<?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 11:38:54"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02SLm0065K08-Lkm25/GenomeThreader_SGN_E_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02SLm0065K08-Lkm25/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" 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-C02SLm0065K08-Lkm25/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" ref_id="SGN-E551088" ref_strand="+" ref_description="SGN-E551088 [TUS-55-C7]">
      <seq>tagtttgattattatttgttttgttacagaagatggacaagtcgaaaccggaatcgtcaaaattgttgtgtgggagcagtagcaaagtagagactagaagccctataacatttgttcttctacttagtacatttgctgctgcttgtggttctatagcctatggatttgctgtcggatattcatctccagctgaagcagggatcatggatgatctgggcttgtctcttgcaaattattcagcattcagttcattactgacacttggaggagccattggtgcactaatcagtggcagagtggcagagtctgttggccgaagagttacaatgtggctgttagagttatgttttatcatagggtggctttccataatatttgccaagaatatttggtggctcaatgctggaagattactcatgggaattggagctggacttcattgctatgtggcaccaatatatgt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02SLm0065K08-Lkm25/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C02SLm0065K08.2" temp_strand="-" temp_description="C02SLm0065K08.2  AC215483.2 htgs_phase:3 submitted_to_sgn_as:C02SLm0065K08 sequenced_by:kribb upload_account_name:korea">
        <position start="29817" stop="27297"/>
      </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="29517" g_stop="29348" g_length="170"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="170" r_length="170" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="29347" i_stop="29004" i_length="344">
            <donor d_prob="0.971" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="29003" g_stop="28941" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="171" r_stop="233" r_length="63" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="28940" i_stop="28197" i_length="744">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.390" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="28196" g_stop="28107" g_length="90"/>
          <reference_exon_boundary r_type="cDNA" r_start="234" r_stop="323" r_length="90" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="28106" i_stop="28009" i_length="98">
            <donor d_prob="0.983" d_score="1.00"/>
            <acceptor a_prob="0.735" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="28008" g_stop="27949" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="324" r_stop="383" r_length="60" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="27948" i_stop="27666" i_length="283">
            <donor d_prob="0.193" d_score="1.00"/>
            <acceptor a_prob="0.640" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="27665" g_stop="27600" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="384" r_stop="449" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="27599" i_stop="27517" i_length="83">
            <donor d_prob="0.965" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="27516" g_stop="27503" g_length="14"/>
          <reference_exon_boundary r_type="cDNA" r_start="450" r_stop="463" r_length="14" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02SLm0065K08.2" gen_strand="-" ref_id="SGN-E551088" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>463</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02SLm0065K08.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E551088" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="29517" e_stop="29348"/>
