<?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="2009-01-16 17:38:52"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C06HBa0218N05-1hy1d/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C06HBa0218N05-1hy1d/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_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-C06HBa0218N05-1hy1d/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U335931" ref_strand="+" ref_description="SGN-U335931        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: gi|47824972|gb|AAT38745.1| putative polyprotein, 3'-partial [Solanum demissum] (evalue: 1e-33, score=146)">
      <seq>acctagcccatctggtactaaggcggtgacacctccaccaactgaggaagtggtaagagagggtgaggatggggagaatgaacaagtgcagaatgaggaattgccaccccaacctacccaagagatgatcaatcaggttcttgcttaccttagcgggttatctgatcaaggccaagcacctccagtgttttctgcactagcacctcaggctccggaggtacaacatgcgcctactgtgactccccgcatcgatacctcattggaaataggaacgtttccccgtctgactacagggcctataatgacaaatgatcagcatgaactttttagtaagttcttgaaattgaaacctcaagtctacaagggtgttgaatctgaggatgcctacgattttctggttgactgtcatgagctactacacaagatgggtatagtagaacggtttggtgttgagtttgtgacttatcagtttcaagggaacgccaaaatgtggtggcggtcacatgttgagtgtcaaccaacagaggcaccacgtatgacttgggcatcattct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0218N05-1hy1d/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0218N05.1" temp_strand="+" temp_description="C06HBa0218N05.1  AC216651.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0218N05 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="47053" stop="48205"/>
      </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="47353" g_stop="47905" g_length="553"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="554" r_length="554" r_score="0.919"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C06HBa0218N05.1" gen_strand="+" ref_id="SGN-U335931" ref_strand="+">
        <total_alignment_score>0.919</total_alignment_score>
        <cumulative_length_of_scored_exons>553</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0218N05.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U335931" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="47353" e_stop="47905"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACCTAGCCCATCTGATACTAGGGCAGTGACTCCTCCACCGACTGAAGAAGTAGTAAGAG-GGGTGAGGAAGGGGAAACTGAACAAGTACAGAATGAGGGATTGCCTCCCCAACCTACCCCAGAGATGATCAATCAGGTTCTTGCTTATCTTAGTGGGTTATCTGATCAAGGTCAAACACCTCCAGTGTTTTTTGCACCAGCACCTCAGGGTCCGGAGGTACAGCATGCAGCTACTGCGGCTCCCCGCATGGATGTTCCATTGGAAATAGGCATGTTTCCTCGTCTGACTACAGGGCCTATAATGACAAATGATCAACATGAACTTTTCAGTAAGTTCTTGAAATTGAAACCTCCAGTCTTCAAGGGTGCTGAATCTGAGGATGCCTATGATTTTCTGGTTGACTGTCATGAGCTACTACACAAAATGGGTATAGTAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAGGGAACGTCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCACCTATGACTTGGGCATCATTCT</genome_strand>
        <mrna_strand>ACCTAGCCCATCTGGTACTAAGGCGGTGACACCTCCACCAACTGAGGAAGTGGTAAGAGAGGGTGAGGATGGGGAGAATGAACAAGTGCAGAATGAGGAATTGCCACCCCAACCTACCCAAGAGATGATCAATCAGGTTCTTGCTTACCTTAGCGGGTTATCTGATCAAGGCCAAGCACCTCCAGTGTTTTCTGCACTAGCACCTCAGGCTCCGGAGGTACAACATGCGCCTACTGTGACTCCCCGCATCGATACCTCATTGGAAATAGGAACGTTTCCCCGTCTGACTACAGGGCCTATAATGACAAATGATCAGCATGAACTTTTTAGTAAGTTCTTGAAATTGAAACCTCAAGTCTACAAGGGTGTTGAATCTGAGGATGCCTACGATTTTCTGGTTGACTGTCATGAGCTACTACACAAGATGGGTATAGTAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAGGGAACGCCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCACGTATGACTTGGGCATCATTCT</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-C06HBa0218N05-1hy1d/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U317064" ref_strand="+" ref_description="SGN-U317064        Tomato 200607 #1 [6 ESTs aligned] genbank/nr: gi|47824972|gb|AAT38745.1| putative polyprotein, 3'-partial [Solanum demissum] (evalue: 5e-64, score=248)">
      <seq>acgaataggcatatcaagaaattcacaatgtaaatttagaccattagcaaatgaggaagatacataagaaaacgtggatccaggatcaaacaatacggaagccatgcaatcacaaactagaagattacctgtgatgacagcatcagatgcctccgcttcagaccgcccagggaaagcgtaacaatgggccctatcgtttgtctgcccattgcccctaccatgttgtgatgtagtggccccagtttgcccattacctctgccgttttggtgaccaccattacctcgaccaccacgtcctccagaataacggcctctaccatgaccacctctacctctagctattgggggtctataacttggtccgggacaatttatcctaatatgtccaatctccccacatccataacattctctggagtcactcataggccccttggagaagtgttgaccggtctgaggtggacccccaactacagtctgtagtgaagactgaatgggtcgagctgagtaacctccggaaccttgtcctctagagtaagaacccttaaactcacctccctttcgaaacctctttgatgtcgatgtcgtggtgaagtcgtctggcttcactccttccacttctatcacaaagtctaccacttcttggaaggattttgccgttgccgctacctgtaaggacgaaatccgcaattctgacctcaaccccttcacaaaccggcgaatccgctcttgaggactgaaacagagttgagtggcatatctggatagtgcacgaaacttagcctcataagcattaactgacaccctaccttgctctaggctcaagaactcatcccttttcttatccctcaaagtccgggggatatacttctccataaacaaactatagaatgaggcccaagtcataggtgatgcctctattggttgacactcgatatgtgaccgccaccacatttgggcgttcccttgaaactgataagtcacaaactccacaccaaaccgttctactatacccatcttgtgtagtagctcgtgacagtcaaccagaaaatcataagcatcctccgattcagcacccttgaagaccggaggtttcaatttcaagaacttactgaaaagttcatgctgatcatttgtcattatagggacagtagtcaaacgtggaaatgtgcctatgtccaatggaacatccatgcggggagccatagtagccgcatgttgtacttctgaaaccggaggtgttggcgcagaaaacactggaggtgcttgaccttgatcagataacccgctaagataagccagaacctgattgatcatctctggggtaggttggggtggcatttcctcattttgcacttgttcagtttccccatccctccctttctctattacttcctcagtcagtggaagagtcactgccctagtatcagatgggct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0218N05-1hy1d/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0218N05.1" temp_strand="-" temp_description="C06HBa0218N05.1  AC216651.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0218N05 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="49092" stop="47057"/>
      </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="48792" g_stop="47357" g_length="1436"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="1437" r_length="1437" r_score="0.903"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C06HBa0218N05.1" gen_strand="-" ref_id="SGN-U317064" ref_strand="+">
        <total_alignment_score>0.903</total_alignment_score>
        <cumulative_length_of_scored_exons>1436</cumulative_length_of_scored_exons>
        <coverage percentage="0.999" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0218N05.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U317064" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="48792" e_stop="47357"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACGAATAGGTATGTCAAGCAATTCACAATGTAAATTAAGACCATTAGCAAATGAGGAAGATACATATGAAAATGTGGAGCCAGGATCAAATAATATAGAAGCCATGCAATCACAAACCAAAAGATTACCTGTGATGACAGCATCTGATGTCTCCGCTTCTGACCGCCCAGGGAAAGCATAACAATGGGCCCTCTCACCTGTCTGTCCGTTGCCCCTACCATGTTGTGATATAGTGGCTCCAGTTTGCCCATCACCCCGGCCGTTTTGATGACCACCATTACCTCGGCCACCACGTCCTCCAGAATAACGGCCTCTACCATGACCACCTTTATCTCTAGCTATTGGGGGTCTATAACTCTATTTTGGACAATTCCTCCTAATATGTCCAGTCTCCCCACATCCATAACACTCTCTGGAGTCAAGCATAGGTCTCTCAGAGAAGTGTTGACCGGTCTGAGGCGGACCCCCAACTACAGTTTGTAGTGAAGACTGAATTGGTCGAACTGAGTAACCTCCTGAACCCTGTCCTCTAGAGTAAGAACCATTAAACTCACCTCCCTTTCGAAACCTTTTTGATGTTGATGCCATGGTGAAGTCATCTGGCTTCACTCCCTCTACCTCTATCACGAAGTCTACCACTTCTTGAAAAGATTTTGCTGTAGCCGCTACCTGTAAGGCTGAAATCCGCAATTCTGACCTCAACCCCTTCACAAAACGGCGAATCCGCTCTTGTGGACTGAAACAAAGCTGAGTGGCATATCTGGAAAGTGCACGAAACTTAGCCTCATATGCAGTAATTGACATCCTACCTTGCTCTAGACTCAAGAATTCATCTCTTTTCCTATCCCTCAAAGTCCGGGGAATATACTTCTCCATAAACAAGCTAGAGAATGATGCCCAAGTCATAGGTGGTGCCTCTGTTGGTTGACACTCAACATGTGACCGCCACCACATTTTGACGTTCCCTTGAAACTGATAAGTCACAAACTCAACACCAAACCGTTCTACTATACCCATTTTGTGTAGTAGCTCATGACAGTCAACCAGAAAATCATAGGCATCCTCAGATTCAGCACCCTTGAAGACTGGAGGTTTCAATTTCAAGAACTTACTGAAAAGTTCATGTTGATCATTTGTCATTATAGGCCCTGTAGTCAGACGAGGAAACATGCCTATTTCCAATGGAACATCCATGCGGGGAGCCGCAGTAGCTGCATGCTGTACCTCCGGACCCTGAGGTGCTGGTGCAAAAAACACTGGAGGTGTTTGACCTTGATCAGATAACCCACTAAGATAAGCAAGAACCTGATTGATCATCTCTGGGGTAGGTTGGGGAGGCAATCCCTCATTCTGTACTTGTTCAGTTTCCCCTTCCTCACCCCTCT-TACTACTTCTTCAGTCGGTGGAGGAGTCACTGCCCTAGTATCAGATGGGCT</genome_strand>
        <mrna_strand>ACGAATAGGCATATCAAGAAATTCACAATGTAAATTTAGACCATTAGCAAATGAGGAAGATACATAAGAAAACGTGGATCCAGGATCAAACAATACGGAAGCCATGCAATCACAAACTAGAAGATTACCTGTGATGACAGCATCAGATGCCTCCGCTTCAGACCGCCCAGGGAAAGCGTAACAATGGGCCCTATCGTTTGTCTGCCCATTGCCCCTACCATGTTGTGATGTAGTGGCCCCAGTTTGCCCATTACCTCTGCCGTTTTGGTGACCACCATTACCTCGACCACCACGTCCTCCAGAATAACGGCCTCTACCATGACCACCTCTACCTCTAGCTATTGGGGGTCTATAACTTGGTCCGGGACAATTTATCCTAATATGTCCAATCTCCCCACATCCATAACATTCTCTGGAGTCACTCATAGGCCCCTTGGAGAAGTGTTGACCGGTCTGAGGTGGACCCCCAACTACAGTCTGTAGTGAAGACTGAATGGGTCGAGCTGAGTAACCTCCGGAACCTTGTCCTCTAGAGTAAGAACCCTTAAACTCACCTCCCTTTCGAAACCTCTTTGATGTCGATGTCGTGGTGAAGTCGTCTGGCTTCACTCCTTCCACTTCTATCACAAAGTCTACCACTTCTTGGAAGGATTTTGCCGTTGCCGCTACCTGTAAGGACGAAATCCGCAATTCTGACCTCAACCCCTTCACAAACCGGCGAATCCGCTCTTGAGGACTGAAACAGAGTTGAGTGGCATATCTGGATAGTGCACGAAACTTAGCCTCATAAGCATTAACTGACACCCTACCTTGCTCTAGGCTCAAGAACTCATCCCTTTTCTTATCCCTCAAAGTCCGGGGGATATACTTCTCCATAAACAAACTATAGAATGAGGCCCAAGTCATAGGTGATGCCTCTATTGGTTGACACTCGATATGTGACCGCCACCACATTTGGGCGTTCCCTTGAAACTGATAAGTCACAAACTCCACACCAAACCGTTCTACTATACCCATCTTGTGTAGTAGCTCGTGACAGTCAACCAGAAAATCATAAGCATCCTCCGATTCAGCACCCTTGAAGACCGGAGGTTTCAATTTCAAGAACTTACTGAAAAGTTCATGCTGATCATTTGTCATTATAGGGACAGTAGTCAAACGTGGAAATGTGCCTATGTCCAATGGAACATCCATGCGGGGAGCCATAGTAGCCGCATGTTGTACTTCTGAAACCGGAGGTGTTGGCGCAGAAAACACTGGAGGTGCTTGACCTTGATCAGATAACCCGCTAAGATAAGCCAGAACCTGATTGATCATCTCTGGGGTAGGTTGGGGTGGCATTTCCTCATTTTGCACTTGTTCAGTTTCCCCATCCCTCCCTTTCTCTATTACTTCCTCAGTCAGTGGAAGAGTCACTGCCCTAGTATCAGATGGGCT</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-C06HBa0218N05-1hy1d/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U335937" ref_strand="+" ref_description="SGN-U335937        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: beta-galactosidase(evalue: 3e-30, score=135)">
