[med-svn] [circlator] 02/07: Imported Upstream version 1.3.0
Afif Elghraoui
afif at moszumanska.debian.org
Tue Aug 16 07:07:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository circlator.
commit cd946212b81d9b7e90ea717582b649e717811057
Author: Afif Elghraoui <afif at debian.org>
Date: Mon Aug 15 20:54:23 2016 -0700
Imported Upstream version 1.3.0
---
.travis.yml | 4 -
circlator/__init__.py | 2 +-
circlator/external_progs.py | 45 +-
circlator/fixstart.py | 55 --
circlator/program.py | 55 +-
circlator/start_fixer.py | 337 +++++++++
circlator/tasks/all.py | 5 +-
circlator/tasks/fixstart.py | 6 +-
circlator/tasks/progcheck.py | 6 +-
...tart_fixer_find_circular_using_prodigal.ctgs.fa | 109 +++
...art_fixer_find_circular_using_promer.contigs.fa | 168 +++++
.../start_fixer_find_circular_using_promer.refs.fa | 75 ++
circlator/tests/data/start_fixer_init_contigs.fa | 4 +
circlator/tests/data/start_fixer_init_dnaA.fa | 2 +
circlator/tests/data/start_fixer_init_ignore_ids | 2 +
.../data/start_fixer_max_length_from_fasta_file.fa | 6 +
.../data/start_fixer_rearrange_contigs.expect.fa | 776 +++++++++++++++++++++
.../data/start_fixer_rearrange_contigs.expect.log | 8 +
.../tests/data/start_fixer_rearrange_contigs.in.fa | 776 +++++++++++++++++++++
.../data/start_fixer_rearrange_contigs.refs.fa | 50 ++
.../data/start_fixer_run_bit_of_everything.ctg.fa | 282 ++++++++
.../start_fixer_run_bit_of_everything.expect.fa | 282 ++++++++
.../data/start_fixer_run_bit_of_everything.ignore | 1 +
.../data/start_fixer_run_bit_of_everything.ref.fa | 25 +
.../data/start_fixer_run_ignore_all.expect.fa | 2 +
circlator/tests/data/start_fixer_run_ignore_all.fa | 2 +
.../data/start_fixer_run_ignore_all.to_ignore | 1 +
.../data/start_fixer_run_none_for_prodigal.ctg.fa | 91 +++
.../start_fixer_run_none_for_prodigal.expect.fa | 91 +++
.../data/start_fixer_run_none_for_prodigal.ref.fa | 25 +
..._fixer_write_fasta_plus_circularized_ends.in.fa | 8 +
...fixer_write_fasta_plus_circularized_ends.out.fa | 12 +
...rite_fasta_plus_circularized_ends.out.ignore.fa | 6 +
.../data/start_fixer_write_renamed_contigs.fa | 4 +
circlator/tests/start_fixer_test.py | 225 ++++++
circlator/versions.py | 7 +-
install_dependencies.sh | 2 +-
setup.py | 5 +-
38 files changed, 3451 insertions(+), 111 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index adc52ee..fde9749 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,10 +4,6 @@ addons:
packages:
- zlib1g-dev
- libncurses5-dev
-cache:
- directories:
- - "build"
- - "$HOME/.cache/pip"
python:
- "3.4"
sudo: false
diff --git a/circlator/__init__.py b/circlator/__init__.py
index 4d4e7b9..3df9ce1 100644
--- a/circlator/__init__.py
+++ b/circlator/__init__.py
@@ -14,11 +14,11 @@ __all__ = [
'common',
'dnaa',
'external_progs',
- 'fixstart',
'mapping',
'merge',
'minimus2',
'program',
+ 'start_fixer',
'tasks',
'versions',
]
diff --git a/circlator/external_progs.py b/circlator/external_progs.py
index 9bf3efe..c3b8527 100644
--- a/circlator/external_progs.py
+++ b/circlator/external_progs.py
@@ -8,15 +8,6 @@ import pyfastaq
class Error (Exception): pass
-# Travis is using python3.4, and actually "python" in travis means
-# python3.4, not python2. SPAdes throws an error about not being
-# compatible with python3.4.
-# This means we need to explicitly run SPAdes with python2.
-class Spades(program.Program):
- def exe(self):
- return 'python2 ' + shutil.which(self.path)
-
-
prog_to_env_var = {
'samtools': 'CIRCLATOR_SAMTOOLS',
'spades': 'CIRCLATOR_SPADES',
@@ -37,7 +28,7 @@ min_versions = {
'nucmer': '3.1',
'prodigal': '2.6',
'samtools': '0.1.19',
- 'spades': '3.5.0',
+ 'spades': '3.6.2', # this is the first version to support python3
}
@@ -55,11 +46,6 @@ prog_name_to_default = {
}
-prog_builders = {
- 'spades': Spades
-}
-
-
def handle_error(message, raise_error=True):
if raise_error:
raise Error(message + '\nCannot continue')
@@ -67,42 +53,47 @@ def handle_error(message, raise_error=True):
print(message)
-def make_and_check_prog(name, verbose=False, raise_error=True, filehandle=None):
- builder = prog_builders.get(name, program.Program)
- p = builder(
+def make_and_check_prog(name, verbose=False, raise_error=True, filehandle=None, debug=False):
+ p = program.Program(
prog_name_to_default[name],
prog_to_version_cmd[name][0],
prog_to_version_cmd[name][1],
- environment_var=prog_to_env_var.get(name, None)
+ environment_var=prog_to_env_var.get(name, None),
+ debug=debug
)
if not p.in_path():
handle_error("Didn't find " + name + " in path. Looked for:" + p.path, raise_error=raise_error)
return p
- version = p.version()
+ version = p.version
if version is None:
handle_error('Found ' + name + " but couldn't get version.", raise_error=raise_error)
return p
if not p.version_at_least(min_versions[name]):
- handle_error('Version of ' + name + ' too low. I found ' + p.version() + ', but must be at least ' + min_versions[name] + '. Found here:\n' + p.full_path, raise_error=raise_error)
+ handle_error('Version of ' + name + ' too low. I found ' + p.version + ', but must be at least ' + min_versions[name] + '. Found here:\n' + p.from_which, raise_error=raise_error)
return p
- if name == 'spades' and p.version() == bad_versions['spades']:
- handle_error('ERROR! SPAdes version ' + bad_versions['spades'] + ' is incompatible with Circlator. Please update SPAdes to the latest version', raise_error=raise_error)
+ if name == 'spades' and p.version == bad_versions['spades']:
+ handle_error('ERROR! SPAdes version ' + bad_versions['spades'] + ' is incompatible with Circlator. Please use SPAdes 3.7.1', raise_error=raise_error)
return p
+ if name == 'spades' and not p.version.startswith('3.7.'):
+ print('WARNING: SPAdes version', p.version, 'is being used. It will work, but better results are usually obtained from Circlator using SPAdes version 3.7.1. Although 3.7.1 is not the latest version, we recommend it for Circlator.', file=sys.stderr)
+
if verbose:
- print(name, p.version(), p.full_path, sep='\t')
+ print(name, p.version, p.from_which, sep='\t')
if filehandle:
- print(name, p.version(), p.full_path, sep='\t', file=filehandle)
+ print(name, p.version, p.from_which, sep='\t', file=filehandle)
return p
-def check_all_progs(verbose=False, raise_error=False, filehandle=None):
+def check_all_progs(verbose=False, raise_error=False, filehandle=None, debug=False):
for prog in sorted(prog_name_to_default):
- make_and_check_prog(prog, verbose=verbose, raise_error=raise_error, filehandle=filehandle)
+ if debug:
+ print('__________ checking', prog, '____________', flush=True)
+ make_and_check_prog(prog, verbose=verbose, raise_error=raise_error, filehandle=filehandle, debug=debug)
diff --git a/circlator/fixstart.py b/circlator/fixstart.py
deleted file mode 100644
index 60e3fb0..0000000
--- a/circlator/fixstart.py
+++ /dev/null
@@ -1,55 +0,0 @@
-import os
-import shutil
-import tempfile
-import circlator
-from bio_assembly_refinement import contig_break_finder
-
-class Error (Exception): pass
-
-class StartFixer:
- def __init__(self,
- assembly_fa,
- outprefix,
- min_percent_identity=70,
- genes_fa=None,
- ignore=None,
- ):
- if genes_fa is None:
- d = os.path.abspath(os.path.dirname(circlator.__file__))
- self.genes_fa = os.path.join(d, 'data', 'dnaA.fasta')
- assert os.path.exists(self.genes_fa)
- else:
- self.genes_fa = os.path.abspath(genes_fa)
-
- self.min_percent_identity = min_percent_identity
- self.assembly_fa = os.path.abspath(assembly_fa)
- self.outprefix = os.path.abspath(outprefix)
-
- if ignore is None:
- self.ignore = None
- else:
- self.ignore = os.path.abspath(ignore)
-
-
- def run(self):
- original_dir = os.getcwd()
- tmpdir = tempfile.mkdtemp(prefix=self.outprefix + '.tmp.circlator.fixstart.', dir=os.getcwd())
- os.chdir(tmpdir)
-
- break_finder = contig_break_finder.ContigBreakFinder(
- fasta_file=self.assembly_fa,
- gene_file=self.genes_fa,
- hit_percent_id=self.min_percent_identity,
- skip=self.ignore,
- rename=False,
- summary_prefix='[fixstart]',
- )
- break_finder.run()
-
- # move output files and delete tmp dir
- assert os.path.exists(break_finder.output_file)
- assert os.path.exists(break_finder.summary_file)
- os.rename(break_finder.output_file, self.outprefix + '.fasta')
- os.rename(break_finder.summary_file, self.outprefix + '.log')
- os.chdir(original_dir)
- shutil.rmtree(tmpdir)
diff --git a/circlator/program.py b/circlator/program.py
index ff58c14..13b87bb 100644
--- a/circlator/program.py
+++ b/circlator/program.py
@@ -7,48 +7,83 @@ from circlator import common
class Program:
- def __init__(self, name, version_cmd, version_regex, environment_var=None):
+ def __init__(self, name, version_cmd, version_regex, environment_var=None, debug=False):
self.name = name
+ self.debug = debug
+
if environment_var is not None and environment_var in os.environ:
+ if self.debug:
+ print(self.name, '- getting path from environment variable', environment_var, '=', os.environ[environment_var], flush=True)
self.path = os.environ[environment_var]
else:
+ if self.debug:
+ print(self.name, '- not using environment variable', flush=True)
self.path = name
self.version_cmd = version_cmd
self.version_regex = version_regex
- self.full_path = shutil.which(self.path)
+
+ if self.debug:
+ print(self.name, '- checking which(' + self.path + ')', flush=True)
+
+ self.from_which = shutil.which(self.path)
+
+ if self.debug:
+ print(' ... got: "', self.from_which, '"', sep='', flush=True)
+
+ self._set_version()
def in_path(self):
'''Returns true iff it is in the path'''
- return shutil.which(self.path) is not None
+ return self.from_which is not None
- def version(self):
- '''Returns version. If not in path, or in path but can't get the version, returns None'''
+ def _set_version(self):
+ self.version = None
+
+ if self.debug:
+ print(self.name, '- checking version ...')
+
if not self.in_path():
- return None
+ if self.debug:
+ print(' ... not in path so cannot get version', flush=True)
+ return
cmd = self.exe() + ' ' + self.version_cmd
+ if self.debug:
+ print('Running this command to get version:', cmd)
cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
cmd_output = common.decode(cmd_output[0]).split('\n')[:-1] + common.decode(cmd_output[1]).split('\n')[:-1]
+ if self.debug:
+ print('__________ (begin output from ', cmd, ')___________', sep='')
+ print(*cmd_output, sep='\n')
+ print('__________ (end of output from ', cmd, ')___________', sep='')
+ print('Looking far a match to the regex "', self.version_regex.pattern, '" in the above output', sep='', flush=True)
for line in cmd_output:
hits = self.version_regex.search(line)
if hits:
- return hits.group(1)
- return None
+ if self.debug:
+ print('Match to this line:', line)
+ print('Got version:', hits.group(1), flush=True)
+ self.version = hits.group(1)
+ break
+ else:
+ if self.debug:
+ print('No match found to the regex', flush=True)
+
def version_at_least(self, min_version):
- v = self.version()
+ v = self.version
if v is None:
return None
return LooseVersion(v) >= LooseVersion(min_version)
def version_at_most(self, max_version):
- v = self.version()
+ v = self.version
if v is None:
return None
return LooseVersion(v) <= LooseVersion(max_version)
diff --git a/circlator/start_fixer.py b/circlator/start_fixer.py
new file mode 100644
index 0000000..18db867
--- /dev/null
+++ b/circlator/start_fixer.py
@@ -0,0 +1,337 @@
+import os
+import shutil
+import copy
+import tempfile
+from distutils.version import LooseVersion
+import pyfastaq
+import pymummer
+import circlator
+
+class Error (Exception): pass
+
+class StartFixer:
+ def __init__(self,
+ input_assembly_fa,
+ outprefix,
+ min_percent_identity=70,
+ genes_fa=None,
+ ignore=None,
+ verbose=False,
+ ):
+ if genes_fa is None:
+ d = os.path.abspath(os.path.dirname(circlator.__file__))
+ self.genes_fa = os.path.join(d, 'data', 'dnaA.fasta')
+ assert os.path.exists(self.genes_fa)
+ else:
+ if not os.path.exists(genes_fa):
+ raise Error('Genes file "' + genes_fa + '" not found. Cannot continue')
+ self.genes_fa = os.path.abspath(genes_fa)
+
+ if not os.path.exists(input_assembly_fa):
+ raise Error('Error! File not found: ' + input_assembly_fa)
+ self.input_assembly = {}
+ pyfastaq.tasks.file_to_dict(input_assembly_fa, self.input_assembly)
+
+ self.min_percent_identity = min_percent_identity
+ self.outprefix = os.path.abspath(outprefix)
+ self.verbose = verbose
+
+ if ignore is None:
+ self.ignore = set()
+ else:
+ with open(ignore) as f:
+ self.ignore = {x.rstrip().split()[0] for x in f}
+
+
+ @classmethod
+ def _rename_contigs(cls, contigs_dict):
+ rename_dict = {}
+ new_contigs_dict = {}
+ for old_name, contig in contigs_dict.items():
+ new_name = old_name.split()[0]
+ if new_name in rename_dict:
+ raise Error('Non-unique name "' + new_name + '" in input contigs. Cannot continue')
+ rename_dict[new_name] = old_name
+ new_contigs_dict[new_name] = pyfastaq.sequences.Fasta(new_name, contig.seq)
+
+ return new_contigs_dict, rename_dict
+
+
+ @classmethod
+ def _write_renamed_contigs(cls, contigs_dict, rename_dict, outfile):
+ f = pyfastaq.utils.open_file_write(outfile)
+
+ for old_name, contig in sorted(contigs_dict.items()):
+ contig.id = rename_dict[old_name]
+ print(contig, file=f)
+
+ pyfastaq.utils.close(f)
+
+
+ @classmethod
+ def _max_length_from_fasta_file(cls, infile):
+ freader = pyfastaq.sequences.file_reader(infile)
+ return max([len(x) for x in freader])
+
+
+ @classmethod
+ def _write_fasta_plus_circularized_ends(cls, contigs, outfile, end_length, ignore=None):
+ if ignore is None:
+ ignore = set()
+
+ if ignore.issuperset(set(contigs.keys())):
+ return 0
+
+ f = pyfastaq.utils.open_file_write(outfile)
+ used_names = set(contigs.keys())
+ seqs_written = 0
+
+ for contig_name, contig in sorted(contigs.items()):
+ if contig_name in ignore:
+ continue
+
+ print(contig, file=f)
+ seqs_written += 1
+
+ if len(contig) >= 2 * end_length:
+ start_coord = end_length - 1
+ end_coord = len(contig) - end_length
+ new_name = contig.id + '__ends'
+ assert new_name not in used_names
+ used_names.add(new_name)
+ new_contig = pyfastaq.sequences.Fasta(new_name, contig[end_coord:] + contig[:start_coord + 1])
+ print(new_contig, file=f)
+ seqs_written += 1
+
+ pyfastaq.utils.close(f)
+ return seqs_written
+
+
+ @classmethod
+ def _find_circular_using_promer(cls, outprefix, ref_genes_fa, contigs_dict, min_percent_id, end_length, log_fh, ignore=None):
+ if ignore is None:
+ ignore = set()
+ promer_out = outprefix + '.promer'
+ contigs_with_ends = outprefix + '.contigs_with_ends.fa'
+ sequences_written = StartFixer._write_fasta_plus_circularized_ends(contigs_dict, contigs_with_ends, end_length, ignore=ignore)
+ if sequences_written == 0:
+ print('No sequences to check with promer. Skipping', file=log_fh)
+ return {}
+
+ prunner = pymummer.nucmer.Runner(
+ contigs_with_ends,
+ ref_genes_fa,
+ promer_out,
+ min_id=min_percent_id,
+ promer=True,
+ verbose=False,
+ maxmatch=True,
+ )
+ prunner.run()
+
+ circularized = {} # original_contig_name -> promer match
+ file_reader = pymummer.coords_file.reader(promer_out)
+
+ for match in file_reader:
+ if match.ref_name.endswith('__ends'):
+ original_contig_name = match.ref_name[:-len('__ends')]
+ else:
+ original_contig_name = match.ref_name
+
+ if match.hit_length_qry == match.qry_length and match.percent_identity >= min_percent_id:
+ if original_contig_name not in circularized or circularized[original_contig_name].percent_identity < match.percent_identity:
+ circularized[original_contig_name] = copy.copy(match)
+
+ if len(circularized):
+ print('Using the following promer matches to circularize contigs:', file=log_fh)
+ for contig_name in circularized:
+ print(circularized[contig_name], file=log_fh)
+ else:
+ print('No suitable promer matches found', file=log_fh)
+
+ return circularized
+
+
+ @classmethod
+ def _find_circular_using_prodigal(cls, outprefix, contigs_dict, circular_from_promer, log_fh, ignore=None):
+ if ignore is None:
+ ignore = set()
+
+ all_to_ignore = copy.copy(ignore)
+ all_to_ignore.update(set(circular_from_promer.keys()))
+ if all_to_ignore.issuperset(set(contigs_dict.keys())):
+ print('No sequences left for which to look for genes using prodigal. Skipping', file=log_fh)
+ return {}
+
+ prodigal = circlator.external_progs.make_and_check_prog('prodigal')
+ total_contig_length = 0
+ prodigal_input_file = outprefix + '.for_prodigal.fa'
+ prodigal_output_file = outprefix + '.prodigal.gff'
+ with open(prodigal_input_file, 'w') as f:
+ for seq_name in sorted(contigs_dict):
+ if seq_name not in circular_from_promer and seq_name not in ignore:
+ total_contig_length += len(contigs_dict[seq_name])
+ print(contigs_dict[seq_name], file=f)
+
+
+ if (total_contig_length < 20000):
+ # prodigal needs -p meta option for sequences less than 20000
+ # annoyingly newer version of prodigal has different -p option!
+ if LooseVersion(prodigal.version) >= LooseVersion('3.0'):
+ p_option = "-p anon"
+ else:
+ p_option = "-p meta"
+ else:
+ p_option = ''
+
+ cmd = ' '.join([
+ 'prodigal',
+ '-i', prodigal_input_file,
+ '-o', prodigal_output_file,
+ '-f gff -c -q',
+ p_option
+ ])
+
+ circlator.common.syscall(cmd)
+ circularized = {}
+ best_dist = {}
+
+ with open(prodigal_output_file) as f:
+ for line in f:
+ if line.startswith('#'):
+ continue
+
+ contig, x, y, start, end, *z = line.rstrip().split('\t')
+ new_inter = pyfastaq.intervals.Interval(int(start), int(end))
+ new_dist = new_inter.distance_to_point(int(len(contigs_dict[contig])/2))
+
+ if contig in circularized:
+ assert contig in best_dist
+ if new_dist < best_dist[contig]:
+ best_dist[contig] = new_dist
+ circularized[contig] = line.rstrip()
+ else:
+ best_dist[contig] = new_dist
+ circularized[contig] = line.rstrip()
+
+ if len(circularized):
+ print('Using the following prodigal predictions to circularize contigs:', file=log_fh)
+ for contig_name in circularized:
+ print(circularized[contig_name], file=log_fh)
+ else:
+ print('No prodigal matches found', file=log_fh)
+
+ return circularized
+
+
+ @classmethod
+ def _rearrange_contigs(cls, contigs_dict, circular_from_promer, circular_from_prodigal, to_ignore, end_length, log_filename):
+ log_fh = pyfastaq.utils.open_file_write(log_filename)
+ log_prefix = '[fixstart]'
+ print(log_prefix, 'id', 'break_point', 'gene_name', 'gene_reversed', 'new_name', 'skipped', sep='\t', file=log_fh)
+ for contig_name, contig in sorted(contigs_dict.items()):
+ original_length = len(contig)
+ if contig.id in circular_from_promer:
+ match = circular_from_promer[contig.id]
+ if contig.id == match.ref_name:
+ if match.on_same_strand():
+ position = min(match.ref_start, match.ref_end)
+ contig.seq = contig.seq[position:] + contig.seq[:position]
+ print(log_prefix, contig.id, position + 1, match.qry_name, 'no', '-', '-', sep='\t', file=log_fh)
+ else:
+ position = max(match.ref_start, match.ref_end) + 1
+ contig.seq = contig.seq[position:] + contig.seq[:position]
+ contig.revcomp()
+ print(log_prefix, contig.id, position, match.qry_name, 'yes', '-', '-', sep='\t', file=log_fh)
+ else:
+ assert contig.id + '__ends' == match.ref_name
+ if match.on_same_strand():
+ start_in_ends_contig = min(match.ref_start, match.ref_end)
+ else:
+ start_in_ends_contig = max(match.ref_start, match.ref_end) + 1
+
+ if start_in_ends_contig < end_length:
+ position = len(contig) - end_length + start_in_ends_contig
+ else:
+ position = start_in_ends_contig - end_length
+
+ if match.on_same_strand():
+ contig.seq = contig.seq[position:] + contig.seq[:position]
+ print(log_prefix, contig.id, position + 1, match.qry_name, 'no', '-', '-', sep='\t', file=log_fh)
+ else:
+ contig.seq = contig.seq[position:] + contig.seq[:position]
+ contig.revcomp()
+ print(log_prefix, contig.id, position, match.qry_name, 'yes', '-', '-', sep='\t', file=log_fh)
+ elif contig.id in circular_from_prodigal:
+ gff_contig_name, x, y, start, end, score, strand, *z = circular_from_prodigal[contig.id].rstrip().split('\t')
+ assert contig.id == gff_contig_name
+
+ if strand == '+':
+ position = int(start) - 1
+ contig.seq = contig.seq[position:] + contig.seq[:position]
+ print(log_prefix, contig.id, position + 1, 'prodigal', 'no', '-', '-', sep='\t', file=log_fh)
+ else:
+ assert strand == '-'
+ position = int(end)
+ contig.seq = contig.seq[position:] + contig.seq[:position]
+ contig.revcomp()
+ print(log_prefix, contig.id, position + 1, 'prodigal', 'yes', '-', '-', sep='\t', file=log_fh)
+ elif contig.id in to_ignore:
+ print(log_prefix, contig.id, '-', '-', '-', '-', 'skipped', sep='\t', file=log_fh)
+ else:
+ print(log_prefix, contig.id, '-', '-', '-', '-', '-', sep='\t', file=log_fh)
+
+ assert original_length == len(contig)
+
+ pyfastaq.utils.close(log_fh)
+
+
+ def run(self):
+ renamed_contigs, contig_rename_dict = StartFixer._rename_contigs(self.input_assembly)
+ if self.verbose:
+ print('[fixstart] loaded input contigs', flush=True)
+
+ end_extend = StartFixer._max_length_from_fasta_file(self.genes_fa)
+ log_fh = pyfastaq.utils.open_file_write(self.outprefix + '.detailed.log')
+
+ if self.verbose:
+ print('[fixstart] Running promer to look for reference genes', flush=True)
+ circ_with_promer = StartFixer._find_circular_using_promer(
+ self.outprefix + '.promer',
+ self.genes_fa,
+ renamed_contigs,
+ self.min_percent_identity,
+ end_extend,
+ log_fh,
+ ignore=self.ignore
+ )
+
+ if self.verbose:
+ print('[fixstart] Running prodigal on sequences that had no promer match', flush=True)
+ circ_with_prodigal = StartFixer._find_circular_using_prodigal(
+ self.outprefix + '.prodigal',
+ renamed_contigs,
+ circ_with_promer,
+ log_fh,
+ ignore=self.ignore)
+
+ if self.verbose:
+ print('[fixstart] Fixing start positions of contigs', flush=True)
+ StartFixer._rearrange_contigs(
+ renamed_contigs,
+ circ_with_promer,
+ circ_with_prodigal,
+ self.ignore,
+ end_extend,
+ self.outprefix + '.log'
+ )
+
+ pyfastaq.utils.close(log_fh)
+
+ if self.verbose:
+ print('[fixstart] Writing final FASTA file of contigs', flush=True)
+ StartFixer._write_renamed_contigs(
+ renamed_contigs,
+ contig_rename_dict,
+ self.outprefix + '.fasta'
+ )
diff --git a/circlator/tasks/all.py b/circlator/tasks/all.py
index 5ada723..8ab2fb3 100644
--- a/circlator/tasks/all.py
+++ b/circlator/tasks/all.py
@@ -245,12 +245,13 @@ def run():
#-------------------------------- fixstart -------------------------------
print_message('{:_^79}'.format(' Running fixstart '), options)
- fixer = circlator.fixstart.StartFixer(
+ fixer = circlator.start_fixer.StartFixer(
clean_fasta,
fixstart_prefix,
min_percent_identity=options.fixstart_min_id,
genes_fa=options.genes_fa,
- ignore=not_fix_start_file
+ ignore=not_fix_start_file,
+ verbose=options.verbose
)
fixer.run()
diff --git a/circlator/tasks/fixstart.py b/circlator/tasks/fixstart.py
index e17ca00..abd1884 100644
--- a/circlator/tasks/fixstart.py
+++ b/circlator/tasks/fixstart.py
@@ -8,15 +8,17 @@ def run():
parser.add_argument('--genes_fa', help='FASTA file of genes to search for to use as start point. If this option is not used, a built-in set of dnaA genes is used', metavar='FILENAME')
parser.add_argument('--ignore', help='Absolute path to file of IDs of contigs to not change', metavar='FILENAME')
parser.add_argument('--min_id', type=float, help='Minimum percent identity of promer match between contigs and gene(s) to use as start point [%(default)s]', default=70, metavar='FLOAT')
+ parser.add_argument('--verbose', action='store_true', help='Be verbose')
parser.add_argument('assembly_fa', help='Name of input FASTA file', metavar='assembly.fasta')
parser.add_argument('outprefix', help='Prefix of output files')
options = parser.parse_args()
- fixer = circlator.fixstart.StartFixer(
+ fixer = circlator.start_fixer.StartFixer(
options.assembly_fa,
options.outprefix,
min_percent_identity=options.min_id,
genes_fa=options.genes_fa,
- ignore=options.ignore
+ ignore=options.ignore,
+ verbose=options.verbose,
)
fixer.run()
diff --git a/circlator/tasks/progcheck.py b/circlator/tasks/progcheck.py
index 86ca05a..3448246 100644
--- a/circlator/tasks/progcheck.py
+++ b/circlator/tasks/progcheck.py
@@ -5,6 +5,8 @@ from circlator import versions
def run():
parser = argparse.ArgumentParser(
description = 'Checks all dependencies are found and are correct versions',
- usage = 'circlator progcheck')
