<?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="2009-01-15 23:40:09"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C05HBa0003C20-FONp9/GenomeThreader_SGN_E_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C05HBa0003C20-FONp9/gth_cdna_fileCXGN::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-C05HBa0003C20-FONp9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E744681" ref_strand="+" ref_description="SGN-E744681 [GI|30519753]">
      <seq>ggggtttatggttatggtggaggaggttggattgatgctcatgcaactttttatgggggtggtgatgcttctggaacaatgggtggggcttgtggatatgggaatctttatagtcaagggtatggcacaaatacagcagctttaagtactgctatgttcaacaatgggttgagctgtggttcttgttttgaattaaggtgtgtaaatgacagacaagggtgtttgcctggttctattgtggttactgctacaaatttttgcccaccaaacaatgccctccctaataatgcaggtggctggtgtaatcctccacttcaccattttgacctctctcagcctattttccaacacattgctcattacaaagctggaattgtccctgttgcttatagaagggtaccctgtagaagaaggggaggaataaggttcacaatcaatggacactcatacttcaacttagtactagtaacaaacgttggtggtggtggtgatgttcattcagtagctgttaaaggatcaagaacaggttggcagccaatgtcaagaaactggggacaaaactggcaaaacaacaacgaccttaatggacaaacactatcatttaaggttacaacaggtgatggtagaagtttgatctcatacaatgttgcacctgctcactggtcatttggacagacatatactggtgctcaattccactaaaaaaaggcattaaatggggttttttttttcttcaagtttttgaaagtatatttactagaattactattatcattactagtattagtatgcatactgatttggtcactagtattattgtgactatttagtatagaggtattttggttgtaaaggtgtggtctttaaggtaaaaaaaaatgaaaaaagggcatattttaaaattgtcctctttttcattttgattgaattaagggtatcttactttggggaccctaatttttgaggccacacttagtagttttttttggttttggagggtattttggtaatttttccttctgttaagggcagaagtggaaagcagtggtggacttttaccncccccagttggtaggtgggggtatttttggcaactttttttttaagcttcagcctgtagctgaagatggactttgtatgtgtgagactatgaaatgtaaagaaccntttaactagtaatgattcagaagattatggttatgtattttaacttttgtaatgcctctctcggttttaatttgtttgacnggttncaaaaaaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C05HBa0003C20-FONp9/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C05HBa0003C20.1" temp_strand="+" temp_description="C05HBa0003C20.1  AC212299.1 htgs_phase:3 submitted_to_sgn_as:C05HBa0003C20 sequenced_by:iitg upload_account_name:india complete sequence">
        <position start="4767" stop="7611"/>
      </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="5064" g_stop="5145" g_length="82"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="82" r_length="82" r_score="0.963"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="5146" i_stop="5237" i_length="92">
            <donor d_prob="0.999" 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="5238" g_stop="5550" g_length="313"/>
          <reference_exon_boundary r_type="cDNA" r_start="83" r_stop="395" r_length="313" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="5551" i_stop="6427" i_length="877">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="6428" g_stop="7308" g_length="881"/>
          <reference_exon_boundary r_type="cDNA" r_start="396" r_stop="1249" r_length="854" r_score="0.961"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="1255" polyA_stop="1280"/>
      <MATCH_line gen_id="C05HBa0003C20.1" gen_strand="+" ref_id="SGN-E744681" ref_strand="+">
        <total_alignment_score>0.971</total_alignment_score>
        <cumulative_length_of_scored_exons>1276</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C05HBa0003C20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-E744681" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="5064" e_stop="5145"/>
          <exon e_start="5238" e_stop="5550"/>
