<?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="2008-02-20 07:29:35"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C07HBa0114J16-ccCh5/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-8YEIm2/lycopersicum_combined_unigene_seqs" 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/cxgn-bacpublish-resources-8YEIm2/lycopersicum_combined_unigene_seqs" ref_id="SGN-U346798" ref_strand="+" ref_description="SGN-U346798        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT4G23160.1 | Symbol: None | protein kinase family protein, contains Pfam domain PF00069: Protein kinase domain | chr4:12129496-12134198 FORWARD | Aliases: F21P8.50, F21P8_50 (evalue: 1e-36, score=149) genbank/nr: gi|37530894|ref|NP_919749.1| putative gag-pol polyprotein [Oryza sativa (japonica cultivar-group)] gi|18642681|gb|AAK02020.2| Putative gag-pol polyprotein [Oryza sativa] gi|31430072|gb|AAP52036.1| putative gag-pol polyprotein [Oryza sativa (japonica cultivar-group)](evalue: 3e-43, score=178)">
      <seq>tcatccacaatacacacgcaaccaccacccacacgcacaagcaacccgaaccaccccatacccacaacatctccaacccgatccgttttgggtccttaccggccacccccgaatcaccaccgcccgtgccaccccccaatactcatcccatgttaacccgtggcaaagccggtatctttaaacccaaaacctttcaggctaccatactaccaaatacaccccttcccgatagtgaaccaacaacctactctgttgcctcaaaaaatgcttattggcgtcatgctatggatgacgagtttaaggctttgactgatcaggaaacttgggttcttgtacctaagccccatgggcggcacccagtgggctgtaaatgggtgtacaaaattaaacacaatgcggatggcagtatttccaggtacaaggctcgtttggttgctaaaggctacaatcaggagtatggtcttgattactccgagacattcagtc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0114J16-ccCh5/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C07HBa0114J16.1" temp_strand="+" temp_description="C07HBa0114J16.1  AC210355.1 htgs_phase:2 submitted_to_sgn_as:C07HBa0114J16 upload_account_name:france">
        <position start="72731" stop="73816"/>
      </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="73031" g_stop="73516" g_length="486"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="486" r_length="486" r_score="0.957"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0114J16.1" gen_strand="+" ref_id="SGN-U346798" ref_strand="+">
        <total_alignment_score>0.957</total_alignment_score>
        <cumulative_length_of_scored_exons>486</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0114J16.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U346798" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="73031" e_stop="73516"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCACCCACAATACACCCGCAACCACCACCCACACTCACAACCAATCCGAACAACCCCATACACACAACATCTCCAGCCCGATCCGTTTTGGGTCCTTCCCGGCCACCCCCGAATCACCACCACCCGTGCCACCCCCCAATACTCATCCCATGTTAACCCGTGGCAAAGCCGGTATCTTTAAACCCAAAACCTTTCAGGCTACCATACTACCAAATATACCCTTTCCCGATAGTGAACCAACAACCTACTCTGTTGCCTTAAAAAATGCTTATTGGCGTCATGCTATGGATGACGAGTTTAAGGCTTTGACTGATCAGAAAACTTGGGTTCTTGTACCTAAGCCCCATGGGCGGCACCCAGTGTGCTGTAAATGGGTGTATAAAATTAAACACAATGCAGATGGCAGTATTTCCAGGTACAAGGCTCGTTTGGTTGCTGAAGTCTACAATCAGGAGTATGGGCTTGATTACTCCGAGACATTTAGTC</genome_strand>
        <mrna_strand>TCATCCACAATACACACGCAACCACCACCCACACGCACAAGCAACCCGAACCACCCCATACCCACAACATCTCCAACCCGATCCGTTTTGGGTCCTTACCGGCCACCCCCGAATCACCACCGCCCGTGCCACCCCCCAATACTCATCCCATGTTAACCCGTGGCAAAGCCGGTATCTTTAAACCCAAAACCTTTCAGGCTACCATACTACCAAATACACCCCTTCCCGATAGTGAACCAACAACCTACTCTGTTGCCTCAAAAAATGCTTATTGGCGTCATGCTATGGATGACGAGTTTAAGGCTTTGACTGATCAGGAAACTTGGGTTCTTGTACCTAAGCCCCATGGGCGGCACCCAGTGGGCTGTAAATGGGTGTACAAAATTAAACACAATGCGGATGGCAGTATTTCCAGGTACAAGGCTCGTTTGGTTGCTAAAGGCTACAATCAGGAGTATGGTCTTGATTACTCCGAGACATTCAGTC</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/cxgn-bacpublish-resources-8YEIm2/lycopersicum_combined_unigene_seqs" ref_id="SGN-U344877" ref_strand="+" ref_description="SGN-U344877        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT4G23160.1 | Symbol: None | protein kinase family protein, contains Pfam domain PF00069: Protein kinase domain | chr4:12129496-12134198 FORWARD | Aliases: F21P8.50, F21P8_50 (evalue: 2e-36, score=149) genbank/nr: retrotransposon(evalue: 5e-50, score=201)">
