<?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 02:20:37"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0119A16-4ftES/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0119A16-4ftES/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-C04HBa0119A16-4ftES/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-C04HBa0119A16-4ftES/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0119A16.1" temp_strand="+" temp_description="C04HBa0119A16.1  CT573298.1 htgs_phase:3 submitted_to_sgn_as:C04HBa0119A16 sequenced_by:sanger upload_account_name:uk">
        <position start="1" stop="896"/>
      </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="43" g_stop="596" g_length="554"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="554" r_length="554" r_score="0.922"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0119A16.1" gen_strand="+" ref_id="SGN-U335931" ref_strand="+">
        <total_alignment_score>0.922</total_alignment_score>
        <cumulative_length_of_scored_exons>554</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0119A16.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U335931" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="43" e_stop="596"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCCCGTCCCATCTAGTACTAGGGCGGTGACTCCTCCACCGACTAAAGAAGTAGTAAGAGAGGGTGAGGAAGGGGAAACTGAGCAAGTGCAGAATGAGGAACTACCACCCCAACCTACCCCAGAGATGATAAATCAGGTCCTTACTTATCTTAGTGGGTTATCTGATCAAGGTCAAACACCTCCAGTGTTTTCTGCACCAGCACCTCAGGCTCTGGAGGTACAACATGCGGCTACTATGGCTCCCCGCATGGATGCCTCATTGGAAATAGGTACGTTTCCTCGTCTGACTACAGGGCCGATAATGACAAATGATCAGCATGAACTTTTCAGTAAGTTCTTGAAATTGAAACCTCCAGTCTTCAAGGGTGCTGAATCTGAGGATGCCTACGATTTTTTGGTTAACTATCATGAGCTACTACACAAGATGGGTATAGTAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAGGGAACGCCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCACCTATGACTTGGGCATCATTCT</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-C04HBa0119A16-4ftES/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U335930" ref_strand="+" ref_description="SGN-U335930        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: hypothetical(evalue: 7e-35, score=150)">
      <seq>aaacacgaataggcatatcaagtaattcacaatgtaaagttagaccattagcaaatgaggaagatacataagaaaatgtggatccaggatcaaacaatacagaagccatgcaatcacaaaccaaaagattacctgtgatgacaacatcagattcctccgcttcagaccgcccagggaaagcgtaacaatgggccctatcattcttatgtctgttgcccctaccatgttgtgatgtagtggctccagtttgcccatcacctcggccgttttggtgaccaccatttcctcgaccgccacgtcctccagaataacggactctgccatgaccacctctacctctaacctttggaggtctgtaactctgttttggacaatatctcttaatatgtccaatctccccacacccatagcactctctgggttcatgcataagtctctcagagaagtgttgaccggtcgaaggtggacccccaactacagtctgtagtgaagactgaattggtcggactgagtaacttcccgaaccctgtcctctagtgtaagcaccattaaactcacc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0119A16-4ftES/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0119A16.1" temp_strand="-" temp_description="C04HBa0119A16.1  CT573298.1 htgs_phase:3 submitted_to_sgn_as:C04HBa0119A16 sequenced_by:sanger upload_account_name:uk">
        <position start="1787" stop="629"/>
      </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="1487" g_stop="929" g_length="559"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="559" r_length="559" r_score="0.914"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0119A16.1" gen_strand="-" ref_id="SGN-U335930" ref_strand="+">
        <total_alignment_score>0.914</total_alignment_score>
        <cumulative_length_of_scored_exons>559</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0119A16.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U335930" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1487" e_stop="929"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAACACGAATAGGCATGTCAAGCAATTCACAATGTAAATTATGACCATTAGCAAATGAGGAAGATATATAAGAAAATGTGGATCCAGGGTCAAATAATACAGAAGCCATACAATCACAAACCAAAAGATTACCTGTGATAACAGCATCTGATGTCTCCGCTTCCGACCGCCCAGGGAAAGCGTAACAATGGGCCCTCTCACCTGTCTGTCCGTTGCCCCTACCATGTTGTGATGTAGTGGCTCCAGTTTGCCCATCACCCCGGCCGTTTTGGTGACCACCATTACCTCGACCACCGCGTCCTCCAGAATGACGGCCTCTTCCATAACCACCTCTACCTCTAACATTTGGAGGTCTGTAACTCTGTTTTGGACAATACCTCTTAATGTGTCCAGTCTCCCCACATCCATAACACTTTCTGGATTCAAGCATAGTTCTCTCAGAGAAGTGTTGACCGGTCTGAGGTGGACCCCCAACTACAGTCTGTAGTGAAGACTGAATTGGTCAGACTGAGTAACCTCCTGAACCCTGTCCTCTAGAGTAAGAACCATTAAACTCACC</genome_strand>
