<?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="2009-01-16 11:42:53"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C06SLm0113N10-0ouk2/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C06SLm0113N10-0ouk2/gth_cdna_fileCXGN::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-C06SLm0113N10-0ouk2/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M7603" ref_strand="+" ref_description="SGN-M7603 C2_At3g03130 [cosii_markers]">
      <seq>ctcccccaagcaatcgtagatcgatttcctgtttcagttcagcagcagagatggatttccacagcctcgctaggagagaattgcaagctctttgcaagaagaacaagatcccagctaacatgaccaatgtcgccatggctgatgctcttcaatctcttgaatttgttgatggtattgaagaggtcttgaaaacatgtgagtctgatggtgccaactcatccatggaatcccctggaaagtcagaagcattagcaagtgtacctcggactggtcgccgaactacacaacgaaagacaatcaaacatgactcagaaactttgcagaccacgacaaggagtcactgcagaacaagaggaacagtggtaagagacgttgatgaagcaaaaaatgatatgctggagactcctgcattgccaactaccagaaggagggctgcaacaacttcagttcgtgctaagctggaatctgcaatgaaggaatgtgaaccaaaagaggaaattgtggatcaggttgaggaagaaaggaaagacgttccaaagacaccagcagctgctctcactagccaaagaaaggaagtgaaggcaaagagttcagttaggcaagtgtacagcactcgtcgatcagtgaggttagctgggaaacctatg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C06SLm0113N10-0ouk2/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C06SLm0113N10.1" temp_strand="+" temp_description="C06SLm0113N10.1  AC219227.1 htgs_phase:3 submitted_to_sgn_as:C06SLm0113N10 sequenced_by:cbsg upload_account_name:netherlands [organism=Solanum lycopersicum]">
        <position start="34621" stop="36659"/>
      </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="34921" g_stop="35084" g_length="164"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="164" r_length="164" r_score="0.957"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="35085" i_stop="35876" i_length="792">
            <donor d_prob="1.000" d_score="0.96"/>
            <acceptor a_prob="0.907" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="35877" g_stop="36359" g_length="483"/>
          <reference_exon_boundary r_type="cDNA" r_start="165" r_stop="647" r_length="483" r_score="0.973"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C06SLm0113N10.1" gen_strand="+" ref_id="SGN-M7603" ref_strand="+">
        <total_alignment_score>0.969</total_alignment_score>
        <cumulative_length_of_scored_exons>647</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C06SLm0113N10.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M7603" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="34921" e_stop="35084"/>
          <exon e_start="35877" e_stop="36359"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCCCCCAAACAATCGTAAATCGATTTCCTGTTTCATTTTAGCAGCTGAGATGGATTTCCACAGCCTCGCTAGGAGAGAATTGCAAGCTCTTTGCAAGAAGAACAAGATCCCAGCTAACATAACCAATGTTGCCATGGCTGATGCTCTTCAATCTCTTGAATTTGTAAGTTTTCTTAAATCTAAATATGATAATTTTGTTCCTGTGTTGTAGAATTGATGAGTTTTATTTGAAATGAAAAATGAAATCTGTAGCATTTCTAATGGTTACAGTAGGAAGATGAGTTACCAGTATCTGCCAATATTTTTGTTGTTGGATCGATTTGGTTTACCTAATTTCACTTGCAGTTACCTCTCTTGAGTTTCTGAAATCAAAATGACTACTGAGTCTGTTTAAAATGGGAATAAACTATGCAGCATTTCAATTGGTTACACTAGGAAGAAGAATATCTGTATTTGATTCGATGTGCGAGTGTTTTGATTATTGGATCGATTTGTGAATCGGTTAAATCTTATTTCATTTGGAGTCAACTCTCTCGGGTTTGTCAGTTTTTTTCATTCAAAGCCATTGCTGAGTTTGCTTAAAATGACAAACAATAAGCAGCATCTCAAATGGTTACATAGAACGATGAATATCAATTACTGCTTCGATCTGCAATTTTAATTTTGGTTGGATCGGTATTTAAATCGTTTATTCATTTCACGTTCAGTCACCTTTATGGTACCAAGTCTTTTCCAGCTTATCAATCATCTTCAGACAATTTGAGAATGTGAGGAAGCTGTGGACTGTAATTTCTATACTAAAAAGTCATTCCTGCTTGTTGGATTGTGTGAACCACCTAATAATTCCCCAGCTGGATTTCTATAGCTGCTAATAACATATTTACTTAATGTTTAACCGATTAATACATTGACATTGCACATCAGAAACGAAATTCAGAAATGTTTCGATATGCAGGTTGACGGTATTGAAGAGGTCTTGAAAACATGTGAATCTGATGTTGCCAACTCATCCATGGAATCCCCTGGAAAGTCAGAAGCATTAGCAAGTGTACCTCGGACTGGTCGCCGAACTACACAACGAAAGACTATCAAACATGACTCAGAAACTATGCAGACCACGACAAGGAGTCACTGCAGAACAAGAGGAACGGTGGTAAGAGACATTGATGAAGCCAAAAAGGATATGCTGGAGACTCCTGCATTGCCAACTACCAGAAGGAGGGCTGCAACAACTTCAGTTCGTGTTAAGCTGGAATCTGCAATGAAGGAATGTGAACCAAAAGAGGAAATTGTGGATCAGGTTGAGGAAGAAAAGAAAGATGTTCCAAAGACACCAGCAGCTGCTCTCACTAGCCAAAGAAAGGAAGTGAAGGCAAAGAGTTCAGTTAGGCAAGTGTACAGCACTCGTCGATCAGTGAGGTTAGCTGGGAAACCTACG</genome_strand>
        <mrna_strand>CTCCCCCAAGCAATCGTAGATCGATTTCCTGTTTCAGTTCAGCAGCAGAGATGGATTTCCACAGCCTCGCTAGGAGAGAATTGCAAGCTCTTTGCAAGAAGAACAAGATCCCAGCTAACATGACCAATGTCGCCATGGCTGATGCTCTTCAATCTCTTGAATTT........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTGATGGTATTGAAGAGGTCTTGAAAACATGTGAGTCTGATGGTGCCAACTCATCCATGGAATCCCCTGGAAAGTCAGAAGCATTAGCAAGTGTACCTCGGACTGGTCGCCGAACTACACAACGAAAGACAATCAAACATGACTCAGAAACTTTGCAGACCACGACAAGGAGTCACTGCAGAACAAGAGGAACAGTGGTAAGAGACGTTGATGAAGCAAAAAATGATATGCTGGAGACTCCTGCATTGCCAACTACCAGAAGGAGGGCTGCAACAACTTCAGTTCGTGCTAAGCTGGAATCTGCAATGAAGGAATGTGAACCAAAAGAGGAAATTGTGGATCAGGTTGAGGAAGAAAGGAAAGACGTTCCAAAGACACCAGCAGCTGCTCTCACTAGCCAAAGAAAGGAAGTGAAGGCAAAGAGTTCAGTTAGGCAAGTGTACAGCACTCGTCGATCAGTGAGGTTAGCTGGGAAACCTATG</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="34921" PGL_stop="36359"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="34921" e_stop="35084"/>
            <exon e_start="35877" e_stop="36359"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.907" e_score="0.957"/>
          <exon-only e_score="0.973"/>
        </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="0.957">
            <gDNA_exon_boundary e_start="34921" e_stop="35084" e_length="164"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.907">
            <gDNA_intron_boundary i_start="35085" i_stop="35876" i_length="792"/>
          </intron>
          <exon e_serial="2" e_score="0.973">
            <gDNA_exon_boundary e_start="35877" e_stop="36359" e_length="483"/>
          </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="34921" stop="35084"/>
              <exon start="35877" stop="36359"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7603" 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>CTCCCCCAAACAATCGTAAATCGATTTCCTGTTTCATTTTAGCAGCTGAGATGGATTTCCACAGCCTCGCTAGGAGAGAATTGCAAGCTCTTTGCAAGAAGAACAAGATCCCAGCTAACATAACCAATGTTGCCATGGCTGATGCTCTTCAATCTCTTGAATTT : GTTGACGGTATTGAAGAGGTCTTGAAAACATGTGAATCTGATGTTGCCAACTCATCCATGGAATCCCCTGGAAAGTCAGAAGCATTAGCAAGTGTACCTCGGACTGGTCGCCGAACTACACAACGAAAGACTATCAAACATGACTCAGAAACTATGCAGACCACGACAAGGAGTCACTGCAGAACAAGAGGAACGGTGGTAAGAGACATTGATGAAGCCAAAAAGGATATGCTGGAGACTCCTGCATTGCCAACTACCAGAAGGAGGGCTGCAACAACTTCAGTTCGTGTTAAGCTGGAATCTGCAATGAAGGAATGTGAACCAAAAGAGGAAATTGTGGATCAGGTTGAGGAAGAAAAGAAAGATGTTCCAAAGACACCAGCAGCTGCTCTCACTAGCCAAAGAAAGGAAGTGAAGGCAAAGAGTTCAGTTAGGCAAGTGTACAGCACTCGTCGATCAGTGAGGTTAGCTGGGAAACCTACG</gDNA_template>
