<?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="2009-11-30 18:29:12"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00SLm0103M17-zUfTZ/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00SLm0103M17-zUfTZ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" 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/bac-submission-temp-C00SLm0103M17-zUfTZ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At4g18230" ref_strand="+" ref_description="C2_At4g18230">
      <seq>attttgtgctgaattccgattgattttttcgccggccgatttgaaaagacagcaggatctctgtcttcagctgaggtgcagagcttcttgtaatggagaagggggatttttgcatctccactatggcatcatcaaatatcggagttctattaactattggtgtcatcactgtacttgtgatacgaattatttatgtgattaataggagcagaaagccgcttcactccaaatctccacaatccctcagtactcttattgttctgggttcaggtggtcacacagcagaaatgctatacttattatatgtccttcaaacagagaggtttaagccgaggtattatattgccgctgctactgataatatgagtctccaaaaagcacttgtgtttgaggattccttgctcggtaaggaagcgctcaaggaagtagggggggctgaattcatgcagatatatcgaagtcgagaggttggtcaatcgtatataacctcagttggaaccacattggttgcaattgcacatgcgttgtggttaatgatcaagatcagaccccaagtgattctgtgcaatggccctggaacgtgtattccactatgtgtaattgccttccttttcaaggttttgggaattaggtggtcatcgattttctatgtcgagagcattgcaagagtcaggaagatgtct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0103M17-zUfTZ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00SLm0103M17.2" temp_strand="-" temp_description="C00SLm0103M17.2  CU468238.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0103M17 sequenced_by:sanger upload_account_name:uk">
        <position start="37857" stop="33654"/>
      </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="37557" g_stop="37503" g_length="55"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="55" r_length="55" r_score="0.927"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="37502" i_stop="36379" i_length="1124">
            <donor d_prob="0.962" d_score="0.92"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="36378" g_stop="36164" g_length="215"/>
          <reference_exon_boundary r_type="cDNA" r_start="56" r_stop="270" r_length="215" r_score="0.963"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="36163" i_stop="36077" i_length="87">
            <donor d_prob="0.963" d_score="0.94"/>
            <acceptor a_prob="0.990" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="36076" g_stop="35937" g_length="140"/>
          <reference_exon_boundary r_type="cDNA" r_start="271" r_stop="410" r_length="140" r_score="0.957"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="35936" i_stop="34933" i_length="1004">
            <donor d_prob="0.994" d_score="0.96"/>
            <acceptor a_prob="0.993" a_score="0.92"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="34932" g_stop="34786" g_length="147"/>
          <reference_exon_boundary r_type="cDNA" r_start="411" r_stop="557" r_length="147" r_score="0.959"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="34785" i_stop="34660" i_length="126">
            <donor d_prob="0.892" d_score="0.96"/>
            <acceptor a_prob="0.950" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="34659" g_stop="34600" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="558" r_stop="617" r_length="60" r_score="0.983"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="34599" i_stop="34020" i_length="580">
            <donor d_prob="0.975" d_score="0.98"/>
            <acceptor a_prob="0.719" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="34019" g_stop="33954" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="618" r_stop="683" r_length="66" r_score="0.970"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0103M17.2" gen_strand="-" ref_id="C2_At4g18230" ref_strand="+">
        <total_alignment_score>0.960</total_alignment_score>
        <cumulative_length_of_scored_exons>683</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0103M17.2" gen_strand="-"/>
        <rDNA rDNA_id="C2_At4g18230" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="37557" e_stop="37503"/>
          <exon e_start="36378" e_stop="36164"/>
          <exon e_start="36076" e_stop="35937"/>
          <exon e_start="34932" e_stop="34786"/>
          <exon e_start="34659" e_stop="34600"/>