      <seq>gatctgtcccaggcttggctaacgtcacagttttagcattacaatccaagattgcaaaatttggagaaagccaagtcatacccagaattacatcaaaatcaaccatttctaagataaccaagtctacataagtattgctccccacaaaagtcaccagaccagacctatatactttttcaactatcacagactcacccaccggagtagaaacacgaataggcatgtcaagcaattcataatttaatttaagaccagtagcaaatgaggaagatacatatgaaaatgtggatccagggtcaaataatacaaaagccatgcaatcacaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0218N05-1hy1d/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0218N05.1" temp_strand="-" temp_description="C06HBa0218N05.1  AC216651.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0218N05 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="49303" stop="48373"/>
      </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="49003" g_stop="48673" g_length="331"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="331" r_length="331" r_score="0.915"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C06HBa0218N05.1" gen_strand="-" ref_id="SGN-U335937" ref_strand="+">
        <total_alignment_score>0.915</total_alignment_score>
        <cumulative_length_of_scored_exons>331</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0218N05.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U335937" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="49003" e_stop="48673"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GATCCGTCCCAGGCTTGGCTAACGTCACTGTTTTAGCATTACAATCCAAGATCGCAAAATTCGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCAACTATGTCTAAGATAACCAAGTCTACATAAGTATTATTCCCCCCAAAATTCACCAAACAAGACCTATATATCCTTTCAACTATTACAGACTCACCCACCGGAGTAGACACACGAATAGGTATGTCAAGCAATTCACAATGTAAATTAAGACCATTAGCAAATGAGGAAGATACATATGAAAATGTGGAGCCAGGATCAAATAATATAGAAGCCATGCAATCACAAACCAA</genome_strand>
        <mrna_strand>GATCTGTCCCAGGCTTGGCTAACGTCACAGTTTTAGCATTACAATCCAAGATTGCAAAATTTGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCAACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCACAGACTCACCCACCGGAGTAGAAACACGAATAGGCATGTCAAGCAATTCATAATTTAATTTAAGACCAGTAGCAAATGAGGAAGATACATATGAAAATGTGGATCCAGGGTCAAATAATACAAAAGCCATGCAATCACAAAAAAA</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-C06HBa0218N05-1hy1d/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U336382" ref_strand="+" ref_description="SGN-U336382        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: gi|49533772|gb|AAT66771.1| putative polyprotein [Solanum demissum] (evalue: 3e-75, score=284)">
      <seq>tcggcatgtactgttttccaaaacttagaagtaaattgcgtacctctatctgatatgatggagagtggaactccgtgcaatcgaacaatttctaagatgtaaagtttggctaacttctctgcattgtaagtcaccttaaccgaaatagagtgagcagacttagttaatctgtcaacaatcacccaaatagagtcatacctacccatcgtctttggatgactaaccacgaagtccattgcaattctctcccacttccattcaggaatgggcattctctgaagtgtccctccaggcctctggtgttcatactttacttgctgacaattcgggcattgagcaacaaaattaacaatgtcacgcttcatcctactccaccaaaaatgttgctttaggtcacgatacatcttgtttgcaccaggatgtatagagtacttcgaactatgagcctatataagaatagtgtgaatcaaatcatcgacgcggggtacacatactccttcccttattctcaaaacaccttcctcatcgatttttgcttcttt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0218N05-1hy1d/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0218N05.1" temp_strand="-" temp_description="C06HBa0218N05.1  AC216651.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0218N05 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="50867" stop="49726"/>
      </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="50567" g_stop="50026" g_length="542"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="542" r_length="542" r_score="0.900"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C06HBa0218N05.1" gen_strand="-" ref_id="SGN-U336382" ref_strand="+">
        <total_alignment_score>0.900</total_alignment_score>
        <cumulative_length_of_scored_exons>542</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0218N05.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U336382" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="50567" e_stop="50026"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTGCATGCAATGTTTTCCAAAACTTAGAAGTAAACTGCGTACCTTTATCTGATATGATGGAGAGTGGAACCCCATGCAACCGAACAATTTCTGAGATATAGATTTTGGCTAACTTCTCTGCATTGTAAGTCACCTTGACCGGAATGAAATGAGCAGACTTAGTTAACCTATCAACAATCACCCAAATAGAGTCATACTTACCCATTGTCTTTGGAAGACCAACCACGAAATCCATTGCAATCCTTTCCCACTTCCATTCAGGAATGGACATTCTCTGAAGTGTTCCTCCGGGCCTCTGGTGTTCATACTTTACTTGCTGGCAATTTGGACATTTGACAATAAAATTAACAATATCACGCTTCATCCTACTCCACCAAAAGTGTTGCTTTAGGTCACGATACATCTTGGTTGCACCAAGATGTATAGAATACCTTGAACTATGAGCCTCTGTCAGAATAGTGTTGATCAAATCATCGACGCGGGGTACACATAC-CCTTCCCTTGATTCTCAAAACACCTTTCTCATCGATTTGTGCTTCCTT</genome_strand>