      <seq>gtttggttgctaaaggctacaatcaggagtatgggcttgattactccgagacattcagtcctgttattcggcaggaaaccattcgcctggtactgtcactcgccgtgcgcaacaattggctcatcaatcagttggatgtttccaatgcttttcttcatggcatgcttgatgaaacaatctacatgacgcaaccaccgggctatgttgatcctcgcttccctcaacatgtttgcaaactccagaagtctctgtatgggctcaagcaagccccccgtgcttggtacgcacgtctgaaaacgtt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0114J16-ccCh5/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C07HBa0114J16.1" temp_strand="+" temp_description="C07HBa0114J16.1  AC210355.1 htgs_phase:2 submitted_to_sgn_as:C07HBa0114J16 upload_account_name:france">
        <position start="73157" stop="74057"/>
      </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="73457" g_stop="73757" g_length="301"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="301" r_length="301" r_score="0.937"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0114J16.1" gen_strand="+" ref_id="SGN-U344877" ref_strand="+">
        <total_alignment_score>0.937</total_alignment_score>
        <cumulative_length_of_scored_exons>301</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0114J16.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U344877" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="73457" e_stop="73757"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTTTGGTTGCTGAAGTCTACAATCAGGAGTATGGGCTTGATTACTCCGAGACATTTAGTCCTGTTATTAGGCAGGAAACCATTCGCCTGGTACTGTCACTCGCCGTGCGCAACAATTGGCTAATCAATCAGTTGGATATTTCCAATTCTTTTCTTCATGGCATGCTTGATGAAACTATCTACATGACGCAACCACCGGGCTATGTTTATCCCCGCTTCCCTAAACATGTTTTCAAACTCTAGAAGTCTCTGTATGGGATCATGCAAGCCCCCCGTGCTTGCTACACACGACTGAAAACATT</genome_strand>
        <mrna_strand>GTTTGGTTGCTAAAGGCTACAATCAGGAGTATGGGCTTGATTACTCCGAGACATTCAGTCCTGTTATTCGGCAGGAAACCATTCGCCTGGTACTGTCACTCGCCGTGCGCAACAATTGGCTCATCAATCAGTTGGATGTTTCCAATGCTTTTCTTCATGGCATGCTTGATGAAACAATCTACATGACGCAACCACCGGGCTATGTTGATCCTCGCTTCCCTCAACATGTTTGCAAACTCCAGAAGTCTCTGTATGGGCTCAAGCAAGCCCCCCGTGCTTGGTACGCACGTCTGAAAACGTT</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/cxgn-bacpublish-resources-8YEIm2/lycopersicum_combined_unigene_seqs" ref_id="SGN-U334737" ref_strand="+" ref_description="SGN-U334737        Tomato 200607 #1 [1 ESTs aligned]">
      <seq>cgagggtctttgttctaatacacttcaactcttggaatttgggtactgggatcacttctctgaacttcacgacgaacctgcaggacggaccgtcagatccacgacggaccgtcacaagcttcgtaatcccacacttagtcagacttccctatcttccttcagcagctgcactacgcttccacctacggaccgtcacaagcacgacggaccgtcataagctccgtaggtggtttcttctgcatttcttcgctcaaaatctccgcattcagctttggacagatttcctgcaaaacaaagagtaacttatataaaaattagcacaaaaaggcttttggacacactaagcttaaggaaaaagtattaataataccgtgaaaccacggtatatcaacaccctcaacttaaattagttgtttgtcctcaagcgacgcactatgactcactacacaatctttgtacaatagtatccatgttttatcctttgcaatcatttggctatcaatcccgattaatctcatcaaatctatgcatgctatcactattaggtttgaattttgtgggatcagaatatgacacagacttaccatgcactaacacctatcctcttcaatttctcaccgaggtgctaacaattctagtattgcaactagtgtcctcactataagacaaaatcctcctttttcacacagtgattttagtttgagtataaggattac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0114J16-ccCh5/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C07HBa0114J16.1" temp_strand="+" temp_description="C07HBa0114J16.1  AC210355.1 htgs_phase:2 submitted_to_sgn_as:C07HBa0114J16 upload_account_name:france">
        <position start="75811" stop="77124"/>
      </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="76111" g_stop="76824" g_length="714"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="716" r_length="716" r_score="0.910"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0114J16.1" gen_strand="+" ref_id="SGN-U334737" ref_strand="+">
        <total_alignment_score>0.910</total_alignment_score>
        <cumulative_length_of_scored_exons>714</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0114J16.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U334737" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="76111" e_stop="76824"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CGAGGGTCTCGATTC-AAAATACTTCAACTCTTGGAATCTGGGTACTTGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATAGCAATGACGGACCGTCACAATCTTCGTAATCCCACACTTTGTCAGACTTCCCCATCTTCTTTCAGCAGCTTCTCTACGCTGCCACCTACGGACTGTTACATGCATGACAGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTACATTT-TTCGCTCAAAATCTCCGCATTCAGCTTTGGACAGATTTCCTGTAAAACAAAGAGAAACTTATATCAAAATTAGCACAAAAAGGGCTTTCAGACACACTAAACATAAGGAAAAAGTATTAATTATACCGTGAAACCACGGTATATCAACACCCTCAACTTAAATTTGTTGTTTGTCCTCAAGCGACGCACTATGACTCACTACACAATCTTTGTACAATAGTATTCATGTTTTATCCTTTGCAATCATTTGGCTATCAATCTCGATTAATCTCATCAAATATATGCATGCTATCACTATTAGGCTTGAATTTTATGGGATTCGAACATGACACAGACTCACCATGCACTAACACCTATCCTCTTCAATTTCTCACCGAGGTGCTAATAATTCCGGTATAGCAACTAGTGTCCTCACTTTAGAACAAAATACT-CATTTTCAAACAATGATTTAAGTTTAAGTATAAGGATTAC</genome_strand>
