test_identify_chimeric_seqs.py

#!/usr/bin/env python
from __future__ import division

__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.9.1"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"

from shutil import rmtree
from glob import glob
from os import getenv
from os.path import basename, exists, join, isfile, getsize
from tempfile import NamedTemporaryFile, mkdtemp
from unittest import TestCase, main

from skbio.util import remove_files

from qiime.util import (get_qiime_temp_dir, load_qiime_config)
from qiime.test import initiate_timeout, disable_timeout
from qiime.parse import fields_to_dict
from qiime.parallel.identify_chimeric_seqs import ParallelChimericSequenceIdentifier


class ParallelChimericSequenceIdentifierTests(TestCase):

    def setUp(self):
        """ """
        self.dirs_to_remove = []

        tmp_dir = get_qiime_temp_dir()
        self.test_out = mkdtemp(dir=tmp_dir,
                                prefix='qiime_parallel_chimeric_sequence_identifier_tests_',
                                suffix='')
        self.dirs_to_remove.append(self.test_out)

        self.in_seqs_f = NamedTemporaryFile(
            prefix='qiime_parallel_chimeric_sequence_identifier_tests_input',
            suffix='.fasta', dir=tmp_dir)
        self.in_seqs_f.write(in_seqs)
        self.in_seqs_f.seek(0)

        self.reference_seqs_f = NamedTemporaryFile(
            prefix='qiime_parallel_chimeric_sequence_identifier_tests_refs',
            suffix='.fasta', dir=tmp_dir)
        self.reference_seqs_f.write(ref_seqs)
        self.reference_seqs_f.seek(0)

        self.id_to_tax_f = NamedTemporaryFile(
            prefix='qiime_parallel_chimeric_sequence_identifier_tests_id_tax',
            suffix='.txt', dir=tmp_dir)
        self.id_to_tax_f.write(id_to_tax)
        self.id_to_tax_f.seek(0)

        self.in_seqs_aligned_f = NamedTemporaryFile(
            prefix='qiime_parallel_chimeric_sequence_identifier_tests_aligned',
            suffix='.fasta', dir=tmp_dir)
        self.in_seqs_aligned_f.write(in_seqs_aligned)
        self.in_seqs_aligned_f.seek(0)

        initiate_timeout(180)

    def tearDown(self):
        """ """
        disable_timeout()
        for d in self.dirs_to_remove:
            if exists(d):
                rmtree(d)

    def test_parallel_chimeric_sequence_identifier_blast_fragments(self):
        """Test ParallelChimericSequenceIdentifier using blast_fragments."""
        params = {
            'id_to_taxonomy_fp': self.id_to_tax_f.name,
            'reference_seqs_fp': self.reference_seqs_f.name,
            'chimera_detection_method': 'blast_fragments',
            'num_fragments': 3,
            'taxonomy_depth': 4,
            'max_e_value': 1e-30,
            'min_div_ratio': None,
            'output_fp': self.test_out + '/blast_fragments_out.txt'
        }

        app = ParallelChimericSequenceIdentifier()
        r = app(self.in_seqs_f.name,
                self.test_out,
                params,
                job_prefix='CHIMTEST',
                poll_directly=True,
                suppress_submit_jobs=False)

        # We should get an empty file.
        results = [line for line in open(join(self.test_out,
                   'blast_fragments_out.txt'), 'U')]
        self.assertEqual(results, [])

    def test_parallel_chimeric_sequence_identifier_chimera_slayer(self):
        """Test ParallelChimericSequenceIdentifier using ChimeraSlayer."""
        qiime_config = load_qiime_config()
        params = {
            'reference_seqs_fp': None,
            'aligned_reference_seqs_fp': qiime_config['pynast_template_alignment_fp'],
            'chimera_detection_method': 'ChimeraSlayer',
            'num_fragments': 3,
            'taxonomy_depth': 4,
            'max_e_value': 1e-30,
            'min_div_ratio': None,
            'output_fp': self.test_out + '/ChimeraSlayer_out.txt'
        }

        app = ParallelChimericSequenceIdentifier()
        r = app(self.in_seqs_aligned_f.name,
                self.test_out,
                params,
                job_prefix='CHIMTEST',
                poll_directly=True,
                suppress_submit_jobs=False)

        output_filepath = join(self.test_out, 'ChimeraSlayer_out.txt')
        self.assertTrue(isfile(output_filepath) and
                        (getsize(output_filepath) > 0))

