<?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="2009-12-01 05:57:16"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0164O03-7Kr3M/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0164O03-7Kr3M/gth_cdna_fileCXGN::TomatoGenome::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-C00HBa0164O03-7Kr3M/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U590648" ref_strand="+" ref_description="SGN-U590648 Tomato 200607#2 [1 ESTs aligned] (*GB) gi|113205316|gb|ABI34339.1| (e_value=2e-17) Polyprotein,; ">
      <seq>gcacctagcccatctggtactaaggcggtgacacctccaccaactgaggaagtggtaagagagggtgaggatggggagaatgaacaagtgcagaatgaggaattgccaccccaacctacccaagagatgatcaatcaggttcttgcttaccttagcgggttatctgatcaaggccaagcacctccagtgttttctgcactagcacctcaggctccggaggtacaacatgcgcctactgtgactccccgcatcgatacctcattggaaataggaacgtttccccgtctgactacagggcctataatgacaaatgatcagcatgaactttttagtaagttcttgaaattgaaacctcaagtctacaagggtgttgaatctgaggatgcctacgattttctggttgactgtcatgagctactacacaagatgggtatagtagaacggtttggtgttgagtttgtgacttatcagtttcaagggaacgccaaaatgtggtggcggtcacatgttgagtgtcaaccaacagaggcaccacgtatgacttgggcatcattct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0164O03-7Kr3M/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0164O03.2" temp_strand="+" temp_description="C00HBa0164O03.2  CU571242.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0164O03 sequenced_by:sanger upload_account_name:uk">
        <position start="80757" stop="81912"/>
      </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="81057" g_stop="81612" g_length="556"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="556" r_length="556" r_score="0.912"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0164O03.2" gen_strand="+" ref_id="SGN-U590648" ref_strand="+">
        <total_alignment_score>0.912</total_alignment_score>
        <cumulative_length_of_scored_exons>556</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0164O03.2" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U590648" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="81057" e_stop="81612"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GCACCTAGCCCATCTGGCACTAGGGCGGTGACTCCTCCACCGGCTGAAGAAGTAGTAAGAGAGGGGGAGGATAGGGAAAATAAGAATGCACAGAATGACGAATTACCACCCCAACCTACCCCAAATATGATCAATCAGGTTCTTGCTTATCTTAGCGAGTTATCTGATCAAGACCAGACACCTCCAGTGTTTTCTGCACCAGCAACTCAGGTTCCAGAGGTACTACATGCGGCTACTGTGGCTCCCCGCATGGATACCTCATTGGAAATAGGCACGTTTCCTCGTCTGACTCTAGGGCCTATAATGACAAATGATCAGCATGAACTTTTCAGTAAGTTCTTGAAATTGAAACCTCCAGTCTTCAAGGGTGCTGAATCTGAGGATGCCTATGATTTTCTGGTTGATTGTCATGAGCTACTACACAAGATGGGTATAATAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAAGAAACGCCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCATCTATGACTTGGGCATCATTCT</genome_strand>
