<?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 10:56:03"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02SLe0026H18-MNs3q/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02SLe0026H18-MNs3q/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-C02SLe0026H18-MNs3q/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At4g35550" ref_strand="+" ref_description="C2_At4g35550">
      <seq>ctttactttctggttaccctttttttactcactctctctgtttacttcaactctcagaaacagatacaattttgtgatgacccttttaaggaattgactaaaacaagaggaaattatggagtgggaaaaacagcagcagcagcagcagccggtgtcggcgccgcagcagacggtggaggaattgaacggagcagttagtggtgggatgtttgtgaaagtgatgacggatgagcaaatggaagttttaaggaagcaaatcgctgtttatgctactatttgtgaacaacttgttgatttgcataaatccatggcttcacaacacgatcttgctggagccaggctgggaaatttgtactgcgatccactagtgacatccgctggccataaaatcactggtagacaacgctggactccaacgcctatgcaacttcagattcttgagcgcatatttgaacaaggcaatggaactccaaccaaacagaagatcaaagatataacttctgaattatctcaacatggacaaatttctgaaacaaatgtgtataattggtttcaaaataggcgtgctcgatcaaaaaggaagcaacaggttgcagcaacaaacaccactgaatcagaggtggagacagaggttgagtcacccaatgaaaagaaaacaaagccagaggatctgcagtcttctcacatgcctacttcaatggctgaagatcttggctatgagaaccctgacgtgagctctggcatgcattcactaaatccacgaaccagtaaacccgagcctatgtttccatcagacggtagtttaaaacctgc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02SLe0026H18-MNs3q/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02SLe0026H18.1" temp_strand="-" temp_description="C02SLe0026H18.1  AC215450.2 htgs_phase:3 submitted_to_sgn_as:C02SLe0026H18 sequenced_by:kribb upload_account_name:korea">
        <position start="67581" stop="65135"/>
      </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="67229" g_stop="66962" g_length="268"/>
          <reference_exon_boundary r_type="cDNA" r_start="64" r_stop="332" r_length="269" r_score="0.951"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="66961" i_stop="65916" i_length="1046">
            <donor d_prob="0.995" d_score="0.98"/>
            <acceptor a_prob="0.899" a_score="0.92"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="65915" g_stop="65435" g_length="481"/>
          <reference_exon_boundary r_type="cDNA" r_start="333" r_stop="813" r_length="481" r_score="0.975"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02SLe0026H18.1" gen_strand="-" ref_id="C2_At4g35550" ref_strand="+">
        <total_alignment_score>0.967</total_alignment_score>
        <cumulative_length_of_scored_exons>749</cumulative_length_of_scored_exons>
        <coverage percentage="0.921" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02SLe0026H18.1" gen_strand="-"/>
        <rDNA rDNA_id="C2_At4g35550" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="67229" e_stop="66962"/>
