<?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="2009-01-15 20:42:04"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04SLm0134J13-CJRF9/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04SLm0134J13-CJRF9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato_potato" 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-C04SLm0134J13-CJRF9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato_potato" ref_id="SGN-E261310" ref_strand="+" ref_description="SGN-E261310 [cLEG-68-F10]">
      <seq>ggacatgttccttgctgaaaatggctataaaaggaagtcaaattttgattttttaaacactgaaaatttttctttctctgcatttatttttctctcaaataaaatcaaagtgtcgatcgactgagtctgtgtgacttgttgttgttcttaagttcgttgaagttaaagaagtttgaggtaccgctatttctttaacaggtttaatccgttttatcttgagagaaatt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0134J13-CJRF9/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C04SLm0134J13.1" temp_strand="-" temp_description="C04SLm0134J13.1  CU302233.8 htgs_phase:3 submitted_to_sgn_as:C04SLm0134J13 sequenced_by:sanger upload_account_name:uk">
        <position start="739" stop="1"/>
      </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="440" g_stop="214" g_length="227"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="227" r_length="227" r_score="0.916"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0134J13.1" gen_strand="-" ref_id="SGN-E261310" ref_strand="+">
        <total_alignment_score>0.916</total_alignment_score>
        <cumulative_length_of_scored_exons>227</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0134J13.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E261310" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="440" e_stop="214"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGACATGTTTCTTGCTGAAAATGGCTATAAAAGGAAGGCAATTTTTGATTTTTCAAACACTTAAAATTTTTCTTTCTGTGCATTTATT-TTCTCTCAAATAAAAATCAAAGTGTCGATCGACTGAGTCTGTGTGACTAGTTGATGTTCTTAAGTTCATTGAAGTTAATGAAATTTAAAGTACCGCTATTTCTTTAATAGGTTTAATCCGTTTTATCTTGGGAGAAATT</genome_strand>
        <mrna_strand>GGACATGTTCCTTGCTGAAAATGGCTATAAAAGGAAGTCAAATTTTGATTTTTTAAACACTGAAAATTTTTCTTTCTCTGCATTTATTTTTCTCTCAAAT-AAAATCAAAGTGTCGATCGACTGAGTCTGTGTGACTTGTTGTTGTTCTTAAGTTCGTTGAAGTTAAAGAAGTTTGAGGTACCGCTATTTCTTTAACAGGTTTAATCCGTTTTATCTTGAGAGAAATT</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-C04SLm0134J13-CJRF9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato_potato" ref_id="SGN-E369759" ref_strand="+" ref_description="SGN-E369759 [TUS-25-O3](-)">
      <seq>taaggttgagaatcgaagaggataataaggctgcagaaaagaggtcacgtggtaattcagcaatatctggagtaaattttgttgaagaagattccacaaaattcaagaaaagaaagaaagcatctggtccaaaacgcaatcctcctaagaagaaattcaatggaaactgctttaattgtggtaaacatggtcatagggctaatgaatgccggggtcctaagaaggacaagaaaaagaaggatcaagcaaacttggctgaatccaaaggagaaatggacgatctctgtgcaatgctttcagaatgtaacttggttggaaatccaagagaatggtggatagattctggtgcctcatgccatgtttgtgccaacaaagaattattttcatcatatactctagcacttacagatgaaaaattatttatggcaaactccgctgttgcaaaggtggaaggaactggcaaagtcctattaaagatgacatcaggcaaggtagtgactttgaatatggtctcatatgttccagaattgagaaataatttagtttcaattccaattctgaccaagaatggatttaaatgtgtatttgtttctgataaagtagtagtaagcaaaaatgatatgtatgtaggaaaagactaccttagtgatggccttttcaaactcaatgtaattgcagttgatatgaataaagattttgcttcttcttaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0134J13-CJRF9/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C04SLm0134J13.1" temp_strand="-" temp_description="C04SLm0134J13.1  CU302233.8 htgs_phase:3 submitted_to_sgn_as:C04SLm0134J13 sequenced_by:sanger upload_account_name:uk">
        <position start="4885" stop="3629"/>
      </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="4577" g_stop="3929" g_length="649"/>
