<?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="2009-07-24 21:32:40"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C07SLe0088K03-UeAvk/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C07SLe0088K03-UeAvk/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-C07SLe0088K03-UeAvk/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M2243" ref_strand="+" ref_description="SGN-M2243 T1750 [cos_markers]">
      <seq>ttttctccagtactaaatcaacctaattaagttgatatggcaataatatctattcctagtagcaccacaatgtttccaatgcctcaacaagtattgagacgaaataaagaggttgttatggctgaggaaatgggttgcgctagaatgctcaccttgaatcggcctgataatttaaattatatatcagccaaagtggcattagcactcgggcagaactttgagaaatatgagaatgatgataatgctgattttgtaatcatcaagggggctggtcgtactttttctgctggtggagacttacatatgttctatgatggacgaaacacaagggattctggcattgaatgtatttatagaatgtattggctttgctaccacattcatacttacaagaaaccgcatattgctcttgttcatggaatgtcagtgggtgggggtgcatccttgatgactccaatgaaattctctgtcgtcactgagaaagcgttt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07SLe0088K03-UeAvk/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07SLe0088K03.2" temp_strand="-" temp_description="C07SLe0088K03.2  AC234407.2 htgs_phase:2 submitted_to_sgn_as:gi|238909038|gb|AC234407.2| upload_account_name:france Solanum lycopersicum chromosome 7 clone C07SLe0088K03, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces">
        <position start="74653" stop="72934"/>
      </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="74353" g_stop="74243" g_length="111"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="111" r_length="111" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="74242" i_stop="74136" i_length="107">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="74135" g_stop="74052" g_length="84"/>
          <reference_exon_boundary r_type="cDNA" r_start="112" r_stop="195" r_length="84" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="74051" i_stop="73952" i_length="100">
            <donor d_prob="0.891" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="73951" g_stop="73883" g_length="69"/>
          <reference_exon_boundary r_type="cDNA" r_start="196" r_stop="264" r_length="69" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="73882" i_stop="73581" i_length="302">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.982" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="73580" g_stop="73517" g_length="64"/>
          <reference_exon_boundary r_type="cDNA" r_start="265" r_stop="328" r_length="64" r_score="1.000"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="73516" i_stop="73394" i_length="123">
            <donor d_prob="0.981" d_score="1.00"/>
            <acceptor a_prob="0.889" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="73393" g_stop="73236" g_length="158"/>
          <reference_exon_boundary r_type="cDNA" r_start="329" r_stop="486" r_length="158" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07SLe0088K03.2" gen_strand="-" ref_id="SGN-M2243" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>486</cumulative_length_of_scored_exons>
        <coverage percentage="0.994" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07SLe0088K03.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M2243" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="74353" e_stop="74243"/>
          <exon e_start="74135" e_stop="74052"/>
          <exon e_start="73951" e_stop="73883"/>
          <exon e_start="73580" e_stop="73517"/>
          <exon e_start="73393" e_stop="73236"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTTTCTCCAGTACTAAATCAACCTAATTAAGTTGATATGGCAATAATATCTATTCCTAGTAGCACCACAATGTTTCCAATGCCTCAACAAGTATTGAGACGAAATAAAGAGGTAATTACAACGTTACTAAAACAACTTATTAATGTCAAAAATATTATTCGATATTATCGATCTTCGGTCCGATATATGTAGCTTAATATATCTTTGGTTGTCATTAGGTTGTTATGGCTGAGGAAATGGGTTGCGCTAGAATGCTCACCTTGAATCGGCCTGATAATTTAAATTATATATCAGCCAAAGTGGTATATATTTAATAATTTATACTATATACTATATATGTATGGTTATAAAATGGCTATTGCAATGTTCACCTTAATTATAAAATTTCTTTTAAATAATTAGGCATTAGCACTCGGGCAGAACTTTGAGAAATATGAGAATGATGATAATGCTGATTTTGTAATCATCAAGGTAAGGACTTATTTAAGAAGTATCTATTTTGCTTTTTTTTTCTTTTTCTTTTATAACGCATAAACGTGTCCTTTTTACTTGGTATTGGCTGACATCTATACCTTGGAATGTGCACAAACAGACACACATACGACGTCATGTAATATGCAAATTATCATGTAGGATCGACGTGCATGGGTGTCTATTTGTTTAATTGTTGGAAGGCAATAACTGTCTGTTATAAGAACAAGTTAAAAGACATTTATATGTATTATATCTTTTGATTTTGCCAATTTAATTCTCATTAATTTGCACATATATAGGGGGCTGGTCGTACTTTTTCTGCTGGTGGAGACTTACATATGTTCTATGATGGACGAAACACAAGTAACTATTTTTTTTCATTTGTTACTATATATATGTCAGAACTATACTATTATTGAAATTATTAATTAATTACTACATGTTCAATTCATTTAAACTAATGAGTATATTAATTGTTTGAATTAGGGGATTCTGGCATTGAATGTATTTATAGAATGTATTGGCTTTGCTACCACATTCATACTTACAAGAAACCGCATATTGCTCTTGTTCATGGAATGTCAGTGGGTGGGGGTGCATCCTTGATGACTCCAATGAAATTCTCTGTCGTCACTGAGAAAGCG</genome_strand>