          <exon e_start="65915" e_stop="65435"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATACAATTTTGTGATGACCCTTTTAAGGAATTGACTAAAACAAAGAGGAAAATTATGGATTGGGAAAAACAGCAGCAGCAGC--CA-CCGGTGTCGGCGCCGCAGCAGACGGCGGAGGAATTGAACGGAACAGTCAGTGGTGGGATGTTTGTGAAAGTGATGACGGATGAGCAAATGGAAGTTTTAAGGAAGCAAATCGCTGTTTATGCTACTATTTGTGAACAGCTTGTTGATTTGCATAAATCCATGGCTTCACAACACGATCTTGCTGGTTCGTCTATTTTTATATTTATATTTGGTCTTGATATCTAATTGGGCCTTTTTTTTTTCTGTTAATTTTATCAATTTTTGTGTCTTTTTTAGCTATGGTTTCTCTATTCTGTTTCTTTTGGTTGATTTTGTCTTTTTTTTTTCCTCTAGGAATTGAAGTTCAAAAACTTGAGAGAAAATAGAAAAATGAAATCATTTCATAATTCTTACCTTTTCTGTTAATTTTGGTAAAAATAAATTCAAATAGTTCTATTCAGCTTAAATGTCTCAAAGATTCAAAGTTTTGTGTTTCCTTTTGGTATAGAATTTCATTGTATTGATTCTCCTTAAGTTTTTGAATTTTTTTACTTTTGGTATAGAATCTCATTTGATTCTTTAGTTTTATTTCTTACTCTACCCATCCAAATATAGTTCCCTCTAGGTTATCTCTCCCACATAATCCTTTGAGAATCCTGTAACGCTATGTGCGGGGTCCGGGGAAGGACCGAACTGTTAGGGTCTATTGTACGTAATTTTACCATGCATTAGCTTGAACCCTTGATCTCCCCGTAACATGACAACAACTTTACTAGTTAGGCGACTTGTAAAAAATGTAGTAGTGAAACTTGCCAGTAACATGGAAGCTGGAAATCTTTCAATCCATGACTGTATGCTGAAATCTTTAATTGATTGCAATGTTCAATGACAGGTGGATTTTGCAGACTTTAGGTTTCATATTTTTATTCGATGAAATCGATTCAAAGGAAACCCAATATAACCTCCTCCTTTTGAGTGGTTCTTCAAATTTTTTGTATATGATAAACGACCATTTCCATGTTTCAAGATACTAGTATTGGTTTCATTCGACTTTAGAGTGAATGATTGTACTGTTAACCATGATGCAAGAAGCTGGAGGACGATAGTTTTCTCAGTTAGACTTATTAATGGTCTTAATTTGTTGTGCTTAACATCCATATGTTCAACTTGATGTGTTTGTAGTGATCGCTAATATTACTTTCTGAATTTGAATTCATCTAATGTGAGCAAAATCTGTACCTGCAACCTCAGGAGCCAGGCTGGGAAATCTGTACTGCGATCCACTGGTGACATCTGCTGGTCATAAAATCACTGGTAGACAACGCTGGACTCCAACACCTATGCAACTTCAGATTCTTGAGCGCATATTTGAACAAGGCAATGGAACTCCAACCAAACAGAAGATCAAAGAGATAACTTCTGAATTATCTCAACATGGCCAAATTTCTGAAACAAATGTGTATAATTGGTTTCAAAATAGGCGTGCTCGATCAAAAAGGAAGCAACAGGTTGCAGCAACAAACAACACTGAATCAGAGGTGGAGACAGAGGTTGAGTCGCCCAATGAAAAGAAAACAAAGCCAGAGGATCTGCAGTCTTCTCACATGCCTACTTCAATGGCTGAAGATCTTGGCTATGAGAACCCTGACGTGAGCTCTGGAATGCATTCACTAGATCCACGAACCAGTAAACCCGAGCCTATGTTTCCATCAGACGGTAGTTCAAAACCTGC</genome_strand>
        <mrna_strand>ATACAATTTTGTGATGACCCTTTTAAGGAATTGACTAAAACAA-GAGG-AAATTATGGAGTGGGAAAAACAGCAGCAGCAGCAGCAGCCGGTGTCGGCGCCGCAGCAGACGGTGGAGGAATTGAACGGAGCAGTTAGTGGTGGGATGTTTGTGAAAGTGATGACGGATGAGCAAATGGAAGTTTTAAGGAAGCAAATCGCTGTTTATGCTACTATTTGTGAACAACTTGTTGATTTGCATAAATCCATGGCTTCACAACACGATCTTGCTG......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAGCCAGGCTGGGAAATTTGTACTGCGATCCACTAGTGACATCCGCTGGCCATAAAATCACTGGTAGACAACGCTGGACTCCAACGCCTATGCAACTTCAGATTCTTGAGCGCATATTTGAACAAGGCAATGGAACTCCAACCAAACAGAAGATCAAAGATATAACTTCTGAATTATCTCAACATGGACAAATTTCTGAAACAAATGTGTATAATTGGTTTCAAAATAGGCGTGCTCGATCAAAAAGGAAGCAACAGGTTGCAGCAACAAACACCACTGAATCAGAGGTGGAGACAGAGGTTGAGTCACCCAATGAAAAGAAAACAAAGCCAGAGGATCTGCAGTCTTCTCACATGCCTACTTCAATGGCTGAAGATCTTGGCTATGAGAACCCTGACGTGAGCTCTGGCATGCATTCACTAAATCCACGAACCAGTAAACCCGAGCCTATGTTTCCATCAGACGGTAGTTTAAAACCTGC</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-C02SLe0026H18-MNs3q/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At4g35560" ref_strand="+" ref_description="C2_At4g35560">
      <seq>tcagcagagtgaggacaacctttccttaagtggtgtacccttaacggcattatgtcttacatctgacttacatatcctcatttctggtgatcaaagtggaacggtacgtatctacaagttcaaaactgagttttttgccccagatactagttttctatcctttcaaggttcaaagaaaggaagcaacccaatccagagcattaagcttgtcaaagttaatggagctgtactttctataagtaccagtgaggattctaagtattttgctgttggttctgaccaaggatatgtggtattaattgattctgacagcaagactatactgtatcaaacacatattgccagtgaactctgtgcaggtgtcatgtctatgcagttcaacacgtgtagcttgcatggattcgacaagaatatcttagtggtagcgactaaggattcatcagtcttggcccttgagacagaaacaggaaatatattaagcccttccagtgtccatccaaagaaaccttccagagctttacttatgcagattttggatggacttgaaatgtctggtcgaggattaagcatttcagatggtatagacattattaaggggaattcggataatgttgcatcaaagcaaccattagtattgatctgttctgaaaaggctgtgtatgtctattccttattgcatattattcagggtattaagaaaggatactacaaaagaagtccattccacgctatgttgctgggcatcaacatttgacatgccctgagcgggccttatgcttc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02SLe0026H18-MNs3q/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02SLe0026H18.1" temp_strand="+" temp_description="C02SLe0026H18.1  