<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2008-02-20 09:19:45"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M7104" ref_strand="+" ref_description="SGN-M7104 C2_At1g79050 [cosii_markers]">
      <seq>ctcgtgccgatggaactccggcgacagcatagcctaagctccttcttcagcaaggagaactgagcttaagtatagtaatatctttcaatccgcttgaactttgtagtccaagagaacggagcttttaagctagaaactttaatggagttaactttcccagtgaaagctcagttatttggctccaaaattggtcacaaatctctaagctactcaacttcagtaaaattctaccagaaagtatctcgtcctcaattttcagcatgtggaatcagggttcgttcggaatttgaccataaaatcaatggcgctttctctcctgattctgacgctcggattctcgaccggcaaaaagcattggatgctgcaatgaacgatataaacagctcgtttggcaaaggaagcgttactagattgggtagtgctggcggagctctggttgaaacttttccgagtggctgcttgacgctagactttgctttaggtggtggcattcccaaaggcagaattgttgagatatatgggcccgaaagtagtggaaagactaccttagctctccatgctattgcagaagtacagaagctaggaggcaatgcaatgcttgttgatgctgagcatgcttttgatcctgcatactccaaagcacttggagtagatgtagaagaatttgatcgtctgccagcctgataatggagagatggctctagaatcgcagaccggatgtgtagatcaggtgccgtagatctcatttgcattgattcagtctcagc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="+" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="43617" stop="46061"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="43916" g_stop="44259" g_length="344"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="345" r_length="345" r_score="0.985"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="44260" i_stop="44360" i_length="101">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.970" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="44361" g_stop="44452" g_length="92"/>
          <reference_exon_boundary r_type="cDNA" r_start="346" r_stop="437" r_length="92" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="44453" i_stop="44647" i_length="195">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="44648" g_stop="44723" g_length="76"/>
          <reference_exon_boundary r_type="cDNA" r_start="438" r_stop="513" r_length="76" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="44724" i_stop="45068" i_length="345">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="45069" g_stop="45131" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="514" r_stop="576" r_length="63" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="45132" i_stop="45444" i_length="313">
            <donor d_prob="0.850" d_score="1.00"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="45445" g_stop="45574" g_length="130"/>
          <reference_exon_boundary r_type="cDNA" r_start="577" r_stop="706" r_length="130" r_score="0.977"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="45575" i_stop="45700" i_length="126">
            <donor d_prob="0.977" d_score="0.94"/>
            <acceptor a_prob="0.835" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="45701" g_stop="45761" g_length="61"/>
          <reference_exon_boundary r_type="cDNA" r_start="707" r_stop="767" r_length="61" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="+" ref_id="SGN-M7104" ref_strand="+">
        <total_alignment_score>0.990</total_alignment_score>
        <cumulative_length_of_scored_exons>766</cumulative_length_of_scored_exons>
        <coverage percentage="0.999" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M7104" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="43916" e_stop="44259"/>
          <exon e_start="44361" e_stop="44452"/>
          <exon e_start="44648" e_stop="44723"/>
          <exon e_start="45069" e_stop="45131"/>
          <exon e_start="45445" e_stop="45574"/>
          <exon e_start="45701" e_stop="45761"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGCGCC-ATGGAACTCCGGCGACAGCATAGCCTAAGCTCCTTCTTCAGCAAGGAGAACTGAGCTTAAGTATAGTAATATCTTTCAATCCGCTTGAACTTTGTAGTCCAAGAGAACGGAGCTTTTAAGCTAGAAACTTTAATGGAGTTAACTTTCCCAGTGAAAGCTCAGTTATTTGGCTCCAAAATTGGTCACAAATCTCTAAGCTACTCAACTTCAGTAAAATTCTACCAGAAAGTATCTCGTCCTCAATTTTCAGCATGTGGAATCAGGGTTCGTTCGGAATTTGACCATAAAATCAATGGCGCTTTCTCTCCTGATTCTGACGCTCGGATTCTCGACCGGGTATCTCTTTCTCTCTCTACATATGTTTGTATTTATAGTTCTGTATGTTGCTTTACTGAAGAATTCCATGTGACTGACTTCCCTAACTCCTCCTGCTTCAGCAAAAAGCATTGGATGCTGCAATGAACGATATAAACAGCTCGTTTGGCAAAGGAAGCGTTACTAGATTGGGTAGTGCTGGCGGAGCTCTGGTGTATGTAATTTTTTTACTGAATTCAAAAAAAGTTATATTTAGTTTCTGCACAGGAACCATGTCGAAACAAACATGAAATGTTTTGGGGAAAAGAAGCAGAAAATGAAAATGGAGAAAAATATTCTGCCCAAAATTTTGATCATTGTTAGACTATATCATTCTTACAAGCACTTGTGTATCTGCTTCTTTATGCAGTGAAACTTTTCCGAGTGGCTGCTTGACGCTAGACTTTGCTTTAGGTGGTGGCATTCCCAAAGGCAGAATTGTTGAGGTTTAAATTTCTATCTTTTTCATTTGTATTTTCAGTATGCATTAGTTATTACTGGTTATTCGCCATCTATTTGGTTTCAAATGCTTGGCTGCTTAGTTATTACTAACTTTTGGTTTTGATTACACATAGTGGACTAACTCCTACATGAAGATGAATAGAACAGTTATATTGACCTGTTAATAGAGTGAGTGCGTTAGAAATTTACTTATTTCATTAATAGGCTGGGGTATTTGATTCTGATGTTTGTCCACATCCTGAACTTCTCAACTGATGTGAGCATGTGGAATATTAACAAGGTTGCTGCAATTTGTTGTCTAATTGCTTTCCTCATATTTTTCTTTACAGATATATGGGCCCGAAAGTAGTGGAAAGACTACCTTAGCTCTCCATGCTATTGCAGAAGTACAGGTGCAGTATGTGTTTGGTTTATTCTACTCATCAGCTTGGAACTTCTATAGGCATGGGGCTGCACTTGGAAGGGGAGGGGGCATTTGATTGTTTGGATGAAAAAGGAAGTCATATGCTTCTATCTTACAGATGAAGTGAAAGAAAATAATGGACAATTTGGAAGTCTAGAAAGCAAACTTAGAATCCTTTCCAGCATCCATTGGAGCTTTATTATTGTGACCAATCCACTGAAACCACTTGCCTTAGGCTTATTACTGAAAATGTTCTCATGTAAAAGGAGACAGATTATAAAATGTTAAATATTGTTATGCAGAAGCTAGGAGGCAATGCAATGCTTGTTGATGCTGAGCATGCTTTTGATCCTGCATACTCCAAAGCACTTGGAGTAGATGTAG-AGAATTTGATCGTCTGCCAGCCTGATAATGGAGAGATGGCTCTAGAAAGTAACAACTTTTCCTTGTTTACACCATTAGAAATGATTTTTCAGTTTTTTGTGCTAGCAACCTTGTCAATAATCATGGTGGTCTTACTAGAGTTTGTACTTTCAACCAAACTTTTGTCTATCTCAGTCGCAGACCGGATGTGTAGATCAGGTGCCGTAGATCTCATTTGCATTGATTCAGTCTCAGC</genome_strand>
        <mrna_strand>CTCGTGCCGATGGAACTCCGGCGACAGCATAGCCTAAGCTCCTTCTTCAGCAAGGAGAACTGAGCTTAAGTATAGTAATATCTTTCAATCCGCTTGAACTTTGTAGTCCAAGAGAACGGAGCTTTTAAGCTAGAAACTTTAATGGAGTTAACTTTCCCAGTGAAAGCTCAGTTATTTGGCTCCAAAATTGGTCACAAATCTCTAAGCTACTCAACTTCAGTAAAATTCTACCAGAAAGTATCTCGTCCTCAATTTTCAGCATGTGGAATCAGGGTTCGTTCGGAATTTGACCATAAAATCAATGGCGCTTTCTCTCCTGATTCTGACGCTCGGATTCTCGACCGG.....................................................................................................CAAAAAGCATTGGATGCTGCAATGAACGATATAAACAGCTCGTTTGGCAAAGGAAGCGTTACTAGATTGGGTAGTGCTGGCGGAGCTCTGGT...................................................................................................................................................................................................TGAAACTTTTCCGAGTGGCTGCTTGACGCTAGACTTTGCTTTAGGTGGTGGCATTCCCAAAGGCAGAATTGTTGAG.........................................................................................................................................................................................................................................................................................................................................................ATATATGGGCCCGAAAGTAGTGGAAAGACTACCTTAGCTCTCCATGCTATTGCAGAAGTACAG.........................................................................................................................................................................................................................................................................................................................AAGCTAGGAGGCAATGCAATGCTTGTTGATGCTGAGCATGCTTTTGATCCTGCATACTCCAAAGCACTTGGAGTAGATGTAGAAGAATTTGATCGTCTGCCAGCCTGATAATGGAGAGATGGCTCTAG-AA..............................................................................................................................TCGCAGACCGGATGTGTAGATCAGGTGCCGTAGATCTCATTTGCATTGATTCAGTCTCAGC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M1936" ref_strand="+" ref_description="SGN-M1936 T1336 [cos_markers]">
      <seq>ggcgacagcatagcctaagctccttcttcagcaaggagaactgagcttaagtatagtaatatttttcaatccgcttgaactttgtagtccaagagaacggagcttttaagcttagactagaaacttcaatggagttaactttcccagtgaaagctcagttatttggctccaaaattggtcacaaatctctaagctactcaacttcagtaaaattctaccagaaagtatctcgccctcaattttcagcatgtggaatcagggttcgttcggaatttgaccataaaatcaatggcgctttctctcctgattctgacgctcggattctcgaccggcaaaaagcattggatgctgcaatgaacgatataaacagctcgtttggcaaaggaagcgttactagattgggtagtgccggcggagctctggttgaaacttttccgagtggctgcttgacgctagactttgctttaggtggtggcattcccaaaggcagaattgttgagatatatgggcccgaaagtagtggaaagactaccttagctctccatgctattgcagaagtacagaagctaggaggcaatgcaatgcttgttgatgctgagcatgcttttgatcctgcatactccaaagca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="+" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="43634" stop="45810"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="43934" g_stop="44259" g_length="326"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="332" r_length="332" r_score="0.954"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="44260" i_stop="44360" i_length="101">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.970" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="44361" g_stop="44452" g_length="92"/>