          <exon e_start="6428" e_stop="7308"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTGTTTATGGTTATGGTGGAGGAGGTTGGATTGATGCTCATGCAACTTTTTATGGGGGTGGTGATGCTTCTGGAACAATGGGTATGCAACATTTCCTTTAAATTCCCCAAAAGTTTGATTTTTGAGTAAATTTAGGGTATAAATTTGTGCTGATTCTTGATTTCTTTGAATAGGTGGGGCTTGTGGATATGGGAATCTTTATAGTCAAGGGTATGGCACAAATACAGCAGCTTTAAGTACTGCTATGTTCAACAATGGGTTGAGCTGTGGTTCTTGTTTTGAATTAAGGTGTGTAAATGACAGACAAGGGTGTTTGCCTGGTTCTATTGTGGTTACTGCTACAAATTTTTGCCCACCAAACAATGCCCTCCCTAATAATGCAGGTGGCTGGTGTAATCCTCCACTTCACCATTTTGACCTCTCTCAGCCTATTTTCCAACACATTGCTCATTACAAAGCTGGAATTGTCCCTGTTGCTTATAGAAGGTAAATTCTTGGTAAAAATATGTTAGTTGTAGAACTATATGCTGTTTGTATCTTGCTATGTATGTATGATGTTGTTTGAGTACTATAAAAGAGTGGCAAGGAGAGTTTTGTCTTTTCACAAATGCTAAACCTTAGTCATGTCTAAATTGCTTAAGCCCAAAGGTTTGAAATTTCTAAATGGTCCCTTTTAAATGACCTTAATTTACTTGTGCATGCTAATAGAAAAATGAAATGGTGGAACCACATGGTGTGGACCCTTTTGATAAAGGTTTTAACTTTATCACAAGAAGTTTCCCATTTGGCTATTTTCAATGGAGTACTCTTTAGCATTTACTTCTTTCTTGGTTGTTGTAATAGTAGAAGATTCATAAAGTTACATATATTGTTCCCATTTGTCTCTTTACTTGTTTCAATTGTGCTCTTTATCCTTGACTTGTTTCTTAAATTTGGTAAAACTTGGAAAAGCATGAGAAACAAAGTTACAAACTTTAACACCATATAAAAACATAACATAACCAATCTTGCAAATTTTAATAGCTTAGTTTGTTGACAAGCCATACCTTTACCCTATGAACAATCTTGATAATCTTATTAGCTTAGTAAGTTGACTATCTGAAGTTTCACGTTTCGACAAATCTTGTTTATTTTAGTAGCTTAATTGTCTCACTATCTAGACTTTCATATTATACAACCAATCTTAGTTGTTAGAATACCTGAACTTTTTATGTTATGACTAATCTTGACAATCTCAGTAGCTCAATTGGTTGACTCCCTGAACTTTTCATGTTATAACTAATCTTGACAATCTTAGTAGCTTAGTTAGTTGACTATCTGAATTTCCATGTCTCAACTAATCTTTTGTCGAAATAAATTACAGGGTACCCTGTAGAAGAAGGGGAGGAATAAGGTTCACAATCAATGGACACTCATACTTCAACTTAGTACTAGTAACAAATGTTGGTGGTGGTGGTGATGTTCATTCAGTAGCTGTTAAAGGATCAAGAACAGGTTGGCAGCCAATGTCAAGAAACTGGGGACAAAACTGGCAAAACAACAACAACCTTAATGGACAAACACTATCATTTAAGGTTACAACAGGTGATGGTAGAAGTTTGATCTCATACAATGTTGCACCTGCTCACTGGTCATTTGGACAGACATATACTGGTGCTCAATTCCACTAAAAAAAGGCATTAAATGGGGTTTTTTTTTTCTTCAAGTTTTTGAAAGTATATTTACTAGAATTACTATTATCATTACTAGTATTAGTATGCATACTGATTTGGTCACTAGTATTAGTATTGTGACTATTTAGTATAGAGGTATTTTGGTTGTAAAGGTGTGGTCTTTAAGGTAAAAAAAAATGAAAAAAGGGCATATTTTAAAATTGTCCTCTTTTTCATTTTGATTGAATTAAGGGTATCTTACTTTTGGGGACCCTAATTCTTGAGGCCACACTTAGTAGTTTTTTTTGGTTTTGGAGGGTATTTTGGTAATTTTTCCTTCTGTTAAGGGCAGAAGTGGAAAGCAGTGGTGGACTTTTACCACCCGCAGTTGGTAGGTGGGGGTGGGGGTGGGGTGGGGTGGGGGTATTTTTGGCAACTTTTTTTTTAAGCTTCAGCCTGTAGCTGAAGATGGACTTTGTATGTGTGAGACTATGAAATGTAAAGAACCATTTAACTAGTAATGATTCAAGAAGATTATGGTTATGTATTTTAACTTTTGTAATGCCTCTCTCGGTTTTAATTTGTTTGACAG</genome_strand>
        <mrna_strand>GGGGTTTATGGTTATGGTGGAGGAGGTTGGATTGATGCTCATGCAACTTTTTATGGGGGTGGTGATGCTTCTGGAACAATGG............................................................................................GTGGGGCTTGTGGATATGGGAATCTTTATAGTCAAGGGTATGGCACAAATACAGCAGCTTTAAGTACTGCTATGTTCAACAATGGGTTGAGCTGTGGTTCTTGTTTTGAATTAAGGTGTGTAAATGACAGACAAGGGTGTTTGCCTGGTTCTATTGTGGTTACTGCTACAAATTTTTGCCCACCAAACAATGCCCTCCCTAATAATGCAGGTGGCTGGTGTAATCCTCCACTTCACCATTTTGACCTCTCTCAGCCTATTTTCCAACACATTGCTCATTACAAAGCTGGAATTGTCCCTGTTGCTTATAGAAG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GGTACCCTGTAGAAGAAGGGGAGGAATAAGGTTCACAATCAATGGACACTCATACTTCAACTTAGTACTAGTAACAAACGTTGGTGGTGGTGGTGATGTTCATTCAGTAGCTGTTAAAGGATCAAGAACAGGTTGGCAGCCAATGTCAAGAAACTGGGGACAAAACTGGCAAAACAACAACGACCTTAATGGACAAACACTATCATTTAAGGTTACAACAGGTGATGGTAGAAGTTTGATCTCATACAATGTTGCACCTGCTCACTGGTCATTTGGACAGACATATACTGGTGCTCAATTCCACTAAAAAAAGGCATTAAATGGGGTTTTTTTTTTCTTCAAGTTTTTGAAAGTATATTTACTAGAATTACTATTATCATTACTAGTATTAGTATGCATACTGATTTGGTCACTAGTA-T--TATTGTGACTATTTAGTATAGAGGTATTTTGGTTGTAAAGGTGTGGTCTTTAAGGTAAAAAAAAATGAAAAAAGGGCATATTTTAAAATTGTCCTCTTTTTCATTTTGATTGAATTAAGGGTATCTTAC-TTTGGGGACCCTAATTTTTGAGGCCACACTTAGTAGTTTTTTTTGGTTTTGGAGGGTATTTTGGTAATTTTTCCTTCTGTTAAGGGCAGAAGTGGAAAGCAGTGGTGGACTTTTACCNCCCCCAGTTGGTA----------------------GGTGGGGGTATTTTTGGCAACTTTTTTTTTAAGCTTCAGCCTGTAGCTGAAGATGGACTTTGTATGTGTGAGACTATGAAATGTAAAGAACCNTTTAACTAGTAATGATTC-AGAAGATTATGGTTATGTATTTTAACTTTTGTAATGCCTCTCTCGGTTTTAATTTGTTTGACNG</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-C05HBa0003C20-FONp9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E303220" ref_strand="+" ref_description="SGN-E303220 [cLEX-5-I11]">
