<?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="2008-04-10 05:34:06"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0303A06-k0SfX/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-Lf1GlD/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-Lf1GlD/lycopersicum_combined_unigene_seqs" ref_id="SGN-U343604" ref_strand="+" ref_description="SGN-U343604        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT2G45400.1 | Symbol: None | dihydroflavonol 4-reductase family / dihydrokaempferol 4-reductase family, similar to dihydroflavonol 4-reductase (SP:P51102), vestitone reductase (Medicago sativa, GI:973249) | chr2:18710903-18713319 REVERSE | Aliases: F4L23.9 (evalue: 1e-42, score=107) genbank/nr: gi|6573167|gb|AAF17576.1| 2'-hydroxy isoflavone/dihydroflavonol reductase homolog [Glycine max](evalue: 4e-52, score=142)">
      <seq>gaaaagaaagaagagcgattaaaggagatatggaagaagtgatgttgaaggagaaaggaaaggtatgtgtagcaggaggaagtggttatcttggatcatggatggttatgagacttcttcaaattggttattatgttaacacaactattagagatggcaagaaggatgtgagctacctcagaaatctcccaggtgcacacgaaagattaaatatttttaatgttgatctacacaaaccacaaagtttcaatgcaccaaattgaaggctgcatcggtgtatttgatgttgcacatccaattgattttgaagacaaagaaacagaagaaagaataacacaaagatcaattaatgggacaataggtattttacaggcatatctcgattcaaaaacagttaaacacgttgtatacacttgtagtgcatcaaccgttgtgggtactggaagttccaacgtcataattgatgaatgctcgtggatagatgtagatgttatgagaacattgaagccttttgcaagttgttacgcgattagtaagacattaacagaaaaagcatctcttggatttgctgaaaaaaatggtattgatcttgtgactgtaattccaacttggatacatggtaccttttgttactcctcaaattcctggctctgttcgttcatcgatgaaaatgattcttgctacgtcttaaanaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0303A06-k0SfX/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0303A06.1" temp_strand="-" temp_description="C04HBa0303A06.1  CU468237.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0303A06 sequenced_by:sanger upload_account_name:uk">
        <position start="86024" stop="81807"/>
      </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="85741" g_stop="85588" g_length="154"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="153" r_length="153" r_score="0.981"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="85587" i_stop="82655" i_length="2933">
            <donor d_prob="0.933" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="82654" g_stop="82103" g_length="552"/>
          <reference_exon_boundary r_type="cDNA" r_start="154" r_stop="705" r_length="552" r_score="0.984"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0303A06.1" gen_strand="-" ref_id="SGN-U343604" ref_strand="+">
        <total_alignment_score>0.983</total_alignment_score>
        <cumulative_length_of_scored_exons>706</cumulative_length_of_scored_exons>
        <coverage percentage="1.001" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0303A06.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U343604" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="85741" e_stop="85588"/>
          <exon e_start="82654" e_stop="82103"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAAAAGAAAGAAGAGATGAATAAAGGAGATATGGAAGAAGTGATGTTGAAGGAGAAAGGAAAGGTATGTGTAGCAGGAGGAAGTGGTTATCTTGGATCATGGATGGTTATGAGACTTCTTCAAATTGGTTATTATGTTAACACAACTATTAGAGGTAATTTCTTAGTTGTTTAATTCTACTTTAAATCTTTCGTAAGCTCATCATATCGAGTAATATAAATCTATCATGTAATTGGCGCTTAAGTTTACGTTTCTTTACTTTGTGTATGCACAATTAATCACTCTTTAACGGAGTAACTTCCATTTCTATTTTGTGATGGCATGGTGTTTAAGCGGAGCTTACACTAAAATAAAAATAATTTTTAGTAGCATTAAATATTGATATTAATAAAGATTGCTAAAGTTTTTGTCGGCATTTGTTAAGTGTTATTAGAACTAATGTTGCTAAAGGTTTTAGGCACATATACCAAGAGTGTTAATTATCTTTCCACTAAAAATACATATTTAATTGCCGCTAATAATCATTTTTGATGTATTATCATTGACATATCTTAAAGTTGAGACTCACGTTAAGTAGGTTTTGATTATTTTAAATACTTTAAGTAAAGGTTTGATGTGTGTTATTTTAATGCTTTATGTTTAGTGACAGGCGTATTTCACTCATTTTTAGTGCGTGAGGAACAATTTTTAATGTAATATTATCGCGCCTCTTTGCTTTCATTTTTGTTCCTGCCCCCTAAATCACCTCCATCGTGAAAAGATCTTGATAAATATTTTTACAAAACATAATATAAAGAAAATAATAAAAATAAAAAACATTAGACTAATTTAATTTTTATTATAAGAACATGAAAAGGCAAGATGTGAAATGAAAGGAAAATAAAAGAAGAGCCCTAGACCCTCATATAAAGATAGTATCAATAGAATATTTGTCCAAATCAAATCTACGACACAAAAAAAAAATTGAAAAGAAAAAAACAAAGTGAAGGAAGAACAAAAGGGGATTTCAAAAGAGTATGTGCCTTCAAGAAAGGGGAAGGTGGGGTGGGAGGTAAGTTGGAGGGGATAAACGATCGGAGTAGTCATTTTATTATTATTATTTTTATTTAAAAAGAAAACCTCAACAGAGATAAATACAAGTAAAAGGGGCAAATCTTACCTTACCAATTGTAATGAGGTACAATACCTTTACTAATTAAATCGCATGAAGAAAACAAAAGTTAGAGAGAACTAAGTATTGTATGATCATCATAGAGTTTATAATACAATGTATGATGATATTACAAATGAGAATGCTTAAGTAGTACAAAAGTATAAAGCCATGATGAGATTTGAGTGATTAAACTCAAACTTAATGTTACAAAAGTATGAACTAAAAAAGATAGATTGCCCTTCTAAAGTAACTTGGAGTGTTTTTCTCTTGTCTTCTGCTTCAAATCTGTCTAACAATATTTGATAGTTCATCAAATCTTCTTAGATTTATTGGATCTCGTAAAGTTGTTGACACTGTCATGTGATTCTGCTTTATCAGTCGCATCGGTAGGTGCCTTGGAAGAAACTCCTTAGTCATCTTACCGTCCCAACTATTTTTTCTTCCAAGCTTCTTTTTTTTTTGTTTCATTGTTGCCTAGGAGAAATATCTGCATCCCTAGCTGCATTTACAAAACAATAATTCAACATATCCTATTCTTCACTTCATCAAAGGTGTCCTTGTCTTGTAGGTTAGCTAATTTATTTTTGGAGAAAGAACTACTACAAACATCTATTTGTGTCATTTGTCTCAATCTATGTGATGCATATTATTTTTCAAGTGTCAATTAAGCTTGATCAAAAATTTGTTTATATTTTTTTTTATTTTTTAAGAAATGAAATTTGTATATTTGTAAACTATTTTTTAAAATAATAAGGGTAAATGCACAAGTACCCTCTAGACTATGACCGAAATCTCAGAGAAACACCTTAACTAACTAAGGTCCTATTACCCCCTGAACTTATCTTTTTTTTGTAATTTTGTGCACCTTTTTGTCTTATGTGGCATCTAAATATCTCTCACGCCATCAATTGCGTGGAGTCACGGAGTGTGTCTCGTAAAACAAAAGGTGTATAAAATTACGAAATAAATAAGTTTAGAAGAATAATAGGACCTTATTTAGTTAAGGCGTGTCTCTGAAATTTCAATCATAGTCTAGGGTGCATTTTCCCCAAATAAGAATAATATAAGTCACAATAATCAATAATTAAAAATAGGGATAATGTCCAAGTACTCCCTCAACCTATGCCCGAAATCTCAGAGACACACTTATACTATATTAAGGTCCTACCCTGAACTTATTTTATTAATAATTTTTTACCCCTTTTCGACCTACGTGACACTATCTTGTGGGCCCAACGATGGTTGACTTTTTTTTTTTCAAACTAGTGCCACGTAGGCTAAAAGGGGTAGAAAATTACTTATAAAATAAGTTCAGGGGGTAATAGGACCTTAATATAGTATAAGTGTGTCTCTGGAATTTCGGGCATAGGTTGAGAGGGTACTTGTGCATTTTTCCTTTAAAATATTTAAAAGAAATACTAATTTTTTTTAATAGTACCTCCACATAAACTAGAACAGACAGTGACGAAGCCAGAATTGTTGCCAAGACTGTTCATACATTAGGACAAGTAAAAATATAAACCTTGCTAGTCGTGTATTTGCTTGACATTTTCATCTCGACCTAGTTGATTTTGAGGTGCCAAACTTGTTTTGGATACTCTAAAAAAATCTTTCTCCAAACTCATTGAACTCCAAACTGGAATAGTAGTCAAGTATATCAAACTTACTAAAAATCATCCACAATACACCAAAATAGTTGATCAATACTCAAATAAATAAAATAGCTTTTAAAATAAAACTTATTAAGATATTCAAGTATTTCAAACACATGATTAGAAAAAATTAAACTAAAGGAAAAAAATAATTGAGATATACCTTTTCACACTTCAATGATGGTTGATGAAGAAATATACTGAACAGAGTATAACTAATTTATGTCATTGTTGTCCAGTTAAAATTATATATCTTTTTAGCCTAACTATCATTGATTGTAGATGGCAAGAAGGATGTGAGCTACCTCAGAAATCTCCCAGGTGCACACGAAAGATTAAATATTTTTAATGTTGATCTACACAAACCACAAAGTTTCAATGCACCAAATTGAAGGCTGCATCGGTGTATTTGATGTTGCACATCCAATTGATTTTGAAGACAAAGAAACAGAAGAAAGAATAACACAAAGATCAATTAATGGGACAATAGGTATTTTACAGGCATATCTCGATTCAAAAACAGTTAAACACGTTGTATACACTTGTAGTGCATCAACCGTTGTGGGTACTGGAAGTTCCAACGTCATAATTGATGAATGCTCGTGGATAGATGTAGATGTTATGAGAACATTGAAGCCTTTTGCAAGTTGTTACGCGATTAGTAAGACATTAACAGAAAAAGCATCTCTTGGATTTGCTGAAAAAAATGGTATTGATCTTGTGACTGTAATTCCAACTTGGATACATGGTACCTTTTGTTACTCCTCAAATTCCTGGCTCTGTTCGTTCATCGATGAAAATGATTCTTGCTACGTCTTAAAATATCATAACTTT</genome_strand>
        <mrna_strand>GAAAAGAAAGAAGAG-CGATTAAAGGAGATATGGAAGAAGTGATGTTGAAGGAGAAAGGAAAGGTATGTGTAGCAGGAGGAAGTGGTTATCTTGGATCATGGATGGTTATGAGACTTCTTCAAATTGGTTATTATGTTAACACAACTATTAGAG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATGGCAAGAAGGATGTGAGCTACCTCAGAAATCTCCCAGGTGCACACGAAAGATTAAATATTTTTAATGTTGATCTACACAAACCACAAAGTTTCAATGCACCAAATTGAAGGCTGCATCGGTGTATTTGATGTTGCACATCCAATTGATTTTGAAGACAAAGAAACAGAAGAAAGAATAACACAAAGATCAATTAATGGGACAATAGGTATTTTACAGGCATATCTCGATTCAAAAACAGTTAAACACGTTGTATACACTTGTAGTGCATCAACCGTTGTGGGTACTGGAAGTTCCAACGTCATAATTGATGAATGCTCGTGGATAGATGTAGATGTTATGAGAACATTGAAGCCTTTTGCAAGTTGTTACGCGATTAGTAAGACATTAACAGAAAAAGCATCTCTTGGATTTGCTGAAAAAAATGGTATTGATCTTGTGACTGTAATTCCAACTTGGATACATGGTACCTTTTGTTACTCCTCAAATTCCTGGCTCTGTTCGTTCATCGATGAAAATGATTCTTGCTACGTCTTAAANAAAAAAAAAAAA</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-Lf1GlD/lycopersicum_combined_unigene_seqs" ref_id="SGN-U344585" ref_strand="+" ref_description="SGN-U344585        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT2G45400.1 | Symbol: None | dihydroflavonol 4-reductase family / dihydrokaempferol 4-reductase family, similar to dihydroflavonol 4-reductase (SP:P51102), vestitone reductase (Medicago sativa, GI:973249) | chr2:18710903-18713319 REVERSE | Aliases: F4L23.9 (evalue: 1e-11, score=45.4) genbank/nr: gi|6573167|gb|AAF17576.1| 2'-hydroxy isoflavone/dihydroflavonol reductase homolog [Glycine max](evalue: 1e-10, score=53.9)">
      <seq>ctctggaatttcgggcataggttgagagggtacttgtgcatttttcctttaaaatatttaaaagaaatactaattttttttaatagtacctccacataaactagaacagacagtgacgaagccagaattgttgccaagactgttcatacattaggacaagtaaaaatataaaccttgctagtcgtgtatttgcttgacattttcatctcgacctagttgattttgaggtgccaaacttgttttggatactctaaaaaaatctttctccaaactcattgaactccaaactggaatagtagtcaagtatatcaaacttactaaaaatcatccacaatacaccaaaatagttgatcaatactcaaataaataaaatagcttttaaaataaaacttattaagatattcaagtatttcaaacacatgattagaaaaaattaaactaaaggaaaaaaataattgagatataccttttcacacttcaatgatggttgatgaagaaatatactgaacagagtataactaatttatgtcattgttgcccagttaaaattatatatctttttagcctaactatcattgattgtagatggcaagaaggatgtgagctacc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0303A06-k0SfX/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0303A06.1" temp_strand="-" temp_description="C04HBa0303A06.1  CU468237.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0303A06 sequenced_by:sanger upload_account_name:uk">
