<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-01-19 11:22:08"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09SLf0089D12-clscI/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09SLf0089D12-clscI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U340296" ref_strand="+" ref_description="SGN-U340296        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT1G04645.1 | Symbol: None | self-incompatibility protein-related, similar to S3 self-incompatibility protein (Papaver rhoeas) GI:1107841 | chr1:1293769-1294262 REVERSE | Aliases: None (evalue: 1e-11, score=67) genbank/nr: gi|13016738|emb|CAC29426.1| S-protein homologue [Lycopersicon esculentum](evalue: 8e-35, score=150)">
      <seq>caccagatttttttctttttgcttatcactccactcaacctttcaatagcaaaacattgtccatttggttcgagatacacggtatatgttaccaacaaacttcctttcgactcttcaaaattgtcatttcattgtgcttcaaaaaatgatgatctcggatatcacgatcttgctataaatcaagtgtttaattggtcgttttgcgaggcaattttcagtagaactttattcttttgtcatttttggtggggttcaaaagagaaagcattcgatgtgtttaacgatccatatacatgtgttaaaggtacaggaaatccaaatattttaactaattgtaaatgggaggcaagggcagatggtttttatttggaattgtttaatagtacaagtgagacatattatatgtatcattatttagagtggtcttagggaattaatatgtttgtgtcatattttaatttagataaaatgagaagtaaaaaaaaaaaagaattccaaagtgtattatttc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09SLf0089D12.1" temp_strand="-" temp_description="C09SLf0089D12.1  AC234217.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLf0089D12 upload_account_name:spain (1 - 32889)">
        <position start="4816" stop="3708"/>
      </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="4518" g_stop="4008" g_length="511"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="511" r_length="511" r_score="0.992"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLf0089D12.1" gen_strand="-" ref_id="SGN-U340296" ref_strand="+">
        <total_alignment_score>0.992</total_alignment_score>
        <cumulative_length_of_scored_exons>511</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLf0089D12.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U340296" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4518" e_stop="4008"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATCAACATTTTTTTCTTTTTGCTTATCACTCCACTCAACCTTTCAATAGCAAAACATTGTCCATTTGGTTCGAGATACACGGTATATGTTACCAACAAACTTCCTTTCGACTCTTCAAAATTGTCATTTCATTGTGCTTCAAAAAATGATGATCTCGGATATCACGATCTTGCTATAAATCAAGTGTTTAATTGGTCGTTTTGCGAGGCAATTTTCAGTAGAACTTTATTCTTTTGTCATTTTTGGTGGGGTTCAAAAGAGAAAGCATTCGATGTGTTTAACGATCCATATACATGTGTTAAAGGTACAGGAAATCCAAATATTTTAACTAATTGTAAATGGGAGGCAAGGGCAGATGGTTTTTATTTGGAATTGTTTAATAGTACAAGTGAGACATATTATATGTATCATTATTTAGAGTGGTCTTAGGGAATTAATATGTTTGTGTCATATTTTAATTTAGATAAAATGAGAAGTAAAAAAAAAAAAGAATTCCAAAGTGTATTATTTC</genome_strand>
        <mrna_strand>CACCAGATTTTTTTCTTTTTGCTTATCACTCCACTCAACCTTTCAATAGCAAAACATTGTCCATTTGGTTCGAGATACACGGTATATGTTACCAACAAACTTCCTTTCGACTCTTCAAAATTGTCATTTCATTGTGCTTCAAAAAATGATGATCTCGGATATCACGATCTTGCTATAAATCAAGTGTTTAATTGGTCGTTTTGCGAGGCAATTTTCAGTAGAACTTTATTCTTTTGTCATTTTTGGTGGGGTTCAAAAGAGAAAGCATTCGATGTGTTTAACGATCCATATACATGTGTTAAAGGTACAGGAAATCCAAATATTTTAACTAATTGTAAATGGGAGGCAAGGGCAGATGGTTTTTATTTGGAATTGTTTAATAGTACAAGTGAGACATATTATATGTATCATTATTTAGAGTGGTCTTAGGGAATTAATATGTTTGTGTCATATTTTAATTTAGATAAAATGAGAAGTAAAAAAAAAAAAGAATTCCAAAGTGTATTATTTC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U345335" ref_strand="+" ref_description="SGN-U345335        Tomato 200607 #1 [1 ESTs aligned] arabidopsis/peptide: AT4G16195.1 | Symbol: None | self-incompatibility protein-related, similar to S1 self-incompatibility protein (Papaver rhoeas) GI:452430 | chr4:9173180-9173665 REVERSE | Aliases: None (evalue: 4e-08, score=54.3) genbank/nr: gi|13016738|emb|CAC29426.1| S-protein homologue [Lycopersicon esculentum](evalue: 5e-78, score=292)">
      <seq>gaattcggcacgagaatatgactctttatttcaacatcttttttttcttgttattgatcactcctaatcttgacctttcgctagcggaaaattgctttattttaccaagttatgaggtacatattatcaacaaacttcctactaatacctcacaattgcaagttcattgcacgtcaaaggatgacgaaactagaaatgcatatcttaacatagatgaagacttacattggtcattttgcgagtcattttttggtaatacttcgtttttttgtaacttttggtggggttcaatgaataagtctattacagtgtttgatgacccaggcacttgtgttcatagtggtcagtatacaaattatcattactcttgcaaatgggaagtaagacaagatggtttttatttggagatgtttaattataagaatatgacatattttatggatcacattagtgattggtcttagggaattaatataatatgttccattgatgttttgtatatttaaatttggaaggaaatatattatcatggaattttagtgtg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09SLf0089D12.1" temp_strand="-" temp_description="C09SLf0089D12.1  AC234217.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLf0089D12 upload_account_name:spain (1 - 32889)">
        <position start="8893" stop="7762"/>
      </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="8606" g_stop="8062" g_length="545"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="544" r_length="544" r_score="0.983"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLf0089D12.1" gen_strand="-" ref_id="SGN-U345335" ref_strand="+">
        <total_alignment_score>0.983</total_alignment_score>
        <cumulative_length_of_scored_exons>545</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLf0089D12.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U345335" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="8606" e_stop="8062"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCTTCTCCCAAATATAATATGACTCTTTATTTCAACATCTTTTTTTTCTTGTTATTGATCACTCCTAATCTTGACCTTTCGCTAGCGGAAAATTGCTTTATTTTACCAAGTTATGAGGTACATATTATCAACAAACTTCCTACTAATACCTCACAATTGCAAGTTCATTGCACGTCAAAGGATGACGAAACTAGAAATGCATATCTTAACATAGATGAAGACTTACATTGGTCATTTTGCGAGTCATTTTTTGGTAATACTTCGTTTTTTTGTAACTTTTGGTGGGGTTCAATGAATAAGTCTATTACAGTGTTTGATGACCCAGGCACTTGTGTTCATAGTGGTCAGTATACAAATTATCATTACTCTTGCAAATGGGAAGTAAGACAAGATGGTTTTTATTTGGAGATGTTTAATTATAAGAATATGACATATTTTATGGATCACATTAGTGATTGGTCTTAGGGAATTAATATAATATGTTCCATTGATGTTTTGTATATTTAAATTTGGAAGGAAATATATTATCATGGAATTTTAGTGTG</genome_strand>
        <mrna_strand>GAAT-TCGGCACGAGAATATGACTCTTTATTTCAACATCTTTTTTTTCTTGTTATTGATCACTCCTAATCTTGACCTTTCGCTAGCGGAAAATTGCTTTATTTTACCAAGTTATGAGGTACATATTATCAACAAACTTCCTACTAATACCTCACAATTGCAAGTTCATTGCACGTCAAAGGATGACGAAACTAGAAATGCATATCTTAACATAGATGAAGACTTACATTGGTCATTTTGCGAGTCATTTTTTGGTAATACTTCGTTTTTTTGTAACTTTTGGTGGGGTTCAATGAATAAGTCTATTACAGTGTTTGATGACCCAGGCACTTGTGTTCATAGTGGTCAGTATACAAATTATCATTACTCTTGCAAATGGGAAGTAAGACAAGATGGTTTTTATTTGGAGATGTTTAATTATAAGAATATGACATATTTTATGGATCACATTAGTGATTGGTCTTAGGGAATTAATATAATATGTTCCATTGATGTTTTGTATATTTAAATTTGGAAGGAAATATATTATCATGGAATTTTAGTGTG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U322585" ref_strand="+" ref_description="SGN-U322585        Tomato 200607 #1 [7 ESTs aligned] arabidopsis/peptide: | Symbol: None | retinoblastoma-related protein (RBR1), nearly identical to retinoblastoma-related protein (Arabidopsis thaliana) GI:8777927; contains Pfam profiles: PF01858 retinoblastoma-associated protein A domain, PF01857 retinoblastoma-associated protein B domain | chr3:3913419-3919087 REVERSE | Aliases: F28J15.11(evalue: 1e-100, score=363) genbank/nr: retinoblastoma(evalue: 3e-123, score=444)">
      <seq>tgttgagacatccatcaatgtattctttggcaagattgtgaagttggctgctgtcagaatcaatggcatgattgagcggctacagctttctcaacaaataagagagactgtatattgcctttttcagaagattctcagtcagaggacaagtcttttcttcagcagacatattgaccagatcatcctttgctctttctatggagttgccaagatttcacaacttaacttgaccttcaaagaaatcatatacaactaccgaaagcaacctcagtgcaaaccacaagtttttcgaagtgtttttgttgactggacatcagcgcgtcacaatgggaaaacaggttcagaacatgtggatatcatcacgttctacaatgaaatgtttattccttctgttaagccattattagttgagcttgcacctgctggaaatgagcaaaagaataaccatgttgaaaaaaccaagaaggacgggcaaggaccagcatcccccagatcatcttcatttcccagtctccccgacatgtctccaaagaaagtatctgctgttcataatgtttatgtctccccgctgcgatcatcgaagatggatgcgttgatttcccatagctctaaaagctattatgcttgtgtgggagaaagcactcatgcttatcagagcccctcaaaagatttgacagtaatcaacaaccgcttgaatggcaatcggaagctcagaggcgctcttaattttgatgacgttgatgctgtgggcttggttagtgattccatagttgccaacaccctttaccttcaaaacgggaactgcatatcatcacctcgtgcagctgtgaagactgagcagcccgagccctaatacctggacaaacttgcactgtaaataggctttcggattatgacatttctttttcctagttttttaagggtatcctaaacgtagagagatgtataggggtgttgaatgagcggtatgtttatgtaaaatgcccgccaccaacccgatgcttcttttttaactgttgatttctgattctgggaatatatatagggatagatagtcttgttccttaataagagtaatagttgtacattaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09SLf0089D12.1" temp_strand="-" temp_description="C09SLf0089D12.1  AC234217.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLf0089D12 upload_account_name:spain (1 - 32889)">
        <position start="21811" stop="19153"/>
      </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="21511" g_stop="21478" g_length="34"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="34" r_length="34" r_score="0.971"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="21477" i_stop="21035" i_length="443">
            <donor d_prob="1.000" d_score="0.00"/>