          <reference_exon_boundary r_type="cDNA" r_start="333" r_stop="424" r_length="92" r_score="0.989"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="44453" i_stop="44647" i_length="195">
            <donor d_prob="0.991" d_score="0.98"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="44648" g_stop="44723" g_length="76"/>
          <reference_exon_boundary r_type="cDNA" r_start="425" r_stop="500" r_length="76" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="44724" i_stop="45068" i_length="345">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="45069" g_stop="45131" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="501" r_stop="563" r_length="63" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="45132" i_stop="45444" i_length="313">
            <donor d_prob="0.850" d_score="1.00"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="45445" g_stop="45510" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="564" r_stop="629" r_length="66" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="+" ref_id="SGN-M1936" ref_strand="+">
        <total_alignment_score>0.974</total_alignment_score>
        <cumulative_length_of_scored_exons>623</cumulative_length_of_scored_exons>
        <coverage percentage="0.990" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1936" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="43934" e_stop="44259"/>
          <exon e_start="44361" e_stop="44452"/>
          <exon e_start="44648" e_stop="44723"/>
          <exon e_start="45069" e_stop="45131"/>
          <exon e_start="45445" e_stop="45510"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGCGACAGCATAGCCTAAGCTCCTTCTTCAGCAAGGAGAACTGAGCTTAAGTATAGTAATATCTTTCAATCCGCTTGAACTTTGTAGTCCAAGAGAACGGAGCTTTT-A----AG-CTAGAAACTTTAATGGAGTTAACTTTCCCAGTGAAAGCTCAGTTATTTGGCTCCAAAATTGGTCACAAATCTCTAAGCTACTCAACTTCAGTAAAATTCTACCAGAAAGTATCTCGTCCTCAATTTTCAGCATGTGGAATCAGGGTTCGTTCGGAATTTGACCATAAAATCAATGGCGCTTTCTCTCCTGATTCTGACGCTCGGATTCTCGACCGGGTATCTCTTTCTCTCTCTACATATGTTTGTATTTATAGTTCTGTATGTTGCTTTACTGAAGAATTCCATGTGACTGACTTCCCTAACTCCTCCTGCTTCAGCAAAAAGCATTGGATGCTGCAATGAACGATATAAACAGCTCGTTTGGCAAAGGAAGCGTTACTAGATTGGGTAGTGCTGGCGGAGCTCTGGTGTATGTAATTTTTTTACTGAATTCAAAAAAAGTTATATTTAGTTTCTGCACAGGAACCATGTCGAAACAAACATGAAATGTTTTGGGGAAAAGAAGCAGAAAATGAAAATGGAGAAAAATATTCTGCCCAAAATTTTGATCATTGTTAGACTATATCATTCTTACAAGCACTTGTGTATCTGCTTCTTTATGCAGTGAAACTTTTCCGAGTGGCTGCTTGACGCTAGACTTTGCTTTAGGTGGTGGCATTCCCAAAGGCAGAATTGTTGAGGTTTAAATTTCTATCTTTTTCATTTGTATTTTCAGTATGCATTAGTTATTACTGGTTATTCGCCATCTATTTGGTTTCAAATGCTTGGCTGCTTAGTTATTACTAACTTTTGGTTTTGATTACACATAGTGGACTAACTCCTACATGAAGATGAATAGAACAGTTATATTGACCTGTTAATAGAGTGAGTGCGTTAGAAATTTACTTATTTCATTAATAGGCTGGGGTATTTGATTCTGATGTTTGTCCACATCCTGAACTTCTCAACTGATGTGAGCATGTGGAATATTAACAAGGTTGCTGCAATTTGTTGTCTAATTGCTTTCCTCATATTTTTCTTTACAGATATATGGGCCCGAAAGTAGTGGAAAGACTACCTTAGCTCTCCATGCTATTGCAGAAGTACAGGTGCAGTATGTGTTTGGTTTATTCTACTCATCAGCTTGGAACTTCTATAGGCATGGGGCTGCACTTGGAAGGGGAGGGGGCATTTGATTGTTTGGATGAAAAAGGAAGTCATATGCTTCTATCTTACAGATGAAGTGAAAGAAAATAATGGACAATTTGGAAGTCTAGAAAGCAAACTTAGAATCCTTTCCAGCATCCATTGGAGCTTTATTATTGTGACCAATCCACTGAAACCACTTGCCTTAGGCTTATTACTGAAAATGTTCTCATGTAAAAGGAGACAGATTATAAAATGTTAAATATTGTTATGCAGAAGCTAGGAGGCAATGCAATGCTTGTTGATGCTGAGCATGCTTTTGATCCTGCATACTCCAAAGCA</genome_strand>
        <mrna_strand>GGCGACAGCATAGCCTAAGCTCCTTCTTCAGCAAGGAGAACTGAGCTTAAGTATAGTAATATTTTTCAATCCGCTTGAACTTTGTAGTCCAAGAGAACGGAGCTTTTAAGCTTAGACTAGAAACTTCAATGGAGTTAACTTTCCCAGTGAAAGCTCAGTTATTTGGCTCCAAAATTGGTCACAAATCTCTAAGCTACTCAACTTCAGTAAAATTCTACCAGAAAGTATCTCGCCCTCAATTTTCAGCATGTGGAATCAGGGTTCGTTCGGAATTTGACCATAAAATCAATGGCGCTTTCTCTCCTGATTCTGACGCTCGGATTCTCGACCGG.....................................................................................................CAAAAAGCATTGGATGCTGCAATGAACGATATAAACAGCTCGTTTGGCAAAGGAAGCGTTACTAGATTGGGTAGTGCCGGCGGAGCTCTGGT...................................................................................................................................................................................................TGAAACTTTTCCGAGTGGCTGCTTGACGCTAGACTTTGCTTTAGGTGGTGGCATTCCCAAAGGCAGAATTGTTGAG.........................................................................................................................................................................................................................................................................................................................................................ATATATGGGCCCGAAAGTAGTGGAAAGACTACCTTAGCTCTCCATGCTATTGCAGAAGTACAG.........................................................................................................................................................................................................................................................................................................................AAGCTAGGAGGCAATGCAATGCTTGTTGATGCTGAGCATGCTTTTGATCCTGCATACTCCAAAGCA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M7104-2" ref_strand="+" ref_description="SGN-M7104-2 C2_At1g79050-2 [cosii_markers]">
      <seq>catcaaggagaactgagcttaagtatagcattatttttcaatccgcttgaactttgtagtcaaagagaacggagctttaagctagaaactttaatggagttaactttcccagtgaaagctcagttttttggctccaaaattggttacaaatcccaaagctactcaacttcagtaaaattctatcagaaagtatctcgtcctcaatttccagcacgtggaattagggttcgttcggaatttgaccataaaatcaatggcgctttctctcctgattctgacgctcggtttctcgaccggcaaaaagcattggatgctgcaatgaacgatataaacagctcgtttggcaaaggaagcgttactagattgggtagtgctggcggagctctggttgaaacttttccgagtggctgcttgacgctagactttgctttaggtggtggcattcccaaaggcagaattgttgagatatatgggcccgaaagtagtggaaagactaccttagctctccatgctattgcagaagtacagaagctaggaggcaatgcaatgtttgttgatgctgagcat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="+" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="43662" stop="45783"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="43962" g_stop="44259" g_length="298"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="297" r_length="297" r_score="0.950"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="44260" i_stop="44360" i_length="101">
            <donor d_prob="1.000" d_score="0.98"/>
            <acceptor a_prob="0.970" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="44361" g_stop="44452" g_length="92"/>
          <reference_exon_boundary r_type="cDNA" r_start="298" r_stop="389" r_length="92" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="44453" i_stop="44647" i_length="195">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.987" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="44648" g_stop="44723" g_length="76"/>
          <reference_exon_boundary r_type="cDNA" r_start="390" r_stop="465" r_length="76" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="44724" i_stop="45068" i_length="345">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="45069" g_stop="45131" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="466" r_stop="528" r_length="63" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="45132" i_stop="45444" i_length="313">
            <donor d_prob="0.850" d_score="1.00"/>
            <acceptor a_prob="0.987" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="45445" g_stop="45483" g_length="39"/>
          <reference_exon_boundary r_type="cDNA" r_start="529" r_stop="567" r_length="39" r_score="0.974"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="+" ref_id="SGN-M7104-2" ref_strand="+">
        <total_alignment_score>0.972</total_alignment_score>
        <cumulative_length_of_scored_exons>568</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M7104-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="43962" e_stop="44259"/>
          <exon e_start="44361" e_stop="44452"/>
          <exon e_start="44648" e_stop="44723"/>
          <exon e_start="45069" e_stop="45131"/>