      <seq>caacacattgctcattacaaagctggaattgtccctgttgcttatagaagggtaccctgtagaagaaggggaggaataaggttcacaatcaatggacactcatacttcaacttagtactagtaacaaatgttggtggtggtggtgatgttcattcagtagctgttaaaggatcaagaacaggttggcagccaatgtcaagaaactggggacaaaactggcaaaacaacaacaaccttaatggacaaacactatcatttaaggttacaacaggtgatggtagaagtttgatctcatacaatgttgcacctgctcactggtcatttggacagacatatactggtgctcaattccactaaaaaaaggcattaaatggggctttttttttcttcaagtttttgaaagtatatttactagaattactattatcattactagtattagtatgcatactgatttggtcactagtattagtattgtgactatttagtatacaggtattttggttgtaaaggtgtggtctttaaggtaaaaaaaaatgaaaaaagggcatatttta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C05HBa0003C20-FONp9/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C05HBa0003C20.1" temp_strand="+" temp_description="C05HBa0003C20.1  AC212299.1 htgs_phase:3 submitted_to_sgn_as:C05HBa0003C20 sequenced_by:iitg upload_account_name:india complete sequence">
        <position start="5201" stop="7234"/>
      </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="5501" g_stop="5550" g_length="50"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="50" r_length="50" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="5551" i_stop="6427" i_length="877">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.988" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="6428" g_stop="6934" g_length="507"/>
          <reference_exon_boundary r_type="cDNA" r_start="51" r_stop="557" r_length="507" r_score="0.996"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C05HBa0003C20.1" gen_strand="+" ref_id="SGN-E303220" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>557</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C05HBa0003C20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-E303220" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="5501" e_stop="5550"/>
          <exon e_start="6428" e_stop="6934"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAACACATTGCTCATTACAAAGCTGGAATTGTCCCTGTTGCTTATAGAAGGTAAATTCTTGGTAAAAATATGTTAGTTGTAGAACTATATGCTGTTTGTATCTTGCTATGTATGTATGATGTTGTTTGAGTACTATAAAAGAGTGGCAAGGAGAGTTTTGTCTTTTCACAAATGCTAAACCTTAGTCATGTCTAAATTGCTTAAGCCCAAAGGTTTGAAATTTCTAAATGGTCCCTTTTAAATGACCTTAATTTACTTGTGCATGCTAATAGAAAAATGAAATGGTGGAACCACATGGTGTGGACCCTTTTGATAAAGGTTTTAACTTTATCACAAGAAGTTTCCCATTTGGCTATTTTCAATGGAGTACTCTTTAGCATTTACTTCTTTCTTGGTTGTTGTAATAGTAGAAGATTCATAAAGTTACATATATTGTTCCCATTTGTCTCTTTACTTGTTTCAATTGTGCTCTTTATCCTTGACTTGTTTCTTAAATTTGGTAAAACTTGGAAAAGCATGAGAAACAAAGTTACAAACTTTAACACCATATAAAAACATAACATAACCAATCTTGCAAATTTTAATAGCTTAGTTTGTTGACAAGCCATACCTTTACCCTATGAACAATCTTGATAATCTTATTAGCTTAGTAAGTTGACTATCTGAAGTTTCACGTTTCGACAAATCTTGTTTATTTTAGTAGCTTAATTGTCTCACTATCTAGACTTTCATATTATACAACCAATCTTAGTTGTTAGAATACCTGAACTTTTTATGTTATGACTAATCTTGACAATCTCAGTAGCTCAATTGGTTGACTCCCTGAACTTTTCATGTTATAACTAATCTTGACAATCTTAGTAGCTTAGTTAGTTGACTATCTGAATTTCCATGTCTCAACTAATCTTTTGTCGAAATAAATTACAGGGTACCCTGTAGAAGAAGGGGAGGAATAAGGTTCACAATCAATGGACACTCATACTTCAACTTAGTACTAGTAACAAATGTTGGTGGTGGTGGTGATGTTCATTCAGTAGCTGTTAAAGGATCAAGAACAGGTTGGCAGCCAATGTCAAGAAACTGGGGACAAAACTGGCAAAACAACAACAACCTTAATGGACAAACACTATCATTTAAGGTTACAACAGGTGATGGTAGAAGTTTGATCTCATACAATGTTGCACCTGCTCACTGGTCATTTGGACAGACATATACTGGTGCTCAATTCCACTAAAAAAAGGCATTAAATGGGGTTTTTTTTTTCTTCAAGTTTTTGAAAGTATATTTACTAGAATTACTATTATCATTACTAGTATTAGTATGCATACTGATTTGGTCACTAGTATTAGTATTGTGACTATTTAGTATAGAGGTATTTTGGTTGTAAAGGTGTGGTCTTTAAGGTAAAAAAAAATGAAAAAAGGGCATATTTTA</genome_strand>
        <mrna_strand>CAACACATTGCTCATTACAAAGCTGGAATTGTCCCTGTTGCTTATAGAAG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GGTACCCTGTAGAAGAAGGGGAGGAATAAGGTTCACAATCAATGGACACTCATACTTCAACTTAGTACTAGTAACAAATGTTGGTGGTGGTGGTGATGTTCATTCAGTAGCTGTTAAAGGATCAAGAACAGGTTGGCAGCCAATGTCAAGAAACTGGGGACAAAACTGGCAAAACAACAACAACCTTAATGGACAAACACTATCATTTAAGGTTACAACAGGTGATGGTAGAAGTTTGATCTCATACAATGTTGCACCTGCTCACTGGTCATTTGGACAGACATATACTGGTGCTCAATTCCACTAAAAAAAGGCATTAAATGGGGCTTTTTTTTTCTTCAAGTTTTTGAAAGTATATTTACTAGAATTACTATTATCATTACTAGTATTAGTATGCATACTGATTTGGTCACTAGTATTAGTATTGTGACTATTTAGTATACAGGTATTTTGGTTGTAAAGGTGTGGTCTTTAAGGTAAAAAAAAATGAAAAAAGGGCATATTTTA</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-C05HBa0003C20-FONp9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E317861" ref_strand="-" ref_description="SGN-E317861 [cTOA-30-B18]">