            <acceptor a_prob="0.979" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="21034" g_stop="20858" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="35" r_stop="211" r_length="177" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="20857" i_stop="20772" i_length="86">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.980" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="20771" g_stop="20652" g_length="120"/>
          <reference_exon_boundary r_type="cDNA" r_start="212" r_stop="331" r_length="120" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="20651" i_stop="20567" i_length="85">
            <donor d_prob="0.604" d_score="1.00"/>
            <acceptor a_prob="0.829" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="20566" g_stop="20428" g_length="139"/>
          <reference_exon_boundary r_type="cDNA" r_start="332" r_stop="470" r_length="139" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="20427" i_stop="20300" i_length="128">
            <donor d_prob="0.972" d_score="1.00"/>
            <acceptor a_prob="0.973" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="20299" g_stop="20187" g_length="113"/>
          <reference_exon_boundary r_type="cDNA" r_start="471" r_stop="583" r_length="113" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="20186" i_stop="20036" i_length="151">
            <donor d_prob="0.989" d_score="1.00"/>
            <acceptor a_prob="0.829" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="20035" g_stop="19920" g_length="116"/>
          <reference_exon_boundary r_type="cDNA" r_start="584" r_stop="699" r_length="116" r_score="1.000"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="19919" i_stop="19846" i_length="74">
            <donor d_prob="0.982" d_score="1.00"/>
            <acceptor a_prob="0.874" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="19845" g_stop="19453" g_length="393"/>
          <reference_exon_boundary r_type="cDNA" r_start="700" r_stop="1092" r_length="393" r_score="0.997"/>
        </exon>
        <intron i_serial="7">
          <gDNA_intron_boundary i_start="19452" i_stop="19389" i_length="64">
            <donor d_prob="0.000" d_score="0.98"/>
            <acceptor a_prob="0.983" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="8">
          <gDNA_exon_boundary g_start="19388" g_stop="19376" g_length="13"/>
          <reference_exon_boundary r_type="cDNA" r_start="1093" r_stop="1105" r_length="13" r_score="0.692"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLf0089D12.1" gen_strand="-" ref_id="SGN-U322585" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>1105</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLf0089D12.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U322585" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="21511" e_stop="21478"/>
          <exon e_start="21034" e_stop="20858"/>
          <exon e_start="20771" e_stop="20652"/>
          <exon e_start="20566" e_stop="20428"/>
          <exon e_start="20299" e_stop="20187"/>
          <exon e_start="20035" e_stop="19920"/>
          <exon e_start="19845" e_stop="19453"/>
          <exon e_start="19388" e_stop="19376"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TGCTGAGACATCCATCAATGTATTCTTTGGCAAGGTAAAACTGTCAATTATTCCATCAGTTTTTATGTTGATTATGCTGTGTCAATCTCTTTTTGAAGTGGTTATCACATTTTTAAGTTGTTCAAATGCTCACATGCTGGTTAGCCATTTAGTGCCAGAAGTGCTCCTCTGGGTTCTCAATTTCCAACTTCTTTTTGGAAAAGAACTTACATCTCTTTAACAACCAACTTTTTATCCAGTAATTTTTGACATGAGATCTTGATTTTAATCTTCTGGTAGCTCCTTACAATATTTAAGTAAATGTGAACTGTGAATGGCAGATGCAAATAGTGGGATCTAGCAGTTCGAATATGGATATCCTGGATTCTGATTCTTCTGTTAGATGCTAATTAGATGTTTTTTCTCGATCAAGTTCTTTGGTTTAGCCTGCTGATTATTTGACCATTCCTTTTTTCTCTTATGTCATGTTCCACCTAGATTGTGAAGTTGGCTGCTGTCAGAATCAATGGCATGATTGAGCGGCTACAGCTTTCTCAACAAATAAGAGAGACTGTATATTGCCTTTTTCAGAAGATTCTCAGTCAGAGGACAAGTCTTTTCTTCAGCAGACATATTGACCAGATCATCCTTTGCTCTTTCTATGGAGTTGCCAAGGTAAACGTTGGGGGAAAAGGGAGATAGCTGGAGCTGATAGTCTGTAATTCTCTTATTTCACACCTTGTTTCTTGATTATATTGCAGATTTCACAACTTAACTTGACCTTCAAAGAAATCATATACAACTACCGAAAGCAACCTCAGTGCAAACCACAAGTTTTTCGAAGTGTTTTTGTTGACTGGACATCAGCGCGTCACAATGGGGTAATGTCATCAGTCTTTAGATCGTTGACACGAGTCTCTTACAGTTTCTAGAACCACTGACCAATTTCTTTTGGATTTAAAACAGAAAACAGGTTCAGAACATGTGGATATCATCACGTTCTACAATGAAATGTTTATTCCTTCTGTTAAGCCATTATTAGTTGAGCTTGCACCTGCTGGAAATGAGCAAAAGAATAACCATGTTGAAAAAACCAAGAAGGACGGTGAGTTCTCTTTATTATGCGGTTGTGAAGTACTATTTTTCTTCTCGTTTGGTTTCTCTATATGATTTCTTTCTCATGTACAAAATTGTCCAACCTGTGGCCTTTTTTGTTTTCTTCATCTCATTCAGGGCAAGGACCAGCATCCCCCAGATCATCTTCATTTCCCAGTCTCCCCGACATGTCTCCAAAGAAAGTATCTGCTGTTCATAATGTTTATGTCTCCCCGCTGCGATCATCGAAGGTTAGTGTCTATGTTTTTCCAGTGTGACTTGAAGTTCATATTTCGAATGTTTCAGAGTTGAGAAATATGGGATTTTGAATGAATATACCACCTTTCATGACCCCTCTTTGGTCCATTATTTCTCGCATTCATCTCTTATTTCTGATTTCAGATGGATGCGTTGATTTCCCATAGCTCTAAAAGCTATTATGCTTGTGTGGGAGAAAGCACTCATGCTTATCAGAGCCCCTCAAAAGATTTGACAGTAATCAACAACCGCTTGAATGGGTACGTGGTTCTTTTACCTATCAGCAAAACTCCTTTATCTAAATACAATTCGACTCAAATCCTCTCATCTGCAGCAATCGGAAGCTCAGAGGCGCTCTTAATTTTGATGACGTTGATGCTGTGGGCTTGGTTAGTGATTCCATAGTTGCCAACACCCTTTACCTTCAAAACGGGAACTGCATATCATCACCTCGTGCAGCTGTGAAGACTGAGCAGCCCGAGCCCTAATACCTGGACAAACTTGCACTGTAAATAGGCTTTCGGATTATGACATTTCTTTTTCCTAGTTTTTTAAGGGTATCCTAAACGTAGAGAGATGTATAGGGGTGTTGAATGAGCGGTATGTTTATGTAAAATGCCCGCCACCAACCCGATGCTTCTTTTTTAACTGTTGATTTCTGATTCTGGGAATATATATAGGGATAGATAGTCTTGTTCCTTAATAAGAGTAATAGTTGTACATTACACCACTGGTGTTTTTCTCTGATTTTTCTCAACAACGATGCTCGTTCTCTTCGATGTTTTTTTTAGGAAAAGAAAATAG</genome_strand>
        <mrna_strand>TGTTGAGACATCCATCAATGTATTCTTTGGCAAG...........................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGTGAAGTTGGCTGCTGTCAGAATCAATGGCATGATTGAGCGGCTACAGCTTTCTCAACAAATAAGAGAGACTGTATATTGCCTTTTTCAGAAGATTCTCAGTCAGAGGACAAGTCTTTTCTTCAGCAGACATATTGACCAGATCATCCTTTGCTCTTTCTATGGAGTTGCCAAG......................................................................................ATTTCACAACTTAACTTGACCTTCAAAGAAATCATATACAACTACCGAAAGCAACCTCAGTGCAAACCACAAGTTTTTCGAAGTGTTTTTGTTGACTGGACATCAGCGCGTCACAATGGG.....................................................................................AAAACAGGTTCAGAACATGTGGATATCATCACGTTCTACAATGAAATGTTTATTCCTTCTGTTAAGCCATTATTAGTTGAGCTTGCACCTGCTGGAAATGAGCAAAAGAATAACCATGTTGAAAAAACCAAGAAGGACG................................................................................................................................GGCAAGGACCAGCATCCCCCAGATCATCTTCATTTCCCAGTCTCCCCGACATGTCTCCAAAGAAAGTATCTGCTGTTCATAATGTTTATGTCTCCCCGCTGCGATCATCGAAG.......................................................................................................................................................ATGGATGCGTTGATTTCCCATAGCTCTAAAAGCTATTATGCTTGTGTGGGAGAAAGCACTCATGCTTATCAGAGCCCCTCAAAAGATTTGACAGTAATCAACAACCGCTTGAATGG..........................................................................CAATCGGAAGCTCAGAGGCGCTCTTAATTTTGATGACGTTGATGCTGTGGGCTTGGTTAGTGATTCCATAGTTGCCAACACCCTTTACCTTCAAAACGGGAACTGCATATCATCACCTCGTGCAGCTGTGAAGACTGAGCAGCCCGAGCCCTAATACCTGGACAAACTTGCACTGTAAATAGGCTTTCGGATTATGACATTTCTTTTTCCTAGTTTTTTAAGGGTATCCTAAACGTAGAGAGATGTATAGGGGTGTTGAATGAGCGGTATGTTTATGTAAAATGCCCGCCACCAACCCGATGCTTCTTTTTTAACTGTTGATTTCTGATTCTGGGAATATATATAGGGATAGATAGTCTTGTTCCTTAATAAGAGTAATAGTTGTACATTAAA................................................................AAAAAAAAAAAAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U330582" ref_strand="+" ref_description="SGN-U330582        Tomato 200607 #1 [2 ESTs aligned] arabidopsis/peptide: | Symbol: None | retinoblastoma-related protein (RBR1), nearly identical to retinoblastoma-related protein (Arabidopsis thaliana) GI:8777927; contains Pfam profiles: PF01858 retinoblastoma-associated protein A domain, PF01857 retinoblastoma-associated protein B domain | chr3:3913419-3919087 REVERSE | Aliases: F28J15.11(evalue: 6e-100, score=361) genbank/nr: retinoblastoma(evalue: 4e-156, score=554)">
      <seq>tagagagagaaaggcgagggaaaatcaggggcttttttagtttttgaagaatttggatctaattatacagatctgagaaatttgtacaattttgggttctgggtttgggtttctttagttagttgtggatgaatatggaggagctgaagaatcattcgaattctgaagagaatggttcggtggactctcttgaagttcgatttactgatttctgcaagaatggattgtctatgggtgagagttttatggtagaagctagaaagctgtttatggactgtaaacatcttttactgtcaaataatgctgctcttggagctataacgcctgaggaagttgaacggtattggtttgtgtttgttctgttctccgtgaagagattacgtgagaatgaagctaggaattcgagtaatgggaatgaaggaaatggatttgatctatgccaaattctgcgaggggcgaaactcaatgttctagatttcttcaaagaattaccacagtttattgttaaagttggtccagtattaagcaacctatatggttcagattgggagaagagacttcaggcaaaggaattgcagaccaactttgtgcatttgagccttttaagcaagtactacaagcgcgcatatcaggagctgtttttgtcaagtgataacaatgaagtaaatcagtctgctacttctaattcgattgtcctcttgccacagtattatcgttttggctggttgctttttctttcacttcgcgaacatgtattcagccgcttcaaggaccttgtgacatgcacaaatggtttagtttctgtgctggcaatcttaataatacatgtgcctgtatgcttcagaaatttcaacatcaatgactccccacgatttgttaagaaaggagacaaagtggacttgcttgtttcattaagcagcatttaccagacctcgatagatgacttaagggagaccatggacaaagttaataatctaataacagtaaagttgaagaaggaactttgtttggcttcagaatgcagggcaaagaacctggacaatatcgacgcagatggtttgacgtatttcgaaaatttactggaggaatcatctttatcgtcaagtatatgtatactggagaaggattacaatgatgcaattcagaacaagggtgaattggatgagaggattttttgtcatgatgaggatagcttgctggggtcagggagcttgtctggaggtgcagtcaatatgaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09SLf0089D12.1" temp_strand="-" temp_description="C09SLf0089D12.1  AC234217.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLf0089D12 upload_account_name:spain (1 - 32889)">
