_random_samples), "\n")
+ pops <- levels(pop(microbov))
+ pops <- pops[pops %in% pop(microbov)[ten_random_samples]]
+ loci <- microbov at loc.fac[microbov at loc.fac %in% two_random_loci]
+ loci <- factor(loci)
+
+ mic10 <- microbov[ten_random_samples]
+ mic2Loc <- microbov[loc = two_random_loci]
+ mic2Loc10 <- microbov[ten_random_samples, loc = two_random_loci]
+
+ names(two_random_loci) <- two_random_loci
+ two_random_loci <- two_random_loci[levels(loci)]
+
+ expect_that(nInd(mic10), equals(10))
+ expect_that(nInd(mic2Loc), equals(nInd(microbov)))
+ expect_that(nInd(mic2Loc10), equals(10))
+
+ expect_that(nLoc(mic10), equals(nLoc(microbov)))
+ expect_that(nLoc(mic2Loc), equals(2))
+ expect_that(nLoc(mic2Loc10), equals(2))
+
+ expect_equivalent(popNames(mic10), pops)
+ expect_equivalent(popNames(mic2Loc10), pops)
+ expect_that(nPop(mic10), equals(length(pops)))
+ expect_that(nPop(mic2Loc10), equals(length(pops)))
+
+ expect_that(length(mic10 at loc.fac), equals(ncol(tab(microbov))))
+ expect_that(mic2Loc at loc.fac, equals(loci))
+ expect_that(mic2Loc10 at loc.fac, equals(loci))
+
+ expect_that(mic10 at loc.n.all, equals(microbov at loc.n.all))
+ expect_that(mic2Loc at loc.n.all, equals(microbov at loc.n.all[two_random_loci]))
+ expect_that(mic2Loc10 at loc.n.all, equals(microbov at loc.n.all[two_random_loci]))
+})
+
+test_that("'[' method works for genind objects with drop = TRUE", {
+ skip_on_cran()
+ two_random_loci <- sample(locNames(microbov), 2)
+ ten_random_samples <- sample(nInd(microbov), 10)
+# cat("\nLoci:", dput(two_random_loci),
+# "\nSamples:", dput(ten_random_samples), "\n")
+ pops <- levels(pop(microbov))
+ pops <- pops[pops %in% pop(microbov)[ten_random_samples]]
+ j <- microbov at loc.fac %in% two_random_loci
+ loci <- microbov at loc.fac[j]
+ loci <- factor(loci)
+ loci <- loci[colSums(tab(microbov)[, j], na.rm = TRUE) > 0]
+ ten_ind_loci <- colSums(tab(microbov[ten_random_samples, ]), na.rm = TRUE) > 0
+
+
+ mic10 <- microbov[ten_random_samples, , drop = TRUE]
+ mic2Loc <- microbov[loc = two_random_loci]
+ mic2Loc10 <- microbov[ten_random_samples, loc = two_random_loci, drop = TRUE]
+
+ names(two_random_loci) <- two_random_loci
+ two_random_loci <- two_random_loci[levels(loci)]
+
+ expect_that(nInd(mic10), equals(10))
+ expect_that(nInd(mic2Loc), equals(nInd(microbov)))
+ expect_that(nInd(mic2Loc10), equals(10))
+
+ expect_that(nLoc(mic10), equals(nLoc(microbov)))
+ expect_that(nLoc(mic2Loc), equals(2))
+ expect_that(nLoc(mic2Loc10), equals(2))
+
+ expect_equivalent(popNames(mic10), pops)
+ expect_equivalent(popNames(mic2Loc10), pops)
+ expect_that(nPop(mic10), equals(length(pops)))
+ expect_that(nPop(mic2Loc10), equals(length(pops)))
+
+ ten_ind_loci2 <- factor(mic10 at loc.fac[mic10 at loc.fac %in% levels(loci)])
+ expect_that(length(mic10 at loc.fac), equals(ncol(tab(microbov)[, ten_ind_loci])))
+ expect_that(mic2Loc at loc.fac, equals(loci))
+ expect_that(mic2Loc10 at loc.fac, equals(ten_ind_loci2))
+
+ expect_true(all(mic10 at loc.n.all <= microbov at loc.n.all))
+ expect_that(mic2Loc at loc.n.all, equals(microbov at loc.n.all[two_random_loci]))
+ expect_that(names(mic2Loc10 at loc.n.all), equals(names(microbov at loc.n.all[two_random_loci])))
+ expect_true(all(mic2Loc10 at loc.n.all <= microbov at loc.n.all[two_random_loci]))
+})
+
+test_that("tab will retain dimensions", {
+ skip_on_cran()
+ micpop <- genind2genpop(microbov[pop(microbov) %in% popNames(microbov)[1]], quiet = TRUE)