      <seq>gtaaaggtgtggtctttaaggtaaaaaaaaatgaaaaaagggcatattttaaaattgtcctctttttcattttgattgaattaagggtatcttacttttggggaccctaattcttgaggccacacttagtagttttttttggttttggagggtattttggtaatttttccttctgttaagggcagaagtggaaagcagtggtggacttttaccacccgcagttggtaggtgggggtgggggtggggtggggtgggggtatttttgggcctttttttttaagcttcagcctgtagctgaagatggactttgtatgtgtgagactatgaaatgtaaagacccatttaactagtaatgattcaagaagattatggttatgtattttaacttttgtaatgcctctctcggttttaatttgtttgacaaacaaaaaaaaaaaaaaaaaactc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C05HBa0003C20-FONp9/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C05HBa0003C20.1" temp_strand="+" temp_description="C05HBa0003C20.1  AC212299.1 htgs_phase:3 submitted_to_sgn_as:C05HBa0003C20 sequenced_by:iitg upload_account_name:india complete sequence">
        <position start="6584" stop="7614"/>
      </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="6884" g_stop="7308" g_length="425"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="424" r_length="424" r_score="0.988"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="425" polyA_stop="444"/>
      <MATCH_line gen_id="C05HBa0003C20.1" gen_strand="+" ref_id="SGN-E317861" ref_strand="-">
        <total_alignment_score>0.988</total_alignment_score>
        <cumulative_length_of_scored_exons>425</cumulative_length_of_scored_exons>
        <coverage percentage="0.951" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C05HBa0003C20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-E317861" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="6884" e_stop="7308"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTAAAGGTGTGGTCTTTAAGGTAAAAAAAAATGAAAAAAGGGCATATTTTAAAATTGTCCTCTTTTTCATTTTGATTGAATTAAGGGTATCTTACTTTTGGGGACCCTAATTCTTGAGGCCACACTTAGTAGTTTTTTTTGGTTTTGGAGGGTATTTTGGTAATTTTTCCTTCTGTTAAGGGCAGAAGTGGAAAGCAGTGGTGGACTTTTACCACCCGCAGTTGGTAGGTGGGGGTGGGGGTGGGGTGGGGTGGGGGTATTTTTGGCAACTTTTTTTTTAAGCTTCAGCCTGTAGCTGAAGATGGACTTTGTATGTGTGAGACTATGAAATGTAAAGAACCATTTAACTAGTAATGATTCAAGAAGATTATGGTTATGTATTTTAACTTTTGTAATGCCTCTCTCGGTTTTAATTTGTTTGACAG</genome_strand>
        <mrna_strand>GTAAAGGTGTGGTCTTTAAGGTAAAAAAAAATGAAAAAAGGGCATATTTTAAAATTGTCCTCTTTTTCATTTTGATTGAATTAAGGGTATCTTACTTTTGGGGACCCTAATTCTTGAGGCCACACTTAGTAGTTTTTTTTGGTTTTGGAGGGTATTTTGGTAATTTTTCCTTCTGTTAAGGGCAGAAGTGGAAAGCAGTGGTGGACTTTTACCACCCGCAGTTGGTAGGTGGGGGTGGGGGTGGGGTGGGGTGGGGGTATTTTTGG-GCCTTTTTTTTTAAGCTTCAGCCTGTAGCTGAAGATGGACTTTGTATGTGTGAGACTATGAAATGTAAAGACCCATTTAACTAGTAATGATTCAAGAAGATTATGGTTATGTATTTTAACTTTTGTAATGCCTCTCTCGGTTTTAATTTGTTTGACAA</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-C05HBa0003C20-FONp9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato" ref_id="SGN-E703862" ref_strand="+" ref_description="SGN-E703862 [FA22CG01]">
      <seq>ccttacttcaactgactgtggtctcaaattcagggagaaaatactctatcttcaagaactcaatatcaatcccagtaaagttcttcaactaaacccccatttacgatcagcaacgctcgattcaatcagatctgttgaagtatgtctgttttcaatggggattgaacggtcggcaattggtcgaatacttgatatgcatcctcagcttttaacctccgacccatatatccacctttacccaattttcgatttcttgttaaacgacgtcgttatccctttccatgacattcggaaatccattatccgatgtccgagaattcttgtttgtagtgttgaagatcaattgaaacccacatttgagtttttgaaggaatttgggtttgtgggtcagaatcgaattacttgtcagactactgttttgcttgtgtccagtgttgagctaactttgaaccctaaaattgattacatgttgagtttgggatttgaactcgatgatgtggctaatatggttttgagatcacctgggttgttgacatttagtattgagaaaaactttaggccaaaagttgagtattttttgaaggagatgaatggggatataagggaattgaagaggtttcctcagtacttttcgtttagtttggagaggaagattaagcctcggcataggcttttggtggagcatgggtttacgctgtctttatcggagatgttgaaggttagtgatggagaattcaatgccagattgatttgaatgcgattgaggttagtggatgataagcaaatgtagtacgtaattaactc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C05HBa0003C20-FONp9/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C05HBa0003C20.1" temp_strand="+" temp_description="C05HBa0003C20.1  AC212299.1 htgs_phase:3 submitted_to_sgn_as:C05HBa0003C20 sequenced_by:iitg upload_account_name:india complete sequence">