          <exon e_start="45445" e_stop="45483"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAGCAAGGAGAACTGAGCTTAAGTATAGTAATATCTTTCAATCCGCTTGAACTTTGTAGTCCAAGAGAACGGAGCTTTTAAGCTAGAAACTTTAATGGAGTTAACTTTCCCAGTGAAAGCTCAGTTATTTGGCTCCAAAATTGGTCACAAATCTCTAAGCTACTCAACTTCAGTAAAATTCTACCAGAAAGTATCTCGTCCTCAATTTTCAGCATGTGGAATCAGGGTTCGTTCGGAATTTGACCATAAAATCAATGGCGCTTTCTCTCCTGATTCTGACGCTCGGATTCTCGACCGGGTATCTCTTTCTCTCTCTACATATGTTTGTATTTATAGTTCTGTATGTTGCTTTACTGAAGAATTCCATGTGACTGACTTCCCTAACTCCTCCTGCTTCAGCAAAAAGCATTGGATGCTGCAATGAACGATATAAACAGCTCGTTTGGCAAAGGAAGCGTTACTAGATTGGGTAGTGCTGGCGGAGCTCTGGTGTATGTAATTTTTTTACTGAATTCAAAAAAAGTTATATTTAGTTTCTGCACAGGAACCATGTCGAAACAAACATGAAATGTTTTGGGGAAAAGAAGCAGAAAATGAAAATGGAGAAAAATATTCTGCCCAAAATTTTGATCATTGTTAGACTATATCATTCTTACAAGCACTTGTGTATCTGCTTCTTTATGCAGTGAAACTTTTCCGAGTGGCTGCTTGACGCTAGACTTTGCTTTAGGTGGTGGCATTCCCAAAGGCAGAATTGTTGAGGTTTAAATTTCTATCTTTTTCATTTGTATTTTCAGTATGCATTAGTTATTACTGGTTATTCGCCATCTATTTGGTTTCAAATGCTTGGCTGCTTAGTTATTACTAACTTTTGGTTTTGATTACACATAGTGGACTAACTCCTACATGAAGATGAATAGAACAGTTATATTGACCTGTTAATAGAGTGAGTGCGTTAGAAATTTACTTATTTCATTAATAGGCTGGGGTATTTGATTCTGATGTTTGTCCACATCCTGAACTTCTCAACTGATGTGAGCATGTGGAATATTAACAAGGTTGCTGCAATTTGTTGTCTAATTGCTTTCCTCATATTTTTCTTTACAGATATATGGGCCCGAAAGTAGTGGAAAGACTACCTTAGCTCTCCATGCTATTGCAGAAGTACAGGTGCAGTATGTGTTTGGTTTATTCTACTCATCAGCTTGGAACTTCTATAGGCATGGGGCTGCACTTGGAAGGGGAGGGGGCATTTGATTGTTTGGATGAAAAAGGAAGTCATATGCTTCTATCTTACAGATGAAGTGAAAGAAAATAATGGACAATTTGGAAGTCTAGAAAGCAAACTTAGAATCCTTTCCAGCATCCATTGGAGCTTTATTATTGTGACCAATCCACTGAAACCACTTGCCTTAGGCTTATTACTGAAAATGTTCTCATGTAAAAGGAGACAGATTATAAAATGTTAAATATTGTTATGCAGAAGCTAGGAGGCAATGCAATGCTTGTTGATGCTGAGCAT</genome_strand>
        <mrna_strand>CATCAAGGAGAACTGAGCTTAAGTATAGCATTATTTTTCAATCCGCTTGAACTTTGTAGTCAAAGAGAACGGAGC-TTTAAGCTAGAAACTTTAATGGAGTTAACTTTCCCAGTGAAAGCTCAGTTTTTTGGCTCCAAAATTGGTTACAAATCCCAAAGCTACTCAACTTCAGTAAAATTCTATCAGAAAGTATCTCGTCCTCAATTTCCAGCACGTGGAATTAGGGTTCGTTCGGAATTTGACCATAAAATCAATGGCGCTTTCTCTCCTGATTCTGACGCTCGGTTTCTCGACCGG.....................................................................................................CAAAAAGCATTGGATGCTGCAATGAACGATATAAACAGCTCGTTTGGCAAAGGAAGCGTTACTAGATTGGGTAGTGCTGGCGGAGCTCTGGT...................................................................................................................................................................................................TGAAACTTTTCCGAGTGGCTGCTTGACGCTAGACTTTGCTTTAGGTGGTGGCATTCCCAAAGGCAGAATTGTTGAG.........................................................................................................................................................................................................................................................................................................................................................ATATATGGGCCCGAAAGTAGTGGAAAGACTACCTTAGCTCTCCATGCTATTGCAGAAGTACAG.........................................................................................................................................................................................................................................................................................................................AAGCTAGGAGGCAATGCAATGTTTGTTGATGCTGAGCAT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M1647" ref_strand="+" ref_description="SGN-M1647 T0876 [cos_markers]">
      <seq>agtaatgagctcattgagcctaaagccaactttcactctggagaaaatatcagtgaaagggcttccatcacttactagatcttcttcttccttcaaagttgtggctagtggtgttaagaagcttaagactgacaaaccctatggaattaatggaagcatggccttgagagatggggttgatgcctcaggcaggaagcccaagggaaagggtgtgtaccaatatgttgacaaatatggagctaatgttgatggatacagtcccatctacaacacggatgaatggtctccaagtggtgatgtctatgttggaggtaccactgggctagccatatgggcggtgaccttgcttggcattcttgcaggaggtgctctccttgtctacaacacaagtgctttggcgcaatagatgttatccttgtattgtactattaagtttaagttgtattccatgttatcttttcaaaatatttcttggcatcttcattaatatgtaattgctgtgattntactgtggataatattacatctaatggtgctggtttaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="-" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="50651" stop="48554"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="50351" g_stop="50209" g_length="143"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="143" r_length="143" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="50208" i_stop="49597" i_length="612">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="49596" g_stop="49538" g_length="59"/>
          <reference_exon_boundary r_type="cDNA" r_start="144" r_stop="202" r_length="59" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="49537" i_stop="49382" i_length="156">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.980" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="49381" g_stop="49326" g_length="56"/>
          <reference_exon_boundary r_type="cDNA" r_start="203" r_stop="258" r_length="56" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="49325" i_stop="49250" i_length="76">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="49249" g_stop="49197" g_length="53"/>
          <reference_exon_boundary r_type="cDNA" r_start="259" r_stop="311" r_length="53" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="49196" i_stop="49086" i_length="111">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="49085" g_stop="48853" g_length="233"/>
          <reference_exon_boundary r_type="cDNA" r_start="312" r_stop="544" r_length="233" r_score="0.974"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="545" polyA_stop="554"/>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="-" ref_id="SGN-M1647" ref_strand="+">
        <total_alignment_score>0.989</total_alignment_score>
        <cumulative_length_of_scored_exons>544</cumulative_length_of_scored_exons>
        <coverage percentage="0.982" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1647" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="50351" e_stop="50209"/>
          <exon e_start="49596" e_stop="49538"/>
          <exon e_start="49381" e_stop="49326"/>
          <exon e_start="49249" e_stop="49197"/>
          <exon e_start="49085" e_stop="48853"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGTAATGAGCTCATTGAGCCTAAAGCCAACTTTCACTCTGGAGAAAATATCAGTGAAAGGGCTTCCATCACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATGGTATGTAATTAATAATCCAGTTTTAACTTATATACACCAACAATATTATTTGTCTAATTTGTCATGTCCCTTGTGATTTAGCTTTTAAGTTGTGACTTTATAATAGTATAGGAAATATTATATGTTGTCCGTGTATATATTCATCAAACTCTGCATATTTACTCATGACTTAATTGTATCATGTGGGTGCATTTTGGGGCTGTTGTTGTTAGTGAATTGTCTCATATTTGTCCTTGATGTTAATTAAGCTCTAGTTTAGATTGAGAGGAATTTAGGAGTAAAAAAGTTCAAATATGATTTAACCAATTAATTACCTGCTTCGGATTGGAGCTGTGTTAGGGTTAAGGGCTAACATCTGCTAAGTATAGTGGAGGCTAAAATTAGGATAATTGGTATAGAGAGTAGGTAGGTGTGTTTTTAATCCCTTTTCTCTCAAACTCTTTGATGAAAGCAGCTTGGTATACAAAGCATCCCATATTCGTAGGATTTGAGAAAGGGCCACAGCCTAAGAGATGTGATATAGACAATCTATCCTAATGCAAAACCAGAGATAGAATATTGTAATACAAAATTAATACTACCTGCTGATTATGAAGTGGATTTTGTTACTAGGAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAGGTTTGTTTCTACTTCTACCTTTGATAATATATAAGAATATCATTAATTAGTAGTAAAATAATTTTTTTCAAAATAAAAGAATGTGAATTATAGCAATTACTTTTCTCTGTGTGTATTTTAATTTCTAATATATGAGCAAAACATGGTGATGTTTAGGGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAGGTTAGTTAAATACTTGTTAGTTTGCACTAATATGAAACAATTAAAATCTTATACTTTGTGTGATTTTGAAATGCAGTCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAGGTATGATTGTTTTTTTTAACTCGAACTATGTATATATACTCAACAACGTTTATAATTAAGTCACTACTCATTTTGAATCTAGATCCTAAATCACATGTAATATGATTGCAGGTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGCTGTGATTTTACTGTGGATAATATTACATCTAATGTTGCTGTTTTAG</genome_strand>
        <mrna_strand>AGTAATGAGCTCATTGAGCCTAAAGCCAACTTTCACTCTGGAGAAAATATCAGTGAAAGGGCTTCCATCACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAG............................................................................................................................................................GGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAG............................................................................TCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAG...............................................................................................................GTACCACTGGGCTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGCTGTGATTNTACTGTGGATAATATTACATCTAATGGTGCTGGTTTAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M542-R" ref_strand="+" ref_description="SGN-M542-R CT223-R [rflp_markers_reverse]">
      <seq>cttccatcacttactagatcttcttcttccttcaaagttgtggctagtggtgttaagaagcttaagactgacaaaccctatggaattaatggaagcatggccttgagagatggggttgatgcctcaggcaggaagcccaagggaaagggtgtgtaccaatatgttgacaaatatggagctaatgttgatggatacagtcccatctacaacacggatgaatggtctccaagtggtgatgtctatgttggaggtaccactggcttagccatatgggcggtgaccttgcttggcattcttgcaggaggtgctctccttgtctacaacacaagtgctttggcgcaatagatgttatccttgtattgtactattaagtttaagttgtattccatgttatcttttcaaaatatttcttggcatcttcattaatatgtaattgctgtgattttactgtggataatattacatctaatgttgctgttttaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="-" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="50590" stop="48554"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="50290" g_stop="50209" g_length="82"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="82" r_length="82" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="50208" i_stop="49597" i_length="612">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="49596" g_stop="49538" g_length="59"/>