# This test data is taken from qiime_test_data.
in_seqs = """
>11472286
GATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGAACACTTTGTGTTTTGAGTTAATAGTTCGATAGTAGATAGTAAATAGTGAACACTATGAACTAGTAAACTATTTAACTAGAAACTCTTAAACGCAGAGCGTTTAGTGGCGAACGGGTGAGTAATACATTGGTATCTACCTCGGAGAAGGACATAGCCTGCCGAAAGGTGGGGTAATTTCCTATAGTCCCCGCACATATTTGTTCTTAAATCTGTTAAAATGATTATATGTTTTATGTTTATTTGATAAAAAGCAGCAAGACAAATGAGTTTTATATTGGTTATACAGCAGATTTAAAAAATAGAATTAGGTCTCATAATCAGGGAGAAAACAAATCAACTAAATCTAAAATACCTTGGGAATTGGTTTACTATGAAGCCTACAAAAACCAAACATCAGCAAGGGTTAGAGAATCAAAGTTGAAACATTATGGGCAATCATTAACTAGACTTAAGAGAAGAATTGGTTTTTGAGAACAAATATGTGCGGGGTAAAGCAGCAATGCGCTCCGAGAGGAACCTCTGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGACGGGTAGCTGGTGTGAGAGCACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTCCACAATGGGCGCAAGCCTGATGGAGCAATGCCGCGTGAAGGATGAAGATTTTCGGATTGTAAACTTCTTTTAAGTAGGAAGATTATGACGGTACTACTTGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATTACTGGGCGTAAAGCGTGTGTAGGTGGTTTATTAAGTTAAATGTTAAATTTTCAGGCTTAACTTGGAAACCGCATTTAATACTGGTAGACTTTGAGGACAAGAGAGGCAGGCGGAATTAGCGGAGTAGCGGTGAAATGCGTAGATATCGCTAAGAACACCAATGGCGAAGGCAGCCTGCTGGTTTGCACCTGACACTGAGATACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACGATGGTCACTAGCTGTTAGGGGCTCGACCCCTTTAGTAGCGAAGCTAACGCGTTAAGTGACCCGCCTGGGGAGTACGATCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAACGTGAGGTTTAATTCGTCTCTAAGCGAAAAACCTTACCGAGGCTTGACATCTCCGGAAGACCTTAGAAATAAGGTTGTGCCCGAAAGGGAGCCGGATGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTCGGTTAAGTCCGTTAACGAGCGCAACCCTTGCTGTGTGTTGTATTTTTCACACAGGACTATCCTGGTCAACAGGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCTCTTACGCCTCGGGCTACACTCGCGTTACAATGGCCGGTACAATGGGCTGCCAACTCGTAAGGGGGAGCTAATCCCATCAAAACCGGTCCCAGTTCGGATTGAGGGCTGCAATTCGCCCTCATGAAGTCGGAATCGCTAGTAACCGCGAATCAGCACGTCGCGGTGAATGCGTTCTCGGGTCTTGTACACACTGCCCGTCACACCACGAAAGTTAGTAACGCCCGAAGTGCCCTGTATGGGGTCCTAAGGTGGGGCTAGCGATTGGGGTG
>11472384
AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAAACGCCGTGGTTAATACCCGTGGCGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTCCGCTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGGCGGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTCGGGTCTTCATTGACTTGGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTATGGAATCCTGCTGAGAGGTGGGAGTGCCCGAAAGGGAGCCATAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCCTAGTTGCTACGCAAGAGCACTCTAGGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTCGCCAACCCGCGAGGGGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGCACTCTGCAACTCGAGTGCGTGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTCGAGCGAACGTGTCGAACGTTGAGCGCTCACGCTTATCGGCTGTGAAATTAGGACAGTAAGTCAGACAGACTGAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGATGGTTCGAATCCATCCAGACCCACCATTGTCT
>11468680
TAAACTGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGTGCTTGCACCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACATGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGATCTACGGATGAAAGCGGGGGACCTTCGGGCCTCGCGCTATAGGGTTGGCCGATGGCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAATCCTTGGCTCTAATACAGTCGGGGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTGCTAAGACCGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTGGTGACTGGCAGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTTGGGGATTCATTTCCTTAGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGGTCGGAATCCCGCTGAGAGGTGGGAGTGCTCGAAAGAGAACCGGCGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTTAGTTGCTACGCAAGAGCACTCTAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTTGCCAACCCGCGAGGGGGAGCTAATCCCAGAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCCAGAGCTATCTCGCAAAGTTGAGCGCTCACGCTTATCGGCTGTAAATTTAAAGACAGACTCAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGTTGGTTCGAATCCAACCAGACCCACCATTGTCTG
>11458037
GACGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGTTTCGAAGATCGGACTTCGAATTTCGAATTTCGATCATCGAGATAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTACCCATAAAGCCGGGACAACCCTTGGAAACGAGGGCTAATACCGGATAAGCTTGAGAAGTGGCATCACTTTTTAAGGAAAGGTGGCCGATGAGAATGCTGCCGATTATGGATGGACCCGCGTCTGATTAGCTGGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCCGGCCTGAGAGGGTGAACGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGTATGATGAAGGTTTTCGGATTGTAAAGTACTGTCTATGGGGAAGAATGGTGTGCTTGAGAATATTAAGTACAAATGACGGTACCCAAGGAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGATAGTTAAGTCCGGTGTGAAAGATCAGGGCTCAACCCTGAGAGTGCATCGGAAACTGGGTATCTTGAGGACAGGAGAGGAAAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGTGCTAGGTGTAGAGGGTATCGACCCCTTCTGTGCCGCAGTTAACACAATAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCAGGGCTTGACATCCTCTGAACTTGCTGGAAACAGGAAGGTGCCCTTCGGGGAGCAGAGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAATCCCGCAACGAGCGCAACCCCTGTATTTAGTTGCTAACGCGTAGAGGCGAGCACTCTGGATAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTTCTGGGCTACACACGTGCTACAATGGCCGGTACAGACGGAAGCGAAGCCGCGAGGCGGAGCAAATCCGAGAAAGCCGGTCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCTGCAACACCCGAAGCCGGTGAGGTAACCGACTCGAGATTCGAGGCTCGAAGTTCGAGGATCGAAGTGTAAGCGAAATTAATAAGTCTTAGTAAAGCTAAAAAGCATTAAGACCGATAAGATGATCTTGCAATCGAACATCGAACATCGAATTTCGAACCTCGAGTTGGAGCTAGCCGTCGAAGGTGGGGCCGATAATTGGGGTG
>11469739
AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAGAAGCTAACTTCTGATTCCTTCGGGATGATGAGGTTAGCAGAAAGTGGCGAACGGGTGAGTAACGCGTGGGTAATCTACCCTGTAAGTGGGGGATAACCCTCCGAAAGGAGGGCTAATACCGCATAATATCTTTATCCCAAAAGAGGTAAAGATTAAAGATGGCCTCTATACTATGCTATCGCTTCAGGATGAGTCCGCGTCCTATTAGTTAGTTGGTGGGGTAATGGCCTACCAAGACGACAATGGGTAGCCGGTCTGAGAGGATGTACGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGACAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCCTTGGGTTGTAAAATCCTGTTCTGGGGGAAGAAAGCTTAAAGGTCCAATAAACCCTTAAGCCTGACGGTACCCCAAGAGAAAGCTCCGGCTAATTATGTGCCAGCAGCCGCGGTAATACATAAGGAGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTCTTAAAAGTCAGTTGTGAAATTATCAGGCTCAACCTGATAAGGTCATCTGAAACTCTAAGACTTGAGGTTAGAAGAGGAAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTATCTCTGACGCTGAGGAGCGAAAGCTAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTAGCTGTAAACGATGGATACTAGGTGTGGGAGGTATCGACCCCTTCTGTGCCGTAGCTAACGCATTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCGGGACTTGACATTATCTTGCCCGTCTAAGAAATTAGATCTTCTTCCTTTGGAAGACAGGATAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCACAACGAGCGCAACCCTTGTGCTTAGTTGCTAACTTGTTTTACAAGTGCACTCTAGGCAGACTGCCGCAGATAATGCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTACGTCCCGGGCTACACACGTGCTACAATGGCCTGTACAGAGGGTAGCGAAAGAGCGATCTTAAGCCAATCCCAAAAAGCAGGCCCCAGTTCGGATTGGAGGCTGCAACTCGCCTCCATGAAGTAGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTTGGCGATACCTGAAGTTACTAGGCTAACCTGGCACTCAACTAAGTTCACTAACTTATTTGCTTAAAATAAGGCTTAATGTGCTTAGTTGAGTGCCGGGAGGCAGGTACCGAAGGTATGGCTGGCGATTGGGGTGAAGTCGTAACAAGGTGGAAA
>11469752
AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGCAGCGAGTTCCTCACCGAGGTTCGGAACAGTTGACAGTAAACAGTTGACAGTAAACAGTAACTTCAGAAATGAAGCGGACTGTGAACTGTTTACTGTAACCTGTTAGCTATTATTTCGAGCTTTAGTGAGGAATGTCGGCGAGCGGCGGACGGCTGAGTAACGCGTAGGAACGTACCCCAAACTGAGGGATAAGCACCAGAAATGGTGTCTAATACCGCATATGGCCCAGCACCTTTTTTAATCAACCACGACCCTAAAATCGTGAATAATTGGTAGGAAAAGGTGTTGGGTTAAAGCTTCGGCGGTTTGGGAACGGCCTGCGTATGATTAGCTTGTTGGTGAGGTAAAAGCTCACCAAGGCGACGATCATTAGCTGGTCTGAGAGGATGATCAGCCAGACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGGCGAAAGCCTGATGGAGCAACGCCGTGTGCAGGATGAAAGCCTTCGGGTCGTAAACTGCTTTTATATGTGAAGACTTCGACGGTAGCATATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTCATACGGAGGATCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGTTGGTAGTGAAATTGTGTGGCTCAACCATACACCCATTACTAAAACTGCTAAGCTAGAGTATATGAGAGGTAGCTGGAATTCCTAGTGTAGGAGTGAAATCCGTANATATTAGGAGGAACACCGATGGCGTAGGCAGGCTACTGGCATATTACTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCTGTAAACGATGGATGCTAGCTGTTATGAGTATCGACCCTTGTAGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACGAGCGCAAGCTTAAAACATAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGATGATAAGCGAAGAACCTTACCAAGGCTTGACATCCCTGGAATTTCTCCGAAAGGAGAGAGTGCCTTCGGGAATCAGGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATTAACGAGCGCAACCCTTGTAAATAGTTGGATTTTTCTATTTAGACTGCCTCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCAGTATTTCTCTTACGCCTTGGGCTACAAACACGCTACAATGGCCGGTACAAAGGGCAGCCAACCCGCGAGGGGGAGCAAATCCCATCAAAGCCGGTCTCAGTTCGGATAGCAGGCTGAAATTCGCCTGCTTGAAGTCGGAATCGCTAGTAACGGTGAGTCAGCTATATTACCGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCAAGGCATGAAAGTCATCAATACCTGACGTCTGGATTTATTCTGGCCTAAGGTAGGGGCGATGATTGGGCCTAAGTCGTAACAAGGTAA
>11460523
AGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCGAAATCGGGCACTCAATTTTGCTTTTCAAACATTAACTGATGAAACGACCAGAGAGATTGTTCCAGTTTAAAGAGTGAAAAGCAGGCTTGAGTGCCTGAGAGTAGAGTGGCGCACGGGTGAGTAACGCGTAAATAATCTACCCCTGCATCTGGGATAACCCACCGAAAGGTGAGCTAATACCGGATACGTTCTTTTAACCGCGAGGTTTTAAGAAGAAAGGTGGCCTCTGATATAAGCTACTGTGCGGGGAGGAGTTTGCGTACCATTAGCTAGTTGGTAGGGTAATGGCCTACCAAGGCATCGATGGTTAGCGGGTCTGAGAGGATGATCCGCCACACTGGAACTGGAACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCTTCGGGTCGTAAAATCCTGTCAGATGGAAAGAAGTGTTATATGGATAATACCTGTATAGCTTGACGGTACCATCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGTCTGTTATGTCAGATGTGAAAGTCCACGGCTCAACCGTGGAAGTGCATTTGAAACTGACAGACTTGAGTACTGGAGGGGGTGGTGGAATTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAATACCGGTGGCGAAGGCGACCACCTGGCCAGATACTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCAACTAGGTGTTGGGATGGTTAATCGTCTCATTGCCGGAGCTAACGCATTAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGACGCAACGCGCAGAACCTTACCTGGTCTTGACATCCCGAGAATCTCAAGGAAACTTGAGAGTGCCTCTTGAGGAACTCGGTGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTTTAGTTGCCATCATTAAGTTGGGCACTCTAAAGAGACTGCCGGTGTCAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGACCAGGGCTACACACGTACTACAATGGCATAGACAAAGGGCAGCGACATCGCGAGGTGAAGCGAATCCCATAAACCATGTCTCAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGGGAGTTGGTTGTACCAGAAGCAGTTGAGCGAACTATTCGTAGACGCAGGCTGCCAAGGTATGATTGGTAACTGGGGTGAAGTCGTAACAAGGTAACC
>11460543
TGGTTTGATCCTGGCTCAGGACAAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAGAAGCCAGCTTTTGATTCCTTCGGGATGAGAAAGCAGGTAGAAAGTGGCGAACGGGTGAGTAACGCGTGGGTAATCTACCCTGTAAGTAGGGGATAACCCTCTGAAAAGAGGGCTAATACCGCATAATATCTTTACCCCATAAGAAGTAAAGATTAAAGATGGCCTCTGTATATGCTATCGCTTCAGGATGAGCCCGCGTCCTATTAGTTAGTTGGTAAGGTAATGGCTTACCAAGACCACGATGGGTAGCCGGTCTGAGAGGATGTACGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCTTCGGGTTGTAAAATCCTGTTTTGGGGGACGAAACCTTAAGGGTCCAATAAACCCTTAAATTGACGGTACCCCAAGAGAAAGCTCCGGCTAATTATGTGCCAGCAGCCGCGGTAATACATAAGGAGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGTTCGTAGGCGGTCTTAAAAGTCAGGTGTGAAATTATCAGGCTTAACCTGATACGGTCATCTGAAACTTTAAGACTTGAGGTTAGGAGAGGAAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGCCTAACTCTGACGCTGAGGAACGAAAGCTAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTAGCTGTAAACGATGGATACTAGGTGTGGGAGGTATCGACCCCTTCTGTGCCGWCACTAACGCATTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCGGGGCTTGACATTGTCTTGCCCGTTTAAGAAATTAAATTTTCTTCCCTTTTAGGGAAGACAAGATAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCACAACGAGCGCAACCCTTATTCTTAGTTGCTAGTTTGTTTACAAACGCACTCTAAAGAGACTGCCGCAGATAATGCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTACGTCCCGGGCTACACACGTGCTACAATGGCCTGTACAGAGGGTAGCGAAAGAGCGATCTCAAGCTAATCCCTTAAAACAGGTCTCAGTTCGGATTGGAGGCTGCAACTCGCCTCCATGAAGTCGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGAAAGTTGGCGATACCTGAAGTTACTGTGCTAACCCGGCACTCAACTAAGTACATTAAGTCTTATTTTAAGCTATTGTATTTAGTTGAGTGCCGGGAGGCAGGTACCTAAGGTATGGCTAGCGATTGGGGTGAAGTCGTAACAAGGTAGCCG
>11480235
TGGTTTGATCCTGGCTCAGGATTAACGCTGGCGGCGCGCCTTATACATGCAAGTCGAACGAGCCTTGTGCTTCGCACAAGGAAATTCCAAGCACCAAGCACCAAATCTCAAACAAATCCCAATGACCAAAATTCCAAAAACCTAAACATTTTAAATGTTTAGAATTTGGAAAATTGGAATTTGGAATTTATTTGTTATTTGGAATTTATGATTTGGGATTTTCTCGCGCGGAGANCNTNAGTGGCGAACGGGTGAGTAATACGTTGGTATCTACCCCAAAGTAGAGAATAAGCCCGAGAAATCGGGGTTAATACTCTATGTGTTCGAAAGAACAAAGACTTCGGTTGCTTTGGGAAGAACCTGCGGCCTATCAGCTTGTTGGTAAGGTAACGGCTTACCAAGGCTTTGACGGGTAGCTGGTCTGGGAAGACGACCAGCCACAATGGGACTTAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGCCCGAAAGGTGACCGAGCGACGCCGCGTAGAGGAAGAAGATCTTTGGATTGTAAACTCTTTTTCTCCTAGACAAAGTTCTGATTGTATAGGAGGAATAAGGGGTTTCTAAACTCGTGCCAGCAGAAGCGGTAATACGAGTGCCCCAAGCGTTATCCGGAATCATTGGGCGTAGAGCGTTGTATAGGTGGTTTAAAAAGTCCAAAATTAAATCTTTAGGCTCAACCTAAAATCTGTTTTGGAAACTTTTAGACTTGAATAAAATCGACGSGAGTGGAACTTCCAGAGTAGGGGTTACATCCGTTGATACTGGAAGGAACGCCGAAGGCGAAAGCAACTCGCGAGATTTTATTGACGCCGCGTACACGAAAGCGTGGGGAGCGAAAAGTATTAGATACACTTGTAGTCCACGCCGTAAACTATGGATACTAGCAATTTGAAGCTTCGACCCTTCAAGTTGCGGACTAACGCGTTAAGTATCTCGCCTGGGAAGTACGGCCGCAAGGCTAAAACTCAAAGGAATAGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGATAAGCGTGGAACCTTACCAGGGCTTAGACGTACAGAGAATTCCTTGGAAACAAGGAAGTGCTTCGGGAACTCTGTACTCAGGTACTGCATGGCTGTCGTCAGTATGTACTGTGAAGCACTCCCTTAATTGGGGCAACATACGCAACCCCTATCCTAAGTTAGAAATGTCTTAGGAAACCGCTTCGATTCATCGGAGAGGAAGATGGGGACGACGTCAAGTCAGCATGGTCCTTGATGTCCTGGGCGACACACGTGCTACAATGGCTAGTATAACGGGATGCGTAGGTGCGAACCGAAGCTAATCCTTAAAAAACTAGTCTAAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGCCGGAATCGCTAGTAACCGCAAATCAGCCACGTTGCGGTGAATACGTTCTCGGGCCTTGTACTCACTGCCCGTCACGTCAAAAAAGTCGGTAATACCCGAAGCACCCTTTTAAAGGGTTCTAAGGTAGGACCGATGATTGGGACGAAGTCGTAACAAGGTAGCCG
>11480408
AATTTAGCGGCCGCGAATTCGCCCTTGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGGGATATCCGAGCGGAAGGTTTCGGCCGGAAGGTTGGGTATTCGAGTGGCGGACGGGTGAGTAACGCGTGAGCAATCTGTCCCGGACAGGGGGATAACACTTGGAAACAGGTGCTAATACCGCATAAGACCACAGCATCGCATGGTGCAGGGGTAAAAGGAGCGATCCGGTCTGGGGTGAGCTCGCGTCCGATTAGATAGTTGGTGAGGTAACGGCCCACCAAGTCAACGATCGGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGAACTGAGAGACGGTCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTGTTATGCGAGACGAAGGAAGTGACGGTATCGCATAAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGTGTAGGCGGCCGTTTAAGTATGGAGTGAAAGTCCATTTTTCAAGGATGGAATTGCTTTGTAGACTGGATGGCTTGAGTGCGGAAGAGGTAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGAGGAACACCAGTGGCGAAGGCGACTTACTGGGCCGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCGGTAAACGATGAATGCTAGGTGTTGCGGGTATCGACCCCTGCAGTGCCGGAGTAAACACAATAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAGGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTTGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCAGTTAAGCTCATAGAGATATGAGGTCCCTTCGGGGGAACTGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATGGTCAGTTACTAACGCGTGAAGGCGAGGACTCTGACGAGACTGCCGGGGACAACTCGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACAAACGTGCTACAATGGTGACTACAAAGAGGAGCGAGACTGTAAAGTGGAGCGGATCTCAAAAAAGTCATCCCAGTTCGGATTGTGGGCTGCAACCCGCCCACATGAAGTTGGAGTTGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGGAGCACCCGAAGTCAGTGAGGTAACCGGAAGGAGCCAGCTGCCGAAGGTGAGACCGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTAAGGGCGAATTCGTTTAAACCTGCAGGACTAG
"""