        <mrna_strand>TCGGCATGTACTGTTTTCCAAAACTTAGAAGTAAATTGCGTACCTCTATCTGATATGATGGAGAGTGGAACTCCGTGCAATCGAACAATTTCTAAGATGTAAAGTTTGGCTAACTTCTCTGCATTGTAAGTCACCTTAACCGAAATAGAGTGAGCAGACTTAGTTAATCTGTCAACAATCACCCAAATAGAGTCATACCTACCCATCGTCTTTGGATGACTAACCACGAAGTCCATTGCAATTCTCTCCCACTTCCATTCAGGAATGGGCATTCTCTGAAGTGTCCCTCCAGGCCTCTGGTGTTCATACTTTACTTGCTGACAATTCGGGCATTGAGCAACAAAATTAACAATGTCACGCTTCATCCTACTCCACCAAAAATGTTGCTTTAGGTCACGATACATCTTGTTTGCACCAGGATGTATAGAGTACTTCGAACTATGAGCCTATATAAGAATAGTGTGAATCAAATCATCGACGCGGGGTACACATACTCCTTCCCTT-ATTCTCAAAACACCTTCCTCATCGATTTTTGCTTCTTT</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-C06HBa0218N05-1hy1d/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U331063" ref_strand="+" ref_description="SGN-U331063        Tomato 200607 #1 [2 ESTs aligned] genbank/nr: gi|530742|emb|CAA56791.1| integrase [Nicotiana tabacum] (evalue: 3e-63, score=243)">
      <seq>aggatacatttttatcttctcatcataagaatgagaaggagagctaaatgtagtatctcttgatcgaatctgcattgacaattgtgtcaattgcctttccctccatatccgccaattccaaagctcctttggataacacttgcttaataacataagggccttgccaatttggagaaaactttcccttggcctcgtcttggtggggaaggatacgtttcacaacaagttgacccacttcaaaattccttgggcgtactttcttattatatgcccgagccatcctctgctgatataattgaccaaaacaaattgatgtcaatcgtttttcttctatcagtgctaattgttctaacctcgatttaacccattctttatcctcgatttctgcttcaacaatggttcgaagagaagggacttcaacttctgcgggtatgacagcctcagttccataaaccaataagtaaggagttacaccgactgacgtacgaacagtcgtgcgatatcccatgagagcgaagggtaatttctcatgccacttcctagatccttgcaccattttcctaagaatcttnctgatatttcttatcgcagcttcaacagccccatttgctttggg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06HBa0218N05-1hy1d/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C06HBa0218N05.1" temp_strand="+" temp_description="C06HBa0218N05.1  AC216651.1 htgs_phase:1 submitted_to_sgn_as:C06HBa0218N05 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="62073" stop="63288"/>
      </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="62372" g_stop="62988" g_length="617"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="616" r_length="616" r_score="0.917"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C06HBa0218N05.1" gen_strand="+" ref_id="SGN-U331063" ref_strand="+">
        <total_alignment_score>0.917</total_alignment_score>
        <cumulative_length_of_scored_exons>617</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06HBa0218N05.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U331063" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="62372" e_stop="62988"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAGATACATTTTAATCTTCTCATCATAAAAACGACAAGGAGTGCTAAATGTAGTATCTCTTGATCGAATCTGAATTGAAAATCGTGTAAATCGCCTTTCCCTCCATATCCGCCAATTTTAAAGCTCCTTTGGATAACATTTGCTTAATAACATAAGGGCCTTGCCAATTTGGAGAAAACTTTCCCTTAACCTCGTCTTGGTGGGGGAGGATACGTTTCACAACTAGTTGACCCACTTCAAAATTTCTTGGGCGTACTTTCTTATTATAAGCCCAAGCCATCCTCTGCTGATATAATTGACCAAAATAAATTGATGTCAATCGTTTTTCTTCTATCAGTGCTAATTGTTCTAACCTCGATTTAACCCATTTTGTATCCTCGATTTCTGCTTCAACAATGGCTATAAGAGAAGGGATTTCAACTTCTACGGATATGACAACCTCAGTTCCGTAAACCAATAAGTAGGGAGTTGCACCGATTGATGAACGAACAGTCGTTCGTTATCCCATGAGAGCGAAGGGTAATTTCTCATGCCACTGTCTAGATCATTGCACCATTTTCCTAAGAATCTTTTTGATGTTTTTATTCGCAGCTTCAACAACCCTATTTTCTTTGGG</genome_strand>
        <mrna_strand>AG-GATACATTTTTATCTTCTCATCATAAGAATGAGAAGGAGAGCTAAATGTAGTATCTCTTGATCGAATCTGCATTGACAATTGTGTCAATTGCCTTTCCCTCCATATCCGCCAATTCCAAAGCTCCTTTGGATAACACTTGCTTAATAACATAAGGGCCTTGCCAATTTGGAGAAAACTTTCCCTTGGCCTCGTCTTGGTGGGGAAGGATACGTTTCACAACAAGTTGACCCACTTCAAAATTCCTTGGGCGTACTTTCTTATTATATGCCCGAGCCATCCTCTGCTGATATAATTGACCAAAACAAATTGATGTCAATCGTTTTTCTTCTATCAGTGCTAATTGTTCTAACCTCGATTTAACCCATTCTTTATCCTCGATTTCTGCTTCAACAATGGTTCGAAGAGAAGGGACTTCAACTTCTGCGGGTATGACAGCCTCAGTTCCATAAACCAATAAGTAAGGAGTTACACCGACTGACGTACGAACAGTCGTGCGATATCCCATGAGAGCGAAGGGTAATTTCTCATGCCACTTCCTAGATCCTTGCACCATTTTCCTAAGAATCTTNCTGATATTTCTTATCGCAGCTTCAACAGCCCCATTTGCTTTGGG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>5</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="47353" PGL_stop="47905"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="47353" e_stop="47905"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.919"/>
        </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="0.919">
            <gDNA_exon_boundary e_start="47353" e_stop="47905" e_length="553"/>