        <position start="83539" stop="82331"/>
      </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="83239" g_stop="82631" g_length="609"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="609" r_length="609" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0303A06.1" gen_strand="-" ref_id="SGN-U344585" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>609</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0303A06.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U344585" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="83239" e_stop="82631"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCTGGAATTTCGGGCATAGGTTGAGAGGGTACTTGTGCATTTTTCCTTTAAAATATTTAAAAGAAATACTAATTTTTTTTAATAGTACCTCCACATAAACTAGAACAGACAGTGACGAAGCCAGAATTGTTGCCAAGACTGTTCATACATTAGGACAAGTAAAAATATAAACCTTGCTAGTCGTGTATTTGCTTGACATTTTCATCTCGACCTAGTTGATTTTGAGGTGCCAAACTTGTTTTGGATACTCTAAAAAAATCTTTCTCCAAACTCATTGAACTCCAAACTGGAATAGTAGTCAAGTATATCAAACTTACTAAAAATCATCCACAATACACCAAAATAGTTGATCAATACTCAAATAAATAAAATAGCTTTTAAAATAAAACTTATTAAGATATTCAAGTATTTCAAACACATGATTAGAAAAAATTAAACTAAAGGAAAAAAATAATTGAGATATACCTTTTCACACTTCAATGATGGTTGATGAAGAAATATACTGAACAGAGTATAACTAATTTATGTCATTGTTGTCCAGTTAAAATTATATATCTTTTTAGCCTAACTATCATTGATTGTAGATGGCAAGAAGGATGTGAGCTACC</genome_strand>
        <mrna_strand>CTCTGGAATTTCGGGCATAGGTTGAGAGGGTACTTGTGCATTTTTCCTTTAAAATATTTAAAAGAAATACTAATTTTTTTTAATAGTACCTCCACATAAACTAGAACAGACAGTGACGAAGCCAGAATTGTTGCCAAGACTGTTCATACATTAGGACAAGTAAAAATATAAACCTTGCTAGTCGTGTATTTGCTTGACATTTTCATCTCGACCTAGTTGATTTTGAGGTGCCAAACTTGTTTTGGATACTCTAAAAAAATCTTTCTCCAAACTCATTGAACTCCAAACTGGAATAGTAGTCAAGTATATCAAACTTACTAAAAATCATCCACAATACACCAAAATAGTTGATCAATACTCAAATAAATAAAATAGCTTTTAAAATAAAACTTATTAAGATATTCAAGTATTTCAAACACATGATTAGAAAAAATTAAACTAAAGGAAAAAAATAATTGAGATATACCTTTTCACACTTCAATGATGGTTGATGAAGAAATATACTGAACAGAGTATAACTAATTTATGTCATTGTTGCCCAGTTAAAATTATATATCTTTTTAGCCTAACTATCATTGATTGTAGATGGCAAGAAGGATGTGAGCTACC</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-Lf1GlD/lycopersicum_combined_unigene_seqs" ref_id="SGN-U345812" ref_strand="+" ref_description="SGN-U345812        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-39, score=159) genbank/nr: gi|77548751|gb|ABA91548.1| retrotransposon protein, putative, Ty1-copia sub-class [Oryza sativa (japonica cultivar-group)] >gi|62701868|gb|AAX92941.1| retrotransposon protein, putative, Ty1-copia sub-class [Oryza sativa (japonica cultivar-group)] (evalue: 1e-101, score=372)">
      <seq>gtttccaagttccagggaaggaaaatcacgtctgcaagttgaagaagtccttatatggacttaagcagtctccaaggcagtggtataaaaggtttgacagctatatggtgaagttgggctatactcggagctcatatgattgttgtgtctactacaataggctcaatgatgattcattcatctatctggtgctttatgtagatgatatgttgatagctgcaaagaagaagtatgacattcagaagctgaagggtttacttagtgctgagtttgagatgaaggatctgggagccgctcggaagattttagggatggagatcattagagacagagagagaaggaaacttttcttgtcacagagaagctacattcagaaggtcttggcgaggtttggcatgtcttcatctaagcccattgatacccccagtgctgccaatatccatctcactgccatgttcgctccacagtcagaagaagagaaggagtatatgtcacgagtcccttatgccagtgccgtaagaagtttgatgtatgctatggtctgtacaaggccagatttagcacatgcagtcagtgtagtgagcagattcatgggacaaccagggagagaacattggcaggctgtgaagagaattttccggtaccttagaggtacatctgacgttggtctcatttatggaggtgatactcagtgcttggttactggctattctgattcagactatgctggagatgttgacacaagaagatcgatgactggctatgtgtttaccctgggaggatctgtcgtcagttggaaggcaacttt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0303A06-k0SfX/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0303A06.1" temp_strand="-" temp_description="C04HBa0303A06.1  CU468237.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0303A06 sequenced_by:sanger upload_account_name:uk">
        <position start="97290" stop="95883"/>
      </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="96990" g_stop="96183" g_length="808"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="808" r_length="808" r_score="0.973"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0303A06.1" gen_strand="-" ref_id="SGN-U345812" ref_strand="+">
        <total_alignment_score>0.973</total_alignment_score>