        <mrna_strand>CGAGGGTCTTTGTTCTAATACACTTCAACTCTTGGAATTTGGGTACTGGGATCACTTCTCTGAACTTCACGACGAACCTGCAGGACGGACCGTCAGATCCACGACGGACCGTCACAAGCTTCGTAATCCCACACTTAGTCAGACTTCCCTATCTTCCTTCAGCAGCTGCACTACGCTTCCACCTACGGACCGTCACAAGCACGACGGACCGTCATAAGCTCCGTAGGTGGTTTCTTCTGCATTTCTTCGCTCAAAATCTCCGCATTCAGCTTTGGACAGATTTCCTGCAAAACAAAGAGTAACTTATATAAAAATTAGCACAAAAA-GGCTTTTGGACACACTAAGCTTAAGGAAAAAGTATTAATAATACCGTGAAACCACGGTATATCAACACCCTCAACTTAAATTAGTTGTTTGTCCTCAAGCGACGCACTATGACTCACTACACAATCTTTGTACAATAGTATCCATGTTTTATCCTTTGCAATCATTTGGCTATCAATCCCGATTAATCTCATCAAATCTATGCATGCTATCACTATTAGGTTTGAATTTTGTGGGATCAGAATATGACACAGACTTACCATGCACTAACACCTATCCTCTTCAATTTCTCACCGAGGTGCTAACAATTCTAGTATTGCAACTAGTGTCCTCACTATAAGACAAAATCCTCCTTTTTCACACAGTGATTTTAGTTTGAGTATAAGGATTAC</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/cxgn-bacpublish-resources-8YEIm2/lycopersicum_combined_unigene_seqs" ref_id="SGN-U341497" ref_strand="+" ref_description="SGN-U341497        Tomato 200607 #1 [1 ESTs aligned]">
      <seq>ccccctcgagagagtgccaagaggcgtaggggccgatcagaggatgaggcacaagcaaagaagaaggagcgccgagagatggaggctgcgaggagagcctcgctgagacggaggcacaccaaatcagagcatcgcagatagcggatggggcgtctagctcccgcactgtagagatagcaagaggcactactgatggtgcggttgttgctgaggacatcactgagggtgtccagattgctgaggacaccactgagggtgtccagattgcagaggatgtgggttccaggaaaccggacccaccatcttgttaaatcgacggtgctttgcgccacaggtttgcttcacctaccactctaatatttagattttttatgcattggggacagttgcatgcttttttgttgggggtggggtaaatggaaagtgagtgttagggtgaagtctgagtagcccaactcactatcctcttttggggttttcttgcctgtgttctttttccccaaaagactgattactttttttgttgaaccgacacgttatatatttt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0114J16-ccCh5/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C07HBa0114J16.1" temp_strand="-" temp_description="C07HBa0114J16.1  AC210355.1 htgs_phase:2 submitted_to_sgn_as:C07HBa0114J16 upload_account_name:france">
        <position start="78697" stop="77551"/>
      </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="78399" g_stop="77851" g_length="549"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="547" r_length="547" r_score="0.905"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0114J16.1" gen_strand="-" ref_id="SGN-U341497" ref_strand="+">
        <total_alignment_score>0.905</total_alignment_score>
        <cumulative_length_of_scored_exons>549</cumulative_length_of_scored_exons>
        <coverage percentage="1.004" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0114J16.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U341497" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="78399" e_stop="77851"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTCCCTCGAGAGAGTGCAAAGAGGCGTAGGGGTCGATCAGAGGATGAGGCGCGAGCAGGGAAGAAGGAGCGCCGAGAGATGGAGGCCGCGAGGAGAGCCTCACTTGCTGAGGCGGAGGCACACCAAATCAGAGCATCGCAGATAGCGGCTGGGGCGTCTAGCTCCCGCACTGTAGAGACAACAGGAGGCACTACTTATGGTGCGGTTGTTGTTGAGGACATCACTTAGGGTGTCCAGATTGCTGAGGACACCCCTGAGGGTGTCCAGATTGCGTAGGATGTGGGTTCTGGGAAACCAGACCCACCAGCTTGTT-GATCGATGGCGCTATGCGCCACAGTTTTGCTTCACCTACCCCTCTAATCTTTCGATTTCTTTATGCATTGGGGACAATTGCATG-TTTTTT-TTGGGGGTGGGGTAAATGGAAAGTGAGTGTTAGGTTGAAGTCTGAGTAGCCCAACTCACTATCCTCTTTTGGGGTTTTATTGCCTGTGTTCTTTTTCCTCAAAAGACTGATTACTTTTTCTTTTAAACCGGCACGTTATATCTTTT</genome_strand>
        <mrna_strand>CCCCCTCGAGAGAGTGCCAAGAGGCGTAGGGGCCGATCAGAGGATGAGGCACAAGCAAAGAAGAAGGAGCGCCGAGAGATGGAGGCTGCGAGGAGAGCCT--C--GCTGAGACGGAGGCACACCAAATCAGAGCATCGCAGATAGCGGATGGGGCGTCTAGCTCCCGCACTGTAGAGATAGCAAGAGGCACTACTGATGGTGCGGTTGTTGCTGAGGACATCACTGAGGGTGTCCAGATTGCTGAGGACACCACTGAGGGTGTCCAGATTGCAGAGGATGTGGGTTCCAGGAAACCGGACCCACCATCTTGTTAAATCGACGGTGCTTTGCGCCACAGGTTTGCTTCACCTACCACTCTAATATTTAGATTT-TTTATGCATTGGGGACAGTTGCATGCTTTTTTGTTGGGGGTGGGGTAAATGGAAAGTGAGTGTTAGGGTGAAGTCTGAGTAGCCCAACTCACTATCCTCTTTTGGGGTTTTCTTGCCTGTGTTCTTTTTCCCCAAAAGACTGATTACTTTTTTTGTTGAACCGACACGTTATATATTTT</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/cxgn-bacpublish-resources-8YEIm2/lycopersicum_combined_unigene_seqs" ref_id="SGN-U339767" ref_strand="+" ref_description="SGN-U339767        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: ATMG00860.1 | Symbol: ORF158 | hypothetical protein | chrM:235916-236392 FORWARD | Aliases: ORF158 (evalue: 4e-13, score=72) genbank/nr: gi|47824956|gb|AAT38730.1| putative reverse transcriptase [Solanum demissum] (evalue: 4e-93, score=343)">