          <reference_exon_boundary r_type="cDNA" r_start="61" r_stop="709" r_length="649" r_score="0.948"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0134J13.1" gen_strand="-" ref_id="SGN-E369759" ref_strand="+">
        <total_alignment_score>0.948</total_alignment_score>
        <cumulative_length_of_scored_exons>649</cumulative_length_of_scored_exons>
        <coverage percentage="0.904" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0134J13.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E369759" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4577" e_stop="3929"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAACAGTTTGTGTAAATTTTGTTGAAGAAGATTCAACAAAATTAAAGAAAAGAAAGAAAGCATCTGGTCCAAAAAGCAATCCTCCTAAGAAGAAATTCAATGGAAACTGCTTTATTTGTGATAAACATGGTCATAGGGCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAAGATCAAGCAAACTTGGCTTAATCCAAAGGAGAAATGGATGATCTCTGTTCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCAAACAAAGAATTATTTTCATCATATACTCCAGCACTTACAGATGAAAAATTATTCATGGCAAACTCCGTTGTTGCAAAGGTAGAAGGATCTGGAAAAGTCCTATTAAAGATGACTTTAGGCAAGGTGGTGACTTTGAATAGGGTTTCATATGTTCCAGAATTGAGAAAGAATTTAGTTTCAATTCCAGTTCTGAACAAGAATGGATTTAAATGTGTATTTGTTTCTGATAAAGTAGTAGTAAGCAAAACTGATATGTATGTAGGAAAAGGCTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAGAGATTTTTCTTCTTCTTA</genome_strand>
        <mrna_strand>CAATATCTGGAGTAAATTTTGTTGAAGAAGATTCCACAAAATTCAAGAAAAGAAAGAAAGCATCTGGTCCAAAACGCAATCCTCCTAAGAAGAAATTCAATGGAAACTGCTTTAATTGTGGTAAACATGGTCATAGGGCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAGGATCAAGCAAACTTGGCTGAATCCAAAGGAGAAATGGACGATCTCTGTGCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCCAACAAAGAATTATTTTCATCATATACTCTAGCACTTACAGATGAAAAATTATTTATGGCAAACTCCGCTGTTGCAAAGGTGGAAGGAACTGGCAAAGTCCTATTAAAGATGACATCAGGCAAGGTAGTGACTTTGAATATGGTCTCATATGTTCCAGAATTGAGAAATAATTTAGTTTCAATTCCAATTCTGACCAAGAATGGATTTAAATGTGTATTTGTTTCTGATAAAGTAGTAGTAAGCAAAAATGATATGTATGTAGGAAAAGACTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAAAGATTTTGCTTCTTCTTA</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-C04SLm0134J13-CJRF9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato_potato" ref_id="SGN-E395006" ref_strand="-" ref_description="SGN-E395006 [TUS-34-O4]">
      <seq>aagaaattcaatggaaactgctttaattgtggtaaacatggtcataggggtaatgaatgccggggtcctaagaaggacaagaaaaagaaggatcaagcaaacttggctgaatccaaaggagaaatggacgatctctgtgcaatgctttcagaatgtaacttggttggaaatccaagagaatggtggatagattctggtgcctcatgccatgtttgtgccaacaaagaattattttcatcatatactctagcacttacagatgaaaaattatttatggcaaactccgctgttgcaaaggtggaaggaactggcaaagtcctattaaagatgacatcaggcaaggtagtgactttgaatatggtctcatatgttccagaattgagaaataatttagtttcaattccaattctgaccaagaatggatttaaatgtgtatttgtttttgataaagtagtagtaagcaaaaatgatatgtatgtaggaaaagactaccttagtgatggccttttcaaactcaatgtaattgcagttgatatgaataaagattttgcttctttttaaaaaaaaaaaaaaaaaaaaactcga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0134J13-CJRF9/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C04SLm0134J13.1" temp_strand="-" temp_description="C04SLm0134J13.1  CU302233.8 htgs_phase:3 submitted_to_sgn_as:C04SLm0134J13 sequenced_by:sanger upload_account_name:uk">
        <position start="4788" stop="3629"/>
      </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="4488" g_stop="3929" g_length="560"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="560" r_length="560" r_score="0.950"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="561" polyA_stop="581"/>
      <MATCH_line gen_id="C04SLm0134J13.1" gen_strand="-" ref_id="SGN-E395006" ref_strand="-">