        <cumulative_length_of_scored_exons>808</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0303A06.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U345812" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="96990" e_stop="96183"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTTTCCAAGTTCCAGGGAAGGAAAATCACGTTTGCAAGTTGAAGAAGTCCTTATATGGACTTGAGCAGTCTCCAAGGCAGTGGTACAAAAGGTTTGATAGCTATATGGTGAAGTTGGGATATACTCGGAGCTCATATGATTGTTGTGTCTACTACAATAGGCTCAAGGATGATTCATTCATCTATCTGGTGCTTTATGTAGATGATATGTTGATAGCTGCAAAGAAGAAGTATGACATTCAGAAGCTGAAGGGTTTACTTAGTGCTGAGTTTGAGATGAAGGATCTGGGAGCCGCTCGGAAGATTCTAGGGATGGAGATCATTAGAGACAGAGAGAGAATGAAACTTTTCTTTTCACAGAGAAGCTACATTCAGAAGGTCTTGGCGAGGTTTGGCATGTCTGTATCTAAGCCTATTGATACCCCCAGTGCTGCCAATATCCATTTCACTGCCATGTTCGCTCCACAGTCAGAAGAAGAGAAGGAGTATATGTCACGAGTCCCTTATGCCAGTGCCATAGGAAGTTTGATGTATGCTATGGTCTGTACAAGGCCAGATTTAGCACATGCAGTCAGTGTAGTGAGCTGATTCATGGGACAACTAGGGAAAGAACATTGGCAGGCTGTGAAGAGAATTTTCCGGTACCTTAGAGGTACATCTGACGTTGGTCTCATTTATGGAGGTGATACTCAGTGTTTGGTTACTGGCTATTCTGATTCTGACTATGCTGGAGATGTTGACACAAGAAGATTGATGACTGGCTATGTGTTTACCCTTGGAGGATCTGTCGTCAGTTGGAAGGCAACTTT</genome_strand>
        <mrna_strand>GTTTCCAAGTTCCAGGGAAGGAAAATCACGTCTGCAAGTTGAAGAAGTCCTTATATGGACTTAAGCAGTCTCCAAGGCAGTGGTATAAAAGGTTTGACAGCTATATGGTGAAGTTGGGCTATACTCGGAGCTCATATGATTGTTGTGTCTACTACAATAGGCTCAATGATGATTCATTCATCTATCTGGTGCTTTATGTAGATGATATGTTGATAGCTGCAAAGAAGAAGTATGACATTCAGAAGCTGAAGGGTTTACTTAGTGCTGAGTTTGAGATGAAGGATCTGGGAGCCGCTCGGAAGATTTTAGGGATGGAGATCATTAGAGACAGAGAGAGAAGGAAACTTTTCTTGTCACAGAGAAGCTACATTCAGAAGGTCTTGGCGAGGTTTGGCATGTCTTCATCTAAGCCCATTGATACCCCCAGTGCTGCCAATATCCATCTCACTGCCATGTTCGCTCCACAGTCAGAAGAAGAGAAGGAGTATATGTCACGAGTCCCTTATGCCAGTGCCGTAAGAAGTTTGATGTATGCTATGGTCTGTACAAGGCCAGATTTAGCACATGCAGTCAGTGTAGTGAGCAGATTCATGGGACAACCAGGGAGAGAACATTGGCAGGCTGTGAAGAGAATTTTCCGGTACCTTAGAGGTACATCTGACGTTGGTCTCATTTATGGAGGTGATACTCAGTGCTTGGTTACTGGCTATTCTGATTCAGACTATGCTGGAGATGTTGACACAAGAAGATCGATGACTGGCTATGTGTTTACCCTGGGAGGATCTGTCGTCAGTTGGAAGGCAACTTT</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-Lf1GlD/lycopersicum_combined_unigene_seqs" ref_id="SGN-U330105" ref_strand="+" ref_description="SGN-U330105        Tomato 200607 #1 [2 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: 3e-26, score=115) genbank/nr: putative(evalue: 9e-48, score=192)">
      <seq>tacgtcagaaactaggagtcttgacaaacaggtggagtttcaagtcattcagaacgagagcgatttaaaggaacctgaagaggaggatcaagagccacagactgaaactgatattccagaatctatgccatcagatatccatcagagtatagctcaagatcggccaaggagggttggagttcggccacctacgaggtatggttttgaggacatggtgggttatgcactgcaggttgctgaagaggtagatacatctgagccgtctacttacaaagaagccattttaagttctgattctgaaaaatggtttgccgctatgggagatgagatggagtccctacacaagaatcagacatgggatctggtcatacagccttcggggagaaagattattacttgcaaatgggttttcaagaagaaggaagggatatcaccagcagaaggagtcaagtataaagtcagggttgttgctagaggtttcaaccaaagagagggagtggactacaatgagatcttctcaccagtggtcagacatacttccatccgagtgttactagcgatagttgcacatcagaatctggagcttgaaacacttgatgtgaagacagcgtttctacatggagagttggaggaagagatatacatgact</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0303A06-k0SfX/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0303A06.1" temp_strand="-" temp_description="C04HBa0303A06.1  CU468237.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0303A06 sequenced_by:sanger upload_account_name:uk">
        <position start="97947" stop="96701"/>
      </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="97647" g_stop="97001" g_length="647"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="649" r_length="649" r_score="0.955"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0303A06.1" gen_strand="-" ref_id="SGN-U330105" ref_strand="+">
        <total_alignment_score>0.955</total_alignment_score>
        <cumulative_length_of_scored_exons>647</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0303A06.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U330105" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="97647" e_stop="97001"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TACGTCAGAAACTGGGAGTCTTGATAAATAGGTGGAGTTTCAAGTCATTCAGAACGAGAGCGATTTAAAAGAACCTGAAGAGGAGGATCAAGAGCCACAGACAGAAACTGATATCCCAGAATCTATGCCATGAGATATCCATCAGAGTATAGCTCAAGATCGGCCAAAGAGGGTTGGAGTTCAGCCACCTACGAGGTATGGTTTTGAGGACATGGTGGGTTATGCACTGCAGGTTGCTGAAGAGGTAGATACATCTGAGCCATCTACTTACAAAGAAGCCATTTTAAGTCCTGATTCTTAAAAATGGTTTGCTGCTAT-GG-GATGAGATGGAGTCCCTACACAAGAATCAGACATGGGATCTGGTCATACAGCCTTCGGGGAGAAAGATTATTACTTGCAAATGGGTTTTCAAGAAGAAGGAAGGGATATCACCAGCAGAAAGAATCATCTATAAAGCCAGGGTTGTTGCCAGAGGTTTCAACCAAAGAGAGGGAGTGAACTACAATGAGATCTTTTCACCAGTGGTCAGACATACTTCCATCCGAGTGTTACTAGCGATAGTTACACATCAGAATCTGGAGCTTGAACAACTTGATGTGAAGACAACGTTTCTACATGGAGAGTTGGAGGAAGAGATATACATGACT</genome_strand>