ref_seqs = """
>AY800210
TTCCGGTTGATCCTGCCGGACCCGACTGCTATCCGGATGCGACTAAGCCATGCTAGTCTAACGGATCTTCGGATCCGTGGCATACCGCTCTGTAACACGTAGATAACCTACCCTGAGGTCGGGGAAACTCCCGGGAAACTGGGCCTAATCCCCGATAGATAATTTGTACTGGAATGTCTTTTTATTGAAACCTCCGAGGCCTCAGGATGGGTCTGCGCCAGATTATGGTCGTAGGTGGGGTAACGGCCCACCTAGCCTTTGATCTGTACCGGACATGAGAGTGTGTGCCGGGAGATGGCCACTGAGACAAGGGGCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTCACAATGCCCGCAAGGGTGATGAGGGTATCCGAGTGCTACCTTAGCCGGTAGCTTTTATTCAGTGTAAATAGCTAGATGAATAAGGGGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCCCGAGTGGTCGGGATTTTTATTGGGCCTAAAGCGTCCGTAGCCGGGCGTGCAAGTCATTGGTTAAATATCGGGTCTTAAGCCCGAACCTGCTAGTGATACTACACGCCTTGGGACCGGAAGAGGCAAATGGTACGTTGAGGGTAGGGGTGAAATCCTGTAATCCCCAACGGACCACCGGTGGCGAAGCTTGTTCAGTCATGAACAACTCTACACAAGGCGATTTGCTGGGACGGATCCGACGGTGAGGGACGAAACCCAGGGGAGCGAGCGGGATTAGATACCCCGGTAGTCCTGGGCGTAAACGATGCGAACTAGGTGTTGGCGGAGCCACGAGCTCTGTCGGTGCCGAAGCGAAGGCGTTAAGTTCGCCGCCAGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCAC
>EU883771
TGGCGTACGGCTCAGTAACACGTGGATAACTTACCCTTAGGACTGGGATAACTCTGGGAAACTGGGGATAATACTGGATATTAGGCTATGCCTGGAATGGTTTGCCTTTGAAATGTTTTTTTTCGCCTAAGGATAGGTCTGCGGCTGATTAGGTCGTTGGTGGGGTAATGGCCCACCAAGCCGATGATCGGTACGGGTTGTGAGAGCAAGGGCCCGGAGATGGAACCTGAGACAAGGTTCCAGACCCTACGGGGTGCAGCAGGCGCGAAACCTCCGCAATGTACGAAAGTGCGACGGGGGGATCCCAAGTGTTATGCTTTTTTGTATGACTTTTCATTAGTGTAAAAAGCTTTTAGAATAAGAGCTGGGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCAGCTCGAGTGGTGACCACTTTTATTGGGCTTAAAGCGTTCGTAGCTTGATTTTTAAGTCTCTTGGGAAATCTCACGGCTTAACTGTGAGGCGTCTAAGAGATACTGGGAATCTAGGGACCGGGAGAGGTAAGAGGTACTTCAGGGGTAGAAGTGAAATTCTGTAATCCTTGAGGGACCACCGATGGCGAAGGCATCTTACCAGAACGGCTTCGACAGTGAGGAACGAAAGCTGGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTGCCTGTAACTACGAGTTACCGGGGTGCCGAAGTGAAAACGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACGGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGCAGCTCACCGGATAGGACAGCGGAATGATAGCCGGGCTGAAGACCTTGCTTGACCAGCTGAGA
>EF503699
AAGAATGGGGATAGCATGCGAGTCACGCCGCAATGTGTGGCATACGGCTCAGTAACACGTAGTCAACATGCCCAGAGGACGTGGACACCTCGGGAAACTGAGGATAAACCGCGATAGGCCACTACTTCTGGAATGAGCCATGACCCAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGGAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCACGAAACCTCTGCAATAGGCGAAAGCTTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCCGCTTAACGGATGGGCTGCGGAGGATACTGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCTTTGATCTACTGAAGACCACCAGTGGTGAAGGCGGTTCGCCAGAACGCGCTCGAACGGTGAGGATGAAAGCTGGGGGAGCAAACCGGAATAGATACCCGAGTAATCCCAACTGTAAACGATGGCAACTCGGGGATGGGTTGGCCTCCAACCAACCCCATGGCCGCAGGGAAGCCGTTTAGCTCTCCCGCCTGGGGAATACGGTCCGCAGAATTGAACCTTAAAGGAATTTGGCGGGGAACCCCCACAAGGGGGAAAACCGTGCGGTTCAATTGGAATCCACCCCCCGGAAACTTTACCCGGGCGCG
>DQ260310
GATACCCCCGGAAACTGGGGATTATACCGGATATGTGGGGCTGCCTGGAATGGTACCTCATTGAAATGCTCCCGCGCCTAAAGATGGATCTGCCGCAGAATAAGTAGTTTGCGGGGTAAATGGCCACCCAGCCAGTAATCCGTACCGGTTGTGAAAACCAGAACCCCGAGATGGAAACTGAAACAAAGGTTCAAGGCCTACCGGGCACAACAAGCGCCAAAACTCCGCCATGCGAGCCATCGCGACGGGGGAAAACCAAGTACCACTCCTAACGGGGTGGTTTTTCCGAAGTGGAAAAAGCCTCCAGGAATAAGAACCTGGGCCAGAACCGTGGCCAGCCGCCGCCGTTACACCCGCCAGCTCGAGTTGTTGGCCGGTTTTATTGGGGCCTAAAGCCGGTCCGTAGCCCGTTTTGATAAGGTCTCTCTGGTGAAATTCTACAGCTTAACCTGTGGGAATTGCTGGAGGATACTATTCAAGCTTGAAGCCGGGAGAAGCCTGGAAGTACTCCCGGGGGTAAGGGGTGAAATTCTATTATCCCCGGAAGACCAACTGGTGCCGAAGCGGTCCAGCCTGGAACCGAACTTGACCGTGAGTTACGAAAAGCCAAGGGGCGCGGACCGGAATAAAATAACCAGGGTAGTCCTGGCCGTAAACGATGTGAACTTGGTGGTGGGAATGGCTTCGAACTGCCCAATTGCCGAAAGGAAGCTGTAAATTCACCCGCCTTGGAAGTACGGTCGCAAGACTGGAACCTAAAAGGAATTGGCGGGGGGACACCACAACGCGTGGAGCCTGGCGGTTTTATTGGGATTCCACGCAGACATCTCACTCAGGGGCGACAGCAGAAATGATGGGCAGGTTGATGACCTTGCTTGACAAGCTGAAAAGGAGGTGCAT
>EF503697
TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC
"""