          <exon e_start="34019" e_stop="33954"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATTTTGCGCTGAATTCCGATTGATTTTTTCGTCGGCCGATTTCAATAGACAGCAGGTTAGTGACAGATTTAGCTCTTTGTCTCGTCGAAGTAAATTTTTCTGTTTCATTGTTTGCAATTTTTTTTTGTGATTTTGTTTCTACTGTATGAAGATAAGTTTCAAATTTCATTTATATGAATTGGGTTTAGCAAAATTTTGATTTTCTTCCCACTGTATGAAGAAAAGTTTCCATTTTTCTGAATTGGGTTTGTAAAATTTTGGTTTTGTTCGTTTGAAATTTCATTTTTTTCTGAATTGGGTTTGCAAATATTTTCATTTAGTTGCGATGTGTTAAGTTGATAATGGCTTCAAACTATGAAGGTTGTGCTGATCTGCCTTTTTAGTGTTACTAAATACTGATTAGATTACTGAATATTTTTCTCGAAAAGAAATGACAAGTTGTGGTAGGAAATTGTAAGTGAAGTTATTAAGCTTCCCAAAAATACGAGCACAGGAATAGTTGTGATGGATTTAACAATTGGTATAAGCTAAAATAAAATGAAAAAAGAGTTGTAGACAGTGTTACTAATAGGAGATGTTGAAGAAGCCTTATAAGAGTATAGCAAAGGCAAATTATTGAAAAATATGTGAACTAAATTAATCTAGTATAGCATAATGGATAACGAGGATTCATATTGCCGATTCCTAGTGTCTTTTTTTAATTTTTATTTGAAGGAATAGCTTATTGATTGATGTGAAATGTTCACGACAAGTGTTCTAGATTTGGGATGAAAAGTTTGAAGTCATATACCAAATCCTTCTATCGATACGGTGGATTTTAATATTAAACCTTTCAAATAAATTGATCAGTAATAACCATAAAATCCTAATCTCTACTCCAACAGACATTTGAGTTAATGTTTATTATGTAATGTGACTTCGACAGTTATTATATCCTGTGACTAATAGTTGTGTAGTCTATCAAGGCAGTTAACCATAGAGACTGTTCTGCATTATGCATAGCCATTCAAGCTTCTCATTTAGTTTTTGTAAGCAAAACATATCTAATCAATGCGCATCTTATATAATCGGTATTTGAATTTCCATTTGAAGCATCCCTCTGGTTAATTAAATTAATACCATTTACCTTTATAAGCTTGTGCTTTGGAATTTATGCTGATTGATTGAAATGTAATCCTGGATCTCTGTCTTCAGCTGAGGTGCAGAGCTTCTTGTAATGGAGAAGGGGGATTTTTGCATCTCCACTATGGCATCATCAAATATCGCAGTTCTATTAGCTATTGGTGTCATCACTTTACTTGTGATACGAATTATTTATGTTATTAATAGGAGAAGAAAGCCGCTTCACTCCAAATCACCACGATCCCTCAGTACACTTATTGTTCTGGGTTCAGGTCTAGTTTTATGTCTGATAGTATTTCTTCTGTTTTACTGCCTTTTCCTTATACTTGTTCTAAATCTTAAGTTCAACTATGATGTAGGTGGTCACACAGCAGAAATGTTAAACTTATTATATGTCCTCCAAACAGAGAGGTTTAAGCCGAGGTATTATATTGCTGCTGCTACTGATAATATGAGTCTCCAAAAAGCACACGTGTTTGAGGATTCCTTGCTCGGTAAGGTATAGTACATCAGTTTAATTTATTTGTCGGTTTTTCGTTCCCCCTTTTTATCAGACAACGATATGTCAAAAAAATGACGAGTGGAATGGTGTGTGGTTTCTTGTGACTATGAACCAAGAGAGGATAACATTTTTGTATTAGGCTGTTAACACATTATTCTTGTGACTTTTCTCAATTCCTTTATCAGTTTTGAATTAGGCTTCTAAGTTTTCTTTTGGATTTTAACACCTCGTTCACTGTGTCCAAATATTTAATTGCCTTAGTTGTTAAGTGACTAGTATAGCCATCAGTCACCCAGCTCCATCATTGTTCCCAGTTGCTTGCTCATGCAGTTCAATGTGAAAAGTTAGACTTCACTTTTTGTACCGGCAGAGGTGTTAAAGTGCCAAACCATGTATGTTCAACATCAGGCGGCAATTCTTAGGAAGTTTGGCTTGCATATCATCGTAGCCTAATGATCTCTCCAAATCAAAATGTGTTGCTTCTTGTAGAGCCTAATCTTAGAACTCATAGACTGGCAGTCCTTATCGTTTACAAATATATCAAAAATAAAGATTCATAGAATGCTCAAACACCGATTTGTGCATCTAGTATGGTAAATCACATGATTTCTCATATGATCAAAAGAATTTTAGAAAATCAAATTATGTATCTCAATGCATCAAACAATTGGTATACCAAGTCCTTTTACTTATTATTTGCAGTAAGAGATGAAAAATGTTTCTGCAAATGTGTTCCATGTATATATGTAACATTTAGCTATAATTGTCTGCATACAAGTATGTGTACCTTGCTTTTCGTCTCTGAGATAAAACCATAGTCTGTATGTTCTTTCAGATTGTCTAACTTAGGTTTGGAGGGGTCTTCATTCTCTTCTAGTTGTTTAGACTTCAGAGTATTTGAAATACATATCCTACACCACAGAAGCCTCCTCTTCTCCCGGAACTGATCATGATATTCTATTCTTAATTGGCTATATTAATAGGACTACCTCTTATTCTAGGAAGCGCCTGAGGAAGTAGGGGGAGCTGAATTCATGCAGATATATCGAAGTCGAGAGGTTGGTCAATCGTATATAACCTCAGTTGGAACCACATTGGTTGCAATTGCACATGCGTTATGGTTAATGATCAAGACCAGACCCCAAGTGGTATCAGACAAACCTTCTCATATTACCATTTACTCCCCTTTGAAATTGAAATTACCAATCTGCAGATACTTTCTCCTTTATATATCCTGGTCTTCTGATTTATCTTTATTTGGTACTTTGTCTCAGATTCTGTGCAATGGCCCTGGAACGTGTATTCCACTATGTGTAATTGCTTTCCTTTTCAAGGTTTGTTTATTAGATAGTAATCTTTTGTTCTTTTAACTTATTTGTTTTGTCAAATTGGATGCTAGAATACTGATTACATGCAGAATATCTCTGTTAACGTCCCGATTTAGAAAAAAAATGGATCATACTACCTTGATCTCAAAGTCAAGTCCATTCCTGTATTTTCAACTATCTTGCTTGGACTCTTAAAAATGCCGACAGCTGCATGTCGGATCCTCCAAAAGTACAGTGTATTTCGGAGTATTCGAGAGGTGATGCCACATTTTTGGTGTCCTAGCAACATAGATTTCCAAGTGTGTAGGATGACAACAACTTGGACCATTTTGTCTTTTCCTTGTCGGTTCATAAATATTTGCCTCGACTTATTTGGTTTCACGGCCTCTCCAAGCTTATTTGGCACCATCCCTTTAAAAAGTGTGAACAAACCTAACAAAAGGAGGAAGAGAACAGTCAATGAATCAAAAGAGAGCACTTGACTACTCACAGAGTCACATTGATATCGAACTTGCAAACGCTTTTAGTTTCTTATGATCCTTCAAGGTGACATTTGAGGTGCTAATTGAAAGTTCAACTTCTTCAGGTTTTGGGAATTAGGTGGTCATCAATTTTCTATGTCGAGAGCATTGCAAGAGTCAGGAAGCTGTCT</genome_strand>
        <mrna_strand>ATTTTGTGCTGAATTCCGATTGATTTTTTCGCCGGCCGATTTGAAAAGACAGCAG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATCTCTGTCTTCAGCTGAGGTGCAGAGCTTCTTGTAATGGAGAAGGGGGATTTTTGCATCTCCACTATGGCATCATCAAATATCGGAGTTCTATTAACTATTGGTGTCATCACTGTACTTGTGATACGAATTATTTATGTGATTAATAGGAGCAGAAAGCCGCTTCACTCCAAATCTCCACAATCCCTCAGTACTCTTATTGTTCTGGGTTCAG.......................................................................................GTGGTCACACAGCAGAAATGCTATACTTATTATATGTCCTTCAAACAGAGAGGTTTAAGCCGAGGTATTATATTGCCGCTGCTACTGATAATATGAGTCTCCAAAAAGCACTTGTGTTTGAGGATTCCTTGCTCGGTAAG............