AC215450.2 htgs_phase:3 submitted_to_sgn_as:C02SLe0026H18 sequenced_by:kribb upload_account_name:korea">
        <position start="97485" stop="99796"/>
      </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="97785" g_stop="97887" g_length="103"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="103" r_length="103" r_score="0.990"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="97888" i_stop="97970" i_length="83">
            <donor d_prob="0.911" d_score="1.00"/>
            <acceptor a_prob="0.816" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="97971" g_stop="98034" g_length="64"/>
          <reference_exon_boundary r_type="cDNA" r_start="104" r_stop="167" r_length="64" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="98035" i_stop="98207" i_length="173">
            <donor d_prob="0.897" d_score="1.00"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="98208" g_stop="98329" g_length="122"/>
          <reference_exon_boundary r_type="cDNA" r_start="168" r_stop="289" r_length="122" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="98330" i_stop="98806" i_length="477">
            <donor d_prob="0.987" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="98807" g_stop="99053" g_length="247"/>
          <reference_exon_boundary r_type="cDNA" r_start="290" r_stop="536" r_length="247" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="99054" i_stop="99162" i_length="109">
            <donor d_prob="0.701" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="99163" g_stop="99314" g_length="152"/>
          <reference_exon_boundary r_type="cDNA" r_start="537" r_stop="688" r_length="152" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="99315" i_stop="99402" i_length="88">
            <donor d_prob="0.891" d_score="1.00"/>
            <acceptor a_prob="0.815" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="99403" g_stop="99496" g_length="94"/>
          <reference_exon_boundary r_type="cDNA" r_start="689" r_stop="780" r_length="92" r_score="0.926"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02SLe0026H18.1" gen_strand="+" ref_id="C2_At4g35560" ref_strand="+">
        <total_alignment_score>0.990</total_alignment_score>
        <cumulative_length_of_scored_exons>782</cumulative_length_of_scored_exons>
        <coverage percentage="1.003" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02SLe0026H18.1" gen_strand="+"/>
        <rDNA rDNA_id="C2_At4g35560" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="97785" e_stop="97887"/>
          <exon e_start="97971" e_stop="98034"/>
          <exon e_start="98208" e_stop="98329"/>
