<?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 13:02:23"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09HBa0166O16-9aHHw/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09HBa0166O16-9aHHw/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-C09HBa0166O16-9aHHw/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U327089" ref_strand="+" ref_description="SGN-U327089        Tomato 200607 #1 [4 ESTs aligned]">
      <seq>ccaacgtttctagtagtcctagaagaaacgtgtatgataaaaacgatcttaccgcacctctacatcgtccctttcatgcgtctcttcacacgattcccagcagtagctcgccttagaagccatagcgcgtgaggcgtcttcctcagcgtctcccctccattttgtagattgttgacagttgcagcagcaagtcaagtgaagttgtccttgaaagcttgaaatttagccatgtcgcttgccaaggacaatcgatttgatctgttcgtcctttctcctttactatttaggaatggattcacgctttagaaaaatatggtatacctctaatcgtgaaagaattcaaattatgatttctcgatgggctttgaaccccaattggatccgtttttccctgattttcaagccctaaattccctctataaaagatctcttttcttcatctcagggggcttgccggaaaaagattggaaaaaagggttggatatttttagttggaaaattggaagggattttcgagttgagaatttctaatagaaagataggagaaaagttgacgattttcagttgggttattatttggtctaaaagaccaaaaaatctttttagcagaaacatgagaatagctttagaaacgggtagttatacactatactttagaatagagaacttcttggatttctacctcgtctccttagtcgtgagtgttcgatgtgttcgtggtgaaagtcattacctctctgctcgtgctgttgctgcctcggagaaagtaaattttcctcctaaatttttactcgtctgatgtatttttgatttaatgaagtaaagtgatttgttgaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09HBa0166O16-9aHHw/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C09HBa0166O16.1" temp_strand="-" temp_description="C09HBa0166O16.1  AC233064.1 htgs_phase:3 submitted_to_sgn_as:gnl|gbrgsp|C09HBa0166O16 upload_account_name:spain (1 - 118985)">
        <position start="73595" stop="72160"/>
      </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="73295" g_stop="72461" g_length="835"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="835" r_length="835" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="836" polyA_stop="846"/>
      <MATCH_line gen_id="C09HBa0166O16.1" gen_strand="-" ref_id="SGN-U327089" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>835</cumulative_length_of_scored_exons>
        <coverage percentage="0.987" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09HBa0166O16.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U327089" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="73295" e_stop="72461"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCAACGTTTCTAGTAGTCCTAGAAGAAACGTGTATGATAAAAACGATCTTACCGCACCTCTACATCGTCCCTTTCATGCGTCTCTTCACACGATTCCCAGCAGTAGCTCGCCTTAGAAGCCATAGCGCGTGAGGCGTCTTCCTCAGCGTCTCCCCTCCATTTTGTAGATTGTTGACAGTTGCAGCAGCAAGTCAAGTGAAGTTGTCCTTGAAAGCTTGAAATTTAGCCATGTCGCTTGCCAAGGACAATCGATTTGATCTGTTCGTCCTTTCTCCTTTACTATTTAGGAATGGATTCACGCTTTAGAAAAATATGGTATACCTCTAATCGTGAAAGAATTCAAATTATGATTTCTCGATGGGCTTTGAACCCCAATTGGATCCGTTTTTCCCTGATTTTCAAGCCCTAAATTCCCTCTATAAAAGATCTCTTTTCTTCATCTCAGGGGGCTTGCCGGAAAAAGATTGGAAAAAAGGGTTGGATATTTTTAGTTGGAAAATTGGAAGGGATTTTCGAGTTGAGAATTTCTAATAGAAAGATAGGAGAAAAGTTGACGATTTTCAGTTGGGTTATTATTTGGTCTAAAAGACCAAAAAATCTTTTTAGCAGAAACATGAGAATAGCTTTAGAAACGGGTAGTTATACACTATACTTTAGAATAGAGAACTTCTTGGATTTCTACCTCGTCTCCTTAGTCGTGAGTGTTCGATGTGTTCGTGGTGAAAGTCATTACCTCTCTGCTCGTGCTGTTGCTGCCTCGGAGAAAGTAAATTTTCCTCCTAAATTTTTACTCGTCTGATGTATTTTTGATTTAATGAAGTAAAGTGATTTGTTG</genome_strand>