        <mrna_strand>AAACACGAATAGGCATATCAAGTAATTCACAATGTAAAGTTAGACCATTAGCAAATGAGGAAGATACATAAGAAAATGTGGATCCAGGATCAAACAATACAGAAGCCATGCAATCACAAACCAAAAGATTACCTGTGATGACAACATCAGATTCCTCCGCTTCAGACCGCCCAGGGAAAGCGTAACAATGGGCCCTATCATTCTTATGTCTGTTGCCCCTACCATGTTGTGATGTAGTGGCTCCAGTTTGCCCATCACCTCGGCCGTTTTGGTGACCACCATTTCCTCGACCGCCACGTCCTCCAGAATAACGGACTCTGCCATGACCACCTCTACCTCTAACCTTTGGAGGTCTGTAACTCTGTTTTGGACAATATCTCTTAATATGTCCAATCTCCCCACACCCATAGCACTCTCTGGGTTCATGCATAAGTCTCTCAGAGAAGTGTTGACCGGTCGAAGGTGGACCCCCAACTACAGTCTGTAGTGAAGACTGAATTGGTCGGACTGAGTAACTTCCCGAACCCTGTCCTCTAGTGTAAGCACCATTAAACTCACC</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-C04HBa0119A16-4ftES/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U317065" ref_strand="+" ref_description="SGN-U317065        Tomato 200607 #1 [3 ESTs aligned] genbank/nr: gi|49533772|gb|AAT66771.1| putative polyprotein [Solanum demissum] (evalue: 3e-84, score=314)">
      <seq>cggaaactcccatccttcttcttcacaaacaaaatcggagcaccccaaggagatgcacttggtctaatgaaacctttgctcaacaactcttgaagttgggcctttaactctcttaactctacgggagccattctataagggggtatagaaatggggcgtgtgcccggttcaagatcgatacagaagtcaatatccctatctggtggcataccaggaagatctgcagggaacacatccaaaaactcacagactataaaaaccgactcaatcgaaggtacttgggtagtgtcatccttgagatgtgccaagaaagctaaacaccctttactaaccattttcttagcacgaagaaaggagatgatgcacaccggattggaagtgtagtcaccctcccacactaacggatctgtcccaggcttggctaatgtcaccgttttagcattacaatccaagatcgcaaattgcggagaaagccaagtcatacccagaattacatcaaaatcaaccatttctaagataaccaaatctacataagtgttgctccccacaaagttcaccaaacaagacctatataccttttcaactaccacagactcacccaccggagtagaaacacgaataggcatatcaagtaattcacaatgtaaatttagaccgttagcaaatgaggaagatacantagaaaacgtggatcccaggatcaacaatacagaagccatgcaatcacaatcgaaagattacctgtgatgacagcatc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0119A16-4ftES/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0119A16.1" temp_strand="-" temp_description="C04HBa0119A16.1  CT573298.1 htgs_phase:3 submitted_to_sgn_as:C04HBa0119A16 sequenced_by:sanger upload_account_name:uk">
        <position start="2397" stop="1040"/>
      </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="2097" g_stop="1340" g_length="758"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="757" r_length="757" r_score="0.901"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0119A16.1" gen_strand="-" ref_id="SGN-U317065" ref_strand="+">
        <total_alignment_score>0.901</total_alignment_score>
        <cumulative_length_of_scored_exons>758</cumulative_length_of_scored_exons>
        <coverage percentage="1.001" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0119A16.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U317065" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="2097" e_stop="1340"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CGAAAACTCCCATCCTTCTTCTTCACAAATAACACTGGAGCTTCCCAAGGGGATGCACTTGGTCTAATGAAGCCTTTGCTTAACAACTCTTGAAGTTAAGCTTTTAACTCTCTTAACTCCGCGGGAGCCATTTTATAAGGGGGTATAGAAATGGGGCGAGTACCCGGTTCAAGATCAATGCAGAAGTCAATATCCCTATCTGGTGGCATACCAGGAAGATCTGCAGGGAACACATCCAGAAACTCACGGACTACCGAAACCGACTCAATTGGAGGTACTTGGGTAGTATCATCTCGGAGGTGTGCCAAGAACGCTAAACAACCCTTACTAACCATTTTCTTAGCACGAAGAAAGGAGATAATACGAACCGGATTGGAAGTGTAGTCACCCTCCCACACTAATGGATCTGTACCAGGCTTGGCTAACGTCACGGTTTTAGCATTGCAATCCAAGATCGCAAAATTCGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCCACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCACAGACTCACCCACCGGAGTAGAAACACGAATAGGCATGTCAAGCAATTCACAATGTAAATTATGACCATTAGCAAATGAGGAAGATATATAAGAAAATGTGGATCCAGGGTCAAATAATACAGAAGCCATACAATCACAAACCAAAAGATTACCTGTGATAACAGCATC</genome_strand>