          <exon e_start="29003" e_stop="28941"/>
          <exon e_start="28196" e_stop="28107"/>
          <exon e_start="28008" e_stop="27949"/>
          <exon e_start="27665" e_stop="27600"/>
          <exon e_start="27516" e_stop="27503"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAGTTTGATTATTATTTGTTTTGTTACAGAAGATGGACAAGTCGAAACCGGAATCGTCAAAATTGTTGTGTGGGAGCAGTAGCAAAGTAGAGACTAGAAGCCCTATAACATTTGTTCTTCTACTTAGTACATTTGCTGCTGCTTGTGGTTCTATAGCCTATGGATTTGCTGTAAGTATGCATTCCCACCCCTTCTGTAAACACAGACACTTGAATGCCATGTTTTCTTGTACATTACTGGCGTTTCTCATTTAAGCAAAACACCTCACATGGCCATACACTATACTGTTCCCTATTGTTAACATGTCTAAAATCATTCCTCCAAATTAATTGCCACACCATATACAATCTGACCCACTCTAACAAATGTTGAGAGGCATAAACCCGAGGTCTGAAACCACACGGGTAGTTTAAGTTTATAGGTTCTATGTAAACATTGATGAGTATTTTGTCATATGAATCAACAAATAATTCTCTGTTTCTAATACAGCAAATTATTGGTTTTCTACTTGTAGGTCGGATATTCATCTCCAGCTGAAGCAGGGATCATGGATGATCTGGGCTTGTCTCTTGCAAATGTATGCAGCTTTTATATTGTTCTCAACTTGCACTATCTGTGTCCTACACCTGTTCATTCTGGAAACAAGTATCATATGGATCAAATAGTAATTATTACATTACTCTTCGCTTCCATCTTATAAATAGACAAATTTAGATATGTATATGTAAAATCTAGGGTATTTTTGCCTTGGTTGGAGAAATATTTGTTTTTTTTCTTTAGGGTTGTACTAACCTCAAAAATGTGTTTGCAACAAAATGTATTTAGCAAAGGGAAGGAAAAGAGGTAATTAGGGTTGTGGTCATCAGTGAAATCAACCACGATGGTACCAATTGGCAGTGTAGGTTGAAGGTTGAAAAATATCCCCACTGACGTCAGCCACCGACCATAGAGTTCCACTTGTGAGCAATTGTTTTATTGCAACTTCATATGCATGTTTTCAATTACTGGTAGTCTGTTAATGAATGTATGGAGCTCTATATTGCATTTTTATATGCTGTAAATCATGAACATTATTCTGAGGCACAACCCCTGGGAAAGTTTCTAGAAGCGCCATATTAAGATTCACATTTCCGATTTTGAAGCTATCGGATTCAGTGTCATCAAATAAACCAACTTGTGTTTTTTTTGAACATTTTCAATGATGAACCCATAGTATTTGAAATTATTTTTTGTCAATGGTGAATTTAACCACATGAATACCTGTAAATTAGTTCTTTGACCCCACTGTCTGATATTCTTATCTTCCGACAACATTCTGAAGTATTCAGCATTCAGTTCATTACTGACACTTGGAGGAGCCATTGGTGCACTAATCAGTGGCAGAGTGGCAGAGTCTGTTGGCCGAAGAGTTGTATGTTATTTGCTTTTCTTAGAAACTCTCTGGCTTCCAAAATATTATGCTTGTTATATTTCCTTTAAGTTGCGGATCTGATACATTCCTCATTGCAGACAATGTGGCTGTTAGAGTTATGTTTTATCATAGGGTGGCTTTCCATAATATTTGCCAAGGTGTGTGCAAAACATTATACTTTTCTTAAATTTAGCAGTTGTGACTAAAGGAATCTATTAATACTCACATGATAACTCGGACATTTCTTAACTCCTAGTACATGTTCATCCTAATTATGGAGAATTGATGCATGTATTCCTCATTTGTACACTCACTGAACAATTACAATTATTATTTCATTGGTACATTCTTAACTATTGCTTATCATAACTCAGAGACTATATTTGTGTCTAAGGGAACGTAGTTTCAAAATTTATAATATGTTTGATTACTTAATTAAAGAATATTTGGTGGCTCAATGCTGGAAGATTACTCATGGGAATTGGAGCTGGACTTCATTGCTATGTGGTAAACCTTGCAAATTTCCCAACGGATATCTTATGTTCCTCTTTGATTAGAACATAATCAAATTTCCATTAAAATTAAAGCAGGCACCAATATATGT</genome_strand>
        <mrna_strand>TAGTTTGATTATTATTTGTTTTGTTACAGAAGATGGACAAGTCGAAACCGGAATCGTCAAAATTGTTGTGTGGGAGCAGTAGCAAAGTAGAGACTAGAAGCCCTATAACATTTGTTCTTCTACTTAGTACATTTGCTGCTGCTTGTGGTTCTATAGCCTATGGATTTGCT........................................................................................................................................................................................................................................................................................................................................................GTCGGATATTCATCTCCAGCTGAAGCAGGGATCATGGATGATCTGGGCTTGTCTCTTGCAAAT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATTCAGCATTCAGTTCATTACTGACACTTGGAGGAGCCATTGGTGCACTAATCAGTGGCAGAGTGGCAGAGTCTGTTGGCCGAAGAGTT..................................................................................................ACAATGTGGCTGTTAGAGTTATGTTTTATCATAGGGTGGCTTTCCATAATATTTGCCAAG...........................................................................