          </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="47353" stop="47905"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U335931" 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>ACCTAGCCCATCTGATACTAGGGCAGTGACTCCTCCACCGACTGAAGAAGTAGTAAGAGGGGTGAGGAAGGGGAAACTGAACAAGTACAGAATGAGGGATTGCCTCCCCAACCTACCCCAGAGATGATCAATCAGGTTCTTGCTTATCTTAGTGGGTTATCTGATCAAGGTCAAACACCTCCAGTGTTTTTTGCACCAGCACCTCAGGGTCCGGAGGTACAGCATGCAGCTACTGCGGCTCCCCGCATGGATGTTCCATTGGAAATAGGCATGTTTCCTCGTCTGACTACAGGGCCTATAATGACAAATGATCAACATGAACTTTTCAGTAAGTTCTTGAAATTGAAACCTCCAGTCTTCAAGGGTGCTGAATCTGAGGATGCCTATGATTTTCTGGTTGACTGTCATGAGCTACTACACAAAATGGGTATAGTAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAGGGAACGTCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCACCTATGACTTGGGCATCATTCT</gDNA_template>
            <first_frame> T  *  P  I  *  Y  *  G  S  D  S  S  T  D  *  R  S  S  K  R  G  E  E  G  E  T  E  Q  V  Q  N  E  G  L  P  P  Q  P  T  P  E  M  I  N  Q  V  L  A  Y  L  S  G  L  S  D  Q  G  Q  T  P  P  V  F  F  A  P  A  P  Q  G  P  E  V  Q  H  A  A  T  A  A  P  R  M  D  V  P  L  E  I  G  M  F  P  R  L  T  T  G  P  I  M  T  N  D  Q  H  E  L  F  S  K  F  L  K  L  K  P  P  V  F  K  G  A  E  S  E  D  A  Y  D  F  L  V  D  C  H  E  L  L  H  K  M  G  I  V  E  R  F  G  V  E  F  V  T  Y  Q  F  Q  G  N  V  K  M  W  W  R  S  H  V  E  C  Q  P  T  E  A  P  P  M  T  W  A  S  F  </first_frame>
            <second_frame>  P  S  P  S  D  T  R  A  V  T  P  P  P  T  E  E  V  V  R  G  V  R  K  G  K  L  N  K  Y  R  M  R  D  C  L  P  N  L  P  Q  R  *  S  I  R  F  L  L  I  L  V  G  Y  L  I  K  V  K  H  L  Q  C  F  L  H  Q  H  L  R  V  R  R  Y  S  M  Q  L  L  R  L  P  A  W  M  F  H  W  K  *  A  C  F  L  V  *  L  Q  G  L  *  *  Q  M  I  N  M  N  F  S  V  S  S  *  N  *  N  L  Q  S  S  R  V  L  N  L  R  M  P  M  I  F  W  L  T  V  M  S  Y  Y  T  K  W  V  *  *  N  G  L  V  L  S  L  *  L  I  S  F  K  G  T  S  K  C  G  G  G  H  M  L  S  V  N  Q  Q  R  H  H  L  *  L  G  H  H  S </second_frame>
            <third_frame>   L  A  H  L  I  L  G  Q  *  L  L  H  R  L  K  K  *  *  E  G  *  G  R  G  N  *  T  S  T  E  *  G  I  A  S  P  T  Y  P  R  D  D  Q  S  G  S  C  L  S  *  W  V  I  *  S  R  S  N  T  S  S  V  F  C  T  S  T  S  G  S  G  G  T  A  C  S  Y  C  G  S  P  H  G  C  S  I  G  N  R  H  V  S  S  S  D  Y  R  A  Y  N  D  K  *  S  T  *  T  F  Q  *  V  L  E  I  E  T  S  S  L  Q  G  C  *  I  *  G  C  L  *  F  S  G  *  L  S  *  A  T  T  Q  N  G  Y  S  R  T  V  W  C  *  V  C  D  L  S  V  S  R  E  R  Q  N  V  V  A  V  T  C  *  V  S  T  N  R  G  T  T  Y  D  L  G  I  I   </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="C06HBa0218N05.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="47398" stop="47904"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>507</number_coding_nucleotides>
                  <number_encoded_amino_acids>169</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RSSKRGEEGETEQVQNEGLPPQPTPEMINQVLAYLSGLSDQGQTPPVFFAPAPQGPEVQHAATAAPRMDVPLEIGMFPRLTTGPIMTNDQHELFSKFLKLKPPVFKGAESEDAYDFLVDCHELLHKMGIVERFGVEFVTYQFQGNVKMWWRSHVECQPTEAPPMTWASF</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="49003" PGL_stop="47357"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="49003" e_stop="47357"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.903"/>
        </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="0.903">
            <gDNA_exon_boundary e_start="49003" e_stop="47357" e_length="1647"/>
          </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="49003" stop="48673"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U335937" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="48792" stop="47357"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U317064" 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>GATCCGTCCCAGGCTTGGCTAACGTCACTGTTTTAGCATTACAATCCAAGATCGCAAAATTCGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCAACTATGTCTAAGATAACCAAGTCTACATAAGTATTATTCCCCCCAAAATTCACCAAACAAGACCTATATATCCTTTCAACTATTACAGACTCACCCACCGGAGTAGACACACGAATAGGTATGTCAAGCAATTCACAATGTAAATTAAGACCATTAGCAAATGAGGAAGATACATATGAAAATGTGGAGCCAGGATCAAATAATATAGAAGCCATGCAATCACAAACCAAAAGATTACCTGTGATGACAGCATCTGATGTCTCCGCTTCTGACCGCCCAGGGAAAGCATAACAATGGGCCCTCTCACCTGTCTGTCCGTTGCCCCTACCATGTTGTGATATAGTGGCTCCAGTTTGCCCATCACCCCGGCCGTTTTGATGACCACCATTACCTCGGCCACCACGTCCTCCAGAATAACGGCCTCTACCATGACCACCTTTATCTCTAGCTATTGGGGGTCTATAACTCTATTTTGGACAATTCCTCCTAATATGTCCAGTCTCCCCACATCCATAACACTCTCTGGAGTCAAGCATAGGTCTCTCAGAGAAGTGTTGACCGGTCTGAGGCGGACCCCCAACTACAGTTTGTAGTGAAGACTGAATTGGTCGAACTGAGTAACCTCCTGAACCCTGTCCTCTAGAGTAAGAACCATTAAACTCACCTCCCTTTCGAAACCTTTTTGATGTTGATGCCATGGTGAAGTCATCTGGCTTCACTCCCTCTACCTCTATCACGAAGTCTACCACTTCTTGAAAAGATTTTGCTGTAGCCGCTACCTGTAAGGCTGAAATCCGCAATTCTGACCTCAACCCCTTCACAAAACGGCGAATCCGCTCTTGTGGACTGAAACAAAGCTGAGTGGCATATCTGGAAAGTGCACGAAACTTAGCCTCATATGCAGTAATTGACATCCTACCTTGCTCTAGACTCAAGAATTCATCTCTTTTCCTATCCCTCAAAGTCCGGGGAATATACTTCTCCATAAACAAGCTAGAGAATGATGCCCAAGTCATAGGTGGTGCCTCTGTTGGTTGACACTCAACATGTGACCGCCACCACATTTTGACGTTCCCTTGAAACTGATAAGTCACAAACTCAACACCAAACCGTTCTACTATACCCATTTTGTGTAGTAGCTCATGACAGTCAACCAGAAAATCATAGGCATCCTCAGATTCAGCACCCTTGAAGACTGGAGGTTTCAATTTCAAGAACTTACTGAAAAGTTCATGTTGATCATTTGTCATTATAGGCCCTGTAGTCAGACGAGGAAACATGCCTATTTCCAATGGAACATCCATGCGGGGAGCCGCAGTAGCTGCATGCTGTACCTCCGGACCCTGAGGTGCTGGTGCAAAAAACACTGGAGGTGTTTGACCTTGATCAGATAACCCACTAAGATAAGCAAGAACCTGATTGATCATCTCTGGGGTAGGTTGGGGAGGCAATCCCTCATTCTGTACTTGTTCAGTTTCCCCTTCCTCACCCCTCTTACTACTTCTTCAGTCGGTGGAGGAGTCACTGCCCTAGTATCAGATGGGCT</gDNA_template>