      <seq>ctctatgactctagtacctagcaaataggagcaaaatatctcaaaagcaaagactactgcgaggagttcatgctcagtcactgtgtagttcttctgggcttcatttagggctttactagcatagtaaattgggtgaaggattttgtttcttctctgtcccaatactacaccaagagccaccccactagcatcgcacattacctcaaatggacttttccaatccggagaaataatgataggtgcagacactaacttctcttttagctcactgaatgctttaagacaggactcatcaaaacaaaatttacattctttcttcagtaatttgcacaatgggtgtgcaatctttgaaaagtctttgatgaatctccgataaaaacctgcatgcccaagaaagcttctcacacctttcatagagatcggtgggggaagtctctctattacctcaactttagctcgatcaacctctattcccttttctgaaatgcgatgacccaacacaatacctttttttaccatgaaatgacacttttcccagtttagtaccagattgcagtcttcacatctcttaagaacctcagattaattggtcaagcatcgctcaattgaatcaccaaccacagaaaaatcatccataaaaacctctatagtatcctccaccatgtcagaaaatattgacatcatatatctctgaaaggttgcgggtgcattgcacaacctaaatggcattcttc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07HBa0114J16-ccCh5/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C07HBa0114J16.1" temp_strand="+" temp_description="C07HBa0114J16.1  AC210355.1 htgs_phase:2 submitted_to_sgn_as:C07HBa0114J16 upload_account_name:france">
        <position start="82957" stop="84291"/>
      </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="83257" g_stop="83991" g_length="735"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="734" r_length="734" r_score="0.940"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07HBa0114J16.1" gen_strand="+" ref_id="SGN-U339767" ref_strand="+">
        <total_alignment_score>0.940</total_alignment_score>
        <cumulative_length_of_scored_exons>735</cumulative_length_of_scored_exons>
        <coverage percentage="1.001" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07HBa0114J16.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U339767" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="83257" e_stop="83991"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CACTATAACTCTAGTACCTAGAAAATAGGAGCAAAATTTCTCAAAAGCAAAGACTACTACGAGGAGTTCTTGCTCAGTCACTGTGTAGTTCTTCTAGGCTTCATTTAGGGCTTTATTAGCATAGTAAATTGGGTGAAGGATTTTGTTTCTTCTCTGTCCCAATACTACACCAAGAGCCACCCTACTAGCATCGCACATTACCTCAAATGGACTGTTCTAATCCGGAGAAATAATGATAGGCGCATACACTAACTTTTCTTTTAGCTCACCGAATGCTTTATGACAGGATTCATCAAAGCAAAATTTACATTCTTTCTCAAGCAATTTGCACAATGATTGTGCAATCTTTGAAAAGTCTTTGATGAATCTCTGATAAAAAAACTGCATGCCCAAGAAAGCTTCTCACACCTTTCACAGAGATCGGTGGGGGAAGTCTCTCTATTACCTTAACTTTGGCTCAATCAACCTCTATGCCCTTTTCTAAAATGCGATGACCCAACACAATACCCTCTTTCACCATGAAATGACACTTTTCCCAGTTTAGTACCAAATTGCAGTCTTCACATCTCTTAAGAACCTCAGATAAATTGGTCAAGCACCGCTCGAATGAATCACCAACCACAGAAAAATCATCCATAAAAACCTCTATAGTATCCTCCACCATGTTAGAAAATATTGACATCATACATCTCTGAAAGGTTGCGGGTGCATTGCACAACCCAAACGGCATTCTTC</genome_strand>
        <mrna_strand>CTCTATGACTCTAGTACCTAGCAAATAGGAGCAAAATATCTCAAAAGCAAAGACTACTGCGAGGAGTTCATGCTCAGTCACTGTGTAGTTCTTCTGGGCTTCATTTAGGGCTTTACTAGCATAGTAAATTGGGTGAAGGATTTTGTTTCTTCTCTGTCCCAATACTACACCAAGAGCCACCCCACTAGCATCGCACATTACCTCAAATGGACTTTTCCAATCCGGAGAAATAATGATAGGTGCAGACACTAACTTCTCTTTTAGCTCACTGAATGCTTTAAGACAGGACTCATCAAAACAAAATTTACATTCTTTCTTCAGTAATTTGCACAATGGGTGTGCAATCTTTGAAAAGTCTTTGATGAATCTCCGAT-AAAAACCTGCATGCCCAAGAAAGCTTCTCACACCTTTCATAGAGATCGGTGGGGGAAGTCTCTCTATTACCTCAACTTTAGCTCGATCAACCTCTATTCCCTTTTCTGAAATGCGATGACCCAACACAATACCTTTTTTTACCATGAAATGACACTTTTCCCAGTTTAGTACCAGATTGCAGTCTTCACATCTCTTAAGAACCTCAGATTAATTGGTCAAGCATCGCTCAATTGAATCACCAACCACAGAAAAATCATCCATAAAAACCTCTATAGTATCCTCCACCATGTCAGAAAATATTGACATCATATATCTCTGAAAGGTTGCGGGTGCATTGCACAACCTAAATGGCATTCTTC</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="73031" PGL_stop="73757"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="73031" e_stop="73757"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.957"/>
        </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="0.957">
            <gDNA_exon_boundary e_start="73031" e_stop="73757" e_length="727"/>