        <mrna_strand>CGGAAACTCCCATCCTTCTTCTTCACAAACAAAATCGGAGCACCCCAAGGAGATGCACTTGGTCTAATGAAACCTTTGCTCAACAACTCTTGAAGTTGGGCCTTTAACTCTCTTAACTCTACGGGAGCCATTCTATAAGGGGGTATAGAAATGGGGCGTGTGCCCGGTTCAAGATCGATACAGAAGTCAATATCCCTATCTGGTGGCATACCAGGAAGATCTGCAGGGAACACATCCAAAAACTCACAGACTATAAAAACCGACTCAATCGAAGGTACTTGGGTAGTGTCATCCTTGAGATGTGCCAAGAAAGCTAAACACCCTTTACTAACCATTTTCTTAGCACGAAGAAAGGAGATGATGCACACCGGATTGGAAGTGTAGTCACCCTCCCACACTAACGGATCTGTCCCAGGCTTGGCTAATGTCACCGTTTTAGCATTACAATCCAAGATCGCAAATTGCGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCAACCATTTCTAAGATAACCAAATCTACATAAGTGTTGCTCCCCACAAAGTTCACCAAACAAGACCTATATACCTTTTCAACTACCACAGACTCACCCACCGGAGTAGAAACACGAATAGGCATATCAAGTAATTCACAATGTAAATTTAGACCGTTAGCAAATGAGGAAGATACANTAGAAAACGTGGATCCCAGGATCAACAATACAGAAGCCATGCAATCAC-AATCGAAAGATTACCTGTGATGACAGCATC</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-C04HBa0119A16-4ftES/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-C04HBa0119A16-4ftES/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0119A16.1" temp_strand="-" temp_description="C04HBa0119A16.1  CT573298.1 htgs_phase:3 submitted_to_sgn_as:C04HBa0119A16 sequenced_by:sanger upload_account_name:uk">
        <position start="1994" stop="1064"/>
      </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="1694" g_stop="1364" g_length="331"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="331" r_length="331" r_score="0.949"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0119A16.1" gen_strand="-" ref_id="SGN-U335937" ref_strand="+">
        <total_alignment_score>0.949</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="C04HBa0119A16.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U335937" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1694" e_stop="1364"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GATCTGTACCAGGCTTGGCTAACGTCACGGTTTTAGCATTGCAATCCAAGATCGCAAAATTCGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCCACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCACAGACTCACCCACCGGAGTAGAAACACGAATAGGCATGTCAAGCAATTCACAATGTAAATTATGACCATTAGCAAATGAGGAAGATATATAAGAAAATGTGGATCCAGGGTCAAATAATACAGAAGCCATACAATCACAAACCAA</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-C04HBa0119A16-4ftES/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U326740" ref_strand="+" ref_description="SGN-U326740        Tomato 200607 #1 [4 ESTs aligned] arabidopsis/peptide: ATMG00860.1 | Symbol: ORF158 | hypothetical protein | chrM:235916-236392 FORWARD | Aliases: ORF158 (evalue: 2e-15, score=79.3) genbank/nr: RNA-directed(evalue: 2e-101, score=370)">
      <seq>gaatcccttgacaaatcggcggtagtagctagctaacccaacaaagctccttatttctgacacattagtaggtcttacccaattcttcactgtctcaatcttagaaggatccaccatcactccatccttagaaaccacgttccccaagaaggacactacatctagccaaaactcacacttagagaacttggcataaaactttttctccctcaacatttccaataccattctcaaatgctcttcatgttcctccttacttttagagtatatcagtatatcatcaataaatacgatcacaaagagatccaaatatggcttaaaaatcccttttattaaactcataaacgcagcaggggcattcataagaccaaaagacatcactacaaatttgtaatgcccatacctggttctaaaagcagtctttggcacatccgttgcccgtattttcaattgatgataaccggatctcaagtcaatcttagaaaagacacaagcaccttgtaactgatcgaacaagtcattaatgcgaggaagaggatacttgttctttatggttaccttgttcaactgccggtagcctatgcacatccgaaaactccaatccttcttctttacaaacaaaaccggagcaccccaaggagatgcagttggtctaatgaagcctttgctcacaactctttgaagtggtcttttaactctcttaactctgcgg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0119A16-4ftES/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0119A16.1" temp_strand="-" temp_description="C04HBa0119A16.1  CT573298.1 htgs_phase:3 submitted_to_sgn_as:C04HBa0119A16 sequenced_by:sanger upload_account_name:uk">
        <position start="2986" stop="1674"/>
      </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="2686" g_stop="1974" g_length="713"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="712" r_length="712" r_score="0.905"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0119A16.1" gen_strand="-" ref_id="SGN-U326740" ref_strand="+">