        <position start="12110" stop="13513"/>
      </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="12410" g_stop="13213" g_length="804"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="804" r_length="804" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C05HBa0003C20.1" gen_strand="+" ref_id="SGN-E703862" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>804</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C05HBa0003C20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-E703862" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="12410" e_stop="13213"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCTTACTTCAACTGACTGTGGTCTCAAATTCAGGGAGAAAATACTCTATCTTCAAGAACTCAATATCAATCCCAGTAAAGTTCTTCAACTAAACCCCCATTTACGATCAGCAACGCTCGATTCAATCAGATCTGTTGAAGTATGTCTGTTTTCAATGGGGATTGAACGGTCGGCAATTGGTCGAATACTTGATATGCATCCTCAGCTTTTAACCTCCGACCCATATATCCACCTTTACCCAATTTTCGATTTCTTGTTAAACGACGTCGTTATCCCTTTCCATGACATTCGGAAATCCATTATCCGATGTCCGAGAATTCTTGTTTGTAGTGTTGAAGATCAATTGAAACCCACATTTGAGTTTTTGAAGGAATTTGGGTTTGTGGGTCAGAATCGAATTACTTGTCAGACTACTGTTTTGCTTGTGTCCAGTGTTGAGCTAACTTTGAACCCTAAAATTGATTACATGTTGAGTTTGGGATTTGAACTCGATGATGTGGCTAATATGGTTTTGAGATCACCTGGGTTGTTGACATTTAGTATTGAGAAAAACTTTAGGCCAAAAGTTGAGTATTTTTTGAAGGAGATGAATGGGGATATAAGGGAATTGAAGAGGTTTCCTCAGTACTTTTCGTTTAGTTTGGAGAGGAAGATTAAGCCTCGGCATAGGCTTTTGGTGGAGCATGGGTTTACGCTGTCTTTATCGGAGATGTTGAAGGTTAGTGATGGAGAATTCAATGCCAGATTGATTGAAATGCGATTGAGGTTAGTGGATGATAAGCAAATGTAGTACGTAATTAACTC</genome_strand>
        <mrna_strand>CCTTACTTCAACTGACTGTGGTCTCAAATTCAGGGAGAAAATACTCTATCTTCAAGAACTCAATATCAATCCCAGTAAAGTTCTTCAACTAAACCCCCATTTACGATCAGCAACGCTCGATTCAATCAGATCTGTTGAAGTATGTCTGTTTTCAATGGGGATTGAACGGTCGGCAATTGGTCGAATACTTGATATGCATCCTCAGCTTTTAACCTCCGACCCATATATCCACCTTTACCCAATTTTCGATTTCTTGTTAAACGACGTCGTTATCCCTTTCCATGACATTCGGAAATCCATTATCCGATGTCCGAGAATTCTTGTTTGTAGTGTTGAAGATCAATTGAAACCCACATTTGAGTTTTTGAAGGAATTTGGGTTTGTGGGTCAGAATCGAATTACTTGTCAGACTACTGTTTTGCTTGTGTCCAGTGTTGAGCTAACTTTGAACCCTAAAATTGATTACATGTTGAGTTTGGGATTTGAACTCGATGATGTGGCTAATATGGTTTTGAGATCACCTGGGTTGTTGACATTTAGTATTGAGAAAAACTTTAGGCCAAAAGTTGAGTATTTTTTGAAGGAGATGAATGGGGATATAAGGGAATTGAAGAGGTTTCCTCAGTACTTTTCGTTTAGTTTGGAGAGGAAGATTAAGCCTCGGCATAGGCTTTTGGTGGAGCATGGGTTTACGCTGTCTTTATCGGAGATGTTGAAGGTTAGTGATGGAGAATTCAATGCCAGATTGATTTGAATGCGATTGAGGTTAGTGGATGATAAGCAAATGTAGTACGTAATTAACTC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>4</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="+" PGL_start="5064" PGL_stop="7308"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="5064" e_stop="5145"/>
            <exon e_start="5238" e_stop="5550"/>
            <exon e_start="6428" e_stop="7308"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="1.000" e_score="0.963"/>
          <exon-intron don_prob="0.997" acc_prob="0.988" e_score="1.000"/>
          <exon-only e_score="0.961"/>
        </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="0.963">
            <gDNA_exon_boundary e_start="5064" e_stop="5145" e_length="82"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="1.000">
            <gDNA_intron_boundary i_start="5146" i_stop="5237" i_length="92"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="5238" e_stop="5550" e_length="313"/>
          </exon>
          <intron i_serial="2" don_prob="0.997" acc_prob="0.988">
            <gDNA_intron_boundary i_start="5551" i_stop="6427" i_length="877"/>
          </intron>
          <exon e_serial="3" e_score="0.961">
            <gDNA_exon_boundary e_start="6428" e_stop="7308" e_length="881"/>
