<?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 05:23:13"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0044A14-hzP7G/GenomeThreader_SGN_E_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0044A14-hzP7G/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_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-C00HBa0044A14-hzP7G/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" ref_id="SGN-E577891" ref_strand="+" ref_description="SGN-E577891 [LE08BA04]">
      <seq>ttcgtttcaaaatacttcagctcttggaatctgggtactggaatcacttctctgatcttcacgacgaacctgcaggacggaccgtcatagccatgacggaccgtcacaatcttcgtaatcccacacttggtgagacttccccatcttccttcagcagcttctctacgctgccacctacggagcgtcaaaggcacgatggaccgtcataagctcagtaggtggtctcttctacattttttcgctcaaaatctctgctttcagctttggacagatttcctgcaaaataaagagaaacttataccaaaattagcacaaaaaggcttacggacacactaaacttaaggcaaaagtattaattataccgtgaaaccacggtatatcagggacatgaactcgaaggccattgttggc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0044A14-hzP7G/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00HBa0044A14.1" temp_strand="-" temp_description="C00HBa0044A14.1  CU927994.5 htgs_phase:3 submitted_to_sgn_as:C00HBa0044A14 sequenced_by:sanger upload_account_name:uk">
        <position start="102531" stop="101551"/>
      </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="102232" g_stop="101859" g_length="374"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="374" r_length="374" r_score="0.925"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0044A14.1" gen_strand="-" ref_id="SGN-E577891" ref_strand="+">
        <total_alignment_score>0.925</total_alignment_score>
        <cumulative_length_of_scored_exons>374</cumulative_length_of_scored_exons>
        <coverage percentage="0.910" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0044A14.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E577891" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="102232" e_stop="101859"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCGTTTCAAAACACTTCAACTCTTGGAATCTAGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGATTGACCATCATAGCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACGCTGCCACCTACGGACCGTCATAGGCAAGACGGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTGCA-TTTTTCGCTCAAAATCTCCGCATTCAGCTTTGGACAGATTTCCTGTAAAACAAAGAGAAACTTATATCAAAATTAGCACAAAAGGGGCTTTCGGACACACTAAACTTAAGGAAAAAGTATTAATTATACCGTGAAACTACG</genome_strand>
        <mrna_strand>TTCGTTTCAAAATACTTCAGCTCTTGGAATCTGGGTACTGGAATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATAGCCATGACGGACCGTCACAATCTTCGTAATCCCACACTTGGTGAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACGCTGCCACCTACGGAGCGTCAAAGGCACGATGGACCGTCATAAGCTCAGTAGGTGGTCTCTTCTACATTTTTTCGCTCAAAATCTCTGCTTTCAGCTTTGGACAGATTTCCTGCAAAATAAAGAGAAACTTATACCAAAATTAGCACAAAA-AGGCTTACGGACACACTAAACTTAAGGCAAAAGTATTAATTATACCGTGAAACCACG</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-C00HBa0044A14-hzP7G/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_E_tomato" ref_id="SGN-E243969" ref_strand="+" ref_description="SGN-E243969 [cLEE-1-A19]">