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAAGCGCTCAAGGAAGTAGGGGGGGCTGAATTCATGCAGATATATCGAAGTCGAGAGGTTGGTCAATCGTATATAACCTCAGTTGGAACCACATTGGTTGCAATTGCACATGCGTTGTGGTTAATGATCAAGATCAGACCCCAAGTG..............................................................................................................................ATTCTGTGCAATGGCCCTGGAACGTGTATTCCACTATGTGTAATTGCCTTCCTTTTCAAG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTTGGGAATTAGGTGGTCATCGATTTTCTATGTCGAGAGCATTGCAAGAGTCAGGAAGATGTCT</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/bac-submission-temp-C00SLm0103M17-zUfTZ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="CD55-F" ref_strand="+" ref_description="CD55-F">
      <seq>catcctcactatatcggtagagatccaaagtcgtgacacctaaatattcgataccaatagatctgttcttataacctatctaatcaatgtttccccacagatgttcagtgtgtgtcgaatcctctttttgaagagtccgagcacatagtacaccctaaggtaagaacaacagagcaggaccacaaccactgatttgtgggatcattcactaaaatttgggtaaggacgaaaagtaaaagttgtatcttgcaatggagcagcttactcctgacatggatcatggaattgaatttatacaaaaaaatgatttttcaagtttcttaatcgaaataaactatcactaactatttatcgaaacacaactcatctattaattgttcacaaactctttttagattttgccctaatgtttgattaatttttacgaattagggcgatatcgcacaccaatctctctatatatacttttatatttctcggcattgatataaaaatataattgtacttataataattttaacgagatatctggaccattaagaataaaatgttgttaatgatatcaattaata</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0103M17-zUfTZ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00SLm0103M17.2" temp_strand="-" temp_description="C00SLm0103M17.2  CU468238.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0103M17 sequenced_by:sanger upload_account_name:uk">
        <position start="39969" stop="38799"/>
      </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="39669" g_stop="39099" g_length="571"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="572" r_length="572" r_score="0.988"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0103M17.2" gen_strand="-" ref_id="CD55-F" ref_strand="+">
        <total_alignment_score>0.988</total_alignment_score>
        <cumulative_length_of_scored_exons>571</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0103M17.2" gen_strand="-"/>
        <rDNA rDNA_id="CD55-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="39669" e_stop="39099"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CATCCTCACTATATC-GTAGAGATCCAAAGTCGTGACACCTAAATATTCAATACCAATAGATCTGTTCTTATAACCTATCTAATCAATGTTTCCCCACAGATGTTCAGTGTGTGTCGAATCCTCTTTTTGAAGAGTCCGAGCACATAGTACACCCTAAGGTAAGAACAACAGAGCAGGACCACAACCACTGATTTGTGGGATCATTCACTAAAATTTGGGTAAGGACGAAAAGTAAAAGTTGTATCTTGCAATGGAGCAGCTTACTCCTGACATGGATCATGGAATTGAATTTATACAAAAAAATGATTTTTCAAGTTTCTTAATCGAAATAAACTATCACTAACTATTTATCGAAACACAACTCATCTATTAATTGTTCAGAAACTCTTTTTAGATTTTGCCCTAATGTTTGATTAATTTTTACGAATTAGGGCGATATCGCACACCAATCTCTCTATATATACTTTTATATTTCTCGGCATTGATATAAAAATATAATTTTACTTATAATAATTTTAACGAAATATCTGGACCATTAAGAATAAAATGTTGTTAATAATATCAATTAATA</genome_strand>
        <mrna_strand>CATCCTCACTATATCGGTAGAGATCCAAAGTCGTGACACCTAAATATTCGATACCAATAGATCTGTTCTTATAACCTATCTAATCAATGTTTCCCCACAGATGTTCAGTGTGTGTCGAATCCTCTTTTTGAAGAGTCCGAGCACATAGTACACCCTAAGGTAAGAACAACAGAGCAGGACCACAACCACTGATTTGTGGGATCATTCACTAAAATTTGGGTAAGGACGAAAAGTAAAAGTTGTATCTTGCAATGGAGCAGCTTACTCCTGACATGGATCATGGAATTGAATTTATACAAAAAAATGATTTTTCAAGTTTCTTAATCGAAATAAACTATCACTAACTATTTATCGAAACACAACTCATCTATTAATTGTTCACAAACTCTTTTTAGATTTTGCCCTAATGTTTGATTAATTTTTACGAATTAGGGCGATATCGCACACCAATCTCTCTATATATACTTTTATATTTCTCGGCATTGATATAAAAATATAATTGTACTTATAATAATTTTAACGAGATATCTGGACCATTAAGAATAAAATGTTGTTAATGATATCAATTAATA</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/bac-submission-temp-C00SLm0103M17-zUfTZ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="TG453-F" ref_strand="+" ref_description="TG453-F">
      <seq>atgggctatgcttggtgctcttggatgtgtcttccctgagctattggcccgtaacggtgtcaagttcggtgaggctgtgtggttcaaggccggatcccagatcttcagcgagggaggacttgactacttgggcaacccaagcttggtccatgcacagagcatcttggccatctgggcttgccaagttgtcttgatgggagccgttgaaggttaccgtattgctggtggacctcttggtgaggttgtcgacccactctaccccggtggcagcttcgacccattaggccttgctgaagaccccgaggcatttgctgagctcaaggtaaaggagattaagaacggcagacttgctatgttctctatgttcggattctttgttcaggccattgttaccggaaagggtccattggagaaccttgctgaccaccttgcagaccccgttaacaacaacgcttgggctttcgccacaaactttgtccccggaaaatgaatatcataat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0103M17-zUfTZ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00SLm0103M17.2" temp_strand="-" temp_description="C00SLm0103M17.2  CU468238.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0103M17 sequenced_by:sanger upload_account_name:uk">
