<?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="2009-12-03 20:50:25"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C01HBa0131F15-8RaTJ/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C01HBa0131F15-8RaTJ/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-C01HBa0131F15-8RaTJ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="TG158-R" ref_strand="+" ref_description="TG158-R">
      <seq>tatttgtttttatcacgctgttgcgtggtccgtttcacaatgtcttgtttgatttttcaaggtcgaactagtacttccaagaacagttcattctatgttttattgtttccattatttgttttgttgtatcttttttatagggtggaggcttgctttatgtaggagccaaagcccaacgaatccaatcaccaaatctattgaaatgaatacatgttgctgaggcctaaattgttaaaaatagatactgtcgtttgtctaacaccctccccatgtatatatgacccactaaaacagcaattttattaccttacaaaaaaattaatttcttctttttattaattttctattagttttggtccaaactcaaatattggtggttgttgttaagcctcattttgagttgacagaaaggcagcactttcttttgatacccggcttttccaagagcttttatcatcacacgagtcttttaatgttagtacttt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0131F15-8RaTJ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0131F15.1" temp_strand="+" temp_description="C01HBa0131F15.1  AC238909.3 htgs_phase:2 submitted_to_sgn_as:C01HBa0131F15 upload_account_name:manual">
        <position start="36719" stop="37803"/>
      </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="37019" g_stop="37503" g_length="485"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="485" r_length="485" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0131F15.1" gen_strand="+" ref_id="TG158-R" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>485</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0131F15.1" gen_strand="+"/>
        <rDNA rDNA_id="TG158-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="37019" e_stop="37503"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TATTTGTTTTTATCACGCTGTTGCGTGGTCCGTTTCACAATGTCTTGTTTGATTTTTCAAGGTCGAACTAGTACTTCCAAGAACAGTTCATTCTATGTTTTATTGTTTCCATTATTTGTTTTGTTGTATCTTTTTTATAGGGTGGAGGCTTGCTTTATGTAGGAGCCAAAGCCCAACGAATCCAATCACCAAATCTATTGAAATGAATACATGTTGCTGAGGCCTAAATTGTTAAAAATAGATACTGTCGTTTGTCTAACACCCTCCCCATGTATATATGACCCACTAAAACAGCAATTTTATTACCTTACAAAAAAATTAATTTCTTCTTTTTATTAATTTTCTATTAGTTTTGGTCCAAACTCAAATATTGGTGGTTGTTGTTAAGCCTCATTTTGAGTTGACAGAAAGGCAGCACTTTCTTTTGATACCCGGCTTTTCCAAGAGCTTTTATCATCACACGAGTCTTTTAATGTTAGTACTTT</genome_strand>
        <mrna_strand>TATTTGTTTTTATCACGCTGTTGCGTGGTCCGTTTCACAATGTCTTGTTTGATTTTTCAAGGTCGAACTAGTACTTCCAAGAACAGTTCATTCTATGTTTTATTGTTTCCATTATTTGTTTTGTTGTATCTTTTTTATAGGGTGGAGGCTTGCTTTATGTAGGAGCCAAAGCCCAACGAATCCAATCACCAAATCTATTGAAATGAATACATGTTGCTGAGGCCTAAATTGTTAAAAATAGATACTGTCGTTTGTCTAACACCCTCCCCATGTATATATGACCCACTAAAACAGCAATTTTATTACCTTACAAAAAAATTAATTTCTTCTTTTTATTAATTTTCTATTAGTTTTGGTCCAAACTCAAATATTGGTGGTTGTTGTTAAGCCTCATTTTGAGTTGACAGAAAGGCAGCACTTTCTTTTGATACCCGGCTTTTCCAAGAGCTTTTATCATCACACGAGTCTTTTAATGTTAGTACTTT</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-C01HBa0131F15-8RaTJ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="TG158-F" ref_strand="+" ref_description="TG158-F">
      <seq>ataagtaagaagtaacctacttgtttttcttttagaatgaagtaacctacattttttttttgtagaatgaagtaacctacttgtttgttttttttacaatgaagtaacctacttattcaagtgcaacaatatccaaattcaattttagaagcaaaagaaatactctagtaggttagaatgtcagccaaattaaatttgtactgctcccctaagactctccagattattactactgtgcctcaaccactcagccaaccccttggatatgaaaaacaagtgtaccttgatgcattttggaattgttatctctctaatagtctaatttcatgataactgctgtgcacatgaaaatatcctctcctactttctttgttctatcctctttcctcggagagcagataaatacttgtatgtgcccatgaagaagtattaccctaattaagccaataaatctaac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0131F15-8RaTJ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0131F15.1" temp_strand="-" temp_description="C01HBa0131F15.1  AC238909.3 htgs_phase:2 submitted_to_sgn_as:C01HBa0131F15 upload_account_name:manual">
        <position start="39191" stop="38135"/>
      </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="38891" g_stop="38435" g_length="457"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="457" r_length="457" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0131F15.1" gen_strand="-" ref_id="TG158-F" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>457</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0131F15.1" gen_strand="-"/>