        <mrna_strand>TACGTCAGAAACTAGGAGTCTTGACAAACAGGTGGAGTTTCAAGTCATTCAGAACGAGAGCGATTTAAAGGAACCTGAAGAGGAGGATCAAGAGCCACAGACTGAAACTGATATTCCAGAATCTATGCCATCAGATATCCATCAGAGTATAGCTCAAGATCGGCCAAGGAGGGTTGGAGTTCGGCCACCTACGAGGTATGGTTTTGAGGACATGGTGGGTTATGCACTGCAGGTTGCTGAAGAGGTAGATACATCTGAGCCGTCTACTTACAAAGAAGCCATTTTAAGTTCTGATTCTGAAAAATGGTTTGCCGCTATGGGAGATGAGATGGAGTCCCTACACAAGAATCAGACATGGGATCTGGTCATACAGCCTTCGGGGAGAAAGATTATTACTTGCAAATGGGTTTTCAAGAAGAAGGAAGGGATATCACCAGCAGAAGGAGTCAAGTATAAAGTCAGGGTTGTTGCTAGAGGTTTCAACCAAAGAGAGGGAGTGGACTACAATGAGATCTTCTCACCAGTGGTCAGACATACTTCCATCCGAGTGTTACTAGCGATAGTTGCACATCAGAATCTGGAGCTTGAAACACTTGATGTGAAGACAGCGTTTCTACATGGAGAGTTGGAGGAAGAGATATACATGACT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>4</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="-" PGL_start="85741" PGL_stop="82103"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="85741" e_stop="85588"/>
            <exon e_start="82654" e_stop="82103"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.933" acc_prob="0.995" e_score="0.981"/>
          <exon-only e_score="0.984"/>
        </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="0.981">
            <gDNA_exon_boundary e_start="85741" e_stop="85588" e_length="154"/>
          </exon>
          <intron i_serial="1" don_prob="0.933" acc_prob="0.995">
            <gDNA_intron_boundary i_start="85587" i_stop="82655" i_length="2933"/>
          </intron>
          <exon e_serial="2" e_score="0.984">
            <gDNA_exon_boundary e_start="82654" e_stop="82103" e_length="552"/>
          </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="85741" stop="85588"/>
              <exon start="82654" stop="82103"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U343604" 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>GAAAAGAAAGAAGAGATGAATAAAGGAGATATGGAAGAAGTGATGTTGAAGGAGAAAGGAAAGGTATGTGTAGCAGGAGGAAGTGGTTATCTTGGATCATGGATGGTTATGAGACTTCTTCAAATTGGTTATTATGTTAACACAACTATTAGAG : ATGGCAAGAAGGATGTGAGCTACCTCAGAAATCTCCCAGGTGCACACGAAAGATTAAATATTTTTAATGTTGATCTACACAAACCACAAAGTTTCAATGCACCAAATTGAAGGCTGCATCGGTGTATTTGATGTTGCACATCCAATTGATTTTGAAGACAAAGAAACAGAAGAAAGAATAACACAAAGATCAATTAATGGGACAATAGGTATTTTACAGGCATATCTCGATTCAAAAACAGTTAAACACGTTGTATACACTTGTAGTGCATCAACCGTTGTGGGTACTGGAAGTTCCAACGTCATAATTGATGAATGCTCGTGGATAGATGTAGATGTTATGAGAACATTGAAGCCTTTTGCAAGTTGTTACGCGATTAGTAAGACATTAACAGAAAAAGCATCTCTTGGATTTGCTGAAAAAAATGGTATTGATCTTGTGACTGTAATTCCAACTTGGATACATGGTACCTTTTGTTACTCCTCAAATTCCTGGCTCTGTTCGTTCATCGATGAAAATGATTCTTGCTACGTCTTAAAATATCATAACTTT</gDNA_template>
            <first_frame> E  K  K  E  E  M  N  K  G  D  M  E  E  V  M  L  K  E  K  G  K  V  C  V  A  G  G  S  G  Y  L  G  S  W  M  V  M  R  L  L  Q  I  G  Y  Y  V  N  T  T  I  R   : D  G  K  K  D  V  S  Y  L  R  N  L  P  G  A  H  E  R  L  N  I  F  N  V  D  L  H  K  P  Q  S  F  N  A  P  N  *  R  L  H  R  C  I  *  C  C  T  S  N  *  F  *  R  Q  R  N  R  R  K  N  N  T  K  I  N  *  W  D  N  R  Y  F  T  G  I  S  R  F  K  N  S  *  T  R  C  I  H  L  *  C  I  N  R  C  G  Y  W  K  F  Q  R  H  N  *  *  M  L  V  D  R  C  R  C  Y  E  N  I  E  A  F  C  K  L  L  R  D  *  *  D  I  N  R  K  S  I  S  W  I  C  *  K  K  W  Y  *  S  C  D  C  N  S  N  L  D  T  W  Y  L  L  L  L  L  K  F  L  A  L  F  V  H  R  *  K  *  F  L  L  R  L  K  I  S  *  L  </first_frame>
            <second_frame>  K  R  K  K  R  *  I  K  E  I  W  K  K  *  C  *  R  R  K  E  R  Y  V  *  Q  E  E  V  V  I  L  D  H  G  W  L  *  D  F  F  K  L  V  I  M  L  T  Q  L  L  E  :  M  A  R  R  M  *  A  T  S  E  I  S  Q  V  H  T  K  D  *  I  F  L  M  L  I  Y  T  N  H  K  V  S  M  H  Q  I  E  G  C  I  G  V  F  D  V  A  H  P  I  D  F  E  D  K  E  T  E  E  R  I  T  Q  R  S  I  N  G  T  I  G  I  L  Q  A  Y  L  D  S  K  T  V  K  H  V  V  Y  T  C  S  A  S  T  V  V  G  T  G  S  S  N  V  I  I  D  E  C  S  W  I  D  V  D  V  M  R  T  L  K  P  F  A  S  C  Y  A  I  S  K  T  L  T  E  K  A  S  L  G  F  A  E  K  N  G  I  D  L  V  T  V  I  P  T  W  I  H  G  T  F  C  Y  S  S  N  S  W  L  C  S  F  I  D  E  N  D  S  C  Y  V  L  K  Y  H  N  F </second_frame>
