<?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="2009-12-01 08:09:51"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02HBa0023N04-TqhHf/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02HBa0023N04-TqhHf/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-C02HBa0023N04-TqhHf/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1711" ref_strand="+" ref_description="T1711">
      <seq>ggtttaatatggaacacagatcttatagagactattgagttggaaaatcttttaattaatgcatgcatcaccatgcactcagccgaggcaagaaaagaaagcagaggagctcatgctcgtgaagattttacgaaaagagatgatgagaagtggatgaaacacaccataggatattgggaggacgagaaagttcggctagaatacagaccagtgcatatgaacactctagatgacgaagtcgagtcgttcccaccaaaggctcgtgtctactgatatactcatttatagggggatttggatggcgtagaagttgataataaggaaggttgcaataaatcgcgaaaattgtgaaattttggtaataactgtttgatttatttgtgcgatgaattgtaagcagcctgtgaagtgttcataaatattagaagcagaacaccgtttgtcttgtaatcaggaagcaaggcttcctgacttttcgatcttgtagaagatgatggaatcacttgtttatgctcttatatactctacttcttgcattttgacacgattgaagacattatctcattaccctgg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0023N04-TqhHf/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0023N04.3" temp_strand="-" temp_description="C02HBa0023N04.3  AC215358.2 htgs_phase:3 submitted_to_sgn_as:C02HBa0023N04 sequenced_by:kribb upload_account_name:korea">
        <position start="39865" stop="37591"/>
      </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="39663" g_stop="39653" g_length="11"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="11" r_length="11" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="39652" i_stop="39559" i_length="94">
            <donor d_prob="0.000" d_score="0.00"/>
            <acceptor a_prob="0.969" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="39558" g_stop="39438" g_length="121"/>
          <reference_exon_boundary r_type="cDNA" r_start="12" r_stop="132" r_length="121" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="39437" i_stop="39350" i_length="88">
            <donor d_prob="0.986" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="39349" g_stop="39312" g_length="38"/>
          <reference_exon_boundary r_type="cDNA" r_start="133" r_stop="170" r_length="38" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="39311" i_stop="38295" i_length="1017">
            <donor d_prob="0.999" d_score="0.00"/>
            <acceptor a_prob="0.935" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="38294" g_stop="37891" g_length="404"/>
          <reference_exon_boundary r_type="cDNA" r_start="171" r_stop="573" r_length="403" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0023N04.3" gen_strand="-" ref_id="T1711" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>574</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0023N04.3" gen_strand="-"/>
        <rDNA rDNA_id="T1711" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="39663" e_stop="39653"/>
          <exon e_start="39558" e_stop="39438"/>
          <exon e_start="39349" e_stop="39312"/>