            <first_frame> L  P  Q  T  I  V  N  R  F  P  V  S  F  *  Q  L  R  W  I  S  T  A  S  L  G  E  N  C  K  L  F  A  R  R  T  R  S  Q  L  T  *  P  M  L  P  W  L  M  L  F  N  L  L  N  L :   L  T  V  L  K  R  S  *  K  H  V  N  L  M  L  P  T  H  P  W  N  P  L  E  S  Q  K  H  *  Q  V  Y  L  G  L  V  A  E  L  H  N  E  R  L  S  N  M  T  Q  K  L  C  R  P  R  Q  G  V  T  A  E  Q  E  E  R  W  *  E  T  L  M  K  P  K  R  I  C  W  R  L  L  H  C  Q  L  P  E  G  G  L  Q  Q  L  Q  F  V  L  S  W  N  L  Q  *  R  N  V  N  Q  K  R  K  L  W  I  R  L  R  K  K  R  K  M  F  Q  R  H  Q  Q  L  L  S  L  A  K  E  R  K  *  R  Q  R  V  Q  L  G  K  C  T  A  L  V  D  Q  *  G  *  L  G  N  L   </first_frame>
            <second_frame>  S  P  K  Q  S  *  I  D  F  L  F  H  F  S  S  *  D  G  F  P  Q  P  R  *  E  R  I  A  S  S  L  Q  E  E  Q  D  P  S  *  H  N  Q  C  C  H  G  *  C  S  S  I  S  *  I   : C  *  R  Y  *  R  G  L  E  N  M  *  I  *  C  C  Q  L  I  H  G  I  P  W  K  V  R  S  I  S  K  C  T  S  D  W  S  P  N  Y  T  T  K  D  Y  Q  T  *  L  R  N  Y  A  D  H  D  K  E  S  L  Q  N  K  R  N  G  G  K  R  H  *  *  S  Q  K  G  Y  A  G  D  S  C  I  A  N  Y  Q  K  E  G  C  N  N  F  S  S  C  *  A  G  I  C  N  E  G  M  *  T  K  R  G  N  C  G  S  G  *  G  R  K  E  R  C  S  K  D  T  S  S  C  S  H  *  P  K  K  G  S  E  G  K  E  F  S  *  A  S  V  Q  H  S  S  I  S  E  V  S  W  E  T  Y  </second_frame>
            <third_frame>   P  P  N  N  R  K  S  I  S  C  F  I  L  A  A  E  M  D  F  H  S  L  A  R  R  E  L  Q  A  L  C  K  K  N  K  I  P  A  N  I  T  N  V  A  M  A  D  A  L  Q  S  L  E  F  :  V  D  G  I  E  E  V  L  K  T  C  E  S  D  V  A  N  S  S  M  E  S  P  G  K  S  E  A  L  A  S  V  P  R  T  G  R  R  T  T  Q  R  K  T  I  K  H  D  S  E  T  M  Q  T  T  T  R  S  H  C  R  T  R  G  T  V  V  R  D  I  D  E  A  K  K  D  M  L  E  T  P  A  L  P  T  T  R  R  R  A  A  T  T  S  V  R  V  K  L  E  S  A  M  K  E  C  E  P  K  E  E  I  V  D  Q  V  E  E  E  K  K  D  V  P  K  T  P  A  A  A  L  T  S  Q  R  K  E  V  K  A  K  S  S  V  R  Q  V  Y  S  T  R  R  S  V  R  L  A  G  K  P  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="C06SLm0113N10.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="34923" stop="35084"/>
                    <exon start="35877" stop="36359"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>645</number_coding_nucleotides>
                  <number_encoded_amino_acids>215</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>PPNNRKSISCFILAAEMDFHSLARRELQALCKKNKIPANITNVAMADALQSLEFVDGIEEVLKTCESDVANSSMESPGKSEALASVPRTGRRTTQRKTIKHDSETMQTTTRSHCRTRGTVVRDIDEAKKDMLETPALPTTRRRAATTSVRVKLESAMKECEPKEEIVDQVEEEKKDVPKTPAAALTSQRKEVKAKSSVRQVYSTRRSVRLAGKPT</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 6 chains have been computed
$ 
$ memory statistics:
$ 2536 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2536 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
$ 6 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 11:42:57
-->