        <position start="41384" stop="40290"/>
      </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="41084" g_stop="40599" g_length="486"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="486" r_length="486" r_score="0.903"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0103M17.2" gen_strand="-" ref_id="TG453-F" ref_strand="+">
        <total_alignment_score>0.903</total_alignment_score>
        <cumulative_length_of_scored_exons>486</cumulative_length_of_scored_exons>
        <coverage percentage="0.972" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0103M17.2" gen_strand="-"/>
        <rDNA rDNA_id="TG453-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="41084" e_stop="40599"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGGCCATGCTTGGTGCTCTTGGATGTGTATTCCCCGAGCTTTTGGCCCGTAATGGTGTTAAGTTCGGTGAAGCTGTATGGTTCAAGGCTGGATCACAAATTTTCAGCGAGGGTGGACTTGACTACTTGGGAAACCCAAGCTTGGTCCATGCACAAAGCATTTTGGCTATCTGGGCTTGCCAAGTTGTGTTGATGGGAGCCGTTGAGGGTTACCGTATTGCTGGTGGGCCTCTTGGTGAGGTTGTTGACCCACTCTACCCTGGTGGTAGCTTTGACCCACTGGGCCTTGCTGATGACCCAGAGGCTTTTGCTGAGCTCAAGGTAAAAGAGATCAAGAATGGTAGACTTGCTATGTTCTCCATGTTCGGATTCTTTGTTCAAGCTATCGTCACCGGAAAGGGTCCATTGGAGAACCTTGCTGACCATCTCGCTGATCCAGTCAATAACAATGCTTGGGCCTTCGCCACAAACTTTGTCCCCGGAAA</genome_strand>
        <mrna_strand>ATGGGCTATGCTTGGTGCTCTTGGATGTGTCTTCCCTGAGCTATTGGCCCGTAACGGTGTCAAGTTCGGTGAGGCTGTGTGGTTCAAGGCCGGATCCCAGATCTTCAGCGAGGGAGGACTTGACTACTTGGGCAACCCAAGCTTGGTCCATGCACAGAGCATCTTGGCCATCTGGGCTTGCCAAGTTGTCTTGATGGGAGCCGTTGAAGGTTACCGTATTGCTGGTGGACCTCTTGGTGAGGTTGTCGACCCACTCTACCCCGGTGGCAGCTTCGACCCATTAGGCCTTGCTGAAGACCCCGAGGCATTTGCTGAGCTCAAGGTAAAGGAGATTAAGAACGGCAGACTTGCTATGTTCTCTATGTTCGGATTCTTTGTTCAGGCCATTGTTACCGGAAAGGGTCCATTGGAGAACCTTGCTGACCACCTTGCAGACCCCGTTAACAACAACGCTTGGGCTTTCGCCACAAACTTTGTCCCCGGAAA</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/bac-submission-temp-C00SLm0103M17-zUfTZ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="TG145-F" ref_strand="+" ref_description="TG145-F">
      <seq>atgggctatgcttggtgctcttggatgtgtcttccctgagctattggcccgtaatggtgtcaagttcggtgaggctgtgtggttcaaggctggatcccagatcttcagcgagggtggacttgattacttgggcaacccaagcttggtccatgcacaaagcatcttggccatctgggcttgccaagttgtgttgatgggagccgttgagggataccgcattgctggtggacctcttggtgaggttgtcgacccactctaccccggtggcagcttcgacccattaggccttgctgaagacccggaggcatttgctgagcttaaggttaaggagatcaagaacggcagacttgctatgttctctatgtttgggttctttgttcaggccattgttaccggaaagggtccattggagaacctcgctgaccacctt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0103M17-zUfTZ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00SLm0103M17.2" temp_strand="-" temp_description="C00SLm0103M17.2  CU468238.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0103M17 sequenced_by:sanger upload_account_name:uk">
        <position start="41384" stop="40356"/>
      </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="41084" g_stop="40655" g_length="430"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="430" r_length="430" r_score="0.905"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0103M17.2" gen_strand="-" ref_id="TG145-F" ref_strand="+">
        <total_alignment_score>0.905</total_alignment_score>
        <cumulative_length_of_scored_exons>430</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0103M17.2" gen_strand="-"/>
        <rDNA rDNA_id="TG145-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="41084" e_stop="40655"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGGGCCATGCTTGGTGCTCTTGGATGTGTATTCCCCGAGCTTTTGGCCCGTAATGGTGTTAAGTTCGGTGAAGCTGTATGGTTCAAGGCTGGATCACAAATTTTCAGCGAGGGTGGACTTGACTACTTGGGAAACCCAAGCTTGGTCCATGCACAAAGCATTTTGGCTATCTGGGCTTGCCAAGTTGTGTTGATGGGAGCCGTTGAGGGTTACCGTATTGCTGGTGGGCCTCTTGGTGAGGTTGTTGACCCACTCTACCCTGGTGGTAGCTTTGACCCACTGGGCCTTGCTGATGACCCAGAGGCTTTTGCTGAGCTCAAGGTAAAAGAGATCAAGAATGGTAGACTTGCTATGTTCTCCATGTTCGGATTCTTTGTTCAAGCTATCGTCACCGGAAAGGGTCCATTGGAGAACCTTGCTGACCATCTC</genome_strand>