        <total_alignment_score>0.905</total_alignment_score>
        <cumulative_length_of_scored_exons>713</cumulative_length_of_scored_exons>
        <coverage percentage="1.001" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0119A16.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U326740" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="2686" e_stop="1974"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAATCCCTTGACAAATCGACGGTAATAGCTAGCTAAACCAACAAAGCTCCTTATTTCTGACACATTAGTAGGTCTTACCCAATTCTTTACTGTCTCAATCTTAGAAGGATAGACCATCACCTCATCCTTAGAAACCACATTCCCCAAGAAGGACACTGCATCTAGCCAAAACTCACACTTGGAGAATTTGGCATAAAGCTTTTTCTCCCTCAACATTTCCAATACAATTCTCAAGTGCTTCTCGTGTTCCTTCTTGCTCTTTGAGTATACCAATATATCATCAATAAATACGATCACAAAGAGATCCAGATATGGCTTAAAAATCCCGTTCATCAAGCTCATGAAAGCAGCAGGGGCATTCGTAAGACCAAAAGACATCACTACAAATTCGTAATGCCCATACCTGGTCCGAAAAGCAGTTTTTGGCACATCCATTGCCAGTATCTTCAATTGATGATAACCGAACCTCAAGTCAATCTTAGAGAAGACACAAGCACCTTGTAACTGATCGAACAAGTCATCAATGCGAGGAATGGGATACTTGTTCTTAATAGTTACCTTGTTCAACTGCCGGTAGTTTATGCACATCCGAAAACTCCCATCCTTCTTCTTCACAAATAACACTGGAGCTTCCCAAGGGGATGCACTTGGTCTAATGAAGCCTTTGCTTAACAACTCTTGAAGTTAAGCTTTTAACTCTCTTAACTCCGCGG</genome_strand>
        <mrna_strand>GAATCCCTTGACAAATCGGCGGTAGTAGCTAGCTAACCCAACAAAGCTCCTTATTTCTGACACATTAGTAGGTCTTACCCAATTCTTCACTGTCTCAATCTTAGAAGGATCCACCATCACTCCATCCTTAGAAACCACGTTCCCCAAGAAGGACACTACATCTAGCCAAAACTCACACTTAGAGAACTTGGCATAAAACTTTTTCTCCCTCAACATTTCCAATACCATTCTCAAATGCTCTTCATGTTCCTCCTTACTTTTAGAGTATATCAGTATATCATCAATAAATACGATCACAAAGAGATCCAAATATGGCTTAAAAATCCCTTTTATTAAACTCATAAACGCAGCAGGGGCATTCATAAGACCAAAAGACATCACTACAAATTTGTAATGCCCATACCTGGTTCTAAAAGCAGTCTTTGGCACATCCGTTGCCCGTATTTTCAATTGATGATAACCGGATCTCAAGTCAATCTTAGAAAAGACACAAGCACCTTGTAACTGATCGAACAAGTCATTAATGCGAGGAAGAGGATACTTGTTCTTTATGGTTACCTTGTTCAACTGCCGGTAGCCTATGCACATCCGAAAACTCCAATCCTTCTTCTTTACAAACAAAACCGGAGCACCCCAAGGAGATGCAGTTGGTCTAATGAAGCCTTTGC-TCACAACTCTTTGAAGTGGTCTTTTAACTCTCTTAACTCTGCGG</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-C04HBa0119A16-4ftES/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U345909" ref_strand="+" ref_description="SGN-U345909        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: beta-galactosidase(evalue: 1e-29, score=133)">
      <seq>ctacatctcctaccatacaatgcttcaaatggagccatatcaatgcttgattgatagctattattgtatgaaaactccgctaagggtaggaagctatcccaatgaccaccaaactctatcacacacgcacgaagcatattctccaacacttgaatcgttcgctcagactgaccatcgggagaactagt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0119A16-4ftES/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0119A16.1" temp_strand="-" temp_description="C04HBa0119A16.1  CT573298.1 htgs_phase:3 submitted_to_sgn_as:C04HBa0119A16 sequenced_by:sanger upload_account_name:uk">
        <position start="4467" stop="3690"/>
      </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="4167" g_stop="3991" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="177" r_length="177" r_score="0.904"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0119A16.1" gen_strand="-" ref_id="SGN-U345909" ref_strand="+">
        <total_alignment_score>0.904</total_alignment_score>
        <cumulative_length_of_scored_exons>177</cumulative_length_of_scored_exons>
        <coverage percentage="0.941" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0119A16.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U345909" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4167" e_stop="3991"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTACATCTCCTTCCATACAGTGCTTCAAATGGGGCCATATCAATACTTGAGTGATAGATATTGTTGTAGGAGAACTCCGCTAAGGGTAAGAAGTTATCCCAATGAACTCCAAATTCTATCACACATGCACGAAGCATATCCTCCAACACTTGAATCGTTCGCTCAGACTAACCATCG</genome_strand>