          <reference_exon_boundary r_type="cDNA" r_start="83" r_stop="141" r_length="59" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="49537" i_stop="49382" i_length="156">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.980" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="49381" g_stop="49326" g_length="56"/>
          <reference_exon_boundary r_type="cDNA" r_start="142" r_stop="197" r_length="56" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="49325" i_stop="49250" i_length="76">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="49249" g_stop="49197" g_length="53"/>
          <reference_exon_boundary r_type="cDNA" r_start="198" r_stop="250" r_length="53" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="49196" i_stop="49086" i_length="111">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="49085" g_stop="48853" g_length="233"/>
          <reference_exon_boundary r_type="cDNA" r_start="251" r_stop="483" r_length="233" r_score="0.996"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="484" polyA_stop="501"/>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="-" ref_id="SGN-M542-R" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>483</cumulative_length_of_scored_exons>
        <coverage percentage="0.964" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M542-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="50290" e_stop="50209"/>
          <exon e_start="49596" e_stop="49538"/>
          <exon e_start="49381" e_stop="49326"/>
          <exon e_start="49249" e_stop="49197"/>
          <exon e_start="49085" e_stop="48853"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTTCCATCACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATGGTATGTAATTAATAATCCAGTTTTAACTTATATACACCAACAATATTATTTGTCTAATTTGTCATGTCCCTTGTGATTTAGCTTTTAAGTTGTGACTTTATAATAGTATAGGAAATATTATATGTTGTCCGTGTATATATTCATCAAACTCTGCATATTTACTCATGACTTAATTGTATCATGTGGGTGCATTTTGGGGCTGTTGTTGTTAGTGAATTGTCTCATATTTGTCCTTGATGTTAATTAAGCTCTAGTTTAGATTGAGAGGAATTTAGGAGTAAAAAAGTTCAAATATGATTTAACCAATTAATTACCTGCTTCGGATTGGAGCTGTGTTAGGGTTAAGGGCTAACATCTGCTAAGTATAGTGGAGGCTAAAATTAGGATAATTGGTATAGAGAGTAGGTAGGTGTGTTTTTAATCCCTTTTCTCTCAAACTCTTTGATGAAAGCAGCTTGGTATACAAAGCATCCCATATTCGTAGGATTTGAGAAAGGGCCACAGCCTAAGAGATGTGATATAGACAATCTATCCTAATGCAAAACCAGAGATAGAATATTGTAATACAAAATTAATACTACCTGCTGATTATGAAGTGGATTTTGTTACTAGGAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAGGTTTGTTTCTACTTCTACCTTTGATAATATATAAGAATATCATTAATTAGTAGTAAAATAATTTTTTTCAAAATAAAAGAATGTGAATTATAGCAATTACTTTTCTCTGTGTGTATTTTAATTTCTAATATATGAGCAAAACATGGTGATGTTTAGGGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAGGTTAGTTAAATACTTGTTAGTTTGCACTAATATGAAACAATTAAAATCTTATACTTTGTGTGATTTTGAAATGCAGTCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAGGTATGATTGTTTTTTTTAACTCGAACTATGTATATATACTCAACAACGTTTATAATTAAGTCACTACTCATTTTGAATCTAGATCCTAAATCACATGTAATATGATTGCAGGTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGCTGTGATTTTACTGTGGATAATATTACATCTAATGTTGCTGTTTTAG</genome_strand>
        <mrna_strand>CTTCCATCACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAG............................................................................................................................................................GGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAG............................................................................TCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAG...............................................................................................................GTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGCTGTGATTTTACTGTGGATAATATTACATCTAATGTTGCTGTTTTAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M542-F" ref_strand="-" ref_description="SGN-M542-F CT223-F [rflp_markers_forward]">
      <seq>acttactagatcttcttcttccttcaaagttgtggctagtggtgttaagaagcttaagactgacaaaccctatggaattaatggaagcatgcccttgagagatggggttgatgcctcaggcaggaagcccaagggaaagggtgtgtaccaatatgttgacaaatatggagctaatgttgatggatacagtcccatctacaacacggatgaatggtctccaagtggtgatgtctatgttggaggtaccactggcttagccatatgggcggtgaccttgcttggcattcttgcaggaggtgctctccttgtctacaacacaagtgctttggcgcaatagatgttatccttgtattgtactattaagtttaagttgtattccatgttatcttttcaaaatatttcttggcatcttcattaatatgtaattgctgtgattttactgtggataatattacatctaatgttgctgttttaaaaaaaaaaaaaaaaaaaaaaaaag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="-" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="50582" stop="48554"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="50282" g_stop="50209" g_length="74"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="74" r_length="74" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="50208" i_stop="49597" i_length="612">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="49596" g_stop="49538" g_length="59"/>
          <reference_exon_boundary r_type="cDNA" r_start="75" r_stop="133" r_length="59" r_score="0.983"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="49537" i_stop="49382" i_length="156">
            <donor d_prob="1.000" d_score="0.98"/>
            <acceptor a_prob="0.980" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="49381" g_stop="49326" g_length="56"/>
          <reference_exon_boundary r_type="cDNA" r_start="134" r_stop="189" r_length="56" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="49325" i_stop="49250" i_length="76">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="49249" g_stop="49197" g_length="53"/>
          <reference_exon_boundary r_type="cDNA" r_start="190" r_stop="242" r_length="53" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="49196" i_stop="49086" i_length="111">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="49085" g_stop="48853" g_length="233"/>
          <reference_exon_boundary r_type="cDNA" r_start="243" r_stop="475" r_length="233" r_score="0.996"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="476" polyA_stop="499"/>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="-" ref_id="SGN-M542-F" ref_strand="-">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>475</cumulative_length_of_scored_exons>
        <coverage percentage="0.952" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M542-F" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="50282" e_stop="50209"/>
          <exon e_start="49596" e_stop="49538"/>
          <exon e_start="49381" e_stop="49326"/>
          <exon e_start="49249" e_stop="49197"/>
          <exon e_start="49085" e_stop="48853"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATGGTATGTAATTAATAATCCAGTTTTAACTTATATACACCAACAATATTATTTGTCTAATTTGTCATGTCCCTTGTGATTTAGCTTTTAAGTTGTGACTTTATAATAGTATAGGAAATATTATATGTTGTCCGTGTATATATTCATCAAACTCTGCATATTTACTCATGACTTAATTGTATCATGTGGGTGCATTTTGGGGCTGTTGTTGTTAGTGAATTGTCTCATATTTGTCCTTGATGTTAATTAAGCTCTAGTTTAGATTGAGAGGAATTTAGGAGTAAAAAAGTTCAAATATGATTTAACCAATTAATTACCTGCTTCGGATTGGAGCTGTGTTAGGGTTAAGGGCTAACATCTGCTAAGTATAGTGGAGGCTAAAATTAGGATAATTGGTATAGAGAGTAGGTAGGTGTGTTTTTAATCCCTTTTCTCTCAAACTCTTTGATGAAAGCAGCTTGGTATACAAAGCATCCCATATTCGTAGGATTTGAGAAAGGGCCACAGCCTAAGAGATGTGATATAGACAATCTATCCTAATGCAAAACCAGAGATAGAATATTGTAATACAAAATTAATACTACCTGCTGATTATGAAGTGGATTTTGTTACTAGGAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAGGTTTGTTTCTACTTCTACCTTTGATAATATATAAGAATATCATTAATTAGTAGTAAAATAATTTTTTTCAAAATAAAAGAATGTGAATTATAGCAATTACTTTTCTCTGTGTGTATTTTAATTTCTAATATATGAGCAAAACATGGTGATGTTTAGGGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAGGTTAGTTAAATACTTGTTAGTTTGCACTAATATGAAACAATTAAAATCTTATACTTTGTGTGATTTTGAAATGCAGTCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAGGTATGATTGTTTTTTTTAACTCGAACTATGTATATATACTCAACAACGTTTATAATTAAGTCACTACTCATTTTGAATCTAGATCCTAAATCACATGTAATATGATTGCAGGTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGCTGTGATTTTACTGTGGATAATATTACATCTAATGTTGCTGTTTTAG</genome_strand>