        <mrna_strand>ATGGGCTATGCTTGGTGCTCTTGGATGTGTCTTCCCTGAGCTATTGGCCCGTAATGGTGTCAAGTTCGGTGAGGCTGTGTGGTTCAAGGCTGGATCCCAGATCTTCAGCGAGGGTGGACTTGATTACTTGGGCAACCCAAGCTTGGTCCATGCACAAAGCATCTTGGCCATCTGGGCTTGCCAAGTTGTGTTGATGGGAGCCGTTGAGGGATACCGCATTGCTGGTGGACCTCTTGGTGAGGTTGTCGACCCACTCTACCCCGGTGGCAGCTTCGACCCATTAGGCCTTGCTGAAGACCCGGAGGCATTTGCTGAGCTTAAGGTTAAGGAGATCAAGAACGGCAGACTTGCTATGTTCTCTATGTTTGGGTTCTTTGTTCAGGCCATTGTTACCGGAAAGGGTCCATTGGAGAACCTCGCTGACCACCTT</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/bac-submission-temp-C00SLm0103M17-zUfTZ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="CT128-R" ref_strand="+" ref_description="CT128-R">
      <seq>ctggtgattacgggtgggataccgctggactttcagcagaccctgaaacttttgccaagaaccgtgaacttgaggtgatccactgcagatgggctatgcttggtgctcttggatgtgtcttccctgagctcttggcccgtaatggtgtcaagttcggtgaggctgtgtggttcaaggccggatcccagatcttcagtgaaggtggacttgactacttgggcaacccaagcttggtccatgcacaaagcatcttggccatctgggcttgccaagttgtgttgatgggagctgttgagggataccgtattgctggtgggacctcttggtgaggttgtcgacccactctaccctggtggcagcttcgacccattaggccttgctgaagacccagaggcatttgctgagctcaaggtaaaggagatcaagaacggtagacttgctatgttctctatgtttggattctttgttcaagctattgtcaccggaaagggtcca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLm0103M17-zUfTZ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00SLm0103M17.2" temp_strand="-" temp_description="C00SLm0103M17.2  CU468238.3 htgs_phase:3 submitted_to_sgn_as:C04SLm0103M17 sequenced_by:sanger upload_account_name:uk">
        <position start="41472" stop="40379"/>
      </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="41172" g_stop="40679" g_length="494"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="495" r_length="495" r_score="0.907"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLm0103M17.2" gen_strand="-" ref_id="CT128-R" ref_strand="+">
        <total_alignment_score>0.907</total_alignment_score>
        <cumulative_length_of_scored_exons>494</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLm0103M17.2" gen_strand="-"/>
        <rDNA rDNA_id="CT128-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="41172" e_stop="40679"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTGGTGATTACGGATGGGACACTGCTGGACTTTCAGCTGACCCTGAAACATTCGCTAAGAACCGTGAGTTGGAGGTTATTCATTGTAGATGGGCCATGCTTGGTGCTCTTGGATGTGTATTCCCCGAGCTTTTGGCCCGTAATGGTGTTAAGTTCGGTGAAGCTGTATGGTTCAAGGCTGGATCACAAATTTTCAGCGAGGGTGGACTTGACTACTTGGGAAACCCAAGCTTGGTCCATGCACAAAGCATTTTGGCTATCTGGGCTTGCCAAGTTGTGTTGATGGGAGCCGTTGAGGGTTACCGTATTGCTGGTGGG-CCTCTTGGTGAGGTTGTTGACCCACTCTACCCTGGTGGTAGCTTTGACCCACTGGGCCTTGCTGATGACCCAGAGGCTTTTGCTGAGCTCAAGGTAAAAGAGATCAAGAATGGTAGACTTGCTATGTTCTCCATGTTCGGATTCTTTGTTCAAGCTATCGTCACCGGAAAGGGTCCA</genome_strand>
        <mrna_strand>CTGGTGATTACGGGTGGGATACCGCTGGACTTTCAGCAGACCCTGAAACTTTTGCCAAGAACCGTGAACTTGAGGTGATCCACTGCAGATGGGCTATGCTTGGTGCTCTTGGATGTGTCTTCCCTGAGCTCTTGGCCCGTAATGGTGTCAAGTTCGGTGAGGCTGTGTGGTTCAAGGCCGGATCCCAGATCTTCAGTGAAGGTGGACTTGACTACTTGGGCAACCCAAGCTTGGTCCATGCACAAAGCATCTTGGCCATCTGGGCTTGCCAAGTTGTGTTGATGGGAGCTGTTGAGGGATACCGTATTGCTGGTGGGACCTCTTGGTGAGGTTGTCGACCCACTCTACCCTGGTGGCAGCTTCGACCCATTAGGCCTTGCTGAAGACCCAGAGGCATTTGCTGAGCTCAAGGTAAAGGAGATCAAGAACGGTAGACTTGCTATGTTCTCTATGTTTGGATTCTTTGTTCAAGCTATTGTCACCGGAAAGGGTCCA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>5</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="37557" PGL_stop="33954"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="37557" e_stop="37503"/>
            <exon e_start="36378" e_stop="36164"/>
            <exon e_start="36076" e_stop="35937"/>
            <exon e_start="34932" e_stop="34786"/>
            <exon e_start="34659" e_stop="34600"/>
            <exon e_start="34019" e_stop="33954"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.962" acc_prob="0.000" e_score="0.927"/>
          <exon-intron don_prob="0.963" acc_prob="0.990" e_score="0.963"/>
          <exon-intron don_prob="0.994" acc_prob="0.993" e_score="0.957"/>
          <exon-intron don_prob="0.892" acc_prob="0.950" e_score="0.959"/>
          <exon-intron don_prob="0.975" acc_prob="0.719" e_score="0.983"/>
          <exon-only e_score="0.970"/>
        </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="0.927">
            <gDNA_exon_boundary e_start="37557" e_stop="37503" e_length="55"/>
          </exon>
          <intron i_serial="1" don_prob="0.962" acc_prob="0.000">
            <gDNA_intron_boundary i_start="37502" i_stop="36379" i_length="1124"/>
          </intron>
          <exon e_serial="2" e_score="0.963">
            <gDNA_exon_boundary e_start="36378" e_stop="36164" e_length="215"/>