        <mrna_strand>CTACATCTCCTACCATACAATGCTTCAAATGGAGCCATATCAATGCTTGATTGATAGCTATTATTGTATGAAAACTCCGCTAAGGGTAGGAAGCTATCCCAATGACCACCAAACTCTATCACACACGCACGAAGCATATTCTCCAACACTTGAATCGTTCGCTCAGACTGACCATCG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>6</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="43" PGL_stop="596"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="43" e_stop="596"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.922"/>
        </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="0.922">
            <gDNA_exon_boundary e_start="43" e_stop="596" e_length="554"/>
          </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="43" stop="596"/>
            </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>GCCCGTCCCATCTAGTACTAGGGCGGTGACTCCTCCACCGACTAAAGAAGTAGTAAGAGAGGGTGAGGAAGGGGAAACTGAGCAAGTGCAGAATGAGGAACTACCACCCCAACCTACCCCAGAGATGATAAATCAGGTCCTTACTTATCTTAGTGGGTTATCTGATCAAGGTCAAACACCTCCAGTGTTTTCTGCACCAGCACCTCAGGCTCTGGAGGTACAACATGCGGCTACTATGGCTCCCCGCATGGATGCCTCATTGGAAATAGGTACGTTTCCTCGTCTGACTACAGGGCCGATAATGACAAATGATCAGCATGAACTTTTCAGTAAGTTCTTGAAATTGAAACCTCCAGTCTTCAAGGGTGCTGAATCTGAGGATGCCTACGATTTTTTGGTTAACTATCATGAGCTACTACACAAGATGGGTATAGTAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAGGGAACGCCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCACCTATGACTTGGGCATCATTCT</gDNA_template>
            <first_frame> A  R  P  I  *  Y  *  G  G  D  S  S  T  D  *  R  S  S  K  R  G  *  G  R  G  N  *  A  S  A  E  *  G  T  T  T  P  T  Y  P  R  D  D  K  S  G  P  Y  L  S  *  W  V  I  *  S  R  S  N  T  S  S  V  F  C  T  S  T  S  G  S  G  G  T  T  C  G  Y  Y  G  S  P  H  G  C  L  I  G  N  R  Y  V  S  S  S  D  Y  R  A  D  N  D  K  *  S  A  *  T  F  Q  *  V  L  E  I  E  T  S  S  L  Q  G  C  *  I  *  G  C  L  R  F  F  G  *  L  S  *  A  T  T  Q  D  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   </first_frame>
            <second_frame>  P  V  P  S  S  T  R  A  V  T  P  P  P  T  K  E  V  V  R  E  G  E  E  G  E  T  E  Q  V  Q  N  E  E  L  P  P  Q  P  T  P  E  M  I  N  Q  V  L  T  Y  L  S  G  L  S  D  Q  G  Q  T  P  P  V  F  S  A  P  A  P  Q  A  L  E  V  Q  H  A  A  T  M  A  P  R  M  D  A  S  L  E  I  G  T  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  N  Y  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  A  K  M  W  W  R  S  H  V  E  C  Q  P  T  E  A  P  P  M  T  W  A  S  F  </second_frame>
            <third_frame>   P  S  H  L  V  L  G  R  *  L  L  H  R  L  K  K  *  *  E  R  V  R  K  G  K  L  S  K  C  R  M  R  N  Y  H  P  N  L  P  Q  R  *  *  I  R  S  L  L  I  L  V  G  Y  L  I  K  V  K  H  L  Q  C  F  L  H  Q  H  L  R  L  W  R  Y  N  M  R  L  L  W  L  P  A  W  M  P  H  W  K  *  V  R  F  L  V  *  L  Q  G  R  *  *  Q  M  I  S  M  N  F  S  V  S  S  *  N  *  N  L  Q  S  S  R  V  L  N  L  R  M  P  T  I  F  W  L  T  I  M  S  Y  Y  T  R  W  V  *  *  N  G  L  V  L  S  L  *  L  I  S  F  K  G  T  P  K  C  G  G  G  H  M  L  S  V  N  Q  Q  R  H  H  L  *  L  G  H  H  S </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="C04HBa0119A16.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="44" stop="595"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>552</number_coding_nucleotides>
                  <number_encoded_amino_acids>184</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>PVPSSTRAVTPPPTKEVVREGEEGETEQVQNEELPPQPTPEMINQVLTYLSGLSDQGQTPPVFSAPAPQALEVQHAATMAPRMDASLEIGTFPRLTTGPIMTNDQHELFSKFLKLKPPVFKGAESEDAYDFLVNYHELLHKMGIVERFGVEFVTYQFQGNAKMWWRSHVECQPTEAPPMTWASF</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="2686" PGL_stop="929"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="2686" e_stop="929"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.901"/>
        </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="0.901">
            <gDNA_exon_boundary e_start="2686" e_stop="929" e_length="1758"/>