          <exon e_start="38294" e_stop="37891"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGTTTAATATGGTATTATGGAGGAGATTATGAATCGTTATTAAATATTAGGTCTTCCTTTTCGTCTTGTTGTGTTCCTGAATTTCCTTCTATTTCAAATTCATAGGAACACAGATCTTATAGAGACTATTGAGTTGGAAAATCTTTTAATTAATGCATGCATCACCATGCACTCAGCCGAGGCAAGAAAAGAAAGCAGAGGAGCTCATGCTCGTGAAGATTTTACGGTCAGTTTCAATTTCTTATGAATCAGATAGTAGTGCTCTTTTTTTTCTTGTTTGTTCCTAATGGTTTGAACTTTTGATGGTTTTGCAGAAAAGAGATGATGAGAAGTGGATGAAACACACCATAGGGTAAGTGTTTTCCTTGTTTATTTTGATGGCTTACTTCTAGTCATCTTTCCTTAGTCTCTGCAATTGATGAAAGGTTTGCTTGATCATCCATTAAATCACCTTTCCATGAACATATCTTGTTGGGAGGGAGGGAAAGCGGAGGAGTATTGCAACCATTTTTGAGAATCTGTACCTAGTGTGATCTCACAAGTGGAATTTGGAAAGGTGGGGTGTATGCAGACCTTACGCCGACCTTGTTGAGGTAGAAAAGTAGTTTCTGACAGATCCTCGGCTCAAGAAAAGCATGATCTAAAACTGATCTGACAAATACTAAAGTAAAAGCTATAGTGAAAATTTTATGGAAATGAGAAGTAGGGGCAACAAAAACAATAAAGATAGCCTCAGTAAAAGAGACAACAACAAAAATAGCTGAAAAACTGAAGAATAGGATAATAATAATAATAATTCTGATAAGAGGGAGCAAACAAGGTGCTCTAAGCTAGTAGCCTGGAACCATGCTCTCCCGTGGGAAAGAGAGAAATTGCTTGATTACCTACTAACCCCCTCTACCCTGCCTTCATGTTTTCCCATCTTTGGTCATGTTCTCAATGAGCTGAAGATGTGTTATATTATGTCTTAATTGTTTCTCCCCAATTCTTTTTCGGTCTACCTCTACCTCTTGTTGGGCCCATCACTGGCAGCCTCTCTCAAGTCTCACCTCTTCATTGGAACTTTTGTGTTCCTTCTCTCTACATGTCCGAACAATCTCTAATCCTTCCTTCCTGCATCTTTTCTCTCGTAGTGTATCCATACATCCATCATCTCGTGAAATTGATGTAATACTTCAAAAAATTATTTTTTTTTTGTTAAAATAGTATTATCCTTCAAAAATTATTATCCATCGGAATGTGTTCCTGTGGTAGTGACTTAATTGTTCTCCAGTGCTCTTACCATGATTGATGCGCTCTACCGATTAAAGAAATCATGGTAGATGTACCCTACCAAGTGTTCAGCTTAACAAAGTTCATATATCTGCAGATATTGGGAGGACGAGAAAGTTCGGCTAGAATACAGACCAGTGCATATGAACACTCTAGATGACGAAGTCGAGTCGTTCCCACCAAAGGCTCGTGTCTACTGATATACTCATTTATAGGGGGGATTTGGATGGCGTAGAAGTTGATAATAAGGAAGGTTGCAATAAATCGCGAAAATTGTGAAATTTTGGTAATAACTGTTTGATTTATTTGTGCGATGAATTGTAAGCAGCCTGTGAAGTGTTCATAAATATTAGAAGCAGAACACCGTTTGTCTTGTAATCAGGAAGCAAGGCTTCCTGACTTTTCGATCTTGTAGAAGATGATGGAATCACTTGTTTATGCTCTTATATACTCTACTTCTTGCATTTTGACACGATTGAAGACATTATCTCATTACCCTGG</genome_strand>
        <mrna_strand>GGTTTAATATG..............................................................................................GAACACAGATCTTATAGAGACTATTGAGTTGGAAAATCTTTTAATTAATGCATGCATCACCATGCACTCAGCCGAGGCAAGAAAAGAAAGCAGAGGAGCTCATGCTCGTGAAGATTTTACG........................................................................................AAAAGAGATGATGAGAAGTGGATGAAACACACCATAGG.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATATTGGGAGGACGAGAAAGTTCGGCTAGAATACAGACCAGTGCATATGAACACTCTAGATGACGAAGTCGAGTCGTTCCCACCAAAGGCTCGTGTCTACTGATATACTCATTTATA-GGGGGATTTGGATGGCGTAGAAGTTGATAATAAGGAAGGTTGCAATAAATCGCGAAAATTGTGAAATTTTGGTAATAACTGTTTGATTTATTTGTGCGATGAATTGTAAGCAGCCTGTGAAGTGTTCATAAATATTAGAAGCAGAACACCGTTTGTCTTGTAATCAGGAAGCAAGGCTTCCTGACTTTTCGATCTTGTAGAAGATGATGGAATCACTTGTTTATGCTCTTATATACTCTACTTCTTGCATTTTGACACGATTGAAGACATTATCTCATTACCCTGG</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-C02HBa0023N04-TqhHf/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At3g50660" ref_strand="+" ref_description="C2_At3g50660">
      <seq>agcttattgagtattgaaactgaaaaaaggaaaaaaaacagagaagaagaaaaggaaaaacagtgaaatcatcaatgtctgacttagagttttttctttttcttgttcctccaatcttggcagtccttattattcttaatctattcaaaagaaaacacaaatttcaaaatcttccaccaggggatatgggttggccttttcttggtgaaactattggttatttgagaccttactcagttactactattggagatttcatgcaagatcatatctcaaggtatgggaaaattttcaagtcaaatttgtttggagagccaacaatagtttcagcagatgcagggcttaacagatacattctgcagaatgaagggagattatttgagtgtaattatccaagaagtataggtgggatacttggtaaatggtctatgttggttcaagttggacaaatgcatagagatatgaggatgatttctctgaattttttgagcaatgctagactcaggaatcaacttttaagtgaagttgaaaagcatactgtgcttgttcttggctcttggaaacaggattctgttgtttgtgcacaagatgaagcaaagaagtttacattcaactttatggcagagcatatcatgagtctacaacctggaaatccagagacagagaagctgaagaaagagtacatcacatttatgaaaaggagtggtttctgctccattgaattttccaggaacagcttacagaaaggccttacagtctcgatcaacattcttgga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0023N04-TqhHf/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0023N04.3" temp_strand="-" temp_description="C02HBa0023N04.3  