+ tabdim <- dim(micpop at tab)
+ expect_that(tabdim, equals(dim(tab(micpop))))
+ expect_that(tabdim, equals(dim(tab(micpop, freq = TRUE))))
+})
+
+test_that("tab will return frequencies for PA data", {
+ skip_on_cran()
+ x <- read.table(system.file("files/AFLP.txt", package = "adegenet"))
+ aflp <- df2genind(x, type = "PA", ploidy = 1, pop = c(rep(1, 4), rep(2, 3)))
+ apop <- genind2genpop(aflp)
+ atab <- tab(apop, freq = TRUE)
+ res <- tab(apop)/rowSums(tab(apop))
+ expect_equivalent(atab, res)
+})
diff --git a/tests/testthat/test_constructors.R b/tests/testthat/test_constructors.R
new file mode 100644
index 0000000..9c97730
--- /dev/null
+++ b/tests/testthat/test_constructors.R
@@ -0,0 +1,15 @@
+context("constructor tests")
+
+test_that("genind objects can be constructed with nothing", {
+ skip_on_cran()
+ gen <- genind()
+ expect_that(gen, is_a("genind"))
+ expect_true(is.genind(gen))
+})
+
+test_that("genpop objects can be constructed with nothing", {
+ skip_on_cran()
+ gen <- genpop()
+ expect_that(gen, is_a("genpop"))
+ expect_true(is.genpop(gen))
+})
\ No newline at end of file
diff --git a/tests/testthat/test_genlight.R b/tests/testthat/test_genlight.R
new file mode 100644
index 0000000..0c2ae5b
--- /dev/null
+++ b/tests/testthat/test_genlight.R
@@ -0,0 +1,106 @@
+context("Genlight construction")
+
+
+test_that("glSim does not call parallel by default", {
+ skip_on_cran()
+ if ("parallel" %in% sessionInfo()$basePkgs){
+ skip("parallel is already loaded")
+ }
+ no_parallel <- sessionInfo()$basePkgs
+ expect_false("parallel" %in% no_parallel)
+ x <- glSim(2, n.snp.nonstruc = 10, n.snp.struc = 10, parallel = FALSE)
+ check_parallel <- sessionInfo()$basePkgs
+ expect_false("parallel" %in% check_parallel)
+ expect_is(x, "genlight")
+})
+
+test_that("Genlight objects can be created predictably", {
+ skip_on_cran()
+ expect_warning(a <- new("genlight", list(c(1,0,1), c(0,0,1,0)), parallel = FALSE ))
+ expect_warning(b <- new("genlight", list(c(1,0,1,1,1,1), c(1,0)), parallel = FALSE ))
+ locNames(a) <- letters[1:4]
+ locNames(b) <- 1:6
+ c <- cbind(a, b, parallel = FALSE)
+ cbound <- cbind(as.matrix(a), as.matrix(b))
+ rbound <- rbind(as.matrix(a),as.matrix(a))
+ expect_identical(as.matrix(c), cbound)
+ expect_identical(as.matrix(rbind(a, a, parallel = FALSE)), rbound)
+})
+
+
+x <- new("genlight", list(a=1,b=0,c=1), other=list(1:3, letters, data.frame(2:4)), parallel = FALSE)
+pop(x) <- c("pop1","pop1", "pop2")
+
+test_that("subsetting with/without @other works", {
+ skip_on_cran()
+ expect_that(x[1:2, ]@other[[1]], equals(1:2))
+ expect_that(x[1:2, ]@other[[2]], equals(letters))
+ expect_that(x[1:2, ]@other[[3]], equals(x at other[[3]][1:2, , drop = FALSE]))
+})
+
+test_that("population accessors work", {
+ skip_on_cran()
+ expect_that(nPop(x), equals(2))
+ expect_that(pop(x), is_equivalent_to(factor(c("pop1","pop1", "pop2"))))
+ expect_that(popNames(x), equals(levels(pop(x))))
+ popNames(x)[1] <- "replacement"
+ expect_that(popNames(x), equals(c("replacement", "pop2")))
+ expect_error(popNames(x) <- NULL)
+ expect_error(popNames(x)[2] <- NA)
+})
+
+x <- "
+X13049 X13050 X13051 X13052 X13053
+AA36881 2 NA 2 2 2
+AA36883 2 2 2 2 2
+AA36884 2 2 2 2 2
+AA36802 NA 2 2 2 2
+AA36803 2 2 2 2 2
+AA36804 2 NA 2 2 2
+AA36181 2 NA 2 2 2
+AA36183 2 2 2 2 2"
+
+xxdf <- read.table(text = x)
+xx <- new("genlight", xxdf, parallel = FALSE)
+pop(xx) <- rep(LETTERS[1:2], each = 4)