          </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="73031" stop="73516"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U346798" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="73457" stop="73757"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U344877" 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>TCACCCACAATACACCCGCAACCACCACCCACACTCACAACCAATCCGAACAACCCCATACACACAACATCTCCAGCCCGATCCGTTTTGGGTCCTTCCCGGCCACCCCCGAATCACCACCACCCGTGCCACCCCCCAATACTCATCCCATGTTAACCCGTGGCAAAGCCGGTATCTTTAAACCCAAAACCTTTCAGGCTACCATACTACCAAATATACCCTTTCCCGATAGTGAACCAACAACCTACTCTGTTGCCTTAAAAAATGCTTATTGGCGTCATGCTATGGATGACGAGTTTAAGGCTTTGACTGATCAGAAAACTTGGGTTCTTGTACCTAAGCCCCATGGGCGGCACCCAGTGTGCTGTAAATGGGTGTATAAAATTAAACACAATGCAGATGGCAGTATTTCCAGGTACAAGGCTCGTTTGGTTGCTGAAGTCTACAATCAGGAGTATGGGCTTGATTACTCCGAGACATTTAGTCCTGTTATTAGGCAGGAAACCATTCGCCTGGTACTGTCACTCGCCGTGCGCAACAATTGGCTAATCAATCAGTTGGATATTTCCAATTCTTTTCTTCATGGCATGCTTGATGAAACTATCTACATGACGCAACCACCGGGCTATGTTTATCCCCGCTTCCCTAAACATGTTTTCAAACTCTAGAAGTCTCTGTATGGGATCATGCAAGCCCCCCGTGCTTGCTACACACGACTGAAAACATT</gDNA_template>
            <first_frame> S  P  T  I  H  P  Q  P  P  P  T  L  T  T  N  P  N  N  P  I  H  T  T  S  P  A  R  S  V  L  G  P  S  R  P  P  P  N  H  H  H  P  C  H  P  P  I  L  I  P  C  *  P  V  A  K  P  V  S  L  N  P  K  P  F  R  L  P  Y  Y  Q  I  Y  P  F  P  I  V  N  Q  Q  P  T  L  L  P  *  K  M  L  I  G  V  M  L  W  M  T  S  L  R  L  *  L  I  R  K  L  G  F  L  Y  L  S  P  M  G  G  T  Q  C  A  V  N  G  C  I  K  L  N  T  M  Q  M  A  V  F  P  G  T  R  L  V  W  L  L  K  S  T  I  R  S  M  G  L  I  T  P  R  H  L  V  L  L  L  G  R  K  P  F  A  W  Y  C  H  S  P  C  A  T  I  G  *  S  I  S  W  I  F  P  I  L  F  F  M  A  C  L  M  K  L  S  T  *  R  N  H  R  A  M  F  I  P  A  S  L  N  M  F  S  N  S  R  S  L  C  M  G  S  C  K  P  P  V  L  A  T  H  D  *  K  H  </first_frame>
            <second_frame>  H  P  Q  Y  T  R  N  H  H  P  H  S  Q  P  I  R  T  T  P  Y  T  Q  H  L  Q  P  D  P  F  W  V  L  P  G  H  P  R  I  T  T  T  R  A  T  P  Q  Y  S  S  H  V  N  P  W  Q  S  R  Y  L  *  T  Q  N  L  S  G  Y  H  T  T  K  Y  T  L  S  R  *  *  T  N  N  L  L  C  C  L  K  K  C  L  L  A  S  C  Y  G  *  R  V  *  G  F  D  *  S  E  N  L  G  S  C  T  *  A  P  W  A  A  P  S  V  L  *  M  G  V  *  N  *  T  Q  C  R  W  Q  Y  F  Q  V  Q  G  S  F  G  C  *  S  L  Q  S  G  V  W  A  *  L  L  R  D  I  *  S  C  Y  *  A  G  N  H  S  P  G  T  V  T  R  R  A  Q  Q  L  A  N  Q  S  V  G  Y  F  Q  F  F  S  S  W  H  A  *  *  N  Y  L  H  D  A  T  T  G  L  C  L  S  P  L  P  *  T  C  F  Q  T  L  E  V  S  V  W  D  H  A  S  P  P  C  L  L  H  T  T  E  N  I </second_frame>
            <third_frame>   T  H  N  T  P  A  T  T  T  H  T  H  N  Q  S  E  Q  P  H  T  H  N  I  S  S  P  I  R  F  G  S  F  P  A  T  P  E  S  P  P  P  V  P  P  P  N  T  H  P  M  L  T  R  G  K  A  G  I  F  K  P  K  T  F  Q  A  T  I  L  P  N  I  P  F  P  D  S  E  P  T  T  Y  S  V  A  L  K  N  A  Y  W  R  H  A  M  D  D  E  F  K  A  L  T  D  Q  K  T  W  V  L  V  P  K  P  H  G  R  H  P  V  C  C  K  W  V  Y  K  I  K  H  N  A  D  G  S  I  S  R  Y  K  A  R  L  V  A  E  V  Y  N  Q  E  Y  G  L  D  Y  S  E  T  F  S  P  V  I  R  Q  E  T  I  R  L  V  L  S  L  A  V  R  N  N  W  L  I  N  Q  L  D  I  S  N  S  F  L  H  G  M  L  D  E  T  I  Y  M  T  Q  P  P  G  Y  V  Y  P  R  F  P  K  H  V  F  K  L  *  K  S  L  Y  G  I  M  Q  A  P  R  A  C  Y  T  R  L  K  T   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0114J16.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="73033" stop="73698"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>663</number_coding_nucleotides>
                  <number_encoded_amino_acids>221</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>THNTPATTTHTHNQSEQPHTHNISSPIRFGSFPATPESPPPVPPPNTHPMLTRGKAGIFKPKTFQATILPNIPFPDSEPTTYSVALKNAYWRHAMDDEFKALTDQKTWVLVPKPHGRHPVCCKWVYKIKHNADGSISRYKARLVAEVYNQEYGLDYSETFSPVIRQETIRLVLSLAVRNNWLINQLDISNSFLHGMLDETIYMTQPPGYVYPRFPKHVFKL*</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="76111" PGL_stop="76824"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="76111" e_stop="76824"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.910"/>
        </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="0.910">
            <gDNA_exon_boundary e_start="76111" e_stop="76824" e_length="714"/>