        <mrna_strand>GCACCTAGCCCATCTGGTACTAAGGCGGTGACACCTCCACCAACTGAGGAAGTGGTAAGAGAGGGTGAGGATGGGGAGAATGAACAAGTGCAGAATGAGGAATTGCCACCCCAACCTACCCAAGAGATGATCAATCAGGTTCTTGCTTACCTTAGCGGGTTATCTGATCAAGGCCAAGCACCTCCAGTGTTTTCTGCACTAGCACCTCAGGCTCCGGAGGTACAACATGCGCCTACTGTGACTCCCCGCATCGATACCTCATTGGAAATAGGAACGTTTCCCCGTCTGACTACAGGGCCTATAATGACAAATGATCAGCATGAACTTTTTAGTAAGTTCTTGAAATTGAAACCTCAAGTCTACAAGGGTGTTGAATCTGAGGATGCCTACGATTTTCTGGTTGACTGTCATGAGCTACTACACAAGATGGGTATAGTAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAGGGAACGCCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCACGTATGACTTGGGCATCATTCT</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-C00HBa0164O03-7Kr3M/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U591718" ref_strand="+" ref_description="SGN-U591718 Tomato 200607#2 [1 ESTs aligned] (*GB) gi|48057631|gb|AAT39954.1| (e_value=1e-28) putative integrase [Solanum demissum]; ">
      <seq>gggatctgtcccaggcttggctaacgtcacagttttagcattacaatccaagattgcaaaatttggagaaagccaagtcatacccagaattacatcaaaatcaaccatttctaagataaccaagtctacataagtattgctccccacaaaagtcaccagaccagacctatatactttttcaactatcacagactcacccaccggagtagaaacacgaataggcatgtcaagcaattcataatttaatttaagaccagtagcaaatgaggaagatacatatgaaaatgtggatccagggtcaaataatacaaaagccatgcaatcac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0164O03-7Kr3M/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0164O03.2" temp_strand="-" temp_description="C00HBa0164O03.2  CU571242.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0164O03 sequenced_by:sanger upload_account_name:uk">
        <position start="83013" stop="82087"/>
      </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="82714" g_stop="82387" g_length="328"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="326" r_length="326" r_score="0.936"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0164O03.2" gen_strand="-" ref_id="SGN-U591718" ref_strand="+">
        <total_alignment_score>0.936</total_alignment_score>
        <cumulative_length_of_scored_exons>328</cumulative_length_of_scored_exons>
        <coverage percentage="1.006" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0164O03.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U591718" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="82714" e_stop="82387"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CGGATCTGTCCTAGGATTGGCTAATGTCACAGTTTTTAGTATTACAATCCAAGATCGCAAAAATTCGGAGAAAGCCAAGTCATACCCAGAATTACATAAAAATCAACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCATAGACTCACCCACCGGAATAGAAACACGAATAGGCATGTCAAGCAATTCACAATATAAATTAAGACCATTAGCAAATGAGGAAGATACATATGAAAATGTGGAGCCAGGATCAAATAATACCGAAGCTATGCAATCAC</genome_strand>
        <mrna_strand>GGGATCTGTCCCAGGCTTGGCTAACGTCACAG-TTTTAGCATTACAATCCAAGATTGC-AAAATTTGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCAACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCACAGACTCACCCACCGGAGTAGAAACACGAATAGGCATGTCAAGCAATTCATAATTTAATTTAAGACCAGTAGCAAATGAGGAAGATACATATGAAAATGTGGATCCAGGGTCAAATAATACAAAAGCCATGCAATCAC</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-C00HBa0164O03-7Kr3M/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U575265" ref_strand="+" ref_description="SGN-U575265 Tomato 200607#2 [3 ESTs aligned] (*GB) gi|113205316|gb|ABI34339.1| (e_value=2e-65) Polyprotein,; (*SWP) sp|P04323|POL3_DROME (e_value=2e-11) Retrovirus-related Pol polyprotein from transposon 17.6 OS=Drosophila melanogaster GN=pol; ">