        <rDNA rDNA_id="TG158-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="38891" e_stop="38435"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATAAGTAAGAAGTAACCTACTTGTTTTTCTTTTAGAATGAAGTAACCTACATTTTTTTTTTGTAGAATGAAGTAACCTACTTGTTTGTTTTTTTTACAATGAAGTAACCTACTTATTCAAGTGCAACAATATCCAAATTCAATTTTAGAAGCAAAAGAAATACTCTAGTAGGTTAGAATGTCAGCCAAATTAAATTTGTACTGCTCCCCTAAGACTCTCCAGATTATTACTACTGTGCCTCAACCACTCAGCCAACCCCTTGGATATGAAAAACAAGTGTACCTTGATGCATTTTGGAATTGTTATCTCTCTAATAGTCTAATTTCATGATAACTGCTGTGCACATGAAAATATCCTCTCCTACTTTCTTTGTTCTATCCTCTTTCCTCGGAGAGCAGATAAATACTTGTATGTGCCCATGAAGAAGTATTACCCTAATTAAGCCAATAAATCTAAC</genome_strand>
        <mrna_strand>ATAAGTAAGAAGTAACCTACTTGTTTTTCTTTTAGAATGAAGTAACCTACATTTTTTTTTTGTAGAATGAAGTAACCTACTTGTTTGTTTTTTTTACAATGAAGTAACCTACTTATTCAAGTGCAACAATATCCAAATTCAATTTTAGAAGCAAAAGAAATACTCTAGTAGGTTAGAATGTCAGCCAAATTAAATTTGTACTGCTCCCCTAAGACTCTCCAGATTATTACTACTGTGCCTCAACCACTCAGCCAACCCCTTGGATATGAAAAACAAGTGTACCTTGATGCATTTTGGAATTGTTATCTCTCTAATAGTCTAATTTCATGATAACTGCTGTGCACATGAAAATATCCTCTCCTACTTTCTTTGTTCTATCCTCTTTCCTCGGAGAGCAGATAAATACTTGTATGTGCCCATGAAGAAGTATTACCCTAATTAAGCCAATAAATCTAAC</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-C01HBa0131F15-8RaTJ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At2g21440" ref_strand="+" ref_description="C2_At2g21440">
      <seq>gtgatatgtcaaagcgcaaggggctgcaagaaaagaagattatcaaactgaagtccccaaatttccatgtgtcaaggacacggctgattatgtacaatattcccaagtcaatgactgaaaaacagctgaagacactttgcattgatgcagttacttctcgtgctactaagcaaaagcctgttatccggcagataaagtttttgaaggacgtcaaaaaaggacaagcagtggcaaagagtcattctcgtggagtagcttttcttgagttctcagagcatgaacatgcacttgtggctttgagagttcttaacaacaatcctgagacttttggtcccgagcatcgaccaatagtggagtttgctcttgataatatccaaacaatgaagcttcgtcagaaatttcagcagcaaggttttaacaggaacaaagaagatttgcagaagaatgacaatacaaatgaacgggatccccatgataaacagtcaagaaaacgaaaggcaacaggagaggatgaagcaaataacaagcgtgtcagaggtgccacttcgagggaaggcaatgtgtcgtcagtttcaggtagtaaagatggagatcaaccgaaaaacaaaggtgttaaaggagccaccttctctgcagaagaaagagatgagaagaagaacaagaagaaggaaggtaaaacgctaggaggtgcaaaacagaaactaaaagataatcaagaaggaaaaaggcatggtggctttggtagtgaaaaatcaggtaatgctactcccaaggttggacataaagaagatgttgcagcaagagcaacaaagaggaaatttgaagataaaactaaccaacaaaaacaaagcatcagtttacagaacaggaaaaaggataaaaagaagaaagacgcagttggacgagatggagtagacaagctagatatgcttattgaacaatatacatccaaattcactcgcaacagttctaatcaaactgatagtaaccagcagcgctctaagcagcttaagagatggttccaatcctaaaccattcacaggttttcgtgtagcttaattttatggtgatattaagaagaggtgagagtcatcgtttgtggtttgtattttttgttgtattttccccgtaaaatatctcataacaattttagttttaaaatatgggattacaattttggtcaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0131F15-8RaTJ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0131F15.1" temp_strand="-" temp_description="C01HBa0131F15.1  AC238909.3 htgs_phase:2 submitted_to_sgn_as:C01HBa0131F15 upload_account_name:manual">
        <position start="67417" stop="64529"/>
      </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="67117" g_stop="67096" g_length="22"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="22" r_length="22" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="67095" i_stop="66155" i_length="941">
            <donor d_prob="0.996" d_score="0.00"/>
            <acceptor a_prob="0.999" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="66154" g_stop="65986" g_length="169"/>
          <reference_exon_boundary r_type="cDNA" r_start="23" r_stop="191" r_length="169" r_score="0.988"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="65985" i_stop="65906" i_length="80">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="65905" g_stop="65776" g_length="130"/>
          <reference_exon_boundary r_type="cDNA" r_start="192" r_stop="321" r_length="130" r_score="0.977"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="65775" i_stop="65697" i_length="79">
            <donor d_prob="0.984" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="65696" g_stop="64824" g_length="873"/>
          <reference_exon_boundary r_type="cDNA" r_start="322" r_stop="1192" r_length="871" r_score="0.922"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0131F15.1" gen_strand="-" ref_id="C2_At2g21440" ref_strand="+">
        <total_alignment_score>0.938</total_alignment_score>
        <cumulative_length_of_scored_exons>1194</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0131F15.1" gen_strand="-"/>
        <rDNA rDNA_id="C2_At2g21440" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="67117" e_stop="67096"/>
          <exon e_start="66154" e_stop="65986"/>
          <exon e_start="65905" e_stop="65776"/>