          </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="76111" stop="76824"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U334737" 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>CGAGGGTCTCGATTCAAAATACTTCAACTCTTGGAATCTGGGTACTTGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATAGCAATGACGGACCGTCACAATCTTCGTAATCCCACACTTTGTCAGACTTCCCCATCTTCTTTCAGCAGCTTCTCTACGCTGCCACCTACGGACTGTTACATGCATGACAGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTACATTTTTCGCTCAAAATCTCCGCATTCAGCTTTGGACAGATTTCCTGTAAAACAAAGAGAAACTTATATCAAAATTAGCACAAAAAGGGCTTTCAGACACACTAAACATAAGGAAAAAGTATTAATTATACCGTGAAACCACGGTATATCAACACCCTCAACTTAAATTTGTTGTTTGTCCTCAAGCGACGCACTATGACTCACTACACAATCTTTGTACAATAGTATTCATGTTTTATCCTTTGCAATCATTTGGCTATCAATCTCGATTAATCTCATCAAATATATGCATGCTATCACTATTAGGCTTGAATTTTATGGGATTCGAACATGACACAGACTCACCATGCACTAACACCTATCCTCTTCAATTTCTCACCGAGGTGCTAATAATTCCGGTATAGCAACTAGTGTCCTCACTTTAGAACAAAATACTCATTTTCAAACAATGATTTAAGTTTAAGTATAAGGATTAC</gDNA_template>
            <first_frame> R  G  S  R  F  K  I  L  Q  L  L  E  S  G  Y  L  D  H  F  S  D  L  H  D  E  P  A  G  R  T  V  I  A  M  T  D  R  H  N  L  R  N  P  T  L  C  Q  T  S  P  S  S  F  S  S  F  S  T  L  P  P  T  D  C  Y  M  H  D  R  P  S  *  A  P  *  V  V  S  S  T  F  F  A  Q  N  L  R  I  Q  L  W  T  D  F  L  *  N  K  E  K  L  I  S  K  L  A  Q  K  G  L  S  D  T  L  N  I  R  K  K  Y  *  L  Y  R  E  T  T  V  Y  Q  H  P  Q  L  K  F  V  V  C  P  Q  A  T  H  Y  D  S  L  H  N  L  C  T  I  V  F  M  F  Y  P  L  Q  S  F  G  Y  Q  S  R  L  I  S  S  N  I  C  M  L  S  L  L  G  L  N  F  M  G  F  E  H  D  T  D  S  P  C  T  N  T  Y  P  L  Q  F  L  T  E  V  L  I  I  P  V  *  Q  L  V  S  S  L  *  N  K  I  L  I  F  K  Q  *  F  K  F  K  Y  K  D  Y </first_frame>
            <second_frame>  E  G  L  D  S  K  Y  F  N  S  W  N  L  G  T  W  I  T  S  L  I  F  T  T  N  L  Q  D  G  P  S  *  Q  *  R  T  V  T  I  F  V  I  P  H  F  V  R  L  P  H  L  L  S  A  A  S  L  R  C  H  L  R  T  V  T  C  M  T  D  R  H  K  L  R  R  W  S  L  L  H  F  S  L  K  I  S  A  F  S  F  G  Q  I  S  C  K  T  K  R  N  L  Y  Q  N  *  H  K  K  G  F  Q  T  H  *  T  *  G  K  S  I  N  Y  T  V  K  P  R  Y  I  N  T  L  N  L  N  L  L  F  V  L  K  R  R  T  M  T  H  Y  T  I  F  V  Q  *  Y  S  C  F  I  L  C  N  H  L  A  I  N  L  D  *  S  H  Q  I  Y  A  C  Y  H  Y  *  A  *  I  L  W  D  S  N  M  T  Q  T  H  H  A  L  T  P  I  L  F  N  F  S  P  R  C  *  *  F  R  Y  S  N  *  C  P  H  F  R  T  K  Y  S  F  S  N  N  D  L  S  L  S  I  R  I   </second_frame>
            <third_frame>   R  V  S  I  Q  N  T  S  T  L  G  I  W  V  L  G  S  L  L  *  S  S  R  R  T  C  R  T  D  R  H  S  N  D  G  P  S  Q  S  S  *  S  H  T  L  S  D  F  P  I  F  F  Q  Q  L  L  Y  A  A  T  Y  G  L  L  H  A  *  Q  T  V  I  S  S  V  G  G  L  F  Y  I  F  R  S  K  S  P  H  S  A  L  D  R  F  P  V  K  Q  R  E  T  Y  I  K  I  S  T  K  R  A  F  R  H  T  K  H  K  E  K  V  L  I  I  P  *  N  H  G  I  S  T  P  S  T  *  I  C  C  L  S  S  S  D  A  L  *  L  T  T  Q  S  L  Y  N  S  I  H  V  L  S  F  A  I  I  W  L  S  I  S  I  N  L  I  K  Y  M  H  A  I  T  I  R  L  E  F  Y  G  I  R  T  *  H  R  L  T  M  H  *  H  L  S  S  S  I  S  H  R  G  A  N  N  S  G  I  A  T  S  V  L  T  L  E  Q  N  T  H  F  Q  T  M  I  *  V  *  V  *  G  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="C07HBa0114J16.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="76474" stop="76752"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>276</number_coding_nucleotides>
                  <number_encoded_amino_acids>92</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LYRETTVYQHPQLKFVVCPQATHYDSLHNLCTIVFMFYPLQSFGYQSRLISSNICMLSLLGLNFMGFEHDTDSPCTNTYPLQFLTEVLIIPV*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0114J16.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="76111" stop="76326"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>213</number_coding_nucleotides>
                  <number_encoded_amino_acids>71</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RGSRFKILQLLESGYLDHFSDLHDEPAGRTVIAMTDRHNLRNPTLCQTSPSSFSSFSTLPPTDCYMHDRPS*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0114J16.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="3"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="76214" stop="76426"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>210</number_coding_nucleotides>