        <total_alignment_score>0.950</total_alignment_score>
        <cumulative_length_of_scored_exons>560</cumulative_length_of_scored_exons>
        <coverage percentage="0.957" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0134J13.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E395006" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="4488" e_stop="3929"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAGAAATTCAATGGAAACTGCTTTATTTGTGATAAACATGGTCATAGGGCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAAGATCAAGCAAACTTGGCTTAATCCAAAGGAGAAATGGATGATCTCTGTTCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCAAACAAAGAATTATTTTCATCATATACTCCAGCACTTACAGATGAAAAATTATTCATGGCAAACTCCGTTGTTGCAAAGGTAGAAGGATCTGGAAAAGTCCTATTAAAGATGACTTTAGGCAAGGTGGTGACTTTGAATAGGGTTTCATATGTTCCAGAATTGAGAAAGAATTTAGTTTCAATTCCAGTTCTGAACAAGAATGGATTTAAATGTGTATTTGTTTCTGATAAAGTAGTAGTAAGCAAAACTGATATGTATGTAGGAAAAGGCTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAGAGATTTTTCTTCTTCTTA</genome_strand>
        <mrna_strand>AAGAAATTCAATGGAAACTGCTTTAATTGTGGTAAACATGGTCATAGGGGTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAGGATCAAGCAAACTTGGCTGAATCCAAAGGAGAAATGGACGATCTCTGTGCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCCAACAAAGAATTATTTTCATCATATACTCTAGCACTTACAGATGAAAAATTATTTATGGCAAACTCCGCTGTTGCAAAGGTGGAAGGAACTGGCAAAGTCCTATTAAAGATGACATCAGGCAAGGTAGTGACTTTGAATATGGTCTCATATGTTCCAGAATTGAGAAATAATTTAGTTTCAATTCCAATTCTGACCAAGAATGGATTTAAATGTGTATTTGTTTTTGATAAAGTAGTAGTAAGCAAAAATGATATGTATGTAGGAAAAGACTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAAAGATTTTGCTTCTTTTTA</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-C04SLm0134J13-CJRF9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato_potato" ref_id="SGN-E250407" ref_strand="-" ref_description="SGN-E250407 [cLEG-6-H3]">
      <seq>aattgtggtaaacatggtcatagggctaatgaaagccggggtcttaagaaggacaagataaagaaggatcaagcaaacttgggtgaatccaaaggagaaatggacgatctctgtgcaatgctttcagaatgtaacttggttggaaatccaagagaatggtggatagattctggtgcctcatgccatgtttgtgccaacaaagaattattttcatcatatactctagcagttacagatgagaaattatttatggccaactccgctgttgcaaaggtgtaaggaactggcaaagtcctattaaagatgacatcaggcaaggtagtgactttgaatatggtctcatatgttccagaattgagaaataatttagtttcaattccaattctgaccaagaatggatttaaatgtgtatttgtttctgataaagtagtagtaagcaaaaatgatatgtatgtaggaaaagactaccttagtgatggccttttcaaactcaatgtaattgcagttcatatgaataaagattttgcttcttattaaaaaaaaaaaaaaaaaaagactcgac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0134J13-CJRF9/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C04SLm0134J13.1" temp_strand="-" temp_description="C04SLm0134J13.1  CU302233.8 htgs_phase:3 submitted_to_sgn_as:C04SLm0134J13 sequenced_by:sanger upload_account_name:uk">
        <position start="4764" stop="3629"/>
      </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="4464" g_stop="3929" g_length="536"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="536" r_length="536" r_score="0.935"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="537" polyA_stop="556"/>
      <MATCH_line gen_id="C04SLm0134J13.1" gen_strand="-" ref_id="SGN-E250407" ref_strand="-">
        <total_alignment_score>0.935</total_alignment_score>
        <cumulative_length_of_scored_exons>536</cumulative_length_of_scored_exons>