        <mrna_strand>CCAACGTTTCTAGTAGTCCTAGAAGAAACGTGTATGATAAAAACGATCTTACCGCACCTCTACATCGTCCCTTTCATGCGTCTCTTCACACGATTCCCAGCAGTAGCTCGCCTTAGAAGCCATAGCGCGTGAGGCGTCTTCCTCAGCGTCTCCCCTCCATTTTGTAGATTGTTGACAGTTGCAGCAGCAAGTCAAGTGAAGTTGTCCTTGAAAGCTTGAAATTTAGCCATGTCGCTTGCCAAGGACAATCGATTTGATCTGTTCGTCCTTTCTCCTTTACTATTTAGGAATGGATTCACGCTTTAGAAAAATATGGTATACCTCTAATCGTGAAAGAATTCAAATTATGATTTCTCGATGGGCTTTGAACCCCAATTGGATCCGTTTTTCCCTGATTTTCAAGCCCTAAATTCCCTCTATAAAAGATCTCTTTTCTTCATCTCAGGGGGCTTGCCGGAAAAAGATTGGAAAAAAGGGTTGGATATTTTTAGTTGGAAAATTGGAAGGGATTTTCGAGTTGAGAATTTCTAATAGAAAGATAGGAGAAAAGTTGACGATTTTCAGTTGGGTTATTATTTGGTCTAAAAGACCAAAAAATCTTTTTAGCAGAAACATGAGAATAGCTTTAGAAACGGGTAGTTATACACTATACTTTAGAATAGAGAACTTCTTGGATTTCTACCTCGTCTCCTTAGTCGTGAGTGTTCGATGTGTTCGTGGTGAAAGTCATTACCTCTCTGCTCGTGCTGTTGCTGCCTCGGAGAAAGTAAATTTTCCTCCTAAATTTTTACTCGTCTGATGTATTTTTGATTTAATGAAGTAAAGTGATTTGTTG</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>1</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="73295" PGL_stop="72461"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="73295" e_stop="72461"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="1.000"/>
        </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="1.000">
            <gDNA_exon_boundary e_start="73295" e_stop="72461" e_length="835"/>
          </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="73295" stop="72461"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U327089" 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>CCAACGTTTCTAGTAGTCCTAGAAGAAACGTGTATGATAAAAACGATCTTACCGCACCTCTACATCGTCCCTTTCATGCGTCTCTTCACACGATTCCCAGCAGTAGCTCGCCTTAGAAGCCATAGCGCGTGAGGCGTCTTCCTCAGCGTCTCCCCTCCATTTTGTAGATTGTTGACAGTTGCAGCAGCAAGTCAAGTGAAGTTGTCCTTGAAAGCTTGAAATTTAGCCATGTCGCTTGCCAAGGACAATCGATTTGATCTGTTCGTCCTTTCTCCTTTACTATTTAGGAATGGATTCACGCTTTAGAAAAATATGGTATACCTCTAATCGTGAAAGAATTCAAATTATGATTTCTCGATGGGCTTTGAACCCCAATTGGATCCGTTTTTCCCTGATTTTCAAGCCCTAAATTCCCTCTATAAAAGATCTCTTTTCTTCATCTCAGGGGGCTTGCCGGAAAAAGATTGGAAAAAAGGGTTGGATATTTTTAGTTGGAAAATTGGAAGGGATTTTCGAGTTGAGAATTTCTAATAGAAAGATAGGAGAAAAGTTGACGATTTTCAGTTGGGTTATTATTTGGTCTAAAAGACCAAAAAATCTTTTTAGCAGAAACATGAGAATAGCTTTAGAAACGGGTAGTTATACACTATACTTTAGAATAGAGAACTTCTTGGATTTCTACCTCGTCTCCTTAGTCGTGAGTGTTCGATGTGTTCGTGGTGAAAGTCATTACCTCTCTGCTCGTGCTGTTGCTGCCTCGGAGAAAGTAAATTTTCCTCCTAAATTTTTACTCGTCTGATGTATTTTTGATTTAATGAAGTAAAGTGATTTGTTG</gDNA_template>
            <first_frame> P  T  F  L  V  V  L  E  E  T  C  M  I  K  T  I  L  P  H  L  Y  I  V  P  F  M  R  L  F  T  R  F  P  A  V  A  R  L  R  S  H  S  A  *  G  V  F  L  S  V  S  P  P  F  C  R  L  L  T  V  A  A  A  S  Q  V  K  L  S  L  K  A  *  N  L  A  M  S  L  A  K  D  N  R  F  D  L  F  V  L  S  P  L  L  F  R  N  G  F  T  L  *  K  N  M  V  Y  L  *  S  *  K  N  S  N  Y  D  F  S  M  G  F  E  P  Q  L  D  P  F  F  P  D  F  Q  A  L  N  S  L  Y  K  R  S  L  F  F  I  S  G  G  L  P  E  K  D  W  K  K  G  L  D  I  F  S  W  K  I  G  R  D  F  R  V  E  N  F  *  *  K  D  R  R  K  V  D  D  F  Q  L  G  Y  Y  L  V  *  K  T  K  K  S  F  *  Q  K  H  E  N  S  F  R  N  G  *  L  Y  T  I  L  *  N  R  E  L  L  G  F  L  P  R  L  L  S  R  E  C  S  M  C  S  W  *  K  S  L  P  L  C  S  C  C  C  C  L  G  E  S  K  F  S  S  *  I  F  T  R  L  M  Y  F  *  F  N  E  V  K  *  F  V  </first_frame>