            <third_frame>   K  E  R  R  D  E  *  R  R  Y  G  R  S  D  V  E  G  E  R  K  G  M  C  S  R  R  K  W  L  S  W  I  M  D  G  Y  E  T  S  S  N  W  L  L  C  *  H  N  Y  *  R :   W  Q  E  G  C  E  L  P  Q  K  S  P  R  C  T  R  K  I  K  Y  F  *  C  *  S  T  Q  T  T  K  F  Q  C  T  K  L  K  A  A  S  V  Y  L  M  L  H  I  Q  L  I  L  K  T  K  K  Q  K  K  E  *  H  K  D  Q  L  M  G  Q  *  V  F  Y  R  H  I  S  I  Q  K  Q  L  N  T  L  Y  T  L  V  V  H  Q  P  L  W  V  L  E  V  P  T  S  *  L  M  N  A  R  G  *  M  *  M  L  *  E  H  *  S  L  L  Q  V  V  T  R  L  V  R  H  *  Q  K  K  H  L  L  D  L  L  K  K  M  V  L  I  L  *  L  *  F  Q  L  G  Y  M  V  P  F  V  T  P  Q  I  P  G  S  V  R  S  S  M  K  M  I  L  A  T  S  *  N  I  I  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="C04HBa0303A06.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="82597" stop="82103"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>495</number_coding_nucleotides>
                  <number_encoded_amino_acids>165</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IFLMLIYTNHKVSMHQIEGCIGVFDVAHPIDFEDKETEERITQRSINGTIGILQAYLDSKTVKHVVYTCSASTVVGTGSSNVIIDECSWIDVDVMRTLKPFASCYAISKTLTEKASLGFAEKNGIDLVTVIPTWIHGTFCYSSNSWLCSFIDENDSCYVLKYHNF</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
      <AGS_information>
        <AGS_line AGS_serial="2">
          <exon_coordinates>
            <exon e_start="83239" e_stop="82631"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.998"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.998">
            <gDNA_exon_boundary e_start="83239" e_stop="82631" e_length="609"/>
          </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="83239" stop="82631"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U344585" 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="2" gDNA_strand="-"/>
          <translation>
            <gDNA_template>CTCTGGAATTTCGGGCATAGGTTGAGAGGGTACTTGTGCATTTTTCCTTTAAAATATTTAAAAGAAATACTAATTTTTTTTAATAGTACCTCCACATAAACTAGAACAGACAGTGACGAAGCCAGAATTGTTGCCAAGACTGTTCATACATTAGGACAAGTAAAAATATAAACCTTGCTAGTCGTGTATTTGCTTGACATTTTCATCTCGACCTAGTTGATTTTGAGGTGCCAAACTTGTTTTGGATACTCTAAAAAAATCTTTCTCCAAACTCATTGAACTCCAAACTGGAATAGTAGTCAAGTATATCAAACTTACTAAAAATCATCCACAATACACCAAAATAGTTGATCAATACTCAAATAAATAAAATAGCTTTTAAAATAAAACTTATTAAGATATTCAAGTATTTCAAACACATGATTAGAAAAAATTAAACTAAAGGAAAAAAATAATTGAGATATACCTTTTCACACTTCAATGATGGTTGATGAAGAAATATACTGAACAGAGTATAACTAATTTATGTCATTGTTGTCCAGTTAAAATTATATATCTTTTTAGCCTAACTATCATTGATTGTAGATGGCAAGAAGGATGTGAGCTACC</gDNA_template>
            <first_frame> L  W  N  F  G  H  R  L  R  G  Y  L  C  I  F  P  L  K  Y  L  K  E  I  L  I  F  F  N  S  T  S  T  *  T  R  T  D  S  D  E  A  R  I  V  A  K  T  V  H  T  L  G  Q  V  K  I  *  T  L  L  V  V  Y  L  L  D  I  F  I  S  T  *  L  I  L  R  C  Q  T  C  F  G  Y  S  K  K  I  F  L  Q  T  H  *  T  P  N  W  N  S  S  Q  V  Y  Q  T  Y  *  K  S  S  T  I  H  Q  N  S  *  S  I  L  K  *  I  K  *  L  L  K  *  N  L  L  R  Y  S  S  I  S  N  T  *  L  E  K  I  K  L  K  E  K  N  N  *  D  I  P  F  H  T  S  M  M  V  D  E  E  I  Y  *  T  E  Y  N  *  F  M  S  L  L  S  S  *  N  Y  I  S  F  *  P  N  Y  H  *  L  *  M  A  R  R  M  *  A  T </first_frame>
            <second_frame>  S  G  I  S  G  I  G  *  E  G  T  C  A  F  F  L  *  N  I  *  K  K  Y  *  F  F  L  I  V  P  P  H  K  L  E  Q  T  V  T  K  P  E  L  L  P  R  L  F  I  H  *  D  K  *  K  Y  K  P  C  *  S  C  I  C  L  T  F  S  S  R  P  S  *  F  *  G  A  K  L  V  L  D  T  L  K  K  S  F  S  K  L  I  E  L  Q  T  G  I  V  V  K  Y  I  K  L  T  K  N  H  P  Q  Y  T  K  I  V  D  Q  Y  S  N  K  *  N  S  F  *  N  K  T  Y  *  D  I  Q  V  F  Q  T  H  D  *  K  K  L  N  *  R  K  K  I  I  E  I  Y  L  F  T  L  Q  *  W  L  M  K  K  Y  T  E  Q  S  I  T  N  L  C  H  C  C  P  V  K  I  I  Y  L  F  S  L  T  I  I  D  C  R  W  Q  E  G  C  E  L   </second_frame>
            <third_frame>   L  E  F  R  A  *  V  E  R  V  L  V  H  F  S  F  K  I  F  K  R  N  T  N  F  F  *  *  Y  L  H  I  N  *  N  R  Q  *  R  S  Q  N  C  C  Q  D  C  S  Y  I  R  T  S  K  N  I  N  L  A  S  R  V  F  A  *  H  F  H  L  D  L  V  D  F  E  V  P  N  L  F  W  I  L  *  K  N  L  S  P  N  S  L  N  S  K  L  E  *  *  S  S  I  S  N  L  L  K  I  I  H  N  T  P  K  *  L  I  N  T  Q  I  N  K  I  A  F  K  I  K  L  I  K  I  F  K  Y  F  K  H  M  I  R  K  N  *  T  K  G  K  K  *  L  R  Y  T  F  S  H  F  N  D  G  *  *  R  N  I  L  N  R  V  *  L  I  Y  V  I  V  V  Q  L  K  L  Y  I  F  L  A  *  L  S  L  I  V  D  G  K  K  D  V  S  Y  </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="C04HBa0303A06.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="96990" PGL_stop="96183"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="96990" e_stop="96183"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.973"/>