+
+test_that("missing data is properly subset with logical subscripts", {
+ skip_on_cran()
+ Apop <- pop(xx) == "A"
+ Bpop <- pop(xx) == "B"
+ expect_identical(NA.posi(xx), NA.posi(xx[]))
+ expect_identical(xxdf[Apop, ], as.data.frame(xx[Apop, ]))
+ expect_identical(xxdf[Bpop, ], as.data.frame(xx[Bpop, ]))
+ keepers <- c(FALSE, rep(TRUE, 4))
+ expect_identical(xxdf[keepers], as.data.frame(xx[, keepers]))
+})
+
+test_that("missing data is properly subset with positive subscripts", {
+ skip_on_cran()
+ rl <- sample(5)
+ # Can subset single locus
+ expect_identical(xxdf[, 1, drop = FALSE], as.data.frame(xx[, 1]))
+ # Can subset range of loci
+ expect_identical(xxdf[, 1:3, drop = FALSE], as.data.frame(xx[, 1:3]))
+ # Can subset by position
+ expect_identical(xxdf[, rl, drop = FALSE], as.data.frame(xx[, rl]))
+})
+
+test_that("missing data is properly subset with negative subscripts", {
+ skip_on_cran()
+ expect_identical(xxdf[, -1], as.data.frame(xx[, -1]))
+ expect_identical(xxdf[, -c(1, 3)], as.data.frame(xx[, -c(1, 3)]))
+})
+
+test_that("missing data is properly subset with a character vector", {
+ skip_on_cran()
+ lnames <- locNames(xx)
+ rl <- sample(lnames)
+ expect_identical(xxdf[, rl], as.data.frame(xx[, rl]))
+ expect_identical(xxdf[, lnames[1:2]], as.data.frame(xx[, lnames[1:2]]))
+})
+
+test_that("genlight objects do not take a mixture of positive and negative subscripts", {
+ skip_on_cran()
+ expect_error(xx[, c(2, -1)], "subscripts.")
+})
diff --git a/tests/testthat/test_hierarchy.R b/tests/testthat/test_hierarchy.R
new file mode 100644
index 0000000..f64b57e
--- /dev/null
+++ b/tests/testthat/test_hierarchy.R
@@ -0,0 +1,50 @@
+context("Strata methods")
+
+test_that("strata methods work for genind objects.", {
+ skip_on_cran()
+
+ data(microbov, package = "adegenet")
+ expect_null(strata(microbov))
+ strata(microbov) <- data.frame(other(microbov))
+ breeds <- c("Borgou", "Zebu", "Lagunaire", "NDama", "Somba", "Aubrac", "Bazadais",
+ "BlondeAquitaine", "BretPieNoire", "Charolais", "Gascon", "Limousin",
+ "MaineAnjou", "Montbeliard", "Salers")
+
+ expect_that(length(strata(microbov)), equals(3))
+ expect_that(popNames(microbov), equals(breeds))
+ expect_that({microbovsplit <- splitStrata(microbov, ~Pop/Subpop)}, throws_error())
+ nameStrata(microbov) <- ~Country/Breed/Species
+ expect_that(names(strata(microbov)), equals(c("Country", "Breed", "Species")))
+ setPop(microbov) <- ~Country/Species
+ expect_that(popNames(microbov), equals(c("AF_BI", "AF_BT", "FR_BT")))
+})
+
+test_that("strata produce proper errors", {
+ skip_on_cran()
+ expect_warning(setPop(microbov, ~bippity/boppity/boo))
+ strata(microbov) <- data.frame(other(microbov))
+ expect_error({strata(microbov) <- data.frame(a = 1)})
+ expect_error({addStrata(microbov) <- data.frame(a = 1:10)})
+ expect_error(setPop(microbov, ~bippity/boppity/boo))
+ expect_error({strata(microbov) <- "a stratum"})
+ expect_error({setPop(microbov) <- "thepop"})
+})
+
+test_that("strata methods work for genlight objects", {
+ skip_on_cran()
+
+ michier <- data.frame(other(microbov))
+ make_gl <- function(n = 10, hier = michier){
+ objs <- lapply(seq(n), function(x) sample(c(0, 1, NA), 10, replace = TRUE, prob = c(0.49, 0.49, 0.01)))
+ return(new("genlight", objs, strata = hier[sample(704, 10), sample(3, 2)], parallel = FALSE))
+ }
+ set.seed(9999)
+ glTest <- lapply(1:10, function(x, y, z) make_gl(y, z), 10, michier)