          </exon>
          <intron i_serial="2" don_prob="0.963" acc_prob="0.990">
            <gDNA_intron_boundary i_start="36163" i_stop="36077" i_length="87"/>
          </intron>
          <exon e_serial="3" e_score="0.957">
            <gDNA_exon_boundary e_start="36076" e_stop="35937" e_length="140"/>
          </exon>
          <intron i_serial="3" don_prob="0.994" acc_prob="0.993">
            <gDNA_intron_boundary i_start="35936" i_stop="34933" i_length="1004"/>
          </intron>
          <exon e_serial="4" e_score="0.959">
            <gDNA_exon_boundary e_start="34932" e_stop="34786" e_length="147"/>
          </exon>
          <intron i_serial="4" don_prob="0.892" acc_prob="0.950">
            <gDNA_intron_boundary i_start="34785" i_stop="34660" i_length="126"/>
          </intron>
          <exon e_serial="5" e_score="0.983">
            <gDNA_exon_boundary e_start="34659" e_stop="34600" e_length="60"/>
          </exon>
          <intron i_serial="5" don_prob="0.975" acc_prob="0.719">
            <gDNA_intron_boundary i_start="34599" i_stop="34020" i_length="580"/>
          </intron>
          <exon e_serial="6" e_score="0.970">
            <gDNA_exon_boundary e_start="34019" e_stop="33954" e_length="66"/>
          </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="37557" stop="37503"/>
              <exon start="36378" stop="36164"/>
              <exon start="36076" stop="35937"/>
              <exon start="34932" stop="34786"/>
              <exon start="34659" stop="34600"/>
              <exon start="34019" stop="33954"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At4g18230" 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>ATTTTGCGCTGAATTCCGATTGATTTTTTCGTCGGCCGATTTCAATAGACAGCAG : GATCTCTGTCTTCAGCTGAGGTGCAGAGCTTCTTGTAATGGAGAAGGGGGATTTTTGCATCTCCACTATGGCATCATCAAATATCGCAGTTCTATTAGCTATTGGTGTCATCACTTTACTTGTGATACGAATTATTTATGTTATTAATAGGAGAAGAAAGCCGCTTCACTCCAAATCACCACGATCCCTCAGTACACTTATTGTTCTGGGTTCAG : GTGGTCACACAGCAGAAATGTTAAACTTATTATATGTCCTCCAAACAGAGAGGTTTAAGCCGAGGTATTATATTGCTGCTGCTACTGATAATATGAGTCTCCAAAAAGCACACGTGTTTGAGGATTCCTTGCTCGGTAAG : GAAGCGCCTGAGGAAGTAGGGGGAGCTGAATTCATGCAGATATATCGAAGTCGAGAGGTTGGTCAATCGTATATAACCTCAGTTGGAACCACATTGGTTGCAATTGCACATGCGTTATGGTTAATGATCAAGACCAGACCCCAAGTG : ATTCTGTGCAATGGCCCTGGAACGTGTATTCCACTATGTGTAATTGCTTTCCTTTTCAAG : GTTTTGGGAATTAGGTGGTCATCAATTTTCTATGTCGAGAGCATTGCAAGAGTCAGGAAGCTGTCT</gDNA_template>
            <first_frame> I  L  R  *  I  P  I  D  F  F  V  G  R  F  Q  *  T  A   : G  S  L  S  S  A  E  V  Q  S  F  L  *  W  R  R  G  I  F  A  S  P  L  W  H  H  Q  I  S  Q  F  Y  *  L  L  V  S  S  L  Y  L  *  Y  E  L  F  M  L  L  I  G  E  E  S  R  F  T  P  N  H  H  D  P  S  V  H  L  L  F  W  V  Q  :  V  V  T  Q  Q  K  C  *  T  Y  Y  M  S  S  K  Q  R  G  L  S  R  G  I  I  L  L  L  L  L  I  I  *  V  S  K  K  H  T  C  L  R  I  P  C  S  V  R :   K  R  L  R  K  *  G  E  L  N  S  C  R  Y  I  E  V  E  R  L  V  N  R  I  *  P  Q  L  E  P  H  W  L  Q  L  H  M  R  Y  G  *  *  S  R  P  D  P  K  * :   F  C  A  M  A  L  E  R  V  F  H  Y  V  *  L  L  S  F  S  R :   F  W  E  L  G  G  H  Q  F  S  M  S  R  A  L  Q  E  S  G  S  C   </first_frame>
            <second_frame>  F  C  A  E  F  R  L  I  F  S  S  A  D  F  N  R  Q  Q  :  D  L  C  L  Q  L  R  C  R  A  S  C  N  G  E  G  G  F  L  H  L  H  Y  G  I  I  K  Y  R  S  S  I  S  Y  W  C  H  H  F  T  C  D  T  N  Y  L  C  Y  *  *  E  K  K  A  A  S  L  Q  I  T  T  I  P  Q  Y  T  Y  C  S  G  F  R :   W  S  H  S  R  N  V  K  L  I  I  C  P  P  N  R  E  V  *  A  E  V  L  Y  C  C  C  Y  *  *  Y  E  S  P  K  S  T  R  V  *  G  F  L  A  R  *   : G  S  A  *  G  S  R  G  S  *  I  H  A  D  I  S  K  S  R  G  W  S  I  V  Y  N  L  S  W  N  H  I  G  C  N  C  T  C  V  M  V  N  D  Q  D  Q  T  P  S   : D  S  V  Q  W  P  W  N  V  Y  S  T  M  C  N  C  F  P  F  Q   : G  F  G  N  *  V  V  I  N  F  L  C  R  E  H  C  K  S  Q  E  A  V  </second_frame>