        <mrna_strand>ACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAATTAATGGAAGCATGCCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAG............................................................................................................................................................GGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAG............................................................................TCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAG...............................................................................................................GTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGCTGTGATTTTACTGTGGATAATATTACATCTAATGTTGCTGTTTTAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M403-F" ref_strand="+" ref_description="SGN-M403-F CD61-F [rflp_markers_forward]">
      <seq>ctgcagggggggggggggataggagaaaatggcaagcacagtaatgagctcattgagcctaaagccaactttcactctggagaaaatatcagtgaaagggcttccatcacttactagatcttcttcttccttcaaagttgtggctagtggtgttaagaagcttaagactgacaaaccctatggaattaatggaagcatggccttgagagatggggttgatgcctcaggcaggaagcccaagggaaagggtgtgtaccaatatgttgacaaatatggagctaatgttgatggatacagtcccatctacaacacggatgaatggtctccaagtggtgatgtctatgttggaggtaccactggcttagccatatgggcggtgaccttgcttggcattcttgcaggaggtgctctccttgtctacaacacaagtgctttgggcgcatagatgttatccttgtattgtactattaagtttaagttgtattccatgttatctttttcaaatatttcttggcatcttcattaatatgtaattgc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="-" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="50676" stop="48599"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="50375" g_stop="50209" g_length="167"/>
          <reference_exon_boundary r_type="cDNA" r_start="16" r_stop="182" r_length="167" r_score="0.988"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="50208" i_stop="49597" i_length="612">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="49596" g_stop="49538" g_length="59"/>
          <reference_exon_boundary r_type="cDNA" r_start="183" r_stop="241" r_length="59" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="49537" i_stop="49382" i_length="156">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.980" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="49381" g_stop="49326" g_length="56"/>
          <reference_exon_boundary r_type="cDNA" r_start="242" r_stop="297" r_length="56" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="49325" i_stop="49250" i_length="76">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="49249" g_stop="49197" g_length="53"/>
          <reference_exon_boundary r_type="cDNA" r_start="298" r_stop="350" r_length="53" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="49196" i_stop="49086" i_length="111">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="49085" g_stop="48899" g_length="187"/>
          <reference_exon_boundary r_type="cDNA" r_start="351" r_stop="537" r_length="187" r_score="0.973"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="-" ref_id="SGN-M403-F" ref_strand="+">
        <total_alignment_score>0.987</total_alignment_score>
        <cumulative_length_of_scored_exons>522</cumulative_length_of_scored_exons>
        <coverage percentage="0.972" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M403-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="50375" e_stop="50209"/>
          <exon e_start="49596" e_stop="49538"/>
          <exon e_start="49381" e_stop="49326"/>
          <exon e_start="49249" e_stop="49197"/>
          <exon e_start="49085" e_stop="48899"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTAATAGGAGAAAATGGCAAGCACAGTAATGAGCTCATTGAGCCTAAAGCCAACTTTCACTCTGGAGAAAATATCAGTGAAAGGGCTTCCATCACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATGGTATGTAATTAATAATCCAGTTTTAACTTATATACACCAACAATATTATTTGTCTAATTTGTCATGTCCCTTGTGATTTAGCTTTTAAGTTGTGACTTTATAATAGTATAGGAAATATTATATGTTGTCCGTGTATATATTCATCAAACTCTGCATATTTACTCATGACTTAATTGTATCATGTGGGTGCATTTTGGGGCTGTTGTTGTTAGTGAATTGTCTCATATTTGTCCTTGATGTTAATTAAGCTCTAGTTTAGATTGAGAGGAATTTAGGAGTAAAAAAGTTCAAATATGATTTAACCAATTAATTACCTGCTTCGGATTGGAGCTGTGTTAGGGTTAAGGGCTAACATCTGCTAAGTATAGTGGAGGCTAAAATTAGGATAATTGGTATAGAGAGTAGGTAGGTGTGTTTTTAATCCCTTTTCTCTCAAACTCTTTGATGAAAGCAGCTTGGTATACAAAGCATCCCATATTCGTAGGATTTGAGAAAGGGCCACAGCCTAAGAGATGTGATATAGACAATCTATCCTAATGCAAAACCAGAGATAGAATATTGTAATACAAAATTAATACTACCTGCTGATTATGAAGTGGATTTTGTTACTAGGAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAGGTTTGTTTCTACTTCTACCTTTGATAATATATAAGAATATCATTAATTAGTAGTAAAATAATTTTTTTCAAAATAAAAGAATGTGAATTATAGCAATTACTTTTCTCTGTGTGTATTTTAATTTCTAATATATGAGCAAAACATGGTGATGTTTAGGGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAGGTTAGTTAAATACTTGTTAGTTTGCACTAATATGAAACAATTAAAATCTTATACTTTGTGTGATTTTGAAATGCAGTCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAGGTATGATTGTTTTTTTTAACTCGAACTATGTATATATACTCAACAACGTTTATAATTAAGTCACTACTCATTTTGAATCTAGATCCTAAATCACATGTAATATGATTGCAGGTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTT-GGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGC</genome_strand>
        <mrna_strand>GGGATAGGAGAAAATGGCAAGCACAGTAATGAGCTCATTGAGCCTAAAGCCAACTTTCACTCTGGAGAAAATATCAGTGAAAGGGCTTCCATCACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAG............................................................................................................................................................GGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAG............................................................................TCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAG...............................................................................................................GTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGGCGC-ATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTTCAAATATTTCTTGGCATCTTCATTAATATGTAATTGC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M9190" ref_strand="+" ref_description="SGN-M9190 C2_At5g64150 [cosii_markers]">
      <seq>aatgaagttgagcttcattcgaccaatttcatgttgctctgtttcatctccagcaacctcagtgaaacctcaaaaacctatatttttaaggccacccaccttcaaaacaaccatatcagaccttcaaaaatggcatcattgggctaaatccctaatttcttctgtgggttccactttcttggaactggacaatggtccagactccgaattgttgctcagggagctaaattggcttgttgaagatgcaattgaaacaccaaaatctttcttgcaacaaccccacaaaaattacaatgataatagctcagttgcagttcgggcgtctttggaacaactgtatatgttgtggaaacgaagggtagaagaaagaatgccatttcagtatgtggttggctgtgaacattggagggatttggttttgagtgttcaagaaggggttttgattccaaggccagagactgagctgattgtggaccttgtcgatgatgctattaaggagaatggggaattgagggaaggattgtgggctgatttggggactggaagtggtgcacttgctattgggattgcaaggattttgggtacttctggtagagttgttgctactgatttaagccctgttgctactgcagttgcatcttataatgtgcagaggtatgatttggaggaaaaagtgcatgtaaagcaaggatcttggtttgaacctttgagagataatgaaggagaatttgtgggactggtcagtaatccaccatatattccaagcaaagatattggtggactacaagctgaagttggcagacatgaacctagactggcgttagacggtggagcaagtggta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="-" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="81070" stop="78947"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="80770" g_stop="80104" g_length="667"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="667" r_length="667" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="80103" i_stop="79422" i_length="682">
            <donor d_prob="0.981" d_score="1.00"/>
            <acceptor a_prob="0.772" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="79421" g_stop="79247" g_length="175"/>
          <reference_exon_boundary r_type="cDNA" r_start="668" r_stop="842" r_length="175" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="-" ref_id="SGN-M9190" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>842</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M9190" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="80770" e_stop="80104"/>
          <exon e_start="79421" e_stop="79247"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AATGAAGTTGAGCTTCATTCGACCAATTTCATGTTGCTCTGTTTCATCTCCAGCAACCTCAGTGAAACCTCAAAAACCTATATTTTTAAGGCCACCCACCTTCAAAACAACCATATCAGACCTTCAAAAATGGCATCATTGGGCTAAATCCCTAATTTCTTCTGTGGGTTCCACTTTCTTGGAACTGGACAATGGTCCAGACTCCGAATTGTTGCTCAGGGAGCTAAATTGGCTTGTTGAAGATGCAATTGAAACACCAAAATCTTTCTTGCAACAACCCCACAAAAATTACAATGATAATAGCTCAGTTGCAGTTCGGGCGTCTTTGGAACAACTGTATATGTTGTGGAAACGAAGGGTAGAAGAAAGAATGCCATTTCAGTATGTGGTTGGCTGTGAACATTGGAGGGATTTGGTTTTGAGTGTTCAAGAAGGGGTTTTGATTCCAAGGCCAGAGACTGAGCTGATTGTGGACCTTGTCGATGATGCTATTAAGGAGAATGGGGAATTGAGGGAAGGATTGTGGGCTGATTTGGGGACTGGAAGTGGTGCACTTGCTATTGGGATTGCAAGGATTTTGGGTACTTCTGGTAGAGTTGTTGCTACTGATTTAAGCCCTGTTGCTACTGCAGTTGCATCTTATAATGTGCAGAGGTATGATTTGGAGGTTAGTATATTTTGCAATTTGCTTGTTGCTCCTAGTATGGTTTGAAATGAGCTTAAATGAAAGCAGGATTATATAGTCGACCCCAACTTGTTTGGGACCGAGGCGTAGTTGTTGCTCTTAGTATGGTTTAAATGAGCCTTAAATGAAGGCAGGGATTCATATATTGGACCCCAACTTGTTTTGGACTGAGGCGTAGTTGTTGTTGCTCTTAGTATGGTTTGAAATGAGCTTAAATGAAAACGGGGATTCATATAGCTGACCCCAACTTGTTTGGGACTGAGGCATGGTCGTTACTTGTTGCTCTTAGTATGGTTTGATGAGCTTAAAAGAAGGCAGTGATTCATAGAGCTGAACCCAACTTGTTTGGGACTGAGGCATAGTTGTGGTTACTTGTTGCCCTTAGTAAGGTTCCTCTTTGAGATTTTACTTCTGTGTCACTGTATTTTCATAGTTGATTGTCTCAAGCTAGTTGATCTTTAAAGCTAACTGCTATAGTTGTAGAATTGACTAGTTTAGCAAAAGCTTTGATTCTTAAATATTTTTGGCTGAAGAAAAATGGGAACTTGATCAGAAATCAGAATTTTATACATTGTTATAGAATTAGTGAAATAGAGTTTAATCATTGATTAAACTTTCAGGGCTGCAAATTTTGAATAGAGCATTGTCTTGAATTTTGTGCTAGGAAAAAGTGCATGTAAAGCAAGGATCTTGGTTTGAACCTTTGAGAGATAATGAAGGAGAATTTGTGGGACTGGTCAGTAATCCACCATATATTCCAAGCAAAGATATTGGTGGACTACAAGCTGAAGTTGGCAGACATGAACCTAGACTGGCGTTAGACGGTGGAGCAAGTGGTA</genome_strand>