          <exon e_start="65696" e_stop="64824"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTGATATGTCAAAGCGCAAGGGGTCAGTCTCACAAAACTCAAAATTTATCTTATATTCAAACTGGTGAATCTTGAAAGGAAAACATTCCTAACAATTGACTTCATATCAGCTGAGTTCATCTATAGTTTTTTGGCGACAGAAACTGCCCTCCTTTTTTTCTCTACTATAACTCTCTTTTGACAAAAGCTTCTTTAAGGTGTTATGGGACATTAATTCGTAGACCAAGAGTGATCCTTTTAAAGAAGTCTATATGTCCAGAGCACAAAAGCAATATATGATAGGGGTAGATAGATGAACTTGTGGTAATAGTAATGATAATATGTTAAAGAATTGGAGCTCCTCATTAAGACAAGACAATGAAGGTTGATTTTGCTTAGTTTGAAGATTTTCAGTTTTGCCCCCTCAGGCCACATTTCCTATTGGTAGTTACTTCTTTTCAATAATTCTAGCAGGGTTTCTGCATTCAACGGTTAACAAGTGATCTCCTCTTTATTTAATTTTGATCTGCCGGTGCAATTAGCATCGAACTATCTATTCCTTTCTTTTCACTTTATGCTGTACAAATGAATTGATTAGCTAATAAATTAGGTGAATATATAATTATTTACTTTACCTTCTTACTTCTTTTGATGGCCTTTGCAATATTTTTTGTTACTCAAATGTGTTTTTTTGCTATTTAATATATCAAATGAGTTTTTTTTAGGTAATCAATGCTTCAGCAAATAAAAGAACTCATTTGATGCAGAATGCTTTTATTGGCATGACATATGAGTTCAAATGAAGTAACATGGTGAATGAGGATTCATATCGTTAACCACTACTTGTTTGTGACTGAGGTGTAGTGGTAGCTGTTGTATTAGATGCAGAATGTTTAAGGAAGTTCTGGAGCTGTTCTATTGCAGTTTTAAAATGTTTTGTAAGTTCCTGTATAGCTTGCAATGCTAACGTTGTTCATTGTGTAGGCTGCAAGAAAAGAAGATTATCAAGCTGAAGTCCCCAAATTTCCATGTGTCAAGGACACGGCTGATTATGTACAATGTTCCCAAGTCAATGACTGAAAAACAGCTGAAGACACTTTGCATTGATGCAGTTACTTCTCGTGCTACTAAGCAAAAGCCTGTTATCCGGCAGGTGAGCTTTCCTTTGAAGTTTAGTCTTTGCAGTTTGGCTATATTATTCTTGCAACTTCATTATACTTTTCTGTGTTGCAGATAAAGTTTTTGAAGGACGTGAAAAAAGGACAAGCAGTGGCAAAGAATCATTCTCGTGGAGTAGCTTTTCTTGAGTTTTCAGAGCATGAACATGCACTTGTGGCTTTGAGAGTTCTTAACAACAATCCTGGCAAGTGTCTTTAGTTTTTTGATATCTGGTGACTTTTAGCATTTTACATTTCTGTATCTGAGTACTTATCTATTTTCAGAGACTTTTGGTCCTGAGCATCGACCAATAGTGGAGTTTGCTCTTGACAATATCCAAACAATGAAGCTTCGTCAGAAATTTCAGCAGCAAGGTTTTAACAGGAACAAAGAAGATTTGCAGAAGAATGACAATACGAATGAACGGGATACCCGCGATAAACAGTCAAGAAAACGGAAGGCCCCAGGAGAAGATGAAGCAACAAACAAGCGTGTCAGAGGTGTCACTTTAAGGGAAGGCAATGTGTCGTCAGTTTCAGGTAGTAAAGATGGAGATCAACCAAAAAATAAAGGTGTTAAAGGAGCCGCCTTCTCTGCAGAAAAAAGAGATGAGAAGAAGAAC---AAGAAGGAAGGTAAAAAGCTAGGAGGCACAAAACAGAAGCTAAACGATAATCAAGAAGGAAAAAGGCATGGTGGCTTTGGTAGTGAAAAAACAGGTAATGCTACTCCCAAGGTTGGACAAAGCGAATACGTTGCAGCAAGAGCAACAAAGAGGAAATTTGAAGATAAAACTAACCAACAAAAACAAAGCGTCAGTTTACAGAACCGGAAAAAGGATAAAAAGAAGAAAGATGCAGTTGGACGAGATGGAGTAGACAAGCTAGATATGCTAATTGAACAATATACATCCAAATTCACTCGCGGCAGTTCTAATCAAACTAATAGTAATCAGCAGCGCTCTAAGCAGCTTAAGAGATGGTTCCAATCCTAAACCATTCACAGGTTCTTGTGTAGCTTAATTTTATTGTGATAGTAAGAAAAGGTGAGAATCATCGTTTTTGGGTTTGTGTACTATTTTGTTGTATTTTCTCCATAAACTATCTCATAACAATATTTAGTTTTAAAATATGGGATTACATTTTTGGTCATAGATTTTC</genome_strand>
        <mrna_strand>GTGATATGTCAAAGCGCAAGGG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCTGCAAGAAAAGAAGATTATCAAACTGAAGTCCCCAAATTTCCATGTGTCAAGGACACGGCTGATTATGTACAATATTCCCAAGTCAATGACTGAAAAACAGCTGAAGACACTTTGCATTGATGCAGTTACTTCTCGTGCTACTAAGCAAAAGCCTGTTATCCGGCAG................................................................................ATAAAGTTTTTGAAGGACGTCAAAAAAGGACAAGCAGTGGCAAAGAGTCATTCTCGTGGAGTAGCTTTTCTTGAGTTCTCAGAGCATGAACATGCACTTGTGGCTTTGAGAGTTCTTAACAACAATCCTG...............................................................................AGACTTTTGGTCCCGAGCATCGACCAATAGTGGAGTTTGCTCTTGATAATATCCAAACAATGAAGCTTCGTCAGAAATTTCAGCAGCAAGGTTTTAACAGGAACAAAGAAGATTTGCAGAAGAATGACAATACAAATGAACGGGATCCCCATGATAAACAGTCAAGAAAACGAAAGGCAACAGGAGAGGATGAAGCAAATAACAAGCGTGTCAGAGGTGCCACTTCGAGGGAAGGCAATGTGTCGTCAGTTTCAGGTAGTAAAGATGGAGATCAACCGAAAAACAAAGGTGTTAAAGGAGCCACCTTCTCTGCAGAAGAAAGAGATGAGAAGAAGAACAAGAAGAAGGAAGGTAAAACGCTAGGAGGTGCAAAACAGAAACTAAAAGATAATCAAGAAGGAAAAAGGCATGGTGGCTTTGGTAGTGAAAAATCAGGTAATGCTACTCCCAAGGTTGGACATAAAGAAGATGTTGCAGCAAGAGCAACAAAGAGGAAATTTGAAGATAAAACTAACCAACAAAAACAAAGCATCAGTTTACAGAACAGGAAAAAGGATAAAAAGAAGAAAGACGCAGTTGGACGAGATGGAGTAGACAAGCTAGATATGCTTATTGAACAATATACATCCAAATTCACTCGCAACAGTTCTAATCAAACTGATAGTAACCAGCAGCGCTCTAAGCAGCTTAAGAGATGGTTCCAATCCTAAACCATTCACAGGTTTTCGTGTAGCTTAATTTTATGGTGATATTAAGAAGAGGTGAGAGTCATCGTTTGT-GG-TT-TGTA-TTTTTTGTTGTATTTTCCCCGTAAAATATCTCATAACAAT-TTTAGTTTTAAAATATGGGATTACAATTTTGGTCAAAAAAAAAA</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-C01HBa0131F15-8RaTJ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1903" ref_strand="+" ref_description="T1903">
      <seq>gcagatactcctgcaaatggaggttcaaatcctcatgagtccaaaaacaaccaaagtgaactttcagctaccgagaagcaagaagtgcagaacaaactgaccaaacttctgtcaatgctggatgagattgatagaaggtacagacaatattatcatcagatgcaaatagtggtctcatcatttgatgtagtagctggagatggagcagcaaaaccatacacagctcttgctcttcagacaatttccagacactttcgttgcttgcgtgatgcaatctgcgatcagattcgagcatcacgaagaagtcttggagagcaagatgcttcagaaaacagcaaagcgattggaatatcacgcctgcgttttgtggatcagcatattagacagcagagagccctgcagcagcttggtatgatgcaacaacatgcctggaggcctcagaggggattgcctgaaagctctgtttcagttttgcgtgcttggctctttgagcactttcttcatccctacccgaaagattctgaaaaaattatgctagcaaggcaaactggcttaacgagaagtca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0131F15-8RaTJ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0131F15.1" temp_strand="+" temp_description="C01HBa0131F15.1  AC238909.3 htgs_phase:2 submitted_to_sgn_as:C01HBa0131F15 upload_account_name:manual">
