<?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 08:47:29"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C02HBa0054K23-D7rxv/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C02HBa0054K23-D7rxv/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-C02HBa0054K23-D7rxv/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="C2_At3g01180" ref_strand="+" ref_description="C2_At3g01180">
      <seq>tggtggggtctgctatggaaatggaaatttagtgttcattgctaatgattggcatactgctttattgccagtatatctgaaagcttattatcgtgacaatggaattatgaactatacaagatctgtcctggtgattcataacatcgctcatcagggtcgtggtcctttggaggatttttcatatgtagatcttccaccacactatatggaccctttcaagttgtatgacccagtaggaggtgagcatttcaacatttttgcggctggtctaaagacagcagatcgtgtagttacagttagtcatggatattcatgggaactaaagacttcccaaggtggttggggattgcatcagataattaatgagaacgattggaaattacagggtattgtgaatgggattgatacaaaagagtggaaccctgagttggacgttcacttacagtcagatggttacatgaactactccttggacacgctacagactggcaagcctcaatgtaaagctgcattgcagaaggaacttggtttaccagttcgtgatgatgtcccactgatcggtttcattgggaggcttgacccacaaaagggtgttgatctgattgctgaggcagtgcctttggatgatgggtcaggatgtacaaactggtcatgttggggacggggaggcgtgaccttgaacagatgctaaggcaatttgaagtgtcaacacaatg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C02HBa0054K23-D7rxv/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C02HBa0054K23.1" temp_strand="+" temp_description="C02HBa0054K23.1  AC232769.1 htgs_phase:3 submitted_to_sgn_as:C02HBa0054K23 sequenced_by:kribb upload_account_name:korea">
        <position start="19309" stop="21766"/>
      </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="19609" g_stop="19762" g_length="154"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="154" r_length="154" r_score="0.987"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="19763" i_stop="20907" i_length="1145">
            <donor d_prob="0.992" d_score="1.00"/>
            <acceptor a_prob="0.993" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="20908" g_stop="21466" g_length="559"/>
          <reference_exon_boundary r_type="cDNA" r_start="155" r_stop="716" r_length="562" r_score="0.971"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C02HBa0054K23.1" gen_strand="+" ref_id="C2_At3g01180" ref_strand="+">
        <total_alignment_score>0.975</total_alignment_score>
        <cumulative_length_of_scored_exons>713</cumulative_length_of_scored_exons>
        <coverage percentage="0.996" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C02HBa0054K23.1" gen_strand="+"/>
        <rDNA rDNA_id="C2_At3g01180" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="19609" e_stop="19762"/>
          <exon e_start="20908" e_stop="21466"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TGGTGGGGTCTGCTATGGAGATGGAAACTTAGTGTTCATTGCTAATGATTGGCATACTGCTTTATTGCCAGTATATCTGAAAGCTTATTATCGTGACAATGGAATTATGAACTATACAAGATCTGTCCTGGTGATTCATAACATCGCTCATCAGGTCAGTTTCATCAGCAACTAAAGCAGTTTTCTAATCCACCTGTGCATTTTTATTTCCAATAATTTAGCAGTATAGCCATTTTTTAAGTTCCAAAGGTTGGTCGTATATCATGATTTCTATGACTTCTAAGCATAAGATTTAAAATAAATGATTACCTTGATAGGTAAACCGATGGGTGGGGCCCATCATCCACTGAGTTTTGAACTGTGGAGGCCTCGAAAATTTCTCGGTTATCAAAATAATTTAATAACGATGACTAGTTTGATATTATATATCTACTAGGTGTTCGTGGGATAATTATTACTTCCGCGTCACTAAGTTCAATAGCTTAGGTACCCACTGAGAGTACCATATCAGGCTATCAATAAATCTAGTTACAGGTAAAGCATTTTTTATCATGCACAGACCATACTCAGACTTGTTTAGGAGTATTGCCTGATAAGTGAAATTCTTTGAAAAGTTGTTTTCTCATCTCTGTGCGTGAGCCGGTTGAAGAATATGCTTTTTAAGCTTCATACTGGATTATGCTTTGATTTGTAATGATCTACCACAATATGAGATCAACCCCACAAAAAACAAAAGAAAATCTCGAAGAAGTTACCAAAGATATGTCGTACATGAAGTCTTATATTAGCAATGTACAACTCTACCTTTTCCTCATGTGCTAAGGTTAAGCACACTGATGCATTTTGCTTCTACTACTAGTTATCATCTTTTTATTAAATTTTTTCTTGCCTCATTTGATATGTATCTGAATACAACTTTCTTTTTATAATGAATTTTCTTCATGAAAGTTACAAAGAGCGCTGTGGAGTGAGCCAAGATTTTATGCATGTAATGTAAGCAGCAGAGAACTAGAAATACTATGTTCGTCCAATTAAACATGACCTACTTTGACCTGTGCAATTGTTTTCAAATATCTGGTAGATTATAACTTTTAAGTATAATGTGAAGAGTGTAAAATAATAATTTGGAATATAAAACAGTAGAGTAATTGGAGTTATCTCTATCCAAGTTCTGTATTTTGTTAGTATTTTCTGATTTTTGTCATTTATTTTATCTTTTTGTAACGTGAATAAGGGTTATAGCAATCTTAGCCAGCTTTCTATCATTTTCAGCTCTATAATTTGTTCCATCTCATGCAGGGTCGTGGTCCTTTGGAGGATTTTTCATATGTAGATCTTCCACCACACTATATGGACCCTTTCAAATTGTATGACCCAGTAGGAGGTGAGCATTTCAACATTTTTGCGGCTGGTCTAAAGACAGCAGATCGTGTAGTTACAGTTAGTCATGGATATTCATGGGAACTCAAGACTTCCGAAGGTGGTTGGGGATTGCATCAGATAATTAATGAGAACGATTGGAAATTACGGGGTATTGTGAATGGGATTGATACAAAAGAGTGGAACCCTGAGTTGGACGTTCACTTACAGTCAGATGGTTACGTGAACTACTCCTTGGACACACTGCAGACTGGCAAGCCTCAATGTAAAGCTGCATTGCAGAAGGAACTTGGTTTACCAGTTCGTGATGATGTCCCACTGATTGGTTTCATTGGGAGGCTTGACCCACAAAAGGGTGTTGATCTGATTGCTGAGGCAGTGCC-TTGGATGATGGGTCAGGATGTAC-AACTGGTCATGTTGGGTACGGGGAGGCCTGACCTTGAACAGATGCTAAGGCAATTTG-AGTGTCAACACAATG</genome_strand>
        <mrna_strand>TGGTGGGGTCTGCTATGGAAATGGAAATTTAGTGTTCATTGCTAATGATTGGCATACTGCTTTATTGCCAGTATATCTGAAAGCTTATTATCGTGACAATGGAATTATGAACTATACAAGATCTGTCCTGGTGATTCATAACATCGCTCATCAG.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GGTCGTGGTCCTTTGGAGGATTTTTCATATGTAGATCTTCCACCACACTATATGGACCCTTTCAAGTTGTATGACCCAGTAGGAGGTGAGCATTTCAACATTTTTGCGGCTGGTCTAAAGACAGCAGATCGTGTAGTTACAGTTAGTCATGGATATTCATGGGAACTAAAGACTTCCCAAGGTGGTTGGGGATTGCATCAGATAATTAATGAGAACGATTGGAAATTACAGGGTATTGTGAATGGGATTGATACAAAAGAGTGGAACCCTGAGTTGGACGTTCACTTACAGTCAGATGGTTACATGAACTACTCCTTGGACACGCTACAGACTGGCAAGCCTCAATGTAAAGCTGCATTGCAGAAGGAACTTGGTTTACCAGTTCGTGATGATGTCCCACTGATCGGTTTCATTGGGAGGCTTGACCCACAAAAGGGTGTTGATCTGATTGCTGAGGCAGTGCCTTTGGATGATGGGTCAGGATGTACAAACTGGTCATGTTGGGGACGGGGAGGCGTGACCTTGAACAGATGCTAAGGCAATTTGAAGTGTCAACACAATG</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="19609" PGL_stop="21466"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="19609" e_stop="19762"/>
            <exon e_start="20908" e_stop="21466"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.992" acc_prob="0.993" e_score="0.987"/>
          <exon-only e_score="0.971"/>
        </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="0.987">
            <gDNA_exon_boundary e_start="19609" e_stop="19762" e_length="154"/>
          </exon>
          <intron i_serial="1" don_prob="0.992" acc_prob="0.993">
            <gDNA_intron_boundary i_start="19763" i_stop="20907" i_length="1145"/>
          </intron>
          <exon e_serial="2" e_score="0.971">
            <gDNA_exon_boundary e_start="20908" e_stop="21466" e_length="559"/>
          </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="19609" stop="19762"/>
              <exon start="20908" stop="21466"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="C2_At3g01180" 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>TGGTGGGGTCTGCTATGGAGATGGAAACTTAGTGTTCATTGCTAATGATTGGCATACTGCTTTATTGCCAGTATATCTGAAAGCTTATTATCGTGACAATGGAATTATGAACTATACAAGATCTGTCCTGGTGATTCATAACATCGCTCATCAG : GGTCGTGGTCCTTTGGAGGATTTTTCATATGTAGATCTTCCACCACACTATATGGACCCTTTCAAATTGTATGACCCAGTAGGAGGTGAGCATTTCAACATTTTTGCGGCTGGTCTAAAGACAGCAGATCGTGTAGTTACAGTTAGTCATGGATATTCATGGGAACTCAAGACTTCCGAAGGTGGTTGGGGATTGCATCAGATAATTAATGAGAACGATTGGAAATTACGGGGTATTGTGAATGGGATTGATACAAAAGAGTGGAACCCTGAGTTGGACGTTCACTTACAGTCAGATGGTTACGTGAACTACTCCTTGGACACACTGCAGACTGGCAAGCCTCAATGTAAAGCTGCATTGCAGAAGGAACTTGGTTTACCAGTTCGTGATGATGTCCCACTGATTGGTTTCATTGGGAGGCTTGACCCACAAAAGGGTGTTGATCTGATTGCTGAGGCAGTGCCTTGGATGATGGGTCAGGATGTACAACTGGTCATGTTGGGTACGGGGAGGCCTGACCTTGAACAGATGCTAAGGCAATTTGAGTGTCAACACAATG</gDNA_template>