        </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="0.973">
            <gDNA_exon_boundary e_start="96990" e_stop="96183" e_length="808"/>
          </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="96990" stop="96183"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U345812" 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>GTTTCCAAGTTCCAGGGAAGGAAAATCACGTTTGCAAGTTGAAGAAGTCCTTATATGGACTTGAGCAGTCTCCAAGGCAGTGGTACAAAAGGTTTGATAGCTATATGGTGAAGTTGGGATATACTCGGAGCTCATATGATTGTTGTGTCTACTACAATAGGCTCAAGGATGATTCATTCATCTATCTGGTGCTTTATGTAGATGATATGTTGATAGCTGCAAAGAAGAAGTATGACATTCAGAAGCTGAAGGGTTTACTTAGTGCTGAGTTTGAGATGAAGGATCTGGGAGCCGCTCGGAAGATTCTAGGGATGGAGATCATTAGAGACAGAGAGAGAATGAAACTTTTCTTTTCACAGAGAAGCTACATTCAGAAGGTCTTGGCGAGGTTTGGCATGTCTGTATCTAAGCCTATTGATACCCCCAGTGCTGCCAATATCCATTTCACTGCCATGTTCGCTCCACAGTCAGAAGAAGAGAAGGAGTATATGTCACGAGTCCCTTATGCCAGTGCCATAGGAAGTTTGATGTATGCTATGGTCTGTACAAGGCCAGATTTAGCACATGCAGTCAGTGTAGTGAGCTGATTCATGGGACAACTAGGGAAAGAACATTGGCAGGCTGTGAAGAGAATTTTCCGGTACCTTAGAGGTACATCTGACGTTGGTCTCATTTATGGAGGTGATACTCAGTGTTTGGTTACTGGCTATTCTGATTCTGACTATGCTGGAGATGTTGACACAAGAAGATTGATGACTGGCTATGTGTTTACCCTTGGAGGATCTGTCGTCAGTTGGAAGGCAACTTT</gDNA_template>
            <first_frame> V  S  K  F  Q  G  R  K  I  T  F  A  S  *  R  S  P  Y  M  D  L  S  S  L  Q  G  S  G  T  K  G  L  I  A  I  W  *  S  W  D  I  L  G  A  H  M  I  V  V  S  T  T  I  G  S  R  M  I  H  S  S  I  W  C  F  M  *  M  I  C  *  *  L  Q  R  R  S  M  T  F  R  S  *  R  V  Y  L  V  L  S  L  R  *  R  I  W  E  P  L  G  R  F  *  G  W  R  S  L  E  T  E  R  E  *  N  F  S  F  H  R  E  A  T  F  R  R  S  W  R  G  L  A  C  L  Y  L  S  L  L  I  P  P  V  L  P  I  S  I  S  L  P  C  S  L  H  S  Q  K  K  R  R  S  I  C  H  E  S  L  M  P  V  P  *  E  V  *  C  M  L  W  S  V  Q  G  Q  I  *  H  M  Q  S  V  *  *  A  D  S  W  D  N  *  G  K  N  I  G  R  L  *  R  E  F  S  G  T  L  E  V  H  L  T  L  V  S  F  M  E  V  I  L  S  V  W  L  L  A  I  L  I  L  T  M  L  E  M  L  T  Q  E  D  *  *  L  A  M  C  L  P  L  E  D  L  S  S  V  G  R  Q  L  </first_frame>
            <second_frame>  F  P  S  S  R  E  G  K  S  R  L  Q  V  E  E  V  L  I  W  T  *  A  V  S  K  A  V  V  Q  K  V  *  *  L  Y  G  E  V  G  I  Y  S  E  L  I  *  L  L  C  L  L  Q  *  A  Q  G  *  F  I  H  L  S  G  A  L  C  R  *  Y  V  D  S  C  K  E  E  V  *  H  S  E  A  E  G  F  T  *  C  *  V  *  D  E  G  S  G  S  R  S  E  D  S  R  D  G  D  H  *  R  Q  R  E  N  E  T  F  L  F  T  E  K  L  H  S  E  G  L  G  E  V  W  H  V  C  I  *  A  Y  *  Y  P  Q  C  C  Q  Y  P  F  H  C  H  V  R  S  T  V  R  R  R  E  G  V  Y  V  T  S  P  L  C  Q  C  H  R  K  F  D  V  C  Y  G  L  Y  K  A  R  F  S  T  C  S  Q  C  S  E  L  I  H  G  T  T  R  E  R  T  L  A  G  C  E  E  N  F  P  V  P  *  R  Y  I  *  R  W  S  H  L  W  R  *  Y  S  V  F  G  Y  W  L  F  *  F  *  L  C  W  R  C  *  H  K  K  I  D  D  W  L  C  V  Y  P  W  R  I  C  R  Q  L  E  G  N  F </second_frame>
            <third_frame>   F  Q  V  P  G  K  E  N  H  V  C  K  L  K  K  S  L  Y  G  L  E  Q  S  P  R  Q  W  Y  K  R  F  D  S  Y  M  V  K  L  G  Y  T  R  S  S  Y  D  C  C  V  Y  Y  N  R  L  K  D  D  S  F  I  Y  L  V  L  Y  V  D  D  M  L  I  A  A  K  K  K  Y  D  I  Q  K  L  K  G  L  L  S  A  E  F  E  M  K  D  L  G  A  A  R  K  I  L  G  M  E  I  I  R  D  R  E  R  M  K  L  F  F  S  Q  R  S  Y  I  Q  K  V  L  A  R  F  G  M  S  V  S  K  P  I  D  T  P  S  A  A  N  I  H  F  T  A  M  F  A  P  Q  S  E  E  E  K  E  Y  M  S  R  V  P  Y  A  S  A  I  G  S  L  M  Y  A  M  V  C  T  R  P  D  L  A  H  A  V  S  V  V  S  *  F  M  G  Q  L  G  K  E  H  W  Q  A  V  K  R  I  F  R  Y  L  R  G  T  S  D  V  G  L  I  Y  G  G  D  T  Q  C  L  V  T  G  Y  S  D  S  D  Y  A  G  D  V  D  T  R  R  L  M  T  G  Y  V  F  T  L  G  G  S  V  V  S  W  K  A  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="C04HBa0303A06.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="96988" stop="96404"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>582</number_coding_nucleotides>
                  <number_encoded_amino_acids>194</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FQVPGKENHVCKLKKSLYGLEQSPRQWYKRFDSYMVKLGYTRSSYDCCVYYNRLKDDSFIYLVLYVDDMLIAAKKKYDIQKLKGLLSAEFEMKDLGAARKILGMEIIRDRERMKLFFSQRSYIQKVLARFGMSVSKPIDTPSAANIHFTAMFAPQSEEEKEYMSRVPYASAIGSLMYAMVCTRPDLAHAVSVVS*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04HBa0303A06.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="96403" stop="96185"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>219</number_coding_nucleotides>