        <position start="83938" stop="86720"/>
      </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="84237" g_stop="84362" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="126" r_length="126" r_score="0.992"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="84363" i_stop="85848" i_length="1486">
            <donor d_prob="0.994" d_score="1.00"/>
            <acceptor a_prob="0.959" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="85849" g_stop="86228" g_length="380"/>
          <reference_exon_boundary r_type="cDNA" r_start="127" r_stop="506" r_length="380" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="86229" i_stop="86360" i_length="132">
            <donor d_prob="0.967" d_score="1.00"/>
            <acceptor a_prob="0.992" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="86361" g_stop="86420" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="507" r_stop="566" r_length="60" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0131F15.1" gen_strand="+" ref_id="T1903" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>566</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0131F15.1" gen_strand="+"/>
        <rDNA rDNA_id="T1903" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="84237" e_stop="84362"/>
          <exon e_start="85849" e_stop="86228"/>
          <exon e_start="86361" e_stop="86420"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCAGATACTCCTGCAAATGGAGGTTCAAATCCTCATGAGTCCAAAAACAACCAAAGTGAACTTTCAGCTACCGAGAAGCAAGAAGTGCAGAACAAACTGACCAAACTTCTGTCAATGCTGGATGAGGTATGGCCTATGGAAATATTTTTTTGTGTATCAGTTTTGATGATTTCCGATGTTCTAATCCAATGCTTCACAAATTTTTTATTTTCTTATTTCAATTGATGATTGCGTTGAAAGGAGTCAAACTAGTGGCTGCAGTATGTTGAGGACTTCTTTGACTGTCCACATTCATCTTTCCATCGACTTACTTGTCTGAGAGACCTTCTAACTGTGATGAAATAGATTAACTATTATCTGACAAAGAAAATACCATGAATGAAGCATATTATCTGATGATATTTCAACTTCCATGCACATTTTGAAGTTGTTCTCAAATATATTTCCATGAATTTGGTAATACAATAACTTAGTTTGGATACTCACTTCATAGGGTACTAATAGAGAGTTAACTATTATAGCAGTATCATTACTTATTACTATATTTCCAGTGAGTGGCTTCTCTAAAATGGCAAAGTAATGGTTACAAGGCATGACTAACTGCAGAATGATACAAGATATACTCTTGGGTCCTCAGATTTACCTGGGAATGTGGGCAATGAGGGTTGAAGTTGAACAAAACTGCATCAAGGAAATGTTAATCCAAAAACACCTATAGTTATTATTTTCCTTTCCCCCCTCCCTTTCTTTTCTCCCCGCTGCTAGAATGACACTAGAAGTGTAGCTTGGTAGCTAATCTCAGTGGCATAAATTTGTGGAAAGGCCTGCAAAATGTTCAGTTTCATGAGCACATGATTGAAACATGGGTGATACCATGGTGTTATATCTATCTTGGGAAAATAGTCAATTCCTAGTGTAGGATAATGGTTATTTATGTTAAGTTACAGTAACATAGTGTATTCCCACAAGTGAGGTCTGGGAAGGATAGCGAGTACGCGGACCTTACCTCGTTACTTGTGTTCAGTTAATGAAGGGAATTTCTTGTATATTGGCATCCTTCTTTTTACTTGTCCACTTCTGCCAGAGTTTCTAGTAATTAAGTTTATGAATGCACTGATGGTATTGAGAGTTCACAATTAGGCTGCAGTTTATACCTTTGTAGCAGGTATTATTCCTGAATGTATATTCTTCCTTCAATTGTTCTAGTACGTGTCTAGATTTATAATTTAGGGCAAACGTCAAGAATGTAAGAGAGTTCTCCGATCTGCTTACTGAAGACATGATCTTAGATAGGAAAATTCATAGGTCGAGGGTAAGGGCAGATGAGTATAGGTAGCCAAGAGTTGTGGTACATCTTGTTCTCCTAATTTCACTATTACCTATTGTTTCATTTGTTTGGTTTTCCTATTTTGCTGTCGGTTTTTTCTTTTTATCATGATGTTGCATTTGGGTCCATCAGAAACAAACCTCTCTAGCCCACAAAGGTAGGGATAAGGTATGTGTACATCCTACCTCCCCAGGCCCCACTTGTGGAATTACATCGGGTATGTTATTTTTGTTGCCATGTGTAATTTGCATGAAGTGGAAGTTGAACTATGGTGTATTGTCACAGATTGATAGAAGGTACAGACAATATTATCATCAGATGCAAATAGTGGTCTCATCATTTGATGTAGTAGCTGGAGATGGAGCAGCAAAACCATACACAGCTCTTGCTCTTCAGACAATTTCCAGACACTTTCGTTGCTTGCGTGATGCAATCTGCGATCAGATTCGAGCATCACGAAGAAGTCTTGGAGAGCAAGATGCTTCAGAAAACAGCAAAGCGATTGGAATATCACGCCTGCGTTTTGTGGATCAGCATATTAGACAGCAGAGAGCCCTGCAGCAGCTTGGTATGATGCAACAACATGCCTGGAGGCCTCAGAGGGGATTGCCTGAAAGCTCTGTTTCAGTTTTGCGTGCTTGGCTCTTTGAGCACTTTCTTCATCCGTAAGTTGATTAATTTAGACTGCATCCAGCACACGTTATTAAGCTTTTTCTTGAATTTGTATTGTTAGGAGACTTCAGTCATTCAAAAGAACTTTGGTCGTCGTCTAATTTGTAATTGTTTCTCTTTTCCAGCTACCCGAAAGATTCTGAAAAAATTATGCTAGCAAGGCAAACTGGCTTAACGAGAAGTCA</genome_strand>
        <mrna_strand>GCAGATACTCCTGCAAATGGAGGTTCAAATCCTCATGAGTCCAAAAACAACCAAAGTGAACTTTCAGCTACCGAGAAGCAAGAAGTGCAGAACAAACTGACCAAACTTCTGTCAATGCTGGATGAG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGATAGAAGGTACAGACAATATTATCATCAGATGCAAATAGTGGTCTCATCATTTGATGTAGTAGCTGGAGATGGAGCAGCAAAACCATACACAGCTCTTGCTCTTCAGACAATTTCCAGACACTTTCGTTGCTTGCGTGATGCAATCTGCGATCAGATTCGAGCATCACGAAGAAGTCTTGGAGAGCAAGATGCTTCAGAAAACAGCAAAGCGATTGGAATATCACGCCTGCGTTTTGTGGATCAGCATATTAGACAGCAGAGAGCCCTGCAGCAGCTTGGTATGATGCAACAACATGCCTGGAGGCCTCAGAGGGGATTGCCTGAAAGCTCTGTTTCAGTTTTGCGTGCTTGGCTCTTTGAGCACTTTCTTCATCC....................................................................................................................................CTACCCGAAAGATTCTGAAAAAATTATGCTAGCAAGGCAAACTGGCTTAACGAGAAGTCA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>4</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="37019" PGL_stop="37503"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="37019" e_stop="37503"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="37019" e_stop="37503" e_length="485"/>