................................................................................................................................................................................................................AATATTTGGTGGCTCAATGCTGGAAGATTACTCATGGGAATTGGAGCTGGACTTCATTGCTATGTG...................................................................................GCACCAATATATGT</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-C02SLm0065K08-Lkm25/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" ref_id="SGN-E688867" ref_strand="+" ref_description="SGN-E688867 [t3_tus_55_C07]">
      <seq>tagtttgattattatttgttttgttacagaagatggacaagtcgaaaccggaatcgtcaaaattgttgtgtgggagcagtagcaaagtagagactagaagccctataacatttgttcttctacttagtacatttgctgctgcttgtggttctatagcctatggatttgctgtcggatattcatctccagctgaagcagggatcatggatgatctgggcttgtctcttgcaaattattcagcattcagttcattactgacacttggaggagccattggtgcactaatcagtggcagagtggcagagtctgttggccgaagagttacaatgtggctgttagagttatgttttatcatagggtggctttccataatatttgccaagaatatttggtggctcaatgctggaagattactcatgggaattggagctggacttcattgctatgtggcaccaatatatgt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02SLm0065K08-Lkm25/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C02SLm0065K08.2" temp_strand="-" temp_description="C02SLm0065K08.2  AC215483.2 htgs_phase:3 submitted_to_sgn_as:C02SLm0065K08 sequenced_by:kribb upload_account_name:korea">
        <position start="29817" stop="27297"/>
      </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="29517" g_stop="29348" g_length="170"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="170" r_length="170" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="29347" i_stop="29004" i_length="344">
            <donor d_prob="0.971" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="29003" g_stop="28941" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="171" r_stop="233" r_length="63" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="28940" i_stop="28197" i_length="744">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.390" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="28196" g_stop="28107" g_length="90"/>
          <reference_exon_boundary r_type="cDNA" r_start="234" r_stop="323" r_length="90" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="28106" i_stop="28009" i_length="98">
            <donor d_prob="0.983" d_score="1.00"/>
            <acceptor a_prob="0.735" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="28008" g_stop="27949" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="324" r_stop="383" r_length="60" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="27948" i_stop="27666" i_length="283">
            <donor d_prob="0.193" d_score="1.00"/>
            <acceptor a_prob="0.640" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="27665" g_stop="27600" g_length="66"/>
          <reference_exon_boundary r_type="cDNA" r_start="384" r_stop="449" r_length="66" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="27599" i_stop="27517" i_length="83">
            <donor d_prob="0.965" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="27516" g_stop="27503" g_length="14"/>
          <reference_exon_boundary r_type="cDNA" r_start="450" r_stop="463" r_length="14" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02SLm0065K08.2" gen_strand="-" ref_id="SGN-E688867" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>463</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02SLm0065K08.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E688867" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="29517" e_stop="29348"/>