        <mrna_strand>AATGAAGTTGAGCTTCATTCGACCAATTTCATGTTGCTCTGTTTCATCTCCAGCAACCTCAGTGAAACCTCAAAAACCTATATTTTTAAGGCCACCCACCTTCAAAACAACCATATCAGACCTTCAAAAATGGCATCATTGGGCTAAATCCCTAATTTCTTCTGTGGGTTCCACTTTCTTGGAACTGGACAATGGTCCAGACTCCGAATTGTTGCTCAGGGAGCTAAATTGGCTTGTTGAAGATGCAATTGAAACACCAAAATCTTTCTTGCAACAACCCCACAAAAATTACAATGATAATAGCTCAGTTGCAGTTCGGGCGTCTTTGGAACAACTGTATATGTTGTGGAAACGAAGGGTAGAAGAAAGAATGCCATTTCAGTATGTGGTTGGCTGTGAACATTGGAGGGATTTGGTTTTGAGTGTTCAAGAAGGGGTTTTGATTCCAAGGCCAGAGACTGAGCTGATTGTGGACCTTGTCGATGATGCTATTAAGGAGAATGGGGAATTGAGGGAAGGATTGTGGGCTGATTTGGGGACTGGAAGTGGTGCACTTGCTATTGGGATTGCAAGGATTTTGGGTACTTCTGGTAGAGTTGTTGCTACTGATTTAAGCCCTGTTGCTACTGCAGTTGCATCTTATAATGTGCAGAGGTATGATTTGGAG..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAAAAAGTGCATGTAAAGCAAGGATCTTGGTTTGAACCTTTGAGAGATAATGAAGGAGAATTTGTGGGACTGGTCAGTAATCCACCATATATTCCAAGCAAAGATATTGGTGGACTACAAGCTGAAGTTGGCAGACATGAACCTAGACTGGCGTTAGACGGTGGAGCAAGTGGTA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/cxgn-bacpublish-resources-rLT1KL/sgn_marker_seqs" ref_id="SGN-M9190-2" ref_strand="+" ref_description="SGN-M9190-2 C2_At5g64150-2 [cosii_markers]">
      <seq>gcgatttgcgagagattttgaagaaatgaggctaagcttcattcgacccatttcatgttgctctgtttcatctccagctacctcactgaaacttcaaaaaccgctctttttaaggccacccaccttcaaagcaaccatatcagacctcaaaaaatggcacctttgggctaaatccctaacttcttctgtgggttccactttcttggaactggacaatggtccagactccgaattgttgctcagagagctaaattggcttgttgaagatgcaattcaaacacccaaatcgttcttgcaacaaccccaaaaaaattacaatgataatagctctgtttcaattcgggcgtctttggaagaactatatatgttgtggaaacaaagggtagaagaaagaaggccatttcagtatgtggttggttgtgaacattggagggatttggttttgagtgttcaagaaggggttttgattccaaggccagagactgagctgattgtggaccttgtggatgatgctattaaggagaatgaggagttgagggaaggattgtgggctgatttggggactggaagtggtgcacttgctattgggattgcaaggattttgggtagttctggtagagttgttgctactgatttaagccctgttgctactgcagttgcatcttataatg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0179K09-XmROT/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07HBa0179K09.1" temp_strand="-" temp_description="C07HBa0179K09.1  htgs_phase:2 submitted_to_sgn_as:C07HBa0197K09,complete upload_account_name:france sequence">
        <position start="81094" stop="79824"/>
      </template>
    </gDNA_segment>
    <predicted_gene_structure xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
      <exon-intron_info>
        <exon e_serial="1">
          <gDNA_exon_boundary g_start="80794" g_stop="80124" g_length="671"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="671" r_length="671" r_score="0.934"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0179K09.1" gen_strand="-" ref_id="SGN-M9190-2" ref_strand="+">
        <total_alignment_score>0.934</total_alignment_score>
        <cumulative_length_of_scored_exons>671</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0179K09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M9190-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="80794" e_stop="80124"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAGACCTGCCTGTG-TGTCGAAGAAAATGAAGTTGAGCTTCATTCGACCAATTTCATGTTGCTCTGTTTCATCTCCAGCAACCTCAGTGAAACCTCAAAAACCTATATTTTTAAGGCCACCCACCTTCAAAACAACCATATCAGACCTTCAAAAATGGCATCATTGGGCTAAATCCCTAATTTCTTCTGTGGGTTCCACTTTCTTGGAACTGGACAATGGTCCAGACTCCGAATTGTTGCTCAGGGAGCTAAATTGGCTTGTTGAAGATGCAATTGAAACACCAAAATCTTTCTTGCAACAACCCCACAAAAATTACAATGATAATAGCTCAGTTGCAGTTCGGGCGTCTTTGGAACAACTGTATATGTTGTGGAAACGAAGGGTAGAAGAAAGAATGCCATTTCAGTATGTGGTTGGCTGTGAACATTGGAGGGATTTGGTTTTGAGTGTTCAAGAAGGGGTTTTGATTCCAAGGCCAGAGACTGAGCTGATTGTGGACCTTGTCGATGATGCTATTAAGGAGAATGGGGAATTGAGGGAAGGATTGTGGGCTGATTTGGGGACTGGAAGTGGTGCACTTGCTATTGGGATTGCAAGGATTTTGGGTACTTCTGGTAGAGTTGTTGCTACTGATTTAAGCCCTGTTGCTACTGCAGTTGCATCTTATAATG</genome_strand>
        <mrna_strand>GCGATTTGCGAGAGATTTTGAAG-AAATGAGGCTAAGCTTCATTCGACCCATTTCATGTTGCTCTGTTTCATCTCCAGCTACCTCACTGAAACTTCAAAAACCGCTCTTTTTAAGGCCACCCACCTTCAAAGCAACCATATCAGACCTCAAAAAATGGCACCTTTGGGCTAAATCCCTAACTTCTTCTGTGGGTTCCACTTTCTTGGAACTGGACAATGGTCCAGACTCCGAATTGTTGCTCAGAGAGCTAAATTGGCTTGTTGAAGATGCAATTCAAACACCCAAATCGTTCTTGCAACAACCCCAAAAAAATTACAATGATAATAGCTCTGTTTCAATTCGGGCGTCTTTGGAAGAACTATATATGTTGTGGAAACAAAGGGTAGAAGAAAGAAGGCCATTTCAGTATGTGGTTGGTTGTGAACATTGGAGGGATTTGGTTTTGAGTGTTCAAGAAGGGGTTTTGATTCCAAGGCCAGAGACTGAGCTGATTGTGGACCTTGTGGATGATGCTATTAAGGAGAATGAGGAGTTGAGGGAAGGATTGTGGGCTGATTTGGGGACTGGAAGTGGTGCACTTGCTATTGGGATTGCAAGGATTTTGGGTAGTTCTGGTAGAGTTGTTGCTACTGATTTAAGCCCTGTTGCTACTGCAGTTGCATCTTATAATG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>9</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="+" PGL_start="43916" PGL_stop="45761"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="43916" e_stop="44259"/>
            <exon e_start="44361" e_stop="44452"/>
            <exon e_start="44648" e_stop="44723"/>
            <exon e_start="45069" e_stop="45131"/>
            <exon e_start="45445" e_stop="45574"/>
            <exon e_start="45701" e_stop="45761"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.970" e_score="0.985"/>
          <exon-intron don_prob="0.991" acc_prob="0.987" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.850" acc_prob="0.987" e_score="1.000"/>
          <exon-intron don_prob="0.977" acc_prob="0.835" e_score="0.977"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.985">
            <gDNA_exon_boundary e_start="43916" e_stop="44259" e_length="344"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.970">
            <gDNA_intron_boundary i_start="44260" i_stop="44360" i_length="101"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="44361" e_stop="44452" e_length="92"/>
          </exon>
          <intron i_serial="2" don_prob="0.991" acc_prob="0.987">
            <gDNA_intron_boundary i_start="44453" i_stop="44647" i_length="195"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="44648" e_stop="44723" e_length="76"/>
          </exon>
          <intron i_serial="3" don_prob="1.000" acc_prob="0.999">
            <gDNA_intron_boundary i_start="44724" i_stop="45068" i_length="345"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="45069" e_stop="45131" e_length="63"/>
          </exon>
          <intron i_serial="4" don_prob="0.850" acc_prob="0.987">
            <gDNA_intron_boundary i_start="45132" i_stop="45444" i_length="313"/>
          </intron>
          <exon e_serial="5" e_score="0.977">
            <gDNA_exon_boundary e_start="45445" e_stop="45574" e_length="130"/>
          </exon>
          <intron i_serial="5" don_prob="0.977" acc_prob="0.835">
            <gDNA_intron_boundary i_start="45575" i_stop="45700" i_length="126"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="45701" e_stop="45761" e_length="61"/>
          </exon>
        </exon-intron_info>
        <supporting_evidence xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/supporting_evidence/">
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="43916" stop="44259"/>
              <exon start="44361" stop="44452"/>
              <exon start="44648" stop="44723"/>
              <exon start="45069" stop="45131"/>
              <exon start="45445" stop="45574"/>
              <exon start="45701" stop="45761"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7104" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="43934" stop="44259"/>
              <exon start="44361" stop="44452"/>
              <exon start="44648" stop="44723"/>
              <exon start="45069" stop="45131"/>
              <exon start="45445" stop="45510"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1936" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="43962" stop="44259"/>
              <exon start="44361" stop="44452"/>
              <exon start="44648" stop="44723"/>
              <exon start="45069" stop="45131"/>