            <first_frame> W  W  G  L  L  W  R  W  K  L  S  V  H  C  *  *  L  A  Y  C  F  I  A  S  I  S  E  S  L  L  S  *  Q  W  N  Y  E  L  Y  K  I  C  P  G  D  S  *  H  R  S  S   : G  S  W  S  F  G  G  F  F  I  C  R  S  S  T  T  L  Y  G  P  F  Q  I  V  *  P  S  R  R  *  A  F  Q  H  F  C  G  W  S  K  D  S  R  S  C  S  Y  S  *  S  W  I  F  M  G  T  Q  D  F  R  R  W  L  G  I  A  S  D  N  *  *  E  R  L  E  I  T  G  Y  C  E  W  D  *  Y  K  R  V  E  P  *  V  G  R  S  L  T  V  R  W  L  R  E  L  L  L  G  H  T  A  D  W  Q  A  S  M  *  S  C  I  A  E  G  T  W  F  T  S  S  *  *  C  P  T  D  W  F  H  W  E  A  *  P  T  K  G  C  *  S  D  C  *  G  S  A  L  D  D  G  S  G  C  T  T  G  H  V  G  Y  G  E  A  *  P  *  T  D  A  K  A  I  *  V  S  T  Q   </first_frame>
            <second_frame>  G  G  V  C  Y  G  D  G  N  L  V  F  I  A  N  D  W  H  T  A  L  L  P  V  Y  L  K  A  Y  Y  R  D  N  G  I  M  N  Y  T  R  S  V  L  V  I  H  N  I  A  H  Q  :  G  R  G  P  L  E  D  F  S  Y  V  D  L  P  P  H  Y  M  D  P  F  K  L  Y  D  P  V  G  G  E  H  F  N  I  F  A  A  G  L  K  T  A  D  R  V  V  T  V  S  H  G  Y  S  W  E  L  K  T  S  E  G  G  W  G  L  H  Q  I  I  N  E  N  D  W  K  L  R  G  I  V  N  G  I  D  T  K  E  W  N  P  E  L  D  V  H  L  Q  S  D  G  Y  V  N  Y  S  L  D  T  L  Q  T  G  K  P  Q  C  K  A  A  L  Q  K  E  L  G  L  P  V  R  D  D  V  P  L  I  G  F  I  G  R  L  D  P  Q  K  G  V  D  L  I  A  E  A  V  P  W  M  M  G  Q  D  V  Q  L  V  M  L  G  T  G  R  P  D  L  E  Q  M  L  R  Q  F  E  C  Q  H  N  </second_frame>
            <third_frame>   V  G  S  A  M  E  M  E  T  *  C  S  L  L  M  I  G  I  L  L  Y  C  Q  Y  I  *  K  L  I  I  V  T  M  E  L  *  T  I  Q  D  L  S  W  *  F  I  T  S  L  I  R :   V  V  V  L  W  R  I  F  H  M  *  I  F  H  H  T  I  W  T  L  S  N  C  M  T  Q  *  E  V  S  I  S  T  F  L  R  L  V  *  R  Q  Q  I  V  *  L  Q  L  V  M  D  I  H  G  N  S  R  L  P  K  V  V  G  D  C  I  R  *  L  M  R  T  I  G  N  Y  G  V  L  *  M  G  L  I  Q  K  S  G  T  L  S  W  T  F  T  Y  S  Q  M  V  T  *  T  T  P  W  T  H  C  R  L  A  S  L  N  V  K  L  H  C  R  R  N  L  V  Y  Q  F  V  M  M  S  H  *  L  V  S  L  G  G  L  T  H  K  R  V  L  I  *  L  L  R  Q  C  L  G  *  W  V  R  M  Y  N  W  S  C  W  V  R  G  G  L  T  L  N  R  C  *  G  N  L  S  V  N  T  M </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="C02HBa0054K23.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="19610" stop="19762"/>
                    <exon start="20908" stop="21465"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>711</number_coding_nucleotides>
                  <number_encoded_amino_acids>237</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>GGVCYGDGNLVFIANDWHTALLPVYLKAYYRDNGIMNYTRSVLVIHNIAHQGRGPLEDFSYVDLPPHYMDPFKLYDPVGGEHFNIFAAGLKTADRVVTVSHGYSWELKTSEGGWGLHQIINENDWKLRGIVNGIDTKEWNPELDVHLQSDGYVNYSLDTLQTGKPQCKAALQKELGLPVRDDVPLIGFIGRLDPQKGVDLIAEAVPWMMGQDVQLVMLGTGRPDLEQMLRQFECQHN</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 9 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
$ 9 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 08:47:31
-->