          <exon e_start="29003" e_stop="28941"/>
          <exon e_start="28196" e_stop="28107"/>
          <exon e_start="28008" e_stop="27949"/>
          <exon e_start="27665" e_stop="27600"/>
          <exon e_start="27516" e_stop="27503"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAGTTTGATTATTATTTGTTTTGTTACAGAAGATGGACAAGTCGAAACCGGAATCGTCAAAATTGTTGTGTGGGAGCAGTAGCAAAGTAGAGACTAGAAGCCCTATAACATTTGTTCTTCTACTTAGTACATTTGCTGCTGCTTGTGGTTCTATAGCCTATGGATTTGCTGTAAGTATGCATTCCCACCCCTTCTGTAAACACAGACACTTGAATGCCATGTTTTCTTGTACATTACTGGCGTTTCTCATTTAAGCAAAACACCTCACATGGCCATACACTATACTGTTCCCTATTGTTAACATGTCTAAAATCATTCCTCCAAATTAATTGCCACACCATATACAATCTGACCCACTCTAACAAATGTTGAGAGGCATAAACCCGAGGTCTGAAACCACACGGGTAGTTTAAGTTTATAGGTTCTATGTAAACATTGATGAGTATTTTGTCATATGAATCAACAAATAATTCTCTGTTTCTAATACAGCAAATTATTGGTTTTCTACTTGTAGGTCGGATATTCATCTCCAGCTGAAGCAGGGATCATGGATGATCTGGGCTTGTCTCTTGCAAATGTATGCAGCTTTTATATTGTTCTCAACTTGCACTATCTGTGTCCTACACCTGTTCATTCTGGAAACAAGTATCATATGGATCAAATAGTAATTATTACATTACTCTTCGCTTCCATCTTATAAATAGACAAATTTAGATATGTATATGTAAAATCTAGGGTATTTTTGCCTTGGTTGGAGAAATATTTGTTTTTTTTCTTTAGGGTTGTACTAACCTCAAAAATGTGTTTGCAACAAAATGTATTTAGCAAAGGGAAGGAAAAGAGGTAATTAGGGTTGTGGTCATCAGTGAAATCAACCACGATGGTACCAATTGGCAGTGTAGGTTGAAGGTTGAAAAATATCCCCACTGACGTCAGCCACCGACCATAGAGTTCCACTTGTGAGCAATTGTTTTATTGCAACTTCATATGCATGTTTTCAATTACTGGTAGTCTGTTAATGAATGTATGGAGCTCTATATTGCATTTTTATATGCTGTAAATCATGAACATTATTCTGAGGCACAACCCCTGGGAAAGTTTCTAGAAGCGCCATATTAAGATTCACATTTCCGATTTTGAAGCTATCGGATTCAGTGTCATCAAATAAACCAACTTGTGTTTTTTTTGAACATTTTCAATGATGAACCCATAGTATTTGAAATTATTTTTTGTCAATGGTGAATTTAACCACATGAATACCTGTAAATTAGTTCTTTGACCCCACTGTCTGATATTCTTATCTTCCGACAACATTCTGAAGTATTCAGCATTCAGTTCATTACTGACACTTGGAGGAGCCATTGGTGCACTAATCAGTGGCAGAGTGGCAGAGTCTGTTGGCCGAAGAGTTGTATGTTATTTGCTTTTCTTAGAAACTCTCTGGCTTCCAAAATATTATGCTTGTTATATTTCCTTTAAGTTGCGGATCTGATACATTCCTCATTGCAGACAATGTGGCTGTTAGAGTTATGTTTTATCATAGGGTGGCTTTCCATAATATTTGCCAAGGTGTGTGCAAAACATTATACTTTTCTTAAATTTAGCAGTTGTGACTAAAGGAATCTATTAATACTCACATGATAACTCGGACATTTCTTAACTCCTAGTACATGTTCATCCTAATTATGGAGAATTGATGCATGTATTCCTCATTTGTACACTCACTGAACAATTACAATTATTATTTCATTGGTACATTCTTAACTATTGCTTATCATAACTCAGAGACTATATTTGTGTCTAAGGGAACGTAGTTTCAAAATTTATAATATGTTTGATTACTTAATTAAAGAATATTTGGTGGCTCAATGCTGGAAGATTACTCATGGGAATTGGAGCTGGACTTCATTGCTATGTGGTAAACCTTGCAAATTTCCCAACGGATATCTTATGTTCCTCTTTGATTAGAACATAATCAAATTTCCATTAAAATTAAAGCAGGCACCAATATATGT</genome_strand>
        <mrna_strand>TAGTTTGATTATTATTTGTTTTGTTACAGAAGATGGACAAGTCGAAACCGGAATCGTCAAAATTGTTGTGTGGGAGCAGTAGCAAAGTAGAGACTAGAAGCCCTATAACATTTGTTCTTCTACTTAGTACATTTGCTGCTGCTTGTGGTTCTATAGCCTATGGATTTGCT........................................................................................................................................................................................................................................................................................................................................................GTCGGATATTCATCTCCAGCTGAAGCAGGGATCATGGATGATCTGGGCTTGTCTCTTGCAAAT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATTCAGCATTCAGTTCATTACTGACACTTGGAGGAGCCATTGGTGCACTAATCAGTGGCAGAGTGGCAGAGTCTGTTGGCCGAAGAGTT..................................................................................................