                  <number_encoded_amino_acids>70</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RTVTIFVIPHFVRLPHLLSAASLRCHLRTVTCMTDRHKLRRWSLLHFSLKISAFSFGQISCKTKRNLYQN*</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="78399" PGL_stop="77851"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="78399" e_stop="77851"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.905"/>
        </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="0.905">
            <gDNA_exon_boundary e_start="78399" e_stop="77851" e_length="549"/>
          </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="78399" stop="77851"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U341497" 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>TTCCCTCGAGAGAGTGCAAAGAGGCGTAGGGGTCGATCAGAGGATGAGGCGCGAGCAGGGAAGAAGGAGCGCCGAGAGATGGAGGCCGCGAGGAGAGCCTCACTTGCTGAGGCGGAGGCACACCAAATCAGAGCATCGCAGATAGCGGCTGGGGCGTCTAGCTCCCGCACTGTAGAGACAACAGGAGGCACTACTTATGGTGCGGTTGTTGTTGAGGACATCACTTAGGGTGTCCAGATTGCTGAGGACACCCCTGAGGGTGTCCAGATTGCGTAGGATGTGGGTTCTGGGAAACCAGACCCACCAGCTTGTTGATCGATGGCGCTATGCGCCACAGTTTTGCTTCACCTACCCCTCTAATCTTTCGATTTCTTTATGCATTGGGGACAATTGCATGTTTTTTTTGGGGGTGGGGTAAATGGAAAGTGAGTGTTAGGTTGAAGTCTGAGTAGCCCAACTCACTATCCTCTTTTGGGGTTTTATTGCCTGTGTTCTTTTTCCTCAAAAGACTGATTACTTTTTCTTTTAAACCGGCACGTTATATCTTTT</gDNA_template>
            <first_frame> F  P  R  E  S  A  K  R  R  R  G  R  S  E  D  E  A  R  A  G  K  K  E  R  R  E  M  E  A  A  R  R  A  S  L  A  E  A  E  A  H  Q  I  R  A  S  Q  I  A  A  G  A  S  S  S  R  T  V  E  T  T  G  G  T  T  Y  G  A  V  V  V  E  D  I  T  *  G  V  Q  I  A  E  D  T  P  E  G  V  Q  I  A  *  D  V  G  S  G  K  P  D  P  P  A  C  *  S  M  A  L  C  A  T  V  L  L  H  L  P  L  *  S  F  D  F  F  M  H  W  G  Q  L  H  V  F  F  G  G  G  V  N  G  K  *  V  L  G  *  S  L  S  S  P  T  H  Y  P  L  L  G  F  Y  C  L  C  S  F  S  S  K  D  *  L  L  F  L  L  N  R  H  V  I  S  F </first_frame>
            <second_frame>  S  L  E  R  V  Q  R  G  V  G  V  D  Q  R  M  R  R  E  Q  G  R  R  S  A  E  R  W  R  P  R  G  E  P  H  L  L  R  R  R  H  T  K  S  E  H  R  R  *  R  L  G  R  L  A  P  A  L  *  R  Q  Q  E  A  L  L  M  V  R  L  L  L  R  T  S  L  R  V  S  R  L  L  R  T  P  L  R  V  S  R  L  R  R  M  W  V  L  G  N  Q  T  H  Q  L  V  D  R  W  R  Y  A  P  Q  F  C  F  T  Y  P  S  N  L  S  I  S  L  C  I  G  D  N  C  M  F  F  L  G  V  G  *  M  E  S  E  C  *  V  E  V  *  V  A  Q  L  T  I  L  F  W  G  F  I  A  C  V  L  F  P  Q  K  T  D  Y  F  F  F  *  T  G  T  L  Y  L   </second_frame>
            <third_frame>   P  S  R  E  C  K  E  A  *  G  S  I  R  G  *  G  A  S  R  E  E  G  A  P  R  D  G  G  R  E  E  S  L  T  C  *  G  G  G  T  P  N  Q  S  I  A  D  S  G  W  G  V  *  L  P  H  C  R  D  N  R  R  H  Y  L  W  C  G  C  C  *  G  H  H  L  G  C  P  D  C  *  G  H  P  *  G  C  P  D  C  V  G  C  G  F  W  E  T  R  P  T  S  L  L  I  D  G  A  M  R  H  S  F  A  S  P  T  P  L  I  F  R  F  L  Y  A  L  G  T  I  A  C  F  F  W  G  W  G  K  W  K  V  S  V  R  L  K  S  E  *  P  N  S  L  S  S  F  G  V  L  L  P  V  F  F  F  L  K  R  L  I  T  F  S  F  K  P  A  R  Y  I  F  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0114J16.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="78224" stop="77982"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>240</number_coding_nucleotides>
                  <number_encoded_amino_acids>80</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RQQEALLMVRLLLRTSLRVSRLLRTPLRVSRLRRMWVLGNQTHQLVDRWRYAPQFCFTYPSNLSISLCIGDNCMFFLGVG*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0114J16.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="78399" stop="78172"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>225</number_coding_nucleotides>
                  <number_encoded_amino_acids>75</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FPRESAKRRRGRSEDEARAGKKERREMEAARRASLAEAEAHQIRASQIAAGASSSRTVETTGGTTYGAVVVEDIT*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C07HBa0114J16.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="3"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="78142" stop="77948"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>192</number_coding_nucleotides>