              <exon start="45445" stop="45483"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7104-2" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="1" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>ATGGCGCCATGGAACTCCGGCGACAGCATAGCCTAAGCTCCTTCTTCAGCAAGGAGAACTGAGCTTAAGTATAGTAATATCTTTCAATCCGCTTGAACTTTGTAGTCCAAGAGAACGGAGCTTTTAAGCTAGAAACTTTAATGGAGTTAACTTTCCCAGTGAAAGCTCAGTTATTTGGCTCCAAAATTGGTCACAAATCTCTAAGCTACTCAACTTCAGTAAAATTCTACCAGAAAGTATCTCGTCCTCAATTTTCAGCATGTGGAATCAGGGTTCGTTCGGAATTTGACCATAAAATCAATGGCGCTTTCTCTCCTGATTCTGACGCTCGGATTCTCGACCGG : CAAAAAGCATTGGATGCTGCAATGAACGATATAAACAGCTCGTTTGGCAAAGGAAGCGTTACTAGATTGGGTAGTGCTGGCGGAGCTCTGGT : TGAAACTTTTCCGAGTGGCTGCTTGACGCTAGACTTTGCTTTAGGTGGTGGCATTCCCAAAGGCAGAATTGTTGAG : ATATATGGGCCCGAAAGTAGTGGAAAGACTACCTTAGCTCTCCATGCTATTGCAGAAGTACAG : AAGCTAGGAGGCAATGCAATGCTTGTTGATGCTGAGCATGCTTTTGATCCTGCATACTCCAAAGCACTTGGAGTAGATGTAGAGAATTTGATCGTCTGCCAGCCTGATAATGGAGAGATGGCTCTAGAAA : TCGCAGACCGGATGTGTAGATCAGGTGCCGTAGATCTCATTTGCATTGATTCAGTCTCAGC</gDNA_template>
            <first_frame> M  A  P  W  N  S  G  D  S  I  A  *  A  P  S  S  A  R  R  T  E  L  K  Y  S  N  I  F  Q  S  A  *  T  L  *  S  K  R  T  E  L  L  S  *  K  L  *  W  S  *  L  S  Q  *  K  L  S  Y  L  A  P  K  L  V  T  N  L  *  A  T  Q  L  Q  *  N  S  T  R  K  Y  L  V  L  N  F  Q  H  V  E  S  G  F  V  R  N  L  T  I  K  S  M  A  L  S  L  L  I  L  T  L  G  F  S  T  G :   K  K  H  W  M  L  Q  *  T  I  *  T  A  R  L  A  K  E  A  L  L  D  W  V  V  L  A  E  L  W   : L  K  L  F  R  V  A  A  *  R  *  T  L  L  *  V  V  A  F  P  K  A  E  L  L  R :   Y  M  G  P  K  V  V  E  R  L  P  *  L  S  M  L  L  Q  K  Y  R :   S  *  E  A  M  Q  C  L  L  M  L  S  M  L  L  I  L  H  T  P  K  H  L  E  *  M  *  R  I  *  S  S  A  S  L  I  M  E  R  W  L  *  K  :  S  Q  T  G  C  V  D  Q  V  P  *  I  S  F  A  L  I  Q  S  Q  </first_frame>
            <second_frame>  W  R  H  G  T  P  A  T  A  *  P  K  L  L  L  Q  Q  G  E  L  S  L  S  I  V  I  S  F  N  P  L  E  L  C  S  P  R  E  R  S  F  *  A  R  N  F  N  G  V  N  F  P  S  E  S  S  V  I  W  L  Q  N  W  S  Q  I  S  K  L  L  N  F  S  K  I  L  P  E  S  I  S  S  S  I  F  S  M  W  N  Q  G  S  F  G  I  *  P  *  N  Q  W  R  F  L  S  *  F  *  R  S  D  S  R  P   : A  K  S  I  G  C  C  N  E  R  Y  K  Q  L  V  W  Q  R  K  R  Y  *  I  G  *  C  W  R  S  S  G  :  *  N  F  S  E  W  L  L  D  A  R  L  C  F  R  W  W  H  S  Q  R  Q  N  C  *   : D  I  W  A  R  K  *  W  K  D  Y  L  S  S  P  C  Y  C  R  S  T   : E  A  R  R  Q  C  N  A  C  *  C  *  A  C  F  *  S  C  I  L  Q  S  T  W  S  R  C  R  E  F  D  R  L  P  A  *  *  W  R  D  G  S  R  N :   R  R  P  D  V  *  I  R  C  R  R  S  H  L  H  *  F  S  L  S </second_frame>
            <third_frame>   G  A  M  E  L  R  R  Q  H  S  L  S  S  F  F  S  K  E  N  *  A  *  V  *  *  Y  L  S  I  R  L  N  F  V  V  Q  E  N  G  A  F  K  L  E  T  L  M  E  L  T  F  P  V  K  A  Q  L  F  G  S  K  I  G  H  K  S  L  S  Y  S  T  S  V  K  F  Y  Q  K  V  S  R  P  Q  F  S  A  C  G  I  R  V  R  S  E  F  D  H  K  I  N  G  A  F  S  P  D  S  D  A  R  I  L  D  R  :  Q  K  A  L  D  A  A  M  N  D  I  N  S  S  F  G  K  G  S  V  T  R  L  G  S  A  G  G  A  L  V :   E  T  F  P  S  G  C  L  T  L  D  F  A  L  G  G  G  I  P  K  G  R  I  V  E  :  I  Y  G  P  E  S  S  G  K  T  T  L  A  L  H  A  I  A  E  V  Q  :  K  L  G  G  N  A  M  L  V  D  A  E  H  A  F  D  P  A  Y  S  K  A  L  G  V  D  V  E  N  L  I  V  C  Q  P  D  N  G  E  M  A  L  E   : I  A  D  R  M  C  R  S  G  A  V  D  L  I  C  I  D  S  V  S   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0179K09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="43993" stop="44259"/>
                    <exon start="44361" stop="44452"/>
                    <exon start="44648" stop="44723"/>
                    <exon start="45069" stop="45131"/>
                    <exon start="45445" stop="45574"/>
                    <exon start="45701" stop="45759"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>687</number_coding_nucleotides>
                  <number_encoded_amino_acids>229</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>YLSIRLNFVVQENGAFKLETLMELTFPVKAQLFGSKIGHKSLSYSTSVKFYQKVSRPQFSACGIRVRSEFDHKINGAFSPDSDARILDRQKALDAAMNDINSSFGKGSVTRLGSAGGALVETFPSGCLTLDFALGGGIPKGRIVEIYGPESSGKTTLALHAIAEVQKLGGNAMLVDAEHAFDPAYSKALGVDVENLIVCQPDNGEMALEIADRMCRSGAVDLICIDSVS</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="50375" PGL_stop="48853"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="50375" e_stop="50209"/>
            <exon e_start="49596" e_stop="49538"/>
            <exon e_start="49381" e_stop="49326"/>
            <exon e_start="49249" e_stop="49197"/>
            <exon e_start="49085" e_stop="48853"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.996" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.980" e_score="1.000"/>
          <exon-intron don_prob="0.991" acc_prob="0.998" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.998" e_score="1.000"/>
          <exon-only e_score="0.996"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="50375" e_stop="50209" e_length="167"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.996">
            <gDNA_intron_boundary i_start="50208" i_stop="49597" i_length="612"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="49596" e_stop="49538" e_length="59"/>
          </exon>
          <intron i_serial="2" don_prob="1.000" acc_prob="0.980">
            <gDNA_intron_boundary i_start="49537" i_stop="49382" i_length="156"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="49381" e_stop="49326" e_length="56"/>
          </exon>
          <intron i_serial="3" don_prob="0.991" acc_prob="0.998">
            <gDNA_intron_boundary i_start="49325" i_stop="49250" i_length="76"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="49249" e_stop="49197" e_length="53"/>
          </exon>
          <intron i_serial="4" don_prob="0.998" acc_prob="0.998">
            <gDNA_intron_boundary i_start="49196" i_stop="49086" i_length="111"/>
          </intron>
          <exon e_serial="5" e_score="0.996">
            <gDNA_exon_boundary e_start="49085" e_stop="48853" e_length="233"/>
          </exon>
        </exon-intron_info>
        <supporting_evidence xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/supporting_evidence/">
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="50375" stop="50209"/>
              <exon start="49596" stop="49538"/>
              <exon start="49381" stop="49326"/>
              <exon start="49249" stop="49197"/>
              <exon start="49085" stop="48899"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M403-F" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="50351" stop="50209"/>
              <exon start="49596" stop="49538"/>
              <exon start="49381" stop="49326"/>
              <exon start="49249" stop="49197"/>
              <exon start="49085" stop="48853"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1647" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="50290" stop="50209"/>
              <exon start="49596" stop="49538"/>
              <exon start="49381" stop="49326"/>
              <exon start="49249" stop="49197"/>
              <exon start="49085" stop="48853"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M542-R" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="50282" stop="50209"/>
              <exon start="49596" stop="49538"/>
              <exon start="49381" stop="49326"/>
              <exon start="49249" stop="49197"/>
              <exon start="49085" stop="48853"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M542-F" strand="-"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="2" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>GTAATAGGAGAAAATGGCAAGCACAGTAATGAGCTCATTGAGCCTAAAGCCAACTTTCACTCTGGAGAAAATATCAGTGAAAGGGCTTCCATCACTTACTAGATCTTCTTCTTCCTTCAAAGTTGTGGCTAGTGGTGTTAAGAAGCTTAAGACTGACAAACCCTATG : GAATTAATGGAAGCATGGCCTTGAGAGATGGGGTTGATGCCTCAGGCAGGAAGCCCAAG : GGAAAGGGTGTGTACCAATATGTTGACAAATATGGAGCTAATGTTGATGGATACAG : TCCCATCTACAACACGGATGAATGGTCTCCAAGTGGTGATGTCTATGTTGGAG : GTACCACTGGCTTAGCCATATGGGCGGTGACCTTGCTTGGCATTCTTGCAGGAGGTGCTCTCCTTGTCTACAACACAAGTGCTTTGGCGCAATAGATGTTATCCTTGTATTGTACTATTAAGTTTAAGTTGTATTCCATGTTATCTTTTCAAAATATTTCTTGGCATCTTCATTAATATGTAATTGCTGTGATTTTACTGTGGATAATATTACATCTAATGTTGCTGTTTTAG</gDNA_template>