          <exon e_start="98807" e_stop="99053"/>
          <exon e_start="99163" e_stop="99314"/>
          <exon e_start="99403" e_stop="99496"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTGCAGAGTGAGGACAACCTTTCCTTAAGTGGTGTACCCTTAACGGCATTATGTCTTACATCTGACTTACATATCCTCATTTCTGGTGATCAAAGTGGAACGGTAAACTGTCTATAATGGATTTACCAAAATGAAGAAATTTTCTGCATTCTGAGGGTTTTAATTCTTGTATACTTGGCGTGCAGGTACGTATCTACAAGTTCAAAACTGAGTTTTTTGCCCCAGATACTAGTTTTCTATCCTTTCAAGGTATGTAGCATGAATGTCAGGAAAACTTTGAGAATTTGATCTTACATCTTATATTATTAATGGTTTTGCTCTCTTAAAAGATAGACATATCCCTTTCTTTTTTTTATGTAAGCAAATATTTCAAGAATCAGCAAAAAAAATGAATTATTGACTTATTCACCCAACTCCAGTAGGTTCAAAGAAAGGAAGCAACCCAATCCAGAGCATTAAGCTTGTCAAAGTTAATGGAGCTGTACTTTCTATAAGTACCAGTGAGGATTCTAAGTATTTTGCTGTTGGTTCTGACCAAGGATATGTAAGTTTCTGCTTCTATTTTTCCTCCAGCTATACATCATTCATTTTATTCCTTTAGGTTTTCAAGCATTTCAATACTGCACCCTTCTCCTTCCAAGACAAATGTCGGTCTCAATCATTTGGGAATAATGCCGCTACAGTAAGTTTGTAGGACCTGTGCAGAATGTGAACTGTATATCTCAGAATTTTTTGTTAAATGTTATTGTTAATTCTGTTTAATATGGTGGTTCTCTAGTAAGGAGGAGCCTGGAAAACAGCTTGGTTTTACACACACATTTTATAAGGCTCTAGTAACTCTGAGTTTTTAACAAGTACCTTAACTGAATTTATTCGGACCCTTGAGATACAAAGTTCCCAGTGACCTGTTTTCTTGTGATTGTATAAGGGGGAGTATGTGACATATTGAGGATGCTTTTCAAGTCGAGTGTTTGTATTAAAAGATTCGAGTGTTTGAAATCCCATAATTTGTGGTATGCAGGTGGTATTAATTGATTCTGACAGCAAGACTATACTGTATCAAACACATATTGCCAGTGAACTCTGTGCAGGTGTCATGTCTATGCAGTTCAACACGTGTAGCTTGCATGGATTCGACAAGAATATCTTAGTGGTAGCGACTAAGGATTCATCAGTCTTGGCCCTTGAGACAGAAACAGGAAATATATTAAGCCCTTCCAGTGTCCATCCAAAGAAACCTTCCAGAGCTTTACTTATGCAGATTTTGGGTATTTCACGATTTTTTATAGGATCTGTTCATTTTCTCGAAAAGCTTCTCATGAACGCTTGAAACTAACAAAAATTCATGTATTTTCCTTTTCTCTACATTTGATGCAGATGGACTTGAAATGTCTGGTCGAGGATTAAGCATTTCAGATGGTATAGACATTATTAAGGGGAATTCGGATAATGTTGCATCAAAGCAACCATTAGTATTGATCTGTTCTGAAAAGGCTGTGTATGTCTATTCCTTATTGCATATTATTCAGGTATGTGTCTATTTGTCTTGTTGTGCTTATATAAAATTGGTGGACTATCCATCTCAGTGTGTGTTCTCTTTGCTTGAAATATATTCAGGGTATTAAGAAAGTATACTACAAAAAGAAGTTCCATTCCACGCTATGTTGCTGGGCATCAACATTTGACATGCCTGAGGCGGGCCTTATGCTTC</genome_strand>
        <mrna_strand>TCAGCAGAGTGAGGACAACCTTTCCTTAAGTGGTGTACCCTTAACGGCATTATGTCTTACATCTGACTTACATATCCTCATTTCTGGTGATCAAAGTGGAACG...................................................................................GTACGTATCTACAAGTTCAAAACTGAGTTTTTTGCCCCAGATACTAGTTTTCTATCCTTTCAAG.............................................................................................................................................................................GTTCAAAGAAAGGAAGCAACCCAATCCAGAGCATTAAGCTTGTCAAAGTTAATGGAGCTGTACTTTCTATAAGTACCAGTGAGGATTCTAAGTATTTTGCTGTTGGTTCTGACCAAGGATAT.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGGTATTAATTGATTCTGACAGCAAGACTATACTGTATCAAACACATATTGCCAGTGAACTCTGTGCAGGTGTCATGTCTATGCAGTTCAACACGTGTAGCTTGCATGGATTCGACAAGAATATCTTAGTGGTAGCGACTAAGGATTCATCAGTCTTGGCCCTTGAGACAGAAACAGGAAATATATTAAGCCCTTCCAGTGTCCATCCAAAGAAACCTTCCAGAGCTTTACTTATGCAGATTTTGG.............................................................................................................ATGGACTTGAAATGTCTGGTCGAGGATTAAGCATTTCAGATGGTATAGACATTATTAAGGGGAATTCGGATAATGTTGCATCAAAGCAACCATTAGTATTGATCTGTTCTGAAAAGGCTGTGTATGTCTATTCCTTATTGCATATTATTCAG........................................................................................GGTATTAAGAAAGGATACTAC-AAAAGAAG-TCCATTCCACGCTATGTTGCTGGGCATCAACATTTGACATGCCCTGAGCGGGCCTTATGCTTC</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="67229" PGL_stop="65435"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="67229" e_stop="66962"/>