id_to_tax = """
AY800210	Archaea;Euryarchaeota;Halobacteriales;uncultured
EU883771	Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.
EF503699	Archaea;Crenarchaeota;uncultured;uncultured
DQ260310	Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium
EF503697	Archaea;Crenarchaeota;uncultured;uncultured
"""

in_seqs_aligned = """
>11472384 1..1530
---------------------------------------------------------------------------------------------------------------AGAGTTTGAT-CC-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GC-A-TG--C----C-T--TACACA-T-GC-A-AGT-CGA-A-CG----------G-CAG-CA-C------------------------------GG-G-GG----------------------------------------------------CAA------------------------------------------------------------------------------------C-C-CT------------------G-GT--G--GC--G--AG-T-GG-C-GA-A--C-------------GGG-TGAGT-A--AT-AC-A-T-C-GG---A-A--C-GT-G--T-C-CTG--TA-G------------------------------------------------------------------T-GG----GGG-AT-AG-CCC-------------------------G-G-C-----------------------GAA-A---GCC-GGA-TTAA-TA---CC-G--C-AT-A----------C--------------------G-------------------------------------CT-C-----------------------------------------------------------------------------------------------------------------------T-AC-G--------------------------------------------------------------------------------------------------------------------------------------G-A-G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-G-G-GG-----G--GA-T--C--------------------------------------------------------------------------------------------------------------------TTA-G----------------------------------------------------------------------------------------------------------------------G-A--CC-TC--C---C-G--------------C----T-A---C-AG-G---GG---C-G-----G-CCG-ATG--G-CAG--A------TT--A--G-CT-A----G---TTGG-T-G-GG-G-T----AAA-GG-C-C-T-ACCA--A-GG-C-G--A-CG-A------------TCT-G-T------AG-CT-G-G-TCT-G-AG----A--GG-AC--G-AC-C-AG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-G-CCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATT-TTGGA-C-AA-T-GG--GG-GC-A----A-C-CC-T-GA-TC-CA-GCAA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TT-G-T--C-CGG----AA-A--G---AA-AACG---CCGT-GG----T--T--AA-T---A----C-----CC-G-TGG-CGG-AT-GA-CG-GT-A-C-CG-G-AA-G---------AA-----------TAAGC-ACC-GG-C-TAA---C--T-ACGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GT-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGT-GC--G-CA-G-G-C-G------------G--T-CC-G-C-T-AA----G-A-C-A---G-ATG-TG-A-AA-TC--CC-CGG-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-T--------T--GT-G-A-C-T-G-GCG--G-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-A-----T-GG--CA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-C-GT--GT-A-GCA-GTGAAA-TG-CGT-AGAG-A-TG-T-GGA--GG-A-AT-A-CC-GA--T--G--GC-GAA-G--G-C---A----G--C-C-CCCTG------G-GC-CA--------------------------------------------------------------AT-A-C-T--GA--CG-----CT-CA-TG--C-A-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCC-T-AAA--C-GATG-TC--AA-CT---------A-GT--T--G-T-CG-G-GT-C--T---------------------------------------------------------------------------------------TC-AT--------------------------------------------------------------------------------------------------------------------------------------------------T-G-A-CT--T-G-G-T-AA-C------GT--A----GC-TAA--CG-C-G-T--G--AA-GT--T----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----T-C--G-C-A-A-GAT-T--AAA-ACTC-AAA---------GGAA-TTG-ACGGG-G-A-CCCG----C-A--C-A-A-GCG-GT-G--G--AT-GA-T--GT-GGA-TT-AATT-C-G-ATG-CAAC-G-CG-A-AA-A-A-CC-TT-A-CC-TACCC-TT-G-AC-A-T-G--------------TAT-G-G-------------A-AT-C-C-T--GC--T-GA-G-A-G--G-T-G--G-G-A-G--T-GC----CC-------------------------------------G--AA-A------------------------------------------GG---GA----G---CC-ATA---A--CA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TG--TC--C-CTAG--T-T-G-C-T---A--C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G------------A----G---C-A--CT---------------C-T-A-G-G-GA-G--AC-T-G-CCG--G-T------------------------------------G-A---CAA----------------------------------A-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---CTC-A-T-G-G-C-C-CTT----AT-G--GG-T-A-GG-GC-TT-CAC-ACGTC-A--TA--CAATG---G-TCGG-A-A--C-AGA-GG-GT--------------------------------------------------------------------------------------------------C-G-C-C-A--A-CCCG-C--G---------------------------------------A-GG-G-G-----------G--A-G-CC---A----------A--TCC-C------A-G-AAAAC-CG-A-T-C-G-TAG-TCC--------GGA-T-CGCAC-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-AGTGC-G-T-G-AA-G-CT-GGAAT-CG-C-TA--G-TA-AT-C-G-C----GGA-TC-A-G-C-------AT--GCC-GC-G-GT-G-AAT-ACGT-T-CCCGGGTCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-TT-ACC--A-GAA------G--T-GGC-TA-G-T-C-T-AA-C-C-------------------------------------------------------------G-CA-A------------------------------------------------------------------------------------------------------GG-A--GG-A--C---GG-TCA--CC--ACG-G----T-AGG-AT-TCA------------------------TG--ACT-GGGG-TGAAGTCG--TAACAA-GGTAG-CCGT-ATCGGAA-GGTG-CGGC-TGGATCACCTCCTTTCTCGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>11468680 6..1535
------------------------------------------------------------------------------------------------------------TGAAGAGTTTGAT-CC-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GC-A-TG--C-----CT--TACACA-T-GC-A-AGT-CGA-A-CG----------G-CAG-CA-C------------------------------GG-G-TG------------------------------------------------------C-T----------------------------------------------------------------------------------TGCACCT-----------------G-GT--G--GC--G--AG-T-GG-C-GA-A--C-------------GGG-TGAGT-A--AT-AC-A-T-C-GG---A-A--C-AT-G--T-C-CTG--TA-G------------------------------------------------------------------T-GG----GGG-AT-AG-CCC-------------------------G-G-C-----------------------GAA-A---GC--CGGATTAA-TA---CC-G--C-AT-A----------C--------------------G-------------------------------------AT-C-----------------------------------------------------------------------------------------------------------------------T-AC-G--------------------------------------------------------------------------------------------------------------------------------------G-A-T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-C-G-GG-----G--GA-C--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-G--CC-TC--G---C-G--------------C----T-A---T-AG-G---GT---T-G-----G-CCG-ATG--G-CTG--A------TT--A--G-CT-A----G---TTGG-T-G-GG-G-T----AAA-GG-C-C-T-ACCA--A-GG-C-G--A-CG-A------------TCA-G-T------AG-CT-G-G-TCT-G-AG----A--GG-AC--G-AC-C-AG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-G-CCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATT-TTGGA-C-AA-T-GG--GC-GA-A----A-G-CC-T-GA-TC-CA-GCAA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-C-----CTT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TT-G-T--C-CGG----AA-A--G---AA-ATCC---TTGG-CT----C--T--AA-T---A----C------A-G-TCG-GGGGAT-GA-CG-GT-A-C-CG-G-AA-G---------AA-----------TAAGC-ACC-GG-C-TAA---C--T-ACGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GT-AG-GGT-GCG-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGT-GC--G-CA-G-G-C-G------------G--T-TT-G-C-T-AA----G-A-C-C---G-ATG-TG-A-AA-TC--CC-CGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-T--------G--GT-G-A-C-T-G-GCA--G-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-A-----T-GG--CA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-C-GT--GT-A-GCA-GTGAAA-TG-CGT-AGAG-A-TG-T-GGA--GG-A-AT-A-CC-GA--T--G--GC-GAA-G--G-C---A----G