            <first_frame> V  I  G  E  N  G  K  H  S  N  E  L  I  E  P  K  A  N  F  H  S  G  E  N  I  S  E  R  A  S  I  T  Y  *  I  F  F  F  L  Q  S  C  G  *  W  C  *  E  A  *  D  *  Q  T  L  W :   N  *  W  K  H  G  L  E  R  W  G  *  C  L  R  Q  E  A  Q   : G  K  G  C  V  P  I  C  *  Q  I  W  S  *  C  *  W  I  Q  :  S  H  L  Q  H  G  *  M  V  S  K  W  *  C  L  C  W  R :   Y  H  W  L  S  H  M  G  G  D  L  A  W  H  S  C  R  R  C  S  P  C  L  Q  H  K  C  F  G  A  I  D  V  I  L  V  L  Y  Y  *  V  *  V  V  F  H  V  I  F  S  K  Y  F  L  A  S  S  L  I  C  N  C  C  D  F  T  V  D  N  I  T  S  N  V  A  V  L  </first_frame>
            <second_frame>  *  *  E  K  M  A  S  T  V  M  S  S  L  S  L  K  P  T  F  T  L  E  K  I  S  V  K  G  L  P  S  L  T  R  S  S  S  S  F  K  V  V  A  S  G  V  K  K  L  K  T  D  K  P  Y   : G  I  N  G  S  M  A  L  R  D  G  V  D  A  S  G  R  K  P  K  :  G  K  G  V  Y  Q  Y  V  D  K  Y  G  A  N  V  D  G  Y  S :   P  I  Y  N  T  D  E  W  S  P  S  G  D  V  Y  V  G   : G  T  T  G  L  A  I  W  A  V  T  L  L  G  I  L  A  G  G  A  L  L  V  Y  N  T  S  A  L  A  Q  *  M  L  S  L  Y  C  T  I  K  F  K  L  Y  S  M  L  S  F  Q  N  I  S  W  H  L  H  *  Y  V  I  A  V  I  L  L  W  I  I  L  H  L  M  L  L  F  * </second_frame>
            <third_frame>   N  R  R  K  W  Q  A  Q  *  *  A  H  *  A  *  S  Q  L  S  L  W  R  K  Y  Q  *  K  G  F  H  H  L  L  D  L  L  L  P  S  K  L  W  L  V  V  L  R  S  L  R  L  T  N  P  M  :  E  L  M  E  A  W  P  *  E  M  G  L  M  P  Q  A  G  S  P  R :   E  R  V  C  T  N  M  L  T  N  M  E  L  M  L  M  D  T   : V  P  S  T  T  R  M  N  G  L  Q  V  V  M  S  M  L  E  :  V  P  L  A  *  P  Y  G  R  *  P  C  L  A  F  L  Q  E  V  L  S  L  S  T  T  Q  V  L  W  R  N  R  C  Y  P  C  I  V  L  L  S  L  S  C  I  P  C  Y  L  F  K  I  F  L  G  I  F  I  N  M  *  L  L  *  F  Y  C  G  *  Y  Y  I  *  C  C  C  F   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0179K09.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="50368" stop="50209"/>
                    <exon start="49596" stop="49538"/>
                    <exon start="49381" stop="49326"/>
                    <exon start="49249" stop="49197"/>
                    <exon start="49085" stop="48991"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>420</number_coding_nucleotides>
                  <number_encoded_amino_acids>140</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>EKMASTVMSSLSLKPTFTLEKISVKGLPSLTRSSSSFKVVASGVKKLKTDKPYGINGSMALRDGVDASGRKPKGKGVYQYVDKYGANVDGYSPIYNTDEWSPSGDVYVGGTTGLAIWAVTLLGILAGGALLVYNTSALAQ*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="80794" PGL_stop="79247"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="80794" e_stop="80104"/>
            <exon e_start="79421" e_stop="79247"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.981" acc_prob="0.772" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="80794" e_stop="80104" e_length="691"/>
          </exon>
          <intron i_serial="1" don_prob="0.981" acc_prob="0.772">
            <gDNA_intron_boundary i_start="80103" i_stop="79422" i_length="682"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="79421" e_stop="79247" e_length="175"/>
          </exon>
        </exon-intron_info>
        <supporting_evidence xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/supporting_evidence/">
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="80794" stop="80124"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M9190-2" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="80770" stop="80104"/>
              <exon start="79421" stop="79247"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M9190" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="3" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>GAGACCTGCCTGTGTGTCGAAGAAAATGAAGTTGAGCTTCATTCGACCAATTTCATGTTGCTCTGTTTCATCTCCAGCAACCTCAGTGAAACCTCAAAAACCTATATTTTTAAGGCCACCCACCTTCAAAACAACCATATCAGACCTTCAAAAATGGCATCATTGGGCTAAATCCCTAATTTCTTCTGTGGGTTCCACTTTCTTGGAACTGGACAATGGTCCAGACTCCGAATTGTTGCTCAGGGAGCTAAATTGGCTTGTTGAAGATGCAATTGAAACACCAAAATCTTTCTTGCAACAACCCCACAAAAATTACAATGATAATAGCTCAGTTGCAGTTCGGGCGTCTTTGGAACAACTGTATATGTTGTGGAAACGAAGGGTAGAAGAAAGAATGCCATTTCAGTATGTGGTTGGCTGTGAACATTGGAGGGATTTGGTTTTGAGTGTTCAAGAAGGGGTTTTGATTCCAAGGCCAGAGACTGAGCTGATTGTGGACCTTGTCGATGATGCTATTAAGGAGAATGGGGAATTGAGGGAAGGATTGTGGGCTGATTTGGGGACTGGAAGTGGTGCACTTGCTATTGGGATTGCAAGGATTTTGGGTACTTCTGGTAGAGTTGTTGCTACTGATTTAAGCCCTGTTGCTACTGCAGTTGCATCTTATAATGTGCAGAGGTATGATTTGGAG : GAAAAAGTGCATGTAAAGCAAGGATCTTGGTTTGAACCTTTGAGAGATAATGAAGGAGAATTTGTGGGACTGGTCAGTAATCCACCATATATTCCAAGCAAAGATATTGGTGGACTACAAGCTGAAGTTGGCAGACATGAACCTAGACTGGCGTTAGACGGTGGAGCAAGTGGTA</gDNA_template>
            <first_frame> E  T  C  L  C  V  E  E  N  E  V  E  L  H  S  T  N  F  M  L  L  C  F  I  S  S  N  L  S  E  T  S  K  T  Y  I  F  K  A  T  H  L  Q  N  N  H  I  R  P  S  K  M  A  S  L  G  *  I  P  N  F  F  C  G  F  H  F  L  G  T  G  Q  W  S  R  L  R  I  V  A  Q  G  A  K  L  A  C  *  R  C  N  *  N  T  K  I  F  L  A  T  T  P  Q  K  L  Q  *  *  *  L  S  C  S  S  G  V  F  G  T  T  V  Y  V  V  E  T  K  G  R  R  K  N  A  I  S  V  C  G  W  L  *  T  L  E  G  F  G  F  E  C  S  R  R  G  F  D  S  K  A  R  D  *  A  D  C  G  P  C  R  *  C  Y  *  G  E  W  G  I  E  G  R  I  V  G  *  F  G  D  W  K  W  C  T  C  Y  W  D  C  K  D  F  G  Y  F  W  *  S  C  C  Y  *  F  K  P  C  C  Y  C  S  C  I  L  *  C  A  E  V  *  F  G   : G  K  S  A  C  K  A  R  I  L  V  *  T  F  E  R  *  *  R  R  I  C  G  T  G  Q  *  S  T  I  Y  S  K  Q  R  Y  W  W  T  T  S  *  S  W  Q  T  *  T  *  T  G  V  R  R  W  S  K  W   </first_frame>
            <second_frame>  R  P  A  C  V  S  K  K  M  K  L  S  F  I  R  P  I  S  C  C  S  V  S  S  P  A  T  S  V  K  P  Q  K  P  I  F  L  R  P  P  T  F  K  T  T  I  S  D  L  Q  K  W  H  H  W  A  K  S  L  I  S  S  V  G  S  T  F  L  E  L  D  N  G  P  D  S  E  L  L  L  R  E  L  N  W  L  V  E  D  A  I  E  T  P  K  S  F  L  Q  Q  P  H  K  N  Y  N  D  N  S  S  V  A  V  R  A  S  L  E  Q  L  Y  M  L  W  K  R  R  V  E  E  R  M  P  F  Q  Y  V  V  G  C  E  H  W  R  D  L  V  L  S  V  Q  E  G  V  L  I  P  R  P  E  T  E  L  I  V  D  L  V  D  D  A  I  K  E  N  G  E  L  R  E  G  L  W  A  D  L  G  T  G  S  G  A  L  A  I  G  I  A  R  I  L  G  T  S  G  R  V  V  A  T  D  L  S  P  V  A  T  A  V  A  S  Y  N  V  Q  R  Y  D  L  E  :  E  K  V  H  V  K  Q  G  S  W  F  E  P  L  R  D  N  E  G  E  F  V  G  L  V  S  N  P  P  Y  I  P  S  K  D  I  G  G  L  Q  A  E  V  G  R  H  E  P  R  L  A  L  D  G  G  A  S  G  </second_frame>
            <third_frame>   D  L  P  V  C  R  R  K  *  S  *  A  S  F  D  Q  F  H  V  A  L  F  H  L  Q  Q  P  Q  *  N  L  K  N  L  Y  F  *  G  H  P  P  S  K  Q  P  Y  Q  T  F  K  N  G  I  I  G  L  N  P  *  F  L  L  W  V  P  L  S  W  N  W  T  M  V  Q  T  P  N  C  C  S  G  S  *  I  G  L  L  K  M  Q  L  K  H  Q  N  L  S  C  N  N  P  T  K  I  T  M  I  I  A  Q  L  Q  F  G  R  L  W  N  N  C  I  C  C  G  N  E  G  *  K  K  E  C  H  F  S  M  W  L  A  V  N  I  G  G  I  W  F  *  V  F  K  K  G  F  *  F  Q  G  Q  R  L  S  *  L  W  T  L  S  M  M  L  L  R  R  M  G  N  *  G  K  D  C  G  L  I  W  G  L  E  V  V  H  L  L  L  G  L  Q  G  F  W  V  L  L  V  E  L  L  L  L  I  *  A  L  L  L  L  Q  L  H  L  I  M  C  R  G  M  I  W  R :   K  K  C  M  *  S  K  D  L  G  L  N  L  *  E  I  M  K  E  N  L  W  D  W  S  V  I  H  H  I  F  Q  A  K  I  L  V  D  Y  K  L  K  L  A  D  M  N  L  D  W  R  *  T  V  E  Q  V  V </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0179K09.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="80793" stop="80104"/>
                    <exon start="79421" stop="79248"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>864</number_coding_nucleotides>
                  <number_encoded_amino_acids>288</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RPACVSKKMKLSFIRPISCCSVSSPATSVKPQKPIFLRPPTFKTTISDLQKWHHWAKSLISSVGSTFLELDNGPDSELLLRELNWLVEDAIETPKSFLQQPHKNYNDNSSVAVRASLEQLYMLWKRRVEERMPFQYVVGCEHWRDLVLSVQEGVLIPRPETELIVDLVDDAIKENGELREGLWADLGTGSGALAIGIARILGTSGRVVATDLSPVATAVASYNVQRYDLEEKVHVKQGSWFEPLRDNEGEFVGLVSNPPYIPSKDIGGLQAEVGRHEPRLALDGGASG</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 11 chains have been computed
$ 
$ memory statistics:
$ 18744 bytes spliced alignments in total
$ 9 spliced alignments have been stored
$ 2082 bytes was the average size of a spliced alignment
$ 8200 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2733 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 12 backtrace matrices have been allocated
$ 
$ date finished: 2008-02-20 09:19:49
-->