+ usage = 'circlator progcheck'
+ )
+ parser.add_argument('--debug', action='store_true', help='Debug mode with very verbose output')
options = parser.parse_args()
- versions.get_all_versions(sys.stdout, raise_error=False)
+ versions.get_all_versions(sys.stdout, raise_error=False, debug=options.debug)
diff --git a/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa b/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa
new file mode 100644
index 0000000..5a7db22
--- /dev/null
+++ b/circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa
@@ -0,0 +1,109 @@
+>ctg1
+AGTGCTAGCCCATTATTGGTCAGCCAGGCGGCATACCAGCCCTTCTTGTGATCCTGCACT
+GGCGTAAAAATCCTTACAGAGTAACGGTCAACTACAAGCTGAGTAGACTTGGGGGTGTTT
+GGTGTCCCTTAGTATCCGTGCTAGCAGCCTTGGACCCCCGAAAGTGTCAAGGGGGGAGAC
+AATTATCGCTCGTCATCCATAACTATTCCGTGTCGGCGCGTCGTTTGAAGCTAAGGAGTC
+TATCGACCCGGGATGCAAGTCCTTCATCGGGGCTCGATTAAACTCGAATAAGGACACAGA
+TATATTAGGCATTCCCGGGTTCCTGGCCGTGTCCCGCCTTGTGTGAGTGAAGGATAAGGG
+GTGGCGGCCGATCTCGCTGCAGTTGATAGAACACTGAGTCGAAGAAAGTGGACATAAGTA
+GTCTCTACTACTTCACCTTGTTGTGATCGCGCTATGACCTCGCATAGATTGGATCCGTGG
+TACCTGGCAGTCGTCGTTTGCATTGCTGGCGCGTTATCGTCTGCAGGAGGCGCACCCATG
+TACGTCTGAGTCAGGAATTACGTTAAGGTGGTGCACCGCAGGTGCGCCTTCTAGGCTTGA
+CTACCATTTTCCAATAGCCAATCCCATAGTCTAGTCACACATAACCTCCTTAAAAAAATA
+ATGACAATAACGGCGAGGTCGCTATTAATATGCCTGTCGCTGTCCCATATCTGTTAAAAG
+CCAAGCAAGGAAAAAATAGCCACGCGTAAGGTGCACTGACGAACTTTTGGTTTTGACGGC
+ATGCCCTAGGACTCGAGGACCATTTTTTATATCCAGTTTACTTGTGTCAGTTAAAATCTT
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCATCGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGATATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAAGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGACCCCGCTGCGCACCCTCAAGGGGGGGGATTTTCTCC
+GATAACTAACCCGCACGGGAGAGCCTTAATAACAGGGCCACTGCGGACTGTCACCAGGAG
+AACACTAAGGATAAACCCATAGAAGCGCTTACTGGACTCAGCACGACCACCAATCGGTCC
+GAACAACACTTTATCCGATAGGCAGGGATCAGTGGGCGCCACAAGCATGCGGAGTAAATG
+TAAACCGAGATGCGGTGCTGCGACTCCTTGTGAGATCCATGCCTAGCGTGACGTAATTAA
+ATAACATGCGAACTGTCTTCCCCTTCATTCCCTCGAAGCCTTTCACAGAGGGTACGCATT
+CGCCGCTACAGAGACCAGAGAGGGTTTCCGCAGAGTAATCAAGCACGAGTACGCCGTCTA
+TTATGAACATCCCAAGATGGACTGTAGGCGCCATCAAATTCGCCACCATCCACCTACTAT
+ACTGTTAAAGAGGATTGTTTGCACCGCAATCGAGATGACGAGGCATCGAGGGTTCTAGCA
+TCGAACTTGCTTGTATCAGGAGATCGCGACGTTGCTGTCTTCGTACGCCTTCCACCGGCC
+GCGTCCCGAATGCATCAAAGTAGCTGAATACTCTTCCTCTAGCGGAAACGTTTACAAACC
+CTATCAACCGGCAACACAGAATGAGGGTACCGCTGGCTTCGACGCGAACGTTCCTAATGA
+ACCATAAGGCTTCCAGCCATCAGCCCATCAGATTGGGCGATACTGGATCGAAAATTTCAA
+ACGATCTAAGCCGTGCTCGTACAAAAGGGGTTCAAATGTGTAGACCTTCAAAGGTCTGTA
+GTCACGCGTTCTAGTAACTATATC
+>ctg2
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+GGGGGGGGGGGGGGGGGGGGGGGGGGG
+>ctg3
+AGTGCTAGCCCATTATTGGTCAGCCAGGCGGCATACCAGCCCTTCTTGTGATCCTGCACT
+GGCGTAAAAATCCTTACAGAGTAACGGTCAACTACAAGCTGAGTAGACTTGGGGGTGTTT
+GGTGTCCCTTAGTATCCGTGCTAGCAGCCTTGGACCCCCGAAAGTGTCAAGGGGGGAGAC
+AATTATCGCTCGTCATCCATAACTATTCCGTGTCGGCGCGTCGTTTGAAGCTAAGGAGTC
+TATCGACCCGGGATGCAAGTCCTTCATCGGGGCTCGATTAAACTCGAATAAGGACACAGA
+TATATTAGGCATTCCCGGGTTCCTGGCCGTGTCCCGCCTTGTGTGAGTGAAGGATAAGGG
+GTGGCGGCCGATCTCGCTGCAGTTGATAGAACACTGAGTCGAAGAAAGTGGACATAAGTA
+GTCTCTACTACTTCACCTTGTTGTGATCGCGCTATGACCTCGCATAGATTGGATCCGTGG
+TACCTGGCAGTCGTCGTTTGCATTGCTGGCGCGTTATCGTCTGCAGGAGGCGCACCCATG
+TACGTCTGAGTCAGGAATTACGTTAAGGTGGTGCACCGCAGGTGCGCCTTCTAGGCTTGA
+CTACCATTTTCCAATAGCCAATCCCATAGTCTAGTCACACATAACCTCCTTAAAAAAATA
+ATGACAATAACGGCGAGGTCGCTATTAATATGCCTGTCGCTGTCCCATATCTGTTAAAAG
+CCAAGCAAGGAAAAAATAGCCACGCGTAAGGTGCACTGACGAACTTTTGGTTTTGACGGC
+ATGCCCTAGGACTCGAGGACCATTTTTTATATCCAGTTTACTTGTGTCAGTTAAAATCTT
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCATCGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGATATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAAGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGACCCCGCTGCGCACCCTCAAGGGGGGGGATTTTCTCC
+GATAACTAACCCGCACGGGAGAGCCTTAATAACAGGGCCACTGCGGACTGTCACCAGGAG
+AACACTAAGGATAAACCCATAGAAGCGCTTACTGGACTCAGCACGACCACCAATCGGTCC
+GAACAACACTTTATCCGATAGGCAGGGATCAGTGGGCGCCACAAGCATGCGGAGTAAATG
+TAAACCGAGATGCGGTGCTGCGACTCCTTGTGAGATCCATGCCTAGCGTGACGTAATTAA
+ATAACATGCGAACTGTCTTCCCCTTCATTCCCTCGAAGCCTTTCACAGAGGGTACGCATT
+CGCCGCTACAGAGACCAGAGAGGGTTTCCGCAGAGTAATCAAGCACGAGTACGCCGTCTA
+TTATGAACATCCCAAGATGGACTGTAGGCGCCATCAAATTCGCCACCATCCACCTACTAT
+ACTGTTAAAGAGGATTGTTTGCACCGCAATCGAGATGACGAGGCATCGAGGGTTCTAGCA
+TCGAACTTGCTTGTATCAGGAGATCGCGACGTTGCTGTCTTCGTACGCCTTCCACCGGCC
+GCGTCCCGAATGCATCAAAGTAGCTGAATACTCTTCCTCTAGCGGAAACGTTTACAAACC
+CTATCAACCGGCAACACAGAATGAGGGTACCGCTGGCTTCGACGCGAACGTTCCTAATGA
+ACCATAAGGCTTCCAGCCATCAGCCCATCAGATTGGGCGATACTGGATCGAAAATTTCAA
+ACGATCTAAGCCGTGCTCGTACAAAAGGGGTTCAAATGTGTAGACCTTCAAAGGTCTGTA
+GTCACGCGTTCTAGTAACTATATC
diff --git a/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa b/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa
new file mode 100644
index 0000000..1f00a66
--- /dev/null
+++ b/circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa
@@ -0,0 +1,168 @@
+>ctg_DNAA_ECOLI
+ATTGCAGGATAGTCCGGTAACACAAGCTTACAGCCCACTATATGGAATAGTCCCCTGCAC
+GGCCTCACTTAGATTACGTATACAGAGCGTGTTTATCAAGGGCTTCATGAAGGTTAATAG
+CTGTATATAGGACATTACATCCTTACATGTTTCTTCATACACTAAGCACCAATAAGGGGC
+GATCTACAGCGAAACCAACCCACGTCACTGTCCATCGTATAGACGGTCAGCTGTTGGGGG
+AGAACTCGTTGCGCTTCTACACCGGTTTATCAATGCCGGACACGGAGGGGGGGCAACAGA
+CAGAATACGACAAGAACGATAAAGTATCTAATAGATAAATTTTACACCGAGGCTTATATC
+GATTGAGGACAGCAAGGAGCAGGGACATACTAGTCCATCGTAATTCTACGGTCACGCTCT
+ATTCGTATGTTACTAATCGCGCCCCACATGTGCTAGAGGAAATACCCCTCTTAAAGGTGG
+CGTTGTCCACAAAACATAATAGTGAACGGTGACGGTGGATCAGGATTTTCAGTTTCGTAT
+GGCGTTGCATTCAACCCCGGTGGATAACAGAGTCTTAAGCGCGTATATCAGTTCACACCT
+TTGGGGACCAACATGGGTTGGACCTCCGGTCTGGTTGGCCTTAAAGCAGAACTGCTCGTC
+ACGAGGAGCTTTTGTGGAAATTGCAGGCGTCGTCAACGTGATTGGTTGATGAAACCAATG
+ACCCCACACCAGTGGCTTATTCGTTTGTTGCATAAGGGAATGTTCTTGTTCAAAGCTTCA
+TCCAAAGGAGCCGTAGAAGCTGCCGGAGTCCCGTAGCGCAACCGACGAAGCAAAGCAGGT
+CGATCTGCAGTGAGATTCATATACCGCGCGTCCAGGCGTTGCGCCTGCGGTTGGAAATCC
+CTACCCATCTATAGTGTGTTGTCCCGAAATTCCCGACGACGGTGCAATTGTCCTGTTGAC
+ATAAGTAATCATAGTAGGAAGCCGTCTGCTAGCTACGTCCTAGGTCGCATCGTAATTTGT
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGACTGCATATGGATTGGTCCTCGAGCCACCAGCCAAAT
+TGTGAATAAATTCCCTCTAAACTGCCATTCTAACTTTTAAAGGAGCACCGTACTAGGTGT
+CAAGCGCTCTATACTCTGGTAGTGGGAAGACCTACTCAAGACTAGTGTTAAGACTTATAC
+TATAGGGTACGGCCCGCTTGGTAACTCTTCCAAATTGGACAAGATGCTGTTTATTTAGAA
+CAGGCGACACAGCTATAGCATTTGAATCACCGCAGCTCTCACCCGAAGAGCGACCAGGCA
+TCTCAAATCAATTTACCTGGGGGTATGCCCACGGATAGGTACTGCATTCAGCGATACAAG
+CCAAGGTCGCATGCCTCGGATAGAGCCTTCCTCAATTGATAGGCACGGTATTGATGGTTA
+GACAGGTTTTGCTATTAGTCAGTGTAGCTTACCCAATCTGGTCCCACCCCCAATTCACGA
+GTTCCGGGCTAAGAAGTTATGGTGGATGAACAGGCAGGCGACTACCGTACTACCTTTACT
+ATAGAAATGAGGGTACGTTAGGTAGATACATCGTCACAAATCTAGCTAGAAGCAAACAAT
+ACATGCGAGCACTTTGCTTCCCGTCGACCGGCGACGCCTTCTTTGTGCCTGTCGAAACTG
+CGGAACACTTTCCATTGCTGACGGTGGTGAGTGAGGGAAGCCTTCTCGCTGCGGCCAAGC
+CCAGATCTTCCGGGATTATAAGGTAAAGGGAAGCACACGAGAACAGTGCGGGGCTTAACT
+TACAGCAGATTATGAGGCGCTGCTAGCAAAGGCAGATCAGTTTCCCTCACGATGCCTCGT
+GGTGTGTTTTGGGCGCACACCCTGTCGTTAATCGTGTTCCTAGATCAGTAGCCAGGGGAT
+TCAAGTTAACACGTGCACGATCGCAGGATCGTACGGGCCGATAATGCCAATACTTAGGGA
+TCCGTCCCAAGGCACGCATCAGATACCAATCCCCTACCTGGGAT
+>ctg_DNAA_ECOLI_2
+TGGGCTGGATAAGCTCGTGGAAAGCGTACGAGCCACAAAACCACATGAAATGTTACTGCC
+GTCCAGATCAGTAATCCCCAACTGTTCTGGCGGGGAACTAGAGCCTCTGGCTGACATGAA
+TAGCTGATGCTCTTCGGTATGTTCCATCTACACAGGTCACCTCATCGCTAGTCTATAGAT
+CAGGTTCCCACTGCGCCGAAGGGGCCATACTTTCTACAAAACAAAGGCATTCGTCAGAAA
+AAGAATACCTACCTAAGTGGCAGTAGAATTGTTTTGTATTTTTTTGCCCCTAAAAATTTT
+CAGGTGATCCTTACAAGTAAAGCTGAATCGTGTGGCCGCCAAAGCAGGGCGCCTACCGCC
+CTGTCATAGACTACACTCTGGTGGGTCTGACTCGTTCCATATATCGAAAGGTAAATACCG
+CACACGCAGCTTGAGCGGCTCACATTCTACTCCGGTGAATTCCCCCTCACAGGGCACCAC
+TCGTGCAGCCTCAGCACAGGCCCGCACGCTATCTGAACGTGAGCCGGTCCACTCGAATGG
+TACTTTAACAATGCTAGATCATTTATGTCCTGTCGCCGTGCCATCCGATCACGGGGACGG
+GCTGAAGTGAAATGTGTGCCTTGTTGGACTCGAAGGGGGCAATAAGGGTCGACATTCACT
+CCCAGCAATACAAGGTTATGAAGCCATGTCGGCATGTAGGCGCGTGCAATATTTCGTGAT
+TAAGAGCTCGCTGCTTTTTAGCGCCTTGCTCCAGCATGTCCTGCGGCCTGACGGGGTCTT
+GCCTATAGAGAGTCACCATCGGACGTACCAACGACATCTTTCCTCTTACTATCGCCCTCT
+TGTTTCAGAAAGTCCATCCTACCAGAAGATTGTATGGGAGTAGTTCCCTTGTCTACCGCG
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCATCGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGATATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAAGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAGTTAGTCCGGGCGGGGGCAGTGCTACAGAATCTACC
+TGGGGCACGGATCCAGCACTAAGGTGACCGCGATTAAGAGATCGCGTCATGCCCGAAACT
+TCGGTGCACCAGCAGGAGTGGGCGGTCGGACAATTCGTTGCCATCTGAAGGGGAAGGGTC
+CTAAATCAGCGCTAGACGGCCCCGATTGACGGGGGTGAGGGCCATCTAAGCCCAAAATCC
+GGCACCTGTCTACTCTCATCACCTAAAGCGTGGGAGTGCGAATAGAATGTCTTACTGAGC
+AAGGTAATATTGCGGGTGAGTCCACCGGGACCAGAGTTACAAGCCGCCACGGTACACTAG
+CCTAATGTCGCTGCCGTCGGGATTGCCGCCGCGGGTCAAACGTTGCCTCCCAGAGTCGTA
+GCTCGATGGCTTCGACCTGCGCGGCTTTTTCCGACTGCTCGACGCAATGCCAAGAAGGTC
+CCGAATATGACCTTTAATTGATATGCTAAAAAAGTGTGGATCCGCAGCGCTCCTGAGAAT
+ATTATATTACGCCGCATATCAACGACTGTAGCTCGTCATAAGGACCCTACAATCAGCTTG
+TTGCCCTTTGTGTAATTTCACGTGGCCATTGACTGCTGGACGCCTCGAACCGTGCGTGGC
+GTCACGATTAGATCCTTTGACAACAAGGTCTTTACATTTCTTCAAAAAAATGATGTTATG
+GGGCCCGGACGTTTTAGGGCATAAAAGGTCTGGCGAGGTTGATT
+>ctg_DNAA1_CHLPN
+TCGTCGTCGTACGCTCCGGTCGACTTGGTCGCTGTCGAAGACCGATTGATCTCGCGATTC
+GAATGGGGTGTCGCTATCCCGATCCACCCGTTGGTCCAAGAAGGTTTGCGATCGTTCTTG
+ATGCGACAAGTCGAACGATTGTCGATCCGAATCCAAGAAACTGCTTTGGACTTCTTGATC
+TACGCTTTGTCGTCGAATGTCAAGACTTTGTTGCACGCTTTGAATTTGTTGGCTAAGCGA
+GTCATGTACAAGAAGTTGTCGCACCAATTGTTGTACGAAGACGACGTCAAGACTTTGTTG
+AAGGACGTCTTGGAAGCTGCTGGTTCGGTCCGATTGACTCCGTTGAAGATCATCCGAAAT
+GTCGCTCAATACTACGGTGTCTCGCAAGAATCGATCTTGGGTCGATCGCAATCGCGAGAA
+TACGTCTTGCCGCGACAAGTCGCTATGTACTTCTGCCGACAAAAGTTGTCGTTGTCGTAC
+GTCCGAATCGGTGACGTCTTCTCGCGAGACCACTCGACTGTCATCTCGTCGATCCGATTG
+ATCGAACAAAAGATCGAAGAAAATTCGCACGACATCCACATGGCTATCCAAGACATCTCG
+AAGAATTTGAATTCGTTGCACAAGTCGTTGGAATTCTTCCCGTCGGAAGAAATGATCATC
+TGATTTAGAAGATCGCTAACGTATCTGAGGTGGTGAGTTCAGGAGCACCAGGCACAATCC
+CCACCTTAGTTCTTGGTAGAGCCAGCTAGGAGGGCGAGAGTATCGTTTGCCGACATGAGG
+GATTATACCGAACGAGGTGGATCACAGTTCTTTACCTACGGGTCGATAACAAGGATATGG
+CATTTGTACAGCTCCCTGGGTTTTGAAGCAACGAATCACAAGATCCCATGTTTTGCGAGA
+CGCGCGATGGTGGGTGCCTTCTTATTCTCTGTTAGACAACCCCCTCAACGCTCTCGGTGA
+ACATAGTGGTGAGCCGAACAGCGACGGTCGAGCAGCACAGCGCTTGTAGAAACTGGAGGC
+GTATTGTTCGGACCCTTCTCGTCCGAGTCCGCTCCTTTTATCGTGTTTTTCCAAGACCCG
+TCTGAATTAGCGCGGACGCCCCCAAGTGACTGAGTCCTATGTTATATTCGGGCCTGACGT
+AACGGCTCGGAAGCGACGATTGGGCTCCTCCGAACTAATGCGCTGCCATGCTGCAGAAGA
+TGGGAAAGTTAGTACCAATGCTACGGTTGTCACGCCCTGTTTTCTAGACATTGACCGTTC
+TAGACTACGCCACATTGGCCCGTTTACGCGACTTCTTGTGAGAAGCACCAAATCTGGTAA
+CTCGACAGTTGTTCGGACACTGCCTACCAAGCAAAAACCCAGGGAGGGGGCTCTACGGTT
+CATACGACAGTGATACCAAGGACCTCTTTCGTCCGATCAGGATGAAAGGAGTAACATTCT
+TGGGCTCACCGGCGGGCCCGGTCTAGGCTTTTAGCGCACCGGGAATGGGCATCCGACACT
+AATTGATCACACTCGGGAGCCGCATAAAGGTCGACTGATTCAAGCATGTCCAGAATGATT
+TGAAGAGTCCACAGCACCTGGTCGTGTTTCCCGCCGGTAAAACCGTGTTGACCTTCAAAC
+CAGATTCTCTGGTTGCTTCCCTTTTTCAAGATAGTCGCGATGATCCTGACAGAACAATTT
+TCAACTACGAAGCCCCTCACGTATTGCTCTCAATAAGCATTCGGATAAGCACGCAGACTG
+CTCGTATAGATCGTATCTCGCAACGATGAGACCGGGCTAGCGCATGGAACTTGAACACTA
+ATAGACTCATGGATCTTAGCTTGAAATACTGTTAAATGCGGGGCTTGCTCAGAGACACCT
+GAGCCTCCGTAAGAGGTACGACTTATACTGACCGAGCTGGTGGGACAGAGGTTTCGCCGC
+GGGCGCTCCTATTCCGGCTACATACCTGCAGTCTACTATTATCGACATTAAAGGGGAAAT
+CAAATTTAGACTCGCGCTACTGAATTTATTTCGCTGTCTGAGGTGAGAACTAAGGTTGAT
+CCTGGTTGGTGTCATCGTGGCGCTACGCCCGGTCGCAACCGCGCCGTAAGAATTCCCCCG
+GAAGGAAGTTGGAGAGTGTCTAGTCAAAGATTCGTGACGTAGACATAGCGGAGCATTCAG
+TAAAGCGGCCACTCCAAACAGGGAAAGCTAGGGTCACTACGTCACATCGCAAGGCGGCTT
+GCGACCCAGATTGTGCCTGAGTCGACCGAAAATTAGGTTTAATGGGTGATCCAGCTTCGG
+GCGTACAAAACGGCGAGCCACCTCAAACTGTGTACGGCACAGGTTTTGTAAGCCATGCTA
+ACTTCGGTAGCGTTATTGCGTATGTTTGACAACTGGGTCGAGCTACAAGGCGTAAATTGA
+AGACTTCATTCCACCAAGCTCGGGTGCTTATTTCCGGGGCGTAGCTAAATGTTGGCTGGC
+CTAACCGAGGAGGCGATCACCAAAGATAGTCGGATGGACTCGAAAGCAATCCCTAGAGCA
+AGTGTAAGGAGTGGGTACACTCAAAAAATCTATAGTCATATCGGACCGGTCAAAAATCTT
+GGCTGAAAAGGACGCCGCCTAGCAGGTTCCGATTCCCGGCGCTCTCCGACTAACAAGCAT
+AGACAAGTGCAAAATAAAGCATGATGCGAGCTTGGGAAGAATTCTTGTTGTTGCAAGAAA
+AGGAAATCGGTACTAATACTGTCGACAAGTGGTTGCGATCGTTGAAGGTCTTGTGCTTCG
+ACGCTTGCAATTTGTACTTGGAAGCTCAAGACTCGTTCCAAATCACTTGGTTCGAAGAAC
+ACATCCGACACAAGGTCAAGTCGGGTTTGGTCAATAATAATAATAAGCCGATCCGAGTCC
+ACGTCACTTCGGTCGACAAGGCTGCTCCGTTCTACAAGGAAAAGCAAATGCAACAAGAAA
+AGACTGCTTACTTCACTATGCACTACGGTTCGGTCAATCCGGAAATGACTTTCTCGAATT
+TCTTGGTCACTCCGGAAAATGACTTGCCGTTCCGAGTCTTGCAAGAATTCACTAAGTCGC
+CGGACGAAAATGGTGGTGTCACTTTCAATCCGATCTACTTGTTCGGTCCGGAAGGTTCGG
+GTAAGACTCACTTGATGCAATCGGCTATCTCGGTCTTGCGAGAATCGGGTGGTAAGATCT
+TGTACGTCTCGTCGGACTTGTTCACTGAACACTTGGTCTCGGCTATCCGATCGGGTGAAA
+TGCAAAAGTTCCGATCGTTCTACCGAAATATCGACGCTTTGTTCATCGAAGACATCGAAG
+TCTTCTCGGGTAAGTCGGCTACTCAAGAAGAATTCTTCCACACTTTCAATTCGTTGCACT
+CGGAAGGTAAGTTGATCGTCGTC
diff --git a/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa b/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa
new file mode 100644
index 0000000..128c9bf
--- /dev/null
+++ b/circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa
@@ -0,0 +1,75 @@
+>sp|P03004|DNAA_ECOLI Chromosomal replication initiator protein DnaA OS=Escherichia coli (strain K12) GN=dnaA PE=1 SV=2
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGA
+>sp|P03004|DNAA_ECOLI_2 Chromosomal replication initiator protein DnaA OS=Escherichia coli (strain K12) GN=dnaA PE=1 SV=2
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCATCGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGATATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAAGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGA
+>sp|Q9Z8M9|DNAA1_CHLPN Chromosomal replication initiator protein DnaA 1 OS=Chlamydia pneumoniae GN=dnaA1 PE=3 SV=1
+ATGCGAGCTTGGGAAGAATTCTTGTTGTTGCAAGAAAAGGAAATCGGTACTAATACTGTC
+GACAAGTGGTTGCGATCGTTGAAGGTCTTGTGCTTCGACGCTTGCAATTTGTACTTGGAA
+GCTCAAGACTCGTTCCAAATCACTTGGTTCGAAGAACACATCCGACACAAGGTCAAGTCG
+GGTTTGGTCAATAATAATAATAAGCCGATCCGAGTCCACGTCACTTCGGTCGACAAGGCT
+GCTCCGTTCTACAAGGAAAAGCAAATGCAACAAGAAAAGACTGCTTACTTCACTATGCAC
+TACGGTTCGGTCAATCCGGAAATGACTTTCTCGAATTTCTTGGTCACTCCGGAAAATGAC
+TTGCCGTTCCGAGTCTTGCAAGAATTCACTAAGTCGCCGGACGAAAATGGTGGTGTCACT
+TTCAATCCGATCTACTTGTTCGGTCCGGAAGGTTCGGGTAAGACTCACTTGATGCAATCG
+GCTATCTCGGTCTTGCGAGAATCGGGTGGTAAGATCTTGTACGTCTCGTCGGACTTGTTC
+ACTGAACACTTGGTCTCGGCTATCCGATCGGGTGAAATGCAAAAGTTCCGATCGTTCTAC
+CGAAATATCGACGCTTTGTTCATCGAAGACATCGAAGTCTTCTCGGGTAAGTCGGCTACT
+CAAGAAGAATTCTTCCACACTTTCAATTCGTTGCACTCGGAAGGTAAGTTGATCGTCGTC
+TCGTCGTCGTACGCTCCGGTCGACTTGGTCGCTGTCGAAGACCGATTGATCTCGCGATTC
+GAATGGGGTGTCGCTATCCCGATCCACCCGTTGGTCCAAGAAGGTTTGCGATCGTTCTTG
+ATGCGACAAGTCGAACGATTGTCGATCCGAATCCAAGAAACTGCTTTGGACTTCTTGATC
+TACGCTTTGTCGTCGAATGTCAAGACTTTGTTGCACGCTTTGAATTTGTTGGCTAAGCGA
+GTCATGTACAAGAAGTTGTCGCACCAATTGTTGTACGAAGACGACGTCAAGACTTTGTTG
+AAGGACGTCTTGGAAGCTGCTGGTTCGGTCCGATTGACTCCGTTGAAGATCATCCGAAAT
+GTCGCTCAATACTACGGTGTCTCGCAAGAATCGATCTTGGGTCGATCGCAATCGCGAGAA
+TACGTCTTGCCGCGACAAGTCGCTATGTACTTCTGCCGACAAAAGTTGTCGTTGTCGTAC
+GTCCGAATCGGTGACGTCTTCTCGCGAGACCACTCGACTGTCATCTCGTCGATCCGATTG
+ATCGAACAAAAGATCGAAGAAAATTCGCACGACATCCACATGGCTATCCAAGACATCTCG
+AAGAATTTGAATTCGTTGCACAAGTCGTTGGAATTCTTCCCGTCGGAAGAAATGATCATC
+TGA
diff --git a/circlator/tests/data/start_fixer_init_contigs.fa b/circlator/tests/data/start_fixer_init_contigs.fa
new file mode 100644
index 0000000..d7e0bc9
--- /dev/null
+++ b/circlator/tests/data/start_fixer_init_contigs.fa
@@ -0,0 +1,4 @@
+>contig1
+ACGT
+>contig2
+AAAA
diff --git a/circlator/tests/data/start_fixer_init_dnaA.fa b/circlator/tests/data/start_fixer_init_dnaA.fa
new file mode 100644
index 0000000..c33c265
--- /dev/null
+++ b/circlator/tests/data/start_fixer_init_dnaA.fa
@@ -0,0 +1,2 @@
+>dna1
+ACGTACGTA
diff --git a/circlator/tests/data/start_fixer_init_ignore_ids b/circlator/tests/data/start_fixer_init_ignore_ids
new file mode 100644
index 0000000..15a4df1
--- /dev/null
+++ b/circlator/tests/data/start_fixer_init_ignore_ids
@@ -0,0 +1,2 @@
+ignore_me1
+ignore_me2
diff --git a/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa b/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa
new file mode 100644
index 0000000..686ef71
--- /dev/null
+++ b/circlator/tests/data/start_fixer_max_length_from_fasta_file.fa
@@ -0,0 +1,6 @@
+>seq1
+ACGT
+>seq2
+ACGTGTGTCAG
+>seq3
+AA
diff --git a/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa b/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa
new file mode 100644
index 0000000..e0b6584
--- /dev/null
+++ b/circlator/tests/data/start_fixer_rearrange_contigs.expect.fa
@@ -0,0 +1,776 @@
+>promer_ctg1
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAACCTCATAAGGCGGCGCGGCATGCAGTTATTGAGCA
+ATAATGTCTCATAGTAGGCTCAGGGGCACGACTTATCTCCAACGATAATCCGAAGTTGCG
+ACTCATGTCGTCTGAGCTGCCGGGTTAACAATGGGCACAGTCATACTAAGCGCGTCGCAA
+TGAGCACAAGAACAACTCCGGCTGGTGATCTTTTTCGAGTTCGTTCGACCGCTGCGAATT
+TACTCCCACGCGCAGTCCGTAATGCCTACTGCTTTTGCCGACGAACGGAGGATTCCAGTT
+TCGATCTCCAAGCGGACGAGGCCCAGGGTGGGGCTCCCGCCGAACCGCCCTACAATGATA
+GGGTGGATTTGGCTACGTAATCGCTCAAGCATCGAAATCGCAGTGTTAGAAGGGGCGGAG
+GGACCACCGTACATCCGTGCTACGGAGCATTGCTTGACGTGTCTTGCCGCATTCCCAGAC
+TATGTCTATGACCGTGCCCAGCGTCAATTCCTTCAGCTCGCGTGACGCCACCATGGTAAT
+AGCCTAGCAAAGGATGAAGCTCACGCCGCGACATACTCCTCTGGCTCCTTTTATTGAGGC
+AGTGTCGTCCGAACCCGTTCGAGCTCATTTAGTTATCAACATTTAGGGACGCAAAACCCG
+TAATAGGGTCTCTATGGATTGTATCTTGACAGAGAAGTAGCTGATCAGGTCGGTCATATC
+GACAGCAGACCCCGACAGATTGAGCCGTCAACTAAGGGGAGCGCTCTAGAACCCAGTTGG
+AGGAGAGTCATTATTTGACCATGGGCGGAATTTCACTACGTCATGTGCCGTATAAAGGCG
+TCCGGGACGGATGTCGCCCCATGCCAACACTTCCCTTGCCTGTTGATCATGCGGAAATGG
+CCGCAGCAACTGGGGTTGTTTGTGGATATTACTGGTCTTGGACGGAAGATTGGGGAGTAG
+CCACCTTAAGTTAGTCGGGCATGATTGTGGGTTAGATTCGGACGAGTTTCTTCCGTAGCT
+TAGTGATCTTACGTTTCTATAACAGAATCGTTTCCAGACTCTTGGGCCGACCCTAGTATC
+CATCTCGCTGTTGCCGTACTAATCATACGCTAGCTACAGATTATCTCTCGATAGCGAGTT
+TGCGCCCGATCATGTACTCGTAGCCACGGAGGGATAGATGGAGATATGGGTCGTAAAGAT
+TCACGGATAGCGACAGGATAGCTCTTGCCCCAGGCTCGTGATGGCCTGCGATCATTCTAA
+CTATTTCCAGCGACATGGACCTCCTGTGGTCAATAAGATATTGGCCCGATTACAGGACTC
+TGACAGAGCGTCAACCTAACCTGCCTAAGCATGACTACTAGGTTGGCAAGCATGGTAATT
+TCCTAGTGTCACATCCATACTATGTCCCCTTTCCCAAGACACTCCAACAACTCATTATGT
+CAAGCATCCAAAACGACTATGCTGTCGCACTCCAGCTGCGACATGTTGCAGGGTACGTAT
+AAACTATATCTAGACGTGCCGTATTTATTAGCAGGCCTTCTTTATTTACGCTACGCCGAC
+TACGAAACTTCTACGGAGGTAAAATCGGTTAACATCTCGTGCGTACTGCTCTATTCAGGA
+GCACTATGTGGCGCACTAGGTATACCAGCCCCTGGCGTCCTGCTGATTAATGGTCAAAGC
+GAGTCTGGATTACACAGAAAGCCCTAATACCCTGTGATAAGATGTGCCCACATATAAAAT
+TCACTAGTCCGCAGTTGCCCGCCGGCCGGTTCTCCCCAGTCCAAAGCTAAGAGTGTGAGA
+CCTACCAGCAGAGATCTAGACCTTCCCATTTGATGTATCGCAACAGGCATTGGCCATGCC
+GGGCGCGGTATTAACTCTCCAGAGCTTAAGCGTTGAAATCCGCGCTGTCGTGGTCAACGT
+ATTGTGTCTGTGCTGCCTAGGGTGCGACATCCATGAATAACAGCCAGGTATAAAACGAAT
+TTTTTCATTGTGAAGTCTTCTGCATTACTTCGCTGAAGGTTTTCCACTGCGGTGATTCAC
+CACTATCGGCAGCTTAATACCACCACACAGGAGTGGGTACGTGCACGCTTACTATGTGCC
+GTAAAAGTCATCAATGACCCCTGAGACGCCTGCCCACCCGCAACGTGGAAGATATCAAGA
+TATCTGAGGTTATACAGTATATTTGCGGTCGGTTGCCGTCGCGGCGATTCCTTGTGTGTT
+GCACTTTTTAGAAGTTACTACAACCCACGCATGAAGTCTCGGTTGGACTACCCCTCTTAT
+AGTCATCATGCAGTGCGGGTGGCCTGCTTTCGCAAGGCGTTCAGAACTTGGCATAGTGTC
+GCGCGCGGAGTCCTTTGGCTAACGAGACCGGTTAATCAAAGGCACAGCCTAGTGAAGGTC
+GAAATAGTTCCGCCCCGATCATACAAAGATATCTCCACGAATTGGTGTCGTTTTCGAAGG
+AAGGCGGACGCCTAAATGTTTGAGAGTACATCAGTCAATTCTCCCGAATATCGGTATACC
+TGTTAGACTATGAACTCATACTTTTCTAACCACCGCTCATCTCGTTCCTTATCCGTTATG
+TCTATACTGAGTCTACAACATGGACATCGCAGGGAGCTCAATTGGCTATGGGAGCCAACA
+CTCAGGCTGGGTTACGCAACCCAGATGTCTGCTGGAGTGTTAGTGTAAGCTGTAATAAAG
+ACTCTCTCGTGTGCCCTTGAGAGACGACACCCACCGAACTGCGTTTACTCAGGGGCAGAA
+CATCCGAATTTTGCCTTCCCGCACATCAGTGGGGGACGACTGCGGGCAACAGTAAAGCTA
+GTCCGATCGCGCTCTGGATGCTATCCGATGTCGGGGGTGAATAATTGGTGAAACTGCCTC
+CAACAATTCAGAGTCTCTTCTCAACAAGGACGTGTACCGAGGCATAGAGGGGGAATGTCC
+GCCAGGCCCCAGAGATCTTTGCGACCTACATTGCACAGTATTGGTCGTGTTCAATCTTGA
+ACACTTACTATTCACCGAATTGGTGCGCTGTTGACGCTTTCTTCCGTAATCACCTCCAAA
+TCTGGGTGTTAGTAACGAGGCCGGCGTGCTTTGAGGAGAGAATACATGGCACCTTAAAAC
+GACGTACTAGCCTTAGCTTACGCAACCTAGGTTTGTGCACAGGCGTACGATCATTGACAG
+CCGACATCACGAATAACGCGCAAATGGCCTGTATCCTACACGCCTTGCCTGCCAAACCGA
+GTCATTGTGTTGTCGCCGAATGGCATTTCGGCTACGTGAAAATCTTAGATATTTTGCGTG
+GACAATGTTCGCCTACTTGAGTTCTTCTTGGGTATCTCATGTTATTTCCAGGATATAACG
+CGTGTCTCGAAATCGACCACAGGCCTTCCTCATACTCTTATGGATGTTACTGCTGTGTAC
+CGATATGGAGATTCTAGGAGAGGGCAATGGGTTCTTCTTACAATTGGCCGGTCGAGCTCT
+CCACGCCAGATCTCCACTTGACGCCGGGGCGGGAGAAAGTATTAACCTTCCATAGAGTCA
+TCATTATGAATGGCGCCTAATGTAGACAGGAAACGGGCTCAGCTACCGTCTACCGCAGGT
+AGTTCGATTCGAATTCACAACGTTTAGTTCTCGTTAAGTGGACACGATACCGAGCTTTGG
+TTCGAGTTGAAAGTTACGGTGGGTCTAGATGTAATGATCCGAACGGTGCCGCTAATGCGA
+TGACCGTAGGCCCACTCGCTGTGATAGTGGTCCCTCGTATCGCATTGATCCCTTCTGTTT
+CCGCACACTAACATGCATCCCCGGGAACTCCTTACACTTGCGCACCGAATCCCGCTGAAG
+ATGCACCTAGATATGTCCCCCTATGATACACTCCTTTTATCGCTTCGACATCAGCTGTGC
+ATTAAATGATTGTTTGTGCAAATTCATCACCTACTCTCAGAACGATGAAAACAGGTTGAA
+GTCTATGGTGTTTGCATGGCAGCTAAAGTCATCTTTCGTGAACGGCAATCTTGAGAGCTG
+TT
+>promer_ctg3
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAGCCTAAACCGTATGTGCCTCAAAAACAAGCGTACCT
+ACGCAGTCGGGTGTGTTAACTCAGGATCCAACCAGGTGCGGGGCGGAACCGTAGTTGCTA
+GATGTGGCGAAAGTTTTCCGTTCGATTGTTCCGGCTGGCTTCTCGACTGATGCTCGGCTT
+GACCCGCTTACGAACGGTCCGATAAAGTCCAACACAGTCTCCCCACTTGATGTTCCGGAT
+CAGTCCCATTGCTTGCCCCCGGGTGTTCGTTAACCCGCTGCTGGTTTGCCACGTCAAACA
+CCACCGCTCTCAAACGCGGACTCGAAACGGCTGCACCGTAAGGAAGAACCACACAAACAC
+GTATCTTAGGCCAGGTCAGCTGGGGGTTCGTAGTACTCCACGAACCCTACGATGGCCGCA
+ACCTTAAGAAGTTGTAAATATTGCGGTCAGCAGCCCTGACATGATGCAACGCGATTCACA
+TTGACTAAGTGTAGCATCACGACGCCAGCTGGTAGTTAAGTAATGCGTGGATGGCTTGGT
+CCGGGCTTCGCTGCACGTAGTTGGACGCATCAAAGCCAATTCGGGCCCGCCTTACCGCGT
+CCAAGTGGCACCATTGCGGCCAGTAACTCTGACACAATGATGGAGCCCTAATTCGGGCCT
+ATCCACAGCACTGTACATATTCCTCTCGTAGGCATTAAGATACGGACGGATCTATATTTC
+CTGGGTTCGAGTTGAGCACGTTGTCGCTCCTCATATTTTCTGTTGTATCAGCCTTGGATG
+GTTACCGCCGATATCCACCCGTCCTTTCAGAGTCTTCACGCGCTTAGGCGGCCTACTTAC
+CGGGCCCCTGCAAGAATCACAAGTTTCGTACGCCTGTATTTCGCTGAGAAAGCCACGGAT
+CTCTGGGTCATAGGGCTGATTCTTTCAATTTCTTTTTCGGTCATCCACAAGAGCGGTCGG
+ACAGCACGCTTGGCGTACATGAGTGATCGCGATCTATATTGGAAGAAATGCATCCACGCA
+CTCTTTGATGCATGCGGGGATTTAAGAGCGGTTCTGATCTACTATTTCGTATAGTCCGTA
+AGATCCGAGTTCGATCCTTTATAAGAGACGATTTACGTCCTTCATGCCTACAGCCCCAGA
+GTAGCTTACGGGGTGTCCTGGGTGGTGCCTGGCAGGAGCGTGCGATCTCCCAAGATGAAT
+CCTCCCTTGGCCTCATATCCTTTCTGTACTGTTTCCGTATGAGAGGTGGACATATGGTGT
+GTGAGGACTTCCCGCACTGTAGAACAGACTAAGTAATTAGAGAAAAAACCGTCATCGCGC
+CGAGTAAAGGGGAGCTCCGAGTTGGACAGGCTTCCCTGTCGAAGGCTACGGGAGAACTTA
+CAAGAGCGCGCGCTTGTATGTTCGCTCCATCCAAATGACTCGCGCGCCCCCGGTTGATCT
+CCAACAGATCTGCTGTGTACTCCTCCTCATATAGATGACCGCGGTCGGCTCATCCAACGG
+GAGGCGTGGCCGAAAAAACTCTCCTAACCTTCCCGCTTCTGGTGAACTTTATTACGAACT
+CTACGCTACTAGAACGGTACATGGAAGAAACGGAGAAACCTTTCGCAAGTCAGCGGATTG
+CGTTCCCTGTTGTGGTCCTGAAAGTAGTTAAGATATACCGATCGGCTTTTTACGAAGGAC
+ACTGGTCACCTGCATACCCAGGCTAATCCTATAAGTAGGGTGTAACTCCAAGGTCTAGCG
+TGTTCATTCCGTGAGATATATGCGTCCAACGCTGCTATAGAAGAAGTGCGACGCTGAGAT
+ATGTCTTCGTTCGCGTGAAAATGAGAAACTAAGAAAACACCACTTCTCCACGTAGGCCTT
+ACAGAAATAAGCGATGCTTTCTTGCTGCACCTTCGGATGAAGACTAGGTATAAACAATAT
+TAGAATGAGGTCCGTTCTATCGGCGGAATAATTGCGCTCAAAATTTACCATTGGGGCCAA
+CGCGCCCACAGTCGAGACCGAAGGGGATGGCCCTATCACGACTGGCGGAAGCCTCCCGAG
+GAGAAGAGTCTCCTAAGACGATTTATGTGAGCACTGCAGTAGTTTGAAGGCGACCAAGTC
+GGTGCGGGGTCCTGACATGAGAAGTCTCCTACCAGAGCCAGACCCTGTTTCGAATGGTCT
+ACAATCCTTCTCGTCGGAACCATCCCGTGTGTACCACCACGCTGAAATGACTAGTCTATG
+TGAGGAACCACCTTACCGTCCCATTGTCATATCTCTCCTCGTCGAGATAAGCTCGACGCG
+GCAGTGTAAACATGGTCGATCGTTGGGTGGGGGGACCTTGGTGTAGAATATGCGGAGGTC
+TCAAACTCGGGGTAGAGAGGCATTGGAACATCTGGGCCGGCTATAGGTATAATCTTATAG
+ACCAATTCATGGCGATTAGGCCGGTCGGCTACGGCCTTAATCTCACAGTTGCGTGAATGA
+CCTACGACCATCTAGATTGGATAATAATCCGGTAAGCGTTCTCGCCAACTATTGTGGTAT
+TGGATGGAGTCAGAGCCTCGGAAACGACACCTGCCGTAAGAACGAGACTACGTGCAACAC
+GCGAGGTGTCGCCCTGGTGTGCAGAATGCCTCAAACATCTTGCTCCTACCTCAGACTGAT
+ATGGAACTACTGCACGGGCAGTTCCGAATGGCAAGAAGGGATTGCTGCTACCTGTTGTTG
+ATTGAACATTGGATAAGAGGACAGCGCAAACGAACGAATATGCTACCAAAAGATATTTAG
+AACGGACAATTACGGGAGAATAACGGGTGACCATTTGCCGAACCACTCCGAATTCTAAAT
+TCTGGCTGGTAAGGGCTAATTGCTATATTTGAAGCAGCGCACTTTAAGCCGGGCACCATC
+AATAGGGGATCGTCACCATTGAGGAACTTCAGCTAGATGCGGGGCAGCCTATTAGACTAC
+GATGATATCAGGCGACTACGTAAGGACGAGGATGCTCGCCTCTCGGTTAGAATTCGACCC
+CTAGGAAGGCCGCGCAAGCCAGTGTGCCTATGGGCTATCACAGCGTTGTTCCAGCAGACC
+CCATTCTTGCGTTAAGGGAGTTCAGCCCATTTCAGCTTGGGGGTTCTTACAGGGACATAG
+TAAATGTACGGGCACGGAGTTTGCGTCTTGTTTTGGGGCTTGGAGTTAATCGTTGATATT
+ACGGATACTTAACCTACCAGAGTTGGTAGTAAGGACTGGGTGTGTGTTTTTTCCAGAGCC
+AGCTGGCTTTGGTCGATAAGACCTTAAAATCTGCAATTTTTGTCGCAACGCGCAAACGCC
+CAATCCTCCCCAGGTCTAAGGCCAGTGAGATGAGTTTCACCGCTAACGTTTAGGCGGCAT
+CACTGGCTAGCAAACGTAGGGAACCGGGCCCTGCCCCGAGCTTGCTATACTATGCAGGTC
+GATCTTAATAGAGCTGACGCAACTTGGAGGAACCTGACTTGGGCACTTCTGACAAGCACA
+ATAAGATTGCGGATCAGTAGTTCTGATCAGAACATTGACGCACCCTGACGGGCAGGATCA
+TTGTTATGAGAATTGCCTATGCGTCGCCCGTCTAGTAGTTACACCCCTATAACCACATTA
+GGGCCAGAGTCGCTTGGAAAGCCCCTCGCTGATAAATATGGAAGACCCCGAGGCTAGATT
+GAGTGCGGGCAAAGACTCCCAATGCAACCTGGCTGCAACCCAGCGGTCTAAGATAAGTTG