            <first_frame> D  P  S  Q  A  W  L  T  S  L  F  *  H  Y  N  P  R  S  Q  N  S  E  K  A  K  S  Y  P  E  L  H  Q  N  Q  L  C  L  R  *  P  S  L  H  K  Y  Y  S  P  Q  N  S  P  N  K  T  Y  I  S  F  Q  L  L  Q  T  H  P  P  E  *  T  H  E  *  V  C  Q  A  I  H  N  V  N  *  D  H  *  Q  M  R  K  I  H  M  K  M  W  S  Q  D  Q  I  I  *  K  P  C  N  H  K  P  K  D  Y  L  *  *  Q  H  L  M  S  P  L  L  T  A  Q  G  K  H  N  N  G  P  S  H  L  S  V  R  C  P  Y  H  V  V  I  *  W  L  Q  F  A  H  H  P  G  R  F  D  D  H  H  Y  L  G  H  H  V  L  Q  N  N  G  L  Y  H  D  H  L  Y  L  *  L  L  G  V  Y  N  S  I  L  D  N  S  S  *  Y  V  Q  S  P  H  I  H  N  T  L  W  S  Q  A  *  V  S  Q  R  S  V  D  R  S  E  A  D  P  Q  L  Q  F  V  V  K  T  E  L  V  E  L  S  N  L  L  N  P  V  L  *  S  K  N  H  *  T  H  L  P  F  E  T  F  L  M  L  M  P  W  *  S  H  L  A  S  L  P  L  P  L  S  R  S  L  P  L  L  E  K  I  L  L  *  P  L  P  V  R  L  K  S  A  I  L  T  S  T  P  S  Q  N  G  E  S  A  L  V  D  *  N  K  A  E  W  H  I  W  K  V  H  E  T  *  P  H  M  Q  *  L  T  S  Y  L  A  L  D  S  R  I  H  L  F  S  Y  P  S  K  S  G  E  Y  T  S  P  *  T  S  *  R  M  M  P  K  S  *  V  V  P  L  L  V  D  T  Q  H  V  T  A  T  T  F  *  R  S  L  E  T  D  K  S  Q  T  Q  H  Q  T  V  L  L  Y  P  F  C  V  V  A  H  D  S  Q  P  E  N  H  R  H  P  Q  I  Q  H  P  *  R  L  E  V  S  I  S  R  T  Y  *  K  V  H  V  D  H  L  S  L  *  A  L  *  S  D  E  E  T  C  L  F  P  M  E  H  P  C  G  E  P  Q  *  L  H  A  V  P  P  D  P  E  V  L  V  Q  K  T  L  E  V  F  D  L  D  Q  I  T  H  *  D  K  Q  E  P  D  *  S  S  L  G  *  V  G  E  A  I  P  H  S  V  L  V  Q  F  P  L  P  H  P  S  Y  Y  F  F  S  R  W  R  S  H  C  P  S  I  R  W  A </first_frame>
            <second_frame>  I  R  P  R  L  G  *  R  H  C  F  S  I  T  I  Q  D  R  K  I  R  R  K  P  S  H  T  Q  N  Y  I  K  I  N  Y  V  *  D  N  Q  V  Y  I  S  I  I  P  P  K  I  H  Q  T  R  P  I  Y  P  F  N  Y  Y  R  L  T  H  R  S  R  H  T  N  R  Y  V  K  Q  F  T  M  *  I  K  T  I  S  K  *  G  R  Y  I  *  K  C  G  A  R  I  K  *  Y  R  S  H  A  I  T  N  Q  K  I  T  C  D  D  S  I  *  C  L  R  F  *  P  P  R  E  S  I  T  M  G  P  L  T  C  L  S  V  A  P  T  M  L  *  Y  S  G  S  S  L  P  I  T  P  A  V  L  M  T  T  I  T  S  A  T  T  S  S  R  I  T  A  S  T  M  T  T  F  I  S  S  Y  W  G  S  I  T  L  F  W  T  I  P  P  N  M  S  S  L  P  T  S  I  T  L  S  G  V  K  H  R  S  L  R  E  V  L  T  G  L  R  R  T  P  N  Y  S  L  *  *  R  L  N  W  S  N  *  V  T  S  *  T  L  S  S  R  V  R  T  I  K  L  T  S  L  S  K  P  F  *  C  *  C  H  G  E  V  I  W  L  H  S  L  Y  L  Y  H  E  V  Y  H  F  L  K  R  F  C  C  S  R  Y  L  *  G  *  N  P  Q  F  *  P  Q  P  L  H  K  T  A  N  P  L  L  W  T  E  T  K  L  S  G  I  S  G  K  C  T  K  L  S  L  I  C  S  N  *  H  P  T  L  L  *  T  Q  E  F  I  S  F  P  I  P  Q  S  P  G  N  I  L  L  H  K  Q  A  R  E  *  C  P  S  H  R  W  C  L  C  W  L  T  L  N  M  *  P  P  P  H  F  D  V  P  L  K  L  I  S  H  K  L  N  T  K  P  F  Y  Y  T  H  F  V  *  *  L  M  T  V  N  Q  K  I  I  G  I  L  R  F  S  T  L  E  D  W  R  F  Q  F  Q  E  L  T  E  K  F  M  L  I  I  C  H  Y  R  P  C  S  Q  T  R  K  H  A  Y  F  Q  W  N  I  H  A  G  S  R  S  S  C  M  L  Y  L  R  T  L  R  C  W  C  K  K  H  W  R  C  L  T  L  I  R  *  P  T  K  I  S  K  N  L  I  D  H  L  W  G  R  L  G  R  Q  S  L  I  L  Y  L  F  S  F  P  F  L  T  P  L  T  T  S  S  V  G  G  G  V  T  A  L  V  S  D  G   </second_frame>
            <third_frame>   S  V  P  G  L  A  N  V  T  V  L  A  L  Q  S  K  I  A  K  F  G  E  S  Q  V  I  P  R  I  T  S  K  S  T  M  S  K  I  T  K  S  T  *  V  L  F  P  P  K  F  T  K  Q  D  L  Y  I  L  S  T  I  T  D  S  P  T  G  V  D  T  R  I  G  M  S  S  N  S  Q  C  K  L  R  P  L  A  N  E  E  D  T  Y  E  N  V  E  P  G  S  N  N  I  E  A  M  Q  S  Q  T  K  R  L  P  V  M  T  A  S  D  V  S  A  S  D  R  P  G  K  A  *  Q  W  A  L  S  P  V  C  P  L  P  L  P  C  C  D  I  V  A  P  V  C  P  S  P  R  P  F  *  *  P  P  L  P  R  P  P  R  P  P  E  *  R  P  L  P  *  P  P  L  S  L  A  I  G  G  L  *  L  Y  F  G  Q  F  L  L  I  C  P  V  S  P  H  P  *  H  S  L  E  S  S  I  G  L  S  E  K  C  *  P  V  *  G  G  P  P  T  T  V  C  S  E  D  *  I  G  R  T  E  *  P  P  E  P  C  P  L  E  *  E  P  L  N  S  P  P  F  R  N  L  F  D  V  D  A  M  V  K  S  