+ res <- do.call("rbind.genlight", c(glTest, parallel = FALSE))
+ expect_that(res, is_a("genlight"))
+ expect_that(nInd(res), equals(100))
+ expect_that(nLoc(res), equals(10))
+ expect_that(length(strata(res)), equals(3))
+ nameStrata(res) <- ~Hickory/Dickory/Doc
+ expect_that(names(strata(res)), equals(c("Hickory", "Dickory", "Doc")))
+})
diff --git a/tests/testthat/test_import.R b/tests/testthat/test_import.R
new file mode 100644
index 0000000..0519a29
--- /dev/null
+++ b/tests/testthat/test_import.R
@@ -0,0 +1,131 @@
+context("Import Tests")
+
+test_that("df2genind works with haploids", {
+ skip_on_cran()
+ x <- matrix(sample(20), nrow = 10, ncol = 2)
+ res <- df2genind(x, ploidy = 1)
+ expect_that(sum(res at loc.n.all), equals(20))
+ expect_that(nInd(res), equals(10))
+ expect_that(nLoc(res), equals(2))
+ resdf <- genind2df(res)
+ expect_that(as.matrix(resdf), is_equivalent_to(x))
+})
+
+test_that("df2genind makes sense for given example", {
+ skip_on_cran()
+ df <- data.frame(locusA=c("11","11","12","32"),
+ locusB=c(NA,"34","55","15"),
+ locusC=c("22","22","21","22"))
+ row.names(df) <- .genlab("genotype",4)
+ obj <- df2genind(df, ploidy=2, ncode=1)
+ expect_that(nInd(obj), equals(4))
+ expect_that(nLoc(obj), equals(3))
+ expect_that(locNames(obj), equals(colnames(df)))
+ expect_that(indNames(obj), equals(rownames(df)))
+ expect_that(obj at loc.n.all, is_equivalent_to(c(3, 4, 2)))
+ objdf <- genind2df(obj)
+ expect_that(df, is_equivalent_to(df))
+})
+
+test_that("df2genind handles NAs for 'numerically named' samples correctly", {
+ skip_on_cran()
+
+ df <- read.table(text = "
+AnimalID,Samp,INRA21,AHT137,REN169D01,AHTk253
+730,AX.0CCE,092 098,132 132,NA,284 286
+498,AP.07P4,092 092,124 142,204 208,280 280
+677,AP.088P,092 096,140 146,204 204,280 280
+678,AP.088T,096 098,124 148,198 204,280 280
+544,AP.07XM,096 098,134 146,198 198,280 286
+533,AP.07UM,092 098,134 148,198 204,280 286",
+ header = TRUE, sep = ",", colClasses = rep("factor", 6))
+
+ obj <- df2genind(X = df[, !grepl("AnimalID|Samp", colnames(df))], ind.names = df$AnimalID,
+ sep = " ", ncode = 6)
+ g <- tab(obj)
+ expect_that(g["730", grepl("REN169D01", colnames(g))],
+ is_equivalent_to(c(REN169D01.204 = as.integer(NA),
+ REN169D01.208 = as.integer(NA),
+ REN169D01.198 = as.integer(NA)))
+ )
+ })
+
+test_that("df2genind will handle duplicate samples and loci", {
+ skip_on_cran()
+ x <-
+ "A B
+ 1/2 3/4
+ 5/6 4/5
+ 2/6 3/9"
+ xdf <- read.table(text = x, header = TRUE, stringsAsFactors = FALSE)
+ inds <- c("one", "one", "two")
+ loci <- rep("double", 2)
+ expect_warning(xgid <- df2genind(xdf, sep = "/", ind.names = inds, loc.names = loci))
+ expect_that(unique(rowSums(tab(xgid))), is_equivalent_to(4))
+ expect_that(genind2df(xgid, sep = "/"), is_equivalent_to(xdf))
+})
+
+
+test_that("read.X functions work as expected", {
+ skip_on_cran()
+ gpop <- read.genepop(system.file("files/nancycats.gen",package="adegenet"), quiet = TRUE)
+ fsta <- read.fstat(system.file("files/nancycats.dat",package="adegenet"), quiet = TRUE)
+ gntx <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"), quiet = TRUE)
+ stru <- read.structure(system.file("files/nancycats.str",package="adegenet"),
+ onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1,
+ col.pop=2, ask=FALSE, quiet = TRUE)
+ data("nancycats", package = "adegenet")
+ # Making sure that the populations are all named the same. The order of the
+ # isolates are mixed up within these data.