          </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="37019" stop="37503"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="TG158-R" 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>TATTTGTTTTTATCACGCTGTTGCGTGGTCCGTTTCACAATGTCTTGTTTGATTTTTCAAGGTCGAACTAGTACTTCCAAGAACAGTTCATTCTATGTTTTATTGTTTCCATTATTTGTTTTGTTGTATCTTTTTTATAGGGTGGAGGCTTGCTTTATGTAGGAGCCAAAGCCCAACGAATCCAATCACCAAATCTATTGAAATGAATACATGTTGCTGAGGCCTAAATTGTTAAAAATAGATACTGTCGTTTGTCTAACACCCTCCCCATGTATATATGACCCACTAAAACAGCAATTTTATTACCTTACAAAAAAATTAATTTCTTCTTTTTATTAATTTTCTATTAGTTTTGGTCCAAACTCAAATATTGGTGGTTGTTGTTAAGCCTCATTTTGAGTTGACAGAAAGGCAGCACTTTCTTTTGATACCCGGCTTTTCCAAGAGCTTTTATCATCACACGAGTCTTTTAATGTTAGTACTTT</gDNA_template>
            <first_frame> Y  L  F  L  S  R  C  C  V  V  R  F  T  M  S  C  L  I  F  Q  G  R  T  S  T  S  K  N  S  S  F  Y  V  L  L  F  P  L  F  V  L  L  Y  L  F  Y  R  V  E  A  C  F  M  *  E  P  K  P  N  E  S  N  H  Q  I  Y  *  N  E  Y  M  L  L  R  P  K  L  L  K  I  D  T  V  V  C  L  T  P  S  P  C  I  Y  D  P  L  K  Q  Q  F  Y  Y  L  T  K  K  L  I  S  S  F  Y  *  F  S  I  S  F  G  P  N  S  N  I  G  G  C  C  *  A  S  F  *  V  D  R  K  A  A  L  S  F  D  T  R  L  F  Q  E  L  L  S  S  H  E  S  F  N  V  S  T   </first_frame>
            <second_frame>  I  C  F  Y  H  A  V  A  W  S  V  S  Q  C  L  V  *  F  F  K  V  E  L  V  L  P  R  T  V  H  S  M  F  Y  C  F  H  Y  L  F  C  C  I  F  F  I  G  W  R  L  A  L  C  R  S  Q  S  P  T  N  P  I  T  K  S  I  E  M  N  T  C  C  *  G  L  N  C  *  K  *  I  L  S  F  V  *  H  P  P  H  V  Y  M  T  H  *  N  S  N  F  I  T  L  Q  K  N  *  F  L  L  F  I  N  F  L  L  V  L  V  Q  T  Q  I  L  V  V  V  V  K  P  H  F  E  L  T  E  R  Q  H  F  L  L  I  P  G  F  S  K  S  F  Y  H  H  T  S  L  L  M  L  V  L  </second_frame>
            <third_frame>   F  V  F  I  T  L  L  R  G  P  F  H  N  V  L  F  D  F  S  R  S  N  *  Y  F  Q  E  Q  F  I  L  C  F  I  V  S  I  I  C  F  V  V  S  F  L  *  G  G  G  L  L  Y  V  G  A  K  A  Q  R  I  Q  S  P  N  L  L  K  *  I  H  V  A  E  A  *  I  V  K  N  R  Y  C  R  L  S  N  T  L  P  M  Y  I  *  P  T  K  T  A  I  L  L  P  Y  K  K  I  N  F  F  F  L  L  I  F  Y  *  F  W  S  K  L  K  Y  W  W  L  L  L  S  L  I  L  S  *  Q  K  G  S  T  F  F  *  Y  P  A  F  P  R  A  F  I  I  T  R  V  F  *  C  *  Y  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/">
            <none gDNA_id="C01HBa0131F15.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="38891" PGL_stop="38435"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="38891" e_stop="38435"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="38891" e_stop="38435" e_length="457"/>
          </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="38891" stop="38435"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="TG158-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>ATAAGTAAGAAGTAACCTACTTGTTTTTCTTTTAGAATGAAGTAACCTACATTTTTTTTTTGTAGAATGAAGTAACCTACTTGTTTGTTTTTTTTACAATGAAGTAACCTACTTATTCAAGTGCAACAATATCCAAATTCAATTTTAGAAGCAAAAGAAATACTCTAGTAGGTTAGAATGTCAGCCAAATTAAATTTGTACTGCTCCCCTAAGACTCTCCAGATTATTACTACTGTGCCTCAACCACTCAGCCAACCCCTTGGATATGAAAAACAAGTGTACCTTGATGCATTTTGGAATTGTTATCTCTCTAATAGTCTAATTTCATGATAACTGCTGTGCACATGAAAATATCCTCTCCTACTTTCTTTGTTCTATCCTCTTTCCTCGGAGAGCAGATAAATACTTGTATGTGCCCATGAAGAAGTATTACCCTAATTAAGCCAATAAATCTAAC</gDNA_template>
            <first_frame> I  S  K  K  *  P  T  C  F  S  F  R  M  K  *  P  T  F  F  F  C  R  M  K  *  P  T  C  L  F  F  L  Q  *  S  N  L  L  I  Q  V  Q  Q  Y  P  N  S  I  L  E  A  K  E  I  L  *  *  V  R  M  S  A  K  L  N  L  Y  C  S  P  K  T  L  Q  I  I  T  T  V  P  Q  P  L  S  Q  P  L  G  Y  E  K  Q  V  Y  L  D  A  F  W  N  C  Y  L  S  N  S  L  I  S  *  *  L  L  C  T  *  K  Y  P  L  L  L  S  L  F  Y  P  L  S  S  E  S  R  *  I  L  V  C  A  H  E  E  V  L  P  *  L  S  Q  *  I  *  </first_frame>
            <second_frame>  *  V  R  S  N  L  L  V  F  L  L  E  *  S  N  L  H  F  F  F  V  E  *  S  N  L  L  V  C  F  F  Y  N  E  V  T  Y  L  F  K  C  N  N  I  Q  I  Q  F  *  K  Q  K  K  Y  S  S  R  L  E  C  Q  P  N  *  I  C  T  A  P  L  R  L  S  R  L  L  L  L  C  L  N  H  S  A  N  P  L  D  M  K  N  K  C  T  L  M  H  F  G  I  V  I  S  L  I  V  *  F  H  D  N  C  C  A  H  E  N  I  L  S  Y  F  L  C  S  I  L  F  P  R  R  A  D  K  Y  L  Y  V  P  M  K  K  Y  Y  P  N  *  A  N  K  S  N </second_frame>