        <position start="26362" stop="22628"/>
      </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="26062" g_stop="25846" g_length="217"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="218" r_length="218" r_score="0.968"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="25845" i_stop="25187" i_length="659">
            <donor d_prob="0.995" d_score="0.98"/>
            <acceptor a_prob="0.998" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="25186" g_stop="25082" g_length="105"/>
          <reference_exon_boundary r_type="cDNA" r_start="219" r_stop="323" r_length="105" r_score="0.971"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="25081" i_stop="24982" i_length="100">
            <donor d_prob="0.998" d_score="0.96"/>
            <acceptor a_prob="0.947" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="24981" g_stop="24839" g_length="143"/>
          <reference_exon_boundary r_type="cDNA" r_start="324" r_stop="466" r_length="143" r_score="0.979"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="24838" i_stop="24757" i_length="82">
            <donor d_prob="0.972" d_score="1.00"/>
            <acceptor a_prob="0.566" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="24756" g_stop="24660" g_length="97"/>
          <reference_exon_boundary r_type="cDNA" r_start="467" r_stop="563" r_length="97" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="24659" i_stop="24420" i_length="240">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.980" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="24419" g_stop="24373" g_length="47"/>
          <reference_exon_boundary r_type="cDNA" r_start="564" r_stop="610" r_length="47" r_score="1.000"/>
        </exon>
        <intron i_serial="5">
          <gDNA_intron_boundary i_start="24372" i_stop="24254" i_length="119">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.961" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="6">
          <gDNA_exon_boundary g_start="24253" g_stop="24055" g_length="199"/>
          <reference_exon_boundary r_type="cDNA" r_start="611" r_stop="809" r_length="199" r_score="1.000"/>
        </exon>
        <intron i_serial="6">
          <gDNA_intron_boundary i_start="24054" i_stop="23552" i_length="503">
            <donor d_prob="0.972" d_score="1.00"/>
            <acceptor a_prob="0.956" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="7">
          <gDNA_exon_boundary g_start="23551" g_stop="23485" g_length="67"/>
          <reference_exon_boundary r_type="cDNA" r_start="810" r_stop="876" r_length="67" r_score="1.000"/>
        </exon>
        <intron i_serial="7">
          <gDNA_intron_boundary i_start="23484" i_stop="23362" i_length="123">
            <donor d_prob="0.917" d_score="1.00"/>
            <acceptor a_prob="0.273" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="8">
          <gDNA_exon_boundary g_start="23361" g_stop="23185" g_length="177"/>
          <reference_exon_boundary r_type="cDNA" r_start="877" r_stop="1053" r_length="177" r_score="0.994"/>
        </exon>
        <intron i_serial="8">
          <gDNA_intron_boundary i_start="23184" i_stop="23112" i_length="73">
            <donor d_prob="0.987" d_score="1.00"/>
            <acceptor a_prob="0.986" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="9">
          <gDNA_exon_boundary g_start="23111" g_stop="22928" g_length="184"/>
          <reference_exon_boundary r_type="cDNA" r_start="1054" r_stop="1237" r_length="184" r_score="0.978"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLf0089D12.1" gen_strand="-" ref_id="SGN-U330582" ref_strand="+">
        <total_alignment_score>0.985</total_alignment_score>
        <cumulative_length_of_scored_exons>1236</cumulative_length_of_scored_exons>
        <coverage percentage="0.999" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLf0089D12.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U330582" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="26062" e_stop="25846"/>
          <exon e_start="25186" e_stop="25082"/>
          <exon e_start="24981" e_stop="24839"/>
          <exon e_start="24756" e_stop="24660"/>
          <exon e_start="24419" e_stop="24373"/>
          <exon e_start="24253" e_stop="24055"/>
          <exon e_start="23551" e_stop="23485"/>
          <exon e_start="23361" e_stop="23185"/>
          <exon e_start="23111" e_stop="22928"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAGAGAGAGAAAGGCGAGGGAAAATTAGGGG-TTTTTTAGTTTTTGAAGAATTTGGATCTAATTATACAGATCTGAGAAATTTGTAGAATTTTGGGTTCTGGGTTTCCGTTTCTTTAGTTAGTTGTGGATGAATATGGAGGAGCTGAAGAATCATTCGAATTCTGAAGAGAATGGTTCGGTGGACTCTCTTGAAGTTCGATTTAGTGATTTCTGCAAGGTACGTTTGGTTTTGTTGAGTTTGATTTTAGGTTGTAAATACTTCAGCTGATTTTTTTGGGCTTGATTCAGTTGAGAAAGAAGGAAGATTTGGTCGTTGTTGTGTTTTGTTGGTTAATTTGTTTAAAAAAATCATTTTTGTGAAACCCCATGTGTGAAATATTTGTTCTTTAACGGTTTCTGTTATGCGTTTGGCGATTTTAGTATTTTTAGCATTTGTTGTTTGATTTACAGAATGAGTTTCTTGTTTTCTGCATTTTTTTAGTTGTAGCGTCGAGACCCATGTATGCAAATTTTGTTCTTTTCTGGTTTTGTTTATGGATATGACGATTTTAATTTTTTTTAGGTGGGATTATTACGTTTGTTGTTTGATTTACAGAATGTGTTTCTTGTTTCCTGCATTTTGAAATCGTAGCTAAGAGGCCCATGTGTGCAAAATTTGTTCTTTTTCTGGTTTCTTTTATGGGTGTTGCGATTTTAATTTTTTGTTTTTAGGCGAATTTTAGTAGTTTTTTCATTTGTTTGATTTACAGAATGAGTTTCTTGTGTTGCATTTTCTACTTGTAGCTCAAAGACCCATGATGCAAAAATTTTGTTCTGTTACTGATATGGTAAACTTTGGATTTTAGTATTTTTTAACATTTGTTGTTTGATTTACAGAATGGATTGTCGATGGGTGAGAGTTTTATGGTAGAAGCTAGAAAGCTGTTTATGGACAGTAAACATCTTTTACTGTCAAATAATGCTGCTATTGGAGCTATAACGGTAAGTCCTCATGATTCTATCTTTTGCTAATTTAGTGTGAAATGACAAGTTAGGTGGTTTTAATATGGACTAGAATTGACTTGAGTGTGTTCTTTAACAGCCGGAGGAAGTTGAACGGTATTGGTTTGTGTTTGTTCTGTTCTCGGTGAAGAGATTAAGTGAGAATGAAGCTAGGAATTCGAGTAATGGGAATGAAGGAAATGGATTTGATCTATGCCAAATTCTGCGAGGGGCGAAACTCAAGTGCGTTTATCTAATGTTCTTGTGTTTCTTGTAAAAGTCGTGATTTTATCTCTGTTCTTATGAATTTTGTTTCGTTTTTTAGTGTTCTAGATTTCTTCAAAGAATTACCACAGTTTATTGTTAAAGTTGGTCCAGTATTAAGCAACCTATATGGTTCAGATTGGGAGAAGAGACTTCAGGTAATGATGACGTGGAGGGTTAATCTCATGTTCTGCAGCTATTGTTGTTTCTATTGGCTCTCTTTGTCCTAACAATGTGGCACAGTTGGTGGTGACACCGTTGTTTCCAATTATAGACTGTGACATTCTTTTTTGTACACTAAAAAGGAAAGTGTGCCACATGTATTAGGACAGAGGAGTTATATATTATTATTAAGCATTTATTCATGCACTTAAAATTTATTTGAACTGTTGTATTAGGCAAAGGAATTGCAGACCAACTTTGTGCATTTGAGCCTTTTAAGCAAGTGAGTACTCTTTTCAAGCACTAATTTCCTCTACTTATATTGCTTTGTGATGCTCATTCCGTTAATACTCAGGATGTGGCTTTTTGTGGTACATCTGATAACAATTTTACTGCTTTTAGGTACTACAAGCGCGCATATCAGGAGCTGTTTTTGTCAAGTGATAACAATGAAGTAAATCAGTCTGCTACTTCTAATTCGATTGTCCTCTTGCCACAGTATTATCGTTTTGGCTGGTTGCTTTTTCTTTCACTTCGCGAACATGTATTCAGCCGCTTCAAGGACCTTGTGACATGCACAAATGGTTTAGTTTCTGTGCTGGTCAGTTTCTACTCTATTTAGTTGATTCCTTGGATTCTGTCTGGTTTATTATGTTGTGTGTATGTTGTATTGGGCATGCTAATAATAGACTCTGTTTAACTTGTGTGCAATGTTGTAAAGGTTAAGTCACGAAGCTAGGTGCACCTCAGGTTCGGTGCTTAGCATTACGTAAGTGTTTAGTACAAGCACTAGAGTGCTTAAGGTGAAACTCAATGGAAACCTCCTTTTTTTTTCTAAATTGGTAACTTAAGAGGCCAGTGGCTTTATTGATCATCTGCACCAAAATGCATACTTCAGCAAAACTTTTCATTTACACCAGCTGAGCTGGCACATATATACTCCTTTTTGTCTTTGACATAACTAGCACAGCAGTTATGTGTTCAAGAATTAAATACAGTGCATCTAATCATCTTTCCCATTGCAATTCTATGGATTGGATCTTACCATGTTGCTCTTAAGAAATAGGTGACATGTCTGACTACTGTTTTACAACCATGGTGCAGGCAATCTTAATAATACATGTGCCTGTATGCTTCAGAAATTTCAACATCAATGACTCCCCACGATTTGGTAATTATCTTTACATATTTTGCATTAAGAGAGTTGGGGTTTTGGTCCACTACCTCTTCAACTTTTCTGTTTGGAGATCTGTGATGTCGTAGACCTTGTACTAAAAAGCTGATTTTCTTACAGTTAAGAAAGGAGACAAAGTGGACTTGCTTGTTTCATTAAGCAGCATTTACCAGACCTCGATAGATGACTTGAGGGAGACCATGGACAAAGTTAATAATCTAATAACAGTAAAGTTGAAGAAGGAACTTTGTTTGGCTTCAGAATGCAGGGCAAAGAACCTGGACAATATCGACGCAGGTTTGTCTCGACATCAGCAATCTCTTTCTTTAGTTAATTTTGATATTTCTGAAAGTTAGGATGTTTGTTGCAGATGGTTTGACGTATTTCGAAAATTTACTGGAGGAATCATCTTTATCGTCAAGTATATGTATACTGGAGAAGGATTACAATGATGCAATTCAGAACAAGGGTGAATTGGATGAGAGGATTTTTGTCAATGATGAGGATAGCTTGCTGGGGTCAGGGAGCTTGTCTGGAGGTGCAGTCAATATGAA</genome_strand>