      <seq>ggaaatctgccaaaacgcggcttggtcgacggaccacgcgacggaccgtcgtggactctgtcgtcccatacttggtgcaatttcttctgctgctttcttcattcccctcgacggcaagtgtaacggaccgtcataggtacaacggtctgtcgagggtcttcgtttcaaaatacttcaactcttggaatctgggtactgggatcacttctctgatcttcacgacgaacctgcaggacggaccgtcatagccatgacggaccgtcacaagcttcgtaatcccacacttggtcagacttccccatcttccttcagcagcttctctacgctaccacctacggaccgtcacaagcacgacagaccttcaaaagctccgtaggtggtctcttctgcatttttttgctcaaaatctccgctttcagcttttgacagatttcctgcaaaacaaagagaaacttatatcaaaattagcacaaaaaaggctttcggacactttaaacttaaggcaaaagtattaattatacc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0044A14-hzP7G/GenomeThreader_SGN_E_tomato/un_xed_seqs" temp_id="C00HBa0044A14.1" temp_strand="-" temp_description="C00HBa0044A14.1  CU927994.5 htgs_phase:3 submitted_to_sgn_as:C00HBa0044A14 sequenced_by:sanger upload_account_name:uk">
        <position start="102688" stop="101570"/>
      </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="102388" g_stop="101870" g_length="519"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="522" r_length="522" r_score="0.929"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0044A14.1" gen_strand="-" ref_id="SGN-E243969" ref_strand="+">
        <total_alignment_score>0.929</total_alignment_score>
        <cumulative_length_of_scored_exons>519</cumulative_length_of_scored_exons>
        <coverage percentage="0.994" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0044A14.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-E243969" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="102388" e_stop="101870"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGAAATCTGCCAAAACGCGGCTAGGTCGACGGACCACGCGACGGACCGTCGTGGAGTCCGTCGTCCCATACATGGTGCAATT-CTTCTGCTGCTTTATTCATTCCCATCGACGGCAAGTGTGACGGACCATCATAGGCACAACGGTCCGTCGAGGGTC-TCGTTTCAAAACACTTCAACTCTTGGAATCTAGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGATTGACCATCATAGCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACGCTGCCACCTACGGACCGTCATAGGCAAGACGGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTGCA-TTTTTCGCTCAAAATCTCCGCATTCAGCTTTGGACAGATTTCCTGTAAAACAAAGAGAAACTTATATCAAAATTAGCACAAAAGGGGCTTTCGGACACACTAAACTTAAGGAAAAAGTATTAATTATACC</genome_strand>
        <mrna_strand>GGAAATCTGCCAAAACGCGGCTTGGTCGACGGACCACGCGACGGACCGTCGTGGACTCTGTCGTCCCATACTTGGTGCAATTTCTTCTGCTGCTTTCTTCATTCCCCTCGACGGCAAGTGTAACGGACCGTCATAGGTACAACGGTCTGTCGAGGGTCTTCGTTTCAAAATACTTCAACTCTTGGAATCTGGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGACGGACCGTCATAGCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACGCTACCACCTACGGACCGTCACAAGCACGACAGACCTTCAAAAGCTCCGTAGGTGGTCTCTTCTGCATTTTTTTGCTCAAAATCTCCGCTTTCAGCTTTTGACAGATTTCCTGCAAAACAAAGAGAAACTTATATCAAAATTAGCACAAAAAAGGCTTTCGGACACTTTAAACTTAAGGCAAAAGTATTAATTATACC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>2</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="102388" PGL_stop="101859"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="102388" e_stop="101859"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.929"/>
        </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="0.929">
            <gDNA_exon_boundary e_start="102388" e_stop="101859" e_length="530"/>
          </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="102388" stop="101870"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E243969" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="102232" stop="101859"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-E577891" 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>GGAAATCTGCCAAAACGCGGCTAGGTCGACGGACCACGCGACGGACCGTCGTGGAGTCCGTCGTCCCATACATGGTGCAATTCTTCTGCTGCTTTATTCATTCCCATCGACGGCAAGTGTGACGGACCATCATAGGCACAACGGTCCGTCGAGGGTCTCGTTTCAAAACACTTCAACTCTTGGAATCTAGGTACTGGGATCACTTCTCTGATCTTCACGACGAACCTGCAGGATTGACCATCATAGCCATGACGGACCGTCACAAGCTTCGTAATCCCACACTTGGTCAGACTTCCCCATCTTCCTTCAGCAGCTTCTCTACGCTGCCACCTACGGACCGTCATAGGCAAGACGGACCGTCATAAGCTCCGTAGGTGGTCTCTTCTGCATTTTTCGCTCAAAATCTCCGCATTCAGCTTTGGACAGATTTCCTGTAAAACAAAGAGAAACTTATATCAAAATTAGCACAAAAGGGGCTTTCGGACACACTAAACTTAAGGAAAAAGTATTAATTATACCGTGAAACTACG</gDNA_template>