      <seq>ggcctctgtaagaatagtgtgaatcaaatcgtcggcacggggtacacatacctttcccttaatcctcaaaacaccttccttatcgatttttgcttctttagcctctcctcgcattaccttatctcgaatccagatcagtttctcatcggtaaactgctttcctttaatcttatcaagaaaggaagatcttgcctccacacaagccaaaaattctcccttctcatttaattctagcctcataaggtcattagccagagtctgaacctctctagccaatgggcatctagaaacctgcaagtgagctagacttcccatgctccctgcctttctacttaaagcatctgccacaacattagcctttcccggatgatacaagatagtgatatcatagtccttcagtagctccatcgatctcctctgtctcaaattcaaatctttctgagtaaagacatactgtaaactacgatgatccatatagacttcacacttaaccccatagagataatgtctctattactttaatgcaatcactactgccgctaactccaaatcatgggtcggataattacgttcatgcacctttaattg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0164O03-7Kr3M/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0164O03.2" temp_strand="-" temp_description="C00HBa0164O03.2  CU571242.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0164O03 sequenced_by:sanger upload_account_name:uk">
        <position start="84713" stop="83528"/>
      </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="84414" g_stop="83827" g_length="588"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="588" r_length="588" r_score="0.903"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0164O03.2" gen_strand="-" ref_id="SGN-U575265" ref_strand="+">
        <total_alignment_score>0.903</total_alignment_score>
        <cumulative_length_of_scored_exons>588</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0164O03.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U575265" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="84414" e_stop="83827"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGCCTTTGTCAGAATAGTGTTGATCAAATCATCAACGCGGGGTACACATACCCTTCCCTTGATTCTCAAAACACCTTCCTCATCGATTTGTGCTTCCTTAGCCTCTCCTCGCAATACTTTATCTTGAATCCGGATCAGTTTCTCATCGGTAAACTGCTTTCCTTTAATCTTGTCAAGAAAAGAAGATCTTGCCTTCACACAAGCCAACAATCCTCCCTTCTCATTTACTTCTAACCTCATAAAGTCGTTAGCCAGAGTCTGAACCTCTCTAGCCAATGGACGTCTAGAAACTTGCAAGTGAGCTAGACTTCCCATGCTCCCTGCCTTTCTACTTAAGGCGTCTGCTACAACATTAGCCTTTCCCGGATGATACAAGATAGTGATATCGTAGTACTTCAGTAGTTCCATCCATCTCCTCTGTCTCAAATTCAAATCTTTTTGAGTAAAGACATACTGTAGGCTACGATGATCCGTGTAGACTTCACACTTAACCCAATATTAATAATGTCTCCATTGCTTTAATGCAAACACTACCGCAGCCAACTCCAAATCATGGGTCGGATAGTTACGTTCATGTACCTTTGATTA</genome_strand>
        <mrna_strand>GGCCTCTGTAAGAATAGTGTGAATCAAATCGTCGGCACGGGGTACACATACCTTTCCCTTAATCCTCAAAACACCTTCCTTATCGATTTTTGCTTCTTTAGCCTCTCCTCGCATTACCTTATCTCGAATCCAGATCAGTTTCTCATCGGTAAACTGCTTTCCTTTAATCTTATCAAGAAAGGAAGATCTTGCCTCCACACAAGCCAAAAATTCTCCCTTCTCATTTAATTCTAGCCTCATAAGGTCATTAGCCAGAGTCTGAACCTCTCTAGCCAATGGGCATCTAGAAACCTGCAAGTGAGCTAGACTTCCCATGCTCCCTGCCTTTCTACTTAAAGCATCTGCCACAACATTAGCCTTTCCCGGATGATACAAGATAGTGATATCATAGTCCTTCAGTAGCTCCATCGATCTCCTCTGTCTCAAATTCAAATCTTTCTGAGTAAAGACATACTGTAAACTACGATGATCCATATAGACTTCACACTTAACCCCATAGAGATAATGTCTCTATTACTTTAATGCAATCACTACTGCCGCTAACTCCAAATCATGGGTCGGATAATTACGTTCATGCACCTTTAATTG</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-C00HBa0164O03-7Kr3M/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U575264" ref_strand="+" ref_description="SGN-U575264 Tomato 200607#2 [2 ESTs aligned] (*GB) gi|113205363|gb|AAT66771.2| (e_value=2e-67) Putative; (*SWP) sp|Q9UR07|RT23_SCHPO (e_value=5e-21) Retrotransposable element Tf2 155 kDa protein type 3 OS=Schizosaccharomyces pombe GN=Tf2-11; ">