            <third_frame>   F  A  L  N  S  D  *  F  F  R  R  P  I  S  I  D  S  R :   I  S  V  F  S  *  G  A  E  L  L  V  M  E  K  G  D  F  C  I  S  T  M  A  S  S  N  I  A  V  L  L  A  I  G  V  I  T  L  L  V  I  R  I  I  Y  V  I  N  R  R  R  K  P  L  H  S  K  S  P  R  S  L  S  T  L  I  V  L  G  S   : G  G  H  T  A  E  M  L  N  L  L  Y  V  L  Q  T  E  R  F  K  P  R  Y  Y  I  A  A  A  T  D  N  M  S  L  Q  K  A  H  V  F  E  D  S  L  L  G  K  :  E  A  P  E  E  V  G  G  A  E  F  M  Q  I  Y  R  S  R  E  V  G  Q  S  Y  I  T  S  V  G  T  T  L  V  A  I  A  H  A  L  W  L  M  I  K  T  R  P  Q  V  :  I  L  C  N  G  P  G  T  C  I  P  L  C  V  I  A  F  L  F  K  :  V  L  G  I  R  W  S  S  I  F  Y  V  E  S  I  A  R  V  R  K  L  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="C00SLm0103M17.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="36359" stop="36164"/>
                    <exon start="36076" stop="35937"/>
                    <exon start="34932" stop="34786"/>
                    <exon start="34659" stop="34600"/>
                    <exon start="34019" stop="33954"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>609</number_coding_nucleotides>
                  <number_encoded_amino_acids>203</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GAELLVMEKGDFCISTMASSNIAVLLAIGVITLLVIRIIYVINRRRKPLHSKSPRSLSTLIVLGSGGHTAEMLNLLYVLQTERFKPRYYIAAATDNMSLQKAHVFEDSLLGKEAPEEVGGAEFMQIYRSREVGQSYITSVGTTLVAIAHALWLMIKTRPQVILCNGPGTCIPLCVIAFLFKVLGIRWSSIFYVESIARVRKLS</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="39669" PGL_stop="39099"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="39669" e_stop="39099"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.988"/>
        </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="0.988">
            <gDNA_exon_boundary e_start="39669" e_stop="39099" e_length="571"/>
          </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="39669" stop="39099"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="CD55-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>CATCCTCACTATATCGTAGAGATCCAAAGTCGTGACACCTAAATATTCAATACCAATAGATCTGTTCTTATAACCTATCTAATCAATGTTTCCCCACAGATGTTCAGTGTGTGTCGAATCCTCTTTTTGAAGAGTCCGAGCACATAGTACACCCTAAGGTAAGAACAACAGAGCAGGACCACAACCACTGATTTGTGGGATCATTCACTAAAATTTGGGTAAGGACGAAAAGTAAAAGTTGTATCTTGCAATGGAGCAGCTTACTCCTGACATGGATCATGGAATTGAATTTATACAAAAAAATGATTTTTCAAGTTTCTTAATCGAAATAAACTATCACTAACTATTTATCGAAACACAACTCATCTATTAATTGTTCAGAAACTCTTTTTAGATTTTGCCCTAATGTTTGATTAATTTTTACGAATTAGGGCGATATCGCACACCAATCTCTCTATATATACTTTTATATTTCTCGGCATTGATATAAAAATATAATTTTACTTATAATAATTTTAACGAAATATCTGGACCATTAAGAATAAAATGTTGTTAATAATATCAATTAATA</gDNA_template>
            <first_frame> H  P  H  Y  I  V  E  I  Q  S  R  D  T  *  I  F  N  T  N  R  S  V  L  I  T  Y  L  I  N  V  S  P  Q  M  F  S  V  C  R  I  L  F  L  K  S  P  S  T  *  Y  T  L  R  *  E  Q  Q  S  R  T  T  T  T  D  L  W  D  H  S  L  K  F  G  *  G  R  K  V  K  V  V  S  C  N  G  A  A  Y  S  *  H  G  S  W  N  *  I  Y  T  K  K  *  F  F  K  F  L  N  R  N  K  L  S  L  T  I  Y  R  N  T  T  H  L  L  I  V  Q  K  L  F  L  D  F  A  L  M  F  D  *  F  L  R  I  R  A  I  S  H  T  N  L  S  I  Y  T  F  I  F  L  G  I  D  I  K  I  *  F  Y  L  *  *  F  *  R  N  I  W  T  I  K  N  K  M  L  L  I  I  S  I  N  </first_frame>
            <second_frame>  I  L  T  I  S  *  R  S  K  V  V  T  P  K  Y  S  I  P  I  D  L  F  L  *  P  I  *  S  M  F  P  H  R  C  S  V  C  V  E  S  S  F  *  R  V  R  A  H  S  T  P  *  G  K  N  N  R  A  G  P  Q  P  L  I  C  G  I  I  H  *  N  L  G  K  D  E  K  *  K  L  Y  L  A  M  E  Q  L  T  P  D  M  D  H  G  I  E  F  I  Q  K  N  D  F  S  S  F  L  I  E  I  N  Y  H  *  L  F  I  E  T  Q  L  I  Y  *  L  F  R  N  S  F  *  I  L  P  *  C  L  I  N  F  Y  E  L  G  R  Y  R  T  P  I  S  L  Y  I  L  L  Y  F  S  A  L  I  *  K  Y  N  F  T  Y  N  N  F  N  E  I  S  G  P  L  R  I  K  C  C  *  *  Y  Q  L  I </second_frame>
            <third_frame>   S  S  L  Y  R  R  D  P  K  S  *  H  L  N  I  Q  Y  Q  *  I  C  S  Y  N  L  S  N  Q  C  F  P  T  D  V  Q  C  V  S  N  P  L  F  E  E  S  E  H  I  V  H  P  K  V  R  T  T  E  Q  D  H  N  H  *  F  V  G  S  F  T  K  I  W  V  R  T  K  S  K  S  C  I  L  Q  W  S  S  L  L  L  T  W  I  M  E  L  N  L  Y  K  K  M  I  F  Q  V  S  *  S  K  *  T  I  T  N  Y  L  S  K  H  N  S  S  I  N  C  S  E  T  L  F  R  F  C  P  N  V  *  L  I  F  T  N  *  G  D  I  A  H  Q  S  L  Y  I  Y  F  Y  I  S  R  H  *  Y  K  N  I  I  L  L  I  I  I  L  T  K  Y  L  D  H  *  E  *  N  V  V  N  N  I  N  *   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <none gDNA_id="C00SLm0103M17.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="41172" PGL_stop="40599"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="41172" e_stop="40599"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.907"/>