          </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="5064" stop="5145"/>
              <exon start="5238" stop="5550"/>
              <exon start="6428" stop="7308"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E744681" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="5501" stop="5550"/>
              <exon start="6428" stop="6934"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E303220" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="6884" stop="7308"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E317861" 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>TCTGTTTATGGTTATGGTGGAGGAGGTTGGATTGATGCTCATGCAACTTTTTATGGGGGTGGTGATGCTTCTGGAACAATGG : GTGGGGCTTGTGGATATGGGAATCTTTATAGTCAAGGGTATGGCACAAATACAGCAGCTTTAAGTACTGCTATGTTCAACAATGGGTTGAGCTGTGGTTCTTGTTTTGAATTAAGGTGTGTAAATGACAGACAAGGGTGTTTGCCTGGTTCTATTGTGGTTACTGCTACAAATTTTTGCCCACCAAACAATGCCCTCCCTAATAATGCAGGTGGCTGGTGTAATCCTCCACTTCACCATTTTGACCTCTCTCAGCCTATTTTCCAACACATTGCTCATTACAAAGCTGGAATTGTCCCTGTTGCTTATAGAAG : GGTACCCTGTAGAAGAAGGGGAGGAATAAGGTTCACAATCAATGGACACTCATACTTCAACTTAGTACTAGTAACAAATGTTGGTGGTGGTGGTGATGTTCATTCAGTAGCTGTTAAAGGATCAAGAACAGGTTGGCAGCCAATGTCAAGAAACTGGGGACAAAACTGGCAAAACAACAACAACCTTAATGGACAAACACTATCATTTAAGGTTACAACAGGTGATGGTAGAAGTTTGATCTCATACAATGTTGCACCTGCTCACTGGTCATTTGGACAGACATATACTGGTGCTCAATTCCACTAAAAAAAGGCATTAAATGGGGTTTTTTTTTTCTTCAAGTTTTTGAAAGTATATTTACTAGAATTACTATTATCATTACTAGTATTAGTATGCATACTGATTTGGTCACTAGTATTAGTATTGTGACTATTTAGTATAGAGGTATTTTGGTTGTAAAGGTGTGGTCTTTAAGGTAAAAAAAAATGAAAAAAGGGCATATTTTAAAATTGTCCTCTTTTTCATTTTGATTGAATTAAGGGTATCTTACTTTTGGGGACCCTAATTCTTGAGGCCACACTTAGTAGTTTTTTTTGGTTTTGGAGGGTATTTTGGTAATTTTTCCTTCTGTTAAGGGCAGAAGTGGAAAGCAGTGGTGGACTTTTACCACCCGCAGTTGGTAGGTGGGGGTGGGGGTGGGGTGGGGTGGGGGTATTTTTGGCAACTTTTTTTTTAAGCTTCAGCCTGTAGCTGAAGATGGACTTTGTATGTGTGAGACTATGAAATGTAAAGAACCATTTAACTAGTAATGATTCAAGAAGATTATGGTTATGTATTTTAACTTTTGTAATGCCTCTCTCGGTTTTAATTTGTTTGACAG</gDNA_template>
            <first_frame> S  V  Y  G  Y  G  G  G  G  W  I  D  A  H  A  T  F  Y  G  G  G  D  A  S  G  T  M   : G  G  A  C  G  Y  G  N  L  Y  S  Q  G  Y  G  T  N  T  A  A  L  S  T  A  M  F  N  N  G  L  S  C  G  S  C  F  E  L  R  C  V  N  D  R  Q  G  C  L  P  G  S  I  V  V  T  A  T  N  F  C  P  P  N  N  A  L  P  N  N  A  G  G  W  C  N  P  P  L  H  H  F  D  L  S  Q  P  I  F  Q  H  I  A  H  Y  K  A  G  I  V  P  V  A  Y  R  R :   V  P  C  R  R  R  G  G  I  R  F  T  I  N  G  H  S  Y  F  N  L  V  L  V  T  N  V  G  G  G  G  D  V  H  S  V  A  V  K  G  S  R  T  G  W  Q  P  M  S  R  N  W  G  Q  N  W  Q  N  N  N  N  L  N  G  Q  T  L  S  F  K  V  T  T  G  D  G  R  S  L  I  S  Y  N  V  A  P  A  H  W  S  F  G  Q  T  Y  T  G  A  Q  F  H  *  K  K  A  L  N  G  V  F  F  F  F  K  F  L  K  V  Y  L  L  E  L  L  L  S  L  L  V  L  V  C  I  L  I  W  S  L  V  L  V  L  *  L  F  S  I  E  V  F  W  L  *  R  C  G  L  *  G  K  K  K  *  K  K  G  I  F  *  N  C  P  L  F  H  F  D  *  I  K  G  I  L  L  L  G  T  L  I  L  E  A  T  L  S  S  F  F  W  F  W  R  V  F  W  *  F  F  L  L  L  R  A  E  V  E  S  S  G  G  L  L  P  P  A  V  G  R  W  G  W  G  W  G  G  V  G  V  F  L  A  T  F  F  L  S  F  S  L  *  L  K  M  D  F  V  C  V  R  L  *  N  V  K  N  H  L  T  S  N  D  S  R  R  L  W  L  C  I  L  T  F  V  M  P  L  S  V  L  I  C  L  T  </first_frame>
            <second_frame>  L  F  M  V  M  V  E  E  V  G  L  M  L  M  Q  L  F  M  G  V  V  M  L  L  E  Q  W  :  V  G  L  V  D  M  G  I  F  I  V  K  G  M  A  Q  I  Q  Q  L  *  V  L  L  C  S  T  M  G  *  A  V  V  L  V  L  N  *  G  V  *  M  T  D  K  G  V  C  L  V  L  L  W  L  L  L  Q  I  F  A  H  Q  T  M  P  S  L  I  M  Q  V  A  G  V  I  L  H  F  T  I  L  T  S  L  S  L  F  S  N  T  L  L  I  T  K  L  E  L  S  L  L  L  I  E   : G  Y  P  V  E  E  G  E  E  *  G  S  Q  S  M  D  T  H  T  S  T  *  Y  *  *  Q  M  L  V  V  V  V  M  F  I  Q  *  L  L  K  D  Q  E  Q  V  G  S  Q  C  Q  E  