AC215358.2 htgs_phase:3 submitted_to_sgn_as:C02HBa0023N04 sequenced_by:kribb upload_account_name:korea">
        <position start="55399" stop="53600"/>
      </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="55062" g_stop="54856" g_length="207"/>
          <reference_exon_boundary r_type="cDNA" r_start="71" r_stop="277" r_length="207" r_score="0.957"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="54855" i_stop="54790" i_length="66">
            <donor d_prob="0.996" d_score="0.92"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="54789" g_stop="54465" g_length="325"/>
          <reference_exon_boundary r_type="cDNA" r_start="278" r_stop="602" r_length="325" r_score="0.985"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="54464" i_stop="54179" i_length="286">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="0.990" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="54178" g_stop="54026" g_length="153"/>
          <reference_exon_boundary r_type="cDNA" r_start="603" r_stop="756" r_length="154" r_score="0.974"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="54025" i_stop="53921" i_length="105">
            <donor d_prob="0.854" d_score="1.00"/>
            <acceptor a_prob="0.983" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="53920" g_stop="53900" g_length="21"/>
          <reference_exon_boundary r_type="cDNA" r_start="757" r_stop="776" r_length="20" r_score="0.952"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0023N04.3" gen_strand="-" ref_id="C2_At3g50660" ref_strand="+">
        <total_alignment_score>0.974</total_alignment_score>
        <cumulative_length_of_scored_exons>706</cumulative_length_of_scored_exons>
        <coverage percentage="0.910" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0023N04.3" gen_strand="-"/>
        <rDNA rDNA_id="C2_At3g50660" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="55062" e_stop="54856"/>
          <exon e_start="54789" e_stop="54465"/>
          <exon e_start="54178" e_stop="54026"/>
          <exon e_start="53920" e_stop="53900"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATCAATGTCTGACTTAGAGTTTTTTCTTTTTCTTATTCCTCCAATCTTAGCAGTACTTATAATTCTTAATCTATTCAAAAGAAAACACAACTTTCAAAATCTTCCACCAGGGGATATGGGTTGGCCTTTTCTTGGTGAAACTATTGGTTATTTGAGACCTTATTCAGCTACTACTATTGGAGATTTCATGCAAGATCATATTTCTAGGTAAATCCCTTTTTTATTTGTGTGTTTGTTGAATTTTTGTACTGAAAAAATTGGATCTTTTTTCAGGTATGGGAAAATTTTCAAGTCAAATTTGTTTGGAGAGCCAACAATAGTTTCAGCAGATGCAGGGCTAAACAGATACATTCTGCAGAATGAAGGGAGATTATTTGAGTGTAATTATCCAAGAAGTATAGGTGGGATACTTGGTAAATGGTCTATGTTAGTTCAAGTTGGACAAATGCATAGAGATATGAGGATGATTTCTCTGAATTTTTTGAGCAATGCTAGGCTAAGGAATCAACTTTTAAGTGAAGTTGAAAAGCATACTTTGCTTGTTCTTGGCTCTTGGAAACAGGATTCTGTTGTTTGTGCACAAGATGAAGCAAAGAAGGTGAATAAGTGGCTTCGCACTATTTTGTTGTAGTTATTGATCGTATTTTTTCTTCTTTTTTCAATGTATTTTATCATGATTTTTGCACTTCCATAATTTCCTTAAGGTGAGTGTAAAACACTCTACCTTTCAAGGTAGGGTAAGGTTTACACGTTCAATGTACTCTTTCAGACCTCGTTCAATGTACTCTTTCAGACCTCATTTGTATGATTACACTGAGTATGTTATTATTGATGCTACTCTAACTTTGGAAATTGTTGTTGTTTTGTGTGTGAAATTTCTACAGTTAACATTCAACTTTATGGCAGAGCATATCATGAGTCTACAACCTGGAAATCCAGAGACAGAGAAGCTGAAAAAAGAGTACATCACATTTATGA-AAGGAGTGGTTTCTGCTCCATTGAATTTTCCAGGAACAGCTTACAGAAAGGCCTTACAGGTACCATTATAAATCACTAGGACATGAACGTGCTTACCATCTGAACAACCCCTTTTACTTGTTCACTTATTTTCAAGTTACGAATTATTTTTCTCTTTTCAACAGTCTCGATCAACAATTCTTGGA</genome_strand>
        <mrna_strand>ATCAATGTCTGACTTAGAGTTTTTTCTTTTTCTTGTTCCTCCAATCTTGGCAGTCCTTATTATTCTTAATCTATTCAAAAGAAAACACAAATTTCAAAATCTTCCACCAGGGGATATGGGTTGGCCTTTTCTTGGTGAAACTATTGGTTATTTGAGACCTTACTCAGTTACTACTATTGGAGATTTCATGCAAGATCATATCTCAAG..................................................................GTATGGGAAAATTTTCAAGTCAAATTTGTTTGGAGAGCCAACAATAGTTTCAGCAGATGCAGGGCTTAACAGATACATTCTGCAGAATGAAGGGAGATTATTTGAGTGTAATTATCCAAGAAGTATAGGTGGGATACTTGGTAAATGGTCTATGTTGGTTCAAGTTGGACAAATGCATAGAGATATGAGGATGATTTCTCTGAATTTTTTGAGCAATGCTAGACTCAGGAATCAACTTTTAAGTGAAGTTGAAAAGCATACTGTGCTTGTTCTTGGCTCTTGGAAACAGGATTCTGTTGTTTGTGCACAAGATGAAGCAAAGAAG..............................................................................................................................................................................................................................................................................................TTTACATTCAACTTTATGGCAGAGCATATCATGAGTCTACAACCTGGAAATCCAGAGACAGAGAAGCTGAAGAAAGAGTACATCACATTTATGAAAAGGAGTGGTTTCTGCTCCATTGAATTTTCCAGGAACAGCTTACAGAAAGGCCTTACAG.........................................................................................................TCTCGATCAAC-ATTCTTGGA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>2</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="39663" PGL_stop="37891"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="39663" e_stop="39653"/>
            <exon e_start="39558" e_stop="39438"/>
            <exon e_start="39349" e_stop="39312"/>
            <exon e_start="38294" e_stop="37891"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.000" acc_prob="0.969" e_score="1.000"/>
          <exon-intron don_prob="0.986" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.935" e_score="1.000"/>
          <exon-only e_score="0.998"/>
        </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="39663" e_stop="39653" e_length="11"/>
          </exon>
          <intron i_serial="1" don_prob="0.000" acc_prob="0.969">
            <gDNA_intron_boundary i_start="39652" i_stop="39559" i_length="94"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="39558" e_stop="39438" e_length="121"/>
          </exon>
          <intron i_serial="2" don_prob="0.986" acc_prob="1.000">
            <gDNA_intron_boundary i_start="39437" i_stop="39350" i_length="88"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="39349" e_stop="39312" e_length="38"/>
          </exon>
          <intron i_serial="3" don_prob="0.999" acc_prob="0.935">
            <gDNA_intron_boundary i_start="39311" i_stop="38295" i_length="1017"/>
          </intron>
          <exon e_serial="4" e_score="0.998">
            <gDNA_exon_boundary e_start="38294" e_stop="37891" e_length="404"/>