        <mrna_strand>TAGAGAGAGAAAGGCGAGGGAAAATCAGGGGCTTTTTTAGTTTTTGAAGAATTTGGATCTAATTATACAGATCTGAGAAATTTGTACAATTTTGGGTTCTGGGTTTGGGTTTCTTTAGTTAGTTGTGGATGAATATGGAGGAGCTGAAGAATCATTCGAATTCTGAAGAGAATGGTTCGGTGGACTCTCTTGAAGTTCGATTTACTGATTTCTGCAAG...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AATGGATTGTCTATGGGTGAGAGTTTTATGGTAGAAGCTAGAAAGCTGTTTATGGACTGTAAACATCTTTTACTGTCAAATAATGCTGCTCTTGGAGCTATAACG....................................................................................................CCTGAGGAAGTTGAACGGTATTGGTTTGTGTTTGTTCTGTTCTCCGTGAAGAGATTACGTGAGAATGAAGCTAGGAATTCGAGTAATGGGAATGAAGGAAATGGATTTGATCTATGCCAAATTCTGCGAGGGGCGAAACTCAA..................................................................................TGTTCTAGATTTCTTCAAAGAATTACCACAGTTTATTGTTAAAGTTGGTCCAGTATTAAGCAACCTATATGGTTCAGATTGGGAGAAGAGACTTCAG................................................................................................................................................................................................................................................GCAAAGGAATTGCAGACCAACTTTGTGCATTTGAGCCTTTTAAGCAA.......................................................................................................................GTACTACAAGCGCGCATATCAGGAGCTGTTTTTGTCAAGTGATAACAATGAAGTAAATCAGTCTGCTACTTCTAATTCGATTGTCCTCTTGCCACAGTATTATCGTTTTGGCTGGTTGCTTTTTCTTTCACTTCGCGAACATGTATTCAGCCGCTTCAAGGACCTTGTGACATGCACAAATGGTTTAGTTTCTGTGCTG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCAATCTTAATAATACATGTGCCTGTATGCTTCAGAAATTTCAACATCAATGACTCCCCACGATTTG...........................................................................................................................TTAAGAAAGGAGACAAAGTGGACTTGCTTGTTTCATTAAGCAGCATTTACCAGACCTCGATAGATGACTTAAGGGAGACCATGGACAAAGTTAATAATCTAATAACAGTAAAGTTGAAGAAGGAACTTTGTTTGGCTTCAGAATGCAGGGCAAAGAACCTGGACAATATCGACGCAG.........................................................................ATGGTTTGACGTATTTCGAAAATTTACTGGAGGAATCATCTTTATCGTCAAGTATATGTATACTGGAGAAGGATTACAATGATGCAATTCAGAACAAGGGTGAATTGGATGAGAGGATTTTTTGTCATGATGAGGATAGCTTGCTGGGGTCAGGGAGCTTGTCTGGAGGTGCAGTCAATATGAA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U318571" ref_strand="+" ref_description="SGN-U318571        Tomato 200607 #1 [15 ESTs aligned] arabidopsis/peptide: | Symbol: None | expressed protein, similar to unknown protein (emb:CAB67623.1) | chr5:19420399-19421314 REVERSE | Aliases: MCA23.26, MCA23_26(evalue: 5e-33, score=138) genbank/nr: gi|15238843|ref|NP_199603.1| expressed protein [Arabidopsis thaliana] gi|10177928|dbj|BAB11339.1| emb|CAB67623.1~gene_id:MCA23.26~similar to unknown protein [Arabidopsis thaliana] gi|26449488|dbj|BAC41870.1| unknown protein [Arabidopsis thaliana](evalue: 4e-31, score=138)">
      <seq>tttggatgtgtcacacggggagctataaaagaaaagttgtgaagaaaattttggctgtttaaaccatatcaaagtgagatcacttgtaattttggccaagtataaattgatattcaaaagaagtttgctcttgggttggtgttgaacaatttctttaagattatttcagtagtgatgaagaacaactcagcaattaaattcctaaaacatgtcatttcagtactatccacactaaccaaatcaaaatcaacagccatcaaaagcaaaactgaggcaataaaagctaagttaatggtcttatcattgctcaaatccaagaaactctctttatctggcctaggaactaaggccatttctcacaagatccattcactattaggacataaagatcaagatcacgaagacgaaaacaacaaggccattgtactagtctacaaccacgcccctgaagtcggtgaggatcatgtacactatcagcataacgaggctaacgaagagatactactactattaagcaatggagaaaactacgattatgatgatgataagtatccggatttaacacattcattgttcgatgaagaggacgagtacttaggtgatccaaatgcatcagctatagacatggtaaggaatttcaaagaggaagaaggagagaactttgtgcttgaagacgagatcgataacgttgcagacttgttcatcaagaagtttcacaaaaggatgagattacaaaagcttgaatctttcaagaggtatcaagagatgcttcagagaagcacttaaattataagtagattaatgagtattattaattgctaattgaagtttttatctgttaaacttctgcagtattattattattgttgcagtagttcttttgtttcaactatgaagtgtttgctttttttaaataaattttcatgtcctttgttccctagtagcaaaagagagaaaaactaaggacttgtactaataagttgggagaaataggtaagtatgaatcaagattgtgtgtgagtttctaactatgtaaatttaatctctgatatcagtaatcacgatgaacttttggttatttgactttcgtactctgaatccagtcgttcttttcaaaagggagaaagtaat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09SLf0089D12.1" temp_strand="+" temp_description="C09SLf0089D12.1  AC234217.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLf0089D12 upload_account_name:spain (1 - 32889)">
        <position start="29685" stop="31930"/>
      </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="29985" g_stop="30143" g_length="159"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="159" r_length="159" r_score="0.981"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="30144" i_stop="30657" i_length="514">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.997" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="30658" g_stop="31630" g_length="973"/>
          <reference_exon_boundary r_type="cDNA" r_start="160" r_stop="1131" r_length="972" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLf0089D12.1" gen_strand="+" ref_id="SGN-U318571" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>1132</cumulative_length_of_scored_exons>
        <coverage percentage="1.001" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLf0089D12.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U318571" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="29985" e_stop="30143"/>
          <exon e_start="30658" e_stop="31630"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTGGATGTGTCACACAAGGAGCTAGAAAAGAAAAGTTGTGAAGAAAATTTTGGCTGTTTAAACCATATCAAAGTGAGATCACTTGTAATTTTGGCCAAGTATAAATTGATATTCAAAAGAAGTTTGCTCTTGGGTTGGTGTTGAACAATTTCTTTAAGGTAAGATTTGTGAATAATAACTCTTCTTATTCTATGTTTGGAGTACATTATATACTTTTCAATAGTTTGTAATTCTGTCACATGTTTGTACGATTTAGCTCGTAACTAACAAGATTTTTTGGTAATTTGTAGTTAAATTGAATCAGTAACGAGTTATTGTCGTTTAGCGATAGAAGTTGTTTGTCACTAATTCTTGTTGTTCTTACTCCACAAAATGGACATACAAGATCCATCCTATAAACCTGCTAACGCGAGATGCTTTGTGCATCGACATATATAAAATCTTCTCCAGAACTCTGCTAACGTGGGATGTTTTGTGCACCATCTTTGTTAGAATCCTGCTAATACAAGATGCTTTATGCATCGACGTATATAAGATCTTTGCTAGAACCCTACTAATGCGGAATGTTTTGTGCACGACATACAAACTAGAGTTATCATGTCAATATGAGTACTTCATACAATACTTTATATCTTGACTTAAAAACTTGTTTCCTATTTGATGATTTTTCAGATTATTTCAGTAGTGATGAAGAACAACTCAGCAATTAAATTCCTAAAACATGTCATTTCAGTACTATCCACACTAACCAAATCAAAATCAACAGCCATCAAAAGCAAAACTGAGGCAATAAAAGCTAAGTTAATGGTCTTATCATTGCTCAAATCCAAGAAACTCTCTTTATCTGGCCTAGGAACTAAGGCCATTTCTCACAAGATCCATTCACTATTAGGACATAAAGATCAAGATCACGAAGACGAAAACAACAAGGCCATTGTACTAGTCTACAACCACGCCCCTGAAGTCGGTGAGGATCATGTACACTATCAGCATAACGAGGCTAACGAAGAGATACTACTACTATTAAGCAATGGAGAAAACTACGATTATGATGATGATAAGTATCCGGATTTAACACATTCATTGTTCGATGAAGAGGACGAGTACTTAGGTGATCCAAATGCATCAGCTATAGACATGGTAAGGAATTTCAAAGAGGAAGAAGGAGAGAACTTTGTGCTTGAAGACGAGATCGATAACGTTGCAGACTTGTTCATCAAGAAGTTTCACAAAAGGATGAGATTACAAAAGCTTGAATCTTTCAAGAGGTATCAAGAGATGCTTCAGAGAAGCACTTAAATTATAAGTAGATTAATGAGTATTATTAATTGCTAATTGAAGTTTTTATCTGTTAAACTTCTGCAGTATTATTATTATTGTTGCAGTAGTTCTTTTGTTTCAACTATGAAGTGTTTGCTTTTTTTAAATAAATTTTCATGTCCTTTGTTCCCTAGTAGCAAAAGAGAGAAAAACTAAGGACTTGTACTAATAAGTTGGGAGAAATAGGTAAGTATGAATCAAGATTGTGTGTGAGTTTCTAACTATGTAAATTTAATCTCTGATATCAGTAATCACGATGAACTTTTGGTTATTTGACTTTCGTACTCTGAATCCAGTCGTTCTTTTTCAAAACGGAGAAAGTAAT</genome_strand>
        <mrna_strand>TTTGGATGTGTCACACGGGGAGCTATAAAAGAAAAGTTGTGAAGAAAATTTTGGCTGTTTAAACCATATCAAAGTGAGATCACTTGTAATTTTGGCCAAGTATAAATTGATATTCAAAAGAAGTTTGCTCTTGGGTTGGTGTTGAACAATTTCTTTAAG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTATTTCAGTAGTGATGAAGAACAACTCAGCAATTAAATTCCTAAAACATGTCATTTCAGTACTATCCACACTAACCAAATCAAAATCAACAGCCATCAAAAGCAAAACTGAGGCAATAAAAGCTAAGTTAATGGTCTTATCATTGCTCAAATCCAAGAAACTCTCTTTATCTGGCCTAGGAACTAAGGCCATTTCTCACAAGATCCATTCACTATTAGGACATAAAGATCAAGATCACGAAGACGAAAACAACAAGGCCATTGTACTAGTCTACAACCACGCCCCTGAAGTCGGTGAGGATCATGTACACTATCAGCATAACGAGGCTAACGAAGAGATACTACTACTATTAAGCAATGGAGAAAACTACGATTATGATGATGATAAGTATCCGGATTTAACACATTCATTGTTCGATGAAGAGGACGAGTACTTAGGTGATCCAAATGCATCAGCTATAGACATGGTAAGGAATTTCAAAGAGGAAGAAGGAGAGAACTTTGTGCTTGAAGACGAGATCGATAACGTTGCAGACTTGTTCATCAAGAAGTTTCACAAAAGGATGAGATTACAAAAGCTTGAATCTTTCAAGAGGTATCAAGAGATGCTTCAGAGAAGCACTTAAATTATAAGTAGATTAATGAGTATTATTAATTGCTAATTGAAGTTTTTATCTGTTAAACTTCTGCAGTATTATTATTATTGTTGCAGTAGTTCTTTTGTTTCAACTATGAAGTGTTTGCTTTTTTTAAATAAATTTTCATGTCCTTTGTTCCCTAGTAGCAAAAGAGAGAAAAACTAAGGACTTGTACTAATAAGTTGGGAGAAATAGGTAAGTATGAATCAAGATTGTGTGTGAGTTTCTAACTATGTAAATTTAATCTCTGATATCAGTAATCACGATGAACTTTTGGTTATTTGACTTTCGTACTCTGAATCCAGTCGTTC-TTTTCAAAAGGGAGAAAGTAAT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U336562" ref_strand="+" ref_description="SGN-U336562        Tomato 200607 #1 [1 ESTs aligned]">
      <seq>gcaattaaattcctaaaacatgtcatttcagtactatccacactaaccaaatcaaaatcaacagccattttaagcaaaactgaggcaataaaagctgaggtgagtggtcttattattggggaggtccaagaaactctctttatctggcctaggaactaagggcatttctcacaagatccattcactattaggacataaagatcaagatcacgaaga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLf0089D12-clscI/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09SLf0089D12.1" temp_strand="+" temp_description="C09SLf0089D12.1  AC234217.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLf0089D12 upload_account_name:spain (1 - 32889)">
        <position start="30388" stop="31202"/>
      </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="30688" g_stop="30902" g_length="215"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="216" r_length="216" r_score="0.930"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLf0089D12.1" gen_strand="+" ref_id="SGN-U336562" ref_strand="+">