          </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="2686" stop="1974"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U326740" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="2097" stop="1340"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U317065" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1694" stop="1364"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U335937" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="1487" stop="929"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U335930" 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>GAATCCCTTGACAAATCGACGGTAATAGCTAGCTAAACCAACAAAGCTCCTTATTTCTGACACATTAGTAGGTCTTACCCAATTCTTTACTGTCTCAATCTTAGAAGGATAGACCATCACCTCATCCTTAGAAACCACATTCCCCAAGAAGGACACTGCATCTAGCCAAAACTCACACTTGGAGAATTTGGCATAAAGCTTTTTCTCCCTCAACATTTCCAATACAATTCTCAAGTGCTTCTCGTGTTCCTTCTTGCTCTTTGAGTATACCAATATATCATCAATAAATACGATCACAAAGAGATCCAGATATGGCTTAAAAATCCCGTTCATCAAGCTCATGAAAGCAGCAGGGGCATTCGTAAGACCAAAAGACATCACTACAAATTCGTAATGCCCATACCTGGTCCGAAAAGCAGTTTTTGGCACATCCATTGCCAGTATCTTCAATTGATGATAACCGAACCTCAAGTCAATCTTAGAGAAGACACAAGCACCTTGTAACTGATCGAACAAGTCATCAATGCGAGGAATGGGATACTTGTTCTTAATAGTTACCTTGTTCAACTGCCGGTAGTTTATGCACATCCGAAAACTCCCATCCTTCTTCTTCACAAATAACACTGGAGCTTCCCAAGGGGATGCACTTGGTCTAATGAAGCCTTTGCTTAACAACTCTTGAAGTTAAGCTTTTAACTCTCTTAACTCCGCGGGAGCCATTTTATAAGGGGGTATAGAAATGGGGCGAGTACCCGGTTCAAGATCAATGCAGAAGTCAATATCCCTATCTGGTGGCATACCAGGAAGATCTGCAGGGAACACATCCAGAAACTCACGGACTACCGAAACCGACTCAATTGGAGGTACTTGGGTAGTATCATCTCGGAGGTGTGCCAAGAACGCTAAACAACCCTTACTAACCATTTTCTTAGCACGAAGAAAGGAGATAATACGAACCGGATTGGAAGTGTAGTCACCCTCCCACACTAATGGATCTGTACCAGGCTTGGCTAACGTCACGGTTTTAGCATTGCAATCCAAGATCGCAAAATTCGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCCACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCACAGACTCACCCACCGGAGTAGAAACACGAATAGGCATGTCAAGCAATTCACAATGTAAATTATGACCATTAGCAAATGAGGAAGATATATAAGAAAATGTGGATCCAGGGTCAAATAATACAGAAGCCATACAATCACAAACCAAAAGATTACCTGTGATAACAGCATCTGATGTCTCCGCTTCCGACCGCCCAGGGAAAGCGTAACAATGGGCCCTCTCACCTGTCTGTCCGTTGCCCCTACCATGTTGTGATGTAGTGGCTCCAGTTTGCCCATCACCCCGGCCGTTTTGGTGACCACCATTACCTCGACCACCGCGTCCTCCAGAATGACGGCCTCTTCCATAACCACCTCTACCTCTAACATTTGGAGGTCTGTAACTCTGTTTTGGACAATACCTCTTAATGTGTCCAGTCTCCCCACATCCATAACACTTTCTGGATTCAAGCATAGTTCTCTCAGAGAAGTGTTGACCGGTCTGAGGTGGACCCCCAACTACAGTCTGTAGTGAAGACTGAATTGGTCAGACTGAGTAACCTCCTGAACCCTGTCCTCTAGAGTAAGAACCATTAAACTCACC</gDNA_template>
            <first_frame> E  S  L  D  K  S  T  V  I  A  S  *  T  N  K  A  P  Y  F  *  H  I  S  R  S  Y  P  I  L  Y  C  L  N  L  R  R  I  D  H  H  L  I  L  R  N  H  I  P  Q  E  G  H  C  I  *  P  K  L  T  L  G  E  F  G  I  K  L  F  L  P  Q  H  F  Q  Y  N  S  Q  V  L  L  V  F  L  L  A  L  *  V  Y  Q  Y  I  I  N  K  Y  D  H  K  E  I  Q  I  W  L  K  N  P  V  H  Q  A  H  E  S  S  R  G  I  R  K  T  K  R  H  H  Y  K  F  V  M  P  I  P  G  P  K  S  S  F  W  H  I  H  C  Q  Y  L  Q  L  M  I  T  E  P  Q  V  N  L  R  E  D  T  S  T  L  *  L  I  E  Q  V  I  N  A  R  N  G  I  L  V  L  N  S  Y  L  V  Q  L  P  V  V  Y  A  H  P  K  T  P  I  L  L  L  H  K  *  H  W  S  F  P  R  G  C  T  W  S  N  E  A  F  A  *  Q  L  L  K  L  S  F  *  L  S  *  L  R  G  S  H  F  I  R  G  Y  R  N  G  A  S  T  R  F  K  I  N  A  E  V  N  I  P  I  W  W  H  T  R  K  I  C  R  E  H  I  Q  K  L  T  D  Y  R  N  R  L  N  W  R  Y  L  G  S  I  I  S  E  V  C  Q  E  R  *  T  T  L  T  N  H  F  L  S  T  K  K  G  D  N  T  N  R  I  G  S  V  V  T  L  P  H  *  W  I  C  T  R  L  G  *  R  H  G  F  S  I  A  I  Q  D  R  K  I  R  R  K  P  S  H  T  Q  N  Y  I  K  I  H  H  F  *  D  N  Q  V  Y  I  S  I  A  P  H  K  S  H  Q  T  R  P  I  Y  F  F  N  Y  H  R  L  T  H  R  S  R  N  T  N  R  H  V  K  Q  F  T  M  *  I  M  T  I  S  K  *  G  R  Y  I  R  K  C  G  S  R  V  K  *  Y  R  S  H  T  I  T  N  Q  K  I  T  C  D  N  S  I  *  C  L  R  F  R  P  P  R  E  S  V  T  M  G  P  L  T  C  L  S  V  A  P  T  M  L  *  C  S  G  S  S  L  P  I  T  P  A  V  L  V  T  T  I  T  S  T  T  A  S  S  R  M  T  A  S  S  I  T  T  S  T  S  N  I  W  R  S  V  T  L  F  W  T  I  P  L  N  V  S  S  L  P  T  S  I  T  L  S  G  F  K  H  S  S  L  R  E  V  L  T  G  L  R  W  T  P  N  Y  S  L  *  *  R  L  N  W  S  D  *  V  T  S  *  T  L  S  S  R  V  R  T  I  K  L  T </first_frame>