ACAATGTGGCTGTTAGAGTTATGTTTTATCATAGGGTGGCTTTCCATAATATTTGCCAAG...........................................................................................................................................................................................................................................................................................AATATTTGGTGGCTCAATGCTGGAAGATTACTCATGGGAATTGGAGCTGGACTTCATTGCTATGTG...................................................................................GCACCAATATATGT</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-C02SLm0065K08-Lkm25/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" ref_id="SGN-E260180" ref_strand="+" ref_description="SGN-E260180 [cLEG-52-P17]">
      <seq>tttgaagcttatagtttgattattatttcgttttgttacagaagatggacaagtcgaaaccggaatcgtcaaaattgttgtgtgggagcagtagcaaagtagagactataagccctataacatttgttcttctacttaatacatttgctgctgcttggggttctatagcctatggatttgctgtcggatattcatctccagctgaagcatggatcatggatgatctgggcttgtctcttgcgaattattcagcattcaattcattactgacacttggaggagccattggtgcactaatcaatggcagagtggcatagtctgttggccgaagaaatacaatgtggctgatatagttatgttttatcatagggtggctttccataatatttgccaagaatatttggtggctcaatgctgga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02SLm0065K08-Lkm25/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C02SLm0065K08.2" temp_strand="-" temp_description="C02SLm0065K08.2  AC215483.2 htgs_phase:3 submitted_to_sgn_as:C02SLm0065K08 sequenced_by:kribb upload_account_name:korea">
        <position start="29828" stop="27342"/>
      </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="29528" g_stop="29348" g_length="181"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="182" r_length="182" r_score="0.972"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="29347" i_stop="29004" i_length="344">
            <donor d_prob="0.971" d_score="0.96"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="29003" g_stop="28941" g_length="63"/>
          <reference_exon_boundary r_type="cDNA" r_start="183" r_stop="245" r_length="63" r_score="0.968"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="28940" i_stop="28197" i_length="744">
            <donor d_prob="0.997" d_score="0.96"/>
            <acceptor a_prob="0.390" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="28196" g_stop="28107" g_length="90"/>
          <reference_exon_boundary r_type="cDNA" r_start="246" r_stop="335" r_length="90" r_score="0.944"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="28106" i_stop="28009" i_length="98">
            <donor d_prob="0.983" d_score="0.92"/>
            <acceptor a_prob="0.735" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="28008" g_stop="27949" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="336" r_stop="395" r_length="60" r_score="0.967"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="27948" i_stop="27666" i_length="283">
            <donor d_prob="0.193" d_score="0.96"/>
            <acceptor a_prob="0.640" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="27665" g_stop="27642" g_length="24"/>
          <reference_exon_boundary r_type="cDNA" r_start="396" r_stop="419" r_length="24" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02SLm0065K08.2" gen_strand="-" ref_id="SGN-E260180" ref_strand="+">
        <total_alignment_score>0.964</total_alignment_score>