            <third_frame>   K  *  E  V  T  Y  L  F  F  F  *  N  E  V  T  Y  I  F  F  L  *  N  E  V  T  Y  L  F  V  F  F  T  M  K  *  P  T  Y  S  S  A  T  I  S  K  F  N  F  R  S  K  R  N  T  L  V  G  *  N  V  S  Q  I  K  F  V  L  L  P  *  D  S  P  D  Y  Y  Y  C  A  S  T  T  Q  P  T  P  W  I  *  K  T  S  V  P  *  C  I  L  E  L  L  S  L  *  *  S  N  F  M  I  T  A  V  H  M  K  I  S  S  P  T  F  F  V  L  S  S  F  L  G  E  Q  I  N  T  C  M  C  P  *  R  S  I  T  L  I  K  P  I  N  L   </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="C01HBa0131F15.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="67117" PGL_stop="64824"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="67117" e_stop="67096"/>
            <exon e_start="66154" e_stop="65986"/>
            <exon e_start="65905" e_stop="65776"/>
            <exon e_start="65696" e_stop="64824"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.996" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="1.000" e_score="0.988"/>
          <exon-intron don_prob="0.984" acc_prob="0.995" e_score="0.977"/>
          <exon-only e_score="0.922"/>
        </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="67117" e_stop="67096" e_length="22"/>
          </exon>
          <intron i_serial="1" don_prob="0.996" acc_prob="0.999">
            <gDNA_intron_boundary i_start="67095" i_stop="66155" i_length="941"/>
          </intron>
          <exon e_serial="2" e_score="0.988">
            <gDNA_exon_boundary e_start="66154" e_stop="65986" e_length="169"/>
          </exon>
          <intron i_serial="2" don_prob="1.000" acc_prob="1.000">
            <gDNA_intron_boundary i_start="65985" i_stop="65906" i_length="80"/>
          </intron>
          <exon e_serial="3" e_score="0.977">
            <gDNA_exon_boundary e_start="65905" e_stop="65776" e_length="130"/>
          </exon>
          <intron i_serial="3" don_prob="0.984" acc_prob="0.995">
            <gDNA_intron_boundary i_start="65775" i_stop="65697" i_length="79"/>
          </intron>
          <exon e_serial="4" e_score="0.922">
            <gDNA_exon_boundary e_start="65696" e_stop="64824" e_length="873"/>
          </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="67117" stop="67096"/>
              <exon start="66154" stop="65986"/>
              <exon start="65905" stop="65776"/>
              <exon start="65696" stop="64824"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At2g21440" 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>GTGATATGTCAAAGCGCAAGGG : GCTGCAAGAAAAGAAGATTATCAAGCTGAAGTCCCCAAATTTCCATGTGTCAAGGACACGGCTGATTATGTACAATGTTCCCAAGTCAATGACTGAAAAACAGCTGAAGACACTTTGCATTGATGCAGTTACTTCTCGTGCTACTAAGCAAAAGCCTGTTATCCGGCAG : ATAAAGTTTTTGAAGGACGTGAAAAAAGGACAAGCAGTGGCAAAGAATCATTCTCGTGGAGTAGCTTTTCTTGAGTTTTCAGAGCATGAACATGCACTTGTGGCTTTGAGAGTTCTTAACAACAATCCTG : AGACTTTTGGTCCTGAGCATCGACCAATAGTGGAGTTTGCTCTTGACAATATCCAAACAATGAAGCTTCGTCAGAAATTTCAGCAGCAAGGTTTTAACAGGAACAAAGAAGATTTGCAGAAGAATGACAATACGAATGAACGGGATACCCGCGATAAACAGTCAAGAAAACGGAAGGCCCCAGGAGAAGATGAAGCAACAAACAAGCGTGTCAGAGGTGTCACTTTAAGGGAAGGCAATGTGTCGTCAGTTTCAGGTAGTAAAGATGGAGATCAACCAAAAAATAAAGGTGTTAAAGGAGCCGCCTTCTCTGCAGAAAAAAGAGATGAGAAGAAGAACAAGAAGGAAGGTAAAAAGCTAGGAGGCACAAAACAGAAGCTAAACGATAATCAAGAAGGAAAAAGGCATGGTGGCTTTGGTAGTGAAAAAACAGGTAATGCTACTCCCAAGGTTGGACAAAGCGAATACGTTGCAGCAAGAGCAACAAAGAGGAAATTTGAAGATAAAACTAACCAACAAAAACAAAGCGTCAGTTTACAGAACCGGAAAAAGGATAAAAAGAAGAAAGATGCAGTTGGACGAGATGGAGTAGACAAGCTAGATATGCTAATTGAACAATATACATCCAAATTCACTCGCGGCAGTTCTAATCAAACTAATAGTAATCAGCAGCGCTCTAAGCAGCTTAAGAGATGGTTCCAATCCTAAACCATTCACAGGTTCTTGTGTAGCTTAATTTTATTGTGATAGTAAGAAAAGGTGAGAATCATCGTTTTTGGGTTTGTGTACTATTTTGTTGTATTTTCTCCATAAACTATCTCATAACAATATTTAGTTTTAAAATATGGGATTACATTTTTGGTCATAGATTTTC</gDNA_template>