            <exon e_start="65915" e_stop="65435"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.995" acc_prob="0.899" e_score="0.951"/>
          <exon-only e_score="0.975"/>
        </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="0.951">
            <gDNA_exon_boundary e_start="67229" e_stop="66962" e_length="268"/>
          </exon>
          <intron i_serial="1" don_prob="0.995" acc_prob="0.899">
            <gDNA_intron_boundary i_start="66961" i_stop="65916" i_length="1046"/>
          </intron>
          <exon e_serial="2" e_score="0.975">
            <gDNA_exon_boundary e_start="65915" e_stop="65435" e_length="481"/>
          </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="67229" stop="66962"/>
              <exon start="65915" stop="65435"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At4g35550" 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>ATACAATTTTGTGATGACCCTTTTAAGGAATTGACTAAAACAAAGAGGAAAATTATGGATTGGGAAAAACAGCAGCAGCAGCCACCGGTGTCGGCGCCGCAGCAGACGGCGGAGGAATTGAACGGAACAGTCAGTGGTGGGATGTTTGTGAAAGTGATGACGGATGAGCAAATGGAAGTTTTAAGGAAGCAAATCGCTGTTTATGCTACTATTTGTGAACAGCTTGTTGATTTGCATAAATCCATGGCTTCACAACACGATCTTGCTG : GAGCCAGGCTGGGAAATCTGTACTGCGATCCACTGGTGACATCTGCTGGTCATAAAATCACTGGTAGACAACGCTGGACTCCAACACCTATGCAACTTCAGATTCTTGAGCGCATATTTGAACAAGGCAATGGAACTCCAACCAAACAGAAGATCAAAGAGATAACTTCTGAATTATCTCAACATGGCCAAATTTCTGAAACAAATGTGTATAATTGGTTTCAAAATAGGCGTGCTCGATCAAAAAGGAAGCAACAGGTTGCAGCAACAAACAACACTGAATCAGAGGTGGAGACAGAGGTTGAGTCGCCCAATGAAAAGAAAACAAAGCCAGAGGATCTGCAGTCTTCTCACATGCCTACTTCAATGGCTGAAGATCTTGGCTATGAGAACCCTGACGTGAGCTCTGGAATGCATTCACTAGATCCACGAACCAGTAAACCCGAGCCTATGTTTCCATCAGACGGTAGTTCAAAACCTGC</gDNA_template>
            <first_frame> I  Q  F  C  D  D  P  F  K  E  L  T  K  T  K  R  K  I  M  D  W  E  K  Q  Q  Q  Q  P  P  V  S  A  P  Q  Q  T  A  E  E  L  N  G  T  V  S  G  G  M  F  V  K  V  M  T  D  E  Q  M  E  V  L  R  K  Q  I  A  V  Y  A  T  I  C  E  Q  L  V  D  L  H  K  S  M  A  S  Q  H  D  L  A   : G  A  R  L  G  N  L  Y  C  D  P  L  V  T  S  A  G  H  K  I  T  G  R  Q  R  W  T  P  T  P  M  Q  L  Q  I  L  E  R  I  F  E  Q  G  N  G  T  P  T  K  Q  K  I  K  E  I  T  S  E  L  S  Q  H  G  Q  I  S  E  T  N  V  Y  N  W  F  Q  N  R  R  A  R  S  K  R  K  Q  Q  V  A  A  T  N  N  T  E  S  E  V  E  T  E  V  E  S  P  N  E  K  K  T  K  P  E  D  L  Q  S  S  H  M  P  T  S  M  A  E  D  L  G  Y  E  N  P  D  V  S  S  G  M  H  S  L  D  P  R  T  S  K  P  E  P  M  F  P  S  D  G  S  S  K  P   </first_frame>