--C-C-CCCTG------G-GC-CA--------------------------------------------------------------AT-A-C-T--GA--CG-----CT-CA-TG--C-A-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCC-T-AAA--C-GATG-TC--AA-CT---------A-GT--T--G-T-TG-G-GG-A--T---------------------------------------------------------------------------------------TC-AT--------------------------------------------------------------------------------------------------------------------------------------------------T-T-C-CT--T-A-G-T-AA-C------GT--A----GC-TAA--CG-C-G-T--G--AA-GT--T----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----T-C--G-C-A-A-GAT-T--AAA-ACTC-AAA---------GGAA-TTG-ACGGG-G-A-CCCG----C-A--C-A-A-GCG-GT-G--G--AT-GA-T--GT-GGA-TT-AATT-C-G-ATG-CAAC-G-CG-A-AA-A-A-CC-TT-A-CC-TACCC-TT-G-AC-A-T-G--------------GTC-G-G-------------A-AT-C-C-C--GC--T-GA-G-A-G--G-T-G--G-G-A-G--T-GC----TC-------------------------------------G--AA-A------------------------------------------GA---GA----A---CC-GGC---G--CA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TG--TC--C-TTAG--T-T-G-C-T---A--C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G------------A----G---C-A--CT---------------C-T-A-A-G-GA-G--AC-T-G-CCG--G-T------------------------------------G-A---CAA----------------------------------A-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---CTC-A-T-G-G-C-C-CTT----AT-G--GG-T-A-GG-GC-TT-CAC-ACGTC-A--TA--CAATG---G-TCGG-A-A--C-AGA-GG-GT--------------------------------------------------------------------------------------------------T-G-C-C-A--A-CCCG-C--G---------------------------------------A-GG-G-G-----------G--A-G-CT---A----------A--TCC-C------A-G-AAAAC-CG-A-T-C-G-TAG-TCC--------GGA-T-TGCAC-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-AGTGC-A-T-G-AA-G-CT-GGAAT-CG-C-TA--G-TA-AT-C-G-C----GGA-TC-A-G-C-------AT--GCC-GC-G-GT-G-AAT-ACGT-T-CCCGGGTCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-TT-ACC--A-GAA------G--T-GGC-TA-G-T-C-T-AA-C-C-------------------------------------------------------------G-CA-A------------------------------------------------------------------------------------------------------GG-A--GG-A--C---GG-TCA--CC--ACG-G----T-AGG-AT-TCA------------------------TG--ACT-GGGGTGAAGTCGTAACAAGGTAGC----CGTA--TCGGAA-GGTG-CGGC-TGGATCACCTCCTTT-C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>11458037 1..1544
-----------------------------------------------------------------------------------------------------------------------------------------GA-CGAA-C-GC--TGG-C--G-GC-G-TG--C----C-T--AACACA-T-GC-A-AGT-CGA-A-CGG----------------T--TTC-------------------------------------------------------------------------------GAAGAT-CGG-A-CTTCGAA-----------------------------------------------------------------------------------------TTTCGA--A-TTTCGATCATCGAGATAGT-GG-C-GG-A--C-------------GGG-TGAGT-A--AC-GC-G-T-G-GG---TAA--C-CT-A--C-C-CAT--AA-A------------------------------------------------------------------G-CC----GGG-AC-AA-CCC-------------------------T-T-G-----------------------GAA-A---CGA-GGG-CTAA-TA---CC-G--G-AT-A----------A--------------------G-C--T-T-G--A--G-----------------AA---GT-G-----------------------------------------------------------------------------------------------------------------------G-CA-T--------------------------------------------------------------------------------------------------------------------------------------C-A-C--T-T---------------T--T-T-A-A-G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-G-T-GG-----C--C--GA-T--------------------------------------------------------------------------------------------------------------------GAG-A----------------------------------------------------------------------------------------------------------------------A-T--GC-TG--C---C-G--------------A----T-T---A-TG-G---AT---G-G-----A-CCC-GCG--T-CTG--A------TT--A--G-CT-G----G---TTGG-T-G-GG-G-T----AAA-GG-C-C-T-ACCA--A-GG-C-G--A-CG-A------------TCA-G-T------AG-CC-G-G-CCT-G-AG----A--GG-GT--G-AA-C-GG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-G-CCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATC-TTCCG-C-AA-T-GG--AC-GA-A----A-G-TC-T-GA-CG-GA-GCAA-CGCC-G-CG-T---G-T-A--T--GA-T-G--A--A-G-G-TT-----TT-CG---------G-A-T-T-G-T--A---AA-G-TAC--------TG-TC-T-A--T-GGG----GA-A--G---AATGGTG---TGCT-TG----A--G--AA-T---A----T-----TA-A-GTA-CAA-AT-GA-CG-GT-A-C-CC-A-AG-G---------AG-----------GAAGC-CCC-GG-C-TAA---C--T-ACGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GT-AG-GGG-GCA-A-G-CG-TTGT-C-CGG-AA-TT-A--T-T--GGGC-GTA----AA-GGGC-GC--G-TA-G-G-C-G------------G--A-TA-G-T-T-AA----G-T-C-C---G-GTG-TG-A-AA-GA--TC-AGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-C-T-GA-GA-G----T-G-C-A-T-C--------G--GA-A-A-C-T-G-GGT--A-T-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-G-A-----C-AG--GA-G-A------------G-GA-A-AG-T----GG--AATT-CCA-C-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAT-A-TG-T-GGA--GG-A-AC-A-CC-AG--T--G--GC-GAA-G--G-C---G----A--C-T-TTCTG------G-AC-TG--------------------------------------------------------------TA-A-C-T--GA--CG-----CT-GA-GG--C-G-CGA--AA-G-C--------------G-T-GGGGAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CTG-T-AAA--C-GATG-AG--TG-CT---------A-GG--T--G-T-AG-A-GG-G----------------------------------------------------------------------------------------TATC-GA-CC-------------------------------------------------------------------------------------------------------------------------------------------------C-C-TT--C-T-G-T-GC-C------GC--A----GT-TAA--CA-C-A-A--T--AA-GC--A----C-TCC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--GAA-ACTC-AAA---------GGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ACG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-AGGGC-TT-G-AC-A-T-C--------------CTC-T-G-------------A-AC-T-T-G--CT--G-GA-A-A-C--A-G-G--A-A-G-G--T-GC----CC-------------------------------------T--TC-G------------------------------------------GG---GA----G---CA-GAG---A--GA---------------------------------------------------C-A-G-G-T-GGTG-CA-TGG-TT--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-AT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-C-TG--TA--T-TTAG--T-T-G-C-T---AA-C-G--C--G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----G----C-G------------A----G---C-A--CT---------------C-T-G-G-A-TA-G--AC-T-G-CCG--G-T------------------------------------G-A---TAA----------------------------------A-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAAT-C---ATC-A-T-G-C-C-C-CTT----AT-G--TT-C-T-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CCGG-T-A--C-AGA-CG-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--A-GCCG-C--G---------------------------------------A-GG-C-G-----------G--A-G-CA---A----------A--TCC-G------A-G-AAAGC-CG-G-T-C-T-CAG-TTC--------GGA-T-TGCAG-GC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-CCTGC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-C----AGG-TC-A-G-C-------AT--ACT-GC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-CG-AA-A--G---TCT-G-CA-AC-ACC--C-GAA------G--C-CGG-TG-A-G-G-T-AA-C-C-G-----------------------------------------------------------A-CT-C-----------------------------------------------------------------------------------------------------GAG-A--TT-C--G---AG-GCT--CG--AAG-T----T--------CGA------------------------GG--ATC-GAAG-TG-TAA-GCGAAATTA-ATAAG-TCTT-A--GTAA-AGCT-AAAA-AGCATTAAGACCGA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>11469739 1..1595