+TCAAACCCCATTTTAAGTGAATGAAGCCGGACCTAAAGCGGCCCGGAGTAGCTTTCACAA
+TACCTCAGTCATGGTGATGGTGTGCTAGGTCCTCGATTTAGGTTTGGATAGACCAATTTA
+GCACCTCAAGTAGAACGGGATCATGAACTAGGACAGGAGGGAAACTGGGCGCAGACTCCA
+AGATATCGCGTCCGAACAATGGTTTAGAGCCAGCCTATTGTGTGAAGGCTATTACGATGC
+GTTGAACACGTACTAACGTCGATCTCTAGACATGTTCAGGTCTAATTCGCGCATTCCGGG
+GCAA
+>promer_ctg2
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCATCGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGATATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAAGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAAGCCCACCTGATCTGCGTCTGGGGAGCCCGTATCGA
+GTAGGGACTTCGAGTCGATTCGCAAAGCTAAGAAGTCGGACATGTGTTGCACCATAAGTG
+TGAGTGCAGTTCACGGTCCGCGGGTTCTCATCCATGGGCTAATCCAATAGAGGGTACGGG
+ATGAAGGAGTGAGCTGGACTCGCTCGTGGTCGTGAATAAGCGTTTAGTACATGAACATCG
+TTCTTCAGTTTATGCACGGACGCATCTTTCGCATAGCGATTATAATCTATTTTCCAAACG
+CTCCCACGATGCTGGGAACAGCCACCGAGCGCAAAACGCAAAAGCGCCGTATCCTACCTG
+TCTCCTTGCAACATGGAAAGGTCTGGACGGTAACTTAACTCTTAAGAATTAGATCGAGGT
+CGGGCCAGAATAAGTTATACCCTATACGTATTGTGTCTTATATAGAACTGGGCGTGCGTG
+TTGTGGGGAGGTTGGTACCCTGCTACGTTGTGACATCGTAAGCGGCGAGCAAATGGTAAT
+TCTGGGCATCAATCTTAGGATGAAGAAGGAGTACGTCGGTGGACATGTGCGGATTAATCC
+CGTAGGGAGGATGAGTGTTGAGGATCCGTCCTTCTGATCGCTCGACTGACCGCAATCCGT
+ATAGTACAGTTCTCTCACAATGAAGTAATGCCGCCGCCCTCTCCGCTAAAGGATAGCTAG
+ACAGGCAAGTTTAATGAACTTAGATGGCTTCCCTCAGAATACTAGTGATGTTATCATCGT
+CTACGATTTATTGCTTCCCAGAGATAGCGATATGTAAAATCTAATCACGCGGTATGCCGC
+CGTCGTCACTGAAAGAGGACTAAAATAAGTGACCCAACAGTGACCGCGCGGTCCATCTAT
+TCATAGCAAGGCACCGGCCCGGTTCATCAAATTAGGGCCTACATTGACGCATAGCTACCC
+GTTCTCATCCGAGATTTGGCGCCGTCTGTGCAACGTCCTTTGCCGCCTAAGCGTCGGGCG
+TGGGATGCGCTGCGAGCTCAAGTGATCAGTCTCCATAGGATTGAGTGCCTTAACTTTGCT
+GGTTTCTGATCCCATGGACGACGTTCGTCGCAACAAGGAGGAAGAGCCGACTTCTGCGCT
+TCCGGGGCTAAACCTTGTGACAGCCTCAAACAGAAGATGAGCCAGTCCAACGACATTCGA
+TCTAAGAGCTTTCCGGTCACACAGCTTCCACAGTCCACGTTGAGGCACCGGGGTGGCGCG
+GTAACTGGCATCAGCTCTAAACTCGGAGCATCTGACCGGCGTGTCAATGGCACTTGCAGC
+AATGCATACCTAAGCTTGAGTTTTCATGCGGACAATTTCCTAGGATGCAGGTATTCTGAC
+CTGAACCTAGGCGATTATGACGCACGAGTTAGGTGTCAGTGCCAGCGAACTCATACCCCG
+ACGGACAAGGGTGCGTTACTCTAAGCTGTGGGTTGTATGCCACTATCTACCCTGTTTTCC
+TCGCAGATATCCTTTGCACACGCCCTTGCTCTCACCTATTTAAGTGCCGTGTTCTGCAAT
+CTAGTTGGAACCAAACCAAGTTAGAATATGGTTCGCGCGATACGCTAGAACCACAGTACG
+TAAAAACGAAGGAGTTTGTTACCACTGGTCAGATACCCAATAGAGAATTTCCCTGGGTTC
+TGTAGTTTGAACGCGTTCGAGCGAGTCAAGTTCAGGGTCCCGTGATGAACCGGGAAGCGT
+TTCTATGCATCCGTGGAGGGCCCTGTGATCACGAAAGGAACTAAACGCAACATACGACGT
+GGGTGTAGACGCAGCTTTGCGGCCCACGTTATTAGGCCTTTTGTCCGATGCCGGGGACAT
+CATTTCAGCAATATTTCGCCATCTCAAGGGGGGCGTCCAGACGTTCAATATGACTAGCGC
+AGAGGCAAAGTGCAACTAAGCACGCGCCAGTCCCAACTTACCTACAAGACATTGCTTAAA
+GGTGCCAATCGAACTACAGAGGGCTTAGGCTCGATACCGATGCCGAGTACTGTTCGGTCT
+CTCCTGATTTAACTTAGACCTTATGGTCTCATACAACAATACGACGAATACCATCAAAGA
+ATCGCACACGTCCTACTAGGACGCGCACACGGTAGCACCCTAAGTAGATCTCAGAGGAAC
+GGAGGGAGCACAAGTGGTCTCGGGTTGCAATTAATATCAGGTCCCTACATTGAGGGTCGG
+CCCGCCAGGTTTGGCTCTAATTTTGGTCACCCGGACCGTAGCCTACAGAATAACGGTTCC
+TATTGTCGGTCCTAGGAGGAGTGGGTTGGACCTAACAGGACTAACGTCCTATGACACTAG
+CCATGTTTCACCCGCCTCTGCACCCTATCATAACTTTAGCATTGAAATTAATGCCGTGAC
+TTACTACAAAGGGTCCTAACCCATTCAAGCTCTTTAATCCTGATCTCTCCCACCTAATTT
+CATTGCCCCAGCCCAGTATTCGAAACTAACTGTCATAGAAATGAGACTAGCCTATGCCCC
+ATCCACTAAGCTCGCCTTCGTGTTGACAAAATTTGACGGTCGTTTTTCTCACCGTACCCG
+TTCGGAACATACAAGTTAGTGGCCTATACCGTACTCTAGAGCCAGTGAAATGCAGGTCAA
+ATATTCTGTACCCCACGCCGATGGTGTAGATCTCTTCCGGGAAGTCATGCGCGTGATCTG
+TACGTTCCAGCTCGAGTGTTACGCGTAACTGGCAACTAGCGACCGAATTACCCTCTTCAC
+CAATGAACTTAGGGCCAGGATGTCGACTTGTTATTTGGTTTTATCGACCTTACGGTAGGC
+GTAGTGGCCCGGTGTTGACCACCAAGAGTTACTAGCTGACGGCGTACCTGCAGTGGCTTC
+CCCCACTTTGGTAGTGTACGCCCTACTGGTTGGCGCTCTACAACTGAATCTGGGAAGGCT
+ACATGACCTGACACGTCAGATAGCTTCTCTCCTTCTGCTCTGTGATTTAATGTAAGTCTA
+TCCATGATAATCGTGACCCTGGGCCTCGATAACTCGCTTAGTTCCGTGCGAAAAGGTTTG
+CGTTTTTACGATCACCGCCAAGAACTCGGAGCCCCAGTATTTAATGCGGGTTCTCTTGCC
+TTTGCTCAAAGTCTCCCAGACTGTTTTATTGCACCATCAATAAGCACCACATGGTCAAAA
+CGCCGGATCCGGGGCCCTCGCTGACGAGGTCCCGGGGAGCAAGGATTTCCTTGATAGAGG
+GAGTTATGGTTACCGAAAAGCTAAGTAGGTACGGGGACGAGCGCCAACCGGCAAGTCGAC
+CCGAATAGTTATATGGTCAGTAGAAACGACGGTTTCTCGCTGACTTAGCGGCCACGGTAC
+CGTGGCAGGATGATTCCCTTCGCAAGGCCGGGTTGCCCCCCGCTGAATCTCGTCAACAAC
+TAGAGATGGTCCACGACTTGTGATATATGGCGTGCTGGGGCGATCGTTGCGCTTCCCCGA
+GTACGGTCGTCCGTAGGCAAGGCAATCCCGCGCGACTCGGTACACCAACACGATACGGGT
+CGGTGTAATCTAAGTTGGAGGGCGGAATTGAAGTGGGGCAACTAATTAGAGCGGCGATAC
+AATAGGTCCCTCCCTGCCGTCACGGCAACAGCCGACCCTCCGACTCGGTTAGCGATCGGC
+TTTGCCGTAACGAGGAGGACGAGTACCAATTAATAATTCATAGCGTTGGCCACTGGCAGT
+CCTCGCACGATAATATCTAGGGGAGGCCGCGTGGCGACCCCGATCCCCAAGAAGCTTTGG
+GACTCCCACTCAGTAAGCACCTCGATTTGCTCCGGATTTTCACACACATATACAAGGGTC
+AGGACTGTCCAACCCTTCAAAACATTCTCGGCACTCTGCGCGATAGTTCCGATTCACCAC
+TTAAAATGATACGCTATGGTACGGTAACAATCCGATGCATTCGGAAAGCCGAACGATGGT
+GAGAGGTATGAGAAGGATTCTGGGTGCTGGAATGCGGGCGAGCCCTTGATTGTTGTCCAA
+TC
+>prodigal_ctg2
+ATGCGTTATATTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTC
+GCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTG
+GGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAG
+CGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTG
+GATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGAC
+TACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCC
+GCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGC
+CCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGC
+TGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCC
+AGCATGGCCACCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAG
+CAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTG
+CTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGC
+ATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGG
+GATACGCCGGCGACCATAGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTG
+ATCGAGCACTGGCAACGCTAATCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCG
+GGGTTAATGAACCGGCCAAAATGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCA
+ACCAGCCTCGCCCAAGTTCCCTGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGT
+CTCGTACGGCGCCGGTTAGGATCATCATGACTTCGGCAGAACCCCACACTGTCATATCAG
+CCCAGCTCGCATCCAAACGGCCTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCC
+CCTACAACAGTTGTAGCTGGAATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGG
+AAAGGCTCATCTCAAGATTTACTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAG
+ATGCGCGAGGTCGGAACTGCCTCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCAC
+CTGTGTTTGTGGTCCCCCCTGTCTGTCCGACTCATATTAATTCATTATATTAATTGGTAT
+ACCTGCATTAGATTATGCCATTAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAA
+ATGTAGCGCTAAAAGGCGCCGCCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTA
+CGGTATGAATCTCGGATCAAGTAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCAT
+GTACCCATGGATCCTTCGCGTCTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACAC
+ACACCTCTTTACTACGTCTAAGATATATTTTCAACTAACAACGGAGACTCTCGATTCACG
+AAATCCGTACCTATCACTATCGCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTA
+TTCCACGTATGGAGGATCACCAGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTAC
+CGCCCACCCGGGCTGGACGGGATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAAC
+CACCATTCTCTAAGCATCAGTATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGA
+TTCAAGAGTGAACATAGTTCGAGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAAC
+CGACTAACGGACAAGTATTACGAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTA
+CTAGTGCGGGCCGGAACTTGCGGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGC
+GCAACAGGCTCCACCTCGCCTCACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATAT
+AGTATTTTTGGCTGGACGCGAATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGC
+CCATGTGATTGAAAAGCGTACTCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCC
+CTCCCCACCGCGCTTTCTGTAAATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTA
+GCATGTTTGAAAATTTCCTGTCGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATG
+ACGGAAACCTTGGCCCGACAGGCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCT
+CCGCCGATCTGTATACGCCCTGTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCT
+CCCATAACACAATGGCGGATTTTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTT
+CTGAGTCCTCCTAACTGATTATCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCA
+CGCAATGGCAAGTCACAGACTGTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTAT
+CAAATTCCTAAGCAAACGGGAGTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACG
+TGTCTCGCTAGTGCCGGGTAGATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATT
+CTTTTTAGAACACCTTGAAATTTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAA
+GCATTCGAGCGAGAGTAGTTCGGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTA
+AGACTGGCCGGGTCGGGGGACAATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGT
+ATCTCGACAAGGACGCGCGGTAGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGC
+TTATCAACTCTCAGATCTTTAGATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCAT
+CTATCTTACAACCTGCCAATCACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCG
+AGCAGTTGCGGATCCCTCTTATGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCC
+CCATAGCCCCCGAAATAGTTTCGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGG
+ATAAACCTGGCATCGCTTCAGACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGC
+TTAGGGATCTCCGATGCATCTACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCT
+GGTCTGAGAGTCGGAATAGTCGGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTG
+TAATCTGAGTTGGGAGTTGCTAAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGG
+TGTCGACGTGATTCTGTGAGAGTCTCAGCTCTGAAAACAACTCTAATAGTTAACGTGGCT
+TTAACCGCTAGGTGACACGTAACACACCGCTATGCACTAACACGGGCTGAGTACGGATAA
+TTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTGCAC
+GGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGAGTT
+CCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAACAC
+TATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAGACT
+TTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGTTGA
+GCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTAATA
+TTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCCATA
+GACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGCAAT
+GGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATAACC
+TGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCCCGC
+GGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTCTCC
+GGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAAAGA
+GTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGGTTT
+TCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCCTAG
+ATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAACGT
+GAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGATCA
+CCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAACGT
+GCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACTAAT
+TTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAAGCT
+GAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTATAC
+CGCCTAAACCGTATGTGCCTCAAAAACAAGCGTACCTACGCAGTCGGGTGTGTTAACTCA
+GGATCCAACCAGGTGCGGGGCGGAACCGTAGTTGCTAGATGTGGCGAAAGTTTTCCGTTC
+GATTGTTCCGGCTGGCTTCTCGACTGATGCTCGGCTTGACCCGCTTACGAACGGTCCGAT
+AAAGTCCAACACAGTCTCCCCACTTGATGTTCCGGATCAGTCCCATTGCTTGCCCCCGGG
+TGTTCGTTAACCCGCTGCTGGTTTGCCACGTCAAACACCACCGCTCTCAAACGCGGACTC
+GAAACGGCTGCACCGTAAGGAAGAACCACACAAACACGTATCTTAGGCCAGGTCAGCTGG
+GGGTTCGTAGTACTCCACGAACCCTACGATGGCCGCAACCTTAAGAAGTTGTAAATATTG
+CGGTCAGCAGCCCTGACATGATGCAACGCGATTCACATTGACTAAGTGTAGCATCACGAC
+GCCAGCTGGTAGTTAAGTAATGCGTGGATGGCTTGGTCCGGGCTTCGCTGCACGTAGTTG
+GACGCATCAAAGCCAATTCGGGCCCGCCTTACCGCGTCCAAGTGGCACCATTGCGGCCAG
+TAACTCTGACACAATGATGGAGCCCTAATTCGGGCCTATCCACAGCACTGTACATATTCC
+TCTCGTAGGCATTAAGATACGGACGGATCTATATTTCCTGGGTTCGAGTTGAGCACGTTG
+TCGCTCCTCATATTTTCTGTTGTATCAGCCTTGGATGGTTACCGCCGATATCCACCCGTC
+CTTTCAGAGTCTTCACGCGCTTAGGCGGCCTACTTACCGGGCCCCTGCAAGAATCACAAG
+TTTCGTACGCCTGTATTTCGCTGAGAAAGCCACGGATCTCTGGGTCATAGGGCTGATTCT
+TTCAATTTCTTTTTCGGTCATCCACAAGAGCGGTCGGACAGCACGCTTGGCGTATGTCAT
+CAATCCGGCGCCGGCACGCCGCCGCTTCGCTCGACACCCCTGCCGTGGGCGGCAGGCACG
+AACTCGGTCAGAACTTCCTCGTCGACCGAGGTGTATGCACAAGGATCGCCGAGGTCGTCT
+CCTCGACGACGGCCCATCCGGTCCTCGAACTGGGCGCCGGTGACGGTGCCATCACCCGGG
+CCCTGGTCGCGGCGAATCTCCCGGTCACCGCGCTGGAACTCGACCCCCGGCGGGTCCGGC
+GGCTCCAGCGGACCTTCGCCGACGGGGTCACCGTCGTGCACGGGGACATGCTCCGGTACG
+ACTTCGGGCCGTACCCGCACCACGTGGTGTCGACCGTGCCGTTCTCCATCACCACGCCGC
+TGCTCCGGCGCCTGATCGGCCAGCGGTTCTGGCACACCGCGGTGCTGTTGGTGCAGTGGG
+AGGTGGCCCGTAAGCGGGCCGGTGTGGGCGGCACCACGATGCTCACCGCAGCCAGTTGGC
+CGTGGTACGAGTTCACCCTGGTGGAGCGGGTGCCGAAGACCTCGTTCGACCCGGTGCCGA
+GCGTCGACGGCGGCATCCTCGTCATCGAGCGTCGATCCGCGCCGCTGCTCGACGACCGCT
+GCGTGGGTGACTACCAGAACCTGGTACGCGAGGTGTACACCGGTCCCGGTCGTGGTCTGG
+CCGCGATTCTCCGTACCCGTCTGCCCGGTCGTGAGGTGGACGCCTGGCTCCGCCGCGAGC
+GGGTGGACCCGGCGGCCCTGCCCCGCGACCTCAAGGCCGGGCACTGGGCATCCCTCTACC
+GGCTCTACCGGGAGGTGGGTACTCGGCCCGCCCCTGCCGGCCGGTCCGTCCGGGCCCGGC
+CCGGATCCGTCGGCCCCGACCGCTCGCTCCCTCCGCGCGGCCTGCGATCCGGTCCGCCGA
+GGGCTCGACGACGTGGTGGAGGCGCCTGAGACAGGCTTCCCTGTCGAAGGCTACGGGAGA
+ACTTACAAGAGCGCGCGCTTGTATGTTCGCTCCATCCAAATGACTCGCGCGCCCCCGGTT
+GATCTCCAACAGATCTGCTGTGTACTCCTCCTCATATAGATGACCGCGGTCGGCTCATCC
+AACGGGAGGCGTGGCCGAAAAAACTCTCCTAACCTTCCCGCTTCTGGTGAACTTTATTAC
+GAACTCTACGCTACTAGAACGGTACATGGAAGAAACGGAGAAACCTTTCGCAAGTCAGCG
+GATTGCGTTCCCTGTTGTGGTCCTGAAAGTAGTTAAGATATACCGATCGGCTTTTTACGA
+AGGACACTGGTCACCTGCATACCCAGGCTAATCCTATAAGTAGGGTGTAACTCCAAGGTC
+TAGCGTGTTCATTCCGTGAGATATATGCGTCCAACGCTGCTATAGAAGAAGTGCGACGCT
+GAGATATGTCTTCGTTCGCGTGAAAATGAGAAACTAAGAAAACACCACTTCTCCACGTAG
+GCCTTACAGAAATAAGCGATGCTTTCTTGCTGCACCTTCGGATGAAGACTAGGTATAAAC
+AATATTAGAATGAGGTCCGTTCTATCGGCGGAATAATTGCGCTCAAAATTTACCATTGGG
+GCCAACGCGCCCACAGTCGAGACCGAAGGGGATGGCCCTATCACGACTGGCGGAAGCCTC
+CCGAGGAGAAGAGTCTCCTAAGACGATTTATGTGAGCACTGCAGTAGTTTGAAGGCGACC
+AAGTCGGTGCGGGGTCCTGACATGAGAAGTCTCCTACCAGAGCCAGACCCTGTTTCGAAT
+GGTCTACAATCCTTCTCGTCGGAACCATCCCGTGTGTACCACCACGCTGAAATGACTAGT
+CTATGTGAGGAACCACCTTACCGTCCCATTGTCATATCTCTCCTCGTCGAGATAAGCTCG
+ACGCGGCAGTGTAAACATGGTCGATCGTTGGGTGGGGGGACCTTGGTGTAGAATATGCGG
+AGGTCTCAAACTCGGGGTAGAGAGGCATTGGAACATCTGGGCCGGCTATAGGTATAATCT
+TATAGACCAATTCATGGCGATTAGGCCGGTCGGCTACGGCCTTAATCTCACAGTTGCGTG
+AATGACCTACGACCATCTAGATTGGATAATAATCCGGTAAGCGTTCTCGCCAACTATTGT
+GGTATTGGATGGAGTCAGAGCCTCGGAAACGACACCTGCCGTAAGAACGAGACTACGTGC
+AACACGCGAGGTGTCGCCCTGGTGTGCAGAATGCCTCAAACATCTTGCTCCTACCTCAGA
+CTGATATGGAACTACTGCACGGGCAGTTCCGAATGGCAAGAAGGGATTGCTGCTACCTGT
+TGTTGATTGAACATTGGATAAGAGGACAGCGCAAACGAACGAATATGCTACCAAAAGATA
+TTTAGAACGGACAATTACGGGAGAATAACGGGTGACCATTTGCCGAACCACTCCGAATTC
+TAAATTCTGGCTGGTAAGGGCTAATTGCTATATTTGAAGCAGCGCACTTTAAGCCGGGCA
+CCATCAATAGGGGATCGTCACCATTGAGGAACTTCAGCTAGATGCGGGGCAGCCTATTAG
+ACTACGATGATATCAGGCGACTACGTAAGGACGAGGATGCTCGCCTCTCGGTTAGAATTC
+GACCCCTAGGAAGGCCGCGCAAGCCAGTGTGCCTATGGGCTATCACAGCGTTGTTCCAGC
+AGACCCCATTCTTGCGTTAAGGGAGTTCAGCCCATTTCAGCTTGGGGGTTCTTACAGGGA
+CATAGTAAATGTACGGGCACGGAGTTTGCGTCTTGTTTTGGGGCTTGGAGTTAATCGTTG
+ATATTACGGATACTTAACCTACCAGAGTTGGTAGTAAGGACTGGGTGTGTGTTTTTTCCA
+GAGCCAGCTGGCTTTGGTCGATAAGACCTTAAAATCTGCAATTTTTGTCGCAACGCGCAA
+ACGCCCAATCCTCCCCAGGTCTAAGGCCAGTGAGATGAGTTTCACCGCTAACGTTTAGGC
+GGCATCACTGGCTAGCAAACGTAGGGAACCGGGCCCTGCCCCGAGCTTGCTATACTATGC
+AGGTCGATCTTAATAGAGCTGACGCAACTTGGAGGAACCTGACTTGGGCACTTCTGACAA
+GCACAATAAGATTGCGGATCAGTAGTTCTGATCAGAACATTGACGCACCCTGACGGGCAG
+GATCATTGTTATGAGAATTGCCTATGCGTCGCCCGTCTAGTAGTTACACCCCTATAACCA
+CATTAGGGCCAGAGTCGCTTGGAAAGCCCCTCGCTGATAAATATGGAAGACCCCGAGGCT
+AGATTGAGTGCGGGCAAAGACTCCCAATGCAACCTGGCTGCAACCCAGCGGTCTAAGATA
+AGTTGTCAAACCCCATTTTAAGTGAATGAAGCCGGACCTAAAGCGGCCCGGAGTAGCTTT
+CACAATACCTCAGTCATGGTGATGGTGTGCTAGGTCCTCGATTTAGGTTTGGATAGACCA
+ATTTAGCACCTCAAGTAGAACGGGATCATGAACTAGGACAGGAGGGAAACTGGGCGCAGA
+CTCCAAGATATCGCGTCCGAACAATGGTTTAGAGCCAGCCTATTGTGTGAAGGCTATTAC
+GATGCGTTGAACACGTACTAACGTCGATC
+>promer_ctg4
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAGCCTAAACCGTATGTGCCTCAAAAACAAGCGTACCT
+ACGCAGTCGGGTGTGTTAACTCAGGATCCAACCAGGTGCGGGGCGGAACCGTAGTTGCTA
+GATGTGGCGAAAGTTTTCCGTTCGATTGTTCCGGCTGGCTTCTCGACTGATGCTCGGCTT
+GACCCGCTTACGAACGGTCCGATAAAGTCCAACACAGTCTCCCCACTTGATGTTCCGGAT
+CAGTCCCATTGCTTGCCCCCGGGTGTTCGTTAACCCGCTGCTGGTTTGCCACGTCAAACA
+CCACCGCTCTCAAACGCGGACTCGAAACGGCTGCACCGTAAGGAAGAACCACACAAACAC
+GTATCTTAGGCCAGGTCAGCTGGGGGTTCGTAGTACTCCACGAACCCTACGATGGCCGCA
+ACCTTAAGAAGTTGTAAATATTGCGGTCAGCAGCCCTGACATGATGCAACGCGATTCACA
+TTGACTAAGTGTAGCATCACGACGCCAGCTGGTAGTTAAGTAATGCGTGGATGGCTTGGT
+CCGGGCTTCGCTGCACGTAGTTGGACGCATCAAAGCCAATTCGGGCCCGCCTTACCGCGT
+CCAAGTGGCACCATTGCGGCCAGTAACTCTGACACAATGATGGAGCCCTAATTCGGGCCT
+ATCCACAGCACTGTACATATTCCTCTCGTAGGCATTAAGATACGGACGGATCTATATTTC
+CTGGGTTCGAGTTGAGCACGTTGTCGCTCCTCATATTTTCTGTTGTATCAGCCTTGGATG
+GTTACCGCCGATATCCACCCGTCCTTTCAGAGTCTTCACGCGCTTAGGCGGCCTACTTAC
+CGGGCCCCTGCAAGAATCACAAGTTTCGTACGCCTGTATTTCGCTGAGAAAGCCACGGAT
+CTCTGGGTCATAGGGCTGATTCTTTCAATTTCTTTTTCGGTCATCCACAAGAGCGGTCGG
+ACAGCACGCTTGGCGTACATGAGTGATCGCGATCTATATTGGAAGAAATGCATCCACGCA
+CTCTTTGATGCATGCGGGGATTTAAGAGCGGTTCTGATCTACTATTTCGTATAGTCCGTA
+AGATCCGAGTTCGATCCTTTATAAGAGACGATTTACGTCCTTCATGCCTACAGCCCCAGA
+GTAGCTTACGGGGTGTCCTGGGTGGTGCCTGGCAGGAGCGTGCGATCTCCCAAGATGAAT
+CCTCCCTTGGCCTCATATCCTTTCTGTACTGTTTCCGTATGAGAGGTGGACATATGGTGT
+GTGAGGACTTCCCGCACTGTAGAACAGACTAAGTAATTAGAGAAAAAACCGTCATCGCGC
+CGAGTAAAGGGGAGCTCCGAGTTGGACAGGCTTCCCTGTCGAAGGCTACGGGAGAACTTA
+CAAGAGCGCGCGCTTGTATGTTCGCTCCATCCAAATGACTCGCGCGCCCCCGGTTGATCT
+CCAACAGATCTGCTGTGTACTCCTCCTCATATAGATGACCGCGGTCGGCTCATCCAACGG
+GAGGCGTGGCCGAAAAAACTCTCCTAACCTTCCCGCTTCTGGTGAACTTTATTACGAACT
+CTACGCTACTAGAACGGTACATGGAAGAAACGGAGAAACCTTTCGCAAGTCAGCGGATTG
+CGTTCCCTGTTGTGGTCCTGAAAGTAGTTAAGATATACCGATCGGCTTTTTACGAAGGAC
+ACTGGTCACCTGCATACCCAGGCTAATCCTATAAGTAGGGTGTAACTCCAAGGTCTAGCG
+TGTTCATTCCGTGAGATATATGCGTCCAACGCTGCTATAGAAGAAGTGCGACGCTGAGAT
+ATGTCTTCGTTCGCGTGAAAATGAGAAACTAAGAAAACACCACTTCTCCACGTAGGCCTT
+ACAGAAATAAGCGATGCTTTCTTGCTGCACCTTCGGATGAAGACTAGGTATAAACAATAT
+TAGAATGAGGTCCGTTCTATCGGCGGAATAATTGCGCTCAAAATTTACCATTGGGGCCAA
+CGCGCCCACAGTCGAGACCGAAGGGGATGGCCCTATCACGACTGGCGGAAGCCTCCCGAG
+GAGAAGAGTCTCCTAAGACGATTTATGTGAGCACTGCAGTAGTTTGAAGGCGACCAAGTC
+GGTGCGGGGTCCTGACATGAGAAGTCTCCTACCAGAGCCAGACCCTGTTTCGAATGGTCT
+ACAATCCTTCTCGTCGGAACCATCCCGTGTGTACCACCACGCTGAAATGACTAGTCTATG
+TGAGGAACCACCTTACCGTCCCATTGTCATATCTCTCCTCGTCGAGATAAGCTCGACGCG
+GCAGTGTAAACATGGTCGATCGTTGGGTGGGGGGACCTTGGTGTAGAATATGCGGAGGTC
+TCAAACTCGGGGTAGAGAGGCATTGGAACATCTGGGCCGGCTATAGGTATAATCTTATAG
+ACCAATTCATGGCGATTAGGCCGGTCGGCTACGGCCTTAATCTCACAGTTGCGTGAATGA
+CCTACGACCATCTAGATTGGATAATAATCCGGTAAGCGTTCTCGCCAACTATTGTGGTAT
+TGGATGGAGTCAGAGCCTCGGAAACGACACCTGCCGTAAGAACGAGACTACGTGCAACAC
+GCGAGGTGTCGCCCTGGTGTGCAGAATGCCTCAAACATCTTGCTCCTACCTCAGACTGAT
+ATGGAACTACTGCACGGGCAGTTCCGAATGGCAAGAAGGGATTGCTGCTACCTGTTGTTG
+ATTGAACATTGGATAAGAGGACAGCGCAAACGAACGAATATGCTACCAAAAGATATTTAG
+AACGGACAATTACGGGAGAATAACGGGTGACCATTTGCCGAACCACTCCGAATTCTAAAT
+TCTGGCTGGTAAGGGCTAATTGCTATATTTGAAGCAGCGCACTTTAAGCCGGGCACCATC
+AATAGGGGATCGTCACCATTGAGGAACTTCAGCTAGATGCGGGGCAGCCTATTAGACTAC
+GATGATATCAGGCGACTACGTAAGGACGAGGATGCTCGCCTCTCGGTTAGAATTCGACCC
+CTAGGAAGGCCGCGCAAGCCAGTGTGCCTATGGGCTATCACAGCGTTGTTCCAGCAGACC
+CCATTCTTGCGTTAAGGGAGTTCAGCCCATTTCAGCTTGGGGGTTCTTACAGGGACATAG
+TAAATGTACGGGCACGGAGTTTGCGTCTTGTTTTGGGGCTTGGAGTTAATCGTTGATATT
+ACGGATACTTAACCTACCAGAGTTGGTAGTAAGGACTGGGTGTGTGTTTTTTCCAGAGCC
+AGCTGGCTTTGGTCGATAAGACCTTAAAATCTGCAATTTTTGTCGCAACGCGCAAACGCC
+CAATCCTCCCCAGGTCTAAGGCCAGTGAGATGAGTTTCACCGCTAACGTTTAGGCGGCAT
+CACTGGCTAGCAAACGTAGGGAACCGGGCCCTGCCCCGAGCTTGCTATACTATGCAGGTC
+GATCTTAATAGAGCTGACGCAACTTGGAGGAACCTGACTTGGGCACTTCTGACAAGCACA
+ATAAGATTGCGGATCAGTAGTTCTGATCAGAACATTGACGCACCCTGACGGGCAGGATCA
+TTGTTATGAGAATTGCCTATGCGTCGCCCGTCTAGTAGTTACACCCCTATAACCACATTA
+GGGCCAGAGTCGCTTGGAAAGCCCCTCGCTGATAAATATGGAAGACCCCGAGGCTAGATT
+GAGTGCGGGCAAAGACTCCCAATGCAACCTGGCTGCAACCCAGCGGTCTAAGATAAGTTG
+TCAAACCCCATTTTAAGTGAATGAAGCCGGACCTAAAGCGGCCCGGAGTAGCTTTCACAA
+TACCTCAGTCATGGTGATGGTGTGCTAGGTCCTCGATTTAGGTTTGGATAGACCAATTTA
+GCACCTCAAGTAGAACGGGATCATGAACTAGGACAGGAGGGAAACTGGGCGCAGACTCCA
+AGATATCGCGTCCGAACAATGGTTTAGAGCCAGCCTATTGTGTGAAGGCTATTACGATGC
+GTTGAACACGTACTAACGTCGATCTCTAGACATGTTCAGGTCTAATTCGCGCATTCCGGG
+GCAA
+>prodigal_ctg1
+ATGCGTTATATTCGCCTGTGCCTTTTCTCCCTGATTGCCGCCCTGCCACTGGCGGTATTC
+GCCAGCCCTCCGCCGCTTGAGCAAATTACACGCAGCGAAAGTCAGCTGGCGGGCCGCGTG
+GGCTATGTTGAAATGGATCTGGCCAGCGGCCGCACGCTGGCCGCCTGGCGCGCCAGTGAG
+CGCTTTCCGCTGATGAGCACCTTTAAAGTGCTGCTCTGCGGCGCGGTGCTGGCCCGGGTG
+GATGCCGGAGACGAACAGCTGGATCGGCGGATCCGCTACCGCCAGCAGGATCTGGTGGAC
+TACTCCCCGGTCAGCGAAAAACACCTTGCCGACGGGATGACCGTTGGCGAACTCTGCGCC
+GCCGCCATCACCATGAGCGACAACAGCGCCGGCAATCTGCTGTTGAAGAGCGTTGGCGGC
+CCCGCGGGATTGACCGCTTTTTTGCGCCAGATCGGTGACAACGTCACCCGCCTCGACCGC
+TGGGAAACGGAGCTCAATGAAGCGCTTCCCGGCGACGTGCGCGACACCACCACCCCAGCC
+AGCATGGCCACCACCCTGCGCAAGCTGCTAACCAGCCACACTCTGAGCGCCCGTTCGCAG
+CAGCAGCTGCTGCAGTGGATGGTGGACGACCAGGTAGCCGGTCCGCTGATCCGCGCCGTG
+CTGCCGGCGGGCTGGTTTATCGCCGATAAAACCGGGGCCGGCGAGCGGGGCTCACGTGGC
+ATTGTCGCCCTGCTCGGCCCGAACGGCAAAGCGGAGCGCATCGTGGTGATCTATCTGCGG
+GATACGCCGGCGACCATAGCCGAGCGTAACCAGCAGATCGCCAGAATAGGCGCGGCGCTG
+ATCGAGCACTGGCAACGCTAATCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCG
+GGGTTAATGAACCGGCCAAAATGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCA
+ACCAGCCTCGCCCAAGTTCCCTGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGT
+CTCGTACGGCGCCGGTTAGGATCATCATGACTTCGGCAGAACCCCACACTGTCATATCAG
+CCCAGCTCGCATCCAAACGGCCTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCC
+CCTACAACAGTTGTAGCTGGAATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGG
+AAAGGCTCATCTCAAGATTTACTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAG
+ATGCGCGAGGTCGGAACTGCCTCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCAC
+CTGTGTTTGTGGTCCCCCCTGTCTGTCCGACTCATATTAATTCATTATATTAATTGGTAT
+ACCTGCATTAGATTATGCCATTAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAA
+ATGTAGCGCTAAAAGGCGCCGCCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTA
+CGGTATGAATCTCGGATCAAGTAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCAT
+GTACCCATGGATCCTTCGCGTCTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACAC
+ACACCTCTTTACTACGTCTAAGATATATTTTCAACTAACAACGGAGACTCTCGATTCACG
+AAATCCGTACCTATCACTATCGCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTA
+TTCCACGTATGGAGGATCACCAGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTAC
+CGCCCACCCGGGCTGGACGGGATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAAC
+CACCATTCTCTAAGCATCAGTATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGA
+TTCAAGAGTGAACATAGTTCGAGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAAC
+CGACTAACGGACAAGTATTACGAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTA
+CTAGTGCGGGCCGGAACTTGCGGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGC
+GCAACAGGCTCCACCTCGCCTCACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATAT
+AGTATTTTTGGCTGGACGCGAATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGC
+CCATGTGATTGAAAAGCGTACTCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCC
+CTCCCCACCGCGCTTTCTGTAAATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTA
+GCATGTTTGAAAATTTCCTGTCGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATG
+ACGGAAACCTTGGCCCGACAGGCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCT
+CCGCCGATCTGTATACGCCCTGTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCT
+CCCATAACACAATGGCGGATTTTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTT
+CTGAGTCCTCCTAACTGATTATCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCA
+CGCAATGGCAAGTCACAGACTGTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTAT
+CAAATTCCTAAGCAAACGGGAGTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACG
+TGTCTCGCTAGTGCCGGGTAGATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATT
+CTTTTTAGAACACCTTGAAATTTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAA
+GCATTCGAGCGAGAGTAGTTCGGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTA
+AGACTGGCCGGGTCGGGGGACAATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGT
+ATCTCGACAAGGACGCGCGGTAGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGC
+TTATCAACTCTCAGATCTTTAGATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCAT
+CTATCTTACAACCTGCCAATCACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCG
+AGCAGTTGCGGATCCCTCTTATGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCC
+CCATAGCCCCCGAAATAGTTTCGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGG
+ATAAACCTGGCATCGCTTCAGACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGC
+TTAGGGATCTCCGATGCATCTACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCT
+GGTCTGAGAGTCGGAATAGTCGGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTG
+TAATCTGAGTTGGGAGTTGCTAAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGG
+TGTCGACGTGATTCTGTGAGAGTCTCAGCTCTGAAAACAACTCTAATAGTTAACGTGGCT
+TTAACCGCTAGGTGACACGTAACACACCGCTATGCACTAACACGGGCTGAGTACGGATAA
+TTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTGCAC
+GGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGAGTT
+CCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAACAC
+TATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAGACT
+TTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGTTGA
+GCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTAATA
+TTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCCATA
+GACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGCAAT
+GGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATAACC
+TGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCCCGC
+GGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTCTCC
+GGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAAAGA
+GTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGGTTT
+TCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCCTAG
+ATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAACGT
+GAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGATCA
+CCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAACGT
+GCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACTAAT
+TTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAAGCT
+GAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTATAC
+CGCCTAAACCGTATGTGCCTCAAAAACAAGCGTACCTACGCAGTCGGGTGTGTTAACTCA
+GGATCCAACCAGGTGCGGGGCGGAACCGTAGTTGCTAGATGTGGCGAAAGTTTTCCGTTC
+GATTGTTCCGGCTGGCTTCTCGACTGATGCTCGGCTTGACCCGCTTACGAACGGTCCGAT
+AAAGTCCAACACAGTCTCCCCACTTGATGTTCCGGATCAGTCCCATTGCTTGCCCCCGGG
+TGTTCGTTAACCCGCTGCTGGTTTGCCACGTCAAACACCACCGCTCTCAAACGCGGACTC
+GAAACGGCTGCACCGTAAGGAAGAACCACACAAACACGTATCTTAGGCCAGGTCAGCTGG
+GGGTTCGTAGTACTCCACGAACCCTACGATGGCCGCAACCTTAAGAAGTTGTAAATATTG
+CGGTCAGCAGCCCTGACATGATGCAACGCGATTCACATTGACTAAGTGTAGCATCACGAC
+GCCAGCTGGTAGTTAAGTAATGCGTGGATGGCTTGGTCCGGGCTTCGCTGCACGTAGTTG
+GACGCATCAAAGCCAATTCGGGCCCGCCTTACCGCGTCCAAGTGGCACCATTGCGGCCAG
+TAACTCTGACACAATGATGGAGCCCTAATTCGGGCCTATCCACAGCACTGTACATATTCC
+TCTCGTAGGCATTAAGATACGGACGGATCTATATTTCCTGGGTTCGAGTTGAGCACGTTG
+TCGCTCCTCATATTTTCTGTTGTATCAGCCTTGGATGGTTACCGCCGATATCCACCCGTC
+CTTTCAGAGTCTTCACGCGCTTAGGCGGCCTACTTACCGGGCCCCTGCAAGAATCACAAG
+TTTCGTACGCCTGTATTTCGCTGAGAAAGCCACGGATCTCTGGGTCATAGGGCTGATTCT
+TTCAATTTCTTTTTCGGTCATCCACAAGAGCGGTCGGACAGCACGCTTGGCGTATGTCAT
+CAATCCGGCGCCGGCACGCCGCCGCTTCGCTCGACACCCCTGCCGTGGGCGGCAGGCACG
+AACTCGGTCAGAACTTCCTCGTCGACCGAGGTGTATGCACAAGGATCGCCGAGGTCGTCT
+CCTCGACGACGGCCCATCCGGTCCTCGAACTGGGCGCCGGTGACGGTGCCATCACCCGGG
+CCCTGGTCGCGGCGAATCTCCCGGTCACCGCGCTGGAACTCGACCCCCGGCGGGTCCGGC
+GGCTCCAGCGGACCTTCGCCGACGGGGTCACCGTCGTGCACGGGGACATGCTCCGGTACG
+ACTTCGGGCCGTACCCGCACCACGTGGTGTCGACCGTGCCGTTCTCCATCACCACGCCGC
+TGCTCCGGCGCCTGATCGGCCAGCGGTTCTGGCACACCGCGGTGCTGTTGGTGCAGTGGG
+AGGTGGCCCGTAAGCGGGCCGGTGTGGGCGGCACCACGATGCTCACCGCAGCCAGTTGGC
+CGTGGTACGAGTTCACCCTGGTGGAGCGGGTGCCGAAGACCTCGTTCGACCCGGTGCCGA
+GCGTCGACGGCGGCATCCTCGTCATCGAGCGTCGATCCGCGCCGCTGCTCGACGACCGCT
+GCGTGGGTGACTACCAGAACCTGGTACGCGAGGTGTACACCGGTCCCGGTCGTGGTCTGG
+CCGCGATTCTCCGTACCCGTCTGCCCGGTCGTGAGGTGGACGCCTGGCTCCGCCGCGAGC
+GGGTGGACCCGGCGGCCCTGCCCCGCGACCTCAAGGCCGGGCACTGGGCATCCCTCTACC
+GGCTCTACCGGGAGGTGGGTACTCGGCCCGCCCCTGCCGGCCGGTCCGTCCGGGCCCGGC
+CCGGATCCGTCGGCCCCGACCGCTCGCTCCCTCCGCGCGGCCTGCGATCCGGTCCGCCGA
+GGGCTCGACGACGTGGTGGAGGCGCCTGAGACAGGCTTCCCTGTCGAAGGCTACGGGAGA
+ACTTACAAGAGCGCGCGCTTGTATGTTCGCTCCATCCAAATGACTCGCGCGCCCCCGGTT
+GATCTCCAACAGATCTGCTGTGTACTCCTCCTCATATAGATGACCGCGGTCGGCTCATCC
+AACGGGAGGCGTGGCCGAAAAAACTCTCCTAACCTTCCCGCTTCTGGTGAACTTTATTAC
+GAACTCTACGCTACTAGAACGGTACATGGAAGAAACGGAGAAACCTTTCGCAAGTCAGCG
+GATTGCGTTCCCTGTTGTGGTCCTGAAAGTAGTTAAGATATACCGATCGGCTTTTTACGA
+AGGACACTGGTCACCTGCATACCCAGGCTAATCCTATAAGTAGGGTGTAACTCCAAGGTC
+TAGCGTGTTCATTCCGTGAGATATATGCGTCCAACGCTGCTATAGAAGAAGTGCGACGCT
+GAGATATGTCTTCGTTCGCGTGAAAATGAGAAACTAAGAAAACACCACTTCTCCACGTAG
+GCCTTACAGAAATAAGCGATGCTTTCTTGCTGCACCTTCGGATGAAGACTAGGTATAAAC
+AATATTAGAATGAGGTCCGTTCTATCGGCGGAATAATTGCGCTCAAAATTTACCATTGGG
+GCCAACGCGCCCACAGTCGAGACCGAAGGGGATGGCCCTATCACGACTGGCGGAAGCCTC
+CCGAGGAGAAGAGTCTCCTAAGACGATTTATGTGAGCACTGCAGTAGTTTGAAGGCGACC
+AAGTCGGTGCGGGGTCCTGACATGAGAAGTCTCCTACCAGAGCCAGACCCTGTTTCGAAT
+GGTCTACAATCCTTCTCGTCGGAACCATCCCGTGTGTACCACCACGCTGAAATGACTAGT
+CTATGTGAGGAACCACCTTACCGTCCCATTGTCATATCTCTCCTCGTCGAGATAAGCTCG
+ACGCGGCAGTGTAAACATGGTCGATCGTTGGGTGGGGGGACCTTGGTGTAGAATATGCGG
+AGGTCTCAAACTCGGGGTAGAGAGGCATTGGAACATCTGGGCCGGCTATAGGTATAATCT
+TATAGACCAATTCATGGCGATTAGGCCGGTCGGCTACGGCCTTAATCTCACAGTTGCGTG
+AATGACCTACGACCATCTAGATTGGATAATAATCCGGTAAGCGTTCTCGCCAACTATTGT
+GGTATTGGATGGAGTCAGAGCCTCGGAAACGACACCTGCCGTAAGAACGAGACTACGTGC
+AACACGCGAGGTGTCGCCCTGGTGTGCAGAATGCCTCAAACATCTTGCTCCTACCTCAGA
+CTGATATGGAACTACTGCACGGGCAGTTCCGAATGGCAAGAAGGGATTGCTGCTACCTGT
+TGTTGATTGAACATTGGATAAGAGGACAGCGCAAACGAACGAATATGCTACCAAAAGATA
+TTTAGAACGGACAATTACGGGAGAATAACGGGTGACCATTTGCCGAACCACTCCGAATTC
+TAAATTCTGGCTGGTAAGGGCTAATTGCTATATTTGAAGCAGCGCACTTTAAGCCGGGCA
+CCATCAATAGGGGATCGTCACCATTGAGGAACTTCAGCTAGATGCGGGGCAGCCTATTAG
+ACTACGATGATATCAGGCGACTACGTAAGGACGAGGATGCTCGCCTCTCGGTTAGAATTC
+GACCCCTAGGAAGGCCGCGCAAGCCAGTGTGCCTATGGGCTATCACAGCGTTGTTCCAGC
+AGACCCCATTCTTGCGTTAAGGGAGTTCAGCCCATTTCAGCTTGGGGGTTCTTACAGGGA
+CATAGTAAATGTACGGGCACGGAGTTTGCGTCTTGTTTTGGGGCTTGGAGTTAATCGTTG
+ATATTACGGATACTTAACCTACCAGAGTTGGTAGTAAGGACTGGGTGTGTGTTTTTTCCA
+GAGCCAGCTGGCTTTGGTCGATAAGACCTTAAAATCTGCAATTTTTGTCGCAACGCGCAA
+ACGCCCAATCCTCCCCAGGTCTAAGGCCAGTGAGATGAGTTTCACCGCTAACGTTTAGGC
+GGCATCACTGGCTAGCAAACGTAGGGAACCGGGCCCTGCCCCGAGCTTGCTATACTATGC
+AGGTCGATCTTAATAGAGCTGACGCAACTTGGAGGAACCTGACTTGGGCACTTCTGACAA
+GCACAATAAGATTGCGGATCAGTAGTTCTGATCAGAACATTGACGCACCCTGACGGGCAG
+GATCATTGTTATGAGAATTGCCTATGCGTCGCCCGTCTAGTAGTTACACCCCTATAACCA
+CATTAGGGCCAGAGTCGCTTGGAAAGCCCCTCGCTGATAAATATGGAAGACCCCGAGGCT
+AGATTGAGTGCGGGCAAAGACTCCCAATGCAACCTGGCTGCAACCCAGCGGTCTAAGATA
+AGTTGTCAAACCCCATTTTAAGTGAATGAAGCCGGACCTAAAGCGGCCCGGAGTAGCTTT
+CACAATACCTCAGTCATGGTGATGGTGTGCTAGGTCCTCGATTTAGGTTTGGATAGACCA
+ATTTAGCACCTCAAGTAGAACGGGATCATGAACTAGGACAGGAGGGAAACTGGGCGCAGA
+CTCCAAGATATCGCGTCCGAACAATGGTTTAGAGCCAGCCTATTGTGTGAAGGCTATTAC
+GATGCGTTGAACACGTACTAACGTCGATC
+>ignore_ctg
+CCACTGCGGTGATTCACCACTATCGGCAGCTTAATACCACCACACAGGAGTGGGTACGTG
+CACGCTTACTATGTGCCGTAAAAGTCATCAATGACCCCTGAGACGCCTGCCCACCCGCAA
+CGTGGAAGATATCAAGATATCTGAGGTTATACAGTATATTTGCGGTCGGTTGCCGTCGCG
+GCGATTCCTTGTGTGTTGCACTTTTTAGAAGTTACTACAACCCACGCATGAAGTCTCGGT
+TGGACTACCCCTCTTATAGTCATCATGCAGTGCGGGTGGCCTGCTTTCGCAAGGCGTTCA
+GAACTTGGCATAGTGTCGCGCGCGGAGTCCTTTGGCTAACGAGACCGGTTAATCAAAGGC
+ACAGCCTAGTGAAGGTCGAAATAGTTCCGCCCCGATCATACAAAGATATCTCCACGAATT
+GGTGTCGTTTTCGAAGGAAGGCGGACGCCTAAATGTTTGAGAGTACATCAGTCAATTCTC
+CCGAATATCGGTATACCTGTTAGACTATGAACTCATACTTTTCTAACCACCGCTCATCTC
+GTTCCTTATCCGTTATGTCTATACTGAGTCTACAACATGGACATCGCAGGGAGCTCAATT
+GGCTATGGGAGCCAACACTCAGGCTGGGTTACGCAACCCAGATGTCTGCTGGAGTGTTAG
+TGTAAGCTGTAATAAAGACTCTCTCGTGTGCCCTTGAGAGACGACACCCACCGAACTGCG
+TTTACTCAGGGGCAGAACATCCGAATTTTGCCTTCCCGCACATCAGTGGGGGACGACTGC
+GGGCAACAGTAAAGCTAGTCCGATCGCGCTCTGGATGCTATCCGATGTCGGGGGTGAATA
+ATTGGTGAAACTGCCTCCAACAATTCAGAGTCTCTTCTCAACAAGGACGTGTACCGAGGC
+ATAGAGGGGGAATGTCCGCCAGGCCCCAGAGATCTTTGCGACCTACATTGCACAGTATTG
+GTCGTGTTCAATCTTGAACACTTACTATTCACCGAATTGGTGCGCTGTTGACGCTTTCTT
+CCGTAATCACCTCCAAATCTGGGTGTTAGTAACGAGGCCGGCGTGCTTTGAGGAGAGAAT
+ACATGGCACCTTAAAACGACGTACTAGCCTTAGCTTACGCAACCTAGGTTTGTGCACAGG
+CGTACGATCATTGACAGCCGACATCACGAATAACGCGCAAATGGCCTGTATCCTACACGC
+CTTGCCTGCCAAACCGAGTCATTGTGTTGTCGCCGAATGGCATTTCGGCTACGTGAAAAT
+CTTAGATATTTTGCGTGGACAATGTTCGCCTACTTGAGTTCTTCTTGGGTATCTCATGTT
+ATTTCCAGGATATAACGCGTGTCTCGAAATCGACCACAGGCCTTCCTCATACTCTTATGG
+ATGTTACTGCTGTGTACCGATATGGAGATTCTAGGAGAGGGCAATGGGTTCTTCTTACAA
+TTGGCCGGTCGAGCTCTCCACGCCAGATCTCCACTTGACGCCGGGGCGGGAGAAAGTATT
+AACCTTCCATAGAGTCATCATTATGAATGGCGCCTAATGTAGACAGGAAACGGGCTCAGC
+TACCGTCTACCGCAGGTAGTTCGATTCGAATTCACAACGTTTAGTTCTCGTTAAGTGGAC
+ACGATACCGAGCTTTGGTTCGAGTTGAAAGTTACGGTGGGTCTAGATGTAATGATCCGAA
+CGGTGCCGCTAATGCGATGACCGTAGGCCCACTCGCTGTGATAGTGGTCCCTCGTATCGC
+ATTGATCCCTTCTGTTTCCGCACACTAACATGCATCCCCGGGAACTCCTTACACTTGCGC
+ACCGAATCCCGCTGAAGATGCACCTAGATATGTCCCCCTATGATACACTCCTTTTATCGC
+TTCGACATCAGCTGTGCATTAAATGATTGTTTGTGCAAATTCATCACCTACTCTCAGAAC
+GATGAAAACAGGTTGAAGTCTATGGTGTTTGCATGGCAGCTAAAGTCATCTTTCGTGAAC
+GGCAATCTTGAGAGCTGTTATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCA
+AGACGAATTGCCGGCTACTGAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTC
+GGACAATACTTTGGCTTTGTACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAA
+GTACTTGAATAATATCAATGGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATT
+GCGATTCGAAGTCGGTACTAAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAA
+TGTCGCTGCTCCGGCTCAAGTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCG
+ATCGGGTTGGGACAATGTCCCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGT
+CAAGCACACTTTCGACAATTTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGC
+TCGACAAGTCGCTGACAATCCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTAC
+TGGTTTGGGTAAGACTCACTTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCC
+GAATGCTAAGGTCGTCTACATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTT
+GCAAAATAATGCTATCGAAGAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGAT
+CGACGACATCCAATTCTTCGCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTT
+CAATGCTTTGTTGGAAGGTAATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGA
+AATCAATGGTGTCGAAGACCGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTAT
+CGAACCGCCGGAATTGGAAACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGA
+CATCCGATTGCCGGGTGAAGTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCG
+AGAATTGGAAGGTGCTTTGAATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTAT
+CACTATCGACTTCGTCCGAGAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGT
+CACTATCGACAATATCCAAAAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTT
+GTTGTCGAAGCGACGATCGCGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGC
+TAAGGAATTGACTAATCACTCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCA
+CACTACTGTCTTGCACGCTTGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACAT
+CAAGGAAGACTTCTCGAATTTGATCCGAACTTTGTCGTCGTGAACCTCATAAGGCGGCGC
+GGCATGCAGTTATTGAGCAATAATGTCTCATAGTAGGCTCAGGGGCACGACTTATCTCCA
+ACGATAATCCGAAGTTGCGACTCATGTCGTCTGAGCTGCCGGGTTAACAATGGGCACAGT
+CATACTAAGCGCGTCGCAATGAGCACAAGAACAACTCCGGCTGGTGATCTTTTTCGAGTT
+CGTTCGACCGCTGCGAATTTACTCCCACGCGCAGTCCGTAATGCCTACTGCTTTTGCCGA
+CGAACGGAGGATTCCAGTTTCGATCTCCAAGCGGACGAGGCCCAGGGTGGGGCTCCCGCC
+GAACCGCCCTACAATGATAGGGTGGATTTGGCTACGTAATCGCTCAAGCATCGAAATCGC
+AGTGTTAGAAGGGGCGGAGGGACCACCGTACATCCGTGCTACGGAGCATTGCTTGACGTG
+TCTTGCCGCATTCCCAGACTATGTCTATGACCGTGCCCAGCGTCAATTCCTTCAGCTCGC
+GTGACGCCACCATGGTAATAGCCTAGCAAAGGATGAAGCTCACGCCGCGACATACTCCTC
+TGGCTCCTTTTATTGAGGCAGTGTCGTCCGAACCCGTTCGAGCTCATTTAGTTATCAACA
+TTTAGGGACGCAAAACCCGTAATAGGGTCTCTATGGATTGTATCTTGACAGAGAAGTAGC
+TGATCAGGTCGGTCATATCGACAGCAGACCCCGACAGATTGAGCCGTCAACTAAGGGGAG
+CGCTCTAGAACCCAGTTGGAGGAGAGTCATTATTTGACCATGGGCGGAATTTCACTACGT
+CATGTGCCGTATAAAGGCGTCCGGGACGGATGTCGCCCCATGCCAACACTTCCCTTGCCT
+GTTGATCATGCGGAAATGGCCGCAGCAACTGGGGTTGTTTGTGGATATTACTGGTCTTGG
+ACGGAAGATTGGGGAGTAGCCACCTTAAGTTAGTCGGGCATGATTGTGGGTTAGATTCGG
+ACGAGTTTCTTCCGTAGCTTAGTGATCTTACGTTTCTATAACAGAATCGTTTCCAGACTC
+TTGGGCCGACCCTAGTATCCATCTCGCTGTTGCCGTACTAATCATACGCTAGCTACAGAT
+TATCTCTCGATAGCGAGTTTGCGCCCGATCATGTACTCGTAGCCACGGAGGGATAGATGG
+AGATATGGGTCGTAAAGATTCACGGATAGCGACAGGATAGCTCTTGCCCCAGGCTCGTGA
+TGGCCTGCGATCATTCTAACTATTTCCAGCGACATGGACCTCCTGTGGTCAATAAGATAT
+TGGCCCGATTACAGGACTCTGACAGAGCGTCAACCTAACCTGCCTAAGCATGACTACTAG
+GTTGGCAAGCATGGTAATTTCCTAGTGTCACATCCATACTATGTCCCCTTTCCCAAGACA
+CTCCAACAACTCATTATGTCAAGCATCCAAAACGACTATGCTGTCGCACTCCAGCTGCGA
+CATGTTGCAGGGTACGTATAAACTATATCTAGACGTGCCGTATTTATTAGCAGGCCTTCT
+TTATTTACGCTACGCCGACTACGAAACTTCTACGGAGGTAAAATCGGTTAACATCTCGTG
+CGTACTGCTCTATTCAGGAGCACTATGTGGCGCACTAGGTATACCAGCCCCTGGCGTCCT
+GCTGATTAATGGTCAAAGCGAGTCTGGATTACACAGAAAGCCCTAATACCCTGTGATAAG
+ATGTGCCCACATATAAAATTCACTAGTCCGCAGTTGCCCGCCGGCCGGTTCTCCCCAGTC
+CAAAGCTAAGAGTGTGAGACCTACCAGCAGAGATCTAGACCTTCCCATTTGATGTATCGC
+AACAGGCATTGGCCATGCCGGGCGCGGTATTAACTCTCCAGAGCTTAAGCGTTGAAATCC
+GCGCTGTCGTGGTCAACGTATTGTGTCTGTGCTGCCTAGGGTGCGACATCCATGAATAAC
+AGCCAGGTATAAAACGAATTTTTTCATTGTGAAGTCTTCTGCATTACTTCGCTGAAGGTT
+TT
diff --git a/circlator/tests/data/start_fixer_rearrange_contigs.expect.log b/circlator/tests/data/start_fixer_rearrange_contigs.expect.log
new file mode 100644
index 0000000..d280dca
--- /dev/null
+++ b/circlator/tests/data/start_fixer_rearrange_contigs.expect.log
@@ -0,0 +1,8 @@
+[fixstart] id break_point gene_name gene_reversed new_name skipped
+[fixstart] ignore_ctg - - - - skipped
+[fixstart] prodigal_ctg1 4529 prodigal no - -
+[fixstart] prodigal_ctg2 4862 prodigal yes - -
+[fixstart] promer_ctg1 2000 sp|P03004|DNAA_ECOLI no - -
+[fixstart] promer_ctg2 3403 sp|P03004|DNAA_ECOLI_2 yes - -
+[fixstart] promer_ctg3 4745 sp|P03004|DNAA_ECOLI no - -
+[fixstart] promer_ctg4 660 sp|P03004|DNAA_ECOLI yes - -
diff --git a/circlator/tests/data/start_fixer_rearrange_contigs.in.fa b/circlator/tests/data/start_fixer_rearrange_contigs.in.fa
new file mode 100644
index 0000000..324730e
--- /dev/null
+++ b/circlator/tests/data/start_fixer_rearrange_contigs.in.fa
@@ -0,0 +1,776 @@
+>promer_ctg1
+CCACTGCGGTGATTCACCACTATCGGCAGCTTAATACCACCACACAGGAGTGGGTACGTG
+CACGCTTACTATGTGCCGTAAAAGTCATCAATGACCCCTGAGACGCCTGCCCACCCGCAA
+CGTGGAAGATATCAAGATATCTGAGGTTATACAGTATATTTGCGGTCGGTTGCCGTCGCG
+GCGATTCCTTGTGTGTTGCACTTTTTAGAAGTTACTACAACCCACGCATGAAGTCTCGGT
+TGGACTACCCCTCTTATAGTCATCATGCAGTGCGGGTGGCCTGCTTTCGCAAGGCGTTCA
+GAACTTGGCATAGTGTCGCGCGCGGAGTCCTTTGGCTAACGAGACCGGTTAATCAAAGGC
+ACAGCCTAGTGAAGGTCGAAATAGTTCCGCCCCGATCATACAAAGATATCTCCACGAATT
+GGTGTCGTTTTCGAAGGAAGGCGGACGCCTAAATGTTTGAGAGTACATCAGTCAATTCTC
+CCGAATATCGGTATACCTGTTAGACTATGAACTCATACTTTTCTAACCACCGCTCATCTC
+GTTCCTTATCCGTTATGTCTATACTGAGTCTACAACATGGACATCGCAGGGAGCTCAATT
+GGCTATGGGAGCCAACACTCAGGCTGGGTTACGCAACCCAGATGTCTGCTGGAGTGTTAG
+TGTAAGCTGTAATAAAGACTCTCTCGTGTGCCCTTGAGAGACGACACCCACCGAACTGCG
+TTTACTCAGGGGCAGAACATCCGAATTTTGCCTTCCCGCACATCAGTGGGGGACGACTGC
+GGGCAACAGTAAAGCTAGTCCGATCGCGCTCTGGATGCTATCCGATGTCGGGGGTGAATA
+ATTGGTGAAACTGCCTCCAACAATTCAGAGTCTCTTCTCAACAAGGACGTGTACCGAGGC
+ATAGAGGGGGAATGTCCGCCAGGCCCCAGAGATCTTTGCGACCTACATTGCACAGTATTG
+GTCGTGTTCAATCTTGAACACTTACTATTCACCGAATTGGTGCGCTGTTGACGCTTTCTT
+CCGTAATCACCTCCAAATCTGGGTGTTAGTAACGAGGCCGGCGTGCTTTGAGGAGAGAAT
+ACATGGCACCTTAAAACGACGTACTAGCCTTAGCTTACGCAACCTAGGTTTGTGCACAGG
+CGTACGATCATTGACAGCCGACATCACGAATAACGCGCAAATGGCCTGTATCCTACACGC
+CTTGCCTGCCAAACCGAGTCATTGTGTTGTCGCCGAATGGCATTTCGGCTACGTGAAAAT
+CTTAGATATTTTGCGTGGACAATGTTCGCCTACTTGAGTTCTTCTTGGGTATCTCATGTT
+ATTTCCAGGATATAACGCGTGTCTCGAAATCGACCACAGGCCTTCCTCATACTCTTATGG
+ATGTTACTGCTGTGTACCGATATGGAGATTCTAGGAGAGGGCAATGGGTTCTTCTTACAA
+TTGGCCGGTCGAGCTCTCCACGCCAGATCTCCACTTGACGCCGGGGCGGGAGAAAGTATT
+AACCTTCCATAGAGTCATCATTATGAATGGCGCCTAATGTAGACAGGAAACGGGCTCAGC
+TACCGTCTACCGCAGGTAGTTCGATTCGAATTCACAACGTTTAGTTCTCGTTAAGTGGAC
+ACGATACCGAGCTTTGGTTCGAGTTGAAAGTTACGGTGGGTCTAGATGTAATGATCCGAA
+CGGTGCCGCTAATGCGATGACCGTAGGCCCACTCGCTGTGATAGTGGTCCCTCGTATCGC
+ATTGATCCCTTCTGTTTCCGCACACTAACATGCATCCCCGGGAACTCCTTACACTTGCGC
+ACCGAATCCCGCTGAAGATGCACCTAGATATGTCCCCCTATGATACACTCCTTTTATCGC
+TTCGACATCAGCTGTGCATTAAATGATTGTTTGTGCAAATTCATCACCTACTCTCAGAAC
+GATGAAAACAGGTTGAAGTCTATGGTGTTTGCATGGCAGCTAAAGTCATCTTTCGTGAAC
+GGCAATCTTGAGAGCTGTTATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCA
+AGACGAATTGCCGGCTACTGAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTC
+GGACAATACTTTGGCTTTGTACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAA
+GTACTTGAATAATATCAATGGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATT
+GCGATTCGAAGTCGGTACTAAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAA
+TGTCGCTGCTCCGGCTCAAGTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCG
+ATCGGGTTGGGACAATGTCCCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGT
+CAAGCACACTTTCGACAATTTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGC
+TCGACAAGTCGCTGACAATCCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTAC
+TGGTTTGGGTAAGACTCACTTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCC
+GAATGCTAAGGTCGTCTACATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTT
+GCAAAATAATGCTATCGAAGAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGAT
+CGACGACATCCAATTCTTCGCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTT
+CAATGCTTTGTTGGAAGGTAATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGA
+AATCAATGGTGTCGAAGACCGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTAT
+CGAACCGCCGGAATTGGAAACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGA
+CATCCGATTGCCGGGTGAAGTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCG
+AGAATTGGAAGGTGCTTTGAATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTAT
+CACTATCGACTTCGTCCGAGAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGT
+CACTATCGACAATATCCAAAAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTT
+GTTGTCGAAGCGACGATCGCGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGC
+TAAGGAATTGACTAATCACTCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCA
+CACTACTGTCTTGCACGCTTGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACAT
+CAAGGAAGACTTCTCGAATTTGATCCGAACTTTGTCGTCGTGAACCTCATAAGGCGGCGC
+GGCATGCAGTTATTGAGCAATAATGTCTCATAGTAGGCTCAGGGGCACGACTTATCTCCA
+ACGATAATCCGAAGTTGCGACTCATGTCGTCTGAGCTGCCGGGTTAACAATGGGCACAGT
+CATACTAAGCGCGTCGCAATGAGCACAAGAACAACTCCGGCTGGTGATCTTTTTCGAGTT
+CGTTCGACCGCTGCGAATTTACTCCCACGCGCAGTCCGTAATGCCTACTGCTTTTGCCGA
+CGAACGGAGGATTCCAGTTTCGATCTCCAAGCGGACGAGGCCCAGGGTGGGGCTCCCGCC
+GAACCGCCCTACAATGATAGGGTGGATTTGGCTACGTAATCGCTCAAGCATCGAAATCGC
+AGTGTTAGAAGGGGCGGAGGGACCACCGTACATCCGTGCTACGGAGCATTGCTTGACGTG
+TCTTGCCGCATTCCCAGACTATGTCTATGACCGTGCCCAGCGTCAATTCCTTCAGCTCGC
+GTGACGCCACCATGGTAATAGCCTAGCAAAGGATGAAGCTCACGCCGCGACATACTCCTC
+TGGCTCCTTTTATTGAGGCAGTGTCGTCCGAACCCGTTCGAGCTCATTTAGTTATCAACA
+TTTAGGGACGCAAAACCCGTAATAGGGTCTCTATGGATTGTATCTTGACAGAGAAGTAGC
+TGATCAGGTCGGTCATATCGACAGCAGACCCCGACAGATTGAGCCGTCAACTAAGGGGAG
+CGCTCTAGAACCCAGTTGGAGGAGAGTCATTATTTGACCATGGGCGGAATTTCACTACGT
+CATGTGCCGTATAAAGGCGTCCGGGACGGATGTCGCCCCATGCCAACACTTCCCTTGCCT
+GTTGATCATGCGGAAATGGCCGCAGCAACTGGGGTTGTTTGTGGATATTACTGGTCTTGG
+ACGGAAGATTGGGGAGTAGCCACCTTAAGTTAGTCGGGCATGATTGTGGGTTAGATTCGG
+ACGAGTTTCTTCCGTAGCTTAGTGATCTTACGTTTCTATAACAGAATCGTTTCCAGACTC
+TTGGGCCGACCCTAGTATCCATCTCGCTGTTGCCGTACTAATCATACGCTAGCTACAGAT
+TATCTCTCGATAGCGAGTTTGCGCCCGATCATGTACTCGTAGCCACGGAGGGATAGATGG
+AGATATGGGTCGTAAAGATTCACGGATAGCGACAGGATAGCTCTTGCCCCAGGCTCGTGA
+TGGCCTGCGATCATTCTAACTATTTCCAGCGACATGGACCTCCTGTGGTCAATAAGATAT
+TGGCCCGATTACAGGACTCTGACAGAGCGTCAACCTAACCTGCCTAAGCATGACTACTAG
+GTTGGCAAGCATGGTAATTTCCTAGTGTCACATCCATACTATGTCCCCTTTCCCAAGACA
+CTCCAACAACTCATTATGTCAAGCATCCAAAACGACTATGCTGTCGCACTCCAGCTGCGA
+CATGTTGCAGGGTACGTATAAACTATATCTAGACGTGCCGTATTTATTAGCAGGCCTTCT
+TTATTTACGCTACGCCGACTACGAAACTTCTACGGAGGTAAAATCGGTTAACATCTCGTG
+CGTACTGCTCTATTCAGGAGCACTATGTGGCGCACTAGGTATACCAGCCCCTGGCGTCCT
+GCTGATTAATGGTCAAAGCGAGTCTGGATTACACAGAAAGCCCTAATACCCTGTGATAAG
+ATGTGCCCACATATAAAATTCACTAGTCCGCAGTTGCCCGCCGGCCGGTTCTCCCCAGTC
+CAAAGCTAAGAGTGTGAGACCTACCAGCAGAGATCTAGACCTTCCCATTTGATGTATCGC
+AACAGGCATTGGCCATGCCGGGCGCGGTATTAACTCTCCAGAGCTTAAGCGTTGAAATCC
+GCGCTGTCGTGGTCAACGTATTGTGTCTGTGCTGCCTAGGGTGCGACATCCATGAATAAC
+AGCCAGGTATAAAACGAATTTTTTCATTGTGAAGTCTTCTGCATTACTTCGCTGAAGGTT
+TT
+>promer_ctg2
+GCATCGGTATCGAGCCTAAGCCCTCTGTAGTTCGATTGGCACCTTTAAGCAATGTCTTGT
+AGGTAAGTTGGGACTGGCGCGTGCTTAGTTGCACTTTGCCTCTGCGCTAGTCATATTGAA
+CGTCTGGACGCCCCCCTTGAGATGGCGAAATATTGCTGAAATGATGTCCCCGGCATCGGA
+CAAAAGGCCTAATAACGTGGGCCGCAAAGCTGCGTCTACACCCACGTCGTATGTTGCGTT
+TAGTTCCTTTCGTGATCACAGGGCCCTCCACGGATGCATAGAAACGCTTCCCGGTTCATC
+ACGGGACCCTGAACTTGACTCGCTCGAACGCGTTCAAACTACAGAACCCAGGGAAATTCT
+CTATTGGGTATCTGACCAGTGGTAACAAACTCCTTCGTTTTTACGTACTGTGGTTCTAGC
+GTATCGCGCGAACCATATTCTAACTTGGTTTGGTTCCAACTAGATTGCAGAACACGGCAC
+TTAAATAGGTGAGAGCAAGGGCGTGTGCAAAGGATATCTGCGAGGAAAACAGGGTAGATA
+GTGGCATACAACCCACAGCTTAGAGTAACGCACCCTTGTCCGTCGGGGTATGAGTTCGCT
+GGCACTGACACCTAACTCGTGCGTCATAATCGCCTAGGTTCAGGTCAGAATACCTGCATC
+CTAGGAAATTGTCCGCATGAAAACTCAAGCTTAGGTATGCATTGCTGCAAGTGCCATTGA
+CACGCCGGTCAGATGCTCCGAGTTTAGAGCTGATGCCAGTTACCGCGCCACCCCGGTGCC
+TCAACGTGGACTGTGGAAGCTGTGTGACCGGAAAGCTCTTAGATCGAATGTCGTTGGACT
+GGCTCATCTTCTGTTTGAGGCTGTCACAAGGTTTAGCCCCGGAAGCGCAGAAGTCGGCTC
+TTCCTCCTTGTTGCGACGAACGTCGTCCATGGGATCAGAAACCAGCAAAGTTAAGGCACT
+CAATCCTATGGAGACTGATCACTTGAGCTCGCAGCGCATCCCACGCCCGACGCTTAGGCG
+GCAAAGGACGTTGCACAGACGGCGCCAAATCTCGGATGAGAACGGGTAGCTATGCGTCAA
+TGTAGGCCCTAATTTGATGAACCGGGCCGGTGCCTTGCTATGAATAGATGGACCGCGCGG
+TCACTGTTGGGTCACTTATTTTAGTCCTCTTTCAGTGACGACGGCGGCATACCGCGTGAT
+TAGATTTTACATATCGCTATCTCTGGGAAGCAATAAATCGTAGACGATGATAACATCACT
+AGTATTCTGAGGGAAGCCATCTAAGTTCATTAAACTTGCCTGTCTAGCTATCCTTTAGCG
+GAGAGGGCGGCGGCATTACTTCATTGTGAGAGAACTGTACTATACGGATTGCGGTCAGTC
+GAGCGATCAGAAGGACGGATCCTCAACACTCATCCTCCCTACGGGATTAATCCGCACATG
+TCCACCGACGTACTCCTTCTTCATCCTAAGATTGATGCCCAGAATTACCATTTGCTCGCC
+GCTTACGATGTCACAACGTAGCAGGGTACCAACCTCCCCACAACACGCACGCCCAGTTCT
+ATATAAGACACAATACGTATAGGGTATAACTTATTCTGGCCCGACCTCGATCTAATTCTT
+AAGAGTTAAGTTACCGTCCAGACCTTTCCATGTTGCAAGGAGACAGGTAGGATACGGCGC
+TTTTGCGTTTTGCGCTCGGTGGCTGTTCCCAGCATCGTGGGAGCGTTTGGAAAATAGATT
+ATAATCGCTATGCGAAAGATGCGTCCGTGCATAAACTGAAGAACGATGTTCATGTACTAA
+ACGCTTATTCACGACCACGAGCGAGTCCAGCTCACTCCTTCATCCCGTACCCTCTATTGG
+ATTAGCCCATGGATGAGAACCCGCGGACCGTGAACTGCACTCACACTTATGGTGCAACAC
+ATGTCCGACTTCTTAGCTTTGCGAATCGACTCGAAGTCCCTACTCGATACGGGCTCCCCA
+GACGCAGATCAGGTGGGCTTCACGACGACAAAGTTCGGATCAAATTCGAGAAGTCTTCCT
+TGATGTCGTGCGATTCTTCTCGCAATTGTTCGATCTTTCGGCAAGCGTGCAAGACAGTAG
+TGTGGTCTCGACCACCGAAAGCGTCACCGATTTCCGGCAACGAGTGATTAGTCAATTCCT
+TAGCCAAAGCCATAGCCATTTGTCGCGGTCGAGCGACCGATCGCGATCGTCGCTTCGACA
+ACAAGTCAGCGACCTTGATCTTGTAGTATTCAGCGACAGTCTTTTGGATATTGTCGATAG
+TGACCAACTTTTCTTGCAAAGCCAACAAGTCTCGCAAAGCTTCTCGGACGAAGTCGATAG
+TGATAGCTCGACCAGTGAAATTAGCATTAGCGATGACTCGATTCAAAGCACCTTCCAATT
+CTCGGACATTCGATCGCAATCGCTTAGCGATGAAGAAAGCGACTTCACCCGGCAATCGGA
+TGTCATTTTCGTCAGCTTTCTTCATCAAGATAGCGACTCGAGTTTCCAATTCCGGCGGTT
+CGATAGCGACAGTCAAACCCCAACCGAATCGCGACTTCAATCGGTCTTCGACACCATTGA
+TTTCCTTCGGGTATCGGTCCGAAGTCAAGATGATTTGTTGATTACCTTCCAACAAAGCAT
+TGAAAGTGTGGAAGAATTCTTCTTGCGATCGTTCCTTATTAGCGAAGAATTGGATGTCGT
+CGATCAACAAAGCGTCGACCGATCGGTAGTATCGCTTGAATTCTTCGATAGCATTATTTT
+GCAAAGCCTTGACCATGTCTTGGACGAATCGTTCCGAGTGCATGTAGACGACCTTAGCAT
+TCGGCTTTCGAGCCATGATATCATTACCGACAGCGTGCAACAAGTGAGTCTTACCCAAAC
+CAGTACCACCGTACAAGAACAACGGATTGTAAGCACCACCCGGATTGTCAGCGACTTGTC
+GAGCAGCAGCTCGAGCCAATTGATTCGACTTACCTTCGACGAAATTGTCGAAAGTGTGCT
+TGACATTGACATTCGATCGGTAAGTCGGTTCAGCCGGAGCCGGGACATTGTCCCAACCCG
+ATCGAGTCGACGGAGCAGCTCGATGCGGTTGAGTTTGAGCGACTTGAGCCGGAGCAGCGA
+CATTCGAAGTGACAGCAGCTTGCGGAGTTTGAGTGACCGGCTTAGTACCGACTTCGAATC
+GCAATTGCGGAGCGTCAGCACCGCAGAACGAAGTCAACAAACCATTGATATTATTCAAGT
+ACTTGTCTCGGACCCAGTCCAAGACGAATCGATTCGGAGCGTACAAAGCCAAAGTATTGT
+CCGACAATTCAGCTTGCAACGGTCGGATCCACATCGAGAATTCAGTAGCCGGCAATTCGT
+CTTGCAATCGAGCCAAGCATTGTTGCCACAACGACAACGACATGATTGGACAACAATCAA
+GGGCTCGCCCGCATTCCAGCACCCAGAATCCTTCTCATACCTCTCACCATCGTTCGGCTT
+TCCGAATGCATCGGATTGTTACCGTACCATAGCGTATCATTTTAAGTGGTGAATCGGAAC
+TATCGCGCAGAGTGCCGAGAATGTTTTGAAGGGTTGGACAGTCCTGACCCTTGTATATGT
+GTGTGAAAATCCGGAGCAAATCGAGGTGCTTACTGAGTGGGAGTCCCAAAGCTTCTTGGG
+GATCGGGGTCGCCACGCGGCCTCCCCTAGATATTATCGTGCGAGGACTGCCAGTGGCCAA
+CGCTATGAATTATTAATTGGTACTCGTCCTCCTCGTTACGGCAAAGCCGATCGCTAACCG
+AGTCGGAGGGTCGGCTGTTGCCGTGACGGCAGGGAGGGACCTATTGTATCGCCGCTCTAA
+TTAGTTGCCCCACTTCAATTCCGCCCTCCAACTTAGATTACACCGACCCGTATCGTGTTG
+GTGTACCGAGTCGCGCGGGATTGCCTTGCCTACGGACGACCGTACTCGGGGAAGCGCAAC
+GATCGCCCCAGCACGCCATATATCACAAGTCGTGGACCATCTCTAGTTGTTGACGAGATT
+CAGCGGGGGGCAACCCGGCCTTGCGAAGGGAATCATCCTGCCACGGTACCGTGGCCGCTA
+AGTCAGCGAGAAACCGTCGTTTCTACTGACCATATAACTATTCGGGTCGACTTGCCGGTT
+GGCGCTCGTCCCCGTACCTACTTAGCTTTTCGGTAACCATAACTCCCTCTATCAAGGAAA
+TCCTTGCTCCCCGGGACCTCGTCAGCGAGGGCCCCGGATCCGGCGTTTTGACCATGTGGT
+GCTTATTGATGGTGCAATAAAACAGTCTGGGAGACTTTGAGCAAAGGCAAGAGAACCCGC
+ATTAAATACTGGGGCTCCGAGTTCTTGGCGGTGATCGTAAAAACGCAAACCTTTTCGCAC
+GGAACTAAGCGAGTTATCGAGGCCCAGGGTCACGATTATCATGGATAGACTTACATTAAA
+TCACAGAGCAGAAGGAGAGAAGCTATCTGACGTGTCAGGTCATGTAGCCTTCCCAGATTC
+AGTTGTAGAGCGCCAACCAGTAGGGCGTACACTACCAAAGTGGGGGAAGCCACTGCAGGT
+ACGCCGTCAGCTAGTAACTCTTGGTGGTCAACACCGGGCCACTACGCCTACCGTAAGGTC
+GATAAAACCAAATAACAAGTCGACATCCTGGCCCTAAGTTCATTGGTGAAGAGGGTAATT
+CGGTCGCTAGTTGCCAGTTACGCGTAACACTCGAGCTGGAACGTACAGATCACGCGCATG
+ACTTCCCGGAAGAGATCTACACCATCGGCGTGGGGTACAGAATATTTGACCTGCATTTCA
+CTGGCTCTAGAGTACGGTATAGGCCACTAACTTGTATGTTCCGAACGGGTACGGTGAGAA
+AAACGACCGTCAAATTTTGTCAACACGAAGGCGAGCTTAGTGGATGGGGCATAGGCTAGT
+CTCATTTCTATGACAGTTAGTTTCGAATACTGGGCTGGGGCAATGAAATTAGGTGGGAGA
+GATCAGGATTAAAGAGCTTGAATGGGTTAGGACCCTTTGTAGTAAGTCACGGCATTAATT
+TCAATGCTAAAGTTATGATAGGGTGCAGAGGCGGGTGAAACATGGCTAGTGTCATAGGAC
+GTTAGTCCTGTTAGGTCCAACCCACTCCTCCTAGGACCGACAATAGGAACCGTTATTCTG
+TAGGCTACGGTCCGGGTGACCAAAATTAGAGCCAAACCTGGCGGGCCGACCCTCAATGTA
+GGGACCTGATATTAATTGCAACCCGAGACCACTTGTGCTCCCTCCGTTCCTCTGAGATCT
+ACTTAGGGTGCTACCGTGTGCGCGTCCTAGTAGGACGTGTGCGATTCTTTGATGGTATTC
+GTCGTATTGTTGTATGAGACCATAAGGTCTAAGTTAAATCAGGAGAGACCGAACAGTACT
+CG
+>promer_ctg3
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAGCCTAAACCGTATGTGCCTCAAAAACAAGCGTACCT