            <first_frame> V  I  C  Q  S  A  R   : G  C  K  K  R  R  L  S  S  *  S  P  Q  I  S  M  C  Q  G  H  G  *  L  C  T  M  F  P  S  Q  *  L  K  N  S  *  R  H  F  A  L  M  Q  L  L  L  V  L  L  S  K  S  L  L  S  G  R :   *  S  F  *  R  T  *  K  K  D  K  Q  W  Q  R  I  I  L  V  E  *  L  F  L  S  F  Q  S  M  N  M  H  L  W  L  *  E  F  L  T  T  I  L  :  R  L  L  V  L  S  I  D  Q  *  W  S  L  L  L  T  I  S  K  Q  *  S  F  V  R  N  F  S  S  K  V  L  T  G  T  K  K  I  C  R  R  M  T  I  R  M  N  G  I  P  A  I  N  S  Q  E  N  G  R  P  Q  E  K  M  K  Q  Q  T  S  V  S  E  V  S  L  *  G  K  A  M  C  R  Q  F  Q  V  V  K  M  E  I  N  Q  K  I  K  V  L  K  E  P  P  S  L  Q  K  K  E  M  R  R  R  T  R  R  K  V  K  S  *  E  A  Q  N  R  S  *  T  I  I  K  K  E  K  G  M  V  A  L  V  V  K  K  Q  V  M  L  L  P  R  L  D  K  A  N  T  L  Q  Q  E  Q  Q  R  G  N  L  K  I  K  L  T  N  K  N  K  A  S  V  Y  R  T  G  K  R  I  K  R  R  K  M  Q  L  D  E  M  E  *  T  S  *  I  C  *  L  N  N  I  H  P  N  S  L  A  A  V  L  I  K  L  I  V  I  S  S  A  L  S  S  L  R  D  G  S  N  P  K  P  F  T  G  S  C  V  A  *  F  Y  C  D  S  K  K  R  *  E  S  S  F  L  G  L  C  T  I  L  L  Y  F  L  H  K  L  S  H  N  N  I  *  F  *  N  M  G  L  H  F  W  S  *  I  F </first_frame>
            <second_frame>  *  Y  V  K  A  Q  G  :  A  A  R  K  E  D  Y  Q  A  E  V  P  K  F  P  C  V  K  D  T  A  D  Y  V  Q  C  S  Q  V  N  D  *  K  T  A  E  D  T  L  H  *  C  S  Y  F  S  C  Y  *  A  K  A  C  Y  P  A   : D  K  V  F  E  G  R  E  K  R  T  S  S  G  K  E  S  F  S  W  S  S  F  S  *  V  F  R  A  *  T  C  T  C  G  F  E  S  S  *  Q  Q  S  * :   D  F  W  S  *  A  S  T  N  S  G  V  C  S  *  Q  Y  P  N  N  E  A  S  S  E  I  S  A  A  R  F  *  Q  E  Q  R  R  F  A  E  E  *  Q  Y  E  *  T  G  Y  P  R  *  T  V  K  K  T  E  G  P  R  R  R  *  S  N  K  Q  A  C  Q  R  C  H  F  K  G  R  Q  C  V  V  S  F  R  *  *  R  W  R  S  T  K  K  *  R  C  *  R  S  R  L  L  C  R  K  K  R  *  E  E  E  Q  E  G  R  *  K  A  R  R  H  K  T  E  A  K  R  *  S  R  R  K  K  A  W  W  L  W  *  *  K  N  R  *  C  Y  S  Q  G  W  T  K  R  I  R  C  S  K  S  N  K  E  E  I  *  R  *  N  *  P  T  K  T  K  R  Q  F  T  E  P  E  K  G  *  K  E  E  R  C  S  W  T  R  W  S  R  Q  A  R  Y  A  N  *  T  I  Y  I  Q  I  H  S  R  Q  F  *  S  N  *  *  *  S  A  A  L  *  A  A  *  E  M  V  P  I  L  N  H  S  Q  V  L  V  *  L  N  F  I  V  I  V  R  K  G  E  N  H  R  F  W  V  C  V  L  F  C  C  I  F  S  I  N  Y  L  I  T  I  F  S  F  K  I  W  D  Y  I  F  G  H  R  F   </second_frame>
            <third_frame>   D  M  S  K  R  K  G :   L  Q  E  K  K  I  I  K  L  K  S  P  N  F  H  V  S  R  T  R  L  I  M  Y  N  V  P  K  S  M  T  E  K  Q  L  K  T  L  C  I  D  A  V  T  S  R  A  T  K  Q  K  P  V  I  R  Q  :  I  K  F  L  K  D  V  K  K  G  Q  A  V  A  K  N  H  S  R  G  V  A  F  L  E  F  S  E  H  E  H  A  L  V  A  L  R  V  L  N  N  N  P   : E  T  F  G  P  E  H  R  P  I  V  E  F  A  L  D  N  I  Q  T  M  K  L  R  Q  K  F  Q  Q  Q  G  F  N  R  N  K  E  D  L  Q  K  N  D  N  T  N  E  R  D  T  R  D  K  Q  S  R  K  R  K  A  P  G  E  D  E  A  T  N  K  R  V  R  G  V  T  L  R  E  G  N  V  S  S  V  S  G  S  K  D  G  D  Q  P  K  N  K  G  V  K  G  A  A  F  S  A  E  K  R  D  E  K  K  N  K  K  E  G  K  K  L  G  G  T  K  Q  K  L  N  D  N  Q  E  G  K  R  H  G  G  F  G  S  E  K  T  G  N  A  T  P  K  V  G  Q  S  E  Y  V  A  A  R  A  T  K  R  K  F  E  D  K  T  N  Q  Q  K  Q  S  V  S  L  Q  N  R  K  K  D  K  K  K  K  D  A  V  G  R  D  G  V  D  K  L  D  M  L  I  E  Q  Y  T  S  K  F  T  R  G  S  S  N  Q  T  N  S  N  Q  Q  R  S  K  Q  L  K  R  W  F  Q  S  *  T  I  H  R  F  L  C  S  L  I  L  L  *  *  *  E  K  V  R  I  I  V  F  G  F  V  Y  Y  F  V  V  F  S  P  *  T  I  S  *  Q  Y  L  V  L  K  Y  G  I  T  F  L  V  I  D  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="C01HBa0131F15.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="67115" stop="67096"/>
                    <exon start="66154" stop="65986"/>
                    <exon start="65905" stop="65776"/>
                    <exon start="65696" stop="64990"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>1023</number_coding_nucleotides>
                  <number_encoded_amino_acids>341</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>DMSKRKGLQEKKIIKLKSPNFHVSRTRLIMYNVPKSMTEKQLKTLCIDAVTSRATKQKPVIRQIKFLKDVKKGQAVAKNHSRGVAFLEFSEHEHALVALRVLNNNPETFGPEHRPIVEFALDNIQTMKLRQKFQQQGFNRNKEDLQKNDNTNERDTRDKQSRKRKAPGEDEATNKRVRGVTLREGNVSSVSGSKDGDQPKNKGVKGAAFSAEKRDEKKNKKEGKKLGGTKQKLNDNQEGKRHGGFGSEKTGNATPKVGQSEYVAARATKRKFEDKTNQQKQSVSLQNRKKDKKKKDAVGRDGVDKLDMLIEQYTSKFTRGSSNQTNSNQQRSKQLKRWFQS*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="4" PGL_strand="+" PGL_start="84237" PGL_stop="86420"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="84237" e_stop="84362"/>
            <exon e_start="85849" e_stop="86228"/>
            <exon e_start="86361" e_stop="86420"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.994" acc_prob="0.959" e_score="0.992"/>
          <exon-intron don_prob="0.967" acc_prob="0.992" 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="0.992">
