<?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 17:24:09"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0053A08-qpnaw/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0053A08-qpnaw/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-C04HBa0053A08-qpnaw/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M812" ref_strand="+" ref_description="SGN-M812 SSR139 [est_by_read_no_qc_info]">
      <seq>tagagagagaaagtgataatatgggtatgggatttacaccaaaatgtaaagcaaacaacaccaataatagtagtgaaaattggggaatgggttttctcttcatattcttccctgaagaagaagaagaagaagaagagaagaaaaaacccactttctctttcactaattcttcttcttcgtcttcgttgttgccttcgttttcattcaaatcgattaatgcaattcgtaatcgttcaacttcatctcatctcatctcaaaagcacaatccacaatttcaatttgtgtattgttgattttcatcactcttttactcttcactctatcaacttttgaacccaacaattcgttaaatcaaaaacgaaaacccccaattcttaatttccaagagaaattgattttcgcacctgcattgcaaggtatgggttcgttgtatcgaagaggaacaagggctatgaatgacttaatcgtagctcatgtaatcgaatccgtaacggagatcgaactgaaaatgttcctcagattactccatagatccggaatcacttctaaatcagacatattgttcctattttcatcgaaatcaagctcgttggatcacgccattgttgaagagaacaactcctttttgaagctcatcaatggctactacaaatacattaataactcaagttct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0053A08-qpnaw/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0053A08.1" temp_strand="-" temp_description="C04HBa0053A08.1  CU468928.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0053A08 sequenced_by:sanger upload_account_name:uk">
        <position start="17920" stop="16647"/>
      </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="17620" g_stop="16947" g_length="674"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="674" r_length="674" r_score="0.999"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0053A08.1" gen_strand="-" ref_id="SGN-M812" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>674</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0053A08.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M812" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="17620" e_stop="16947"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAGAGAGAGAAAGTGATAATATGGGTATGGGATTTACACCAAAATCTAAAGCAAACAACACCAATAATAGTAGTGAAAATTGGGGAATGGGTTTTCTCTTCATATTCTTCCCTGAAGAAGAAGAAGAAGAAGAAGAGAAGAAAAAACCCACTTTCTCTTTCACTAATTCTTCTTCTTCGTCTTCGTTGTTGCCTTCGTTTTCATTCAAATCGATTAATGCAATTCGTAATCGTTCAACTTCATCTCATCTCATCTCAAAAGCACAATCCACAATTTCAATTTGTGTATTGTTGATTTTCATCACTCTTTTACTCTTCACTCTATCAACTTTTGAACCCAACAATTCGTTAAATCAAAAACGAAAACCCCCAATTCTTAATTTCCAAGAGAAATTGATTTTCGCACCTGCATTGCAAGGTATGGGTTCGTTGTATCGAAGAGGAACAAGGGCTATGAATGACTTAATCGTAGCTCATGTAATCGAATCCGTAACGGAGATCGAACTGAAAATGTTCCTCAGATTACTCCATAGATCCGGAATCACTTCTAAATCAGACATATTGTTCCTATTTTCATCGAAATCAAGCTCGTTGGATCACGCCATTGTTGAAGAGAACAACTCCTTTTTGAAGCTCATCAATGGCTACTACAAATACATTAATAACTCAAGTTCT</genome_strand>
        <mrna_strand>TAGAGAGAGAAAGTGATAATATGGGTATGGGATTTACACCAAAATGTAAAGCAAACAACACCAATAATAGTAGTGAAAATTGGGGAATGGGTTTTCTCTTCATATTCTTCCCTGAAGAAGAAGAAGAAGAAGAAGAGAAGAAAAAACCCACTTTCTCTTTCACTAATTCTTCTTCTTCGTCTTCGTTGTTGCCTTCGTTTTCATTCAAATCGATTAATGCAATTCGTAATCGTTCAACTTCATCTCATCTCATCTCAAAAGCACAATCCACAATTTCAATTTGTGTATTGTTGATTTTCATCACTCTTTTACTCTTCACTCTATCAACTTTTGAACCCAACAATTCGTTAAATCAAAAACGAAAACCCCCAATTCTTAATTTCCAAGAGAAATTGATTTTCGCACCTGCATTGCAAGGTATGGGTTCGTTGTATCGAAGAGGAACAAGGGCTATGAATGACTTAATCGTAGCTCATGTAATCGAATCCGTAACGGAGATCGAACTGAAAATGTTCCTCAGATTACTCCATAGATCCGGAATCACTTCTAAATCAGACATATTGTTCCTATTTTCATCGAAATCAAGCTCGTTGGATCACGCCATTGTTGAAGAGAACAACTCCTTTTTGAAGCTCATCAATGGCTACTACAAATACATTAATAACTCAAGTTCT</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-C04HBa0053A08-qpnaw/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M812-2" ref_strand="+" ref_description="SGN-M812-2 SSR139-2 [est_by_read]">