+ACGCAGTCGGGTGTGTTAACTCAGGATCCAACCAGGTGCGGGGCGGAACCGTAGTTGCTA
+GATGTGGCGAAAGTTTTCCGTTCGATTGTTCCGGCTGGCTTCTCGACTGATGCTCGGCTT
+GACCCGCTTACGAACGGTCCGATAAAGTCCAACACAGTCTCCCCACTTGATGTTCCGGAT
+CAGTCCCATTGCTTGCCCCCGGGTGTTCGTTAACCCGCTGCTGGTTTGCCACGTCAAACA
+CCACCGCTCTCAAACGCGGACTCGAAACGGCTGCACCGTAAGGAAGAACCACACAAACAC
+GTATCTTAGGCCAGGTCAGCTGGGGGTTCGTAGTACTCCACGAACCCTACGATGGCCGCA
+ACCTTAAGAAGTTGTAAATATTGCGGTCAGCAGCCCTGACATGATGCAACGCGATTCACA
+TTGACTAAGTGTAGCATCACGACGCCAGCTGGTAGTTAAGTAATGCGTGGATGGCTTGGT
+CCGGGCTTCGCTGCACGTAGTTGGACGCATCAAAGCCAATTCGGGCCCGCCTTACCGCGT
+CCAAGTGGCACCATTGCGGCCAGTAACTCTGACACAATGATGGAGCCCTAATTCGGGCCT
+ATCCACAGCACTGTACATATTCCTCTCGTAGGCATTAAGATACGGACGGATCTATATTTC
+CTGGGTTCGAGTTGAGCACGTTGTCGCTCCTCATATTTTCTGTTGTATCAGCCTTGGATG
+GTTACCGCCGATATCCACCCGTCCTTTCAGAGTCTTCACGCGCTTAGGCGGCCTACTTAC
+CGGGCCCCTGCAAGAATCACAAGTTTCGTACGCCTGTATTTCGCTGAGAAAGCCACGGAT
+CTCTGGGTCATAGGGCTGATTCTTTCAATTTCTTTTTCGGTCATCCACAAGAGCGGTCGG
+ACAGCACGCTTGGCGTACATGAGTGATCGCGATCTATATTGGAAGAAATGCATCCACGCA
+CTCTTTGATGCATGCGGGGATTTAAGAGCGGTTCTGATCTACTATTTCGTATAGTCCGTA
+AGATCCGAGTTCGATCCTTTATAAGAGACGATTTACGTCCTTCATGCCTACAGCCCCAGA
+GTAGCTTACGGGGTGTCCTGGGTGGTGCCTGGCAGGAGCGTGCGATCTCCCAAGATGAAT
+CCTCCCTTGGCCTCATATCCTTTCTGTACTGTTTCCGTATGAGAGGTGGACATATGGTGT
+GTGAGGACTTCCCGCACTGTAGAACAGACTAAGTAATTAGAGAAAAAACCGTCATCGCGC
+CGAGTAAAGGGGAGCTCCGAGTTGGACAGGCTTCCCTGTCGAAGGCTACGGGAGAACTTA
+CAAGAGCGCGCGCTTGTATGTTCGCTCCATCCAAATGACTCGCGCGCCCCCGGTTGATCT
+CCAACAGATCTGCTGTGTACTCCTCCTCATATAGATGACCGCGGTCGGCTCATCCAACGG
+GAGGCGTGGCCGAAAAAACTCTCCTAACCTTCCCGCTTCTGGTGAACTTTATTACGAACT
+CTACGCTACTAGAACGGTACATGGAAGAAACGGAGAAACCTTTCGCAAGTCAGCGGATTG
+CGTTCCCTGTTGTGGTCCTGAAAGTAGTTAAGATATACCGATCGGCTTTTTACGAAGGAC
+ACTGGTCACCTGCATACCCAGGCTAATCCTATAAGTAGGGTGTAACTCCAAGGTCTAGCG
+TGTTCATTCCGTGAGATATATGCGTCCAACGCTGCTATAGAAGAAGTGCGACGCTGAGAT
+ATGTCTTCGTTCGCGTGAAAATGAGAAACTAAGAAAACACCACTTCTCCACGTAGGCCTT
+ACAGAAATAAGCGATGCTTTCTTGCTGCACCTTCGGATGAAGACTAGGTATAAACAATAT
+TAGAATGAGGTCCGTTCTATCGGCGGAATAATTGCGCTCAAAATTTACCATTGGGGCCAA
+CGCGCCCACAGTCGAGACCGAAGGGGATGGCCCTATCACGACTGGCGGAAGCCTCCCGAG
+GAGAAGAGTCTCCTAAGACGATTTATGTGAGCACTGCAGTAGTTTGAAGGCGACCAAGTC
+GGTGCGGGGTCCTGACATGAGAAGTCTCCTACCAGAGCCAGACCCTGTTTCGAATGGTCT
+ACAATCCTTCTCGTCGGAACCATCCCGTGTGTACCACCACGCTGAAATGACTAGTCTATG
+TGAGGAACCACCTTACCGTCCCATTGTCATATCTCTCCTCGTCGAGATAAGCTCGACGCG
+GCAGTGTAAACATGGTCGATCGTTGGGTGGGGGGACCTTGGTGTAGAATATGCGGAGGTC
+TCAAACTCGGGGTAGAGAGGCATTGGAACATCTGGGCCGGCTATAGGTATAATCTTATAG
+ACCAATTCATGGCGATTAGGCCGGTCGGCTACGGCCTTAATCTCACAGTTGCGTGAATGA
+CCTACGACCATCTAGATTGGATAATAATCCGGTAAGCGTTCTCGCCAACTATTGTGGTAT
+TGGATGGAGTCAGAGCCTCGGAAACGACACCTGCCGTAAGAACGAGACTACGTGCAACAC
+GCGAGGTGTCGCCCTGGTGTGCAGAATGCCTCAAACATCTTGCTCCTACCTCAGACTGAT
+ATGGAACTACTGCACGGGCAGTTCCGAATGGCAAGAAGGGATTGCTGCTACCTGTTGTTG
+ATTGAACATTGGATAAGAGGACAGCGCAAACGAACGAATATGCTACCAAAAGATATTTAG
+AACGGACAATTACGGGAGAATAACGGGTGACCATTTGCCGAACCACTCCGAATTCTAAAT
+TCTGGCTGGTAAGGGCTAATTGCTATATTTGAAGCAGCGCACTTTAAGCCGGGCACCATC
+AATAGGGGATCGTCACCATTGAGGAACTTCAGCTAGATGCGGGGCAGCCTATTAGACTAC
+GATGATATCAGGCGACTACGTAAGGACGAGGATGCTCGCCTCTCGGTTAGAATTCGACCC
+CTAGGAAGGCCGCGCAAGCCAGTGTGCCTATGGGCTATCACAGCGTTGTTCCAGCAGACC
+CCATTCTTGCGTTAAGGGAGTTCAGCCCATTTCAGCTTGGGGGTTCTTACAGGGACATAG
+TAAATGTACGGGCACGGAGTTTGCGTCTTGTTTTGGGGCTTGGAGTTAATCGTTGATATT
+ACGGATACTTAACCTACCAGAGTTGGTAGTAAGGACTGGGTGTGTGTTTTTTCCAGAGCC
+AGCTGGCTTTGGTCGATAAGACCTTAAAATCTGCAATTTTTGTCGCAACGCGCAAACGCC
+CAATCCTCCCCAGGTCTAAGGCCAGTGAGATGAGTTTCACCGCTAACGTTTAGGCGGCAT
+CACTGGCTAGCAAACGTAGGGAACCGGGCCCTGCCCCGAGCTTGCTATACTATGCAGGTC
+GATCTTAATAGAGCTGACGCAACTTGGAGGAACCTGACTTGGGCACTTCTGACAAGCACA
+ATAAGATTGCGGATCAGTAGTTCTGATCAGAACATTGACGCACCCTGACGGGCAGGATCA
+TTGTTATGAGAATTGCCTATGCGTCGCCCGTCTAGTAGTTACACCCCTATAACCACATTA
+GGGCCAGAGTCGCTTGGAAAGCCCCTCGCTGATAAATATGGAAGACCCCGAGGCTAGATT
+GAGTGCGGGCAAAGACTCCCAATGCAACCTGGCTGCAACCCAGCGGTCTAAGATAAGTTG
+TCAAACCCCATTTTAAGTGAATGAAGCCGGACCTAAAGCGGCCCGGAGTAGCTTTCACAA
+TACCTCAGTCATGGTGATGGTGTGCTAGGTCCTCGATTTAGGTTTGGATAGACCAATTTA
+GCACCTCAAGTAGAACGGGATCATGAACTAGGACAGGAGGGAAACTGGGCGCAGACTCCA
+AGATATCGCGTCCGAACAATGGTTTAGAGCCAGCCTATTGTGTGAAGGCTATTACGATGC
+GTTGAACACGTACTAACGTCGATCTCTAGACATGTTCAGGTCTAATTCGCGCATTCCGGG
+GCAAATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGC
+TACTGAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGC
+TTTGTACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATAT
+CAATGGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGG
+TACTAAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGC
+TCAAGTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAA
+TGTCCCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGA
+CAATTTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGA
+CAATCCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGAC
+TCACTTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGT
+CTACATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTAT
+CGAA
+>promer_ctg4
+TTCGATAGCATTATTTTGCAAAGCCTTGACCATGTCTTGGACGAATCGTTCCGAGTGCAT
+GTAGACGACCTTAGCATTCGGCTTTCGAGCCATGATACCATTACCGACAGCGTGCAACAA
+GTGAGTCTTACCCAAACCAGTACCACCGTACAAGAACAACGGATTGTAAGCACCACCCGG
+ATTGTCAGCGACTTGTCGAGCAGCAGCTCGAGCCAATTGATTCGACTTACCTTCGACGAA
+ATTGTCGAAAGTGTGCTTGACATTGACATTCGATCGGTAAGTCGGTTCAGCCGGAGCCGG
+GACATTGTCCCAACCCGATCGAGTCGACGGAGCAGCTCGTTGCGGTTGAGTTTGAGCGAC
+TTGAGCCGGAGCAGCGACATTCGAAGTGACAGCAGCTTGCGGAGTTTGAGTGACCGGCTT
+AGTACCGACTTCGAATCGCAATTGCGGAGCGTCAGCACCGCAGAACGAAGTCAACAAACC
+ATTGATATTATTCAAGTACTTGTCTCGGACCCAGTCCAAGACGAATCGATTCGGAGCGTA
+CAAAGCCAAAGTATTGTCCGACAATTCAGCTTGCAACGGTCGGATCCACATCGAGAATTC
+AGTAGCCGGCAATTCGTCTTGCAATCGAGCCAAGCATTGTTGCCACAACGACAACGACAT
+TTGCCCCGGAATGCGCGAATTAGACCTGAACATGTCTAGAGATCGACGTTAGTACGTGTT
+CAACGCATCGTAATAGCCTTCACACAATAGGCTGGCTCTAAACCATTGTTCGGACGCGAT
+ATCTTGGAGTCTGCGCCCAGTTTCCCTCCTGTCCTAGTTCATGATCCCGTTCTACTTGAG
+GTGCTAAATTGGTCTATCCAAACCTAAATCGAGGACCTAGCACACCATCACCATGACTGA
+GGTATTGTGAAAGCTACTCCGGGCCGCTTTAGGTCCGGCTTCATTCACTTAAAATGGGGT
+TTGACAACTTATCTTAGACCGCTGGGTTGCAGCCAGGTTGCATTGGGAGTCTTTGCCCGC
+ACTCAATCTAGCCTCGGGGTCTTCCATATTTATCAGCGAGGGGCTTTCCAAGCGACTCTG
+GCCCTAATGTGGTTATAGGGGTGTAACTACTAGACGGGCGACGCATAGGCAATTCTCATA
+ACAATGATCCTGCCCGTCAGGGTGCGTCAATGTTCTGATCAGAACTACTGATCCGCAATC
+TTATTGTGCTTGTCAGAAGTGCCCAAGTCAGGTTCCTCCAAGTTGCGTCAGCTCTATTAA
+GATCGACCTGCATAGTATAGCAAGCTCGGGGCAGGGCCCGGTTCCCTACGTTTGCTAGCC
+AGTGATGCCGCCTAAACGTTAGCGGTGAAACTCATCTCACTGGCCTTAGACCTGGGGAGG
+ATTGGGCGTTTGCGCGTTGCGACAAAAATTGCAGATTTTAAGGTCTTATCGACCAAAGCC
+AGCTGGCTCTGGAAAAAACACACACCCAGTCCTTACTACCAACTCTGGTAGGTTAAGTAT
+CCGTAATATCAACGATTAACTCCAAGCCCCAAAACAAGACGCAAACTCCGTGCCCGTACA
+TTTACTATGTCCCTGTAAGAACCCCCAAGCTGAAATGGGCTGAACTCCCTTAACGCAAGA
+ATGGGGTCTGCTGGAACAACGCTGTGATAGCCCATAGGCACACTGGCTTGCGCGGCCTTC
+CTAGGGGTCGAATTCTAACCGAGAGGCGAGCATCCTCGTCCTTACGTAGTCGCCTGATAT
+CATCGTAGTCTAATAGGCTGCCCCGCATCTAGCTGAAGTTCCTCAATGGTGACGATCCCC
+TATTGATGGTGCCCGGCTTAAAGTGCGCTGCTTCAAATATAGCAATTAGCCCTTACCAGC
+CAGAATTTAGAATTCGGAGTGGTTCGGCAAATGGTCACCCGTTATTCTCCCGTAATTGTC
+CGTTCTAAATATCTTTTGGTAGCATATTCGTTCGTTTGCGCTGTCCTCTTATCCAATGTT
+CAATCAACAACAGGTAGCAGCAATCCCTTCTTGCCATTCGGAACTGCCCGTGCAGTAGTT
+CCATATCAGTCTGAGGTAGGAGCAAGATGTTTGAGGCATTCTGCACACCAGGGCGACACC
+TCGCGTGTTGCACGTAGTCTCGTTCTTACGGCAGGTGTCGTTTCCGAGGCTCTGACTCCA
+TCCAATACCACAATAGTTGGCGAGAACGCTTACCGGATTATTATCCAATCTAGATGGTCG
+TAGGTCATTCACGCAACTGTGAGATTAAGGCCGTAGCCGACCGGCCTAATCGCCATGAAT
+TGGTCTATAAGATTATACCTATAGCCGGCCCAGATGTTCCAATGCCTCTCTACCCCGAGT
+TTGAGACCTCCGCATATTCTACACCAAGGTCCCCCCACCCAACGATCGACCATGTTTACA
+CTGCCGCGTCGAGCTTATCTCGACGAGGAGAGATATGACAATGGGACGGTAAGGTGGTTC
+CTCACATAGACTAGTCATTTCAGCGTGGTGGTACACACGGGATGGTTCCGACGAGAAGGA
+TTGTAGACCATTCGAAACAGGGTCTGGCTCTGGTAGGAGACTTCTCATGTCAGGACCCCG
+CACCGACTTGGTCGCCTTCAAACTACTGCAGTGCTCACATAAATCGTCTTAGGAGACTCT
+TCTCCTCGGGAGGCTTCCGCCAGTCGTGATAGGGCCATCCCCTTCGGTCTCGACTGTGGG
+CGCGTTGGCCCCAATGGTAAATTTTGAGCGCAATTATTCCGCCGATAGAACGGACCTCAT
+TCTAATATTGTTTATACCTAGTCTTCATCCGAAGGTGCAGCAAGAAAGCATCGCTTATTT
+CTGTAAGGCCTACGTGGAGAAGTGGTGTTTTCTTAGTTTCTCATTTTCACGCGAACGAAG
+ACATATCTCAGCGTCGCACTTCTTCTATAGCAGCGTTGGACGCATATATCTCACGGAATG
+AACACGCTAGACCTTGGAGTTACACCCTACTTATAGGATTAGCCTGGGTATGCAGGTGAC
+CAGTGTCCTTCGTAAAAAGCCGATCGGTATATCTTAACTACTTTCAGGACCACAACAGGG
+AACGCAATCCGCTGACTTGCGAAAGGTTTCTCCGTTTCTTCCATGTACCGTTCTAGTAGC
+GTAGAGTTCGTAATAAAGTTCACCAGAAGCGGGAAGGTTAGGAGAGTTTTTTCGGCCACG
+CCTCCCGTTGGATGAGCCGACCGCGGTCATCTATATGAGGAGGAGTACACAGCAGATCTG
+TTGGAGATCAACCGGGGGCGCGCGAGTCATTTGGATGGAGCGAACATACAAGCGCGCGCT
+CTTGTAAGTTCTCCCGTAGCCTTCGACAGGGAAGCCTGTCCAACTCGGAGCTCCCCTTTA
+CTCGGCGCGATGACGGTTTTTTCTCTAATTACTTAGTCTGTTCTACAGTGCGGGAAGTCC
+TCACACACCATATGTCCACCTCTCATACGGAAACAGTACAGAAAGGATATGAGGCCAAGG
+GAGGATTCATCTTGGGAGATCGCACGCTCCTGCCAGGCACCACCCAGGACACCCCGTAAG
+CTACTCTGGGGCTGTAGGCATGAAGGACGTAAATCGTCTCTTATAAAGGATCGAACTCGG
+ATCTTACGGACTATACGAAATAGTAGATCAGAACCGCTCTTAAATCCCCGCATGCATCAA
+AGAGTGCGTGGATGCATTTCTTCCAATATAGATCGCGATCACTCATGTACGCCAAGCGTG
+CTGTCCGACCGCTCTTGTGGATGACCGAAAAAGAAATTGAAAGAATCAGCCCTATGACCC
+AGAGATCCGTGGCTTTCTCAGCGAAATACAGGCGTACGAAACTTGTGATTCTTGCAGGGG
+CCCGGTAAGTAGGCCGCCTAAGCGCGTGAAGACTCTGAAAGGACGGGTGGATATCGGCGG
+TAACCATCCAAGGCTGATACAACAGAAAATATGAGGAGCGACAACGTGCTCAACTCGAAC
+CCAGGAAATATAGATCCGTCCGTATCTTAATGCCTACGAGAGGAATATGTACAGTGCTGT
+GGATAGGCCCGAATTAGGGCTCCATCATTGTGTCAGAGTTACTGGCCGCAATGGTGCCAC
+TTGGACGCGGTAAGGCGGGCCCGAATTGGCTTTGATGCGTCCAACTACGTGCAGCGAAGC
+CCGGACCAAGCCATCCACGCATTACTTAACTACCAGCTGGCGTCGTGATGCTACACTTAG
+TCAATGTGAATCGCGTTGCATCATGTCAGGGCTGCTGACCGCAATATTTACAACTTCTTA
+AGGTTGCGGCCATCGTAGGGTTCGTGGAGTACTACGAACCCCCAGCTGACCTGGCCTAAG
+ATACGTGTTTGTGTGGTTCTTCCTTACGGTGCAGCCGTTTCGAGTCCGCGTTTGAGAGCG
+GTGGTGTTTGACGTGGCAAACCAGCAGCGGGTTAACGAACACCCGGGGGCAAGCAATGGG
+ACTGATCCGGAACATCAAGTGGGGAGACTGTGTTGGACTTTATCGGACCGTTCGTAAGCG
+GGTCAAGCCGAGCATCAGTCGAGAAGCCAGCCGGAACAATCGAACGGAAAACTTTCGCCA
+CATCTAGCAACTACGGTTCCGCCCCGCACCTGGTTGGATCCTGAGTTAACACACCCGACT
+GCGTAGGTACGCTTGTTTTTGAGGCACATACGGTTTAGGCTCACGACGACAAAGTTCGGA
+TCAAATTCGAGAAGTCTTCCTTGATGTCGTGCGATTCTTCTCGCAATTGTTCGATCTTTC
+GGCAAGCGTGCAAGACAGTAGTGTGGTCTCGACCACCGAAAGCGTCACCGATTTCCGGCA
+ACGAGTGATTAGTCAATTCCTTAGCCAAAGCCATAGCCATTTGTCGCGGTCGAGCGACCG
+ATCGCGATCGTCGCTTCGACAACAAGTCAGCGACCTTGATCTTGTAGTATTCAGCGACAG
+TCTTTTGGATATTGTCGATAGTGACCAACTTTTCTTGCAAAGCCAACAAGTCTCGCAAAG
+CTTCTCGGACGAAGTCGATAGTGATAGCTCGACCAGTGAAATTAGCATTAGCGATGACTC
+GATTCAAAGCACCTTCCAATTCTCGGACATTCGATCGCAATCGCTTAGCGATGAAGAAAG
+CGACTTCACCCGGCAATCGGATGTCATTTTCGTCAGCCTTCTTCATCAAGATAGCGACTC
+GAGTTTCCAATTCCGGCGGTTCGATAGCGACAGTCAAACCCCAACCGAATCGCGACTTCA
+ATCGGTCTTCGACACCATTGATTTCCTTCGGGTATCGGTCCGAAGTCAAGATGATTTGTT
+GATTACCTTCCAACAAAGCATTGAAAGTGTGGAAGAATTCTTCTTGCGATCGTTCCTTAT
+TAGCGAAGAATTGGATGTCGTCGATCAACAAAGCGTCGACCGATCGGTAGTATCGCTTGA
+ATTC
+>ignore_ctg
+CCACTGCGGTGATTCACCACTATCGGCAGCTTAATACCACCACACAGGAGTGGGTACGTG
+CACGCTTACTATGTGCCGTAAAAGTCATCAATGACCCCTGAGACGCCTGCCCACCCGCAA
+CGTGGAAGATATCAAGATATCTGAGGTTATACAGTATATTTGCGGTCGGTTGCCGTCGCG
+GCGATTCCTTGTGTGTTGCACTTTTTAGAAGTTACTACAACCCACGCATGAAGTCTCGGT
+TGGACTACCCCTCTTATAGTCATCATGCAGTGCGGGTGGCCTGCTTTCGCAAGGCGTTCA
+GAACTTGGCATAGTGTCGCGCGCGGAGTCCTTTGGCTAACGAGACCGGTTAATCAAAGGC
+ACAGCCTAGTGAAGGTCGAAATAGTTCCGCCCCGATCATACAAAGATATCTCCACGAATT
+GGTGTCGTTTTCGAAGGAAGGCGGACGCCTAAATGTTTGAGAGTACATCAGTCAATTCTC
+CCGAATATCGGTATACCTGTTAGACTATGAACTCATACTTTTCTAACCACCGCTCATCTC
+GTTCCTTATCCGTTATGTCTATACTGAGTCTACAACATGGACATCGCAGGGAGCTCAATT
+GGCTATGGGAGCCAACACTCAGGCTGGGTTACGCAACCCAGATGTCTGCTGGAGTGTTAG
+TGTAAGCTGTAATAAAGACTCTCTCGTGTGCCCTTGAGAGACGACACCCACCGAACTGCG
+TTTACTCAGGGGCAGAACATCCGAATTTTGCCTTCCCGCACATCAGTGGGGGACGACTGC
+GGGCAACAGTAAAGCTAGTCCGATCGCGCTCTGGATGCTATCCGATGTCGGGGGTGAATA
+ATTGGTGAAACTGCCTCCAACAATTCAGAGTCTCTTCTCAACAAGGACGTGTACCGAGGC
+ATAGAGGGGGAATGTCCGCCAGGCCCCAGAGATCTTTGCGACCTACATTGCACAGTATTG
+GTCGTGTTCAATCTTGAACACTTACTATTCACCGAATTGGTGCGCTGTTGACGCTTTCTT
+CCGTAATCACCTCCAAATCTGGGTGTTAGTAACGAGGCCGGCGTGCTTTGAGGAGAGAAT
+ACATGGCACCTTAAAACGACGTACTAGCCTTAGCTTACGCAACCTAGGTTTGTGCACAGG
+CGTACGATCATTGACAGCCGACATCACGAATAACGCGCAAATGGCCTGTATCCTACACGC
+CTTGCCTGCCAAACCGAGTCATTGTGTTGTCGCCGAATGGCATTTCGGCTACGTGAAAAT
+CTTAGATATTTTGCGTGGACAATGTTCGCCTACTTGAGTTCTTCTTGGGTATCTCATGTT
+ATTTCCAGGATATAACGCGTGTCTCGAAATCGACCACAGGCCTTCCTCATACTCTTATGG
+ATGTTACTGCTGTGTACCGATATGGAGATTCTAGGAGAGGGCAATGGGTTCTTCTTACAA
+TTGGCCGGTCGAGCTCTCCACGCCAGATCTCCACTTGACGCCGGGGCGGGAGAAAGTATT
+AACCTTCCATAGAGTCATCATTATGAATGGCGCCTAATGTAGACAGGAAACGGGCTCAGC
+TACCGTCTACCGCAGGTAGTTCGATTCGAATTCACAACGTTTAGTTCTCGTTAAGTGGAC
+ACGATACCGAGCTTTGGTTCGAGTTGAAAGTTACGGTGGGTCTAGATGTAATGATCCGAA
+CGGTGCCGCTAATGCGATGACCGTAGGCCCACTCGCTGTGATAGTGGTCCCTCGTATCGC
+ATTGATCCCTTCTGTTTCCGCACACTAACATGCATCCCCGGGAACTCCTTACACTTGCGC
+ACCGAATCCCGCTGAAGATGCACCTAGATATGTCCCCCTATGATACACTCCTTTTATCGC
+TTCGACATCAGCTGTGCATTAAATGATTGTTTGTGCAAATTCATCACCTACTCTCAGAAC
+GATGAAAACAGGTTGAAGTCTATGGTGTTTGCATGGCAGCTAAAGTCATCTTTCGTGAAC
+GGCAATCTTGAGAGCTGTTATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCA
+AGACGAATTGCCGGCTACTGAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTC
+GGACAATACTTTGGCTTTGTACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAA
+GTACTTGAATAATATCAATGGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATT
+GCGATTCGAAGTCGGTACTAAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAA
+TGTCGCTGCTCCGGCTCAAGTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCG
+ATCGGGTTGGGACAATGTCCCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGT
+CAAGCACACTTTCGACAATTTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGC
+TCGACAAGTCGCTGACAATCCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTAC
+TGGTTTGGGTAAGACTCACTTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCC
+GAATGCTAAGGTCGTCTACATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTT
+GCAAAATAATGCTATCGAAGAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGAT
+CGACGACATCCAATTCTTCGCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTT
+CAATGCTTTGTTGGAAGGTAATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGA
+AATCAATGGTGTCGAAGACCGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTAT
+CGAACCGCCGGAATTGGAAACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGA
+CATCCGATTGCCGGGTGAAGTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCG
+AGAATTGGAAGGTGCTTTGAATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTAT
+CACTATCGACTTCGTCCGAGAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGT
+CACTATCGACAATATCCAAAAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTT
+GTTGTCGAAGCGACGATCGCGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGC
+TAAGGAATTGACTAATCACTCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCA
+CACTACTGTCTTGCACGCTTGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACAT
+CAAGGAAGACTTCTCGAATTTGATCCGAACTTTGTCGTCGTGAACCTCATAAGGCGGCGC
+GGCATGCAGTTATTGAGCAATAATGTCTCATAGTAGGCTCAGGGGCACGACTTATCTCCA
+ACGATAATCCGAAGTTGCGACTCATGTCGTCTGAGCTGCCGGGTTAACAATGGGCACAGT
+CATACTAAGCGCGTCGCAATGAGCACAAGAACAACTCCGGCTGGTGATCTTTTTCGAGTT
+CGTTCGACCGCTGCGAATTTACTCCCACGCGCAGTCCGTAATGCCTACTGCTTTTGCCGA
+CGAACGGAGGATTCCAGTTTCGATCTCCAAGCGGACGAGGCCCAGGGTGGGGCTCCCGCC
+GAACCGCCCTACAATGATAGGGTGGATTTGGCTACGTAATCGCTCAAGCATCGAAATCGC
+AGTGTTAGAAGGGGCGGAGGGACCACCGTACATCCGTGCTACGGAGCATTGCTTGACGTG
+TCTTGCCGCATTCCCAGACTATGTCTATGACCGTGCCCAGCGTCAATTCCTTCAGCTCGC
+GTGACGCCACCATGGTAATAGCCTAGCAAAGGATGAAGCTCACGCCGCGACATACTCCTC
+TGGCTCCTTTTATTGAGGCAGTGTCGTCCGAACCCGTTCGAGCTCATTTAGTTATCAACA
+TTTAGGGACGCAAAACCCGTAATAGGGTCTCTATGGATTGTATCTTGACAGAGAAGTAGC
+TGATCAGGTCGGTCATATCGACAGCAGACCCCGACAGATTGAGCCGTCAACTAAGGGGAG
+CGCTCTAGAACCCAGTTGGAGGAGAGTCATTATTTGACCATGGGCGGAATTTCACTACGT
+CATGTGCCGTATAAAGGCGTCCGGGACGGATGTCGCCCCATGCCAACACTTCCCTTGCCT
+GTTGATCATGCGGAAATGGCCGCAGCAACTGGGGTTGTTTGTGGATATTACTGGTCTTGG
+ACGGAAGATTGGGGAGTAGCCACCTTAAGTTAGTCGGGCATGATTGTGGGTTAGATTCGG
+ACGAGTTTCTTCCGTAGCTTAGTGATCTTACGTTTCTATAACAGAATCGTTTCCAGACTC
+TTGGGCCGACCCTAGTATCCATCTCGCTGTTGCCGTACTAATCATACGCTAGCTACAGAT
+TATCTCTCGATAGCGAGTTTGCGCCCGATCATGTACTCGTAGCCACGGAGGGATAGATGG
+AGATATGGGTCGTAAAGATTCACGGATAGCGACAGGATAGCTCTTGCCCCAGGCTCGTGA
+TGGCCTGCGATCATTCTAACTATTTCCAGCGACATGGACCTCCTGTGGTCAATAAGATAT
+TGGCCCGATTACAGGACTCTGACAGAGCGTCAACCTAACCTGCCTAAGCATGACTACTAG
+GTTGGCAAGCATGGTAATTTCCTAGTGTCACATCCATACTATGTCCCCTTTCCCAAGACA
+CTCCAACAACTCATTATGTCAAGCATCCAAAACGACTATGCTGTCGCACTCCAGCTGCGA
+CATGTTGCAGGGTACGTATAAACTATATCTAGACGTGCCGTATTTATTAGCAGGCCTTCT
+TTATTTACGCTACGCCGACTACGAAACTTCTACGGAGGTAAAATCGGTTAACATCTCGTG
+CGTACTGCTCTATTCAGGAGCACTATGTGGCGCACTAGGTATACCAGCCCCTGGCGTCCT
+GCTGATTAATGGTCAAAGCGAGTCTGGATTACACAGAAAGCCCTAATACCCTGTGATAAG
+ATGTGCCCACATATAAAATTCACTAGTCCGCAGTTGCCCGCCGGCCGGTTCTCCCCAGTC
+CAAAGCTAAGAGTGTGAGACCTACCAGCAGAGATCTAGACCTTCCCATTTGATGTATCGC
+AACAGGCATTGGCCATGCCGGGCGCGGTATTAACTCTCCAGAGCTTAAGCGTTGAAATCC
+GCGCTGTCGTGGTCAACGTATTGTGTCTGTGCTGCCTAGGGTGCGACATCCATGAATAAC
+AGCCAGGTATAAAACGAATTTTTTCATTGTGAAGTCTTCTGCATTACTTCGCTGAAGGTT
+TT
+>prodigal_ctg1
+GCCTAAACCGTATGTGCCTCAAAAACAAGCGTACCTACGCAGTCGGGTGTGTTAACTCAG
+GATCCAACCAGGTGCGGGGCGGAACCGTAGTTGCTAGATGTGGCGAAAGTTTTCCGTTCG
+ATTGTTCCGGCTGGCTTCTCGACTGATGCTCGGCTTGACCCGCTTACGAACGGTCCGATA
+AAGTCCAACACAGTCTCCCCACTTGATGTTCCGGATCAGTCCCATTGCTTGCCCCCGGGT
+GTTCGTTAACCCGCTGCTGGTTTGCCACGTCAAACACCACCGCTCTCAAACGCGGACTCG
+AAACGGCTGCACCGTAAGGAAGAACCACACAAACACGTATCTTAGGCCAGGTCAGCTGGG
+GGTTCGTAGTACTCCACGAACCCTACGATGGCCGCAACCTTAAGAAGTTGTAAATATTGC
+GGTCAGCAGCCCTGACATGATGCAACGCGATTCACATTGACTAAGTGTAGCATCACGACG
+CCAGCTGGTAGTTAAGTAATGCGTGGATGGCTTGGTCCGGGCTTCGCTGCACGTAGTTGG
+ACGCATCAAAGCCAATTCGGGCCCGCCTTACCGCGTCCAAGTGGCACCATTGCGGCCAGT
+AACTCTGACACAATGATGGAGCCCTAATTCGGGCCTATCCACAGCACTGTACATATTCCT
+CTCGTAGGCATTAAGATACGGACGGATCTATATTTCCTGGGTTCGAGTTGAGCACGTTGT
+CGCTCCTCATATTTTCTGTTGTATCAGCCTTGGATGGTTACCGCCGATATCCACCCGTCC
+TTTCAGAGTCTTCACGCGCTTAGGCGGCCTACTTACCGGGCCCCTGCAAGAATCACAAGT
+TTCGTACGCCTGTATTTCGCTGAGAAAGCCACGGATCTCTGGGTCATAGGGCTGATTCTT
+TCAATTTCTTTTTCGGTCATCCACAAGAGCGGTCGGACAGCACGCTTGGCGTATGTCATC
+AATCCGGCGCCGGCACGCCGCCGCTTCGCTCGACACCCCTGCCGTGGGCGGCAGGCACGA
+ACTCGGTCAGAACTTCCTCGTCGACCGAGGTGTATGCACAAGGATCGCCGAGGTCGTCTC
+CTCGACGACGGCCCATCCGGTCCTCGAACTGGGCGCCGGTGACGGTGCCATCACCCGGGC
+CCTGGTCGCGGCGAATCTCCCGGTCACCGCGCTGGAACTCGACCCCCGGCGGGTCCGGCG
+GCTCCAGCGGACCTTCGCCGACGGGGTCACCGTCGTGCACGGGGACATGCTCCGGTACGA
+CTTCGGGCCGTACCCGCACCACGTGGTGTCGACCGTGCCGTTCTCCATCACCACGCCGCT
+GCTCCGGCGCCTGATCGGCCAGCGGTTCTGGCACACCGCGGTGCTGTTGGTGCAGTGGGA
+GGTGGCCCGTAAGCGGGCCGGTGTGGGCGGCACCACGATGCTCACCGCAGCCAGTTGGCC
+GTGGTACGAGTTCACCCTGGTGGAGCGGGTGCCGAAGACCTCGTTCGACCCGGTGCCGAG
+CGTCGACGGCGGCATCCTCGTCATCGAGCGTCGATCCGCGCCGCTGCTCGACGACCGCTG
+CGTGGGTGACTACCAGAACCTGGTACGCGAGGTGTACACCGGTCCCGGTCGTGGTCTGGC
+CGCGATTCTCCGTACCCGTCTGCCCGGTCGTGAGGTGGACGCCTGGCTCCGCCGCGAGCG
+GGTGGACCCGGCGGCCCTGCCCCGCGACCTCAAGGCCGGGCACTGGGCATCCCTCTACCG
+GCTCTACCGGGAGGTGGGTACTCGGCCCGCCCCTGCCGGCCGGTCCGTCCGGGCCCGGCC
+CGGATCCGTCGGCCCCGACCGCTCGCTCCCTCCGCGCGGCCTGCGATCCGGTCCGCCGAG
+GGCTCGACGACGTGGTGGAGGCGCCTGAGACAGGCTTCCCTGTCGAAGGCTACGGGAGAA
+CTTACAAGAGCGCGCGCTTGTATGTTCGCTCCATCCAAATGACTCGCGCGCCCCCGGTTG
+ATCTCCAACAGATCTGCTGTGTACTCCTCCTCATATAGATGACCGCGGTCGGCTCATCCA
+ACGGGAGGCGTGGCCGAAAAAACTCTCCTAACCTTCCCGCTTCTGGTGAACTTTATTACG
+AACTCTACGCTACTAGAACGGTACATGGAAGAAACGGAGAAACCTTTCGCAAGTCAGCGG
+ATTGCGTTCCCTGTTGTGGTCCTGAAAGTAGTTAAGATATACCGATCGGCTTTTTACGAA
+GGACACTGGTCACCTGCATACCCAGGCTAATCCTATAAGTAGGGTGTAACTCCAAGGTCT
+AGCGTGTTCATTCCGTGAGATATATGCGTCCAACGCTGCTATAGAAGAAGTGCGACGCTG
+AGATATGTCTTCGTTCGCGTGAAAATGAGAAACTAAGAAAACACCACTTCTCCACGTAGG
+CCTTACAGAAATAAGCGATGCTTTCTTGCTGCACCTTCGGATGAAGACTAGGTATAAACA
+ATATTAGAATGAGGTCCGTTCTATCGGCGGAATAATTGCGCTCAAAATTTACCATTGGGG
+CCAACGCGCCCACAGTCGAGACCGAAGGGGATGGCCCTATCACGACTGGCGGAAGCCTCC
+CGAGGAGAAGAGTCTCCTAAGACGATTTATGTGAGCACTGCAGTAGTTTGAAGGCGACCA
+AGTCGGTGCGGGGTCCTGACATGAGAAGTCTCCTACCAGAGCCAGACCCTGTTTCGAATG
+GTCTACAATCCTTCTCGTCGGAACCATCCCGTGTGTACCACCACGCTGAAATGACTAGTC
+TATGTGAGGAACCACCTTACCGTCCCATTGTCATATCTCTCCTCGTCGAGATAAGCTCGA
+CGCGGCAGTGTAAACATGGTCGATCGTTGGGTGGGGGGACCTTGGTGTAGAATATGCGGA
+GGTCTCAAACTCGGGGTAGAGAGGCATTGGAACATCTGGGCCGGCTATAGGTATAATCTT
+ATAGACCAATTCATGGCGATTAGGCCGGTCGGCTACGGCCTTAATCTCACAGTTGCGTGA
+ATGACCTACGACCATCTAGATTGGATAATAATCCGGTAAGCGTTCTCGCCAACTATTGTG
+GTATTGGATGGAGTCAGAGCCTCGGAAACGACACCTGCCGTAAGAACGAGACTACGTGCA
+ACACGCGAGGTGTCGCCCTGGTGTGCAGAATGCCTCAAACATCTTGCTCCTACCTCAGAC
+TGATATGGAACTACTGCACGGGCAGTTCCGAATGGCAAGAAGGGATTGCTGCTACCTGTT
+GTTGATTGAACATTGGATAAGAGGACAGCGCAAACGAACGAATATGCTACCAAAAGATAT
+TTAGAACGGACAATTACGGGAGAATAACGGGTGACCATTTGCCGAACCACTCCGAATTCT
+AAATTCTGGCTGGTAAGGGCTAATTGCTATATTTGAAGCAGCGCACTTTAAGCCGGGCAC
+CATCAATAGGGGATCGTCACCATTGAGGAACTTCAGCTAGATGCGGGGCAGCCTATTAGA
+CTACGATGATATCAGGCGACTACGTAAGGACGAGGATGCTCGCCTCTCGGTTAGAATTCG
+ACCCCTAGGAAGGCCGCGCAAGCCAGTGTGCCTATGGGCTATCACAGCGTTGTTCCAGCA
+GACCCCATTCTTGCGTTAAGGGAGTTCAGCCCATTTCAGCTTGGGGGTTCTTACAGGGAC
+ATAGTAAATGTACGGGCACGGAGTTTGCGTCTTGTTTTGGGGCTTGGAGTTAATCGTTGA
+TATTACGGATACTTAACCTACCAGAGTTGGTAGTAAGGACTGGGTGTGTGTTTTTTCCAG
+AGCCAGCTGGCTTTGGTCGATAAGACCTTAAAATCTGCAATTTTTGTCGCAACGCGCAAA
+CGCCCAATCCTCCCCAGGTCTAAGGCCAGTGAGATGAGTTTCACCGCTAACGTTTAGGCG
+GCATCACTGGCTAGCAAACGTAGGGAACCGGGCCCTGCCCCGAGCTTGCTATACTATGCA
+GGTCGATCTTAATAGAGCTGACGCAACTTGGAGGAACCTGACTTGGGCACTTCTGACAAG
+CACAATAAGATTGCGGATCAGTAGTTCTGATCAGAACATTGACGCACCCTGACGGGCAGG
+ATCATTGTTATGAGAATTGCCTATGCGTCGCCCGTCTAGTAGTTACACCCCTATAACCAC
+ATTAGGGCCAGAGTCGCTTGGAAAGCCCCTCGCTGATAAATATGGAAGACCCCGAGGCTA
+GATTGAGTGCGGGCAAAGACTCCCAATGCAACCTGGCTGCAACCCAGCGGTCTAAGATAA
+GTTGTCAAACCCCATTTTAAGTGAATGAAGCCGGACCTAAAGCGGCCCGGAGTAGCTTTC
+ACAATACCTCAGTCATGGTGATGGTGTGCTAGGTCCTCGATTTAGGTTTGGATAGACCAA
+TTTAGCACCTCAAGTAGAACGGGATCATGAACTAGGACAGGAGGGAAACTGGGCGCAGAC
+TCCAAGATATCGCGTCCGAACAATGGTTTAGAGCCAGCCTATTGTGTGAAGGCTATTACG
+ATGCGTTGAACACGTACTAACGTCGATCATGCGTTATATTCGCCTGTGCCTTTTCTCCCT
+GATTGCCGCCCTGCCACTGGCGGTATTCGCCAGCCCTCCGCCGCTTGAGCAAATTACACG
+CAGCGAAAGTCAGCTGGCGGGCCGCGTGGGCTATGTTGAAATGGATCTGGCCAGCGGCCG
+CACGCTGGCCGCCTGGCGCGCCAGTGAGCGCTTTCCGCTGATGAGCACCTTTAAAGTGCT
+GCTCTGCGGCGCGGTGCTGGCCCGGGTGGATGCCGGAGACGAACAGCTGGATCGGCGGAT
+CCGCTACCGCCAGCAGGATCTGGTGGACTACTCCCCGGTCAGCGAAAAACACCTTGCCGA
+CGGGATGACCGTTGGCGAACTCTGCGCCGCCGCCATCACCATGAGCGACAACAGCGCCGG
+CAATCTGCTGTTGAAGAGCGTTGGCGGCCCCGCGGGATTGACCGCTTTTTTGCGCCAGAT
+CGGTGACAACGTCACCCGCCTCGACCGCTGGGAAACGGAGCTCAATGAAGCGCTTCCCGG
+CGACGTGCGCGACACCACCACCCCAGCCAGCATGGCCACCACCCTGCGCAAGCTGCTAAC
+CAGCCACACTCTGAGCGCCCGTTCGCAGCAGCAGCTGCTGCAGTGGATGGTGGACGACCA
+GGTAGCCGGTCCGCTGATCCGCGCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAAAC
+CGGGGCCGGCGAGCGGGGCTCACGTGGCATTGTCGCCCTGCTCGGCCCGAACGGCAAAGC
+GGAGCGCATCGTGGTGATCTATCTGCGGGATACGCCGGCGACCATAGCCGAGCGTAACCA
+GCAGATCGCCAGAATAGGCGCGGCGCTGATCGAGCACTGGCAACGCTAATCAGTGCTCAG
+TTAAATGGCGTCTGCAGGATTAATATCGGGGTTAATGAACCGGCCAAAATGTAACATTGG
+CCTCACTGGAACGAAGCTCCTAGTCCCAACCAGCCTCGCCCAAGTTCCCTGTTTGTGATA
+ATGGCCCGAGGTCCAGAGAGTTATCTGTCTCGTACGGCGCCGGTTAGGATCATCATGACT
+TCGGCAGAACCCCACACTGTCATATCAGCCCAGCTCGCATCCAAACGGCCTGCTGCCTGC
+TCCAGCGTCCCCGAATGGCGCGATGTCCCCTACAACAGTTGTAGCTGGAATGAGACGGAT
+GCTGTGTAATGTGTGTTTGCGTCGAAGGAAAGGCTCATCTCAAGATTTACTATCTAATGA
+ACATGCGGCAATCCACGTTGGCAGTAAGATGCGCGAGGTCGGAACTGCCTCCGTGGTTCG
+CAAGTAATGTCGTCCCCCCTGTCTTCACCTGTGTTTGTGGTCCCCCCTGTCTGTCCGACT
+CATATTAATTCATTATATTAATTGGTATACCTGCATTAGATTATGCCATTAATAGTTCGC
+CCGGATCTTTTACGGATCGCCTCCGAAAATGTAGCGCTAAAAGGCGCCGCCCCAATCCCA
+AGATTACGCATTCTAACTTACACGCTTACGGTATGAATCTCGGATCAAGTAAGGTTAGCT
+TTGTAGCATACCCGACCCAAAACTGCATGTACCCATGGATCCTTCGCGTCTTTCTAACTC
+TTAAATGAGCAATTTGAACTACGCACACACACCTCTTTACTACGTCTAAGATATATTTTC
+AACTAACAACGGAGACTCTCGATTCACGAAATCCGTACCTATCACTATCGCTGTATCACA
+TTGTTACCTATAGCAGACGTTTCACGTATTCCACGTATGGAGGATCACCAGGCATGCTTT
+TAGACCACAACAGCTGGCAGAAGTCTACCGCCCACCCGGGCTGGACGGGATCAAGGTCCA
+AACTCAAGGACAGTGATGTTCTGATAACCACCATTCTCTAAGCATCAGTATGAAGATTCT
+TACACAGAGAACTATCCGAATGAGGAGATTCAAGAGTGAACATAGTTCGAGAGATAACCG
+GGGGTAGCGCAGTCGTGGCCTACAAAACCGACTAACGGACAAGTATTACGAAGTCCCACG
+TGTGTTAGGACTTAGTTTAGGCCCTGTACTAGTGCGGGCCGGAACTTGCGGTCAAATGTT
+GGTCGTATTCCCGCATGACAGGCTGGGCGCAACAGGCTCCACCTCGCCTCACGTAATTAG
+CCGATCCGAGAGAATGTGCCCGCCATATAGTATTTTTGGCTGGACGCGAATAGGGAACGG
+GAATCCTAGCTTCTGAGTGAAGGACCGCCCATGTGATTGAAAAGCGTACTCACACGGCTG
+GCTCTTCGCTGATTCGACCATGTTTTCCCTCCCCACCGCGCTTTCTGTAAATACCCCGTT
+GTAAGTGGAGTTCAGGAACTTGAGTCTAGCATGTTTGAAAATTTCCTGTCGAGACAAGTA
+CCCGACCACAGCTAATGAGAAATTAATGACGGAAACCTTGGCCCGACAGGCCGGTACCAA
+GGCTTGGTCTTCCATATGTACCTGGTCTCCGCCGATCTGTATACGCCCTGTTAACTAAAG
+AGTTGCCTCTCTATACACCGCCAGGTCTCCCATAACACAATGGCGGATTTTGTTTCCACG
+CCAGGTGCTAGGCCCGACACTCCAGTTTCTGAGTCCTCCTAACTGATTATCATAAACCAC
+GGTACAGCTGGTAGTATCATGGGGAGCACGCAATGGCAAGTCACAGACTGTGCTTCCCCC
+GAGACCGTGCGTTTTTACTATTTTCTATCAAATTCCTAAGCAAACGGGAGTTCGAACAGC
+AAGACTGTACTGTCGATCAGTTGAAACGTGTCTCGCTAGTGCCGGGTAGATAGCGTTACT
+GTCCAGAATGACATTTCGTCTCAGAATTCTTTTTAGAACACCTTGAAATTTGAGGCTTGG
+CGCCTATCGTAACAAAGACAGCCCGTAAGCATTCGAGCGAGAGTAGTTCGGCTGAATCCT
+GGTCGTCATGCCTCGACGGGAACAGGTAAGACTGGCCGGGTCGGGGGACAATTTACCCGA
+GAACCCAGGACGACTTATCCAAAACAGTATCTCGACAAGGACGCGCGGTAGAAGGAAAAC
