<?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="2010-02-05 14:34:42"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C05HBa0115F01-w1PQQ/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C05HBa0115F01-w1PQQ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" 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-C05HBa0115F01-w1PQQ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="SGN-M3920" ref_strand="+" ref_description="SGN-M3920 cTOS-7-C13 (EST clones)">
      <seq>gattgaagtacttgaaaatggaggtgttacaacaaaaatgaattatgttgatgatcaagttatgaaaaatagcaaagtagtgatgaaaacacacaaaagatcaagtggtgctcatcatgttcatcaaaaaattgatttcaatttggtgagtaaaagaagagttcctaatggtcctgacccaatccacaacagaagagctcggagttctcgtagaccaccaggccaagcttccaaaggaaaactcaacattaagccataattaacaaattaggccaaattagataattaaggtttgtgagatgtgttttttttttttttttgaaaaaaaaaaaaacttgtatgtaattgttgaaaaagggaagtctctatacatattgtcagatga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C05HBa0115F01-w1PQQ/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C05HBa0115F01.1" temp_strand="+" temp_description="C05HBa0115F01.1  AC239565.1 htgs_phase:3 submitted_to_sgn_as:C05HBa0115F01 sequenced_by:iitg upload_account_name:india complete_sequence">
        <position start="90383" stop="93650"/>
      </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="90683" g_stop="90874" g_length="192"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="192" r_length="192" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="90875" i_stop="93159" i_length="2285">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="93160" g_stop="93350" g_length="191"/>
          <reference_exon_boundary r_type="cDNA" r_start="193" r_stop="385" r_length="193" r_score="0.979"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C05HBa0115F01.1" gen_strand="+" ref_id="SGN-M3920" ref_strand="+">
        <total_alignment_score>0.990</total_alignment_score>
        <cumulative_length_of_scored_exons>383</cumulative_length_of_scored_exons>
        <coverage percentage="0.995" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C05HBa0115F01.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M3920" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="90683" e_stop="90874"/>
          <exon e_start="93160" e_stop="93350"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GATTGAAGTACTTGAAAATGGAGGTGTTACAACAAAAATGAATTATGTTGATGATCAAGTTATGAAAAATAGCAAAGTAGTGATGAAAACACACAAAAGATCAAGTGGTGCTCATCATGTTCATCAAAAAATTGATTTCAATTTGGTGAGTAAAAGAAGAGTTCCTAATGGTCCTGACCCAATCCACAACAGGTTTGTCTTTACTTTATTTCTTTATGGAGCTTTTTTTCTCTCTATAAACTTAATTGTCAAAAACATATCTGGATTATCGAGAGTTTTACATACTAATTATATATTAATTGTTCACTTGTCATATCAGAACTATTGTTATCTATGTAGTTATAAAACATACTTTAAGATGTTTAGTTTTCTTACTTGAACTATCACCGTCGTTCATGTACGAAAAGAGAACACGTGATAGTTGAAGTGTGTGTTTAACGAAAGTGGTGATAGTGTCTGTTGAAAAAGGAAATGATTGATAGTTAAAGTATAAAATTTGCGAAAAAATAATATTTAGCTATAAATCAATACTTCTTTAAAGTTGAATATTCTAAATAATTTGATAGTATGAAAAAAAATATGTATATTAATTACATATATGCCCTCACAAACCACATCTTATATAGTTTTTATAAAATATTTACATTATATATAGTATTGATCATATAAATTTTTATATTATAGTGTAGTTTAACCTATTTAGCCGATTTTCTATGTTCTCAATCAACATTTAATAAGTATAAGAGTGACATGTAATGGAAAAATTCTTTTAAACAATTTAATTGTATAAGTTATTATAATTATAATTATAATTATGATCGTCTAATGAGCATTTGATATTAATAATTGATATTTTCAGAAGTTTGGCTCACTTCTAGATGCAATTAGCTAGTGGAAGTAATAAAAAAACTATATTTTAAGACTTCCAAGAGATTTTGCCAATTATAAAAGTAAATTTGAAGTTATATTAAAACAAAAAAAAGTAACTCTATCATATAAATTTTAAAAAAAATCTCTTCAAAGCTATAGATTGTTCTAATAATTATTAATTTTTCTTCCTTTTTTTGGGAATAATTCATCAATTATTTTGAATGAAAAATTTCATATTAATTGATATAGTTCCATGTTCTTTCCCAAATTAAAAGAACAAGACCAATTCAACTTTCTTATGAGGAAAAATTTAATTTCGGATTAATTATCATACTGTTCATTTATTAGCTCATTTCATTTTTATTAATTCATTTTAGTCACCAAAATCGTGATTGATATCGTAGCTTAAATCAATCCATGAAAATCTTATTAAAATATTTTAAAAGGATATAATTTTATCTTATATGTTATATATAGTCATAAATAAAAAAATAGTTTTATTAGGTATTAAAAAATTATTTTATAAAAATATTTAAAACTGAGTATAAATTCAGCGAGTTAGATTTTGACCTATTTTTTAAAGCTCATTTCAACTCATATAACTTTTTACTCGTCTATTTATTAACTCAAAATATTTTAACCCGTTCAAATTAAGTTCGATCGATCTTATTTATTTTACGTAGAGCCCATAAAAGATGTATTTTTGAGACAAAAGTAGTAGGGTTTGCATGCTTAACTGTTACATCAAGTACTCCCACTCTTAGATTCTGTTCAAAGTTTTTGTTTACTGAATTTGTGTAACTTTAAGTTAATGAATAAATAAAATAAAAGGAATTAATTTAGAAAAAAGAAAAAGTATCTGTGTTCTGTTTTGTTGTCTTTCACTTTATTTATTCTCTTATAATTATAAATGAATAATAAAGCTAGCTTAATTATCATGATAATTAATTAACCTTTTCATTTTGTTTTCTATGCAATTTACGAGGTTCTAATTAATTAATTAACCTTTTCATGACATCTCTTTTTTTTTCCTTTTGCTTTCTTTTTTACCCTTTATCACTAAAAAAAAGCTTTTTCATCACTATAGATGCAAATCATATAAATATCTTACATATCAAAAGAATATTTTCTTAACCAAATTTAATTTTCATATATTAACGTTAGAGTCGGAATCAGTATTAAGTTTTGTTAGGGGTTCACAATTAATATTTTTATAATTTTCTAGTACAAATATAAGATATACAGAAAAGATACTGAGTTCGTTTGAATATACAAACCTCGCCTAATTAACGTGTGTGATCAACTCATCTAAGAATTTAAATTTTTATAGCCAAACATGTAAAAAATAAAAAAATTTATAATGGGTGATGATAAGAATATATCGCACTCAGAATTTTGTTTGCTCTAATACTATATTAAAGTACGTAATCTCAAGCTATAATCCCTAACTAAAAAGCTCTAAGTTGATTGAAACTTCTCGTAATTTGTTGTTAATCCATAGCTAAATGAAGTTAACGTGAAAATTTTGTTATTCAGCTACGAAATTTTATCTATGACGTTTGTGTATGTAACTAAATTTATTTATATCTAATTATTTTTTTTAACAGAAGAGCTCGGAGTTCTCGTAGACCACCAGGCCAAGCTTCCAAAGGAAAACTCAACATTAAGCCATAATTAACAAATTAGGCCAAATTAGATAATTAAGGTTTGTGAGATGTGTTT-TTTTTTTTTTTTG-AAAAAAAAAAAACTTGTATGTAATTGTTGAAAAAGGGAAGTCTCTATACATATTGTCAGATGA</genome_strand>
        <mrna_strand>GATTGAAGTACTTGAAAATGGAGGTGTTACAACAAAAATGAATTATGTTGATGATCAAGTTATGAAAAATAGCAAAGTAGTGATGAAAACACACAAAAGATCAAGTGGTGCTCATCATGTTCATCAAAAAATTGATTTCAATTTGGTGAGTAAAAGAAGAGTTCCTAATGGTCCTGACCCAATCCACAACAG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAGAGCTCGGAGTTCTCGTAGACCACCAGGCCAAGCTTCCAAAGGAAAACTCAACATTAAGCCATAATTAACAAATTAGGCCAAATTAGATAATTAAGGTTTGTGAGATGTGTTTTTTTTTTTTTTTTGAAAAAAAAAAAAACTTGTATGTAATTGTTGAAAAAGGGAAGTCTCTATACATATTGTCAGATGA</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="90683" PGL_stop="93350"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="90683" e_stop="90874"/>
            <exon e_start="93160" e_stop="93350"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="1.000" e_score="1.000"/>
          <exon-only e_score="0.979"/>
        </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="90683" e_stop="90874" e_length="192"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="1.000">