------------------------------------------------------------------------------------------------------------AGAGTTT-GA--T-CC-T-G-GCTC-AG-GA-TGAA-C-GC--TGG-C--G-GC-G-TG--C----C-T--AACACA-T-GC-A-AGT-CGA-A-CGA---------G-A---AG-C--------TAACTT--------------CTGA-T-TCC---------------------------------------------------TTC-G---------------------------------------------------------------------------------GGAT-GATGAGGTTA------------GC--A--GA--A--AG-T-GG-C-GA-A--C-------------GGG-TGAGT-A--AC-GC-G-T-G-GG---TAA--T-CT-A--C-C-CTG--TAAG------------------------------------------------------------------T-GG----GGG-AT-AA-CCC-------------------------T-C-C-----------------------GAA-A---GGA-GGG-CTAA-TA---CC-G--C-AT-A----------A--------------------T-A--T-C-T--T--T-----------------AT---CC-C-----------------------------------------------------------------------------------------------------------------------A-AA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-G--G-T---------------A--A-A-G-A-T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAA--G-A-T-GG-----C--CT-C--TA-------------------------------------------------------------------------------------------------------------------TAC-----------------------------------------------------------------------------------------------------------------------TA-T--GC-TA--T---C-G--------------C----T-T---C-AG-G---AT---G-A-----G-TCC-GCG--T-CCT--A------TT--A--G-TT-A----G---TTGG-T-G-GG-G-T----AAT-GG-C-C-T-ACCA--A-GA-C-G--A-CA-A------------TGG-G-T------AG-CC-G-G-TCT-G-AG----A--GG-AT--G-TA-C-GG-CCAC-A-CT-GG-GA-C-TG-A-GA-T-AC-G-G-CCCAGA-CTCC-TAC-G--G-G-A-G-AC-A-GC-A-G-TG---GG-G-A-ATA-TTGCG-C-AA-T-GG--GG-GA-A----A-C-CC-T-GA-CG-CA-GCGA-CGCC-G-CG-T---G-G-A--T--GA-T-G--A--A-G-G-CC-----CT-TG---------G-G-T-T-G-T--A---AA-A-TCC--------TG-TT-C-T--G-GGG----GA-A--G---AA-AGCT---TAAA-GG-T--C--C--AA-T---A----A---A-CC-C-TTA-AGC-CT-GA-CG-GT-A-C-CC-C-AA-G---------AG-----------AAAGC-TCC-GG-C-TAA---T--T-ATGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---AT-AA-GGA-GCA-A-G-CG-TTAT-C-CGG-AA-TT-A--T-T--GGGC-GTA----AA-GAGC-TC--G-TA-G-G-C-G------------G--T-CT-T-A-A-AA----G-T-C-A---G-TTG-TG-A-AA-TT--AT-CAG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-AT-AA-G----G-T-C-A-T-C--------T--GA-A-A-C-T-C-TAA--G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-G-T-----T-AG--AA-G-A------------G-GA-A-AG-T----GG--AATT-CCC-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAT-A-TC-G-GGA--GG-A-AC-A-CC-AG--T--G--GC-GAA-G--G-C---G----G--C-T-TTCTG------G-TC-TA--------------------------------------------------------------TC-T-C-T--GA--CG-----CT-GA-GG--A-G-CGA--AA-G-C--------------T-AGGG-GAG-C-A-AACG--GG-ATTA-G-ATA-C-----CC-C-G-GTA-G-T----C-CT--A-G-CTG-T-AAA--C-GATG-GA--TA-CT---------A-GG--T--G-T-GG-G-AG-G----------------------------------------------------------------------------------------TATC-GA-CC-------------------------------------------------------------------------------------------------------------------------------------------------C-C-TT--C-T-G-T-GC-C------GT--A----GC-TAA--CG-C-A-T--T--AA-GT--A----T-CCC-GCC-T-G-GG-GAG-TA---CGG-----T-C--G-C-A-A-GGC-T--GAA-ACTC-AAA---------GGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ACG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-GGGAC-TT-G-AC-A-T-T------------A-TCT-T-G-------------C-CC-G-T-C--TA--A-GA-A-A-T--T-A-G--A-T-C-T--T-CT----TCC------------------------------------T--T--T-----------------------------------------GGA---AG----A---CA-GGA---T--AA---------------------------------------------------C-A-G-G-T-GGTG-CA-TGG-TT--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-GT-CCCAC-AA--------C-GAG-CGC-A-ACC-C-T-TG--TG--C-TTAG--T-T-G-C-T---AA-C-T--T--GT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---C----A----A-G------------T----G---C-A--CT---------------C-T-A-G-G-CA-G--AC-T-G-CCG--C-A------------------------------------G-A---TAA----------------------------------T-G-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAAT-C---ATC-A-T-G-C-C-C-CTT----AC-G--TC-C-C-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CCTG-T-A--C-AGA-GG-GT--------------------------------------------------------------------------------------------------A-G-C-G-A--A-AGAG-C--G---------------------------------------A-TC-T-T-----------A--A-G-CC---A----------A--TCC-C------A-A-AAAGC-AG-G-C-C-C-CAG-TTC--------GGA-T-TGGAG-GC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-CCTCC-A-T-G-AA-G-TA-GGAAT-CG-C-TA--G-TA-AT-C-G-C----GGA-TC-A-G-C-------AT--GCC-GC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-CG-AA-A--G---TTG-G-CG-AT-ACC--T-GAA------G--T-TAC-TA-G-G-C-T-AA-C-C-TG-----------------------------------------------------GCACTCAACTAA-------------------------------------------------------------------------------------------------GT--TC-A--CT-A--A--CTTATTTGCTT--AAA-A----T-AAG-GCTTAATG----------------------TG--CTT-AGTT-GA-GTG-CCGGGAGGC-AGGTA-CCGA-AGGTATG-GCTGGCGATTGGGGTGAAGTCGTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>11460543 1..1587
-------------------------------------------------------------------------------------------------------------TGGTTT-GA--T-CC-T-G-GCTC-AG-GA-CAAA-C-GC--TGG-C--G-GC-G-TG--C----C-T--AACACA-T-GC-A-AGT-CGA-A-CGA---------G-A---AG-C--------CAGCTT--------------TTGA-T-TCC---------------------------------------------------TTC-G---------------------------------------------------------------------------------GGAT-GAGAAAGCAG------------GT--A--GA--A--AG-T-GG-C-GA-A--C-------------GGG-TGAGT-A--AC-GC-G-T-G-GG---TAA--T-CT-A--C-C-CTG--TAAG------------------------------------------------------------------T-AG----GGG-AT-AA-CCC-------------------------T-C-T-----------------------GAA-A---AGA-GGG-CTAA-TA---CC-G--C-AT-A----------A--------------------T-A--T-C-T--T--T-----------------AC---CC-C-----------------------------------------------------------------------------------------------------------------------A-TA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-A--G-T---------------A--A-A-G-A-T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAA--G-A-T-GG-----C--CT-C--TG-------------------------------------------------------------------------------------------------------------------TA------------------------------------------------------------------------------------------------------------------------TA-T--GC-TA--T---C-G--------------C----T-T---C-AG-G---AT---G-A-----G-CCC-GCG--T-CCT--A------TT--A--G-TT-A----G---TTGG-T-A-AG-G-T----AAT-GG-C-T-T-ACCA--A-GA-C-C--A-CG-A------------TGG-G-T------AG-CC-G-G-TCT-G-AG----A--GG-AT--G-TA-C-GG-CCAC-A-CT-GG-GA-C-TG-A-GA-T-AC-G-G-CCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCG-C-AA-T-GG--GG-GA-A----A-C-CC-T-GA-CG-CA-GCGA-CGCC-G-CG-T---G-G-A--T--GA-T-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-A-TCC--------TG-TT-T-T--G-GGG----GA-C--G---AA-ACCT---TAAG-GG-T--C--C--AA-T---A----A---A-CC-C-TTA-A-A-TT-GA-CG-GT-A-C-CC-C-AA-G---------AG-----------AAAGC-TCC-GG-C-TAA---T--T-ATGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---AT-AA-GGA-GCA-A-G-CG-TTGT-C-CGG-AA-TT-A--T-T--GGGC-GTA----AA-GAGT-TC--G-TA-G-G-C-G------------G--T-CT-T-A-A-AA----G-T-C-A---G-GTG-TG-A-AA-TT--AT-CAG-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CC-T-G-AT-AC-G----G-T-C-A-T-C--------T--GA-A-A-C-T-T-TAA--G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-G-T-----T-AG--GA-G-A------------G-GA-A-AG-T----GG--AATT-CCC-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAT-A-TC-G-GGA--GG-A-AC-A-CC-AG--T--G--GC-GAA-G--G-C---G----G--C-T-TTCTG------G-CC-TA--------------------------------------------------------------AC-T-C-T--GA--CG-----CT-GA-GG--A-A-CGA--AA-G-C--------------T-AGGG-GAG-C-A-AACG--GG-ATTA-G-ATA-C-----CC-C-G-GTA-G