        <total_alignment_score>0.930</total_alignment_score>
        <cumulative_length_of_scored_exons>215</cumulative_length_of_scored_exons>
        <coverage percentage="0.995" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLf0089D12.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U336562" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="30688" e_stop="30902"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCAATTAAATTCCTAAAACATGTCATTTCAGTACTATCCACACTAACCAAATCAAAATCAACAGCCATCAAAAGCAAAACTGAGGCAATAAAAGCT-AAGTTAATGGTCTTATCATTGCTCAAATCCAAGAAACTCTCTTTATCTGGCCTAGGAACTAAGGCCATTTCTCACAAGATCCATTCACTATTAGGACATAAAGATCAAGATCACGAAGA</genome_strand>
        <mrna_strand>GCAATTAAATTCCTAAAACATGTCATTTCAGTACTATCCACACTAACCAAATCAAAATCAACAGCCATTTTAAGCAAAACTGAGGCAATAAAAGCTGAGGTGAGTGGTCTTATTATTGGGGAGGTCCAAGAAACTCTCTTTATCTGGCCTAGGAACTAAGGGCATTTCTCACAAGATCCATTCACTATTAGGACATAAAGATCAAGATCACGAAGA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>6</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="-" PGL_start="4518" PGL_stop="4008"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="4518" e_stop="4008"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.992"/>
        </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="0.992">
            <gDNA_exon_boundary e_start="4518" e_stop="4008" e_length="511"/>
          </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="4518" stop="4008"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U340296" 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>ATCAACATTTTTTTCTTTTTGCTTATCACTCCACTCAACCTTTCAATAGCAAAACATTGTCCATTTGGTTCGAGATACACGGTATATGTTACCAACAAACTTCCTTTCGACTCTTCAAAATTGTCATTTCATTGTGCTTCAAAAAATGATGATCTCGGATATCACGATCTTGCTATAAATCAAGTGTTTAATTGGTCGTTTTGCGAGGCAATTTTCAGTAGAACTTTATTCTTTTGTCATTTTTGGTGGGGTTCAAAAGAGAAAGCATTCGATGTGTTTAACGATCCATATACATGTGTTAAAGGTACAGGAAATCCAAATATTTTAACTAATTGTAAATGGGAGGCAAGGGCAGATGGTTTTTATTTGGAATTGTTTAATAGTACAAGTGAGACATATTATATGTATCATTATTTAGAGTGGTCTTAGGGAATTAATATGTTTGTGTCATATTTTAATTTAGATAAAATGAGAAGTAAAAAAAAAAAAGAATTCCAAAGTGTATTATTTC</gDNA_template>
            <first_frame> I  N  I  F  F  F  L  L  I  T  P  L  N  L  S  I  A  K  H  C  P  F  G  S  R  Y  T  V  Y  V  T  N  K  L  P  F  D  S  S  K  L  S  F  H  C  A  S  K  N  D  D  L  G  Y  H  D  L  A  I  N  Q  V  F  N  W  S  F  C  E  A  I  F  S  R  T  L  F  F  C  H  F  W  W  G  S  K  E  K  A  F  D  V  F  N  D  P  Y  T  C  V  K  G  T  G  N  P  N  I  L  T  N  C  K  W  E  A  R  A  D  G  F  Y  L  E  L  F  N  S  T  S  E  T  Y  Y  M  Y  H  Y  L  E  W  S  *  G  I  N  M  F  V  S  Y  F  N  L  D  K  M  R  S  K  K  K  K  E  F  Q  S  V  L  F  </first_frame>
            <second_frame>  S  T  F  F  S  F  C  L  S  L  H  S  T  F  Q  *  Q  N  I  V  H  L  V  R  D  T  R  Y  M  L  P  T  N  F  L  S  T  L  Q  N  C  H  F  I  V  L  Q  K  M  M  I  S  D  I  T  I  L  L  *  I  K  C  L  I  G  R  F  A  R  Q  F  S  V  E  L  Y  S  F  V  I  F  G  G  V  Q  K  R  K  H  S  M  C  L  T  I  H  I  H  V  L  K  V  Q  E  I  Q  I  F  *  L  I  V  N  G  R  Q  G  Q  M  V  F  I  W  N  C  L  I  V  Q  V  R  H  I  I  C  I  I  I  *  S  G  L  R  E  L  I  C  L  C  H  I  L  I  *  I  K  *  E  V  K  K  K  K  N  S  K  V  Y  Y  F </second_frame>
            <third_frame>   Q  H  F  F  L  F  A  Y  H  S  T  Q  P  F  N  S  K  T  L  S  I  W  F  E  I  H  G  I  C  Y  Q  Q  T  S  F  R  L  F  K  I  V  I  S  L  C  F  K  K  *  *  S  R  I  S  R  S  C  Y  K  S  S  V  *  L  V  V  L  R  G  N  F  Q  *  N  F  I  L  L  S  F  L  V  G  F  K  R  E  S  I  R  C  V  *  R  S  I  Y  M  C  *  R  Y  R  K  S  K  Y  F  N  *  L  *  M  G  G  K  G  R  W  F  L  F  G  I  V  *  *  Y  K  *  D  I  L  Y  V  S  L  F  R  V  V  L  G  N  *  Y  V  C  V  I  F  *  F  R  *  N  E  K  *  K  K  K  R  I  P  K  C  I  I   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C09SLf0089D12.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="4518" stop="4090"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>426</number_coding_nucleotides>
                  <number_encoded_amino_acids>142</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>INIFFFLLITPLNLSIAKHCPFGSRYTVYVTNKLPFDSSKLSFHCASKNDDLGYHDLAINQVFNWSFCEAIFSRTLFFCHFWWGSKEKAFDVFNDPYTCVKGTGNPNILTNCKWEARADGFYLELFNSTSETYYMYHYLEWS*</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="8606" PGL_stop="8062"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="8606" e_stop="8062"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.983"/>
        </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="0.983">
            <gDNA_exon_boundary e_start="8606" e_stop="8062" e_length="545"/>
          </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="8606" stop="8062"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U345335" 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>GCTTCTCCCAAATATAATATGACTCTTTATTTCAACATCTTTTTTTTCTTGTTATTGATCACTCCTAATCTTGACCTTTCGCTAGCGGAAAATTGCTTTATTTTACCAAGTTATGAGGTACATATTATCAACAAACTTCCTACTAATACCTCACAATTGCAAGTTCATTGCACGTCAAAGGATGACGAAACTAGAAATGCATATCTTAACATAGATGAAGACTTACATTGGTCATTTTGCGAGTCATTTTTTGGTAATACTTCGTTTTTTTGTAACTTTTGGTGGGGTTCAATGAATAAGTCTATTACAGTGTTTGATGACCCAGGCACTTGTGTTCATAGTGGTCAGTATACAAATTATCATTACTCTTGCAAATGGGAAGTAAGACAAGATGGTTTTTATTTGGAGATGTTTAATTATAAGAATATGACATATTTTATGGATCACATTAGTGATTGGTCTTAGGGAATTAATATAATATGTTCCATTGATGTTTTGTATATTTAAATTTGGAAGGAAATATATTATCATGGAATTTTAGTGTG</gDNA_template>
            <first_frame> A  S  P  K  Y  N  M  T  L  Y  F  N  I  F  F  F  L  L  L  I  T  P  N  L  D  L  S  L  A  E  N  C  F  I  L  P  S  Y  E  V  H  I  I  N  K  L  P  T  N  T  S  Q  L  Q  V  H  C  T  S  K  D  D  E  T  R  N  A  Y  L  N  I  D  E  D  L  H  W  S  F  C  E  S  F  F  G  N  T  S  F  F  C  N  F  W  W  G  S  M  N  K  S  I  T  V  F  D  D  P  G  T  C  V  H  S  G  Q  Y  T  N  Y  H  Y  S  C  K  W  E  V  R  Q  D  G  F  Y  L  E  M  F  N  Y  K  N  M  T  Y  F  M  D  H  I  S  D  W  S  *  G  I  N  I  I  C  S  I  D  V  L  Y  I  *  I  W  K  E  I  Y  Y  H  G  I  L  V   </first_frame>
            <second_frame>  L  L  P  N  I  I  *  L  F  I  S  T  S  F  F  S  C  Y  *  S  L  L  I  L  T  F  R  *  R  K  I  A  L  F  Y  Q  V  M  R  Y  I  L  S  T  N  F  L  L  I  P  H  N  C  K  F  I  A  R  Q  R  M  T  K  L  E  M  H  I  L  T  *  M  K  T  Y  I  G  H  F  A  S  H  F  L  V  I  L  R  F  F  V  T  F  G  G  V  Q  *  I  S  L  L  Q  C  L  M  T  Q  A  L  V  F  I  V  V  S  I  Q  I  I  I  T  L  A  N  G  K  *  D  K  M  V  F  I  W  R  C  L  I  I  R  I  *  H  I  L  W  I  T  L  V  I  G  L  R  E  L  I  *  Y  V  P  L  M  F  C  I  F  K  F  G  R  K  Y  I  I  M  E  F  *  C  </second_frame>
            <third_frame>   F  S  Q  I  *  Y  D  S  L  F  Q  H  L  F  F  L  V  I  D  H  S  *  S  *  P  F  A  S  G  K  L  L  Y  F  T  K  L  *  G  T  Y  Y  Q  Q  T  S  Y  *  Y  L  T  I  A  S  S  L  H  V  K  G  *  R  N  *  K  C  I  S  *  H  R  *  R  L  T  L  V  I  L  R  V  I  F  W  *  Y  F  V  F  L  *  L  L  V  G  F  N  E  *  V  Y  Y  S  V  *  *  P  R  H  L  C  S  *  W  S  V  Y  K  L  S  L  L  L  Q  M  G  S  K  T  R  W  F  L  F  G  D  V  *  L  *  E  Y  D  I  F  Y  G  S  H  *  *  L  V  L  G  N  *  Y  N  M  F  H  *  C  F  V  Y  L  N  L  E  G  N  I  L  S  W  N  F  S  V </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="C09SLf0089D12.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="8606" stop="8142"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>462</number_coding_nucleotides>
                  <number_encoded_amino_acids>154</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>ASPKYNMTLYFNIFFFLLLITPNLDLSLAENCFILPSYEVHIINKLPTNTSQLQVHCTSKDDETRNAYLNIDEDLHWSFCESFFGNTSFFCNFWWGSMNKSITVFDDPGTCVHSGQYTNYHYSCKWEVRQDGFYLEMFNYKNMTYFMDHISDWS*</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="21511" PGL_stop="19376"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="21511" e_stop="21478"/>
            <exon e_start="21034" e_stop="20858"/>
            <exon e_start="20771" e_stop="20652"/>
            <exon e_start="20566" e_stop="20428"/>
            <exon e_start="20299" e_stop="20187"/>
            <exon e_start="20035" e_stop="19920"/>
            <exon e_start="19845" e_stop="19453"/>
            <exon e_start="19388" e_stop="19376"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.979" e_score="0.971"/>
          <exon-intron don_prob="0.000" acc_prob="0.980" e_score="1.000"/>
          <exon-intron don_prob="0.604" acc_prob="0.829" e_score="1.000"/>
          <exon-intron don_prob="0.972" acc_prob="0.973" e_score="1.000"/>
          <exon-intron don_prob="0.989" acc_prob="0.829" e_score="1.000"/>
          <exon-intron don_prob="0.982" acc_prob="0.874" e_score="1.000"/>
          <exon-intron don_prob="0.000" acc_prob="0.983" e_score="0.997"/>