      <seq>acccaattccgcatgcaatgttttccaaaacttagaagtaaactgcatacctctatctgatatgatggagagtggaaccccatgcaaccgaacaatttctgagacatatattttggctaacttctctgcattgtaagtcaccttgaccggaatgaaatgagcagacttagttaacctatcaacaatcacccaaatagagtcatacttactcattgtctttggaaggccaactacaaaatccattgcaattctctcccacttccattcaggaatgagcattctctgaagtgttcctccaggcctctggtgttcatactttacttgttgacagtttggacatttggcaataaagtcaacaatatcacgcttcattctactccaccaaaagtgttgctttaggtcacggtacatcttggttgcacccggatgtatagaataccttgaactatgagcctctgtcagaatagtgttgatcaaatcatcaactcggggt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0164O03-7Kr3M/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0164O03.2" temp_strand="-" temp_description="C00HBa0164O03.2  CU571242.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0164O03 sequenced_by:sanger upload_account_name:uk">
        <position start="85163" stop="84072"/>
      </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="84863" g_stop="84372" g_length="492"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="493" r_length="493" r_score="0.904"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0164O03.2" gen_strand="-" ref_id="SGN-U575264" ref_strand="+">
        <total_alignment_score>0.904</total_alignment_score>
        <cumulative_length_of_scored_exons>492</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0164O03.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U575264" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="84863" e_stop="84372"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACCCAATTCAGCATGCAAAGTTTTCCAAAACTTAGAAGTAAACTACGTACCTCTATTTGATATGATAGAAAGTGGAACTCCATGCAATCGAACAATCTCTGAGATGTAAAGTTTGGCTAACTTCTCTGCATTGTAAGTCACCTTAACAGGAATGAAGTGAGCAGACATAGTTAACCTATCAACGATTACCCAAATAGAGTCATACTTACCCATT-TTTTTGGAAGACCAACCACGAAGTCCATTGCAATTCTCTCCCACTTCCATTCCGGAATGGGCATTCTCTGAAGTGTTCCTCCGGGCCTCTGGTGTTCACATTTTACTTGCTGACAATTTGGACATTTGGCAATAAAATAAACAATGTCACGCTTCATTATAGTCCACCAAAAATGTTGCTTTAGGTCACGATACATCTTGGTTGCACCAGGATGTATAGAGTACCTCGAACTATGAGCCTTTGTCAGAATAGTGTTGATCAAATCATCAACGCGGGGT</genome_strand>
        <mrna_strand>ACCCAATTCCGCATGCAATGTTTTCCAAAACTTAGAAGTAAACTGCATACCTCTATCTGATATGATGGAGAGTGGAACCCCATGCAACCGAACAATTTCTGAGACATATATTTTGGCTAACTTCTCTGCATTGTAAGTCACCTTGACCGGAATGAAATGAGCAGACTTAGTTAACCTATCAACAATCACCCAAATAGAGTCATACTTACTCATTGTCTTTGGAAGGCCAACTACAAAATCCATTGCAATTCTCTCCCACTTCCATTCAGGAATGAGCATTCTCTGAAGTGTTCCTCCAGGCCTCTGGTGTTCATACTTTACTTGTTGACAGTTTGGACATTTGGCAATAAAGTCAACAATATCACGCTTCATTCTACTCCACCAAAAGTGTTGCTTTAGGTCACGGTACATCTTGGTTGCACCCGGATGTATAGAATACCTTGAACTATGAGCCTCTGTCAGAATAGTGTTGATCAAATCATCAACTCGGGGT</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="81057" PGL_stop="81612"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="81057" e_stop="81612"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.912"/>