+ levels(pop(gpop)) <- levels(pop(nancycats))
+ levels(pop(fsta)) <- levels(pop(nancycats))
+ levels(pop(gntx)) <- levels(pop(nancycats))
+ levels(pop(stru)) <- levels(pop(nancycats))
+
+ # Ensuring that the locus and population summaries are equivalent
+ summary_stats <- summary(nancycats)
+ expect_equivalent(summary(gpop), summary_stats)
+ expect_equivalent(summary(fsta), summary_stats)
+ expect_equivalent(summary(gntx), summary_stats)
+ expect_equivalent(summary(stru), summary_stats)
+})
+
+test_that("read.genpop can import duplicate names", {
+ skip_on_cran()
+ x <- "
+ Microsat on Chiracus radioactivus, a pest species
+ Loc1, Loc2, Loc3, Y-linked, Loc4
+POP
+AA8, 0405 0711 0304 0000 0505
+AA9, 0405 0609 0208 0000 0505
+A10, 0205 0609 0101 0000 0305
+A11, 0405 0606 0102 0000 0504
+A12, 0202 0609 0105 0000 0507
+A13, 0505 0909 0107 0000 0505
+A14, 0202 0609 0207 0000 0503
+A15, 0405 0609 0101 0000 0505
+Pop
+AF, 0000 0000 0000 0000 0505
+AF, 0205 0307 0102 0000 0505
+AF, 0202 0609 0202 0000 0505
+AF, 0205 0909 0000 0000 0505
+AF, 0205 0307 0202 0000 0505
+AF, 0505 0303 0102 0000 0505
+AF, 0205 0700 0000 0000 0505
+AF, 0505 0900 0000 0000 0405
+AF, 0205 0600 0000 0000 0505
+AF, 0505 0606 0202 0000 0505
+pop
+C45, 0505 0606 0202 0000 0505
+C45, 0505 0909 0202 0000 0505
+C45, 0505 0306 0202 0000 0505
+C45, 0505 0909 0102 0000 0405
+C45, 0205 0303 0202 0000 0505
+C45, 0205 0909 0202 0000 0405
+ "
+ tmp <- tempfile(fileext = ".gen")
+ cat(x, file = tmp)
+ expect_warning(gp <- read.genepop(tmp))
+ expect_identical(indNames(gp), .genlab("", nInd(gp)))
+
+})
\ No newline at end of file
diff --git a/tests/testthat/test_repool.R b/tests/testthat/test_repool.R
new file mode 100644
index 0000000..eb4801d
--- /dev/null
+++ b/tests/testthat/test_repool.R
@@ -0,0 +1,35 @@
+context("Repool tests")
+
+data("microbov")
+strata(microbov) <- data.frame(other(microbov))
+
+test_that("slots are equivalent", {
+ skip_on_cran()
+ temp <- seppop(microbov)
+ retemp <- repool(temp)
+ expect_null(other(retemp))
+ expect_that(microbov at call, not(is_equivalent_to(retemp at call)))
+ expect_that(names(microbov), equals(names(retemp)))
+
+# micnames <- names(microbov)
+# micnames <- micnames[!micnames %in% c("other", "call", "all.names")]
+# for (i in micnames){
+# x <- paste0("expect_that(slot(microbov, '", i, "'), is_equivalent_to(slot(retemp, '", i, "')))", "\n")
+# cat(x)
+# }
+ # Alleles in repooled samples are out of order.
+ # This makes sure they are ordered.