            <second_frame>  N  P  L  T  N  R  R  *  *  L  A  K  P  T  K  L  L  I  S  D  T  L  V  G  L  T  Q  F  F  T  V  S  I  L  E  G  *  T  I  T  S  S  L  E  T  T  F  P  K  K  D  T  A  S  S  Q  N  S  H  L  E  N  L  A  *  S  F  F  S  L  N  I  S  N  T  I  L  K  C  F  S  C  S  F  L  L  F  E  Y  T  N  I  S  S  I  N  T  I  T  K  R  S  R  Y  G  L  K  I  P  F  I  K  L  M  K  A  A  G  A  F  V  R  P  K  D  I  T  T  N  S  *  C  P  Y  L  V  R  K  A  V  F  G  T  S  I  A  S  I  F  N  *  *  *  P  N  L  K  S  I  L  E  K  T  Q  A  P  C  N  *  S  N  K  S  S  M  R  G  M  G  Y  L  F  L  I  V  T  L  F  N  C  R  *  F  M  H  I  R  K  L  P  S  F  F  F  T  N  N  T  G  A  S  Q  G  D  A  L  G  L  M  K  P  L  L  N  N  S  *  S  *  A  F  N  S  L  N  S  A  G  A  I  L  *  G  G  I  E  M  G  R  V  P  G  S  R  S  M  Q  K  S  I  S  L  S  G  G  I  P  G  R  S  A  G  N  T  S  R  N  S  R  T  T  E  T  D  S  I  G  G  T  W  V  V  S  S  R  R  C  A  K  N  A  K  Q  P  L  L  T  I  F  L  A  R  R  K  E  I  I  R  T  G  L  E  V  *  S  P  S  H  T  N  G  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  I  S  K  I  T  K  S  T  *  V  L  L  P  T  K  V  T  R  P  D  L  Y  T  F  S  T  I  T  D  S  P  T  G  V  E  T  R  I  G  M  S  S  N  S  Q  C  K  L  *  P  L  A  N  E  E  D  I  *  E  N  V  D  P  G  S  N  N  T  E  A  I  Q  S  Q  T  K  R  L  P  V  I  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  V  V  A  P  V  C  P  S  P  R  P  F  W  *  P  P  L  P  R  P  P  R  P  P  E  *  R  P  L  P  *  P  P  L  P  L  T  F  G  G  L  *  L  C  F  G  Q  Y  L  L  M  C  P  V  S  P  H  P  *  H  F  L  D  S  S  I  V  L  S  E  K  C  *  P  V  *  G  G  P  P  T  T  V  C  S  E  D  *  I  G  Q  T  E  *  P  P  E  P  C  P  L  E  *  E  P  L  N  S   </second_frame>
            <third_frame>   I  P  *  Q  I  D  G  N  S  *  L  N  Q  Q  S  S  L  F  L  T  H  *  *  V  L  P  N  S  L  L  S  Q  S  *  K  D  R  P  S  P  H  P  *  K  P  H  S  P  R  R  T  L  H  L  A  K  T  H  T  W  R  I  W  H  K  A  F  S  P  S  T  F  P  I  Q  F  S  S  A  S  R  V  P  S  C  S  L  S  I  P  I  Y  H  Q  *  I  R  S  Q  R  D  P  D  M  A  *  K  S  R  S  S  S  S  *  K  Q  Q  G  H  S  *  D  Q  K  T  S  L  Q  I  R  N  A  H  T  W  S  E  K  Q  F  L  A  H  P  L  P  V  S  S  I  D  D  N  R  T  S  S  Q  S  *  R  R  H  K  H  L  V  T  D  R  T  S  H  Q  C  E  E  W  D  T  C  S  *  *  L  P  C  S  T  A  G  S  L  C  T  S  E  N  S  H  P  S  S  S  Q  I  T  L  E  L  P  K  G  M  H  L  V  *  *  S  L  C  L  T  T  L  E  V  K  L  L  T  L  L  T  P  R  E  P  F  Y  K  G  V  *  K  W  G  E  Y  P  V  Q  D  Q  C  R  S  Q  Y  P  Y  L  V  A  Y  Q  E  D  L  Q  G  T  H  P  E  T  H  G  L  P  K  P  T  Q  L  E  V  L  G  *  Y  H  L  G  G  V  P  R  T  L  N  N  P  Y  *  P  F  S  *  H  E  E  R  R  *  Y  E  P  D  W  K  C  S  H  P  P  T  L  M  D  L  Y  Q  A  W  L  T  S  R  F  *  H  C  N  P  R  S  Q  N  S  E  K  A  K  S  Y  P  E  L  H  Q  N  P  P  F  L  R  *  P  S  L  H  K  Y  C  S  P  Q  K  S  P  D  Q  T  Y  I  L  F  Q  L  S  Q  T  H  P  P  E  *  K  H  E  *  A  C  Q  A  I  H  N  V  N  Y  D  H  *  Q  M  R  K  I  Y  K  K  M  W  I  Q  G  Q  I  I  Q  K  P  Y  N  H  K  P  K  D  Y  L  *  *  Q  H  L  M  S  P  L  P  T  A  Q  G  K  R  N  N  G  P  S  H  L  S  V  R  C  P  Y  H  V  V  M  *  W  L  Q  F  A  H  H  P  G  R  F  G  D  H  H  Y  L  D  H  R  V  L  Q  N  D  G  L  F  H  N  H  L  Y  L  *  H  L  E  V  C  N  S  V  L  D  N  T  S  *  C  V  Q  S  P  H  I  H  N  T  F  W  I  Q  A  *  F  S  Q  R  S  V  D  R  S  E  V  D  P  Q  L  Q  S  V  V  K  T  E  L  V  R  L  S  N  L  L  N  P  V  L  *  S  K  N  H  *  T  H  </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="C04HBa0119A16.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="1255" stop="1001"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>252</number_coding_nucleotides>