        </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="0.912">
            <gDNA_exon_boundary e_start="81057" e_stop="81612" e_length="556"/>
          </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="81057" stop="81612"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U590648" 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>GCACCTAGCCCATCTGGCACTAGGGCGGTGACTCCTCCACCGGCTGAAGAAGTAGTAAGAGAGGGGGAGGATAGGGAAAATAAGAATGCACAGAATGACGAATTACCACCCCAACCTACCCCAAATATGATCAATCAGGTTCTTGCTTATCTTAGCGAGTTATCTGATCAAGACCAGACACCTCCAGTGTTTTCTGCACCAGCAACTCAGGTTCCAGAGGTACTACATGCGGCTACTGTGGCTCCCCGCATGGATACCTCATTGGAAATAGGCACGTTTCCTCGTCTGACTCTAGGGCCTATAATGACAAATGATCAGCATGAACTTTTCAGTAAGTTCTTGAAATTGAAACCTCCAGTCTTCAAGGGTGCTGAATCTGAGGATGCCTATGATTTTCTGGTTGATTGTCATGAGCTACTACACAAGATGGGTATAATAGAACGGTTTGGTGTTGAGTTTGTGACTTATCAGTTTCAAAGAAACGCCAAAATGTGGTGGCGGTCACATGTTGAGTGTCAACCAACAGAGGCACCATCTATGACTTGGGCATCATTCT</gDNA_template>
            <first_frame> A  P  S  P  S  G  T  R  A  V  T  P  P  P  A  E  E  V  V  R  E  G  E  D  R  E  N  K  N  A  Q  N  D  E  L  P  P  Q  P  T  P  N  M  I  N  Q  V  L  A  Y  L  S  E  L  S  D  Q  D  Q  T  P  P  V  F  S  A  P  A  T  Q  V  P  E  V  L  H  A  A  T  V  A  P  R  M  D  T  S  L  E  I  G  T  F  P  R  L  T  L  G  P  I  M  T  N  D  Q  H  E  L  F  S  K  F  L  K  L  K  P  P  V  F  K  G  A  E  S  E  D  A  Y  D  F  L  V  D  C  H  E  L  L  H  K  M  G  I  I  E  R  F  G  V  E  F  V  T  Y  Q  F  Q  R  N  A  K  M  W  W  R  S  H  V  E  C  Q  P  T  E  A  P  S  M  T  W  A  S  F  </first_frame>
            <second_frame>  H  L  A  H  L  A  L  G  R  *  L  L  H  R  L  K  K  *  *  E  R  G  R  I  G  K  I  R  M  H  R  M  T  N  Y  H  P  N  L  P  Q  I  *  S  I  R  F  L  L  I  L  A  S  Y  L  I  K  T  R  H  L  Q  C  F  L  H  Q  Q  L  R  F  Q  R  Y  Y  M  R  L  L  W  L  P  A  W  I  P  H  W  K  *  A  R  F  L  V  *  L  *  G  L  *  *  Q  M  I  S  M  N  F  S  V  S  S  *  N  *  N  L  Q  S  S  R  V  L  N  L  R  M  P  M  I  F  W  L  I  V  M  S  Y  Y  T  R  W  V  *  *  N  G  L  V  L  S  L  *  L  I  S  F  K  E  T  P  K  C  G  G  G  H  M  L  S  V  N  Q  Q  R  H  H  L  *  L  G  H  H  S </second_frame>
            <third_frame>   T  *  P  I  W  H  *  G  G  D  S  S  T  G  *  R  S  S  K  R  G  G  G  *  G  K  *  E  C  T  E  *  R  I  T  T  P  T  Y  P  K  Y  D  Q  S  G  S  C  L  S  *  R  V  I  *  S  R  P  D  T  S  S  V  F  C  T  S  N  S  G  S  R  G  T  T  C  G  Y  C  G  S  P  H  G  Y  L  I  G  N  R  H  V  S  S  S  D  S  R  A  Y  N  D  K  *  S  A  *  T  F  Q  *  V  L  E  I  E  T  S  S  L  Q  G  C  *  I  *  G  C  L  *  F  S  G  *  L  S  *  A  T  T  Q  D  G  Y  N  R  T  V  W  C  *  V  C  D  L  S  V  S  K  K  R  Q  N  V  V  A  V  T  C  *  V  S  T  N  R  G  T  I  Y  D  L  G  I  I   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C00HBa0164O03.2" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="81057" stop="81611"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>555</number_coding_nucleotides>