          </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="39663" stop="39653"/>
              <exon start="39558" stop="39438"/>
              <exon start="39349" stop="39312"/>
              <exon start="38294" stop="37891"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1711" 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>GGTTTAATATG : GAACACAGATCTTATAGAGACTATTGAGTTGGAAAATCTTTTAATTAATGCATGCATCACCATGCACTCAGCCGAGGCAAGAAAAGAAAGCAGAGGAGCTCATGCTCGTGAAGATTTTACG : AAAAGAGATGATGAGAAGTGGATGAAACACACCATAGG : ATATTGGGAGGACGAGAAAGTTCGGCTAGAATACAGACCAGTGCATATGAACACTCTAGATGACGAAGTCGAGTCGTTCCCACCAAAGGCTCGTGTCTACTGATATACTCATTTATAGGGGGGATTTGGATGGCGTAGAAGTTGATAATAAGGAAGGTTGCAATAAATCGCGAAAATTGTGAAATTTTGGTAATAACTGTTTGATTTATTTGTGCGATGAATTGTAAGCAGCCTGTGAAGTGTTCATAAATATTAGAAGCAGAACACCGTTTGTCTTGTAATCAGGAAGCAAGGCTTCCTGACTTTTCGATCTTGTAGAAGATGATGGAATCACTTGTTTATGCTCTTATATACTCTACTTCTTGCATTTTGACACGATTGAAGACATTATCTCATTACCCTGG</gDNA_template>
            <first_frame> G  L  I  W :   N  T  D  L  I  E  T  I  E  L  E  N  L  L  I  N  A  C  I  T  M  H  S  A  E  A  R  K  E  S  R  G  A  H  A  R  E  D  F  T  :  K  R  D  D  E  K  W  M  K  H  T  I  G :   Y  W  E  D  E  K  V  R  L  E  Y  R  P  V  H  M  N  T  L  D  D  E  V  E  S  F  P  P  K  A  R  V  Y  *  Y  T  H  L  *  G  G  F  G  W  R  R  S  *  *  *  G  R  L  Q  *  I  A  K  I  V  K  F  W  *  *  L  F  D  L  F  V  R  *  I  V  S  S  L  *  S  V  H  K  Y  *  K  Q  N  T  V  C  L  V  I  R  K  Q  G  F  L  T  F  R  S  C  R  R  *  W  N  H  L  F  M  L  L  Y  T  L  L  L  A  F  *  H  D  *  R  H  Y  L  I  T  L  </first_frame>
            <second_frame>  V  *  Y   : G  T  Q  I  L  *  R  L  L  S  W  K  I  F  *  L  M  H  A  S  P  C  T  Q  P  R  Q  E  K  K  A  E  E  L  M  L  V  K  I  L  R :   K  E  M  M  R  S  G  *  N  T  P  *   : D  I  G  R  T  R  K  F  G  *  N  T  D  Q  C  I  *  T  L  *  M  T  K  S  S  R  S  H  Q  R  L  V  S  T  D  I  L  I  Y  R  G  D  L  D  G  V  E  V  D  N  K  E  G  C  N  K  S  R  K  L  *  N  F  G  N  N  C  L  I  Y  L  C  D  E  L  *  A  A  C  E  V  F  I  N  I  R  S  R  T  P  F  V  L  *  S  G  S  K  A  S  *  L  F  D  L  V  E  D  D  G  I  T  C  L  C  S  Y  I  L  Y  F  L  H  F  D  T  I  E  D  I  I  S  L  P  W </second_frame>
            <third_frame>   F  N  M  :  E  H  R  S  Y  R  D  Y  *  V  G  K  S  F  N  *  C  M  H  H  H  A  L  S  R  G  K  K  R  K  Q  R  S  S  C  S  *  R  F  Y   : E  K  R  *  *  E  V  D  E  T  H  H  R  :  I  L  G  G  R  E  S  S  A  R  I  Q  T  S  A  Y  E  H  S  R  *  R  S  R  V  V  P  T  K  G  S  C  L  L  I  Y  S  F  I  G  G  I  W  M  A  *  K  L  I  I  R  K  V  A  I  N  R  E  N  C  E  I  L  V  I  T  V  *  F  I  C  A  M  N  C  K  Q  P  V  K  C  S  *  I  L  E  A  E  H  R  L  S  C  N  Q  E  A  R  L  P  D  F  S  I  L  *  K  M  M  E  S  L  V  Y  A  L  I  Y  S  T  S  C  I  L  T  R  L  K  T  L  S  H  Y  P   </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="C02HBa0023N04.3" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="39663" stop="39653"/>
                    <exon start="39558" stop="39438"/>
                    <exon start="39349" stop="39312"/>
                    <exon start="38294" stop="38192"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>270</number_coding_nucleotides>