+ retempallnames <- lapply(retemp at all.names, sort)
+ retemptab <- retemp at tab[, colnames(microbov at tab)]
+
+ expect_equivalent(slot(microbov, 'tab'), retemptab)
+ expect_equivalent(slot(microbov, 'all.names'), retempallnames)
+ expect_equivalent(slot(microbov, 'strata'), slot(retemp, 'strata'))
+ expect_equivalent(slot(microbov, 'hierarchy'), slot(retemp, 'hierarchy'))
+ expect_equivalent(slot(microbov, 'loc.fac'), slot(retemp, 'loc.fac'))
+ expect_equivalent(slot(microbov, 'loc.n.all'), slot(retemp, 'loc.n.all'))
+ expect_equivalent(slot(microbov, 'pop'), slot(retemp, 'pop'))
+ expect_equivalent(slot(microbov, 'ploidy'), slot(retemp, 'ploidy'))
+ expect_equivalent(slot(microbov, 'type'), slot(retemp, 'type'))
+
+})
diff --git a/tests/testthat/test_subset.R b/tests/testthat/test_subset.R
new file mode 100644
index 0000000..3f01264
--- /dev/null
+++ b/tests/testthat/test_subset.R
@@ -0,0 +1,20 @@
+context("subset tests")
+
+data("nancycats", package = "adegenet")
+
+test_that("subsetters work for genind objects", {
+ skip_on_cran()
+ expect_equivalent(nInd(nancycats[1:10]), 10)
+ expect_equivalent(nLoc(nancycats[loc = locNames(nancycats)[1]]), 1)
+ expect_equivalent(nLoc(nancycats[loc = 1]), 1)
+ expect_equivalent(nLoc(nancycats[loc = -1]), 8)
+})
+
+test_that("subsetters work for genind objects", {
+ skip_on_cran()
+ nanpop <- genind2genpop(nancycats, quiet = TRUE)
+ expect_equivalent(nPop(nanpop[1:10]), 10)
+ expect_equivalent(nLoc(nanpop[loc = locNames(nanpop)[1]]), 1)
+ expect_equivalent(nLoc(nanpop[loc = 1]), 1)
+ expect_equivalent(nLoc(nanpop[loc = -1]), 8)
+})
\ No newline at end of file
diff --git a/tests/testthat/test_summary.R b/tests/testthat/test_summary.R
new file mode 100644
index 0000000..354ae61
--- /dev/null
+++ b/tests/testthat/test_summary.R
@@ -0,0 +1,13 @@
+context("Summary methods")
+
+test_that("Diploid summaries work", {
+ skip_on_cran()
+ data("nancycats", package = "adegenet")
+ nansum <- summary(nancycats, verbose = FALSE)
+ expect_that(nansum, is_a("genindSummary"))
+ expect_that(nansum$n, equals(nInd(nancycats)))
+ expect_that(length(nansum$n.by.pop), equals(length(popNames(nancycats))))
+ expect_that(length(nansum$pop.n.all), equals(length(popNames(nancycats))))
+ expect_that(sample(nansum$Hobs, 1), is_more_than(0))
+ expect_that(sample(nansum$Hexp, 1), is_more_than(0))
+})
diff --git a/tests/testthat/test_xval.R b/tests/testthat/test_xval.R
new file mode 100644
index 0000000..bef12a2
--- /dev/null
+++ b/tests/testthat/test_xval.R
@@ -0,0 +1,31 @@
+context("xvalDapc test")
+
+xvalnames <- c("Cross-Validation Results",
+ "Median and Confidence Interval for Random Chance",
+ "Mean Successful Assignment by Number of PCs of PCA",
+ "Number of PCs Achieving Highest Mean Success",
+ "Root Mean Squared Error by Number of PCs of PCA",
+ "Number of PCs Achieving Lowest MSE",
+ "DAPC")
+
+data(sim2pop)
+
+
+test_that("xvalDapc returns expected results", {
+ skip_on_cran()
+ xval <- xvalDapc(sim2pop at tab, pop(sim2pop), n.pca.max=100, n.rep=3, xval.plot = FALSE)
+ cvr <- xval[["Cross-Validation Results"]]
+ msa <- xval[["Mean Successful Assignment by Number of PCs of PCA"]]
+ expect_that(xval, is_a("list"))
+ expect_equivalent(names(xval), xvalnames)
+ expect_that(xval$DAPC, is_a("dapc"))
+ expect_that(nrow(cvr), equals(3 * length(msa)))
+})
+
+test_that("xvalDapc throws a warning with populations of 1 sample", {
+ skip_on_cran()
+ dat_pop <- as.character(pop(sim2pop))
+ dat_pop[1] <- "Pop C"
+ pop(sim2pop) <- dat_pop
+ expect_warning(xvalDapc(sim2pop at tab, pop(sim2pop), n.pca.max=100, n.rep=3, xval.plot = FALSE))
+})
--
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