+ACACCCAGAGTTTTTCAGTACCGACGGCTTATCAACTCTCAGATCTTTAGATGATCGAGA
+TTGATCATCGGTCAGTACTGAGAGCCATCTATCTTACAACCTGCCAATCACGATGTCGAG
+TTATAGAAGCCCCCGTAATATGAAGGCGAGCAGTTGCGGATCCCTCTTATGTGGGTTGGA
+TCTATTAGACGGAATGCCCCGTGAACCCCCATAGCCCCCGAAATAGTTTCGAAGCAAGGC
+CCCCAGATGGATCCTAGCTGCGCGGGGGATAAACCTGGCATCGCTTCAGACCTGATAGTA
+GTGGCCACAGGACTAGTCACCATCGAGCTTAGGGATCTCCGATGCATCTACTGCCATACT
+CTCATTACGAGTTCGGCGCGTGTGGGCTGGTCTGAGAGTCGGAATAGTCGGGGCAAATCG
+ATAAAGCGGCATGGGGAATGCCGACCTGTAATCTGAGTTGGGAGTTGCTAAAATTCACAT
+GGGGGGCGTTTCGCGTGAACTAGGGAGGTGTCGACGTGATTCTGTGAGAGTCTCAGCTCT
+GAAAACAACTCTAATAGTTAACGTGGCTTTAACCGCTAGGTGACACGTAACACACCGCTA
+TGCACTAACACGGGCTGAGTACGGATAATTGGTGTGTTAAATCTCAGCATAAGAAGCGGA
+ATGGTGTTCTCTGAAAGGATGCCTGCACGGGCACTCGAGACCTGAGGGCGAATTAGTGTA
+CGAACTAAGTGGGCGATCTACGAGAGTTCCGGGATTTTTATACACCCCTAGGTACAGTTG
+CTGGGTCGGTTTTTCTACCCGCAAACACTATCTTCGGCCGTTGTAGGCGTTCACAACCAA
+CTGTTTTATCCTTCTCGCCCGGAAGACTTTGTCAACACTTCAATTTCCCTCTAGCGCTCT
+CTTCACGTCAATGTGTGGGGTACGTTGAGCGATAATTGGGGAAGCAAATTCACGCCTTAT
+TTGAGAAACCGGTCTCTGACACCTAATATTCGACGGTGAATAGGAATCCCTGAATCAACG
+GGTACTTCTAGGGCCGATGGCGGCCATAGACCGCCTGGCTCTTTCTTGTCAGTGTCGATT
+TCGGTGTACTTGGGCAGCGACCTGCAATGGGTGGAAGACCGTCATTTCGCCACCGGGAAA
+TATCTGTCTTACTGCTAACTCTATAACCTGTCTAGTACCCGATTGGCTAAGTTGCATTTT
+CAGATCGAATGATCGACAGCCCCCCCGCGGACCTGACAACTCCCGGTACCGCAAGCTGTA
+GAGTTCTTACCCGTGCCCCATACTCTCCGGGTTTGTGTAACTGTGGTACTGGTTGTGCGA
+GCTGACTTGTATCAGGCTACGCCAAAGAGTAAGTACTGCAATCCGTCTATATCACCTGAG
+TGATTGTGGTTTACCCTTGCGGGGGTTTTCGTGTGGCTCTCTGATCTACGGCGAGTCTCT
+GCGGTGATTGATGTATCAACGCGCCTAGATCTAGCATGTGCCTGTCGGGCCTATAGACAA
+TGTCTTGGGGTGTTCGGTGATTCAACGTGAGATTATTTGCATGGAGACCACTGTGTTACA
+TGCCAGTGGGCTAAGAACCTTTGGATCACCAGATGCCGTGGTAAAGAAGAGCGACCCCGC
+TCAAATACGCACGCATGCGCCCTAACGTGCCAAAACCTTACGCAACGTGGAAGGCCACAC
+CAGGCGAATGCCTGCGCTTCGGACTAATTTAAATAGGCGTACCACGTCAGTACTGATTAC
+CCTTAGGGTGGGTTACCCTAGTGAAGCTGAACCGTACGACATGCCGTTATCGACTGCGTT
+CCTTGGTCCAGTAAGGCATCGTCTATACC
+>prodigal_ctg2
+GGTATAGACGATGCCTTACTGGACCAAGGAACGCAGTCGATAACGGCATGTCGTACGGTT
+CAGCTTCACTAGGGTAACCCACCCTAAGGGTAATCAGTACTGACGTGGTACGCCTATTTA
+AATTAGTCCGAAGCGCAGGCATTCGCCTGGTGTGGCCTTCCACGTTGCGTAAGGTTTTGG
+CACGTTAGGGCGCATGCGTGCGTATTTGAGCGGGGTCGCTCTTCTTTACCACGGCATCTG
+GTGATCCAAAGGTTCTTAGCCCACTGGCATGTAACACAGTGGTCTCCATGCAAATAATCT
+CACGTTGAATCACCGAACACCCCAAGACATTGTCTATAGGCCCGACAGGCACATGCTAGA
+TCTAGGCGCGTTGATACATCAATCACCGCAGAGACTCGCCGTAGATCAGAGAGCCACACG
+AAAACCCCCGCAAGGGTAAACCACAATCACTCAGGTGATATAGACGGATTGCAGTACTTA
+CTCTTTGGCGTAGCCTGATACAAGTCAGCTCGCACAACCAGTACCACAGTTACACAAACC
+CGGAGAGTATGGGGCACGGGTAAGAACTCTACAGCTTGCGGTACCGGGAGTTGTCAGGTC
+CGCGGGGGGGCTGTCGATCATTCGATCTGAAAATGCAACTTAGCCAATCGGGTACTAGAC
+AGGTTATAGAGTTAGCAGTAAGACAGATATTTCCCGGTGGCGAAATGACGGTCTTCCACC
+CATTGCAGGTCGCTGCCCAAGTACACCGAAATCGACACTGACAAGAAAGAGCCAGGCGGT
+CTATGGCCGCCATCGGCCCTAGAAGTACCCGTTGATTCAGGGATTCCTATTCACCGTCGA
+ATATTAGGTGTCAGAGACCGGTTTCTCAAATAAGGCGTGAATTTGCTTCCCCAATTATCG
+CTCAACGTACCCCACACATTGACGTGAAGAGAGCGCTAGAGGGAAATTGAAGTGTTGACA
+AAGTCTTCCGGGCGAGAAGGATAAAACAGTTGGTTGTGAACGCCTACAACGGCCGAAGAT
+AGTGTTTGCGGGTAGAAAAACCGACCCAGCAACTGTACCTAGGGGTGTATAAAAATCCCG
+GAACTCTCGTAGATCGCCCACTTAGTTCGTACACTAATTCGCCCTCAGGTCTCGAGTGCC
+CGTGCAGGCATCCTTTCAGAGAACACCATTCCGCTTCTTATGCTGAGATTTAACACACCA
+ATTATCCGTACTCAGCCCGTGTTAGTGCATAGCGGTGTGTTACGTGTCACCTAGCGGTTA
+AAGCCACGTTAACTATTAGAGTTGTTTTCAGAGCTGAGACTCTCACAGAATCACGTCGAC
+ACCTCCCTAGTTCACGCGAAACGCCCCCCATGTGAATTTTAGCAACTCCCAACTCAGATT
+ACAGGTCGGCATTCCCCATGCCGCTTTATCGATTTGCCCCGACTATTCCGACTCTCAGAC
+CAGCCCACACGCGCCGAACTCGTAATGAGAGTATGGCAGTAGATGCATCGGAGATCCCTA
+AGCTCGATGGTGACTAGTCCTGTGGCCACTACTATCAGGTCTGAAGCGATGCCAGGTTTA
+TCCCCCGCGCAGCTAGGATCCATCTGGGGGCCTTGCTTCGAAACTATTTCGGGGGCTATG
+GGGGTTCACGGGGCATTCCGTCTAATAGATCCAACCCACATAAGAGGGATCCGCAACTGC
+TCGCCTTCATATTACGGGGGCTTCTATAACTCGACATCGTGATTGGCAGGTTGTAAGATA
+GATGGCTCTCAGTACTGACCGATGATCAATCTCGATCATCTAAAGATCTGAGAGTTGATA
+AGCCGTCGGTACTGAAAAACTCTGGGTGTGTTTTCCTTCTACCGCGCGTCCTTGTCGAGA
+TACTGTTTTGGATAAGTCGTCCTGGGTTCTCGGGTAAATTGTCCCCCGACCCGGCCAGTC
+TTACCTGTTCCCGTCGAGGCATGACGACCAGGATTCAGCCGAACTACTCTCGCTCGAATG
+CTTACGGGCTGTCTTTGTTACGATAGGCGCCAAGCCTCAAATTTCAAGGTGTTCTAAAAA
+GAATTCTGAGACGAAATGTCATTCTGGACAGTAACGCTATCTACCCGGCACTAGCGAGAC
+ACGTTTCAACTGATCGACAGTACAGTCTTGCTGTTCGAACTCCCGTTTGCTTAGGAATTT
+GATAGAAAATAGTAAAAACGCACGGTCTCGGGGGAAGCACAGTCTGTGACTTGCCATTGC
+GTGCTCCCCATGATACTACCAGCTGTACCGTGGTTTATGATAATCAGTTAGGAGGACTCA
+GAAACTGGAGTGTCGGGCCTAGCACCTGGCGTGGAAACAAAATCCGCCATTGTGTTATGG
+GAGACCTGGCGGTGTATAGAGAGGCAACTCTTTAGTTAACAGGGCGTATACAGATCGGCG
+GAGACCAGGTACATATGGAAGACCAAGCCTTGGTACCGGCCTGTCGGGCCAAGGTTTCCG
+TCATTAATTTCTCATTAGCTGTGGTCGGGTACTTGTCTCGACAGGAAATTTTCAAACATG
+CTAGACTCAAGTTCCTGAACTCCACTTACAACGGGGTATTTACAGAAAGCGCGGTGGGGA
+GGGAAAACATGGTCGAATCAGCGAAGAGCCAGCCGTGTGAGTACGCTTTTCAATCACATG
+GGCGGTCCTTCACTCAGAAGCTAGGATTCCCGTTCCCTATTCGCGTCCAGCCAAAAATAC
+TATATGGCGGGCACATTCTCTCGGATCGGCTAATTACGTGAGGCGAGGTGGAGCCTGTTG
+CGCCCAGCCTGTCATGCGGGAATACGACCAACATTTGACCGCAAGTTCCGGCCCGCACTA
+GTACAGGGCCTAAACTAAGTCCTAACACACGTGGGACTTCGTAATACTTGTCCGTTAGTC
+GGTTTTGTAGGCCACGACTGCGCTACCCCCGGTTATCTCTCGAACTATGTTCACTCTTGA
+ATCTCCTCATTCGGATAGTTCTCTGTGTAAGAATCTTCATACTGATGCTTAGAGAATGGT
+GGTTATCAGAACATCACTGTCCTTGAGTTTGGACCTTGATCCCGTCCAGCCCGGGTGGGC
+GGTAGACTTCTGCCAGCTGTTGTGGTCTAAAAGCATGCCTGGTGATCCTCCATACGTGGA
+ATACGTGAAACGTCTGCTATAGGTAACAATGTGATACAGCGATAGTGATAGGTACGGATT
+TCGTGAATCGAGAGTCTCCGTTGTTAGTTGAAAATATATCTTAGACGTAGTAAAGAGGTG
+TGTGTGCGTAGTTCAAATTGCTCATTTAAGAGTTAGAAAGACGCGAAGGATCCATGGGTA
+CATGCAGTTTTGGGTCGGGTATGCTACAAAGCTAACCTTACTTGATCCGAGATTCATACC
+GTAAGCGTGTAAGTTAGAATGCGTAATCTTGGGATTGGGGCGGCGCCTTTTAGCGCTACA
+TTTTCGGAGGCGATCCGTAAAAGATCCGGGCGAACTATTAATGGCATAATCTAATGCAGG
+TATACCAATTAATATAATGAATTAATATGAGTCGGACAGACAGGGGGGACCACAAACACA
+GGTGAAGACAGGGGGGACGACATTACTTGCGAACCACGGAGGCAGTTCCGACCTCGCGCA
+TCTTACTGCCAACGTGGATTGCCGCATGTTCATTAGATAGTAAATCTTGAGATGAGCCTT
+TCCTTCGACGCAAACACACATTACACAGCATCCGTCTCATTCCAGCTACAACTGTTGTAG
+GGGACATCGCGCCATTCGGGGACGCTGGAGCAGGCAGCAGGCCGTTTGGATGCGAGCTGG
+GCTGATATGACAGTGTGGGGTTCTGCCGAAGTCATGATGATCCTAACCGGCGCCGTACGA
+GACAGATAACTCTCTGGACCTCGGGCCATTATCACAAACAGGGAACTTGGGCGAGGCTGG
+TTGGGACTAGGAGCTTCGTTCCAGTGAGGCCAATGTTACATTTTGGCCGGTTCATTAACC
+CCGATATTAATCCTGCAGACGCCATTTAACTGAGCACTGATTAGCGTTGCCAGTGCTCGA
+TCAGCGCCGCGCCTATTCTGGCGATCTGCTGGTTACGCTCGGCTATGGTCGCCGGCGTAT
+CCCGCAGATAGATCACCACGATGCGCTCCGCTTTGCCGTTCGGGCCGAGCAGGGCGACAA
+TGCCACGTGAGCCCCGCTCGCCGGCCCCGGTTTTATCGGCGATAAACCAGCCCGCCGGCA
+GCACGGCGCGGATCAGCGGACCGGCTACCTGGTCGTCCACCATCCACTGCAGCAGCTGCT
+GCTGCGAACGGGCGCTCAGAGTGTGGCTGGTTAGCAGCTTGCGCAGGGTGGTGGCCATGC
+TGGCTGGGGTGGTGGTGTCGCGCACGTCGCCGGGAAGCGCTTCATTGAGCTCCGTTTCCC
+AGCGGTCGAGGCGGGTGACGTTGTCACCGATCTGGCGCAAAAAAGCGGTCAATCCCGCGG
+GGCCGCCAACGCTCTTCAACAGCAGATTGCCGGCGCTGTTGTCGCTCATGGTGATGGCGG
+CGGCGCAGAGTTCGCCAACGGTCATCCCGTCGGCAAGGTGTTTTTCGCTGACCGGGGAGT
+AGTCCACCAGATCCTGCTGGCGGTAGCGGATCCGCCGATCCAGCTGTTCGTCTCCGGCAT
+CCACCCGGGCCAGCACCGCGCCGCAGAGCAGCACTTTAAAGGTGCTCATCAGCGGAAAGC
+GCTCACTGGCGCGCCAGGCGGCCAGCGTGCGGCCGCTGGCCAGATCCATTTCAACATAGC
+CCACGCGGCCCGCCAGCTGACTTTCGCTGCGTGTAATTTGCTCAAGCGGCGGAGGGCTGG
+CGAATACCGCCAGTGGCAGGGCGGCAATCAGGGAGAAAAGGCACAGGCGAATATAACGCA
+TGATCGACGTTAGTACGTGTTCAACGCATCGTAATAGCCTTCACACAATAGGCTGGCTCT
+AAACCATTGTTCGGACGCGATATCTTGGAGTCTGCGCCCAGTTTCCCTCCTGTCCTAGTT
+CATGATCCCGTTCTACTTGAGGTGCTAAATTGGTCTATCCAAACCTAAATCGAGGACCTA
+GCACACCATCACCATGACTGAGGTATTGTGAAAGCTACTCCGGGCCGCTTTAGGTCCGGC
+TTCATTCACTTAAAATGGGGTTTGACAACTTATCTTAGACCGCTGGGTTGCAGCCAGGTT
+GCATTGGGAGTCTTTGCCCGCACTCAATCTAGCCTCGGGGTCTTCCATATTTATCAGCGA
+GGGGCTTTCCAAGCGACTCTGGCCCTAATGTGGTTATAGGGGTGTAACTACTAGACGGGC
+GACGCATAGGCAATTCTCATAACAATGATCCTGCCCGTCAGGGTGCGTCAATGTTCTGAT
+CAGAACTACTGATCCGCAATCTTATTGTGCTTGTCAGAAGTGCCCAAGTCAGGTTCCTCC
+AAGTTGCGTCAGCTCTATTAAGATCGACCTGCATAGTATAGCAAGCTCGGGGCAGGGCCC
+GGTTCCCTACGTTTGCTAGCCAGTGATGCCGCCTAAACGTTAGCGGTGAAACTCATCTCA
+CTGGCCTTAGACCTGGGGAGGATTGGGCGTTTGCGCGTTGCGACAAAAATTGCAGATTTT
+AAGGTCTTATCGACCAAAGCCAGCTGGCTCTGGAAAAAACACACACCCAGTCCTTACTAC
+CAACTCTGGTAGGTTAAGTATCCGTAATATCAACGATTAACTCCAAGCCCCAAAACAAGA
+CGCAAACTCCGTGCCCGTACATTTACTATGTCCCTGTAAGAACCCCCAAGCTGAAATGGG
+CTGAACTCCCTTAACGCAAGAATGGGGTCTGCTGGAACAACGCTGTGATAGCCCATAGGC
+ACACTGGCTTGCGCGGCCTTCCTAGGGGTCGAATTCTAACCGAGAGGCGAGCATCCTCGT
+CCTTACGTAGTCGCCTGATATCATCGTAGTCTAATAGGCTGCCCCGCATCTAGCTGAAGT
+TCCTCAATGGTGACGATCCCCTATTGATGGTGCCCGGCTTAAAGTGCGCTGCTTCAAATA
+TAGCAATTAGCCCTTACCAGCCAGAATTTAGAATTCGGAGTGGTTCGGCAAATGGTCACC
+CGTTATTCTCCCGTAATTGTCCGTTCTAAATATCTTTTGGTAGCATATTCGTTCGTTTGC
+GCTGTCCTCTTATCCAATGTTCAATCAACAACAGGTAGCAGCAATCCCTTCTTGCCATTC
+GGAACTGCCCGTGCAGTAGTTCCATATCAGTCTGAGGTAGGAGCAAGATGTTTGAGGCAT
+TCTGCACACCAGGGCGACACCTCGCGTGTTGCACGTAGTCTCGTTCTTACGGCAGGTGTC
+GTTTCCGAGGCTCTGACTCCATCCAATACCACAATAGTTGGCGAGAACGCTTACCGGATT
+ATTATCCAATCTAGATGGTCGTAGGTCATTCACGCAACTGTGAGATTAAGGCCGTAGCCG
+ACCGGCCTAATCGCCATGAATTGGTCTATAAGATTATACCTATAGCCGGCCCAGATGTTC
+CAATGCCTCTCTACCCCGAGTTTGAGACCTCCGCATATTCTACACCAAGGTCCCCCCACC
+CAACGATCGACCATGTTTACACTGCCGCGTCGAGCTTATCTCGACGAGGAGAGATATGAC
+AATGGGACGGTAAGGTGGTTCCTCACATAGACTAGTCATTTCAGCGTGGTGGTACACACG
+GGATGGTTCCGACGAGAAGGATTGTAGACCATTCGAAACAGGGTCTGGCTCTGGTAGGAG
+ACTTCTCATGTCAGGACCCCGCACCGACTTGGTCGCCTTCAAACTACTGCAGTGCTCACA
+TAAATCGTCTTAGGAGACTCTTCTCCTCGGGAGGCTTCCGCCAGTCGTGATAGGGCCATC
+CCCTTCGGTCTCGACTGTGGGCGCGTTGGCCCCAATGGTAAATTTTGAGCGCAATTATTC
+CGCCGATAGAACGGACCTCATTCTAATATTGTTTATACCTAGTCTTCATCCGAAGGTGCA
+GCAAGAAAGCATCGCTTATTTCTGTAAGGCCTACGTGGAGAAGTGGTGTTTTCTTAGTTT
+CTCATTTTCACGCGAACGAAGACATATCTCAGCGTCGCACTTCTTCTATAGCAGCGTTGG
+ACGCATATATCTCACGGAATGAACACGCTAGACCTTGGAGTTACACCCTACTTATAGGAT
+TAGCCTGGGTATGCAGGTGACCAGTGTCCTTCGTAAAAAGCCGATCGGTATATCTTAACT
+ACTTTCAGGACCACAACAGGGAACGCAATCCGCTGACTTGCGAAAGGTTTCTCCGTTTCT
+TCCATGTACCGTTCTAGTAGCGTAGAGTTCGTAATAAAGTTCACCAGAAGCGGGAAGGTT
+AGGAGAGTTTTTTCGGCCACGCCTCCCGTTGGATGAGCCGACCGCGGTCATCTATATGAG
+GAGGAGTACACAGCAGATCTGTTGGAGATCAACCGGGGGCGCGCGAGTCATTTGGATGGA
+GCGAACATACAAGCGCGCGCTCTTGTAAGTTCTCCCGTAGCCTTCGACAGGGAAGCCTGT
+CTCAGGCGCCTCCACCACGTCGTCGAGCCCTCGGCGGACCGGATCGCAGGCCGCGCGGAG
+GGAGCGAGCGGTCGGGGCCGACGGATCCGGGCCGGGCCCGGACGGACCGGCCGGCAGGGG
+CGGGCCGAGTACCCACCTCCCGGTAGAGCCGGTAGAGGGATGCCCAGTGCCCGGCCTTGA
+GGTCGCGGGGCAGGGCCGCCGGGTCCACCCGCTCGCGGCGGAGCCAGGCGTCCACCTCAC
+GACCGGGCAGACGGGTACGGAGAATCGCGGCCAGACCACGACCGGGACCGGTGTACACCT
+CGCGTACCAGGTTCTGGTAGTCACCCACGCAGCGGTCGTCGAGCAGCGGCGCGGATCGAC
+GCTCGATGACGAGGATGCCGCCGTCGACGCTCGGCACCGGGTCGAACGAGGTCTTCGGCA
+CCCGCTCCACCAGGGTGAACTCGTACCACGGCCAACTGGCTGCGGTGAGCATCGTGGTGC
+CGCCCACACCGGCCCGCTTACGGGCCACCTCCCACTGCACCAACAGCACCGCGGTGTGCC
+AGAACCGCTGGCCGATCAGGCGCCGGAGCAGCGGCGTGGTGATGGAGAACGGCACGGTCG
+ACACCACGTGGTGCGGGTACGGCCCGAAGTCGTACCGGAGCATGTCCCCGTGCACGACGG
+TGACCCCGTCGGCGAAGGTCCGCTGGAGCCGCCGGACCCGCCGGGGGTCGAGTTCCAGCG
+CGGTGACCGGGAGATTCGCCGCGACCAGGGCCCGGGTGATGGCACCGTCACCGGCGCCCA
+GTTCGAGGACCGGATGGGCCGTCGTCGAGGAGACGACCTCGGCGATCCTTGTGCATACAC
+CTCGGTCGACGAGGAAGTTCTGACCGAGTTCGTGCCTGCCGCCCACGGCAGGGGTGTCGA
+GCGAAGCGGCGGCGTGCCGGCGCCGGATTGATGACATACGCCAAGCGTGCTGTCCGACCG
+CTCTTGTGGATGACCGAAAAAGAAATTGAAAGAATCAGCCCTATGACCCAGAGATCCGTG
+GCTTTCTCAGCGAAATACAGGCGTACGAAACTTGTGATTCTTGCAGGGGCCCGGTAAGTA
+GGCCGCCTAAGCGCGTGAAGACTCTGAAAGGACGGGTGGATATCGGCGGTAACCATCCAA
+GGCTGATACAACAGAAAATATGAGGAGCGACAACGTGCTCAACTCGAACCCAGGAAATAT
+AGATCCGTCCGTATCTTAATGCCTACGAGAGGAATATGTACAGTGCTGTGGATAGGCCCG
+AATTAGGGCTCCATCATTGTGTCAGAGTTACTGGCCGCAATGGTGCCACTTGGACGCGGT
+AAGGCGGGCCCGAATTGGCTTTGATGCGTCCAACTACGTGCAGCGAAGCCCGGACCAAGC
+CATCCACGCATTACTTAACTACCAGCTGGCGTCGTGATGCTACACTTAGTCAATGTGAAT
+CGCGTTGCATCATGTCAGGGCTGCTGACCGCAATATTTACAACTTCTTAAGGTTGCGGCC
+ATCGTAGGGTTCGTGGAGTACTACGAACCCCCAGCTGACCTGGCCTAAGATACGTGTTTG
+TGTGGTTCTTCCTTACGGTGCAGCCGTTTCGAGTCCGCGTTTGAGAGCGGTGGTGTTTGA
+CGTGGCAAACCAGCAGCGGGTTAACGAACACCCGGGGGCAAGCAATGGGACTGATCCGGA
+ACATCAAGTGGGGAGACTGTGTTGGACTTTATCGGACCGTTCGTAAGCGGGTCAAGCCGA
+GCATCAGTCGAGAAGCCAGCCGGAACAATCGAACGGAAAACTTTCGCCACATCTAGCAAC
+TACGGTTCCGCCCCGCACCTGGTTGGATCCTGAGTTAACACACCCGACTGCGTAGGTACG
+CTTGTTTTTGAGGCACATACGGTTTAGGC
diff --git a/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa b/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa
new file mode 100644
index 0000000..de3140d
--- /dev/null
+++ b/circlator/tests/data/start_fixer_rearrange_contigs.refs.fa
@@ -0,0 +1,50 @@
+>sp|P03004|DNAA_ECOLI Chromosomal replication initiator protein DnaA OS=Escherichia coli (strain K12) GN=dnaA PE=1 SV=2
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGA
+>sp|P03004|DNAA_ECOLI_2 Chromosomal replication initiator protein DnaA OS=Escherichia coli (strain K12) GN=dnaA PE=1 SV=2
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCATCGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGATATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAAGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGA
diff --git a/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa b/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa
new file mode 100644
index 0000000..9088c24
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa
@@ -0,0 +1,282 @@
+>ctg1 extra stuff after a space
+TCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCGGGGTTAATGAACCGGCCAAAA
+TGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCAACCAGCCTCGCCCAAGTTCCC
+TGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGTCTCGTACGGCGCCGGTTAGGA
+TCATCATGACTTCGGCAGAACCCCACACTGTCATATCAGCCCAGCTCGCATCCAAACGGC
+CTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCCCCTACAACAGTTGTAGCTGGA
+ATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGGAAAGGCTCATCTCAAGATTTA
+CTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAGATGCGCGAGGTCGGAACTGCC
+TCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCACCTGTGTTTGTGGTCCCCCCTG
+TCTGTCCGACTCATATTAATTCATTATATTAATTGGTATACCTGCATTAGATTATGCCAT
+TAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAAATGTAGCGCTAAAAGGCGCCG
+CCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTACGGTATGAATCTCGGATCAAG
+TAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCATGTACCCATGGATCCTTCGCGT
+CTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACACACACCTCTTTACTACGTCTAA
+GATATATTTTCAACTAACAACGGAGACTCTCGATTCACGAAATCCGTACCTATCACTATC
+GCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTATTCCACGTATGGAGGATCACC
+AGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTACCGCCCACCCGGGCTGGACGGG
+ATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAACCACCATTCTCTAAGCATCAGT
+ATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGATTCAAGAGTGAACATAGTTCG
+AGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAACCGACTAACGGACAAGTATTAC
+GAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTACTAGTGCGGGCCGGAACTTGC
+GGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGCGCAACAGGCTCCACCTCGCCT
+CACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATATAGTATTTTTGGCTGGACGCGA
+ATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGCCCATGTGATTGAAAAGCGTAC
+TCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCCCTCCCCACCGCGCTTTCTGTA
+AATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTAGCATGTTTGAAAATTTCCTGT
+CGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATGACGGAAACCTTGGCCCGACAG
+GCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCTCCGCCGATCTGTATACGCCCT
+GTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCTCCCATAACACAATGGCGGATT
+TTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTTCTGAGTCCTCCTAACTGATTA
+TCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCACGCAATGGCAAGTCACAGACT
+GTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTATCAAATTCCTAAGCAAACGGGA
+GTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACGTGTCTCGCTAGTGCCGGGTAG
+ATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATTCTTTTTAGAACACCTTGAAAT
+TTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAAGCATTCGAGCGAGAGTAGTTC
+GGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTAAGACTGGCCGGGTCGGGGGAC
+AATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGTATCTCGACAAGGACGCGCGGT
+AGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGCTTATCAACTCTCAGATCTTTA
+GATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCATCTATCTTACAACCTGCCAATC
+ACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCGAGCAGTTGCGGATCCCTCTTA
+TGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCCCCATAGCCCCCGAAATAGTTT
+CGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGGATAAACCTGGCATCGCTTCAG
+ACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGCTTAGGGATCTCCGATGCATCT
+ACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCTGGTCTGAGAGTCGGAATAGTC
+GGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTGTAATCTGAGTTGGGAGTTGCT
+AAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGGTGTCGACGTGATTCTGTGAGA
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAACACACCGCTATGCACTAACACGGGCTGAGTACGGA
+TAATTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTG
+CACGGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGA
+GTTCCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAA
+CACTATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAG
+ACTTTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGT
+TGAGCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTA
+ATATTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCC
+ATAGACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGC
+AATGGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATA
+ACCTGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCC
+CGCGGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTC
+TCCGGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAA
+AGAGTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGG
+TTTTCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCC
+TAGATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAA
+CGTGAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGA
+TCACCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAA
+CGTGCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACT
+AATTTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAA
+GCTGAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTA
+TACC
+>ctg2
+CATCATCTGACTATGCATGACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>ctg3
+TCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCGGGGTTAATGAACCGGCCAAAA
+TGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCAACCAGCCTCGCCCAAGTTCCC
+TGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGTCTCGTACGGCGCCGGTTAGGA
+TCATCATGACTTCGGCAGAACCCCACACTGTCATATCAGCCCAGCTCGCATCCAAACGGC
+CTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCCCCTACAACAGTTGTAGCTGGA
+ATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGGAAAGGCTCATCTCAAGATTTA
+CTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAGATGCGCGAGGTCGGAACTGCC
+TCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCACCTGTGTTTGTGGTCCCCCCTG
+TCTGTCCGACTCATATTAATTCATTATATTAATTGGTATACCTGCATTAGATTATGCCAT
+TAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAAATGTAGCGCTAAAAGGCGCCG
+CCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTACGGTATGAATCTCGGATCAAG
+TAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCATGTACCCATGGATCCTTCGCGT
+CTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACACACACCTCTTTACTACGTCTAA
+GATATATTTTCAACTAACAACGGAGACTCTCGATTCACGAAATCCGTACCTATCACTATC
+GCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTATTCCACGTATGGAGGATCACC
+AGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTACCGCCCACCCGGGCTGGACGGG
+ATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAACCACCATTCTCTAAGCATCAGT
+ATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGATTCAAGAGTGAACATAGTTCG
+AGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAACCGACTAACGGACAAGTATTAC
+GAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTACTAGTGCGGGCCGGAACTTGC
+GGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGCGCAACAGGCTCCACCTCGCCT
+CACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATATAGTATTTTTGGCTGGACGCGA
+ATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGCCCATGTGATTGAAAAGCGTAC
+TCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCCCTCCCCACCGCGCTTTCTGTA
+AATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTAGCATGTTTGAAAATTTCCTGT
+CGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATGACGGAAACCTTGGCCCGACAG
+GCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCTCCGCCGATCTGTATACGCCCT
+GTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCTCCCATAACACAATGGCGGATT
+TTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTTCTGAGTCCTCCTAACTGATTA
+TCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCACGCAATGGCAAGTCACAGACT
+GTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTATCAAATTCCTAAGCAAACGGGA
+GTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACGTGTCTCGCTAGTGCCGGGTAG
+ATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATTCTTTTTAGAACACCTTGAAAT
+TTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAAGCATTCGAGCGAGAGTAGTTC
+GGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTAAGACTGGCCGGGTCGGGGGAC
+AATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGTATCTCGACAAGGACGCGCGGT
+AGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGCTTATCAACTCTCAGATCTTTA
+GATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCATCTATCTTACAACCTGCCAATC
+ACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCGAGCAGTTGCGGATCCCTCTTA
+TGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCCCCATAGCCCCCGAAATAGTTT
+CGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGGATAAACCTGGCATCGCTTCAG
+ACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGCTTAGGGATCTCCGATGCATCT
+ACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCTGGTCTGAGAGTCGGAATAGTC
+GGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTGTAATCTGAGTTGGGAGTTGCT
+AAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGGTGTCGACGTGATTCTGTGAGA
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAACACACCGCTATGCACTAACACGGGCTGAGTACGGA
+TAATTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTG
+CACGGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGA
+GTTCCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAA
+CACTATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAG
+ACTTTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGT
+TGAGCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTA
+ATATTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCC
+ATAGACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGC
+AATGGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATA
+ACCTGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCC
+CGCGGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTC
+TCCGGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAA
+AGAGTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGG
+TTTTCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCC
+TAGATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAA
+CGTGAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGA
+TCACCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAA
+CGTGCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACT
+AATTTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAA
+GCTGAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTA
+TACC
+>ctg4
+ACCAGATTCAGGCCCCAAACTACACCTATTATTACAAAAGCCCCTGCGGTCGTTAATTCA
+GTGAAAGTGATGTTTTGGTTGGCAAGAACAATAGACGTCAGATTCATCTAATGGGTGAAC
+CAGGGGCTTGGACGGCCAACTGTTTCCAGGGATCTCAAACGACTAACGCTCCCTGAACAG
+GCTCCTTTTGTATCAGTATGTAAACATTGACACGGGCTGGGTCGTTGGCTTTCATCGGGT
+CACCGGCCGTCCAGATTTAATTTATGTGGCCCGACTGCTCTCACGTACCCTTCTAGATCT
+ACCACGAAGCCGAACGCTATATTACTCGTTCAAACCACAGTCCGACGAAGTACTCTGGAG
+TTACCGGCGCCACCCAGCCCCACCTACGGCACAAAAAGCGGCCCCTTTACGGATGCGTCT
+CGAGGCTGACGAGTATCAAGAGACCCGAGTTAGGAGGAGTGCACCCTCTTGGGCTTAGAA
+CACGTTAGGGGGGAAGTAAACTATGGGTGGGAATTGTCCAACACAACACAGCATTCATCG
+ACAATAACAGGTGCCCGGCGGTATCTCTATATAAGTCTCAGAATGGAACGGTAACGCGGC
+TTCGAACTATAAAGGTCACGGATACGGAGCCCAACTGCGGGCTTCATAGGGGATGCGACT
+GGATCGCTTGCGGCTCGGGCGTATGTTGACCTCTGCTTGTGTCGATATAGTCTACTATCC
+CCCTTGGTCATTCTGCAGGAGGGACGTACGAAGTAGGTGGCACCAGTTGGTTTTATGTAC
+CCGTATTGAATACAAATTCGGTGGTCCCATTAGATGCAGTCCTAGGGTTGACGGTTCCAC
+TGTTTGCTGCGCCGTATGTACGTGGCACACCCAGATCTTGCTTAGGAGCATCACCATTAG
+ATTAACGCGTCCGTCACGCTGTTGCCTCGCCGGGCGCATAGCAGTCTTAGCATAGCCGCT
+AGACGTTAGGTTGTTACTTCTCGCCAATCGCGAGTAGCCGCGCTTGACTGAGCAGCTGCC
+TGCGAAACTTCGCATTTTGAGAAGGTAACAAAGTTGAACTAGGGCGGGTAGTTAAAGTCG
+AGTCATAACCCCGGGGTACATGCTGATTTAAAACGGACAGTGTGCCTGACAGGTAGTCCC
+CTGCTGTCCACAGCTATGTGGACATGTTCAATAAGAGTCGTTCCCAGGTTGCACCACGAG
+TTTCTGGCATGGAGTACTACTTATAAAGCGTACCTTTACACTTGCAGATTCAAAAGTGCG
+GCGCCCGATAGCACATAGCTCTTGTGGTTGAACTGGAATCCCTAAGATATTCCACCTCCG
+AAACCATGAATACTCGAGGAACCGTTCGGCTATGACCTATAAAACTGTCCGCTGGGAGGG
+CTTTCGAAATGGCTCAGAGGCTCATAACCTGTACCCAGCAGTCGCGATCGCCCCTATTAA
+CAGAGACGATCTGCTGTTGAGCTATTAGAGATCCTCGGTCCAGAGAGAGATGGCCAAATA
+CATCCAAGCACACGTGCCGCTAGCTATCAGCCTGGTCGTCGTTATGAGGTCTATCCGGTT
+CATCGTGCTCGTAGTCTGAGACGAACGTGGAGCCTACTAGGAAACTTGGGGGCAACCTAG