                  <number_encoded_amino_acids>73</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FMGQLGKEHWQAVKRIFRYLRGTSDVGLIYGGDTQCLVTGYSDSDYAGDVDTRRLMTGYVFTLGGSVVSWKAT</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="97647" PGL_stop="97001"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="97647" e_stop="97001"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.955"/>
        </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="0.955">
            <gDNA_exon_boundary e_start="97647" e_stop="97001" e_length="647"/>
          </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="97647" stop="97001"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U330105" 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>TACGTCAGAAACTGGGAGTCTTGATAAATAGGTGGAGTTTCAAGTCATTCAGAACGAGAGCGATTTAAAAGAACCTGAAGAGGAGGATCAAGAGCCACAGACAGAAACTGATATCCCAGAATCTATGCCATGAGATATCCATCAGAGTATAGCTCAAGATCGGCCAAAGAGGGTTGGAGTTCAGCCACCTACGAGGTATGGTTTTGAGGACATGGTGGGTTATGCACTGCAGGTTGCTGAAGAGGTAGATACATCTGAGCCATCTACTTACAAAGAAGCCATTTTAAGTCCTGATTCTTAAAAATGGTTTGCTGCTATGGGATGAGATGGAGTCCCTACACAAGAATCAGACATGGGATCTGGTCATACAGCCTTCGGGGAGAAAGATTATTACTTGCAAATGGGTTTTCAAGAAGAAGGAAGGGATATCACCAGCAGAAAGAATCATCTATAAAGCCAGGGTTGTTGCCAGAGGTTTCAACCAAAGAGAGGGAGTGAACTACAATGAGATCTTTTCACCAGTGGTCAGACATACTTCCATCCGAGTGTTACTAGCGATAGTTACACATCAGAATCTGGAGCTTGAACAACTTGATGTGAAGACAACGTTTCTACATGGAGAGTTGGAGGAAGAGATATACATGACT</gDNA_template>
            <first_frame> Y  V  R  N  W  E  S  *  *  I  G  G  V  S  S  H  S  E  R  E  R  F  K  R  T  *  R  G  G  S  R  A  T  D  R  N  *  Y  P  R  I  Y  A  M  R  Y  P  S  E  Y  S  S  R  S  A  K  E  G  W  S  S  A  T  Y  E  V  W  F  *  G  H  G  G  L  C  T  A  G  C  *  R  G  R  Y  I  *  A  I  Y  L  Q  R  S  H  F  K  S  *  F  L  K  M  V  C  C  Y  G  M  R  W  S  P  Y  T  R  I  R  H  G  I  W  S  Y  S  L  R  G  E  R  L  L  L  A  N  G  F  S  R  R  R  K  G  Y  H  Q  Q  K  E  S  S  I  K  P  G  L  L  P  E  V  S  T  K  E  R  E  *  T  T  M  R  S  F  H  Q  W  S  D  I  L  P  S  E  C  Y  *  R  *  L  H  I  R  I  W  S  L  N  N  L  M  *  R  Q  R  F  Y  M  E  S  W  R  K  R  Y  T  *   </first_frame>
            <second_frame>  T  S  E  T  G  S  L  D  K  *  V  E  F  Q  V  I  Q  N  E  S  D  L  K  E  P  E  E  E  D  Q  E  P  Q  T  E  T  D  I  P  E  S  M  P  *  D  I  H  Q  S  I  A  Q  D  R  P  K  R  V  G  V  Q  P  P  T  R  Y  G  F  E  D  M  V  G  Y  A  L  Q  V  A  E  E  V  D  T  S  E  P  S  T  Y  K  E  A  I  L  S  P  D  S  *  K  W  F  A  A  M  G  *  D  G  V  P  T  Q  E  S  D  M  G  S  G  H  T  A  F  G  E  K  D  Y  Y  L  Q  M  G  F  Q  E  E  G  R  D  I  T  S  R  K  N  H  L  *  S  Q  G  C  C  Q  R  F  Q  P  K  R  G  S  E  L  Q  *  D  L  F  T  S  G  Q  T  Y  F  H  P  S  V  T  S  D  S  Y  T  S  E  S  G  A  *  T  T  *  C  E  D  N  V  S  T  W  R  V  G  G  R  D  I  H  D  </second_frame>
            <third_frame>   R  Q  K  L  G  V  L  I  N  R  W  S  F  K  S  F  R  T  R  A  I  *  K  N  L  K  R  R  I  K  S  H  R  Q  K  L  I  S  Q  N  L  C  H  E  I  S  I  R  V  *  L  K  I  G  Q  R  G  L  E  F  S  H  L  R  G  M  V  L  R  T  W  W  V  M  H  C  R  L  L  K  R  *  I  H  L  S  H  L  L  T  K  K  P  F  *  V  L  I  L  K  N  G  L  L  L  W  D  E  M  E  S  L  H  K  N  Q  T  W  D  L  V  I  Q  P  S  G  R  K  I  I  T  C  K  W  V  F  K  K  K  E  G  I  S  P  A  E  R  I  I  Y  K  A  R  V  V  A  R  G  F  N  Q  R  E  G  V  N  Y  N  E  I  F  S  P  V  V  R  H  T  S  I  R  V  L  L  A  I  V  T  H  Q  N  L  E  L  E  Q  L  D  V  K  T  T  F  L  H  G  E  L  E  E  E  I  Y  M  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="C04HBa0303A06.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="97360" stop="97001"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>360</number_coding_nucleotides>
                  <number_encoded_amino_acids>120</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VLILKNGLLLWDEMESLHKNQTWDLVIQPSGRKIITCKWVFKKKEGISPAERIIYKARVVARGFNQREGVNYNEIFSPVVRHTSIRVLLAIVTHQNLELEQLDVKTTFLHGELEEEIYMT</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 35 chains have been computed
$ 
$ memory statistics:
$ 8912 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 2228 bytes was the average size of a spliced alignment
$ 8000 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2666 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: 2008-04-10 05:34:41
-->