                  <number_encoded_amino_acids>64</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GCPDCVGCGFWETRPTSLLIDGAMRHSFASPTPLIFRFLYALGTIACFFWGWGKWKVSVRLKSE*</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="83257" PGL_stop="83991"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="83257" e_stop="83991"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.940"/>
        </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="0.940">
            <gDNA_exon_boundary e_start="83257" e_stop="83991" e_length="735"/>
          </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="83257" stop="83991"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U339767" 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>CACTATAACTCTAGTACCTAGAAAATAGGAGCAAAATTTCTCAAAAGCAAAGACTACTACGAGGAGTTCTTGCTCAGTCACTGTGTAGTTCTTCTAGGCTTCATTTAGGGCTTTATTAGCATAGTAAATTGGGTGAAGGATTTTGTTTCTTCTCTGTCCCAATACTACACCAAGAGCCACCCTACTAGCATCGCACATTACCTCAAATGGACTGTTCTAATCCGGAGAAATAATGATAGGCGCATACACTAACTTTTCTTTTAGCTCACCGAATGCTTTATGACAGGATTCATCAAAGCAAAATTTACATTCTTTCTCAAGCAATTTGCACAATGATTGTGCAATCTTTGAAAAGTCTTTGATGAATCTCTGATAAAAAAACTGCATGCCCAAGAAAGCTTCTCACACCTTTCACAGAGATCGGTGGGGGAAGTCTCTCTATTACCTTAACTTTGGCTCAATCAACCTCTATGCCCTTTTCTAAAATGCGATGACCCAACACAATACCCTCTTTCACCATGAAATGACACTTTTCCCAGTTTAGTACCAAATTGCAGTCTTCACATCTCTTAAGAACCTCAGATAAATTGGTCAAGCACCGCTCGAATGAATCACCAACCACAGAAAAATCATCCATAAAAACCTCTATAGTATCCTCCACCATGTTAGAAAATATTGACATCATACATCTCTGAAAGGTTGCGGGTGCATTGCACAACCCAAACGGCATTCTTC</gDNA_template>
            <first_frame> H  Y  N  S  S  T  *  K  I  G  A  K  F  L  K  S  K  D  Y  Y  E  E  F  L  L  S  H  C  V  V  L  L  G  F  I  *  G  F  I  S  I  V  N  W  V  K  D  F  V  S  S  L  S  Q  Y  Y  T  K  S  H  P  T  S  I  A  H  Y  L  K  W  T  V  L  I  R  R  N  N  D  R  R  I  H  *  L  F  F  *  L  T  E  C  F  M  T  G  F  I  K  A  K  F  T  F  F  L  K  Q  F  A  Q  *  L  C  N  L  *  K  V  F  D  E  S  L  I  K  K  L  H  A  Q  E  S  F  S  H  L  S  Q  R  S  V  G  E  V  S  L  L  P  *  L  W  L  N  Q  P  L  C  P  F  L  K  C  D  D  P  T  Q  Y  P  L  S  P  *  N  D  T  F  P  S  L  V  P  N  C  S  L  H  I  S  *  E  P  Q  I  N  W  S  S  T  A  R  M  N  H  Q  P  Q  K  N  H  P  *  K  P  L  *  Y  P  P  P  C  *  K  I  L  T  S  Y  I  S  E  R  L  R  V  H  C  T  T  Q  T  A  F  F </first_frame>
            <second_frame>  T  I  T  L  V  P  R  K  *  E  Q  N  F  S  K  A  K  T  T  T  R  S  S  C  S  V  T  V  *  F  F  *  A  S  F  R  A  L  L  A  *  *  I  G  *  R  I  L  F  L  L  C  P  N  T  T  P  R  A  T  L  L  A  S  H  I  T  S  N  G  L  F  *  S  G  E  I  M  I  G  A  Y  T  N  F  S  F  S  S  P  N  A  L  *  Q  D  S  S  K  Q  N  L  H  S  F  S  S  N  L  H  N  D  C  A  I  F  E  K  S  L  M  N  L  *  *  K  N  C  M  P  K  K  A  S  H  T  F  H  R  D  R  W  G  K  S  L  Y  Y  L  N  F  G  S  I  N  L  Y  A  L  F  *  N  A  M  T  Q  H  N  T  L  F  H  H  E  M  T  L  F  P  V  *  Y  Q  I  A  V  F  T  S  L  K  N  L  R  *  I  G  Q  A  P  L  E  *  I  T  N  H  R  K  I  I  H  K  N  L  Y  S  I  L  H  H  V  R  K  Y  *  H  H  T  S  L  K  G  C  G  C  I  A  Q  P  K  R  H  S   </second_frame>
            <third_frame>   L  *  L  *  Y  L  E  N  R  S  K  I  S  Q  K  Q  R  L  L  R  G  V  L  A  Q  S  L  C  S  S  S  R  L  H  L  G  L  Y  *  H  S  K  L  G  E  G  F  C  F  F  S  V  P  I  L  H  Q  E  P  P  Y  *  H  R  T  L  P  Q  M  D  C  S  N  P  E  K  *  *  *  A  H  T  L  T  F  L  L  A  H  R  M  L  Y  D  R  I  H  Q  S  K  I  Y  I  L  S  Q  A  I  C  T  M  I  V  Q  S  L  K  S  L  *  *  I  S  D  K  K  T  A  C  P  R  K  L  L  T  P  F  T  E  I  G  G  G  S  L  S  I  T  L  T  L  A  Q  S  T  S  M  P  F  S  K  M  R  *  P  N  T  I  P  S  F  T  M  K  *  H  F  S  Q  F  S  T  K  L  Q  S  S  H  L  L  R  T  S  D  K  L  V  K  H  R  S  N  E  S  P  T  T  E  K  S  S  I  K  T  S  I  V  S  S  T  M  L  E  N  I  D  I  I  H  L  *  K  V  A  G  A  L  H  N  P  N  G  I  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/">
            <none gDNA_id="C07HBa0114J16.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 35 chains have been computed
$ 
$ memory statistics:
$ 11224 bytes spliced alignments in total
$ 5 spliced alignments have been stored
$ 2244 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
$ 42 backtrace matrices have been allocated
$ 
$ date finished: 2008-02-20 07:30:02
-->