            <gDNA_exon_boundary e_start="84237" e_stop="84362" e_length="126"/>
          </exon>
          <intron i_serial="1" don_prob="0.994" acc_prob="0.959">
            <gDNA_intron_boundary i_start="84363" i_stop="85848" i_length="1486"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="85849" e_stop="86228" e_length="380"/>
          </exon>
          <intron i_serial="2" don_prob="0.967" acc_prob="0.992">
            <gDNA_intron_boundary i_start="86229" i_stop="86360" i_length="132"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="86361" e_stop="86420" e_length="60"/>
          </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="84237" stop="84362"/>
              <exon start="85849" stop="86228"/>
              <exon start="86361" stop="86420"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1903" 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="4" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>TCAGATACTCCTGCAAATGGAGGTTCAAATCCTCATGAGTCCAAAAACAACCAAAGTGAACTTTCAGCTACCGAGAAGCAAGAAGTGCAGAACAAACTGACCAAACTTCTGTCAATGCTGGATGAG : ATTGATAGAAGGTACAGACAATATTATCATCAGATGCAAATAGTGGTCTCATCATTTGATGTAGTAGCTGGAGATGGAGCAGCAAAACCATACACAGCTCTTGCTCTTCAGACAATTTCCAGACACTTTCGTTGCTTGCGTGATGCAATCTGCGATCAGATTCGAGCATCACGAAGAAGTCTTGGAGAGCAAGATGCTTCAGAAAACAGCAAAGCGATTGGAATATCACGCCTGCGTTTTGTGGATCAGCATATTAGACAGCAGAGAGCCCTGCAGCAGCTTGGTATGATGCAACAACATGCCTGGAGGCCTCAGAGGGGATTGCCTGAAAGCTCTGTTTCAGTTTTGCGTGCTTGGCTCTTTGAGCACTTTCTTCATCC : CTACCCGAAAGATTCTGAAAAAATTATGCTAGCAAGGCAAACTGGCTTAACGAGAAGTCA</gDNA_template>
            <first_frame> S  D  T  P  A  N  G  G  S  N  P  H  E  S  K  N  N  Q  S  E  L  S  A  T  E  K  Q  E  V  Q  N  K  L  T  K  L  L  S  M  L  D  E  :  I  D  R  R  Y  R  Q  Y  Y  H  Q  M  Q  I  V  V  S  S  F  D  V  V  A  G  D  G  A  A  K  P  Y  T  A  L  A  L  Q  T  I  S  R  H  F  R  C  L  R  D  A  I  C  D  Q  I  R  A  S  R  R  S  L  G  E  Q  D  A  S  E  N  S  K  A  I  G  I  S  R  L  R  F  V  D  Q  H  I  R  Q  Q  R  A  L  Q  Q  L  G  M  M  Q  Q  H  A  W  R  P  Q  R  G  L  P  E  S  S  V  S  V  L  R  A  W  L  F  E  H  F  L  H  P :   Y  P  K  D  S  E  K  I  M  L  A  R  Q  T  G  L  T  R  S   </first_frame>
            <second_frame>  Q  I  L  L  Q  M  E  V  Q  I  L  M  S  P  K  T  T  K  V  N  F  Q  L  P  R  S  K  K  C  R  T  N  *  P  N  F  C  Q  C  W  M  R :   L  I  E  G  T  D  N  I  I  I  R  C  K  *  W  S  H  H  L  M  *  *  L  E  M  E  Q  Q  N  H  T  Q  L  L  L  F  R  Q  F  P  D  T  F  V  A  C  V  M  Q  S  A  I  R  F  E  H  H  E  E  V  L  E  S  K  M  L  Q  K  T  A  K  R  L  E  Y  H  A  C  V  L  W  I  S  I  L  D  S  R  E  P  C  S  S  L  V  *  C  N  N  M  P  G  G  L  R  G  D  C  L  K  A  L  F  Q  F  C  V  L  G  S  L  S  T  F  F  I   : P  T  R  K  I  L  K  K  L  C  *  Q  G  K  L  A  *  R  E  V  </second_frame>
            <third_frame>   R  Y  S  C  K  W  R  F  K  S  S  *  V  Q  K  Q  P  K  *  T  F  S  Y  R  E  A  R  S  A  E  Q  T  D  Q  T  S  V  N  A  G  *   : D  *  *  K  V  Q  T  I  L  S  S  D  A  N  S  G  L  I  I  *  C  S  S  W  R  W  S  S  K  T  I  H  S  S  C  S  S  D  N  F  Q  T  L  S  L  L  A  *  C  N  L  R  S  D  S  S  I  T  K  K  S  W  R  A  R  C  F  R  K  Q  Q  S  D  W  N  I  T  P  A  F  C  G  S  A  Y  *  T  A  E  S  P  A  A  A  W  Y  D  A  T  T  C  L  E  A  S  E  G  I  A  *  K  L  C  F  S  F  A  C  L  A  L  *  A  L  S  S  S  :  L  P  E  R  F  *  K  N  Y  A  S  K  A  N  W  L  N  E  K  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="C01HBa0131F15.1" strand="+"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="84237" stop="84362"/>
                    <exon start="85849" stop="86228"/>
                    <exon start="86361" stop="86418"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>564</number_coding_nucleotides>
                  <number_encoded_amino_acids>188</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SDTPANGGSNPHESKNNQSELSATEKQEVQNKLTKLLSMLDEIDRRYRQYYHQMQIVVSSFDVVAGDGAAKPYTALALQTISRHFRCLRDAICDQIRASRRSLGEQDASENSKAIGISRLRFVDQHIRQQRALQQLGMMQQHAWRPQRGLPESSVSVLRAWLFEHFLHPYPKDSEKIMLARQTGLTRS</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 10 chains have been computed
$ 
$ memory statistics:
$ 8896 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 2224 bytes was the average size of a spliced alignment
$ 9216 bytes predicted gene locations in total
$ 4 predicted gene locations have been stored
$ 2304 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 10 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-03 20:50:28
-->