            <second_frame>  Q  R  F  *  *  S  *  K  K  R  V  *  *  K  R  S  Y  R  T  S  T  S  S  L  S  C  V  S  S  H  D  S  Q  Q  *  L  A  L  E  A  I  A  R  E  A  S  S  S  A  S  P  L  H  F  V  D  C  *  Q  L  Q  Q  Q  V  K  *  S  C  P  *  K  L  E  I  *  P  C  R  L  P  R  T  I  D  L  I  C  S  S  F  L  L  Y  Y  L  G  M  D  S  R  F  R  K  I  W  Y  T  S  N  R  E  R  I  Q  I  M  I  S  R  W  A  L  N  P  N  W  I  R  F  S  L  I  F  K  P  *  I  P  S  I  K  D  L  F  S  S  S  Q  G  A  C  R  K  K  I  G  K  K  G  W  I  F  L  V  G  K  L  E  G  I  F  E  L  R  I  S  N  R  K  I  G  E  K  L  T  I  F  S  W  V  I  I  W  S  K  R  P  K  N  L  F  S  R  N  M  R  I  A  L  E  T  G  S  Y  T  L  Y  F  R  I  E  N  F  L  D  F  Y  L  V  S  L  V  V  S  V  R  C  V  R  G  E  S  H  Y  L  S  A  R  A  V  A  A  S  E  K  V  N  F  P  P  K  F  L  L  V  *  C  I  F  D  L  M  K  *  S  D  L  L </second_frame>
            <third_frame>   N  V  S  S  S  P  R  R  N  V  Y  D  K  N  D  L  T  A  P  L  H  R  P  F  H  A  S  L  H  T  I  P  S  S  S  S  P  *  K  P  *  R  V  R  R  L  P  Q  R  L  P  S  I  L  *  I  V  D  S  C  S  S  K  S  S  E  V  V  L  E  S  L  K  F  S  H  V  A  C  Q  G  Q  S  I  *  S  V  R  P  F  S  F  T  I  *  E  W  I  H  A  L  E  K  Y  G  I  P  L  I  V  K  E  F  K  L  *  F  L  D  G  L  *  T  P  I  G  S  V  F  P  *  F  S  S  P  K  F  P  L  *  K  I  S  F  L  H  L  R  G  L  A  G  K  R  L  E  K  R  V  G  Y  F  *  L  E  N  W  K  G  F  S  S  *  E  F  L  I  E  R  *  E  K  S  *  R  F  S  V  G  L  L  F  G  L  K  D  Q  K  I  F  L  A  E  T  *  E  *  L  *  K  R  V  V  I  H  Y  T  L  E  *  R  T  S  W  I  S  T  S  S  P  *  S  *  V  F  D  V  F  V  V  K  V  I  T  S  L  L  V  L  L  L  P  R  R  K  *  I  F  L  L  N  F  Y  S  S  D  V  F  L  I  *  *  S  K  V  I  C   </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="C09HBa0166O16.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="72886" stop="72497"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>387</number_coding_nucleotides>
                  <number_encoded_amino_acids>129</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IPSIKDLFSSSQGACRKKIGKKGWIFLVGKLEGIFELRISNRKIGEKLTIFSWVIIWSKRPKNLFSRNMRIALETGSYTLYFRIENFLDFYLVSLVVSVRCVRGESHYLSARAVAASEKVNFPPKFLLV*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 29 chains have been computed
$ 
$ memory statistics:
$ 1528 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 1528 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
$ 0 megabytes was the average size of the backtrace matrix
$ 35 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 13:02:53
-->