          <exon-only e_score="0.692"/>
        </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="0.971">
            <gDNA_exon_boundary e_start="21511" e_stop="21478" e_length="34"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.979">
            <gDNA_intron_boundary i_start="21477" i_stop="21035" i_length="443"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="21034" e_stop="20858" e_length="177"/>
          </exon>
          <intron i_serial="2" don_prob="0.000" acc_prob="0.980">
            <gDNA_intron_boundary i_start="20857" i_stop="20772" i_length="86"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="20771" e_stop="20652" e_length="120"/>
          </exon>
          <intron i_serial="3" don_prob="0.604" acc_prob="0.829">
            <gDNA_intron_boundary i_start="20651" i_stop="20567" i_length="85"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="20566" e_stop="20428" e_length="139"/>
          </exon>
          <intron i_serial="4" don_prob="0.972" acc_prob="0.973">
            <gDNA_intron_boundary i_start="20427" i_stop="20300" i_length="128"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="20299" e_stop="20187" e_length="113"/>
          </exon>
          <intron i_serial="5" don_prob="0.989" acc_prob="0.829">
            <gDNA_intron_boundary i_start="20186" i_stop="20036" i_length="151"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="20035" e_stop="19920" e_length="116"/>
          </exon>
          <intron i_serial="6" don_prob="0.982" acc_prob="0.874">
            <gDNA_intron_boundary i_start="19919" i_stop="19846" i_length="74"/>
          </intron>
          <exon e_serial="7" e_score="0.997">
            <gDNA_exon_boundary e_start="19845" e_stop="19453" e_length="393"/>
          </exon>
          <intron i_serial="7" don_prob="0.000" acc_prob="0.983">
            <gDNA_intron_boundary i_start="19452" i_stop="19389" i_length="64"/>
          </intron>
          <exon e_serial="8" e_score="0.692">
            <gDNA_exon_boundary e_start="19388" e_stop="19376" e_length="13"/>
          </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="21511" stop="21478"/>
              <exon start="21034" stop="20858"/>
              <exon start="20771" stop="20652"/>
              <exon start="20566" stop="20428"/>
              <exon start="20299" stop="20187"/>
              <exon start="20035" stop="19920"/>
              <exon start="19845" stop="19453"/>
              <exon start="19388" stop="19376"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U322585" 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>TGCTGAGACATCCATCAATGTATTCTTTGGCAAG : ATTGTGAAGTTGGCTGCTGTCAGAATCAATGGCATGATTGAGCGGCTACAGCTTTCTCAACAAATAAGAGAGACTGTATATTGCCTTTTTCAGAAGATTCTCAGTCAGAGGACAAGTCTTTTCTTCAGCAGACATATTGACCAGATCATCCTTTGCTCTTTCTATGGAGTTGCCAAG : ATTTCACAACTTAACTTGACCTTCAAAGAAATCATATACAACTACCGAAAGCAACCTCAGTGCAAACCACAAGTTTTTCGAAGTGTTTTTGTTGACTGGACATCAGCGCGTCACAATGGG : AAAACAGGTTCAGAACATGTGGATATCATCACGTTCTACAATGAAATGTTTATTCCTTCTGTTAAGCCATTATTAGTTGAGCTTGCACCTGCTGGAAATGAGCAAAAGAATAACCATGTTGAAAAAACCAAGAAGGACG : GGCAAGGACCAGCATCCCCCAGATCATCTTCATTTCCCAGTCTCCCCGACATGTCTCCAAAGAAAGTATCTGCTGTTCATAATGTTTATGTCTCCCCGCTGCGATCATCGAAG : ATGGATGCGTTGATTTCCCATAGCTCTAAAAGCTATTATGCTTGTGTGGGAGAAAGCACTCATGCTTATCAGAGCCCCTCAAAAGATTTGACAGTAATCAACAACCGCTTGAATGG : CAATCGGAAGCTCAGAGGCGCTCTTAATTTTGATGACGTTGATGCTGTGGGCTTGGTTAGTGATTCCATAGTTGCCAACACCCTTTACCTTCAAAACGGGAACTGCATATCATCACCTCGTGCAGCTGTGAAGACTGAGCAGCCCGAGCCCTAATACCTGGACAAACTTGCACTGTAAATAGGCTTTCGGATTATGACATTTCTTTTTCCTAGTTTTTTAAGGGTATCCTAAACGTAGAGAGATGTATAGGGGTGTTGAATGAGCGGTATGTTTATGTAAAATGCCCGCCACCAACCCGATGCTTCTTTTTTAACTGTTGATTTCTGATTCTGGGAATATATATAGGGATAGATAGTCTTGTTCCTTAATAAGAGTAATAGTTGTACATTACA : GAAAAGAAAATAG</gDNA_template>
            <first_frame> C  *  D  I  H  Q  C  I  L  W  Q   : D  C  E  V  G  C  C  Q  N  Q  W  H  D  *  A  A  T  A  F  S  T  N  K  R  D  C  I  L  P  F  S  E  D  S  Q  S  E  D  K  S  F  L  Q  Q  T  Y  *  P  D  H  P  L  L  F  L  W  S  C  Q   : D  F  T  T  *  L  D  L  Q  R  N  H  I  Q  L  P  K  A  T  S  V  Q  T  T  S  F  S  K  C  F  C  *  L  D  I  S  A  S  Q  W   : E  N  R  F  R  T  C  G  Y  H  H  V  L  Q  *  N  V  Y  S  F  C  *  A  I  I  S  *  A  C  T  C  W  K  *  A  K  E  *  P  C  *  K  N  Q  E  G  R :   A  R  T  S  I  P  Q  I  I  F  I  S  Q  S  P  R  H  V  S  K  E  S  I  C  C  S  *  C  L  C  L  P  A  A  I  I  E   : D  G  C  V  D  F  P  *  L  *  K  L  L  C  L  C  G  R  K  H  S  C  L  S  E  P  L  K  R  F  D  S  N  Q  Q  P  L  E  W  :  Q  S  E  A  Q  R  R  S  *  F  *  *  R  *  C  C  G  L  G  *  *  F  H  S  C  Q  H  P  L  P  S  K  R  E  L  H  I  I  T  S  C  S  C  E  D  *  A  A  R  A  L  I  P  G  Q  T  C  T  V  N  R  L  S  D  Y  D  I  S  F  S  *  F  F  K  G  I  L  N  V  E  R  C  I  G  V  L  N  E  R  Y  V  Y  V  K  C  P  P  P  T  R  C  F  F  F  N  C  *  F  L  I  L  G  I  Y  I  G  I  D  S  L  V  P  *  *  E  *  *  L  Y  I  T  :  E  K  K  I  </first_frame>
            <second_frame>  A  E  T  S  I  N  V  F  F  G  K  :  I  V  K  L  A  A  V  R  I  N  G  M  I  E  R  L  Q  L  S  Q  Q  I  R  E  T  V  Y  C  L  F  Q  K  I  L  S  Q  R  T  S  L  F  F  S  R  H  I  D  Q  I  I  L  C  S  F  Y  G  V  A  K  :  I  S  Q  L  N  L  T  F  K  E  I  I  Y  N  Y  R  K  Q  P  Q  C  K  P  Q  V  F  R  S  V  F  V  D  W  T  S  A  R  H  N  G  :  K  T  G  S  E  H  V  D  I  I  T  F  Y  N  E  M  F  I  P  S  V  K  P  L  L  V  E  L  A  P  A  G  N  E  Q  K  N  N  H  V  E  K  T  K  K  D   : G  Q  G  P  A  S  P  R  S  S  S  F  P  S  L  P  D  M  S  P  K  K  V  S  A  V  H  N  V  Y  V  S  P  L  R  S  S  K  :  M  D  A  L  I  S  H  S  S  K  S  Y  Y  A  C  V  G  E  S  T  H  A  Y  Q  S  P  S  K  D  L  T  V  I  N  N  R  L  N  G :   N  R  K  L  R  G  A  L  N  F  D  D  V  D  A  V  G  L  V  S  D  S  I  V  A  N  T  L  Y  L  Q  N  G  N  C  I  S  S  P  R  A  A  V  K  T  E  Q  P  E  P  *  Y  L  D  K  L  A  L  *  I  G  F  R  I  M  T  F  L  F  P  S  F  L  R  V  S  *  T  *  R  D  V  *  G  C  *  M  S  G  M  F  M  *  N  A  R  H  Q  P  D  A  S  F  L  T  V  D  F  *  F  W  E  Y  I  *  G  *  I  V  L  F  L  N  K  S  N  S  C  T  L  Q :   K  R  K  * </second_frame>
            <third_frame>   L  R  H  P  S  M  Y  S  L  A  R :   L  *  S  W  L  L  S  E  S  M  A  *  L  S  G  Y  S  F  L  N  K  *  E  R  L  Y  I  A  F  F  R  R  F  S  V  R  G  Q  V  F  S  S  A  D  I  L  T  R  S  S  F  A  L  S  M  E  L  P  R :   F  H  N  L  T  *  P  S  K  K  S  Y  T  T  T  E  S  N  L  S  A  N  H  K  F  F  E  V  F  L  L  T  G  H  Q  R  V  T  M  G :   K  Q  V  Q  N  M  W  I  S  S  R  S  T  M  K  C  L  F  L  L  L  S  H  Y  *  L  S  L  H  L  L  E  M  S  K  R  I  T  M  L  K  K  P  R  R  T  :  G  K  D  Q  H  P  P  D  H  L  H  F  P  V  S  P  T  C  L  Q  R  K  Y  L  L  F  I  M  F  M  S  P  R  C  D  H  R  R :   W  M  R  *  F  P  I  A  L  K  A  I  M  L  V  W  E  K  A  L  M  L  I  R  A  P  Q  K  I  *  Q  *  S  T  T  A  *  M   : A  I  G  S  S  E  A  L  L  I  L  M  T  L  M  L  W  A  W  L  V  I  P  *  L  P  T  P  F  T  F  K  T  G  T  A  Y  H  H  L  V  Q  L  *  R  L  S  S  P  S  P  N  T  W  T  N  L  H  C  K  *  A  F  G  L  *  H  F  F  F  L  V  F  *  G  Y  P  K  R  R  E  M  Y  R  G  V  E  *  A  V  C  L  C  K  M  P  A  T  N  P  M  L  L  F  *  L  L  I  S  D  S  G  N  I  Y  R  D  R  *  S  C  S  L  I  R  V  I  V  V  H  Y   : R  K  E  N   </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="C09SLf0089D12.1" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="21510" stop="21478"/>
                    <exon start="21034" stop="20858"/>
                    <exon start="20771" stop="20652"/>
                    <exon start="20566" stop="20428"/>
                    <exon start="20299" stop="20187"/>
                    <exon start="20035" stop="19920"/>
                    <exon start="19845" stop="19692"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>849</number_coding_nucleotides>
                  <number_encoded_amino_acids>283</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>AETSINVFFGKIVKLAAVRINGMIERLQLSQQIRETVYCLFQKILSQRTSLFFSRHIDQIILCSFYGVAKISQLNLTFKEIIYNYRKQPQCKPQVFRSVFVDWTSARHNGKTGSEHVDIITFYNEMFIPSVKPLLVELAPAGNEQKNNHVEKTKKDGQGPASPRSSSFPSLPDMSPKKVSAVHNVYVSPLRSSKMDALISHSSKSYYACVGESTHAYQSPSKDLTVINNRLNGNRKLRGALNFDDVDAVGLVSDSIVANTLYLQNGNCISSPRAAVKTEQPEP*</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="26062" PGL_stop="22928"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="26062" e_stop="25846"/>
            <exon e_start="25186" e_stop="25082"/>
            <exon e_start="24981" e_stop="24839"/>
            <exon e_start="24756" e_stop="24660"/>
            <exon e_start="24419" e_stop="24373"/>
            <exon e_start="24253" e_stop="24055"/>
            <exon e_start="23551" e_stop="23485"/>