            <first_frame> G  N  L  P  K  R  G  *  V  D  G  P  R  D  G  P  S  W  S  P  S  S  H  T  W  C  N  S  S  A  A  L  F  I  P  I  D  G  K  C  D  G  P  S  *  A  Q  R  S  V  E  G  L  V  S  K  H  F  N  S  W  N  L  G  T  G  I  T  S  L  I  F  T  T  N  L  Q  D  *  P  S  *  P  *  R  T  V  T  S  F  V  I  P  H  L  V  R  L  P  H  L  P  S  A  A  S  L  R  C  H  L  R  T  V  I  G  K  T  D  R  H  K  L  R  R  W  S  L  L  H  F  S  L  K  I  S  A  F  S  F  G  Q  I  S  C  K  T  K  R  N  L  Y  Q  N  *  H  K  R  G  F  R  T  H  *  T  *  G  K  S  I  N  Y  T  V  K  L   </first_frame>
            <second_frame>  E  I  C  Q  N  A  A  R  S  T  D  H  A  T  D  R  R  G  V  R  R  P  I  H  G  A  I  L  L  L  L  Y  S  F  P  S  T  A  S  V  T  D  H  H  R  H  N  G  P  S  R  V  S  F  Q  N  T  S  T  L  G  I  *  V  L  G  S  L  L  *  S  S  R  R  T  C  R  I  D  H  H  S  H  D  G  P  S  Q  A  S  *  S  H  T  W  S  D  F  P  I  F  L  Q  Q  L  L  Y  A  A  T  Y  G  P  S  *  A  R  R  T  V  I  S  S  V  G  G  L  F  C  I  F  R  S  K  S  P  H  S  A  L  D  R  F  P  V  K  Q  R  E  T  Y  I  K  I  S  T  K  G  A  F  G  H  T  K  L  K  E  K  V  L  I  I  P  *  N  Y  </second_frame>
            <third_frame>   K  S  A  K  T  R  L  G  R  R  T  T  R  R  T  V  V  E  S  V  V  P  Y  M  V  Q  F  F  C  C  F  I  H  S  H  R  R  Q  V  *  R  T  I  I  G  T  T  V  R  R  G  S  R  F  K  T  L  Q  L  L  E  S  R  Y  W  D  H  F  S  D  L  H  D  E  P  A  G  L  T  I  I  A  M  T  D  R  H  K  L  R  N  P  T  L  G  Q  T  S  P  S  S  F  S  S  F  S  T  L  P  P  T  D  R  H  R  Q  D  G  P  S  *  A  P  *  V  V  S  S  A  F  F  A  Q  N  L  R  I  Q  L  W  T  D  F  L  *  N  K  E  K  L  I  S  K  L  A  Q  K  G  L  S  D  T  L  N  L  R  K  K  Y  *  L  Y  R  E  T  T </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C00HBa0044A14.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="102266" stop="102024"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>240</number_coding_nucleotides>
                  <number_encoded_amino_acids>80</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RTIIGTTVRRGSRFKTLQLLESRYWDHFSDLHDEPAGLTIIAMTDRHKLRNPTLGQTSPSSFSSFSTLPPTDRHRQDGPS*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C00HBa0044A14.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="102136" stop="101924"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>210</number_coding_nucleotides>
                  <number_encoded_amino_acids>70</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RTVTSFVIPHLVRLPHLPSAASLRCHLRTVIGKTDRHKLRRWSLLHFSLKISAFSFGQISCKTKRNLYQN*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 134 chains have been computed
$ 
$ memory statistics:
$ 4080 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2040 bytes was the average size of a spliced alignment
$ 5528 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5528 bytes was the average size of a predicted gene location
$ 3 megabytes was the average size of the backtrace matrix
$ 168 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 05:27:08
-->