                  <number_encoded_amino_acids>90</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GLIWNTDLIETIELENLLINACITMHSAEARKESRGAHAREDFTKRDDEKWMKHTIGYWEDEKVRLEYRPVHMNTLDDEVESFPPKARVY*</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="55062" PGL_stop="53900"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="55062" e_stop="54856"/>
            <exon e_start="54789" e_stop="54465"/>
            <exon e_start="54178" e_stop="54026"/>
            <exon e_start="53920" e_stop="53900"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.996" acc_prob="1.000" e_score="0.957"/>
          <exon-intron don_prob="0.991" acc_prob="0.990" e_score="0.985"/>
          <exon-intron don_prob="0.854" acc_prob="0.983" e_score="0.974"/>
          <exon-only e_score="0.952"/>
        </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="0.957">
            <gDNA_exon_boundary e_start="55062" e_stop="54856" e_length="207"/>
          </exon>
          <intron i_serial="1" don_prob="0.996" acc_prob="1.000">
            <gDNA_intron_boundary i_start="54855" i_stop="54790" i_length="66"/>
          </intron>
          <exon e_serial="2" e_score="0.985">
            <gDNA_exon_boundary e_start="54789" e_stop="54465" e_length="325"/>
          </exon>
          <intron i_serial="2" don_prob="0.991" acc_prob="0.990">
            <gDNA_intron_boundary i_start="54464" i_stop="54179" i_length="286"/>
          </intron>
          <exon e_serial="3" e_score="0.974">
            <gDNA_exon_boundary e_start="54178" e_stop="54026" e_length="153"/>
          </exon>
          <intron i_serial="3" don_prob="0.854" acc_prob="0.983">
            <gDNA_intron_boundary i_start="54025" i_stop="53921" i_length="105"/>
          </intron>
          <exon e_serial="4" e_score="0.952">
            <gDNA_exon_boundary e_start="53920" e_stop="53900" e_length="21"/>
          </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="55062" stop="54856"/>
              <exon start="54789" stop="54465"/>
              <exon start="54178" stop="54026"/>
              <exon start="53920" stop="53900"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At3g50660" 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>ATCAATGTCTGACTTAGAGTTTTTTCTTTTTCTTATTCCTCCAATCTTAGCAGTACTTATAATTCTTAATCTATTCAAAAGAAAACACAACTTTCAAAATCTTCCACCAGGGGATATGGGTTGGCCTTTTCTTGGTGAAACTATTGGTTATTTGAGACCTTATTCAGCTACTACTATTGGAGATTTCATGCAAGATCATATTTCTAG : GTATGGGAAAATTTTCAAGTCAAATTTGTTTGGAGAGCCAACAATAGTTTCAGCAGATGCAGGGCTAAACAGATACATTCTGCAGAATGAAGGGAGATTATTTGAGTGTAATTATCCAAGAAGTATAGGTGGGATACTTGGTAAATGGTCTATGTTAGTTCAAGTTGGACAAATGCATAGAGATATGAGGATGATTTCTCTGAATTTTTTGAGCAATGCTAGGCTAAGGAATCAACTTTTAAGTGAAGTTGAAAAGCATACTTTGCTTGTTCTTGGCTCTTGGAAACAGGATTCTGTTGTTTGTGCACAAGATGAAGCAAAGAAG : TTAACATTCAACTTTATGGCAGAGCATATCATGAGTCTACAACCTGGAAATCCAGAGACAGAGAAGCTGAAAAAAGAGTACATCACATTTATGAAAGGAGTGGTTTCTGCTCCATTGAATTTTCCAGGAACAGCTTACAGAAAGGCCTTACAG : TCTCGATCAACAATTCTTGGA</gDNA_template>