+CTTTACTGGTCTCCTCCGGGTGGCCCTGGACGGAGGCCAAACAACGAAGGACGCAGGCTG
+ACACTAAGTACCGTCAACAGACTACGCCATAATCCGGATTCGGCCATAACACGTCATAAT
+GATCTCCATTCGAATGTAGTTATAAGACGTGCCGTCCATTTTCCCCTTTACTCAATTGGA
+AACTTCGTGAGTTTTTCGCCCAGAGTTACTCCACCCACCAGGGCGAGCATGACCCGTAGT
+TATTTGATATGCCTACTCTTACTTCTATATAAAACGATTTTGATATTTGTAGGCAATGTT
+CCTGTACCTTTGCTTTTAGACTCGGAATTTCACAGCCCGAACAATGTTATGTAGCCGAAT
+TGAGTTTATCACGCTTAGTAGCGGTCCGGCATGGCCTGAAGCGAGTGGTTTAAATTACTG
+GGTTTTATCCACGGCTAGCGCGAAACGTAATCCACCCCATCCCAGGGTGTTACGGTGATC
+GATGGAGAGATGCCATGAGATGGTAATGGATGATGCTAGCTAAGTCGCCCTGAGACGATA
+CCATCTGACCACCAGAAGATCAGGAAAGTCGACCAAAAAAGACTTGCGCCTTCTATCAAT
+ATGGAAAATTTCTGGCAAACTTGCTCGGCTCAATTGGAACAAGAATTGACTCCGCAACAA
+TACTCGGCTTGGATCAAGCCGTTGGCTCCGTTGGACTACGAAGACGGTACTTTGCGAATC
+GCTGCTCCGAATCGATTCAAGTTGGACTGGGTCAAGACTCAATTCGCTGGTCGAATCACT
+TCGATCGCTGCTCAATTCTGGGACATGCCGGTCGACGTCCAATTCGTCTTGGACCCGCGA
+TTGGCTTCGGCTAAGAAGCCGACTACTTCGGCTTCGGTCGCTCCGATCCAATCGGACGAC
+GTCCCGGCTTCGGTCTTGGAACCGATCCCGTCGAATGCTACTGACCACACTCCGCGACGA
+GACCAATCGCGAATCAATACTGCTTTGACTTTCGACTCGTTCGTCACTGGTAAGGCTAAT
+CAATTGGCTCGAGCTGCTGCTATCCAAGTCGCTAATAATCCGGGTTCGTCGTACAATCCG
+TTGTTCTTGTACGGTGGTGTCGGTTTGGGTAAGACTCACTTGATCCACGCTATCGGTAAT
+CAAGTCTTGGCTGACAATCCGGACGTCAAGATCCGATACATCCACGCTGAACAATACGTC
+CGAGACGTCGTCACTGCTTACCAACGAAAGGGTTTCGACGACTTCAAGCGATACTACCAC
+TCGTTGGACTTGTTGTTGATCGACGACATCCAATTCTTCGGTGGTAAGTCGCGAACTCAA
+GAAGAATTCTTCTACGCTTTCGAAGCTTTGATCGCTGCTAAGAAGCAAATCATCATCACT
+TCGGACACTTACCCGAAGGAAATCACTGGTATGGACGACCGATTGATCTCGCGATTCGAC
+TCGGGTTTGACTGTCGCTGTCGAACCGCCGGAATTGGAAATGCGAGTCGCTATCTTGTTG
+AAGAAGGCTGTCCAAGAAGGTGTCACTTTCTCGGACGACGTCGCTTTCTTCGTCGCTAAG
+CACTTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTGCGAAAGATCTTGGCTTACTCG
+CGATTCCACGGTAAGGACATCACTATCGAAGTCGTCAAGGACGCTTTGAAGGACTTGTTG
+TCGGTCCAAAATCGACAAATCTCGGTCGAAAATATCCAAAAGACTGTCGCTGACTTCTTC
+AATATCAAGGTCGCTGACATGTACTCGAAGAAGCGACCGGCTAATATCGCTCGACCGCGA
+CAAATCGCTATGTACTTGGCTAAGGAATTGACTCAAAAGTCGTTGCCGGAAATCGGTGAA
+TTGTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCTGTCCGAAAGATCGCTGCTGAC
+CGAGGTAAGTCGCCGGAATGCAATCACGAATTGCACGTCTTGGAACAAACTTTGAAGGGT
+TGAACGGGATCTTACGCGTCAGACGCATTCGGGGTTCCTCGCACCACAATGCCCCGTCAC
+TCCAGCGATCGGTCCAGCAATCGCCTTCATTGCAGCGGGTTGGTTTTTAGTGCGGACCAT
+GACCGCGCTGAGTGAAAGGATCTACTTGCTGTAAAGCCATATGGTCGGGCCCGACGTGGC
+GCAAGGTTGGCAAGAGAGTCCGCCAGAACAAGCAATCTAACGAGCAGGTCTTTGACATTC
+TACGCCCTTCTGTTTTTTAAGTCTTACAACGAGAATTCGACTATGATGGACAGCTTCCCA
+ACGAACGAGGGACCACCGCTATCAGGGGCACATACGGGGAACGCCAGCGCAAATGCCGAG
+CACCAAAGTCTTCACACAGGGTTGCACAGTCCTACTGCTATACTACGGAATGGCCATTCT
+GCTGCGAGGACCGTGTGACCCTGGCGACATCAGTAGAAATTAATGTGGTCAGATAGCTAG
+TATGTACAGATTATCCTCACGGGCGGCAAAGACATCGCATTAATTCGGGCTTCTTTCGGA
+TATCAGTGATGATTTGCACGACAAACGCGTCACGGGCATAGCCTCATTGACCATAGTGCG
+CGATACACAGCCTCCCTTAACGTAGGACTAGAAGTACTGATCGTTATGTCAAGCGTTTAA
+GTTCCGCGCGGGAAATTGCATCTTTCTAATATACATTATGAGCTGCCAATCGTGGTCGCC
+CCAATGTCCTCAAAACAGATGCGGTAATACGCTCTGGGGCGGCCCTCGGTGCCTCGAGTG
+GCTCTGGATCGACATGTCGTCACGCGTCGAGATACGCGCGGGATCCTGACCACGAATCAT
+AAAAGTGACCTGACCATAAAAAGGCAGTTGCGGTTCTGGCATTGGAGGGCTTCGGTGAAT
+TCAGCATTCTGGTCGCTTAATAGCTAGGATGTGCCATTGACAGGTACTCGTGCACTTCTG
+GGCAGAACCGATGCATCGCTAGCCCCCAAACACCGGCTGGGTCATTGGAAGAGGACGTCG
+CTACGAGTCTACCGGTCGGAGACCCATGTTTTTTGGCAATAATCTCGAACAACAGAAGGG
+AGGGACCATAGGATATTCCGCGTGTGGGCGAAAGGATCAGCCACATCTCGATGTATTTAA
+TGCTCATCTGGTCTTAAGTTTATTACGCTTACGTCCAGGGCATTACCGATGAAACAGGAT
+GACGGCAGAAAGTTAGTATTGTATTGGTGGGCATGTTTACAAAGACACGCCCAAACCTAC
+TAAAACGTGACAGCTAGTCATGCCACTGGATGTAAAAGTCCAGTCCGCCTTCACGAGATT
+ACAGCTACGCATTAGTCAACGTGTTCGTTCTCAGCGCTGGTACCCCTTAGTACAGTGACA
+GTGCTTGCGCGGCAGTGCCGCAGCTATCCGCTTAGTCTGACGAAACAGGCCAGAACTAAC
+ATTACCATCTAAGTTGGAAAGAGGCTGTCCACGTTTATTAATATTTTAATTAAGTACGGG
+CTGAAAGGTAATATGAAACCACGTTAGGACGACCGTAATGATTCAAGTTTGAATTCCATT
+GAATTGCTATCGTGTGCTTGGGCATGTAAAAAGGTCTCAAGAAGTGGAATGTGTCACACA
+ATCTAACTGGAGTTGCTGTAAGACTTGCCAATCCGCCCATGTAGAGTCTGGATAAGAGCG
+TCAACCGCAACCCGGGCTCTAAGCAGCTCGGTTAGGTGCAAGAGGCCGTAGATAGGCGGT
+GATCCGGGGCTCTTTGTATATATTTGTGGGCTGCTACGTGCCGAACTAATTGCGCGTGTC
+AGGTGGTAAAATGCCGGTTAGGGATACATACTCCTATTGGTCGGAAACGTCTATGTCGTG
+CTTCACGAGGGAGCATAGAGATAACCTTCAGGATCGTGAAAAGGCAAATTGCACTCCTAG
+GGTTCCCAGCAGTATAACACGTGAGCCGTACGTGTTCCGCTCAACTAAAGGGCGATACGA
+TTGGACGTTCATAGCTCACCTTTAGCCGAGCCGGTACCAGTCAAGCACCGCGTGCTGGGG
+CTGCGAATATATGGATGTTTTACGTTCCGATGCACCTCTGTGTCGCCTGCATTAGTTCCT
+GAATACCGAATGTCGCTATCTCCCTTGTTTAAACGAAGTGGGAAATCTGATCTCCACGGT
+AACAACAGCCCAATCTGTCGCACGCGCCGAGTCATTTCGGCACCGTAAATGA
diff --git a/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa b/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa
new file mode 100644
index 0000000..f873ed5
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa
@@ -0,0 +1,282 @@
+>ctg1 extra stuff after a space
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAACACACCGCTATGCACTAACACGGGCTGAGTACGGA
+TAATTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTG
+CACGGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGA
+GTTCCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAA
+CACTATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAG
+ACTTTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGT
+TGAGCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTA
+ATATTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCC
+ATAGACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGC
+AATGGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATA
+ACCTGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCC
+CGCGGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTC
+TCCGGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAA
+AGAGTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGG
+TTTTCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCC
+TAGATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAA
+CGTGAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGA
+TCACCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAA
+CGTGCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACT
+AATTTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAA
+GCTGAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTA
+TACCTCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCGGGGTTAATGAACCGGCC
+AAAATGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCAACCAGCCTCGCCCAAGT
+TCCCTGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGTCTCGTACGGCGCCGGTT
+AGGATCATCATGACTTCGGCAGAACCCCACACTGTCATATCAGCCCAGCTCGCATCCAAA
+CGGCCTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCCCCTACAACAGTTGTAGC
+TGGAATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGGAAAGGCTCATCTCAAGA
+TTTACTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAGATGCGCGAGGTCGGAAC
+TGCCTCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCACCTGTGTTTGTGGTCCCC
+CCTGTCTGTCCGACTCATATTAATTCATTATATTAATTGGTATACCTGCATTAGATTATG
+CCATTAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAAATGTAGCGCTAAAAGGC
+GCCGCCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTACGGTATGAATCTCGGAT
+CAAGTAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCATGTACCCATGGATCCTTC
+GCGTCTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACACACACCTCTTTACTACGT
+CTAAGATATATTTTCAACTAACAACGGAGACTCTCGATTCACGAAATCCGTACCTATCAC
+TATCGCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTATTCCACGTATGGAGGAT
+CACCAGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTACCGCCCACCCGGGCTGGA
+CGGGATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAACCACCATTCTCTAAGCAT
+CAGTATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGATTCAAGAGTGAACATAG
+TTCGAGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAACCGACTAACGGACAAGTA
+TTACGAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTACTAGTGCGGGCCGGAAC
+TTGCGGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGCGCAACAGGCTCCACCTC
+GCCTCACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATATAGTATTTTTGGCTGGAC
+GCGAATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGCCCATGTGATTGAAAAGC
+GTACTCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCCCTCCCCACCGCGCTTTC
+TGTAAATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTAGCATGTTTGAAAATTTC
+CTGTCGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATGACGGAAACCTTGGCCCG
+ACAGGCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCTCCGCCGATCTGTATACG
+CCCTGTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCTCCCATAACACAATGGCG
+GATTTTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTTCTGAGTCCTCCTAACTG
+ATTATCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCACGCAATGGCAAGTCACA
+GACTGTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTATCAAATTCCTAAGCAAAC
+GGGAGTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACGTGTCTCGCTAGTGCCGG
+GTAGATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATTCTTTTTAGAACACCTTG
+AAATTTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAAGCATTCGAGCGAGAGTA
+GTTCGGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTAAGACTGGCCGGGTCGGG
+GGACAATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGTATCTCGACAAGGACGCG
+CGGTAGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGCTTATCAACTCTCAGATC
+TTTAGATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCATCTATCTTACAACCTGCC
+AATCACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCGAGCAGTTGCGGATCCCT
+CTTATGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCCCCATAGCCCCCGAAATA
+GTTTCGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGGATAAACCTGGCATCGCT
+TCAGACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGCTTAGGGATCTCCGATGC
+ATCTACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCTGGTCTGAGAGTCGGAAT
+AGTCGGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTGTAATCTGAGTTGGGAGT
+TGCTAAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGGTGTCGACGTGATTCTGT
+GAGA
+>ctg2
+CATCATCTGACTATGCATGACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>ctg3
+TCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCGGGGTTAATGAACCGGCCAAAA
+TGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCAACCAGCCTCGCCCAAGTTCCC
+TGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGTCTCGTACGGCGCCGGTTAGGA
+TCATCATGACTTCGGCAGAACCCCACACTGTCATATCAGCCCAGCTCGCATCCAAACGGC
+CTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCCCCTACAACAGTTGTAGCTGGA
+ATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGGAAAGGCTCATCTCAAGATTTA
+CTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAGATGCGCGAGGTCGGAACTGCC
+TCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCACCTGTGTTTGTGGTCCCCCCTG
+TCTGTCCGACTCATATTAATTCATTATATTAATTGGTATACCTGCATTAGATTATGCCAT
+TAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAAATGTAGCGCTAAAAGGCGCCG
+CCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTACGGTATGAATCTCGGATCAAG
+TAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCATGTACCCATGGATCCTTCGCGT
+CTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACACACACCTCTTTACTACGTCTAA
+GATATATTTTCAACTAACAACGGAGACTCTCGATTCACGAAATCCGTACCTATCACTATC
+GCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTATTCCACGTATGGAGGATCACC
+AGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTACCGCCCACCCGGGCTGGACGGG
+ATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAACCACCATTCTCTAAGCATCAGT
+ATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGATTCAAGAGTGAACATAGTTCG
+AGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAACCGACTAACGGACAAGTATTAC
+GAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTACTAGTGCGGGCCGGAACTTGC
+GGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGCGCAACAGGCTCCACCTCGCCT
+CACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATATAGTATTTTTGGCTGGACGCGA
+ATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGCCCATGTGATTGAAAAGCGTAC
+TCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCCCTCCCCACCGCGCTTTCTGTA
+AATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTAGCATGTTTGAAAATTTCCTGT
+CGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATGACGGAAACCTTGGCCCGACAG
+GCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCTCCGCCGATCTGTATACGCCCT
+GTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCTCCCATAACACAATGGCGGATT
+TTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTTCTGAGTCCTCCTAACTGATTA
+TCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCACGCAATGGCAAGTCACAGACT
+GTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTATCAAATTCCTAAGCAAACGGGA
+GTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACGTGTCTCGCTAGTGCCGGGTAG
+ATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATTCTTTTTAGAACACCTTGAAAT
+TTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAAGCATTCGAGCGAGAGTAGTTC
+GGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTAAGACTGGCCGGGTCGGGGGAC
+AATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGTATCTCGACAAGGACGCGCGGT
+AGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGCTTATCAACTCTCAGATCTTTA
+GATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCATCTATCTTACAACCTGCCAATC
+ACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCGAGCAGTTGCGGATCCCTCTTA
+TGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCCCCATAGCCCCCGAAATAGTTT
+CGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGGATAAACCTGGCATCGCTTCAG
+ACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGCTTAGGGATCTCCGATGCATCT
+ACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCTGGTCTGAGAGTCGGAATAGTC
+GGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTGTAATCTGAGTTGGGAGTTGCT
+AAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGGTGTCGACGTGATTCTGTGAGA
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAACACACCGCTATGCACTAACACGGGCTGAGTACGGA
+TAATTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTG
+CACGGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGA
+GTTCCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAA
+CACTATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAG
+ACTTTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGT
+TGAGCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTA
+ATATTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCC
+ATAGACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGC
+AATGGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATA
+ACCTGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCC
+CGCGGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTC
+TCCGGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAA
+AGAGTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGG
+TTTTCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCC
+TAGATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAA
+CGTGAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGA
+TCACCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAA
+CGTGCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACT
+AATTTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAA
+GCTGAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTA
+TACC
+>ctg4
+ATGGAAAATTTCTGGCAAACTTGCTCGGCTCAATTGGAACAAGAATTGACTCCGCAACAA
+TACTCGGCTTGGATCAAGCCGTTGGCTCCGTTGGACTACGAAGACGGTACTTTGCGAATC
+GCTGCTCCGAATCGATTCAAGTTGGACTGGGTCAAGACTCAATTCGCTGGTCGAATCACT
+TCGATCGCTGCTCAATTCTGGGACATGCCGGTCGACGTCCAATTCGTCTTGGACCCGCGA
+TTGGCTTCGGCTAAGAAGCCGACTACTTCGGCTTCGGTCGCTCCGATCCAATCGGACGAC
+GTCCCGGCTTCGGTCTTGGAACCGATCCCGTCGAATGCTACTGACCACACTCCGCGACGA
+GACCAATCGCGAATCAATACTGCTTTGACTTTCGACTCGTTCGTCACTGGTAAGGCTAAT
+CAATTGGCTCGAGCTGCTGCTATCCAAGTCGCTAATAATCCGGGTTCGTCGTACAATCCG
+TTGTTCTTGTACGGTGGTGTCGGTTTGGGTAAGACTCACTTGATCCACGCTATCGGTAAT
+CAAGTCTTGGCTGACAATCCGGACGTCAAGATCCGATACATCCACGCTGAACAATACGTC
+CGAGACGTCGTCACTGCTTACCAACGAAAGGGTTTCGACGACTTCAAGCGATACTACCAC
+TCGTTGGACTTGTTGTTGATCGACGACATCCAATTCTTCGGTGGTAAGTCGCGAACTCAA
+GAAGAATTCTTCTACGCTTTCGAAGCTTTGATCGCTGCTAAGAAGCAAATCATCATCACT
+TCGGACACTTACCCGAAGGAAATCACTGGTATGGACGACCGATTGATCTCGCGATTCGAC
+TCGGGTTTGACTGTCGCTGTCGAACCGCCGGAATTGGAAATGCGAGTCGCTATCTTGTTG
+AAGAAGGCTGTCCAAGAAGGTGTCACTTTCTCGGACGACGTCGCTTTCTTCGTCGCTAAG
+CACTTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTGCGAAAGATCTTGGCTTACTCG
+CGATTCCACGGTAAGGACATCACTATCGAAGTCGTCAAGGACGCTTTGAAGGACTTGTTG
+TCGGTCCAAAATCGACAAATCTCGGTCGAAAATATCCAAAAGACTGTCGCTGACTTCTTC
+AATATCAAGGTCGCTGACATGTACTCGAAGAAGCGACCGGCTAATATCGCTCGACCGCGA
+CAAATCGCTATGTACTTGGCTAAGGAATTGACTCAAAAGTCGTTGCCGGAAATCGGTGAA
+TTGTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCTGTCCGAAAGATCGCTGCTGAC
+CGAGGTAAGTCGCCGGAATGCAATCACGAATTGCACGTCTTGGAACAAACTTTGAAGGGT
+TGAACGGGATCTTACGCGTCAGACGCATTCGGGGTTCCTCGCACCACAATGCCCCGTCAC
+TCCAGCGATCGGTCCAGCAATCGCCTTCATTGCAGCGGGTTGGTTTTTAGTGCGGACCAT
+GACCGCGCTGAGTGAAAGGATCTACTTGCTGTAAAGCCATATGGTCGGGCCCGACGTGGC
+GCAAGGTTGGCAAGAGAGTCCGCCAGAACAAGCAATCTAACGAGCAGGTCTTTGACATTC
+TACGCCCTTCTGTTTTTTAAGTCTTACAACGAGAATTCGACTATGATGGACAGCTTCCCA
+ACGAACGAGGGACCACCGCTATCAGGGGCACATACGGGGAACGCCAGCGCAAATGCCGAG
+CACCAAAGTCTTCACACAGGGTTGCACAGTCCTACTGCTATACTACGGAATGGCCATTCT
+GCTGCGAGGACCGTGTGACCCTGGCGACATCAGTAGAAATTAATGTGGTCAGATAGCTAG
+TATGTACAGATTATCCTCACGGGCGGCAAAGACATCGCATTAATTCGGGCTTCTTTCGGA
+TATCAGTGATGATTTGCACGACAAACGCGTCACGGGCATAGCCTCATTGACCATAGTGCG
+CGATACACAGCCTCCCTTAACGTAGGACTAGAAGTACTGATCGTTATGTCAAGCGTTTAA
+GTTCCGCGCGGGAAATTGCATCTTTCTAATATACATTATGAGCTGCCAATCGTGGTCGCC
+CCAATGTCCTCAAAACAGATGCGGTAATACGCTCTGGGGCGGCCCTCGGTGCCTCGAGTG
+GCTCTGGATCGACATGTCGTCACGCGTCGAGATACGCGCGGGATCCTGACCACGAATCAT
+AAAAGTGACCTGACCATAAAAAGGCAGTTGCGGTTCTGGCATTGGAGGGCTTCGGTGAAT
+TCAGCATTCTGGTCGCTTAATAGCTAGGATGTGCCATTGACAGGTACTCGTGCACTTCTG
+GGCAGAACCGATGCATCGCTAGCCCCCAAACACCGGCTGGGTCATTGGAAGAGGACGTCG
+CTACGAGTCTACCGGTCGGAGACCCATGTTTTTTGGCAATAATCTCGAACAACAGAAGGG
+AGGGACCATAGGATATTCCGCGTGTGGGCGAAAGGATCAGCCACATCTCGATGTATTTAA
+TGCTCATCTGGTCTTAAGTTTATTACGCTTACGTCCAGGGCATTACCGATGAAACAGGAT
+GACGGCAGAAAGTTAGTATTGTATTGGTGGGCATGTTTACAAAGACACGCCCAAACCTAC
+TAAAACGTGACAGCTAGTCATGCCACTGGATGTAAAAGTCCAGTCCGCCTTCACGAGATT
+ACAGCTACGCATTAGTCAACGTGTTCGTTCTCAGCGCTGGTACCCCTTAGTACAGTGACA
+GTGCTTGCGCGGCAGTGCCGCAGCTATCCGCTTAGTCTGACGAAACAGGCCAGAACTAAC
+ATTACCATCTAAGTTGGAAAGAGGCTGTCCACGTTTATTAATATTTTAATTAAGTACGGG
+CTGAAAGGTAATATGAAACCACGTTAGGACGACCGTAATGATTCAAGTTTGAATTCCATT
+GAATTGCTATCGTGTGCTTGGGCATGTAAAAAGGTCTCAAGAAGTGGAATGTGTCACACA
+ATCTAACTGGAGTTGCTGTAAGACTTGCCAATCCGCCCATGTAGAGTCTGGATAAGAGCG
+TCAACCGCAACCCGGGCTCTAAGCAGCTCGGTTAGGTGCAAGAGGCCGTAGATAGGCGGT
+GATCCGGGGCTCTTTGTATATATTTGTGGGCTGCTACGTGCCGAACTAATTGCGCGTGTC
+AGGTGGTAAAATGCCGGTTAGGGATACATACTCCTATTGGTCGGAAACGTCTATGTCGTG
+CTTCACGAGGGAGCATAGAGATAACCTTCAGGATCGTGAAAAGGCAAATTGCACTCCTAG
+GGTTCCCAGCAGTATAACACGTGAGCCGTACGTGTTCCGCTCAACTAAAGGGCGATACGA
+TTGGACGTTCATAGCTCACCTTTAGCCGAGCCGGTACCAGTCAAGCACCGCGTGCTGGGG
+CTGCGAATATATGGATGTTTTACGTTCCGATGCACCTCTGTGTCGCCTGCATTAGTTCCT
+GAATACCGAATGTCGCTATCTCCCTTGTTTAAACGAAGTGGGAAATCTGATCTCCACGGT
+AACAACAGCCCAATCTGTCGCACGCGCCGAGTCATTTCGGCACCGTAAATGAACCAGATT
+CAGGCCCCAAACTACACCTATTATTACAAAAGCCCCTGCGGTCGTTAATTCAGTGAAAGT
+GATGTTTTGGTTGGCAAGAACAATAGACGTCAGATTCATCTAATGGGTGAACCAGGGGCT
+TGGACGGCCAACTGTTTCCAGGGATCTCAAACGACTAACGCTCCCTGAACAGGCTCCTTT
+TGTATCAGTATGTAAACATTGACACGGGCTGGGTCGTTGGCTTTCATCGGGTCACCGGCC
+GTCCAGATTTAATTTATGTGGCCCGACTGCTCTCACGTACCCTTCTAGATCTACCACGAA
+GCCGAACGCTATATTACTCGTTCAAACCACAGTCCGACGAAGTACTCTGGAGTTACCGGC
+GCCACCCAGCCCCACCTACGGCACAAAAAGCGGCCCCTTTACGGATGCGTCTCGAGGCTG
+ACGAGTATCAAGAGACCCGAGTTAGGAGGAGTGCACCCTCTTGGGCTTAGAACACGTTAG
+GGGGGAAGTAAACTATGGGTGGGAATTGTCCAACACAACACAGCATTCATCGACAATAAC
+AGGTGCCCGGCGGTATCTCTATATAAGTCTCAGAATGGAACGGTAACGCGGCTTCGAACT
+ATAAAGGTCACGGATACGGAGCCCAACTGCGGGCTTCATAGGGGATGCGACTGGATCGCT
+TGCGGCTCGGGCGTATGTTGACCTCTGCTTGTGTCGATATAGTCTACTATCCCCCTTGGT
+CATTCTGCAGGAGGGACGTACGAAGTAGGTGGCACCAGTTGGTTTTATGTACCCGTATTG
+AATACAAATTCGGTGGTCCCATTAGATGCAGTCCTAGGGTTGACGGTTCCACTGTTTGCT
+GCGCCGTATGTACGTGGCACACCCAGATCTTGCTTAGGAGCATCACCATTAGATTAACGC
+GTCCGTCACGCTGTTGCCTCGCCGGGCGCATAGCAGTCTTAGCATAGCCGCTAGACGTTA
+GGTTGTTACTTCTCGCCAATCGCGAGTAGCCGCGCTTGACTGAGCAGCTGCCTGCGAAAC
+TTCGCATTTTGAGAAGGTAACAAAGTTGAACTAGGGCGGGTAGTTAAAGTCGAGTCATAA
+CCCCGGGGTACATGCTGATTTAAAACGGACAGTGTGCCTGACAGGTAGTCCCCTGCTGTC
+CACAGCTATGTGGACATGTTCAATAAGAGTCGTTCCCAGGTTGCACCACGAGTTTCTGGC
+ATGGAGTACTACTTATAAAGCGTACCTTTACACTTGCAGATTCAAAAGTGCGGCGCCCGA
+TAGCACATAGCTCTTGTGGTTGAACTGGAATCCCTAAGATATTCCACCTCCGAAACCATG
+AATACTCGAGGAACCGTTCGGCTATGACCTATAAAACTGTCCGCTGGGAGGGCTTTCGAA
+ATGGCTCAGAGGCTCATAACCTGTACCCAGCAGTCGCGATCGCCCCTATTAACAGAGACG
+ATCTGCTGTTGAGCTATTAGAGATCCTCGGTCCAGAGAGAGATGGCCAAATACATCCAAG
+CACACGTGCCGCTAGCTATCAGCCTGGTCGTCGTTATGAGGTCTATCCGGTTCATCGTGC
+TCGTAGTCTGAGACGAACGTGGAGCCTACTAGGAAACTTGGGGGCAACCTAGCTTTACTG
+GTCTCCTCCGGGTGGCCCTGGACGGAGGCCAAACAACGAAGGACGCAGGCTGACACTAAG
+TACCGTCAACAGACTACGCCATAATCCGGATTCGGCCATAACACGTCATAATGATCTCCA
+TTCGAATGTAGTTATAAGACGTGCCGTCCATTTTCCCCTTTACTCAATTGGAAACTTCGT
+GAGTTTTTCGCCCAGAGTTACTCCACCCACCAGGGCGAGCATGACCCGTAGTTATTTGAT
+ATGCCTACTCTTACTTCTATATAAAACGATTTTGATATTTGTAGGCAATGTTCCTGTACC
+TTTGCTTTTAGACTCGGAATTTCACAGCCCGAACAATGTTATGTAGCCGAATTGAGTTTA
+TCACGCTTAGTAGCGGTCCGGCATGGCCTGAAGCGAGTGGTTTAAATTACTGGGTTTTAT
+CCACGGCTAGCGCGAAACGTAATCCACCCCATCCCAGGGTGTTACGGTGATCGATGGAGA
+GATGCCATGAGATGGTAATGGATGATGCTAGCTAAGTCGCCCTGAGACGATACCATCTGA
+CCACCAGAAGATCAGGAAAGTCGACCAAAAAAGACTTGCGCCTTCTATCAAT
diff --git a/circlator/tests/data/start_fixer_run_bit_of_everything.ignore b/circlator/tests/data/start_fixer_run_bit_of_everything.ignore
new file mode 100644
index 0000000..41573b4
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_bit_of_everything.ignore
@@ -0,0 +1 @@
+ctg3
diff --git a/circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa b/circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa
new file mode 100644
index 0000000..da78adb
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa
@@ -0,0 +1,25 @@
+>dnaa
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGA
diff --git a/circlator/tests/data/start_fixer_run_ignore_all.expect.fa b/circlator/tests/data/start_fixer_run_ignore_all.expect.fa
new file mode 100644
index 0000000..ed64500
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_ignore_all.expect.fa
@@ -0,0 +1,2 @@
+>ctg1
+CTACTACTGACTCATACTTA
diff --git a/circlator/tests/data/start_fixer_run_ignore_all.fa b/circlator/tests/data/start_fixer_run_ignore_all.fa
new file mode 100644
index 0000000..ed64500
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_ignore_all.fa
@@ -0,0 +1,2 @@
+>ctg1
+CTACTACTGACTCATACTTA
diff --git a/circlator/tests/data/start_fixer_run_ignore_all.to_ignore b/circlator/tests/data/start_fixer_run_ignore_all.to_ignore
new file mode 100644
index 0000000..a92f69a
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_ignore_all.to_ignore
@@ -0,0 +1 @@
+ctg1
diff --git a/circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa b/circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa
new file mode 100644
index 0000000..074e845
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa
@@ -0,0 +1,91 @@
+>ctg1
+TCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCGGGGTTAATGAACCGGCCAAAA
+TGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCAACCAGCCTCGCCCAAGTTCCC
+TGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGTCTCGTACGGCGCCGGTTAGGA
+TCATCATGACTTCGGCAGAACCCCACACTGTCATATCAGCCCAGCTCGCATCCAAACGGC
+CTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCCCCTACAACAGTTGTAGCTGGA
+ATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGGAAAGGCTCATCTCAAGATTTA
+CTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAGATGCGCGAGGTCGGAACTGCC
+TCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCACCTGTGTTTGTGGTCCCCCCTG
+TCTGTCCGACTCATATTAATTCATTATATTAATTGGTATACCTGCATTAGATTATGCCAT
+TAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAAATGTAGCGCTAAAAGGCGCCG
+CCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTACGGTATGAATCTCGGATCAAG
+TAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCATGTACCCATGGATCCTTCGCGT
+CTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACACACACCTCTTTACTACGTCTAA
+GATATATTTTCAACTAACAACGGAGACTCTCGATTCACGAAATCCGTACCTATCACTATC
+GCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTATTCCACGTATGGAGGATCACC
+AGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTACCGCCCACCCGGGCTGGACGGG
+ATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAACCACCATTCTCTAAGCATCAGT
+ATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGATTCAAGAGTGAACATAGTTCG
+AGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAACCGACTAACGGACAAGTATTAC
+GAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTACTAGTGCGGGCCGGAACTTGC
+GGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGCGCAACAGGCTCCACCTCGCCT
+CACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATATAGTATTTTTGGCTGGACGCGA
+ATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGCCCATGTGATTGAAAAGCGTAC
+TCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCCCTCCCCACCGCGCTTTCTGTA
+AATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTAGCATGTTTGAAAATTTCCTGT
+CGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATGACGGAAACCTTGGCCCGACAG
+GCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCTCCGCCGATCTGTATACGCCCT
+GTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCTCCCATAACACAATGGCGGATT
+TTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTTCTGAGTCCTCCTAACTGATTA
+TCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCACGCAATGGCAAGTCACAGACT
+GTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTATCAAATTCCTAAGCAAACGGGA
+GTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACGTGTCTCGCTAGTGCCGGGTAG
+ATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATTCTTTTTAGAACACCTTGAAAT
+TTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAAGCATTCGAGCGAGAGTAGTTC
+GGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTAAGACTGGCCGGGTCGGGGGAC
+AATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGTATCTCGACAAGGACGCGCGGT
+AGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGCTTATCAACTCTCAGATCTTTA
+GATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCATCTATCTTACAACCTGCCAATC
+ACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCGAGCAGTTGCGGATCCCTCTTA
+TGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCCCCATAGCCCCCGAAATAGTTT
+CGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGGATAAACCTGGCATCGCTTCAG
+ACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGCTTAGGGATCTCCGATGCATCT
+ACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCTGGTCTGAGAGTCGGAATAGTC
+GGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTGTAATCTGAGTTGGGAGTTGCT
+AAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGGTGTCGACGTGATTCTGTGAGA
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAACACACCGCTATGCACTAACACGGGCTGAGTACGGA
+TAATTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTG
+CACGGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGA
+GTTCCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAA
+CACTATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAG
+ACTTTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGT
+TGAGCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTA
+ATATTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCC
+ATAGACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGC
+AATGGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATA
+ACCTGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCC
+CGCGGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTC
+TCCGGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAA
+AGAGTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGG
+TTTTCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCC
+TAGATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAA
+CGTGAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGA
+TCACCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAA
+CGTGCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACT
+AATTTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAA
+GCTGAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTA
+TACC
diff --git a/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa b/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa
new file mode 100644
index 0000000..b9e97b3
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa
@@ -0,0 +1,91 @@
+>ctg1
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGAACACACCGCTATGCACTAACACGGGCTGAGTACGGA
+TAATTGGTGTGTTAAATCTCAGCATAAGAAGCGGAATGGTGTTCTCTGAAAGGATGCCTG
+CACGGGCACTCGAGACCTGAGGGCGAATTAGTGTACGAACTAAGTGGGCGATCTACGAGA
+GTTCCGGGATTTTTATACACCCCTAGGTACAGTTGCTGGGTCGGTTTTTCTACCCGCAAA
+CACTATCTTCGGCCGTTGTAGGCGTTCACAACCAACTGTTTTATCCTTCTCGCCCGGAAG
+ACTTTGTCAACACTTCAATTTCCCTCTAGCGCTCTCTTCACGTCAATGTGTGGGGTACGT
+TGAGCGATAATTGGGGAAGCAAATTCACGCCTTATTTGAGAAACCGGTCTCTGACACCTA
+ATATTCGACGGTGAATAGGAATCCCTGAATCAACGGGTACTTCTAGGGCCGATGGCGGCC
+ATAGACCGCCTGGCTCTTTCTTGTCAGTGTCGATTTCGGTGTACTTGGGCAGCGACCTGC
+AATGGGTGGAAGACCGTCATTTCGCCACCGGGAAATATCTGTCTTACTGCTAACTCTATA
+ACCTGTCTAGTACCCGATTGGCTAAGTTGCATTTTCAGATCGAATGATCGACAGCCCCCC
+CGCGGACCTGACAACTCCCGGTACCGCAAGCTGTAGAGTTCTTACCCGTGCCCCATACTC
+TCCGGGTTTGTGTAACTGTGGTACTGGTTGTGCGAGCTGACTTGTATCAGGCTACGCCAA
+AGAGTAAGTACTGCAATCCGTCTATATCACCTGAGTGATTGTGGTTTACCCTTGCGGGGG
+TTTTCGTGTGGCTCTCTGATCTACGGCGAGTCTCTGCGGTGATTGATGTATCAACGCGCC
+TAGATCTAGCATGTGCCTGTCGGGCCTATAGACAATGTCTTGGGGTGTTCGGTGATTCAA
+CGTGAGATTATTTGCATGGAGACCACTGTGTTACATGCCAGTGGGCTAAGAACCTTTGGA
+TCACCAGATGCCGTGGTAAAGAAGAGCGACCCCGCTCAAATACGCACGCATGCGCCCTAA
+CGTGCCAAAACCTTACGCAACGTGGAAGGCCACACCAGGCGAATGCCTGCGCTTCGGACT
+AATTTAAATAGGCGTACCACGTCAGTACTGATTACCCTTAGGGTGGGTTACCCTAGTGAA
+GCTGAACCGTACGACATGCCGTTATCGACTGCGTTCCTTGGTCCAGTAAGGCATCGTCTA
+TACCTCAGTGCTCAGTTAAATGGCGTCTGCAGGATTAATATCGGGGTTAATGAACCGGCC
+AAAATGTAACATTGGCCTCACTGGAACGAAGCTCCTAGTCCCAACCAGCCTCGCCCAAGT
+TCCCTGTTTGTGATAATGGCCCGAGGTCCAGAGAGTTATCTGTCTCGTACGGCGCCGGTT
+AGGATCATCATGACTTCGGCAGAACCCCACACTGTCATATCAGCCCAGCTCGCATCCAAA
+CGGCCTGCTGCCTGCTCCAGCGTCCCCGAATGGCGCGATGTCCCCTACAACAGTTGTAGC
+TGGAATGAGACGGATGCTGTGTAATGTGTGTTTGCGTCGAAGGAAAGGCTCATCTCAAGA
+TTTACTATCTAATGAACATGCGGCAATCCACGTTGGCAGTAAGATGCGCGAGGTCGGAAC
+TGCCTCCGTGGTTCGCAAGTAATGTCGTCCCCCCTGTCTTCACCTGTGTTTGTGGTCCCC
+CCTGTCTGTCCGACTCATATTAATTCATTATATTAATTGGTATACCTGCATTAGATTATG
+CCATTAATAGTTCGCCCGGATCTTTTACGGATCGCCTCCGAAAATGTAGCGCTAAAAGGC
+GCCGCCCCAATCCCAAGATTACGCATTCTAACTTACACGCTTACGGTATGAATCTCGGAT
+CAAGTAAGGTTAGCTTTGTAGCATACCCGACCCAAAACTGCATGTACCCATGGATCCTTC
+GCGTCTTTCTAACTCTTAAATGAGCAATTTGAACTACGCACACACACCTCTTTACTACGT
+CTAAGATATATTTTCAACTAACAACGGAGACTCTCGATTCACGAAATCCGTACCTATCAC
+TATCGCTGTATCACATTGTTACCTATAGCAGACGTTTCACGTATTCCACGTATGGAGGAT
+CACCAGGCATGCTTTTAGACCACAACAGCTGGCAGAAGTCTACCGCCCACCCGGGCTGGA
+CGGGATCAAGGTCCAAACTCAAGGACAGTGATGTTCTGATAACCACCATTCTCTAAGCAT
+CAGTATGAAGATTCTTACACAGAGAACTATCCGAATGAGGAGATTCAAGAGTGAACATAG
+TTCGAGAGATAACCGGGGGTAGCGCAGTCGTGGCCTACAAAACCGACTAACGGACAAGTA
+TTACGAAGTCCCACGTGTGTTAGGACTTAGTTTAGGCCCTGTACTAGTGCGGGCCGGAAC
+TTGCGGTCAAATGTTGGTCGTATTCCCGCATGACAGGCTGGGCGCAACAGGCTCCACCTC
+GCCTCACGTAATTAGCCGATCCGAGAGAATGTGCCCGCCATATAGTATTTTTGGCTGGAC
+GCGAATAGGGAACGGGAATCCTAGCTTCTGAGTGAAGGACCGCCCATGTGATTGAAAAGC
+GTACTCACACGGCTGGCTCTTCGCTGATTCGACCATGTTTTCCCTCCCCACCGCGCTTTC
+TGTAAATACCCCGTTGTAAGTGGAGTTCAGGAACTTGAGTCTAGCATGTTTGAAAATTTC
+CTGTCGAGACAAGTACCCGACCACAGCTAATGAGAAATTAATGACGGAAACCTTGGCCCG
+ACAGGCCGGTACCAAGGCTTGGTCTTCCATATGTACCTGGTCTCCGCCGATCTGTATACG
+CCCTGTTAACTAAAGAGTTGCCTCTCTATACACCGCCAGGTCTCCCATAACACAATGGCG
+GATTTTGTTTCCACGCCAGGTGCTAGGCCCGACACTCCAGTTTCTGAGTCCTCCTAACTG
+ATTATCATAAACCACGGTACAGCTGGTAGTATCATGGGGAGCACGCAATGGCAAGTCACA
+GACTGTGCTTCCCCCGAGACCGTGCGTTTTTACTATTTTCTATCAAATTCCTAAGCAAAC
+GGGAGTTCGAACAGCAAGACTGTACTGTCGATCAGTTGAAACGTGTCTCGCTAGTGCCGG
+GTAGATAGCGTTACTGTCCAGAATGACATTTCGTCTCAGAATTCTTTTTAGAACACCTTG
+AAATTTGAGGCTTGGCGCCTATCGTAACAAAGACAGCCCGTAAGCATTCGAGCGAGAGTA
+GTTCGGCTGAATCCTGGTCGTCATGCCTCGACGGGAACAGGTAAGACTGGCCGGGTCGGG
+GGACAATTTACCCGAGAACCCAGGACGACTTATCCAAAACAGTATCTCGACAAGGACGCG
+CGGTAGAAGGAAAACACACCCAGAGTTTTTCAGTACCGACGGCTTATCAACTCTCAGATC
+TTTAGATGATCGAGATTGATCATCGGTCAGTACTGAGAGCCATCTATCTTACAACCTGCC
+AATCACGATGTCGAGTTATAGAAGCCCCCGTAATATGAAGGCGAGCAGTTGCGGATCCCT
+CTTATGTGGGTTGGATCTATTAGACGGAATGCCCCGTGAACCCCCATAGCCCCCGAAATA
+GTTTCGAAGCAAGGCCCCCAGATGGATCCTAGCTGCGCGGGGGATAAACCTGGCATCGCT
+TCAGACCTGATAGTAGTGGCCACAGGACTAGTCACCATCGAGCTTAGGGATCTCCGATGC
+ATCTACTGCCATACTCTCATTACGAGTTCGGCGCGTGTGGGCTGGTCTGAGAGTCGGAAT
+AGTCGGGGCAAATCGATAAAGCGGCATGGGGAATGCCGACCTGTAATCTGAGTTGGGAGT
+TGCTAAAATTCACATGGGGGGCGTTTCGCGTGAACTAGGGAGGTGTCGACGTGATTCTGT
+GAGA
diff --git a/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa b/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa
new file mode 100644
index 0000000..da78adb
--- /dev/null
+++ b/circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa
@@ -0,0 +1,25 @@
+>dnaa
+ATGTCGTTGTCGTTGTGGCAACAATGCTTGGCTCGATTGCAAGACGAATTGCCGGCTACT
+GAATTCTCGATGTGGATCCGACCGTTGCAAGCTGAATTGTCGGACAATACTTTGGCTTTG
+TACGCTCCGAATCGATTCGTCTTGGACTGGGTCCGAGACAAGTACTTGAATAATATCAAT
+GGTTTGTTGACTTCGTTCTGCGGTGCTGACGCTCCGCAATTGCGATTCGAAGTCGGTACT
+AAGCCGGTCACTCAAACTCCGCAAGCTGCTGTCACTTCGAATGTCGCTGCTCCGGCTCAA
+GTCGCTCAAACTCAACCGCAACGAGCTGCTCCGTCGACTCGATCGGGTTGGGACAATGTC
+CCGGCTCCGGCTGAACCGACTTACCGATCGAATGTCAATGTCAAGCACACTTTCGACAAT
+TTCGTCGAAGGTAAGTCGAATCAATTGGCTCGAGCTGCTGCTCGACAAGTCGCTGACAAT
+CCGGGTGGTGCTTACAATCCGTTGTTCTTGTACGGTGGTACTGGTTTGGGTAAGACTCAC
+TTGTTGCACGCTGTCGGTAATGGTATCATGGCTCGAAAGCCGAATGCTAAGGTCGTCTAC
+ATGCACTCGGAACGATTCGTCCAAGACATGGTCAAGGCTTTGCAAAATAATGCTATCGAA
+GAATTCAAGCGATACTACCGATCGGTCGACGCTTTGTTGATCGACGACATCCAATTCTTC
+GCTAATAAGGAACGATCGCAAGAAGAATTCTTCCACACTTTCAATGCTTTGTTGGAAGGT
+AATCAACAAATCATCTTGACTTCGGACCGATACCCGAAGGAAATCAATGGTGTCGAAGAC
+CGATTGAAGTCGCGATTCGGTTGGGGTTTGACTGTCGCTATCGAACCGCCGGAATTGGAA
+ACTCGAGTCGCTATCTTGATGAAGAAGGCTGACGAAAATGACATCCGATTGCCGGGTGAA
+GTCGCTTTCTTCATCGCTAAGCGATTGCGATCGAATGTCCGAGAATTGGAAGGTGCTTTG
+AATCGAGTCATCGCTAATGCTAATTTCACTGGTCGAGCTATCACTATCGACTTCGTCCGA
+GAAGCTTTGCGAGACTTGTTGGCTTTGCAAGAAAAGTTGGTCACTATCGACAATATCCAA
+AAGACTGTCGCTGAATACTACAAGATCAAGGTCGCTGACTTGTTGTCGAAGCGACGATCG
+CGATCGGTCGCTCGACCGCGACAAATGGCTATGGCTTTGGCTAAGGAATTGACTAATCAC
+TCGTTGCCGGAAATCGGTGACGCTTTCGGTGGTCGAGACCACACTACTGTCTTGCACGCT
+TGCCGAAAGATCGAACAATTGCGAGAAGAATCGCACGACATCAAGGAAGACTTCTCGAAT
+TTGATCCGAACTTTGTCGTCGTGA
diff --git a/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa b/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa
new file mode 100644
index 0000000..4a73dca
--- /dev/null
+++ b/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa
@@ -0,0 +1,8 @@
+>seq1
+A
+>seq2
+AGAGATGAA
+>seq3
+ACGTAGCTGC
+>seq4
+GGAGAGAGAAT
diff --git a/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa b/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa
new file mode 100644
index 0000000..7af0064
--- /dev/null
+++ b/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa
@@ -0,0 +1,12 @@
+>seq1
+A
+>seq2
+AGAGATGAA
+>seq3
+ACGTAGCTGC
+>seq3__ends
+GCTGCACGTA
+>seq4
+GGAGAGAGAAT
+>seq4__ends
+AGAATGGAGA
diff --git a/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa b/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa
new file mode 100644
index 0000000..8b86439
--- /dev/null
+++ b/circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa
@@ -0,0 +1,6 @@
+>seq2
+AGAGATGAA
+>seq3
+ACGTAGCTGC
+>seq3__ends
+GCTGCACGTA
diff --git a/circlator/tests/data/start_fixer_write_renamed_contigs.fa b/circlator/tests/data/start_fixer_write_renamed_contigs.fa
new file mode 100644
index 0000000..2a60107
--- /dev/null
+++ b/circlator/tests/data/start_fixer_write_renamed_contigs.fa
@@ -0,0 +1,4 @@
+>ctg1
+ACGT
+>ctg2 foo bar
+AAA
diff --git a/circlator/tests/start_fixer_test.py b/circlator/tests/start_fixer_test.py
new file mode 100644
index 0000000..43af096
--- /dev/null
+++ b/circlator/tests/start_fixer_test.py
@@ -0,0 +1,225 @@
+import unittest
+import shutil
+import filecmp
+import copy
+import os
+import sys
+import pyfastaq
+import pymummer
+from circlator import start_fixer
+
+modules_dir = os.path.dirname(os.path.abspath(start_fixer.__file__))
+data_dir = os.path.join(modules_dir, 'tests', 'data')
+
+
+class TestStartFixer(unittest.TestCase):
+ def test_init(self):
+ '''Test init'''
+ contigs_fa = os.path.join(data_dir, 'start_fixer_init_contigs.fa')
+ dna_da = os.path.join(data_dir, 'start_fixer_init_dnaA.fa')
+
+ with self.assertRaises(start_fixer.Error):
+ sfixer = start_fixer.StartFixer('notafile', 'outprefix')
+
+ sfixer = start_fixer.StartFixer(contigs_fa, 'outprefix')
+ expected_contigs = {
+ 'contig1': pyfastaq.sequences.Fasta('contig1', 'ACGT'),
+ 'contig2': pyfastaq.sequences.Fasta('contig2', 'AAAA'),
+ }
+ self.assertEqual(expected_contigs, sfixer.input_assembly)
+ self.assertEqual(set(), sfixer.ignore)
+
+ with self.assertRaises(start_fixer.Error):
+ sfixer = start_fixer.StartFixer(contigs_fa, 'outprefix', genes_fa='notafile')
+
+ ignore_file = os.path.join(data_dir, 'start_fixer_init_ignore_ids')
+ sfixer = start_fixer.StartFixer(contigs_fa, 'outprefix', ignore=ignore_file)
+ self.assertEqual({'ignore_me1', 'ignore_me2'}, sfixer.ignore)
+
+
+ def test_rename_contigs(self):
+ '''Test _rename_contigs'''
+ contigs_in = {
+ 'ctg1': pyfastaq.sequences.Fasta('ctg1', 'ACGT'),
+ 'ctg2 foo bar': pyfastaq.sequences.Fasta('ctg2 foo bar', 'AAA'),
+ }
+ expected_contigs = {
+ 'ctg1': pyfastaq.sequences.Fasta('ctg1', 'ACGT'),
+ 'ctg2': pyfastaq.sequences.Fasta('ctg2', 'AAA'),
+ }
+ expected_names = {'ctg1': 'ctg1', 'ctg2': 'ctg2 foo bar'}
+ got_contigs, got_names = start_fixer.StartFixer._rename_contigs(contigs_in)
+ self.assertEqual(expected_names, got_names)
+ self.assertEqual(expected_contigs, got_contigs)
+ contigs_in['ctg2 abc'] = pyfastaq.sequences.Fasta('ctg2 abc', 'AAA')
+ with self.assertRaises(start_fixer.Error):
+ start_fixer.StartFixer._rename_contigs(contigs_in)
+
+
+ def test_write_renamed_contigs(self):
+ '''Test _write_renamed_contigs'''
+ contigs_dict = {
+ 'ctg1': pyfastaq.sequences.Fasta('ctg1', 'ACGT'),
+ 'ctg2': pyfastaq.sequences.Fasta('ctg2', 'AAA'),
+ }
+ rename_dict = {'ctg1': 'ctg1', 'ctg2': 'ctg2 foo bar'}
+ tmp_out = 'tmp.test_write_renamed_contigs.fa'
+ start_fixer.StartFixer._write_renamed_contigs(contigs_dict, rename_dict, tmp_out)
+ expected = os.path.join(data_dir, 'start_fixer_write_renamed_contigs.fa')
+ self.assertTrue(filecmp.cmp(expected, tmp_out, shallow=False))
+ os.unlink(tmp_out)
+
+
+ def test_max_length_from_fasta_file(self):
+ '''Test _max_length_from_fasta_file'''
+ infile = os.path.join(data_dir, 'start_fixer_max_length_from_fasta_file.fa')
+ self.assertEqual(11, start_fixer.StartFixer._max_length_from_fasta_file(infile))
+
+
+ def test_write_fasta_plus_circularized_ends(self):
+ '''Test _write_fasta_plus_circularized_ends'''
+ infile = os.path.join(data_dir, 'start_fixer_write_fasta_plus_circularized_ends.in.fa')
+ expected = os.path.join(data_dir, 'start_fixer_write_fasta_plus_circularized_ends.out.fa')
+ expected_ignore = os.path.join(data_dir, 'start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa')
+ tmp_out = 'tmp.test_write_fasta_plus_circularized_ends.fa'
+ contigs = {}
+ pyfastaq.tasks.file_to_dict(infile, contigs)
+ got = start_fixer.StartFixer._write_fasta_plus_circularized_ends(contigs, tmp_out, 5)
+ self.assertEqual(6, got)
+ self.assertTrue(filecmp.cmp(expected, tmp_out, shallow=False))
+ got = start_fixer.StartFixer._write_fasta_plus_circularized_ends(contigs, tmp_out, 5, ignore={'seq1', 'seq4'})
+ self.assertEqual(3, got)
+ self.assertTrue(filecmp.cmp(expected_ignore, tmp_out, shallow=False))
+ os.unlink(tmp_out)
+ got = start_fixer.StartFixer._write_fasta_plus_circularized_ends(contigs, tmp_out, 5, ignore={'seq1', 'seq2', 'seq3', 'seq4'})
+ self.assertEqual(0, got)
+ self.assertFalse(os.path.exists(tmp_out))
+
+
+ def test_find_circular_using_promer(self):
+ '''Test _find_circular_using_promer'''
+ contigs_infile = os.path.join(data_dir, 'start_fixer_find_circular_using_promer.contigs.fa')
+ ref_genes_fa = os.path.join(data_dir, 'start_fixer_find_circular_using_promer.refs.fa')
+ tmp_outprefix = 'tmp.start_fixer_find_circular_using_promer'
+ contigs_dict = {}
+ pyfastaq.tasks.file_to_dict(contigs_infile, contigs_dict)
+ end_extend = start_fixer.StartFixer._max_length_from_fasta_file(ref_genes_fa)
+
+ expected = {
+ 'ctg_DNAA_ECOLI': pymummer.alignment.Alignment('1021\t2424\t1\t1404\t1404\t1404\t100.00\t.\t.\t3404\t1404\t1\t1\tctg_DNAA_ECOLI\tsp|P03004|DNAA_ECOLI\n'),
+ 'ctg_DNAA1_CHLPN': pymummer.alignment.Alignment('685\t2067\t1\t1383\t1383\t1383\t100.00\t.\t.\t2808\t1383\t1\t1\tctg_DNAA1_CHLPN__ends\tsp|Q9Z8M9|DNAA1_CHLPN\n'),
+ 'ctg_DNAA_ECOLI_2': pymummer.alignment.Alignment('901\t2304\t1\t1404\t1404\t1404\t100.00\t.\t.\t3044\t1404\t1\t1\tctg_DNAA_ECOLI_2\tsp|P03004|DNAA_ECOLI_2\n'),
+}
+
+ got = start_fixer.StartFixer._find_circular_using_promer(tmp_outprefix, ref_genes_fa, contigs_dict, 70, end_extend, sys.stdout)
+ self.assertEqual(expected, got)
+ os.unlink(tmp_outprefix + '.contigs_with_ends.fa')
+ os.unlink(tmp_outprefix + '.promer')
+ got = start_fixer.StartFixer._find_circular_using_promer(tmp_outprefix, ref_genes_fa, contigs_dict, 70, end_extend, sys.stdout, ignore={x for x in contigs_dict})
+ self.assertEqual({}, got)
+
+
+ def test_find_circular_using_prodigal(self):
+ '''test _find_circular_using_prodigal'''
+ contigs_infile = os.path.join(data_dir, 'start_fixer_find_circular_using_prodigal.ctgs.fa')
+ outprefix = 'tmp.test_find_circular_using_prodigal'
+ contigs_dict = {}
+ pyfastaq.tasks.file_to_dict(contigs_infile, contigs_dict)
+ circular_from_promer = {'ctg3': 'foo'}
+ got = start_fixer.StartFixer._find_circular_using_prodigal(outprefix, contigs_dict, circular_from_promer, sys.stdout)
+ # We should have a dictionary with one key == "ctg1" and a value like this:
+ # 'ctg1\tProdigal_v2.60\tCDS\t841\t2244\t103.8\t+\t0\tID=1_1;partial=00;start_type=ATG;rbs_motif=TAAAA;rbs_spacer=4bp;gc_cont=0.486;conf=100.00;score=103.84;cscore=95.60;sscore=8.24;rscore=4.24;uscore=-0.13;tscore=4.12;'
+ # ... but this depends on the version of prodigal, so is not predictable
+ self.assertEqual({'ctg1'}, set(got.keys()))
+ got_fields = got['ctg1'].split('\t')
+ self.assertEqual(got_fields[0], 'ctg1')
+ self.assertTrue(got_fields[1].startswith('Prodigal'))
+ os.unlink(outprefix + '.for_prodigal.fa')
+ os.unlink(outprefix + '.prodigal.gff')
+ got = start_fixer.StartFixer._find_circular_using_prodigal(outprefix, contigs_dict, circular_from_promer, sys.stdout, ignore={'ctg1', 'ctg2'})
+ self.assertEqual({}, got)
+
+
+ def test_rearrange_contigs(self):
+ '''test _rearrange_contigs'''
+ # try all the combinations of promer and prodigal and ignore. Also whether or not to
+ # reverse complement and DNAA spanning across start/end of contig
+ # promer_ctg1: has sp|P03004|DNAA_ECOLI starting at position 2000 on fwd strand
+ # promer_ctg2: has sp|P03004|DNAA_ECOLI_2 starting at position 3403 on reverse strand (=revcomp of promer_ctg1)
+ # promer_ctg3: has sp|P03004|DNAA_ECOLI starts at 4745, split over end/start of contig
+ # promer_ctg4: has sp|P03004|DNAA_ECOLI starts at 644, split over start/end of contig (=revcomp of promer_ctg3)
+ # ignore_ctg: same as promer_ctg1, but in the ignore set, so should be unchanged
+ # prodigal_ctg1: has a two genes, nearest to middle starts at 4529
+ # prodigal_ctg2: same as ctg1, but reverse complement, gene starts at 4862 on rev strand
+ contigs_infile = os.path.join(data_dir, 'start_fixer_rearrange_contigs.in.fa')
+ ref_genes_fa = os.path.join(data_dir, 'start_fixer_rearrange_contigs.refs.fa')
+ tmp_outprefix = 'tmp.test_rearrange_contigs'
+ tmp_log = tmp_outprefix + '.log'
+ contigs_dict = {}
+ pyfastaq.tasks.file_to_dict(contigs_infile, contigs_dict)
+ to_ignore = {'ignore_ctg'}
+ end_extend = start_fixer.StartFixer._max_length_from_fasta_file(ref_genes_fa)
+ circ_with_promer = start_fixer.StartFixer._find_circular_using_promer(tmp_outprefix, ref_genes_fa, contigs_dict, 70, end_extend, sys.stdout, ignore=to_ignore)
+ circ_with_prodigal = start_fixer.StartFixer._find_circular_using_prodigal(tmp_outprefix, contigs_dict, circ_with_promer, sys.stdout, ignore=to_ignore)
+ start_fixer.StartFixer._rearrange_contigs(contigs_dict, circ_with_promer, circ_with_prodigal, to_ignore, end_extend, tmp_log)
+ expected_log = os.path.join(data_dir, 'start_fixer_rearrange_contigs.expect.log')
+ self.assertTrue(filecmp.cmp(expected_log, tmp_log, shallow=False))
+ expected_dict = {}
+ expected_fa = os.path.join(data_dir, 'start_fixer_rearrange_contigs.expect.fa')
+ pyfastaq.tasks.file_to_dict(expected_fa, expected_dict)
+ self.assertEqual(expected_dict, contigs_dict)
+ os.unlink(tmp_outprefix + '.contigs_with_ends.fa')
+ os.unlink(tmp_outprefix + '.for_prodigal.fa')
+ os.unlink(tmp_outprefix + '.prodigal.gff')
+ os.unlink(tmp_outprefix + '.promer')
+ os.unlink(tmp_log)
+
+
+ def test_run_ignore_all(self):
+ '''test run when ignoring all sequences'''
+ tmp_prefix = 'tmp.start_fixer.test_run_when_ignoring_all'
+ input_fa = os.path.join(data_dir, 'start_fixer_run_ignore_all.fa')
+ to_ignore = os.path.join(data_dir, 'start_fixer_run_ignore_all.to_ignore')
+ sfixer = start_fixer.StartFixer(input_fa, tmp_prefix, ignore=to_ignore)
+ sfixer.run()
+ expected_fa = os.path.join(data_dir, 'start_fixer_run_ignore_all.expect.fa')
+ self.assertTrue(filecmp.cmp(expected_fa, tmp_prefix + '.fasta'))
+ for suffix in ['detailed.log', 'fasta', 'log', 'promer.contigs_with_ends.fa', 'promer.promer']:
+ try:
+ os.unlink(tmp_prefix + '.' + suffix)
+ except:
+ pass
+
+
+ def test_run_none_for_prodigal(self):
+ '''test run when everthing sorted by promer'''
+ tmp_prefix = 'tmp.start_fixer.test_run_none_for_prodigal'
+ input_ctg = os.path.join(data_dir, 'start_fixer_run_none_for_prodigal.ctg.fa')
+ input_ref = os.path.join(data_dir, 'start_fixer_run_none_for_prodigal.ref.fa')
+ sfixer = start_fixer.StartFixer(input_ctg, tmp_prefix, genes_fa=input_ref)
+ sfixer.run()
+ expected_fa = os.path.join(data_dir, 'start_fixer_run_none_for_prodigal.expect.fa')
+ self.assertTrue(filecmp.cmp(expected_fa, tmp_prefix + '.fasta'))
+ for suffix in ['detailed.log', 'fasta', 'log', 'promer.contigs_with_ends.fa', 'promer.promer']:
+ try:
+ os.unlink(tmp_prefix + '.' + suffix)
+ except:
+ pass
+
+
+ def test_run_bit_of_everything(self):
+ '''test run with promer, prodigal, and ignoring a sequence'''
+ tmp_prefix = 'tmp.start_fixer.test_run_bit_of_everything'
+ input_ctg = os.path.join(data_dir, 'start_fixer_run_bit_of_everything.ctg.fa')
+ input_ref = os.path.join(data_dir, 'start_fixer_run_bit_of_everything.ref.fa')
+ input_ignore = os.path.join(data_dir, 'start_fixer_run_bit_of_everything.ignore')
+ sfixer = start_fixer.StartFixer(input_ctg, tmp_prefix, genes_fa=input_ref, ignore=input_ignore)
+ sfixer.run()
+ expected_fa = os.path.join(data_dir, 'start_fixer_run_bit_of_everything.expect.fa')
+ self.assertTrue(filecmp.cmp(expected_fa, tmp_prefix + '.fasta'))
+
+ for suffix in ['detailed.log', 'fasta', 'log', 'promer.contigs_with_ends.fa', 'promer.promer', 'prodigal.for_prodigal.fa', 'prodigal.prodigal.gff']:
+ try:
+ os.unlink(tmp_prefix + '.' + suffix)
+ except:
+ pass
diff --git a/circlator/versions.py b/circlator/versions.py
index 4358018..fd6e517 100644
--- a/circlator/versions.py
+++ b/circlator/versions.py
@@ -1,5 +1,4 @@
import sys
-import bio_assembly_refinement
import openpyxl
import pyfastaq
import pymummer
@@ -8,12 +7,12 @@ from circlator import external_progs, __version__
from circlator import __version__ as circlator_version
-def get_all_versions(filehandle, raise_error=True):
+def get_all_versions(filehandle, raise_error=True, debug=False):
if filehandle is not None:
print('Circlator version:', circlator_version, file=filehandle)
print('\nExternal dependencies:', file=filehandle)
- external_progs.check_all_progs(verbose=False, raise_error=raise_error, filehandle=filehandle)
+ external_progs.check_all_progs(verbose=False, raise_error=raise_error, filehandle=filehandle, debug=debug)
if filehandle is not None:
print('\nPython version:', file=filehandle)
@@ -22,7 +21,7 @@ def get_all_versions(filehandle, raise_error=True):
found_bad_module = False
- for module in ['bio_assembly_refinement', 'openpyxl', 'pyfastaq', 'pymummer', 'pysam']:
+ for module in ['openpyxl', 'pyfastaq', 'pymummer', 'pysam']:
try:
version = eval(module + '.__version__')
path = eval(module + '.__file__')
diff --git a/install_dependencies.sh b/install_dependencies.sh
index ee12a8d..3fa9560 100644
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -8,7 +8,7 @@ BWA_VERSION=0.7.12
PRODIGAL_VERSION=2.6.2
SAMTOOLS_VERSION=1.3
MUMMER_VERSION=3.23
-SPADES_VERSION=3.6.0
+SPADES_VERSION=3.7.1
BWA_DOWNLOAD_URL="http://downloads.sourceforge.net/project/bio-bwa/bwa-${BWA_VERSION}.tar.bz2"
PRODIGAL_DOWNLOAD_URL="https://github.com/hyattpd/Prodigal/releases/download/v${PRODIGAL_VERSION}/prodigal.linux"
diff --git a/setup.py b/setup.py
index 650acc0..aa02a9a 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@ from setuptools import setup, find_packages
setup(
name='circlator',
- version='1.2.1',
+ version='1.3.0',
description='circlator: a tool to circularise genome assemblies',
packages = find_packages(),
package_data={'circlator': ['data/*']},
@@ -20,9 +20,8 @@ setup(
install_requires=[
'openpyxl',
'pyfastaq >= 3.12.1',
- 'pysam >= 0.8.1, <= 0.8.3',
+ 'pysam >= 0.8.1',
'pymummer>=0.7.1',
- 'bio_assembly_refinement>=0.5.1',
],
license='GPLv3',
classifiers=[
--
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