                  <number_encoded_amino_acids>84</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>CSGSSLPITPAVLVTTITSTTASSRMTASSITTSTSNIWRSVTLFWTIPLNVSSLPTSITLSGFKHSSLREVLTGLRWTPNYSL*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0119A16.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="1959" stop="1714"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>243</number_coding_nucleotides>
                  <number_encoded_amino_acids>81</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GGIEMGRVPGSRSMQKSISLSGGIPGRSAGNTSRNSRTTETDSIGGTWVVSSRRCAKNAKQPLLTIFLARRKEIIRTGLEV*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0119A16.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="3"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="2422" stop="2183"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>237</number_coding_nucleotides>
                  <number_encoded_amino_acids>79</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VYQYIINKYDHKEIQIWLKNPVHQAHESSRGIRKTKRHHYKFVMPIPGPKSSFWHIHCQYLQLMITEPQVNLREDTSTL*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0119A16.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="4"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="1981" stop="1781"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>198</number_coding_nucleotides>
                  <number_encoded_amino_acids>66</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LRGSHFIRGYRNGASTRFKINAEVNIPIWWHTRKICREHIQKLTDYRNRLNWRYLGSIISEVCQER*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0119A16.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="5"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="2490" stop="2293"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>195</number_coding_nucleotides>
                  <number_encoded_amino_acids>65</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SFFSLNISNTILKCFSCSFLLFEYTNISSINTITKRSRYGLKIPFIKLMKAAGAFVRPKDITTNS*</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="4167" PGL_stop="3991"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="4167" e_stop="3991"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.904"/>
        </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="0.904">
            <gDNA_exon_boundary e_start="4167" e_stop="3991" e_length="177"/>
          </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="4167" stop="3991"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U345909" 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>CTACATCTCCTTCCATACAGTGCTTCAAATGGGGCCATATCAATACTTGAGTGATAGATATTGTTGTAGGAGAACTCCGCTAAGGGTAAGAAGTTATCCCAATGAACTCCAAATTCTATCACACATGCACGAAGCATATCCTCCAACACTTGAATCGTTCGCTCAGACTAACCATCG</gDNA_template>
            <first_frame> L  H  L  L  P  Y  S  A  S  N  G  A  I  S  I  L  E  *  *  I  L  L  *  E  N  S  A  K  G  K  K  L  S  Q  *  T  P  N  S  I  T  H  A  R  S  I  S  S  N  T  *  I  V  R  S  D  *  P  S </first_frame>
            <second_frame>  Y  I  S  F  H  T  V  L  Q  M  G  P  Y  Q  Y  L  S  D  R  Y  C  C  R  R  T  P  L  R  V  R  S  Y  P  N  E  L  Q  I  L  S  H  M  H  E  A  Y  P  P  T  L  E  S  F  A  Q  T  N  H   </second_frame>
            <third_frame>   T  S  P  S  I  Q  C  F  K  W  G  H  I  N  T  *  V  I  D  I  V  V  G  E  L  R  *  G  *  E  V  I  P  M  N  S  K  F  Y  H  T  C  T  K  H  I  L  Q  H  L  N  R  S  L  R  L  T  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/">
            <none gDNA_id="C04HBa0119A16.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 35 chains have been computed
$ 
$ memory statistics:
$ 12240 bytes spliced alignments in total
$ 6 spliced alignments have been stored
$ 2040 bytes was the average size of a spliced alignment
$ 7880 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2626 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 41 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 02:20:55
-->