            <gDNA_intron_boundary i_start="90875" i_stop="93159" i_length="2285"/>
          </intron>
          <exon e_serial="2" e_score="0.979">
            <gDNA_exon_boundary e_start="93160" e_stop="93350" e_length="191"/>
          </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="90683" stop="90874"/>
              <exon start="93160" stop="93350"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M3920" 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>GATTGAAGTACTTGAAAATGGAGGTGTTACAACAAAAATGAATTATGTTGATGATCAAGTTATGAAAAATAGCAAAGTAGTGATGAAAACACACAAAAGATCAAGTGGTGCTCATCATGTTCATCAAAAAATTGATTTCAATTTGGTGAGTAAAAGAAGAGTTCCTAATGGTCCTGACCCAATCCACAACAG : AAGAGCTCGGAGTTCTCGTAGACCACCAGGCCAAGCTTCCAAAGGAAAACTCAACATTAAGCCATAATTAACAAATTAGGCCAAATTAGATAATTAAGGTTTGTGAGATGTGTTTTTTTTTTTTTTTGAAAAAAAAAAAACTTGTATGTAATTGTTGAAAAAGGGAAGTCTCTATACATATTGTCAGATGA</gDNA_template>
            <first_frame> D  *  S  T  *  K  W  R  C  Y  N  K  N  E  L  C  *  *  S  S  Y  E  K  *  Q  S  S  D  E  N  T  Q  K  I  K  W  C  S  S  C  S  S  K  N  *  F  Q  F  G  E  *  K  K  S  S  *  W  S  *  P  N  P  Q  Q  :  K  S  S  E  F  S  *  T  T  R  P  S  F  Q  R  K  T  Q  H  *  A  I  I  N  K  L  G  Q  I  R  *  L  R  F  V  R  C  V  F  F  F  F  *  K  K  K  N  L  Y  V  I  V  E  K  G  K  S  L  Y  I  L  S  D   </first_frame>
            <second_frame>  I  E  V  L  E  N  G  G  V  T  T  K  M  N  Y  V  D  D  Q  V  M  K  N  S  K  V  V  M  K  T  H  K  R  S  S  G  A  H  H  V  H  Q  K  I  D  F  N  L  V  S  K  R  R  V  P  N  G  P  D  P  I  H  N  R :   R  A  R  S  S  R  R  P  P  G  Q  A  S  K  G  K  L  N  I  K  P  *  L  T  N  *  A  K  L  D  N  *  G  L  *  D  V  F  F  F  F  F  E  K  K  K  T  C  M  *  L  L  K  K  G  S  L  Y  T  Y  C  Q  M  </second_frame>
            <third_frame>   L  K  Y  L  K  M  E  V  L  Q  Q  K  *  I  M  L  M  I  K  L  *  K  I  A  K  *  *  *  K  H  T  K  D  Q  V  V  L  I  M  F  I  K  K  L  I  S  I  W  *  V  K  E  E  F  L  M  V  L  T  Q  S  T  T   : E  E  L  G  V  L  V  D  H  Q  A  K  L  P  K  E  N  S  T  L  S  H  N  *  Q  I  R  P  N  *  I  I  K  V  C  E  M  C  F  F  F  F  L  K  K  K  K  L  V  C  N  C  *  K  R  E  V  S  I  H  I  V  R  * </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="C05HBa0115F01.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="90684" stop="90874"/>
                    <exon start="93160" stop="93226"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>255</number_coding_nucleotides>
                  <number_encoded_amino_acids>85</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IEVLENGGVTTKMNYVDDQVMKNSKVVMKTHKRSSGAHHVHQKIDFNLVSKRRVPNGPDPIHNRRARSSRRPPGQASKGKLNIKP*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 3 chains have been computed
$ 
$ memory statistics:
$ 2280 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 5560 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5560 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 3 backtrace matrices have been allocated
$ 
$ date finished: 2010-02-05 14:34:44
-->