        <coverage percentage="0.954" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0134J13.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E250407" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="4464" e_stop="3929"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATTTGTGATAAACATGGTCATAGGGCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAAGATCAAGCAAACTTGGCTTAATCCAAAGGAGAAATGGATGATCTCTGTTCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCAAACAAAGAATTATTTTCATCATATACTCCAGCACTTACAGATGAAAAATTATTCATGGCAAACTCCGTTGTTGCAAAGGTAGAAGGATCTGGAAAAGTCCTATTAAAGATGACTTTAGGCAAGGTGGTGACTTTGAATAGGGTTTCATATGTTCCAGAATTGAGAAAGAATTTAGTTTCAATTCCAGTTCTGAACAAGAATGGATTTAAATGTGTATTTGTTTCTGATAAAGTAGTAGTAAGCAAAACTGATATGTATGTAGGAAAAGGCTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAGAGATTTTTCTTCTTCTTA</genome_strand>
        <mrna_strand>AATTGTGGTAAACATGGTCATAGGGCTAATGAAAGCCGGGGTCTTAAGAAGGACAAGATAAAGAAGGATCAAGCAAACTTGGGTGAATCCAAAGGAGAAATGGACGATCTCTGTGCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCCAACAAAGAATTATTTTCATCATATACTCTAGCAGTTACAGATGAGAAATTATTTATGGCCAACTCCGCTGTTGCAAAGGTGTAAGGAACTGGCAAAGTCCTATTAAAGATGACATCAGGCAAGGTAGTGACTTTGAATATGGTCTCATATGTTCCAGAATTGAGAAATAATTTAGTTTCAATTCCAATTCTGACCAAGAATGGATTTAAATGTGTATTTGTTTCTGATAAAGTAGTAGTAAGCAAAAATGATATGTATGTAGGAAAAGACTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTCATATGAATAAAGATTTTGCTTCTTATTA</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-C04SLm0134J13-CJRF9/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_E_tomato_potato" ref_id="SGN-E375520" ref_strand="+" ref_description="SGN-E375520 [TUS-34-B10](-)">
      <seq>atgccggggtcctaagaaggacaagaaaaagaaggatcaagcaaacttggctgaatccaaaggagaaatggacgatctctgtgcaatgctttcagaatgtaacttggttggaaatccaagagaatggtggatagattttggtgcctcatgccatgtttgtgccaacaaagaattattttcatcatatactttagcacttacagatgaaaaattatttatggcaaactccgctgttgcaaaggtggaaggaactggcaaagtcctattaaagatgacatcaggcaaggtagtgactttgaatatggtttcatatgttccagaattgagaaataatttagtttcaattccaattttgaccaagaatggatttaaatgtgtatttgtttttgataaagtagtagtaagcaaaaatgatatgtatgtaggaaaagactaccttagtgatggccttttcaaactcaatgtaattgcagttgatatgaataaagattttgcttttttttaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0134J13-CJRF9/GenomeThreader_SGN_E_tomato_potato/un_xed_seqs" temp_id="C04SLm0134J13.1" temp_strand="-" temp_description="C04SLm0134J13.1  CU302233.8 htgs_phase:3 submitted_to_sgn_as:C04SLm0134J13 sequenced_by:sanger upload_account_name:uk">
        <position start="4732" stop="3629"/>
      </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="4432" g_stop="3929" g_length="504"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="504" r_length="504" r_score="0.944"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="505" polyA_stop="524"/>
      <MATCH_line gen_id="C04SLm0134J13.1" gen_strand="-" ref_id="SGN-E375520" ref_strand="+">
        <total_alignment_score>0.944</total_alignment_score>
        <cumulative_length_of_scored_exons>504</cumulative_length_of_scored_exons>
        <coverage percentage="0.962" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0134J13.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E375520" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4432" e_stop="3929"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAAGATCAAGCAAACTTGGCTTAATCCAAAGGAGAAATGGATGATCTCTGTTCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCAAACAAAGAATTATTTTCATCATATACTCCAGCACTTACAGATGAAAAATTATTCATGGCAAACTCCGTTGTTGCAAAGGTAGAAGGATCTGGAAAAGTCCTATTAAAGATGACTTTAGGCAAGGTGGTGACTTTGAATAGGGTTTCATATGTTCCAGAATTGAGAAAGAATTTAGTTTCAATTCCAGTTCTGAACAAGAATGGATTTAAATGTGTATTTGTTTCTGATAAAGTAGTAGTAAGCAAAACTGATATGTATGTAGGAAAAGGCTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAGAGATTTTTCTTCTTCTTA</genome_strand>