T  G  D  K  T  G  K  T  T  T  T  L  M  D  K  H  Y  H  L  R  L  Q  Q  V  M  V  E  V  *  S  H  T  M  L  H  L  L  T  G  H  L  D  R  H  I  L  V  L  N  S  T  K  K  R  H  *  M  G  F  F  F  S  S  S  F  *  K  Y  I  Y  *  N  Y  Y  Y  H  Y  *  Y  *  Y  A  Y  *  F  G  H  *  Y  *  Y  C  D  Y  L  V  *  R  Y  F  G  C  K  G  V  V  F  K  V  K  K  N  E  K  R  A  Y  F  K  I  V  L  F  F  I  L  I  E  L  R  V  S  Y  F  W  G  P  *  F  L  R  P  H  L  V  V  F  F  G  F  G  G  Y  F  G  N  F  S  F  C  *  G  Q  K  W  K  A  V  V  D  F  Y  H  P  Q  L  V  G  G  G  G  G  G  V  G  W  G  Y  F  W  Q  L  F  F  *  A  S  A  C  S  *  R  W  T  L  Y  V  *  D  Y  E  M  *  R  T  I  *  L  V  M  I  Q  E  D  Y  G  Y  V  F  *  L  L  *  C  L  S  R  F  *  F  V  *  Q </second_frame>
            <third_frame>   C  L  W  L  W  W  R  R  L  D  *  C  S  C  N  F  L  W  G  W  *  C  F  W  N  N  G :   W  G  L  W  I  W  E  S  L  *  S  R  V  W  H  K  Y  S  S  F  K  Y  C  Y  V  Q  Q  W  V  E  L  W  F  L  F  *  I  K  V  C  K  *  Q  T  R  V  F  A  W  F  Y  C  G  Y  C  Y  K  F  L  P  T  K  Q  C  P  P  *  *  C  R  W  L  V  *  S  S  T  S  P  F  *  P  L  S  A  Y  F  P  T  H  C  S  L  Q  S  W  N  C  P  C  C  L  *  K  :  G  T  L  *  K  K  G  R  N  K  V  H  N  Q  W  T  L  I  L  Q  L  S  T  S  N  K  C  W  W  W  W  *  C  S  F  S  S  C  *  R  I  K  N  R  L  A  A  N  V  K  K  L  G  T  K  L  A  K  Q  Q  Q  P  *  W  T  N  T  I  I  *  G  Y  N  R  *  W  *  K  F  D  L  I  Q  C  C  T  C  S  L  V  I  W  T  D  I  Y  W  C  S  I  P  L  K  K  G  I  K  W  G  F  F  F  L  Q  V  F  E  S  I  F  T  R  I  T  I  I  I  T  S  I  S  M  H  T  D  L  V  T  S  I  S  I  V  T  I  *  Y  R  G  I  L  V  V  K  V  W  S  L  R  *  K  K  M  K  K  G  H  I  L  K  L  S  S  F  S  F  *  L  N  *  G  Y  L  T  F  G  D  P  N  S  *  G  H  T  *  *  F  F  L  V  L  E  G  I  L  V  I  F  P  S  V  K  G  R  S  G  K  Q  W  W  T  F  T  T  R  S  W  *  V  G  V  G  V  G  W  G  G  G  I  F  G  N  F  F  F  K  L  Q  P  V  A  E  D  G  L  C  M  C  E  T  M  K  C  K  E  P  F  N  *  *  *  F  K  K  I  M  V  M  Y  F  N  F  C  N  A  S  L  G  F  N  L  F  D   </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="C05HBa0003C20.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="5064" stop="5145"/>
                    <exon start="5238" stop="5550"/>
                    <exon start="6428" stop="6734"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>699</number_coding_nucleotides>
                  <number_encoded_amino_acids>233</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SVYGYGGGGWIDAHATFYGGGDASGTMGGACGYGNLYSQGYGTNTAALSTAMFNNGLSCGSCFELRCVNDRQGCLPGSIVVTATNFCPPNNALPNNAGGWCNPPLHHFDLSQPIFQHIAHYKAGIVPVAYRRVPCRRRGGIRFTINGHSYFNLVLVTNVGGGGDVHSVAVKGSRTGWQPMSRNWGQNWQNNNNLNGQTLSFKVTTGDGRSLISYNVAPAHWSFGQTYTGAQFH*</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="12410" PGL_stop="13213"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="12410" e_stop="13213"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="0.998">
            <gDNA_exon_boundary e_start="12410" e_stop="13213" e_length="804"/>
          </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="12410" stop="13213"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E703862" 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>CCTTACTTCAACTGACTGTGGTCTCAAATTCAGGGAGAAAATACTCTATCTTCAAGAACTCAATATCAATCCCAGTAAAGTTCTTCAACTAAACCCCCATTTACGATCAGCAACGCTCGATTCAATCAGATCTGTTGAAGTATGTCTGTTTTCAATGGGGATTGAACGGTCGGCAATTGGTCGAATACTTGATATGCATCCTCAGCTTTTAACCTCCGACCCATATATCCACCTTTACCCAATTTTCGATTTCTTGTTAAACGACGTCGTTATCCCTTTCCATGACATTCGGAAATCCATTATCCGATGTCCGAGAATTCTTGTTTGTAGTGTTGAAGATCAATTGAAACCCACATTTGAGTTTTTGAAGGAATTTGGGTTTGTGGGTCAGAATCGAATTACTTGTCAGACTACTGTTTTGCTTGTGTCCAGTGTTGAGCTAACTTTGAACCCTAAAATTGATTACATGTTGAGTTTGGGATTTGAACTCGATGATGTGGCTAATATGGTTTTGAGATCACCTGGGTTGTTGACATTTAGTATTGAGAAAAACTTTAGGCCAAAAGTTGAGTATTTTTTGAAGGAGATGAATGGGGATATAAGGGAATTGAAGAGGTTTCCTCAGTACTTTTCGTTTAGTTTGGAGAGGAAGATTAAGCCTCGGCATAGGCTTTTGGTGGAGCATGGGTTTACGCTGTCTTTATCGGAGATGTTGAAGGTTAGTGATGGAGAATTCAATGCCAGATTGATTGAAATGCGATTGAGGTTAGTGGATGATAAGCAAATGTAGTACGTAATTAACTC</gDNA_template>