S  G  F  T  P  S  T  S  I  T  K  S  T  T  S  *  K  D  F  A  V  A  A  T  C  K  A  E  I  R  N  S  D  L  N  P  F  T  K  R  R  I  R  S  C  G  L  K  Q  S  *  V  A  Y  L  E  S  A  R  N  L  A  S  Y  A  V  I  D  I  L  P  C  S  R  L  K  N  S  S  L  F  L  S  L  K  V  R  G  I  Y  F  S  I  N  K  L  E  N  D  A  Q  V  I  G  G  A  S  V  G  *  H  S  T  C  D  R  H  H  I  L  T  F  P  *  N  *  *  V  T  N  S  T  P  N  R  S  T  I  P  I  L  C  S  S  S  *  Q  S  T  R  K  S  *  A  S  S  D  S  A  P  L  K  T  G  G  F  N  F  K  N  L  L  K  S  S  C  *  S  F  V  I  I  G  P  V  V  R  R  G  N  M  P  I  S  N  G  T  S  M  R  G  A  A  V  A  A  C  C  T  S  G  P  *  G  A  G  A  K  N  T  G  G  V  *  P  *  S  D  N  P  L  R  *  A  R  T  *  L  I  I  S  G  V  G  W  G  G  N  P  S  F  C  T  C  S  V  S  P  S  S  P  L  L  L  L  L  Q  S  V  E  E  S  L  P  *  Y  Q  M  G  </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="C06HBa0218N05.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="48872" stop="48612"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>258</number_coding_nucleotides>
                  <number_encoded_amino_acids>86</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VLFPPKFTKQDLYILSTITDSPTGVDTRIGMSSNSQCKLRPLANEEDTYENVEPGSNNIEAMQSQTKRLPVMTASDVSASDRPGKA*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C06HBa0218N05.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="48564" stop="48310"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>252</number_coding_nucleotides>
                  <number_encoded_amino_acids>84</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>YSGSSLPITPAVLMTTITSATTSSRITASTMTTFISSYWGSITLFWTIPPNMSSLPTSITLSGVKHRSLREVLTGLRRTPNYSL*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C06HBa0218N05.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="3"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="47763" stop="47509"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>252</number_coding_nucleotides>
                  <number_encoded_amino_acids>84</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LMTVNQKIIGILRFSTLEDWRFQFQELTEKFMLIICHYRPCSQTRKHAYFQWNIHAGSRSSCMLYLRTLRCWCKKHWRCLTLIR*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="50567" PGL_stop="50026"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="50567" e_stop="50026"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.900"/>
        </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="0.900">
            <gDNA_exon_boundary e_start="50567" e_stop="50026" e_length="542"/>
          </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="50567" stop="50026"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U336382" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="3" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>TCTGCATGCAATGTTTTCCAAAACTTAGAAGTAAACTGCGTACCTTTATCTGATATGATGGAGAGTGGAACCCCATGCAACCGAACAATTTCTGAGATATAGATTTTGGCTAACTTCTCTGCATTGTAAGTCACCTTGACCGGAATGAAATGAGCAGACTTAGTTAACCTATCAACAATCACCCAAATAGAGTCATACTTACCCATTGTCTTTGGAAGACCAACCACGAAATCCATTGCAATCCTTTCCCACTTCCATTCAGGAATGGACATTCTCTGAAGTGTTCCTCCGGGCCTCTGGTGTTCATACTTTACTTGCTGGCAATTTGGACATTTGACAATAAAATTAACAATATCACGCTTCATCCTACTCCACCAAAAGTGTTGCTTTAGGTCACGATACATCTTGGTTGCACCAAGATGTATAGAATACCTTGAACTATGAGCCTCTGTCAGAATAGTGTTGATCAAATCATCGACGCGGGGTACACATACCCTTCCCTTGATTCTCAAAACACCTTTCTCATCGATTTGTGCTTCCTT</gDNA_template>
            <first_frame> S  A  C  N  V  F  Q  N  L  E  V  N  C  V  P  L  S  D  M  M  E  S  G  T  P  C  N  R  T  I  S  E  I  *  I  L  A  N  F  S  A  L  *  V  T  L  T  G  M  K  *  A  D  L  V  N  L  S  T  I  T  Q  I  E  S  Y  L  P  I  V  F  G  R  P  T  T  K  S  I  A  I  L  S  H  F  H  S  G  M  D  I  L  *  S  V  P  P  G  L  W  C  S  Y  F  T  C  W  Q  F  G  H  L  T  I  K  L  T  I  S  R  F  I  L  L  H  Q  K  C  C  F  R  S  R  Y  I  L  V  A  P  R  C  I  E  Y  L  E  L  *  A  S  V  R  I  V  L  I  K  S  S  T  R  G  T  H  T  L  P  L  I  L  K  T  P  F  S  S  I  C  A  S   </first_frame>
            <second_frame>  L  H  A  M  F  S  K  T  *  K  *  T  A  Y  L  Y  L  I  *  W  R  V  E  P  H  A  T  E  Q  F  L  R  Y  R  F  W  L  T  S  L  H  C  K  S  P  *  P  E  *  N  E  Q  T  *  L  T  Y  Q  Q  S  P  K  *  S  H  T  Y  P  L  S  L  E  D  Q  P  R  N  P  L  Q  S  F  P  T  S  I  Q  E  W  T  F  S  E  V  F  L  R  A  S  G  V  H  T  L  L  A  G  N  L  D  I  *  Q  *  N  *  Q  Y  H  A  S  S  Y  S  T  K  S  V  A  L  G  H  D  T  S  W  L  H  Q  D  V  *  N  T  L  N  Y  E  P  L  S  E  *  C  *  S  N  H  R  R  G  V  H  I  P  F  P  *  F  S  K  H  L  S  H  R  F  V  L  P  </second_frame>