      <seq>agagagagaaagtgataatatgggtatgggatttacaccaaaatgtaaagcaaacaacaccaataatagtagtgaaaattggggaatgggttttctcttcatattcttccctgaagaagaagaagaagaagaagagaagaaaaaacccactttctctttcactaattcttcttcttcgtcttcgttgttgccttcgttttcattcaaatcgattaatgcaattcgtaatcgttcaacttcatctcatctcatctcaaaagcacaatccacaatttcaatttgtgtattgttgattttcatcactcttttactcttcactctatcaacttttgaacccaacaattcgttaaatcaaaaacgaaaacccccaattcttaatttccaagagaaattgattttcgcacctgcattgcaaggtatgggttcgttgtatcgaagaggaacaagggctatgaatgacttaatcgtagctcatgtaatcgaatccgtaacggagatcgaactgaaaatgttcctcagattactccatagatccggaatcacttctaaatcagacatattgttcctattttcatcgaaatcaagctcgttggatcacgccatt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0053A08-qpnaw/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0053A08.1" temp_strand="-" temp_description="C04HBa0053A08.1  CU468928.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0053A08 sequenced_by:sanger upload_account_name:uk">
        <position start="17919" stop="16716"/>
      </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="17619" g_stop="17016" g_length="604"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="604" r_length="604" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0053A08.1" gen_strand="-" ref_id="SGN-M812-2" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>604</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0053A08.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M812-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="17619" e_stop="17016"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAGAGAGAAAGTGATAATATGGGTATGGGATTTACACCAAAATCTAAAGCAAACAACACCAATAATAGTAGTGAAAATTGGGGAATGGGTTTTCTCTTCATATTCTTCCCTGAAGAAGAAGAAGAAGAAGAAGAGAAGAAAAAACCCACTTTCTCTTTCACTAATTCTTCTTCTTCGTCTTCGTTGTTGCCTTCGTTTTCATTCAAATCGATTAATGCAATTCGTAATCGTTCAACTTCATCTCATCTCATCTCAAAAGCACAATCCACAATTTCAATTTGTGTATTGTTGATTTTCATCACTCTTTTACTCTTCACTCTATCAACTTTTGAACCCAACAATTCGTTAAATCAAAAACGAAAACCCCCAATTCTTAATTTCCAAGAGAAATTGATTTTCGCACCTGCATTGCAAGGTATGGGTTCGTTGTATCGAAGAGGAACAAGGGCTATGAATGACTTAATCGTAGCTCATGTAATCGAATCCGTAACGGAGATCGAACTGAAAATGTTCCTCAGATTACTCCATAGATCCGGAATCACTTCTAAATCAGACATATTGTTCCTATTTTCATCGAAATCAAGCTCGTTGGATCACGCCATT</genome_strand>
        <mrna_strand>AGAGAGAGAAAGTGATAATATGGGTATGGGATTTACACCAAAATGTAAAGCAAACAACACCAATAATAGTAGTGAAAATTGGGGAATGGGTTTTCTCTTCATATTCTTCCCTGAAGAAGAAGAAGAAGAAGAAGAGAAGAAAAAACCCACTTTCTCTTTCACTAATTCTTCTTCTTCGTCTTCGTTGTTGCCTTCGTTTTCATTCAAATCGATTAATGCAATTCGTAATCGTTCAACTTCATCTCATCTCATCTCAAAAGCACAATCCACAATTTCAATTTGTGTATTGTTGATTTTCATCACTCTTTTACTCTTCACTCTATCAACTTTTGAACCCAACAATTCGTTAAATCAAAAACGAAAACCCCCAATTCTTAATTTCCAAGAGAAATTGATTTTCGCACCTGCATTGCAAGGTATGGGTTCGTTGTATCGAAGAGGAACAAGGGCTATGAATGACTTAATCGTAGCTCATGTAATCGAATCCGTAACGGAGATCGAACTGAAAATGTTCCTCAGATTACTCCATAGATCCGGAATCACTTCTAAATCAGACATATTGTTCCTATTTTCATCGAAATCAAGCTCGTTGGATCACGCCATT</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="17620" PGL_stop="16947"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="17620" e_stop="16947"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.999"/>
        </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="0.999">
            <gDNA_exon_boundary e_start="17620" e_stop="16947" e_length="674"/>