                  <number_encoded_amino_acids>185</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>APSPSGTRAVTPPPAEEVVREGEDRENKNAQNDELPPQPTPNMINQVLAYLSELSDQDQTPPVFSAPATQVPEVLHAATVAPRMDTSLEIGTFPRLTLGPIMTNDQHELFSKFLKLKPPVFKGAESEDAYDFLVDCHELLHKMGIIERFGVEFVTYQFQRNAKMWWRSHVECQPTEAPSMTWASF</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="82714" PGL_stop="82387"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="82714" e_stop="82387"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.936"/>
        </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="0.936">
            <gDNA_exon_boundary e_start="82714" e_stop="82387" e_length="328"/>
          </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="82714" stop="82387"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U591718" 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>CGGATCTGTCCTAGGATTGGCTAATGTCACAGTTTTTAGTATTACAATCCAAGATCGCAAAAATTCGGAGAAAGCCAAGTCATACCCAGAATTACATAAAAATCAACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCATAGACTCACCCACCGGAATAGAAACACGAATAGGCATGTCAAGCAATTCACAATATAAATTAAGACCATTAGCAAATGAGGAAGATACATATGAAAATGTGGAGCCAGGATCAAATAATACCGAAGCTATGCAATCAC</gDNA_template>
            <first_frame> R  I  C  P  R  I  G  *  C  H  S  F  *  Y  Y  N  P  R  S  Q  K  F  G  E  S  Q  V  I  P  R  I  T  *  K  S  T  I  S  K  I  T  K  S  T  *  V  L  L  P  T  K  V  T  R  P  D  L  Y  T  F  S  T  I  I  D  S  P  T  G  I  E  T  R  I  G  M  S  S  N  S  Q  Y  K  L  R  P  L  A  N  E  E  D  T  Y  E  N  V  E  P  G  S  N  N  T  E  A  M  Q  S  </first_frame>
            <second_frame>  G  S  V  L  G  L  A  N  V  T  V  F  S  I  T  I  Q  D  R  K  N  S  E  K  A  K  S  Y  P  E  L  H  K  N  Q  P  F  L  R  *  P  S  L  H  K  Y  C  S  P  Q  K  S  P  D  Q  T  Y  I  L  F  Q  L  S  *  T  H  P  P  E  *  K  H  E  *  A  C  Q  A  I  H  N  I  N  *  D  H  *  Q  M  R  K  I  H  M  K  M  W  S  Q  D  Q  I  I  P  K  L  C  N  H </second_frame>
            <third_frame>   D  L  S  *  D  W  L  M  S  Q  F  L  V  L  Q  S  K  I  A  K  I  R  R  K  P  S  H  T  Q  N  Y  I  K  I  N  H  F  *  D  N  Q  V  Y  I  S  I  A  P  H  K  S  H  Q  T  R  P  I  Y  F  F  N  Y  H  R  L  T  H  R  N  R  N  T  N  R  H  V  K  Q  F  T  I  *  I  K  T  I  S  K  *  G  R  Y  I  *  K  C  G  A  R  I  K  *  Y  R  S  Y  A  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="C00HBa0164O03.2" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="82579" stop="82388"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>192</number_coding_nucleotides>
                  <number_encoded_amino_acids>64</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VLLPTKVTRPDLYTFSTIIDSPTGIETRIGMSSNSQYKLRPLANEEDTYENVEPGSNNTEAMQS</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="84863" PGL_stop="83827"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="84863" e_stop="83827"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.903"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="0.903">