        <mrna_strand>ATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAGGATCAAGCAAACTTGGCTGAATCCAAAGGAGAAATGGACGATCTCTGTGCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTTTGGTGCCTCATGCCATGTTTGTGCCAACAAAGAATTATTTTCATCATATACTTTAGCACTTACAGATGAAAAATTATTTATGGCAAACTCCGCTGTTGCAAAGGTGGAAGGAACTGGCAAAGTCCTATTAAAGATGACATCAGGCAAGGTAGTGACTTTGAATATGGTTTCATATGTTCCAGAATTGAGAAATAATTTAGTTTCAATTCCAATTTTGACCAAGAATGGATTTAAATGTGTATTTGTTTTTGATAAAGTAGTAGTAAGCAAAAATGATATGTATGTAGGAAAAGACTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAAAGATTTTGCTTTTTTTTA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>5</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="-" PGL_start="440" PGL_stop="214"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="440" e_stop="214"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.916"/>
        </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="0.916">
            <gDNA_exon_boundary e_start="440" e_stop="214" e_length="227"/>
          </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="440" stop="214"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E261310" 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>AGACATGTTTCTTGCTGAAAATGGCTATAAAAGGAAGGCAATTTTTGATTTTTCAAACACTTAAAATTTTTCTTTCTGTGCATTTATTTTCTCTCAAATAAAAATCAAAGTGTCGATCGACTGAGTCTGTGTGACTAGTTGATGTTCTTAAGTTCATTGAAGTTAATGAAATTTAAAGTACCGCTATTTCTTTAATAGGTTTAATCCGTTTTATCTTGGGAGAAATT</gDNA_template>
            <first_frame> R  H  V  S  C  *  K  W  L  *  K  E  G  N  F  *  F  F  K  H  L  K  F  F  F  L  C  I  Y  F  L  S  N  K  N  Q  S  V  D  R  L  S  L  C  D  *  L  M  F  L  S  S  L  K  L  M  K  F  K  V  P  L  F  L  *  *  V  *  S  V  L  S  W  E  K   </first_frame>
            <second_frame>  D  M  F  L  A  E  N  G  Y  K  R  K  A  I  F  D  F  S  N  T  *  N  F  S  F  C  A  F  I  F  S  Q  I  K  I  K  V  S  I  D  *  V  C  V  T  S  *  C  S  *  V  H  *  S  *  *  N  L  K  Y  R  Y  F  F  N  R  F  N  P  F  Y  L  G  R  N  </second_frame>
            <third_frame>   T  C  F  L  L  K  M  A  I  K  G  R  Q  F  L  I  F  Q  T  L  K  I  F  L  S  V  H  L  F  S  L  K  *  K  S  K  C  R  S  T  E  S  V  *  L  V  D  V  L  K  F  I  E  V  N  E  I  *  S  T  A  I  S  L  I  G  L  I  R  F  I  L  G  E  I </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <none gDNA_id="C04SLm0134J13.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="4577" PGL_stop="3929"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="4577" e_stop="3929"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.948"/>
        </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="0.948">
            <gDNA_exon_boundary e_start="4577" e_stop="3929" e_length="649"/>
          </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="4577" stop="3929"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E369759" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="4488" stop="3929"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E395006" strand="-"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="4464" stop="3929"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E250407" strand="-"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="4432" stop="3929"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E375520" 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>AAACAGTTTGTGTAAATTTTGTTGAAGAAGATTCAACAAAATTAAAGAAAAGAAAGAAAGCATCTGGTCCAAAAAGCAATCCTCCTAAGAAGAAATTCAATGGAAACTGCTTTATTTGTGATAAACATGGTCATAGGGCTAATGAATGCCGGGGTCCTAAGAAGGACAAGAAAAAGAAAGATCAAGCAAACTTGGCTTAATCCAAAGGAGAAATGGATGATCTCTGTTCAATGCTTTCAGAATGTAACTTGGTTGGAAATCCAAGAGAATGGTGGATAGATTCTGGTGCCTCATGCCATGTTTGTGCAAACAAAGAATTATTTTCATCATATACTCCAGCACTTACAGATGAAAAATTATTCATGGCAAACTCCGTTGTTGCAAAGGTAGAAGGATCTGGAAAAGTCCTATTAAAGATGACTTTAGGCAAGGTGGTGACTTTGAATAGGGTTTCATATGTTCCAGAATTGAGAAAGAATTTAGTTTCAATTCCAGTTCTGAACAAGAATGGATTTAAATGTGTATTTGTTTCTGATAAAGTAGTAGTAAGCAAAACTGATATGTATGTAGGAAAAGGCTACCTTAGTGATGGCCTTTTCAAACTCAATGTAATTGCAGTTGATATGAATAGAGATTTTTCTTCTTCTTA</gDNA_template>