            <second_frame>  Y  N  F  V  M  T  L  L  R  N  *  L  K  Q  R  G  K  L  W  I  G  K  N  S  S  S  S  H  R  C  R  R  R  S  R  R  R  R  N  *  T  E  Q  S  V  V  G  C  L  *  K  *  *  R  M  S  K  W  K  F  *  G  S  K  S  L  F  M  L  L  F  V  N  S  L  L  I  C  I  N  P  W  L  H  N  T  I  L  L  :  E  P  G  W  E  I  C  T  A  I  H  W  *  H  L  L  V  I  K  S  L  V  D  N  A  G  L  Q  H  L  C  N  F  R  F  L  S  A  Y  L  N  K  A  M  E  L  Q  P  N  R  R  S  K  R  *  L  L  N  Y  L  N  M  A  K  F  L  K  Q  M  C  I  I  G  F  K  I  G  V  L  D  Q  K  G  S  N  R  L  Q  Q  Q  T  T  L  N  Q  R  W  R  Q  R  L  S  R  P  M  K  R  K  Q  S  Q  R  I  C  S  L  L  T  C  L  L  Q  W  L  K  I  L  A  M  R  T  L  T  *  A  L  E  C  I  H  *  I  H  E  P  V  N  P  S  L  C  F  H  Q  T  V  V  Q  N  L  </second_frame>
            <third_frame>   T  I  L  *  *  P  F  *  G  I  D  *  N  K  E  E  N  Y  G  L  G  K  T  A  A  A  A  T  G  V  G  A  A  A  D  G  G  G  I  E  R  N  S  Q  W  W  D  V  C  E  S  D  D  G  *  A  N  G  S  F  K  E  A  N  R  C  L  C  Y  Y  L  *  T  A  C  *  F  A  *  I  H  G  F  T  T  R  S  C  W :   S  Q  A  G  K  S  V  L  R  S  T  G  D  I  C  W  S  *  N  H  W  *  T  T  L  D  S  N  T  Y  A  T  S  D  S  *  A  H  I  *  T  R  Q  W  N  S  N  Q  T  E  D  Q  R  D  N  F  *  I  I  S  T  W  P  N  F  *  N  K  C  V  *  L  V  S  K  *  A  C  S  I  K  K  E  A  T  G  C  S  N  K  Q  H  *  I  R  G  G  D  R  G  *  V  A  Q  *  K  E  N  K  A  R  G  S  A  V  F  S  H  A  Y  F  N  G  *  R  S  W  L  *  E  P  *  R  E  L  W  N  A  F  T  R  S  T  N  Q  *  T  R  A  Y  V  S  I  R  R  *  F  K  T  C </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="C02SLe0026H18.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="67229" stop="66962"/>
                    <exon start="65915" stop="65437"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>747</number_coding_nucleotides>
                  <number_encoded_amino_acids>249</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IQFCDDPFKELTKTKRKIMDWEKQQQQPPVSAPQQTAEELNGTVSGGMFVKVMTDEQMEVLRKQIAVYATICEQLVDLHKSMASQHDLAGARLGNLYCDPLVTSAGHKITGRQRWTPTPMQLQILERIFEQGNGTPTKQKIKEITSELSQHGQISETNVYNWFQNRRARSKRKQQVAATNNTESEVETEVESPNEKKTKPEDLQSSHMPTSMAEDLGYENPDVSSGMHSLDPRTSKPEPMFPSDGSSKP</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="97785" PGL_stop="99496"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="97785" e_stop="97887"/>
            <exon e_start="97971" e_stop="98034"/>
            <exon e_start="98208" e_stop="98329"/>
            <exon e_start="98807" e_stop="99053"/>
            <exon e_start="99163" e_stop="99314"/>
            <exon e_start="99403" e_stop="99496"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.911" acc_prob="0.816" e_score="0.990"/>
          <exon-intron don_prob="0.897" acc_prob="0.000" e_score="1.000"/>
          <exon-intron don_prob="0.987" acc_prob="0.991" e_score="1.000"/>
          <exon-intron don_prob="0.701" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.891" acc_prob="0.815" e_score="1.000"/>
          <exon-only e_score="0.926"/>
        </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="0.990">
            <gDNA_exon_boundary e_start="97785" e_stop="97887" e_length="103"/>
          </exon>
          <intron i_serial="1" don_prob="0.911" acc_prob="0.816">