            <first_frame> P  Y  F  N  *  L  W  S  Q  I  Q  G  E  N  T  L  S  S  R  T  Q  Y  Q  S  Q  *  S  S  S  T  K  P  P  F  T  I  S  N  A  R  F  N  Q  I  C  *  S  M  S  V  F  N  G  D  *  T  V  G  N  W  S  N  T  *  Y  A  S  S  A  F  N  L  R  P  I  Y  P  P  L  P  N  F  R  F  L  V  K  R  R  R  Y  P  F  P  *  H  S  E  I  H  Y  P  M  S  E  N  S  C  L  *  C  *  R  S  I  E  T  H  I  *  V  F  E  G  I  W  V  C  G  S  E  S  N  Y  L  S  D  Y  C  F  A  C  V  Q  C  *  A  N  F  E  P  *  N  *  L  H  V  E  F  G  I  *  T  R  *  C  G  *  Y  G  F  E  I  T  W  V  V  D  I  *  Y  *  E  K  L  *  A  K  S  *  V  F  F  E  G  D  E  W  G  Y  K  G  I  E  E  V  S  S  V  L  F  V  *  F  G  E  E  D  *  A  S  A  *  A  F  G  G  A  W  V  Y  A  V  F  I  G  D  V  E  G  *  *  W  R  I  Q  C  Q  I  D  *  N  A  I  E  V  S  G  *  *  A  N  V  V  R  N  *  L </first_frame>
            <second_frame>  L  T  S  T  D  C  G  L  K  F  R  E  K  I  L  Y  L  Q  E  L  N  I  N  P  S  K  V  L  Q  L  N  P  H  L  R  S  A  T  L  D  S  I  R  S  V  E  V  C  L  F  S  M  G  I  E  R  S  A  I  G  R  I  L  D  M  H  P  Q  L  L  T  S  D  P  Y  I  H  L  Y  P  I  F  D  F  L  L  N  D  V  V  I  P  F  H  D  I  R  K  S  I  I  R  C  P  R  I  L  V  C  S  V  E  D  Q  L  K  P  T  F  E  F  L  K  E  F  G  F  V  G  Q  N  R  I  T  C  Q  T  T  V  L  L  V  S  S  V  E  L  T  L  N  P  K  I  D  Y  M  L  S  L  G  F  E  L  D  D  V  A  N  M  V  L  R  S  P  G  L  L  T  F  S  I  E  K  N  F  R  P  K  V  E  Y  F  L  K  E  M  N  G  D  I  R  E  L  K  R  F  P  Q  Y  F  S  F  S  L  E  R  K  I  K  P  R  H  R  L  L  V  E  H  G  F  T  L  S  L  S  E  M  L  K  V  S  D  G  E  F  N  A  R  L  I  E  M  R  L  R  L  V  D  D  K  Q  M  *  Y  V  I  N   </second_frame>
            <third_frame>   L  L  Q  L  T  V  V  S  N  S  G  R  K  Y  S  I  F  K  N  S  I  S  I  P  V  K  F  F  N  *  T  P  I  Y  D  Q  Q  R  S  I  Q  S  D  L  L  K  Y  V  C  F  Q  W  G  L  N  G  R  Q  L  V  E  Y  L  I  C  I  L  S  F  *  P  P  T  H  I  S  T  F  T  Q  F  S  I  S  C  *  T  T  S  L  S  L  S  M  T  F  G  N  P  L  S  D  V  R  E  F  L  F  V  V  L  K  I  N  *  N  P  H  L  S  F  *  R  N  L  G  L  W  V  R  I  E  L  L  V  R  L  L  F  C  L  C  P  V  L  S  *  L  *  T  L  K  L  I  T  C  *  V  W  D  L  N  S  M  M  W  L  I  W  F  *  D  H  L  G  C  *  H  L  V  L  R  K  T  L  G  Q  K  L  S  I  F  *  R  R  *  M  G  I  *  G  N  *  R  G  F  L  S  T  F  R  L  V  W  R  G  R  L  S  L  G  I  G  F  W  W  S  M  G  L  R  C  L  Y  R  R  C  *  R  L  V  M  E  N  S  M  P  D  *  L  K  C  D  *  G  *  W  M  I  S  K  C  S  T  *  L  T  </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="C05HBa0003C20.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="12411" stop="13199"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>786</number_coding_nucleotides>
                  <number_encoded_amino_acids>262</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LTSTDCGLKFREKILYLQELNINPSKVLQLNPHLRSATLDSIRSVEVCLFSMGIERSAIGRILDMHPQLLTSDPYIHLYPIFDFLLNDVVIPFHDIRKSIIRCPRILVCSVEDQLKPTFEFLKEFGFVGQNRITCQTTVLLVSSVELTLNPKIDYMLSLGFELDDVANMVLRSPGLLTFSIEKNFRPKVEYFLKEMNGDIRELKRFPQYFSFSLERKIKPRHRLLVEHGFTLSLSEMLKVSDGEFNARLIEMRLRLVDDKQM*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 4 chains have been computed
$ 
$ memory statistics:
$ 7616 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 1904 bytes was the average size of a spliced alignment
$ 6768 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3384 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 5 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 23:41:08
-->