-T----C-CT--A-G-CTG-T-AAA--C-GATG-GA--TA-CT---------A-GG--T--G-T-GG-G-AG-G----------------------------------------------------------------------------------------TATC-GA-CC-------------------------------------------------------------------------------------------------------------------------------------------------C-C-TT--C-T-G-T-GC-C------GW--C----AC-TAA--CG-C-A-T--T--AA-GT--A----T-CCC-GCC-T-G-GG-GAG-TA---CGG-----T-C--G-C-A-A-GGC-T--AAA-ACTC-AAA---------GGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ACG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-GGGGC-TT-G-AC-A-T-T------------G-TCT-T-G-------------C-CC-G-T-T--TA--A-GA-A-A-T--T-A-A--A-T-T-T--T-CT----TCC---------------------------------CTTT--TA-G-----------------------------------------GGA---AG----A---CA-AGA---T--AA---------------------------------------------------C-A-G-G-T-GGTG-CA-TGG-TT--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-GT-CCCAC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TT--C-TTAG--T-T-G-C-T---AG-T-T--T--G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---C----A----A-A------------C----G---C-A--CT---------------C-T-A-A-A-GA-G--AC-T-G-CCG--C-A------------------------------------G-A---TAA----------------------------------T-G-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAAT-C---ATC-A-T-G-C-C-C-CTT----AC-G--TC-C-C-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CCTG-T-A--C-AGA-GG-GT--------------------------------------------------------------------------------------------------A-G-C-G-A--A-AGAG-C--G---------------------------------------A-TC-T-C-----------A--A-G-CT---A----------A--TCC-C------T-T-AAAAC-AG-G-T-C-T-CAG-TTC--------GGA-T-TGGAG-GC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-CCTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-C----GGA-TC-A-G-C-------AT--GCC-GC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-AA-A--G---TTG-G-CG-AT-ACC--T-GAA------G--T-TAC-TG-T-G-C-T-AA-C-C-CG----------------------------------------------------------G-CA-----------------------------------------------------------------------------------------------------C--TC-A--AC-T--A---AG-TAC--AT--TAA-G-TCTT-ATT-TT-AAG------------------------CT--ATT-GTAT-TTAGTTGAGTGCCGGGAGGCAGGTACCTAAGGTATGGCTAGCGATTGGGGTGAAGTCGTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>11480408 26..1556
------------------------------------------------------------------------------------------------------------TGAGTTT-GA--T-CC-T-G-GCTC-AG-GA-CGAA-C-GC--TGG-C--G-GC-G-TG--C----T-T--AACACA-T-GC-A-AGT-CGA-A-CGG---------G-G-ATATCCGA-------GC------------------GGA---AG--------------------------------------------------GTTTC-G----------------------------------------------------------------------------------GCCGGAAGGTTGGG-------------T--AT-TC--G--AG-T-GG-C-GG-A--C-------------GGG-TGAGT-A--AC-GC-G-T-G-AG---CAA--T-CT-G--T-C-CCG--GA-C------------------------------------------------------------------A-GG----GGG-AT-AA-CAC-------------------------T-T-G-----------------------GAA-A---CAG-GTG-CTAA-TA---CC-G--C-AT-A----------A--------------------G-A--C-C-A--C--A-----------------GC---AT-C-----------------------------------------------------------------------------------------------------------------------G-CA-T--------------------------------------------------------------------------------------------------------------------------------------G-G-T--G-C---------------A--G-G-G-G-T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAA--G-G----------------------------------------------------------------------------------------------------------------------------------------AGC-G----------------------------------------------------------------------------------------------------------------------------------A---TCCG-------------G----T-C---T-GG-G---GT---G-A-----G-CTC-GCG--T-CCG--A------TT--A--G-AT-A----G---TTGG-T-G-AG-G-T----AAC-GG-C-C-C-ACCA--AGT--C-A--A-CG-A------------TCG-G-T------AG-CC-G-A-CCT-G-AG----A--GG-GT--G-AT-C-GG-CCAC-A-TTGGA--A-C-TG-A-GA-G-AC-G-G-TCCAAA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGGG-C-AA-T-GG--GC-GA-A----A-G-CC-T-GA-CC-CA-GCAA-CGCC-G-CG-T---G-A-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CTC--------TG-TT-A-T--G-CGA----GA-C--G---A-----------------------AGGAAG-----------------------------T-GA-CG-GT-A-T-CG-C-AT-A---------AG-----------GAAGC-CCC-GG-C-TAA---C--T-ACGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GT-AG-GGG-GCG-A-G-CG-TTGT-C-CGG-AA-TG-A--C-T--GGGC-GTA----AA-GGGC-GT--G-TA-G-G-C-G------------G----CC-G-TTT-AA----G-T-A-T---G-GAG-TG-A-AA-GT--CC-ATT-T--------------------------------------------------------------------TT-C-AA-------------------------------------------------------------------------GG-A-T-GG-AA-T----T-G-C-T-T-T--------G--TA-G-A-C-T-GGATG--G---C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-T-G-----C-GG--AA-G-A------------G-GT-A-AG-T----GG--AATT-CCC-A-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TT-G-GGA--GG-A-AC-A-CC-AG--T--G--GC-GAA-G--G-C---G----A--C-T-TACTG------G-GC-CG--------------------------------------------------------------TA-A-C-T--GA--CG-----CT-GA-GG--C-G-CGA--AA-G-C--------------G-TGGG-G-AGC-G-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CGG-T-AAA--C-GATG-AA--TG-CT---------A-GG--T--G-T-TGCG-GG-T--A--T-------------------------------------------------------------------------------------C-GA----------------------------------------------------------------------------------------------------------------------------------------------C---C-C-C-TG--C-A-G-T-GC-C------GG--A----GT-AAA--CA-C-A-A--T--AA-GC--A----T-TCC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--GAA-ACTC-AAG---------GGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCA-GC-G--G--AG-CA-T--GT-TGT-TT-AATT-C-G-AAG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-AGGTC-TT-G-AC-A-T-C-------------C-A--GTT-------------A-AG---C-T-CAT--A-GA-G-A-T--A-T-G-AG---G-T--C-------CC-------------------------------------T--TC-G------------------------------------------GG---------G---GAAC-T-G-A--GA---------------------------------------------------C-A-G-G-T-GGTG-CA-TGG-TT--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TG--G-TCAG--T-T-A-C-T---AA-C-G--C--G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----G----C-G------------A----G---G-A--CT---------------C-T-G-A-C-GA-G--AC-T-G-CCG--G-G------------------------------------G-A---CAA----------------------------------C-T-C-G--G-A-GG-A--AGG-T--GGGG-A-CGAC-GTC--AAAT-C---ATC-A-T-G-C-C-C-CTT----AT-G--AC-C-T-GG-GC-TA-CAA-ACGTG-C--TA--CAATG---G-TGAC-T-A--C-AAA-GA-GG--------------------------------------------------------------------------------------------------A-G-C-G-A--G-ACTG-T--A---------------------------------------A-AG-T-G-----------G--A-G-CG---G----------A--TCT-C------A-A-AAAAG-TC-A-T-C-C-CAG-TTC--------GGA-T-TGTGG-GC--T-GCAA-CC-C-------------------------------------------------------------------------------------------------G-CCCAC-A-T-G-AA-G-TT-GGAGT-TG-C-TA--G-TA-AT-C-G-C----GGA-TC-A-G--C------AT--GCC-GC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TTG-G-GA-GC-ACC--C-GAA------G--T-CAG-TG-A-G-G-T-AA-C-C-------------------------------------------------------------G-GA-A------------------------------------------------------------------------------------------------------GG-A--GC-C--A---GC-TGC--CG--AAG-G----T-GAG-AC-CGA------------------------TG--ACT-GGGG-TG-AAG-TCGTAACAA-GGTAG-CCGT-ATCGGAA-GGTG-CGGC-TGGATCACCTCCTTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
"""


if __name__ == "__main__":
    main()