            <third_frame>   C  M  Q  C  F  P  K  L  R  S  K  L  R  T  F  I  *  Y  D  G  E  W  N  P  M  Q  P  N  N  F  *  D  I  D  F  G  *  L  L  C  I  V  S  H  L  D  R  N  E  M  S  R  L  S  *  P  I  N  N  H  P  N  R  V  I  L  T  H  C  L  W  K  T  N  H  E  I  H  C  N  P  F  P  L  P  F  R  N  G  H  S  L  K  C  S  S  G  P  L  V  F  I  L  Y  L  L  A  I  W  T  F  D  N  K  I  N  N  I  T  L  H  P  T  P  P  K  V  L  L  *  V  T  I  H  L  G  C  T  K  M  Y  R  I  P  *  T  M  S  L  C  Q  N  S  V  D  Q  I  I  D  A  G  Y  T  Y  P  S  L  D  S  Q  N  T  F  L  I  D  L  C  F  L </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C06HBa0218N05.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="50400" stop="50176"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>222</number_coding_nucleotides>
                  <number_encoded_amino_acids>74</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>PINNHPNRVILTHCLWKTNHEIHCNPFPLPFRNGHSLKCSSGPLVFILYLLAIWTFDNKINNITLHPTPPKVLL*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="4" PGL_strand="+" PGL_start="62372" PGL_stop="62988"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="62372" e_stop="62988"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.917"/>
        </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="0.917">
            <gDNA_exon_boundary e_start="62372" e_stop="62988" e_length="617"/>
          </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="62372" stop="62988"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U331063" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="4" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>AGAGATACATTTTAATCTTCTCATCATAAAAACGACAAGGAGTGCTAAATGTAGTATCTCTTGATCGAATCTGAATTGAAAATCGTGTAAATCGCCTTTCCCTCCATATCCGCCAATTTTAAAGCTCCTTTGGATAACATTTGCTTAATAACATAAGGGCCTTGCCAATTTGGAGAAAACTTTCCCTTAACCTCGTCTTGGTGGGGGAGGATACGTTTCACAACTAGTTGACCCACTTCAAAATTTCTTGGGCGTACTTTCTTATTATAAGCCCAAGCCATCCTCTGCTGATATAATTGACCAAAATAAATTGATGTCAATCGTTTTTCTTCTATCAGTGCTAATTGTTCTAACCTCGATTTAACCCATTTTGTATCCTCGATTTCTGCTTCAACAATGGCTATAAGAGAAGGGATTTCAACTTCTACGGATATGACAACCTCAGTTCCGTAAACCAATAAGTAGGGAGTTGCACCGATTGATGAACGAACAGTCGTTCGTTATCCCATGAGAGCGAAGGGTAATTTCTCATGCCACTGTCTAGATCATTGCACCATTTTCCTAAGAATCTTTTTGATGTTTTTATTCGCAGCTTCAACAACCCTATTTTCTTTGGG</gDNA_template>
            <first_frame> R  D  T  F  *  S  S  H  H  K  N  D  K  E  C  *  M  *  Y  L  L  I  E  S  E  L  K  I  V  *  I  A  F  P  S  I  S  A  N  F  K  A  P  L  D  N  I  C  L  I  T  *  G  P  C  Q  F  G  E  N  F  P  L  T  S  S  W  W  G  R  I  R  F  T  T  S  *  P  T  S  K  F  L  G  R  T  F  L  L  *  A  Q  A  I  L  C  *  Y  N  *  P  K  *  I  D  V  N  R  F  S  S  I  S  A  N  C  S  N  L  D  L  T  H  F  V  S  S  I  S  A  S  T  M  A  I  R  E  G  I  S  T  S  T  D  M  T  T  S  V  P  *  T  N  K  *  G  V  A  P  I  D  E  R  T  V  V  R  Y  P  M  R  A  K  G  N  F  S  C  H  C  L  D  H  C  T  I  F  L  R  I  F  L  M  F  L  F  A  A  S  T  T  L  F  S  L   </first_frame>
            <second_frame>  E  I  H  F  N  L  L  I  I  K  T  T  R  S  A  K  C  S  I  S  *  S  N  L  N  *  K  S  C  K  S  P  F  P  P  Y  P  P  I  L  K  L  L  W  I  T  F  A  *  *  H  K  G  L  A  N  L  E  K  T  F  P  *  P  R  L  G  G  G  G  Y  V  S  Q  L  V  D  P  L  Q  N  F  L  G  V  L  S  Y  Y  K  P  K  P  S  S  A  D  I  I  D  Q  N  K  L  M  S  I  V  F  L  L  S  V  L  I  V  L  T  S  I  *  P  I  L  Y  P  R  F  L  L  Q  Q  W  L  *  E  K  G  F  Q  L  L  R  I  *  Q  P  Q  F  R  K  P  I  S  R  E  L  H  R  L  M  N  E  Q  S  F  V  I  P  *  E  R  R  V  I  S  H  A  T  V  *  I  I  A  P  F  S  *  E  S  F  *  C  F  Y  S  Q  L  Q  Q  P  Y  F  L  W  </second_frame>
            <third_frame>   R  Y  I  L  I  F  S  S  *  K  R  Q  G  V  L  N  V  V  S  L  D  R  I  *  I  E  N  R  V  N  R  L  S  L  H  I  R  Q  F  *  S  S  F  G  *  H  L  L  N  N  I  R  A  L  P  I  W  R  K  L  S  L  N  L  V  L  V  G  E  D  T  F  H  N  *  L  T  H  F  K  I  S  W  A  Y  F  L  I  I  S  P  S  H  P  L  L  I  *  L  T  K  I  N  *  C  Q  S  F  F  F  Y  Q  C  *  L  F  *  P  R  F  N  P  F  C  I  L  D  F  C  F  N  N  G  Y  K  R  R  D  F  N  F  Y  G  Y  D  N  L  S  S  V  N  Q  *  V  G  S  C  T  D  *  *  T  N  S  R  S  L  S  H  E  S  E  G  *  F  L  M  P  L  S  R  S  L  H  H  F  P  K  N  L  F  D  V  F  I  R  S  F  N  N  P  I  F  F  G </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <none gDNA_id="C06HBa0218N05.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 48 chains have been computed
$ 
$ memory statistics:
$ 11736 bytes spliced alignments in total
$ 5 spliced alignments have been stored
$ 2347 bytes was the average size of a spliced alignment
$ 9056 bytes predicted gene locations in total
$ 4 predicted gene locations have been stored
$ 2264 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 60 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 17:39:38
-->