        <cumulative_length_of_scored_exons>418</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02SLm0065K08.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E260180" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="29528" e_stop="29348"/>
          <exon e_start="29003" e_stop="28941"/>
          <exon e_start="28196" e_stop="28107"/>
          <exon e_start="28008" e_stop="27949"/>
          <exon e_start="27665" e_stop="27642"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTGAAGCTTATAGTTTGATTATTATTT-GTTTTGTTACAGAAGATGGACAAGTCGAAACCGGAATCGTCAAAATTGTTGTGTGGGAGCAGTAGCAAAGTAGAGACTAGAAGCCCTATAACATTTGTTCTTCTACTTAGTACATTTGCTGCTGCTTGTGGTTCTATAGCCTATGGATTTGCTGTAAGTATGCATTCCCACCCCTTCTGTAAACACAGACACTTGAATGCCATGTTTTCTTGTACATTACTGGCGTTTCTCATTTAAGCAAAACACCTCACATGGCCATACACTATACTGTTCCCTATTGTTAACATGTCTAAAATCATTCCTCCAAATTAATTGCCACACCATATACAATCTGACCCACTCTAACAAATGTTGAGAGGCATAAACCCGAGGTCTGAAACCACACGGGTAGTTTAAGTTTATAGGTTCTATGTAAACATTGATGAGTATTTTGTCATATGAATCAACAAATAATTCTCTGTTTCTAATACAGCAAATTATTGGTTTTCTACTTGTAGGTCGGATATTCATCTCCAGCTGAAGCAGGGATCATGGATGATCTGGGCTTGTCTCTTGCAAATGTATGCAGCTTTTATATTGTTCTCAACTTGCACTATCTGTGTCCTACACCTGTTCATTCTGGAAACAAGTATCATATGGATCAAATAGTAATTATTACATTACTCTTCGCTTCCATCTTATAAATAGACAAATTTAGATATGTATATGTAAAATCTAGGGTATTTTTGCCTTGGTTGGAGAAATATTTGTTTTTTTTCTTTAGGGTTGTACTAACCTCAAAAATGTGTTTGCAACAAAATGTATTTAGCAAAGGGAAGGAAAAGAGGTAATTAGGGTTGTGGTCATCAGTGAAATCAACCACGATGGTACCAATTGGCAGTGTAGGTTGAAGGTTGAAAAATATCCCCACTGACGTCAGCCACCGACCATAGAGTTCCACTTGTGAGCAATTGTTTTATTGCAACTTCATATGCATGTTTTCAATTACTGGTAGTCTGTTAATGAATGTATGGAGCTCTATATTGCATTTTTATATGCTGTAAATCATGAACATTATTCTGAGGCACAACCCCTGGGAAAGTTTCTAGAAGCGCCATATTAAGATTCACATTTCCGATTTTGAAGCTATCGGATTCAGTGTCATCAAATAAACCAACTTGTGTTTTTTTTGAACATTTTCAATGATGAACCCATAGTATTTGAAATTATTTTTTGTCAATGGTGAATTTAACCACATGAATACCTGTAAATTAGTTCTTTGACCCCACTGTCTGATATTCTTATCTTCCGACAACATTCTGAAGTATTCAGCATTCAGTTCATTACTGACACTTGGAGGAGCCATTGGTGCACTAATCAGTGGCAGAGTGGCAGAGTCTGTTGGCCGAAGAGTTGTATGTTATTTGCTTTTCTTAGAAACTCTCTGGCTTCCAAAATATTATGCTTGTTATATTTCCTTTAAGTTGCGGATCTGATACATTCCTCATTGCAGACAATGTGGCTGTTAGAGTTATGTTTTATCATAGGGTGGCTTTCCATAATATTTGCCAAGGTGTGTGCAAAACATTATACTTTTCTTAAATTTAGCAGTTGTGACTAAAGGAATCTATTAATACTCACATGATAACTCGGACATTTCTTAACTCCTAGTACATGTTCATCCTAATTATGGAGAATTGATGCATGTATTCCTCATTTGTACACTCACTGAACAATTACAATTATTATTTCATTGGTACATTCTTAACTATTGCTTATCATAACTCAGAGACTATATTTGTGTCTAAGGGAACGTAGTTTCAAAATTTATAATATGTTTGATTACTTAATTAAAGAATATTTGGTGGCTCAATGCTGGA</genome_strand>
        <mrna_strand>TTTGAAGCTTATAGTTTGATTATTATTTCGTTTTGTTACAGAAGATGGACAAGTCGAAACCGGAATCGTCAAAATTGTTGTGTGGGAGCAGTAGCAAAGTAGAGACTATAAGCCCTATAACATTTGTTCTTCTACTTAATACATTTGCTGCTGCTTGGGGTTCTATAGCCTATGGATTTGCT........................................................................................................................................................................................................................................................................................................................................................GTCGGATATTCATCTCCAGCTGAAGCATGGATCATGGATGATCTGGGCTTGTCTCTTGCGAAT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TATTCAGCATTCAATTCATTACTGACACTTGGAGGAGCCATTGGTGCACTAATCAATGGCAGAGTGGCATAGTCTGTTGGCCGAAGAAAT..................................................................................................ACAATGTGGCTGATATAGTTATGTTTTATCATAGGGTGGCTTTCCATAATATTTGCCAAG...........................................................................................................................................................................................................................................................................................AATATTTGGTGGCTCAATGCTGGA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>3</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="29528" PGL_stop="27503"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="29528" e_stop="29348"/>