            <first_frame> I  N  V  *  L  R  V  F  S  F  S  Y  S  S  N  L  S  S  T  Y  N  S  *  S  I  Q  K  K  T  Q  L  S  K  S  S  T  R  G  Y  G  L  A  F  S  W  *  N  Y  W  L  F  E  T  L  F  S  Y  Y  Y  W  R  F  H  A  R  S  Y  F  *  :  V  W  E  N  F  Q  V  K  F  V  W  R  A  N  N  S  F  S  R  C  R  A  K  Q  I  H  S  A  E  *  R  E  I  I  *  V  *  L  S  K  K  Y  R  W  D  T  W  *  M  V  Y  V  S  S  S  W  T  N  A  *  R  Y  E  D  D  F  S  E  F  F  E  Q  C  *  A  K  E  S  T  F  K  *  S  *  K  A  Y  F  A  C  S  W  L  L  E  T  G  F  C  C  L  C  T  R  *  S  K  E   : V  N  I  Q  L  Y  G  R  A  Y  H  E  S  T  T  W  K  S  R  D  R  E  A  E  K  R  V  H  H  I  Y  E  R  S  G  F  C  S  I  E  F  S  R  N  S  L  Q  K  G  L  T   : V  S  I  N  N  S  W  </first_frame>
            <second_frame>  S  M  S  D  L  E  F  F  L  F  L  I  P  P  I  L  A  V  L  I  I  L  N  L  F  K  R  K  H  N  F  Q  N  L  P  P  G  D  M  G  W  P  F  L  G  E  T  I  G  Y  L  R  P  Y  S  A  T  T  I  G  D  F  M  Q  D  H  I  S  R :   Y  G  K  I  F  K  S  N  L  F  G  E  P  T  I  V  S  A  D  A  G  L  N  R  Y  I  L  Q  N  E  G  R  L  F  E  C  N  Y  P  R  S  I  G  G  I  L  G  K  W  S  M  L  V  Q  V  G  Q  M  H  R  D  M  R  M  I  S  L  N  F  L  S  N  A  R  L  R  N  Q  L  L  S  E  V  E  K  H  T  L  L  V  L  G  S  W  K  Q  D  S  V  V  C  A  Q  D  E  A  K  K  :  L  T  F  N  F  M  A  E  H  I  M  S  L  Q  P  G  N  P  E  T  E  K  L  K  K  E  Y  I  T  F  M  K  G  V  V  S  A  P  L  N  F  P  G  T  A  Y  R  K  A  L  Q  :  S  R  S  T  I  L  G </second_frame>
            <third_frame>   Q  C  L  T  *  S  F  F  F  F  L  F  L  Q  S  *  Q  Y  L  *  F  L  I  Y  S  K  E  N  T  T  F  K  I  F  H  Q  G  I  W  V  G  L  F  L  V  K  L  L  V  I  *  D  L  I  Q  L  L  L  L  E  I  S  C  K  I  I  F  L   : G  M  G  K  F  S  S  Q  I  C  L  E  S  Q  Q  *  F  Q  Q  M  Q  G  *  T  D  T  F  C  R  M  K  G  D  Y  L  S  V  I  I  Q  E  V  *  V  G  Y  L  V  N  G  L  C  *  F  K  L  D  K  C  I  E  I  *  G  *  F  L  *  I  F  *  A  M  L  G  *  G  I  N  F  *  V  K  L  K  S  I  L  C  L  F  L  A  L  G  N  R  I  L  L  F  V  H  K  M  K  Q  R  S :   *  H  S  T  L  W  Q  S  I  S  *  V  Y  N  L  E  I  Q  R  Q  R  S  *  K  K  S  T  S  H  L  *  K  E  W  F  L  L  H  *  I  F  Q  E  Q  L  T  E  R  P  Y  S :   L  D  Q  Q  F  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/">
            <orf_entry>
              <id_line>
                <gDNA id="C02HBa0023N04.3" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="55061" stop="54856"/>
                    <exon start="54789" stop="54465"/>
                    <exon start="54178" stop="54026"/>
                    <exon start="53920" stop="53900"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>705</number_coding_nucleotides>
                  <number_encoded_amino_acids>235</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SMSDLEFFLFLIPPILAVLIILNLFKRKHNFQNLPPGDMGWPFLGETIGYLRPYSATTIGDFMQDHISRYGKIFKSNLFGEPTIVSADAGLNRYILQNEGRLFECNYPRSIGGILGKWSMLVQVGQMHRDMRMISLNFLSNARLRNQLLSEVEKHTLLVLGSWKQDSVVCAQDEAKKLTFNFMAEHIMSLQPGNPETEKLKKEYITFMKGVVSAPLNFPGTAYRKALQSRSTILG</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 86 chains have been computed
$ 
$ memory statistics:
$ 4048 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2024 bytes was the average size of a spliced alignment
$ 6896 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3448 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 86 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 08:09:54
-->