            <exon e_start="23361" e_stop="23185"/>
            <exon e_start="23111" e_stop="22928"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.995" acc_prob="0.998" e_score="0.968"/>
          <exon-intron don_prob="0.998" acc_prob="0.947" e_score="0.971"/>
          <exon-intron don_prob="0.972" acc_prob="0.566" e_score="0.979"/>
          <exon-intron don_prob="0.000" acc_prob="0.980" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.961" e_score="1.000"/>
          <exon-intron don_prob="0.972" acc_prob="0.956" e_score="1.000"/>
          <exon-intron don_prob="0.917" acc_prob="0.273" e_score="1.000"/>
          <exon-intron don_prob="0.987" acc_prob="0.986" e_score="0.994"/>
          <exon-only e_score="0.978"/>
        </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="0.968">
            <gDNA_exon_boundary e_start="26062" e_stop="25846" e_length="217"/>
          </exon>
          <intron i_serial="1" don_prob="0.995" acc_prob="0.998">
            <gDNA_intron_boundary i_start="25845" i_stop="25187" i_length="659"/>
          </intron>
          <exon e_serial="2" e_score="0.971">
            <gDNA_exon_boundary e_start="25186" e_stop="25082" e_length="105"/>
          </exon>
          <intron i_serial="2" don_prob="0.998" acc_prob="0.947">
            <gDNA_intron_boundary i_start="25081" i_stop="24982" i_length="100"/>
          </intron>
          <exon e_serial="3" e_score="0.979">
            <gDNA_exon_boundary e_start="24981" e_stop="24839" e_length="143"/>
          </exon>
          <intron i_serial="3" don_prob="0.972" acc_prob="0.566">
            <gDNA_intron_boundary i_start="24838" i_stop="24757" i_length="82"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="24756" e_stop="24660" e_length="97"/>
          </exon>
          <intron i_serial="4" don_prob="0.000" acc_prob="0.980">
            <gDNA_intron_boundary i_start="24659" i_stop="24420" i_length="240"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="24419" e_stop="24373" e_length="47"/>
          </exon>
          <intron i_serial="5" don_prob="0.998" acc_prob="0.961">
            <gDNA_intron_boundary i_start="24372" i_stop="24254" i_length="119"/>
          </intron>
          <exon e_serial="6" e_score="1.000">
            <gDNA_exon_boundary e_start="24253" e_stop="24055" e_length="199"/>
          </exon>
          <intron i_serial="6" don_prob="0.972" acc_prob="0.956">
            <gDNA_intron_boundary i_start="24054" i_stop="23552" i_length="503"/>
          </intron>
          <exon e_serial="7" e_score="1.000">
            <gDNA_exon_boundary e_start="23551" e_stop="23485" e_length="67"/>
          </exon>
          <intron i_serial="7" don_prob="0.917" acc_prob="0.273">
            <gDNA_intron_boundary i_start="23484" i_stop="23362" i_length="123"/>
          </intron>
          <exon e_serial="8" e_score="0.994">
            <gDNA_exon_boundary e_start="23361" e_stop="23185" e_length="177"/>
          </exon>
          <intron i_serial="8" don_prob="0.987" acc_prob="0.986">
            <gDNA_intron_boundary i_start="23184" i_stop="23112" i_length="73"/>
          </intron>
          <exon e_serial="9" e_score="0.978">
            <gDNA_exon_boundary e_start="23111" e_stop="22928" e_length="184"/>
          </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="26062" stop="25846"/>
              <exon start="25186" stop="25082"/>
              <exon start="24981" stop="24839"/>
              <exon start="24756" stop="24660"/>
              <exon start="24419" stop="24373"/>
              <exon start="24253" stop="24055"/>
              <exon start="23551" stop="23485"/>
              <exon start="23361" stop="23185"/>
              <exon start="23111" stop="22928"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U330582" 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>TAGAGAGAGAAAGGCGAGGGAAAATTAGGGGTTTTTTAGTTTTTGAAGAATTTGGATCTAATTATACAGATCTGAGAAATTTGTAGAATTTTGGGTTCTGGGTTTCCGTTTCTTTAGTTAGTTGTGGATGAATATGGAGGAGCTGAAGAATCATTCGAATTCTGAAGAGAATGGTTCGGTGGACTCTCTTGAAGTTCGATTTAGTGATTTCTGCAAG : AATGGATTGTCGATGGGTGAGAGTTTTATGGTAGAAGCTAGAAAGCTGTTTATGGACAGTAAACATCTTTTACTGTCAAATAATGCTGCTATTGGAGCTATAACG : CCGGAGGAAGTTGAACGGTATTGGTTTGTGTTTGTTCTGTTCTCGGTGAAGAGATTAAGTGAGAATGAAGCTAGGAATTCGAGTAATGGGAATGAAGGAAATGGATTTGATCTATGCCAAATTCTGCGAGGGGCGAAACTCAA : TGTTCTAGATTTCTTCAAAGAATTACCACAGTTTATTGTTAAAGTTGGTCCAGTATTAAGCAACCTATATGGTTCAGATTGGGAGAAGAGACTTCAG : GCAAAGGAATTGCAGACCAACTTTGTGCATTTGAGCCTTTTAAGCAA : GTACTACAAGCGCGCATATCAGGAGCTGTTTTTGTCAAGTGATAACAATGAAGTAAATCAGTCTGCTACTTCTAATTCGATTGTCCTCTTGCCACAGTATTATCGTTTTGGCTGGTTGCTTTTTCTTTCACTTCGCGAACATGTATTCAGCCGCTTCAAGGACCTTGTGACATGCACAAATGGTTTAGTTTCTGTGCTG : GCAATCTTAATAATACATGTGCCTGTATGCTTCAGAAATTTCAACATCAATGACTCCCCACGATTTG : TTAAGAAAGGAGACAAAGTGGACTTGCTTGTTTCATTAAGCAGCATTTACCAGACCTCGATAGATGACTTGAGGGAGACCATGGACAAAGTTAATAATCTAATAACAGTAAAGTTGAAGAAGGAACTTTGTTTGGCTTCAGAATGCAGGGCAAAGAACCTGGACAATATCGACGCAG : ATGGTTTGACGTATTTCGAAAATTTACTGGAGGAATCATCTTTATCGTCAAGTATATGTATACTGGAGAAGGATTACAATGATGCAATTCAGAACAAGGGTGAATTGGATGAGAGGATTTTTGTCAATGATGAGGATAGCTTGCTGGGGTCAGGGAGCTTGTCTGGAGGTGCAGTCAATATGAA</gDNA_template>
            <first_frame> *  R  E  K  G  E  G  K  L  G  V  F  *  F  L  K  N  L  D  L  I  I  Q  I  *  E  I  C  R  I  L  G  S  G  F  P  F  L  *  L  V  V  D  E  Y  G  G  A  E  E  S  F  E  F  *  R  E  W  F  G  G  L  S  *  S  S  I  *  *  F  L  Q   : E  W  I  V  D  G  *  E  F  Y  G  R  S  *  K  A  V  Y  G  Q  *  T  S  F  T  V  K  *  C  C  Y  W  S  Y  N   : A  G  G  S  *  T  V  L  V  C  V  C  S  V  L  G  E  E  I  K  *  E  *  S  *  E  F  E  *  W  E  *  R  K  W  I  *  S  M  P  N  S  A  R  G  E  T  Q  :  C  S  R  F  L  Q  R  I  T  T  V  Y  C  *  S  W  S  S  I  K  Q  P  I  W  F  R  L  G  E  E  T  S   : G  K  G  I  A  D  Q  L  C  A  F  E  P  F  K  Q  :  V  L  Q  A  R  I  S  G  A  V  F  V  K  *  *  Q  *  S  K  S  V  C  Y  F  *  F  D  C  P  L  A  T  V  L  S  F  W  L  V  A  F  S  F  T  S  R  T  C  I  Q  P  L  Q  G  P  C  D  M  H  K  W  F  S  F  C  A   : G  N  L  N  N  T  C  A  C  M  L  Q  K  F  Q  H  Q  *  L  P  T  I  C :   *  E  R  R  Q  S  G  L  A  C  F  I  K  Q  H  L  P  D  L  D  R  *  L  E  G  D  H  G  Q  S  *  *  S  N  N  S  K  V  E  E  G  T  L  F  G  F  R  M  Q  G  K  E  P  G  Q  Y  R  R  R :   W  F  D  V  F  R  K  F  T  G  G  I  I  F  I  V  K  Y  M  Y  T  G  E  G  L  Q  *  C  N  S  E  Q  G  *  I  G  *  E  D  F  C  Q  *  *  G  *  L  A  G  V  R  E  L  V  W  R  C  S  Q  Y  E </first_frame>
            <second_frame>  R  E  R  K  A  R  E  N  *  G  F  F  S  F  *  R  I  W  I  *  L  Y  R  S  E  K  F  V  E  F  W  V  L  G  F  R  F  F  S  *  L  W  M  N  M  E  E  L  K  N  H  S  N  S  E  E  N  G  S  V  D  S  L  E  V  R  F  S  D  F  C  K  :  N  G  L  S  M  G  E  S  F  M  V  E  A  R  K  L  F  M  D  S  K  H  L  L  L  S  N  N  A  A  I  G  A  I  T  :  P  E  E  V  E  R  Y  W  F  V  F  V  L  F  S  V  K  R  L  S  E  N  E  A  R  N  S  S  N  G  N  E  G  N  G  F  D  L  C  Q  I  L  R  G  A  K  L  N :   V  L  D  F  F  K  E  L  P  Q  F  I  V  K  V  G  P  V  L  S  N  L  Y  G  S  D  W  E  K  R  L  Q  :  A  K  E  L  Q  T  N  F  V  H  L  S  L  L  S  K :   Y  Y  K  R  A  Y  Q  E  L  F  L  S  S  D  N  N  E  V  N  Q  S  A  T  S  N  S  I  V  L  L  P  Q  Y  Y  R  F  G  W  L  L  F  L  S  L  R  E  H  V  F  S  R  F  K  D  L  V  T  C  T  N  G  L  V  S  V  L  :  A  I  L  I  I  H  V  P  V  C  F  R  N  F  N  I  N  D  S  P  R  F   : V  K  K  G  D  K  V  D  L  L  V  S  L  S  S  I  Y  Q  T  S  I  D  D  L  R  E  T  M  D  K  V  N  N  L  I  T  V  K  L  K  K  E  L  C  L  A  S  E  C  R  A  K  N  L  D  N  I  D  A   : D  G  L  T  Y  F  E  N  L  L  E  E  S  S  L  S  S  S  I  C  I  L  E  K  D  Y  N  D  A  I  Q  N  K  G  E  L  D  E  R  I  F  V  N  D  E  D  S  L  L  G  S  G  S  L  S  G  G  A  V  N  M   </second_frame>
            <third_frame>   E  R  E  R  R  G  K  I  R  G  F  L  V  F  E  E  F  G  S  N  Y  T  D  L  R  N  L  *  N  F  G  F  W  V  S  V  S  L  V  S  C  G  *  I  W  R  S  *  R  I  I  R  I  L  K  R  M  V  R  W  T  L  L  K  F  D  L  V  I  S  A  R :   M  D  C  R  W  V  R  V  L  W  *  K  L  E  S  C  L  W  T  V  N  I  F  Y  C  Q  I  M  L  L  L  E  L  *  R :   R  R  K  L  N  G  I  G  L  C  L  F  C  S  R  *  R  D  *  V  R  M  K  L  G  I  R  V  M  G  M  K  E  M  D  L  I  Y  A  K  F  C  E  G  R  N  S   : M  F  *  I  S  S  K  N  Y  H  S  L  L  L  K  L  V  Q  Y  *  A  T  Y  M  V  Q  I  G  R  R  D  F  R :   Q  R  N  C  R  P  T  L  C  I  *  A  F  *  A   : S  T  T  S  A  H  I  R  S  C  F  C  Q  V  I  T  M  K  *  I  S  L  L  L  L  I  R  L  S  S  C  H  S  I  I  V  L  A  G  C  F  F  F  H  F  A  N  M  Y  S  A  A  S  R  T  L  *  H  A  Q  M  V  *  F  L  C  W :   Q  S  *  *  Y  M  C  L  Y  A  S  E  I  S  T  S  M  T  P  H  D  L  :  L  R  K  E  T  K  W  T  C  L  F  H  *  A  A  F  T  R  P  R  *  M  T  *  G  R  P  W  T  K  L  I  I  *  *  Q  *  S  *  R  R  N  F  V  W  L  Q  N  A  G  Q  R  T  W  T  I  S  T  Q  :  M  V  *  R  I  S  K  I  Y  W  R  N  H  L  Y  R  Q  V  Y  V  Y  W  R  R  I  T  M  M  Q  F  R  T  R  V  N  W  M  R  G  F  L  S  M  M  R  I  A  C  W  G  Q  G  A  C  L  E  V  Q  S  I  *  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C09SLf0089D12.1" strand="-"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="25941" stop="25846"/>