            <exon e_start="29003" e_stop="28941"/>
            <exon e_start="28196" e_stop="28107"/>
            <exon e_start="28008" e_stop="27949"/>
            <exon e_start="27665" e_stop="27600"/>
            <exon e_start="27516" e_stop="27503"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.971" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.997" acc_prob="0.390" e_score="1.000"/>
          <exon-intron don_prob="0.983" acc_prob="0.735" e_score="1.000"/>
          <exon-intron don_prob="0.193" acc_prob="0.640" e_score="1.000"/>
          <exon-intron don_prob="0.965" acc_prob="0.991" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="29528" e_stop="29348" e_length="181"/>
          </exon>
          <intron i_serial="1" don_prob="0.971" acc_prob="1.000">
            <gDNA_intron_boundary i_start="29347" i_stop="29004" i_length="344"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="29003" e_stop="28941" e_length="63"/>
          </exon>
          <intron i_serial="2" don_prob="0.997" acc_prob="0.390">
            <gDNA_intron_boundary i_start="28940" i_stop="28197" i_length="744"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="28196" e_stop="28107" e_length="90"/>
          </exon>
          <intron i_serial="3" don_prob="0.983" acc_prob="0.735">
            <gDNA_intron_boundary i_start="28106" i_stop="28009" i_length="98"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="28008" e_stop="27949" e_length="60"/>
          </exon>
          <intron i_serial="4" don_prob="0.193" acc_prob="0.640">
            <gDNA_intron_boundary i_start="27948" i_stop="27666" i_length="283"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="27665" e_stop="27600" e_length="66"/>
          </exon>
          <intron i_serial="5" don_prob="0.965" acc_prob="0.991">
            <gDNA_intron_boundary i_start="27599" i_stop="27517" i_length="83"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="27516" e_stop="27503" e_length="14"/>
          </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="29528" stop="29348"/>
              <exon start="29003" stop="28941"/>
              <exon start="28196" stop="28107"/>
              <exon start="28008" stop="27949"/>
              <exon start="27665" stop="27642"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E260180" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="29517" stop="29348"/>
              <exon start="29003" stop="28941"/>
              <exon start="28196" stop="28107"/>
              <exon start="28008" stop="27949"/>
              <exon start="27665" stop="27600"/>
              <exon start="27516" stop="27503"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E551088" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="29517" stop="29348"/>
              <exon start="29003" stop="28941"/>
              <exon start="28196" stop="28107"/>
              <exon start="28008" stop="27949"/>
              <exon start="27665" stop="27600"/>