            <first_frame> K  Q  F  V  *  I  L  L  K  K  I  Q  Q  N  *  R  K  E  R  K  H  L  V  Q  K  A  I  L  L  R  R  N  S  M  E  T  A  L  F  V  I  N  M  V  I  G  L  M  N  A  G  V  L  R  R  T  R  K  R  K  I  K  Q  T  W  L  N  P  K  E  K  W  M  I  S  V  Q  C  F  Q  N  V  T  W  L  E  I  Q  E  N  G  G  *  I  L  V  P  H  A  M  F  V  Q  T  K  N  Y  F  H  H  I  L  Q  H  L  Q  M  K  N  Y  S  W  Q  T  P  L  L  Q  R  *  K  D  L  E  K  S  Y  *  R  *  L  *  A  R  W  *  L  *  I  G  F  H  M  F  Q  N  *  E  R  I  *  F  Q  F  Q  F  *  T  R  M  D  L  N  V  Y  L  F  L  I  K  *  *  *  A  K  L  I  C  M  *  E  K  A  T  L  V  M  A  F  S  N  S  M  *  L  Q  L  I  *  I  E  I  F  L  L  L  </first_frame>
            <second_frame>  N  S  L  C  K  F  C  *  R  R  F  N  K  I  K  E  K  K  E  S  I  W  S  K  K  Q  S  S  *  E  E  I  Q  W  K  L  L  Y  L  *  *  T  W  S  *  G  *  *  M  P  G  S  *  E  G  Q  E  K  E  R  S  S  K  L  G  L  I  Q  R  R  N  G  *  S  L  F  N  A  F  R  M  *  L  G  W  K  S  K  R  M  V  D  R  F  W  C  L  M  P  C  L  C  K  Q  R  I  I  F  I  I  Y  S  S  T  Y  R  *  K  I  I  H  G  K  L  R  C  C  K  G  R  R  I  W  K  S  P  I  K  D  D  F  R  Q  G  G  D  F  E  *  G  F  I  C  S  R  I  E  K  E  F  S  F  N  S  S  S  E  Q  E  W  I  *  M  C  I  C  F  *  *  S  S  S  K  Q  N  *  Y  V  C  R  K  R  L  P  *  *  W  P  F  Q  T  Q  C  N  C  S  *  Y  E  *  R  F  F  F  F  L </second_frame>
            <third_frame>   T  V  C  V  N  F  V  E  E  D  S  T  K  L  K  K  R  K  K  A  S  G  P  K  S  N  P  P  K  K  K  F  N  G  N  C  F  I  C  D  K  H  G  H  R  A  N  E  C  R  G  P  K  K  D  K  K  K  K  D  Q  A  N  L  A  *  S  K  G  E  M  D  D  L  C  S  M  L  S  E  C  N  L  V  G  N  P  R  E  W  W  I  D  S  G  A  S  C  H  V  C  A  N  K  E  L  F  S  S  Y  T  P  A  L  T  D  E  K  L  F  M  A  N  S  V  V  A  K  V  E  G  S  G  K  V  L  L  K  M  T  L  G  K  V  V  T  L  N  R  V  S  Y  V  P  E  L  R  K  N  L  V  S  I  P  V  L  N  K  N  G  F  K  C  V  F  V  S  D  K  V  V  V  S  K  T  D  M  Y  V  G  K  G  Y  L  S  D  G  L  F  K  L  N  V  I  A  V  D  M  N  R  D  F  S  S  S   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C04SLm0134J13.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="4377" stop="3931"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>447</number_coding_nucleotides>
                  <number_encoded_amino_acids>149</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SKGEMDDLCSMLSECNLVGNPREWWIDSGASCHVCANKELFSSYTPALTDEKLFMANSVVAKVEGSGKVLLKMTLGKVVTLNRVSYVPELRKNLVSIPVLNKNGFKCVFVSDKVVVSKTDMYVGKGYLSDGLFKLNVIAVDMNRDFSSS</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C04SLm0134J13.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="4575" stop="4378"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>195</number_coding_nucleotides>
                  <number_encoded_amino_acids>65</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>TVCVNFVEEDSTKLKKRKKASGPKSNPPKKKFNGNCFICDKHGHRANECRGPKKDKKKKDQANLA*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 109 chains have been computed
$ 
$ memory statistics:
$ 8152 bytes spliced alignments in total
$ 5 spliced alignments have been stored
$ 1630 bytes was the average size of a spliced alignment
$ 6704 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3352 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 116 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 20:43:46
-->