        </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="0.907">
            <gDNA_exon_boundary e_start="41172" e_stop="40599" e_length="574"/>
          </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="41172" stop="40679"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="CT128-R" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="41084" stop="40599"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="TG453-F" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="41084" stop="40655"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="TG145-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="3" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>CTGGTGATTACGGATGGGACACTGCTGGACTTTCAGCTGACCCTGAAACATTCGCTAAGAACCGTGAGTTGGAGGTTATTCATTGTAGATGGGCCATGCTTGGTGCTCTTGGATGTGTATTCCCCGAGCTTTTGGCCCGTAATGGTGTTAAGTTCGGTGAAGCTGTATGGTTCAAGGCTGGATCACAAATTTTCAGCGAGGGTGGACTTGACTACTTGGGAAACCCAAGCTTGGTCCATGCACAAAGCATTTTGGCTATCTGGGCTTGCCAAGTTGTGTTGATGGGAGCCGTTGAGGGTTACCGTATTGCTGGTGGGCCTCTTGGTGAGGTTGTTGACCCACTCTACCCTGGTGGTAGCTTTGACCCACTGGGCCTTGCTGATGACCCAGAGGCTTTTGCTGAGCTCAAGGTAAAAGAGATCAAGAATGGTAGACTTGCTATGTTCTCCATGTTCGGATTCTTTGTTCAAGCTATCGTCACCGGAAAGGGTCCATTGGAGAACCTTGCTGACCATCTCGCTGATCCAGTCAATAACAATGCTTGGGCCTTCGCCACAAACTTTGTCCCCGGAAA</gDNA_template>
            <first_frame> L  V  I  T  D  G  T  L  L  D  F  Q  L  T  L  K  H  S  L  R  T  V  S  W  R  L  F  I  V  D  G  P  C  L  V  L  L  D  V  Y  S  P  S  F  W  P  V  M  V  L  S  S  V  K  L  Y  G  S  R  L  D  H  K  F  S  A  R  V  D  L  T  T  W  E  T  Q  A  W  S  M  H  K  A  F  W  L  S  G  L  A  K  L  C  *  W  E  P  L  R  V  T  V  L  L  V  G  L  L  V  R  L  L  T  H  S  T  L  V  V  A  L  T  H  W  A  L  L  M  T  Q  R  L  L  L  S  S  R  *  K  R  S  R  M  V  D  L  L  C  S  P  C  S  D  S  L  F  K  L  S  S  P  E  R  V  H  W  R  T  L  L  T  I  S  L  I  Q  S  I  T  M  L  G  P  S  P  Q  T  L  S  P  E  </first_frame>
            <second_frame>  W  *  L  R  M  G  H  C  W  T  F  S  *  P  *  N  I  R  *  E  P  *  V  G  G  Y  S  L  *  M  G  H  A  W  C  S  W  M  C  I  P  R  A  F  G  P  *  W  C  *  V  R  *  S  C  M  V  Q  G  W  I  T  N  F  Q  R  G  W  T  *  L  L  G  K  P  K  L  G  P  C  T  K  H  F  G  Y  L  G  L  P  S  C  V  D  G  S  R  *  G  L  P  Y  C  W  W  A  S  W  *  G  C  *  P  T  L  P  W  W  *  L  *  P  T  G  P  C  *  *  P  R  G  F  C  *  A  Q  G  K  R  D  Q  E  W  *  T  C  Y  V  L  H  V  R  I  L  C  S  S  Y  R  H  R  K  G  S  I  G  E  P  C  *  P  S  R  *  S  S  Q  *  Q  C  L  G  L  R  H  K  L  C  P  R  K </second_frame>
            <third_frame>   G  D  Y  G  W  D  T  A  G  L  S  A  D  P  E  T  F  A  K  N  R  E  L  E  V  I  H  C  R  W  A  M  L  G  A  L  G  C  V  F  P  E  L  L  A  R  N  G  V  K  F  G  E  A  V  W  F  K  A  G  S  Q  I  F  S  E  G  G  L  D  Y  L  G  N  P  S  L  V  H  A  Q  S  I  L  A  I  W  A  C  Q  V  V  L  M  G  A  V  E  G  Y  R  I  A  G  G  P  L  G  E  V  V  D  P  L  Y  P  G  G  S  F  D  P  L  G  L  A  D  D  P  E  A  F  A  E  L  K  V  K  E  I  K  N  G  R  L  A  M  F  S  M  F  G  F  F  V  Q  A  I  V  T  G  K  G  P  L  E  N  L  A  D  H  L  A  D  P  V  N  N  N  A  W  A  F  A  T  N  F  V  P  G   </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="C00SLm0103M17.2" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="41170" stop="40601"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>570</number_coding_nucleotides>
                  <number_encoded_amino_acids>190</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GDYGWDTAGLSADPETFAKNRELEVIHCRWAMLGALGCVFPELLARNGVKFGEAVWFKAGSQIFSEGGLDYLGNPSLVHAQSILAIWACQVVLMGAVEGYRIAGGPLGEVVDPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMFGFFVQAIVTGKGPLENLADHLADPVNNNAWAFATNFVPG</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 54 chains have been computed
$ 
$ memory statistics:
$ 10952 bytes spliced alignments in total
$ 5 spliced alignments have been stored
$ 2190 bytes was the average size of a spliced alignment
$ 8040 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2680 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 56 backtrace matrices have been allocated
$ 
$ date finished: 2009-11-30 18:29:14
-->