              <exon start="27516" stop="27503"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E688867" 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>TTTGAAGCTTATAGTTTGATTATTATTTGTTTTGTTACAGAAGATGGACAAGTCGAAACCGGAATCGTCAAAATTGTTGTGTGGGAGCAGTAGCAAAGTAGAGACTAGAAGCCCTATAACATTTGTTCTTCTACTTAGTACATTTGCTGCTGCTTGTGGTTCTATAGCCTATGGATTTGCT : GTCGGATATTCATCTCCAGCTGAAGCAGGGATCATGGATGATCTGGGCTTGTCTCTTGCAAAT : TATTCAGCATTCAGTTCATTACTGACACTTGGAGGAGCCATTGGTGCACTAATCAGTGGCAGAGTGGCAGAGTCTGTTGGCCGAAGAGTT : ACAATGTGGCTGTTAGAGTTATGTTTTATCATAGGGTGGCTTTCCATAATATTTGCCAAG : AATATTTGGTGGCTCAATGCTGGAAGATTACTCATGGGAATTGGAGCTGGACTTCATTGCTATGTG : GCACCAATATATGT</gDNA_template>
            <first_frame> F  E  A  Y  S  L  I  I  I  C  F  V  T  E  D  G  Q  V  E  T  G  I  V  K  I  V  V  W  E  Q  *  Q  S  R  D  *  K  P  Y  N  I  C  S  S  T  *  Y  I  C  C  C  L  W  F  Y  S  L  W  I  C   : C  R  I  F  I  S  S  *  S  R  D  H  G  *  S  G  L  V  S  C  K   : L  F  S  I  Q  F  I  T  D  T  W  R  S  H  W  C  T  N  Q  W  Q  S  G  R  V  C  W  P  K  S   : Y  N  V  A  V  R  V  M  F  Y  H  R  V  A  F  H  N  I  C  Q   : E  Y  L  V  A  Q  C  W  K  I  T  H  G  N  W  S  W  T  S  L  L  C   : G  T  N  I  C </first_frame>
            <second_frame>  L  K  L  I  V  *  L  L  F  V  L  L  Q  K  M  D  K  S  K  P  E  S  S  K  L  L  C  G  S  S  S  K  V  E  T  R  S  P  I  T  F  V  L  L  L  S  T  F  A  A  A  C  G  S  I  A  Y  G  F  A  :  V  G  Y  S  S  P  A  E  A  G  I  M  D  D  L  G  L  S  L  A  N  :  Y  S  A  F  S  S  L  L  T  L  G  G  A  I  G  A  L  I  S  G  R  V  A  E  S  V  G  R  R  V  :  T  M  W  L  L  E  L  C  F  I  I  G  W  L  S  I  I  F  A  K  :  N  I  W  W  L  N  A  G  R  L  L  M  G  I  G  A  G  L  H  C  Y  V  :  A  P  I  Y   </second_frame>
            <third_frame>   *  S  L  *  F  D  Y  Y  L  F  C  Y  R  R  W  T  S  R  N  R  N  R  Q  N  C  C  V  G  A  V  A  K  *  R  L  E  A  L  *  H  L  F  F  Y  L  V  H  L  L  L  L  V  V  L  *  P  M  D  L  L :   S  D  I  H  L  Q  L  K  Q  G  S  W  M  I  W  A  C  L  L  Q  I :   I  Q  H  S  V  H  Y  *  H  L  E  E  P  L  V  H  *  S  V  A  E  W  Q  S  L  L  A  E  E  L :   Q  C  G  C  *  S  Y  V  L  S  *  G  G  F  P  *  Y  L  P  R :   I  F  G  G  S  M  L  E  D  Y  S  W  E  L  E  L  D  F  I  A  M  W :   H  Q  Y  M  </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="C02SLm0065K08.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="29509" stop="29348"/>
                    <exon start="29003" stop="28941"/>
                    <exon start="28196" stop="28107"/>
                    <exon start="28008" stop="27949"/>
                    <exon start="27665" stop="27600"/>
                    <exon start="27516" stop="27505"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>453</number_coding_nucleotides>
                  <number_encoded_amino_acids>151</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LLFVLLQKMDKSKPESSKLLCGSSSKVETRSPITFVLLLSTFAAACGSIAYGFAVGYSSPAEAGIMDDLGLSLANYSAFSSLLTLGGAIGALISGRVAESVGRRVTMWLLELCFIIGWLSIIFAKNIWWLNAGRLLMGIGAGLHCYVAPIY</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 144 chains have been computed
$ 
$ memory statistics:
$ 6840 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 5688 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5688 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 194 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 11:40:12
-->