            <gDNA_intron_boundary i_start="97888" i_stop="97970" i_length="83"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="97971" e_stop="98034" e_length="64"/>
          </exon>
          <intron i_serial="2" don_prob="0.897" acc_prob="0.000">
            <gDNA_intron_boundary i_start="98035" i_stop="98207" i_length="173"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="98208" e_stop="98329" e_length="122"/>
          </exon>
          <intron i_serial="3" don_prob="0.987" acc_prob="0.991">
            <gDNA_intron_boundary i_start="98330" i_stop="98806" i_length="477"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="98807" e_stop="99053" e_length="247"/>
          </exon>
          <intron i_serial="4" don_prob="0.701" acc_prob="0.995">
            <gDNA_intron_boundary i_start="99054" i_stop="99162" i_length="109"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="99163" e_stop="99314" e_length="152"/>
          </exon>
          <intron i_serial="5" don_prob="0.891" acc_prob="0.815">
            <gDNA_intron_boundary i_start="99315" i_stop="99402" i_length="88"/>
          </intron>
          <exon e_serial="6" e_score="0.926">
            <gDNA_exon_boundary e_start="99403" e_stop="99496" e_length="94"/>
          </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="97785" stop="97887"/>
              <exon start="97971" stop="98034"/>
              <exon start="98208" stop="98329"/>
              <exon start="98807" stop="99053"/>
              <exon start="99163" stop="99314"/>
              <exon start="99403" stop="99496"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At4g35560" 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>TCTGCAGAGTGAGGACAACCTTTCCTTAAGTGGTGTACCCTTAACGGCATTATGTCTTACATCTGACTTACATATCCTCATTTCTGGTGATCAAAGTGGAACG : GTACGTATCTACAAGTTCAAAACTGAGTTTTTTGCCCCAGATACTAGTTTTCTATCCTTTCAAG : GTTCAAAGAAAGGAAGCAACCCAATCCAGAGCATTAAGCTTGTCAAAGTTAATGGAGCTGTACTTTCTATAAGTACCAGTGAGGATTCTAAGTATTTTGCTGTTGGTTCTGACCAAGGATAT : GTGGTATTAATTGATTCTGACAGCAAGACTATACTGTATCAAACACATATTGCCAGTGAACTCTGTGCAGGTGTCATGTCTATGCAGTTCAACACGTGTAGCTTGCATGGATTCGACAAGAATATCTTAGTGGTAGCGACTAAGGATTCATCAGTCTTGGCCCTTGAGACAGAAACAGGAAATATATTAAGCCCTTCCAGTGTCCATCCAAAGAAACCTTCCAGAGCTTTACTTATGCAGATTTTGG : ATGGACTTGAAATGTCTGGTCGAGGATTAAGCATTTCAGATGGTATAGACATTATTAAGGGGAATTCGGATAATGTTGCATCAAAGCAACCATTAGTATTGATCTGTTCTGAAAAGGCTGTGTATGTCTATTCCTTATTGCATATTATTCAG : GGTATTAAGAAAGTATACTACAAAAAGAAGTTCCATTCCACGCTATGTTGCTGGGCATCAACATTTGACATGCCTGAGGCGGGCCTTATGCTTC</gDNA_template>
            <first_frame> S  A  E  *  G  Q  P  F  L  K  W  C  T  L  N  G  I  M  S  Y  I  *  L  T  Y  P  H  F  W  *  S  K  W  N   : G  T  Y  L  Q  V  Q  N  *  V  F  C  P  R  Y  *  F  S  I  L  S  R :   F  K  E  R  K  Q  P  N  P  E  H  *  A  C  Q  S  *  W  S  C  T  F  Y  K  Y  Q  *  G  F  *  V  F  C  C  W  F  *  P  R  I   : C  G  I  N  *  F  *  Q  Q  D  Y  T  V  S  N  T  Y  C  Q  *  T  L  C  R  C  H  V  Y  A  V  Q  H  V  *  L  A  W  I  R  Q  E  Y  L  S  G  S  D  *  G  F  I  S  L  G  P  *  D  R  N  R  K  Y  I  K  P  F  Q  C  P  S  K  E  T  F  Q  S  F  T  Y  A  D  F  G :   W  T  *  N  V  W  S  R  I  K  H  F  R  W  Y  R  H  Y  *  G  E  F  G  *  C  C  I  K  A  T  I  S  I  D  L  F  *  K  G  C  V  C  L  F  L  I  A  Y  Y  S   : G  Y  *  E  S  I  L  Q  K  E  V  P  F  H  A  M  L  L  G  I  N  I  *  H  A  *  G  G  P  Y  A   </first_frame>