            <gDNA_exon_boundary e_start="84863" e_stop="83827" e_length="1037"/>
          </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="84863" stop="84372"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U575264" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="84414" stop="83827"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U575265" 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>ACCCAATTCAGCATGCAAAGTTTTCCAAAACTTAGAAGTAAACTACGTACCTCTATTTGATATGATAGAAAGTGGAACTCCATGCAATCGAACAATCTCTGAGATGTAAAGTTTGGCTAACTTCTCTGCATTGTAAGTCACCTTAACAGGAATGAAGTGAGCAGACATAGTTAACCTATCAACGATTACCCAAATAGAGTCATACTTACCCATTTTTTTGGAAGACCAACCACGAAGTCCATTGCAATTCTCTCCCACTTCCATTCCGGAATGGGCATTCTCTGAAGTGTTCCTCCGGGCCTCTGGTGTTCACATTTTACTTGCTGACAATTTGGACATTTGGCAATAAAATAAACAATGTCACGCTTCATTATAGTCCACCAAAAATGTTGCTTTAGGTCACGATACATCTTGGTTGCACCAGGATGTATAGAGTACCTCGAACTATGAGCCTTTGTCAGAATAGTGTTGATCAAATCATCAACGCGGGGTACACATACCCTTCCCTTGATTCTCAAAACACCTTCCTCATCGATTTGTGCTTCCTTAGCCTCTCCTCGCAATACTTTATCTTGAATCCGGATCAGTTTCTCATCGGTAAACTGCTTTCCTTTAATCTTGTCAAGAAAAGAAGATCTTGCCTTCACACAAGCCAACAATCCTCCCTTCTCATTTACTTCTAACCTCATAAAGTCGTTAGCCAGAGTCTGAACCTCTCTAGCCAATGGACGTCTAGAAACTTGCAAGTGAGCTAGACTTCCCATGCTCCCTGCCTTTCTACTTAAGGCGTCTGCTACAACATTAGCCTTTCCCGGATGATACAAGATAGTGATATCGTAGTACTTCAGTAGTTCCATCCATCTCCTCTGTCTCAAATTCAAATCTTTTTGAGTAAAGACATACTGTAGGCTACGATGATCCGTGTAGACTTCACACTTAACCCAATATTAATAATGTCTCCATTGCTTTAATGCAAACACTACCGCAGCCAACTCCAAATCATGGGTCGGATAGTTACGTTCATGTACCTTTGATTA</gDNA_template>
            <first_frame> T  Q  F  S  M  Q  S  F  P  K  L  R  S  K  L  R  T  S  I  *  Y  D  R  K  W  N  S  M  Q  S  N  N  L  *  D  V  K  F  G  *  L  L  C  I  V  S  H  L  N  R  N  E  V  S  R  H  S  *  P  I  N  D  Y  P  N  R  V  I  L  T  H  F  F  G  R  P  T  T  K  S  I  A  I  L  S  H  F  H  S  G  M  G  I  L  *  S  V  P  P  G  L  W  C  S  H  F  T  C  *  Q  F  G  H  L  A  I  K  *  T  M  S  R  F  I  I  V  H  Q  K  C  C  F  R  S  R  Y  I  L  V  A  P  G  C  I  E  Y  L  E  L  *  A  F  V  R  I  V  L  I  K  S  S  T  R  G  T  H  T  L  P  L  I  L  K  T  P  S  S  S  I  C  A  S  L  A  S  P  R  N  T  L  S  *  I  R  I  S  F  S  S  V  N  C  F  P  L  I  L  S  R  K  E  D  L  A  F  T  Q  A  N  N  P  P  F  S  F  T  S  N  L  I  K  S  L  A  R  V  *  T  S  L  A  N  G  R  L  E  T  C  K  *  A  R  L  P  M  L  P  A  F  L  L  K  A  S  A  T  T  L  A  F  P  G  *  Y  K  I  V  I  S  *  Y  F  S  S  S  I  H  L  L  C  L  K  F  K  S  F  *  V  K  T  Y  C  R  L  R  *  S  V  *  T  S  H  L  T  Q  Y  *  *  C  L  H  C  F  N  A  N  T  T  A  A  N  S  K  S  W  V  G  *  L  R  S  C  T  F  D   </first_frame>