                    <exon start="25186" stop="25082"/>
                    <exon start="24981" stop="24839"/>
                    <exon start="24756" stop="24660"/>
                    <exon start="24419" stop="24373"/>
                    <exon start="24253" stop="24055"/>
                    <exon start="23551" stop="23485"/>
                    <exon start="23361" stop="23185"/>
                    <exon start="23111" stop="22930"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>1113</number_coding_nucleotides>
                  <number_encoded_amino_acids>371</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LWMNMEELKNHSNSEENGSVDSLEVRFSDFCKNGLSMGESFMVEARKLFMDSKHLLLSNNAAIGAITPEEVERYWFVFVLFSVKRLSENEARNSSNGNEGNGFDLCQILRGAKLNVLDFFKELPQFIVKVGPVLSNLYGSDWEKRLQAKELQTNFVHLSLLSKYYKRAYQELFLSSDNNEVNQSATSNSIVLLPQYYRFGWLLFLSLREHVFSRFKDLVTCTNGLVSVLAILIIHVPVCFRNFNINDSPRFVKKGDKVDLLVSLSSIYQTSIDDLRETMDKVNNLITVKLKKELCLASECRAKNLDNIDADGLTYFENLLEESSLSSSICILEKDYNDAIQNKGELDERIFVNDEDSLLGSGSLSGGAVNM</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="5" PGL_strand="+" PGL_start="29985" PGL_stop="31630"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="29985" e_stop="30143"/>
            <exon e_start="30658" e_stop="31630"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.996" acc_prob="0.997" e_score="0.981"/>
          <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="0.981">
            <gDNA_exon_boundary e_start="29985" e_stop="30143" e_length="159"/>
          </exon>
          <intron i_serial="1" don_prob="0.996" acc_prob="0.997">
            <gDNA_intron_boundary i_start="30144" i_stop="30657" i_length="514"/>
          </intron>
          <exon e_serial="2" e_score="0.998">
            <gDNA_exon_boundary e_start="30658" e_stop="31630" e_length="973"/>
          </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="29985" stop="30143"/>
              <exon start="30658" stop="31630"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U318571" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="30688" stop="30902"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U336562" 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="5" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>TTTGGATGTGTCACACAAGGAGCTAGAAAAGAAAAGTTGTGAAGAAAATTTTGGCTGTTTAAACCATATCAAAGTGAGATCACTTGTAATTTTGGCCAAGTATAAATTGATATTCAAAAGAAGTTTGCTCTTGGGTTGGTGTTGAACAATTTCTTTAAG : ATTATTTCAGTAGTGATGAAGAACAACTCAGCAATTAAATTCCTAAAACATGTCATTTCAGTACTATCCACACTAACCAAATCAAAATCAACAGCCATCAAAAGCAAAACTGAGGCAATAAAAGCTAAGTTAATGGTCTTATCATTGCTCAAATCCAAGAAACTCTCTTTATCTGGCCTAGGAACTAAGGCCATTTCTCACAAGATCCATTCACTATTAGGACATAAAGATCAAGATCACGAAGACGAAAACAACAAGGCCATTGTACTAGTCTACAACCACGCCCCTGAAGTCGGTGAGGATCATGTACACTATCAGCATAACGAGGCTAACGAAGAGATACTACTACTATTAAGCAATGGAGAAAACTACGATTATGATGATGATAAGTATCCGGATTTAACACATTCATTGTTCGATGAAGAGGACGAGTACTTAGGTGATCCAAATGCATCAGCTATAGACATGGTAAGGAATTTCAAAGAGGAAGAAGGAGAGAACTTTGTGCTTGAAGACGAGATCGATAACGTTGCAGACTTGTTCATCAAGAAGTTTCACAAAAGGATGAGATTACAAAAGCTTGAATCTTTCAAGAGGTATCAAGAGATGCTTCAGAGAAGCACTTAAATTATAAGTAGATTAATGAGTATTATTAATTGCTAATTGAAGTTTTTATCTGTTAAACTTCTGCAGTATTATTATTATTGTTGCAGTAGTTCTTTTGTTTCAACTATGAAGTGTTTGCTTTTTTTAAATAAATTTTCATGTCCTTTGTTCCCTAGTAGCAAAAGAGAGAAAAACTAAGGACTTGTACTAATAAGTTGGGAGAAATAGGTAAGTATGAATCAAGATTGTGTGTGAGTTTCTAACTATGTAAATTTAATCTCTGATATCAGTAATCACGATGAACTTTTGGTTATTTGACTTTCGTACTCTGAATCCAGTCGTTCTTTTTCAAAACGGAGAAAGTAAT</gDNA_template>
            <first_frame> F  G  C  V  T  Q  G  A  R  K  E  K  L  *  R  K  F  W  L  F  K  P  Y  Q  S  E  I  T  C  N  F  G  Q  V  *  I  D  I  Q  K  K  F  A  L  G  L  V  L  N  N  F  F  K  :  I  I  S  V  V  M  K  N  N  S  A  I  K  F  L  K  H  V  I  S  V  L  S  T  L  T  K  S  K  S  T  A  I  K  S  K  T  E  A  I  K  A  K  L  M  V  L  S  L  L  K  S  K  K  L  S  L  S  G  L  G  T  K  A  I  S  H  K  I  H  S  L  L  G  H  K  D  Q  D  H  E  D  E  N  N  K  A  I  V  L  V  Y  N  H  A  P  E  V  G  E  D  H  V  H  Y  Q  H  N  E  A  N  E  E  I  L  L  L  L  S  N  G  E  N  Y  D  Y  D  D  D  K  Y  P  D  L  T  H  S  L  F  D  E  E  D  E  Y  L  G  D  P  N  A  S  A  I  D  M  V  R  N  F  K  E  E  E  G  E  N  F  V  L  E  D  E  I  D  N  V  A  D  L  F  I  K  K  F  H  K  R  M  R  L  Q  K  L  E  S  F  K  R  Y  Q  E  M  L  Q  R  S  T  *  I  I  S  R  L  M  S  I  I  N  C  *  L  K  F  L  S  V  K  L  L  Q  Y  Y  Y  Y  C  C  S  S  S  F  V  S  T  M  K  C  L  L  F  L  N  K  F  S  C  P  L  F  P  S  S  K  R  E  K  N  *  G  L  V  L  I  S  W  E  K  *  V  S  M  N  Q  D  C  V  *  V  S  N  Y  V  N  L  I  S  D  I  S  N  H  D  E  L  L  V  I  *  L  S  Y  S  E  S  S  R  S  F  S  K  R  R  K  *  </first_frame>
            <second_frame>  L  D  V  S  H  K  E  L  E  K  K  S  C  E  E  N  F  G  C  L  N  H  I  K  V  R  S  L  V  I  L  A  K  Y  K  L  I  F  K  R  S  L  L  L  G  W  C  *  T  I  S  L  R :   L  F  Q  *  *  *  R  T  T  Q  Q  L  N  S  *  N  M  S  F  Q  Y  Y  P  H  *  P  N  Q  N  Q  Q  P  S  K  A  K  L  R  Q  *  K  L  S  *  W  S  Y  H  C  S  N  P  R  N  S  L  Y  L  A  *  E  L  R  P  F  L  T  R  S  I  H  Y  *  D  I  K  I  K  I  T  K  T  K  T  T  R  P  L  Y  *  S  T  T  T  P  L  K  S  V  R  I  M  Y  T  I  S  I  T  R  L  T  K  R  Y  Y  Y  Y  *  A  M  E  K  T  T  I  M  M  M  I  S  I  R  I  *  H  I  H  C  S  M  K  R  T  S  T  *  V  I  Q  M  H  Q  L  *  T  W  *  G  I  S  K  R  K  K  E  R  T  L  C  L  K  T  R  S  I  T  L  Q  T  C  S  S  R  S  F  T  K  G  *  D  Y  K  S  L  N  L  S  R  G  I  K  R  C  F  R  E  A  L  K  L  *  V  D  *  *  V  L  L  I  A  N  *  S  F  Y  L  L  N  F  C  S  I  I  I  I  V  A  V  V  L  L  F  Q  L  *  S  V  C  F  F  *  I  N  F  H  V  L  C  S  L  V  A  K  E  R  K  T  K  D  L  Y  *  *  V  G  R  N  R  *  V  *  I  K  I  V  C  E  F  L  T  M  *  I  *  S  L  I  S  V  I  T  M  N  F  W  L  F  D  F  R  T  L  N  P  V  V  L  F  Q  N  G  E  S  N </second_frame>
            <third_frame>   W  M  C  H  T  R  S  *  K  R  K  V  V  K  K  I  L  A  V  *  T  I  S  K  *  D  H  L  *  F  W  P  S  I  N  *  Y  S  K  E  V  C  S  W  V  G  V  E  Q  F  L  *   : D  Y  F  S  S  D  E  E  Q  L  S  N  *  I  P  K  T  C  H  F  S  T  I  H  T  N  Q  I  K  I  N  S  H  Q  K  Q  N  *  G  N  K  S  *  V  N  G  L  I  I  A  Q  I  Q  E  T  L  F  I  W  P  R  N  *  G  H  F  S  Q  D  P  F  T  I  R  T  *  R  S  R  S  R  R  R  K  Q  Q  G  H  C  T  S  L  Q  P  R  P  *  S  R  *  G  S  C  T  L  S  A  *  R  G  *  R  R  D  T  T  T  I  K  Q  W  R  K  L  R  L  *  *  *  *  V  S  G  F  N  T  F  I  V  R  *  R  G  R  V  L  R  *  S  K  C  I  S  Y  R  H  G  K  E  F  Q  R  G  R  R  R  E  L  C  A  *  R  R  D  R  *  R  C  R  L  V  H  Q  E  V  S  Q  K  D  E  I  T  K  A  *  I  F  Q  E  V  S  R  D  A  S  E  K  H  L  N  Y  K  *  I  N  E  Y  Y  *  L  L  I  E  V  F  I  C  *  T  S  A  V  L  L  L  L  L  Q  *  F  F  C  F  N  Y  E  V  F  A  F  F  K  *  I  F  M  S  F  V  P  *  *  Q  K  R  E  K  L  R  T  C  T  N  K  L  G  E  I  G  K  Y  E  S  R  L  C  V  S  F  *  L  C  K  F  N  L  *  Y  Q  *  S  R  *  T  F  G  Y  L  T  F  V  L  *  I  Q  S  F  F  F  K  T  E  K  V   </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="C09SLf0089D12.1" strand="+"/>
                <serials PGL_serial="5" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="30090" stop="30143"/>
                    <exon start="30658" stop="31284"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>678</number_coding_nucleotides>
                  <number_encoded_amino_acids>226</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IDIQKKFALGLVLNNFFKIISVVMKNNSAIKFLKHVISVLSTLTKSKSTAIKSKTEAIKAKLMVLSLLKSKKLSLSGLGTKAISHKIHSLLGHKDQDHEDENNKAIVLVYNHAPEVGEDHVHYQHNEANEEILLLLSNGENYDYDDDKYPDLTHSLFDEEDEYLGDPNASAIDMVRNFKEEEGENFVLEDEIDNVADLFIKKFHKRMRLQKLESFKRYQEMLQRST*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 8 chains have been computed
$ 
$ memory statistics:
$ 13216 bytes spliced alignments in total
$ 6 spliced alignments have been stored
$ 2202 bytes was the average size of a spliced alignment
$ 10744 bytes predicted gene locations in total
$ 5 predicted gene locations have been stored
$ 2148 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 9 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-19 11:22:23
-->