          </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="17620" stop="16947"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M812" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="17619" stop="17016"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M812-2" 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>TAGAGAGAGAAAGTGATAATATGGGTATGGGATTTACACCAAAATCTAAAGCAAACAACACCAATAATAGTAGTGAAAATTGGGGAATGGGTTTTCTCTTCATATTCTTCCCTGAAGAAGAAGAAGAAGAAGAAGAGAAGAAAAAACCCACTTTCTCTTTCACTAATTCTTCTTCTTCGTCTTCGTTGTTGCCTTCGTTTTCATTCAAATCGATTAATGCAATTCGTAATCGTTCAACTTCATCTCATCTCATCTCAAAAGCACAATCCACAATTTCAATTTGTGTATTGTTGATTTTCATCACTCTTTTACTCTTCACTCTATCAACTTTTGAACCCAACAATTCGTTAAATCAAAAACGAAAACCCCCAATTCTTAATTTCCAAGAGAAATTGATTTTCGCACCTGCATTGCAAGGTATGGGTTCGTTGTATCGAAGAGGAACAAGGGCTATGAATGACTTAATCGTAGCTCATGTAATCGAATCCGTAACGGAGATCGAACTGAAAATGTTCCTCAGATTACTCCATAGATCCGGAATCACTTCTAAATCAGACATATTGTTCCTATTTTCATCGAAATCAAGCTCGTTGGATCACGCCATTGTTGAAGAGAACAACTCCTTTTTGAAGCTCATCAATGGCTACTACAAATACATTAATAACTCAAGTTCT</gDNA_template>
            <first_frame> *  R  E  K  V  I  I  W  V  W  D  L  H  Q  N  L  K  Q  T  T  P  I  I  V  V  K  I  G  E  W  V  F  S  S  Y  S  S  L  K  K  K  K  K  K  K  R  R  K  N  P  L  S  L  S  L  I  L  L  L  R  L  R  C  C  L  R  F  H  S  N  R  L  M  Q  F  V  I  V  Q  L  H  L  I  S  S  Q  K  H  N  P  Q  F  Q  F  V  Y  C  *  F  S  S  L  F  Y  S  S  L  Y  Q  L  L  N  P  T  I  R  *  I  K  N  E  N  P  Q  F  L  I  S  K  R  N  *  F  S  H  L  H  C  K  V  W  V  R  C  I  E  E  E  Q  G  L  *  M  T  *  S  *  L  M  *  S  N  P  *  R  R  S  N  *  K  C  S  S  D  Y  S  I  D  P  E  S  L  L  N  Q  T  Y  C  S  Y  F  H  R  N  Q  A  R  W  I  T  P  L  L  K  R  T  T  P  F  *  S  S  S  M  A  T  T  N  T  L  I  T  Q  V   </first_frame>
            <second_frame>  R  E  R  K  *  *  Y  G  Y  G  I  Y  T  K  I  *  S  K  Q  H  Q  *  *  *  *  K  L  G  N  G  F  S  L  H  I  L  P  *  R  R  R  R  R  R  R  E  E  K  T  H  F  L  F  H  *  F  F  F  F  V  F  V  V  A  F  V  F  I  Q  I  D  *  C  N  S  *  S  F  N  F  I  S  S  H  L  K  S  T  I  H  N  F  N  L  C  I  V  D  F  H  H  S  F  T  L  H  S  I  N  F  *  T  Q  Q  F  V  K  S  K  T  K  T  P  N  S  *  F  P  R  E  I  D  F  R  T  C  I  A  R  Y  G  F  V  V  S  K  R  N  K  G  Y  E  *  L  N  R  S  S  C  N  R  I  R  N  G  D  R  T  E  N  V  P  Q  I  T  P  *  I  R  N  H  F  *  I  R  H  I  V  P  I  F  I  E  I  K  L  V  G  S  R  H  C  *  R  E  Q  L  L  F  E  A  H  Q  W  L  L  Q  I  H  *  *  L  K  F  </second_frame>
            <third_frame>   E  R  E  S  D  N  M  G  M  G  F  T  P  K  S  K  A  N  N  T  N  N  S  S  E  N  W  G  M  G  F  L  F  I  F  F  P  E  E  E  E  E  E  E  E  K  K  K  P  T  F  S  F  T  N  S  S  S  S  S  S  L  L  P  S  F  S  F  K  S  I  N  A  I  R  N  R  S  T  S  S  H  L  I  S  K  A  Q  S  T  I  S  I  C  V  L  L  I  F  I  T  L  L  L  F  T  L  S  T  F  E  P  N  N  S  L  N  Q  K  R  K  P  P  I  L  N  F  Q  E  K  L  I  F  A  P  A  L  Q  G  M  G  S  L  Y  R  R  G  T  R  A  M  N  D  L  I  V  A  H  V  I  E  S  V  T  E  I  E  L  K  M  F  L  R  L  L  H  R  S  G  I  T  S  K  S  D  I  L  F  L  F  S  S  K  S  S  S  L  D  H  A  I  V  E  E  N  N  S  F  L  K  L  I  N  G  Y  Y  K  Y  I  N  N  S  S  S </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="C04HBa0053A08.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="17618" stop="16947"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>672</number_coding_nucleotides>
                  <number_encoded_amino_acids>224</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>ERESDNMGMGFTPKSKANNTNNSSENWGMGFLFIFFPEEEEEEEEKKKPTFSFTNSSSSSSLLPSFSFKSINAIRNRSTSSHLISKAQSTISICVLLIFITLLLFTLSTFEPNNSLNQKRKPPILNFQEKLIFAPALQGMGSLYRRGTRAMNDLIVAHVIESVTEIELKMFLRLLHRSGITSKSDILFLFSSKSSSLDHAIVEENNSFLKLINGYYKYINNSSS</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:
$ 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
$ 0 megabytes was the average size of the backtrace matrix
$ 6 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 17:24:12
-->