            <second_frame>  P  N  S  A  C  K  V  F  Q  N  L  E  V  N  Y  V  P  L  F  D  M  I  E  S  G  T  P  C  N  R  T  I  S  E  M  *  S  L  A  N  F  S  A  L  *  V  T  L  T  G  M  K  *  A  D  I  V  N  L  S  T  I  T  Q  I  E  S  Y  L  P  I  F  L  E  D  Q  P  R  S  P  L  Q  F  S  P  T  S  I  P  E  W  A  F  S  E  V  F  L  R  A  S  G  V  H  I  L  L  A  D  N  L  D  I  W  Q  *  N  K  Q  C  H  A  S  L  *  S  T  K  N  V  A  L  G  H  D  T  S  W  L  H  Q  D  V  *  S  T  S  N  Y  E  P  L  S  E  *  C  *  S  N  H  Q  R  G  V  H  I  P  F  P  *  F  S  K  H  L  P  H  R  F  V  L  P  *  P  L  L  A  I  L  Y  L  E  S  G  S  V  S  H  R  *  T  A  F  L  *  S  C  Q  E  K  K  I  L  P  S  H  K  P  T  I  L  P  S  H  L  L  L  T  S  *  S  R  *  P  E  S  E  P  L  *  P  M  D  V  *  K  L  A  S  E  L  D  F  P  C  S  L  P  F  Y  L  R  R  L  L  Q  H  *  P  F  P  D  D  T  R  *  *  Y  R  S  T  S  V  V  P  S  I  S  S  V  S  N  S  N  L  F  E  *  R  H  T  V  G  Y  D  D  P  C  R  L  H  T  *  P  N  I  N  N  V  S  I  A  L  M  Q  T  L  P  Q  P  T  P  N  H  G  S  D  S  Y  V  H  V  P  L  I  </second_frame>
            <third_frame>   P  I  Q  H  A  K  F  S  K  T  *  K  *  T  T  Y  L  Y  L  I  *  *  K  V  E  L  H  A  I  E  Q  S  L  R  C  K  V  W  L  T  S  L  H  C  K  S  P  *  Q  E  *  S  E  Q  T  *  L  T  Y  Q  R  L  P  K  *  S  H  T  Y  P  F  F  W  K  T  N  H  E  V  H  C  N  S  L  P  L  P  F  R  N  G  H  S  L  K  C  S  S  G  P  L  V  F  T  F  Y  L  L  T  I  W  T  F  G  N  K  I  N  N  V  T  L  H  Y  S  P  P  K  M  L  L  *  V  T  I  H  L  G  C  T  R  M  Y  R  V  P  R  T  M  S  L  C  Q  N  S  V  D  Q  I  I  N  A  G  Y  T  Y  P  S  L  D  S  Q  N  T  F  L  I  D  L  C  F  L  S  L  S  S  Q  Y  F  I  L  N  P  D  Q  F  L  I  G  K  L  L  S  F  N  L  V  K  K  R  R  S  C  L  H  T  S  Q  Q  S  S  L  L  I  Y  F  *  P  H  K  V  V  S  Q  S  L  N  L  S  S  Q  W  T  S  R  N  L  Q  V  S  *  T  S  H  A  P  C  L  S  T  *  G  V  C  Y  N  I  S  L  S  R  M  I  Q  D  S  D  I  V  V  L  Q  *  F  H  P  S  P  L  S  Q  I  Q  I  F  L  S  K  D  I  L  *  A  T  M  I  R  V  D  F  T  L  N  P  I  L  I  M  S  P  L  L  *  C  K  H  Y  R  S  Q  L  Q  I  M  G  R  I  V  T  F  M  Y  L  *  L </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C00HBa0164O03.2" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="84465" stop="84181"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>282</number_coding_nucleotides>
                  <number_encoded_amino_acids>94</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VTIHLGCTRMYRVPRTMSLCQNSVDQIINAGYTYPSLDSQNTFLIDLCFLSLSSQYFILNPDQFLIGKLLSFNLVKKRRSCLHTSQQSSLLIYF*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C00HBa0164O03.2" strand="-"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="84666" stop="84466"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>198</number_coding_nucleotides>
                  <number_encoded_amino_acids>66</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SHTYPFFWKTNHEVHCNSLPLPFRNGHSLKCSSGPLVFTFYLLTIWTFGNKINNVTLHYSPPKMLL*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 81 chains have been computed
$ 
$ memory statistics:
$ 8928 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 2232 bytes was the average size of a spliced alignment
$ 7880 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2626 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 94 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 05:58:08
-->