            <second_frame>  L  Q  S  E  D  N  L  S  L  S  G  V  P  L  T  A  L  C  L  T  S  D  L  H  I  L  I  S  G  D  Q  S  G  T  :  V  R  I  Y  K  F  K  T  E  F  F  A  P  D  T  S  F  L  S  F  Q   : G  S  K  K  G  S  N  P  I  Q  S  I  K  L  V  K  V  N  G  A  V  L  S  I  S  T  S  E  D  S  K  Y  F  A  V  G  S  D  Q  G  Y  :  V  V  L  I  D  S  D  S  K  T  I  L  Y  Q  T  H  I  A  S  E  L  C  A  G  V  M  S  M  Q  F  N  T  C  S  L  H  G  F  D  K  N  I  L  V  V  A  T  K  D  S  S  V  L  A  L  E  T  E  T  G  N  I  L  S  P  S  S  V  H  P  K  K  P  S  R  A  L  L  M  Q  I  L   : D  G  L  E  M  S  G  R  G  L  S  I  S  D  G  I  D  I  I  K  G  N  S  D  N  V  A  S  K  Q  P  L  V  L  I  C  S  E  K  A  V  Y  V  Y  S  L  L  H  I  I  Q  :  G  I  K  K  V  Y  Y  K  K  K  F  H  S  T  L  C  C  W  A  S  T  F  D  M  P  E  A  G  L  M  L  </second_frame>
            <third_frame>   C  R  V  R  T  T  F  P  *  V  V  Y  P  *  R  H  Y  V  L  H  L  T  Y  I  S  S  F  L  V  I  K  V  E  R :   Y  V  S  T  S  S  K  L  S  F  L  P  Q  I  L  V  F  Y  P  F  K  :  V  Q  R  K  E  A  T  Q  S  R  A  L  S  L  S  K  L  M  E  L  Y  F  L  *  V  P  V  R  I  L  S  I  L  L  L  V  L  T  K  D  M :   W  Y  *  L  I  L  T  A  R  L  Y  C  I  K  H  I  L  P  V  N  S  V  Q  V  S  C  L  C  S  S  T  R  V  A  C  M  D  S  T  R  I  S  *  W  *  R  L  R  I  H  Q  S  W  P  L  R  Q  K  Q  E  I  Y  *  A  L  P  V  S  I  Q  R  N  L  P  E  L  Y  L  C  R  F  W  :  M  D  L  K  C  L  V  E  D  *  A  F  Q  M  V  *  T  L  L  R  G  I  R  I  M  L  H  Q  S  N  H  *  Y  *  S  V  L  K  R  L  C  M  S  I  P  Y  C  I  L  F  R :   V  L  R  K  Y  T  T  K  R  S  S  I  P  R  Y  V  A  G  H  Q  H  L  T  C  L  R  R  A  L  C  F </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C02SLe0026H18.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="97786" stop="97887"/>
                    <exon start="97971" stop="98034"/>
                    <exon start="98208" stop="98329"/>
                    <exon start="98807" stop="99053"/>
                    <exon start="99163" stop="99314"/>
                    <exon start="99403" stop="99495"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>780</number_coding_nucleotides>
                  <number_encoded_amino_acids>260</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LQSEDNLSLSGVPLTALCLTSDLHILISGDQSGTVRIYKFKTEFFAPDTSFLSFQGSKKGSNPIQSIKLVKVNGAVLSISTSEDSKYFAVGSDQGYVVLIDSDSKTILYQTHIASELCAGVMSMQFNTCSLHGFDKNILVVATKDSSVLALETETGNILSPSSVHPKKPSRALLMQILDGLEMSGRGLSISDGIDIIKGNSDNVASKQPLVLICSEKAVYVYSLLHIIQGIKKVYYKKKFHSTLCCWASTFDMPEAGLML</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 9 chains have been computed
$ 
$ memory statistics:
$ 4304 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2152 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
$ 11 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 10:56:08
-->