        <mrna_strand>TTTTCTCCAGTACTAAATCAACCTAATTAAGTTGATATGGCAATAATATCTATTCCTAGTAGCACCACAATGTTTCCAATGCCTCAACAAGTATTGAGACGAAATAAAGAG...........................................................................................................GTTGTTATGGCTGAGGAAATGGGTTGCGCTAGAATGCTCACCTTGAATCGGCCTGATAATTTAAATTATATATCAGCCAAAGTG....................................................................................................GCATTAGCACTCGGGCAGAACTTTGAGAAATATGAGAATGATGATAATGCTGATTTTGTAATCATCAAG..............................................................................................................................................................................................................................................................................................................GGGGCTGGTCGTACTTTTTCTGCTGGTGGAGACTTACATATGTTCTATGATGGACGAAACACAA...........................................................................................................................GGGATTCTGGCATTGAATGTATTTATAGAATGTATTGGCTTTGCTACCACATTCATACTTACAAGAAACCGCATATTGCTCTTGTTCATGGAATGTCAGTGGGTGGGGGTGCATCCTTGATGACTCCAATGAAATTCTCTGTCGTCACTGAGAAAGCG</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="74353" PGL_stop="73236"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="74353" e_stop="74243"/>
            <exon e_start="74135" e_stop="74052"/>
            <exon e_start="73951" e_stop="73883"/>
            <exon e_start="73580" e_stop="73517"/>
            <exon e_start="73393" e_stop="73236"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.891" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="1.000" acc_prob="0.982" e_score="1.000"/>
          <exon-intron don_prob="0.981" acc_prob="0.889" e_score="1.000"/>
          <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="74353" e_stop="74243" e_length="111"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.995">
            <gDNA_intron_boundary i_start="74242" i_stop="74136" i_length="107"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="74135" e_stop="74052" e_length="84"/>
          </exon>
          <intron i_serial="2" don_prob="0.891" acc_prob="0.999">
            <gDNA_intron_boundary i_start="74051" i_stop="73952" i_length="100"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="73951" e_stop="73883" e_length="69"/>
          </exon>
          <intron i_serial="3" don_prob="1.000" acc_prob="0.982">
            <gDNA_intron_boundary i_start="73882" i_stop="73581" i_length="302"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="73580" e_stop="73517" e_length="64"/>
          </exon>
          <intron i_serial="4" don_prob="0.981" acc_prob="0.889">
            <gDNA_intron_boundary i_start="73516" i_stop="73394" i_length="123"/>
          </intron>
          <exon e_serial="5" e_score="1.000">
            <gDNA_exon_boundary e_start="73393" e_stop="73236" e_length="158"/>
          </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="74353" stop="74243"/>
              <exon start="74135" stop="74052"/>
              <exon start="73951" stop="73883"/>
              <exon start="73580" stop="73517"/>
              <exon start="73393" stop="73236"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M2243" 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>TTTTCTCCAGTACTAAATCAACCTAATTAAGTTGATATGGCAATAATATCTATTCCTAGTAGCACCACAATGTTTCCAATGCCTCAACAAGTATTGAGACGAAATAAAGAG : GTTGTTATGGCTGAGGAAATGGGTTGCGCTAGAATGCTCACCTTGAATCGGCCTGATAATTTAAATTATATATCAGCCAAAGTG : GCATTAGCACTCGGGCAGAACTTTGAGAAATATGAGAATGATGATAATGCTGATTTTGTAATCATCAAG : GGGGCTGGTCGTACTTTTTCTGCTGGTGGAGACTTACATATGTTCTATGATGGACGAAACACAA : GGGATTCTGGCATTGAATGTATTTATAGAATGTATTGGCTTTGCTACCACATTCATACTTACAAGAAACCGCATATTGCTCTTGTTCATGGAATGTCAGTGGGTGGGGGTGCATCCTTGATGACTCCAATGAAATTCTCTGTCGTCACTGAGAAAGCG</gDNA_template>
            <first_frame> F  S  P  V  L  N  Q  P  N  *  V  D  M  A  I  I  S  I  P  S  S  T  T  M  F  P  M  P  Q  Q  V  L  R  R  N  K  E  :  V  V  M  A  E  E  M  G  C  A  R  M  L  T  L  N  R  P  D  N  L  N  Y  I  S  A  K  V  :  A  L  A  L  G  Q  N  F  E  K  Y  E  N  D  D  N  A  D  F  V  I  I  K  :  G  A  G  R  T  F  S  A  G  G  D  L  H  M  F  Y  D  G  R  N  T   : R  D  S  G  I  E  C  I  Y  R  M  Y  W  L  C  Y  H  I  H  T  Y  K  K  P  H  I  A  L  V  H  G  M  S  V  G  G  G  A  S  L  M  T  P  M  K  F  S  V  V  T  E  K  A </first_frame>
            <second_frame>  F  L  Q  Y  *  I  N  L  I  K  L  I  W  Q  *  Y  L  F  L  V  A  P  Q  C  F  Q  C  L  N  K  Y  *  D  E  I  K  R :   L  L  W  L  R  K  W  V  A  L  E  C  S  P  *  I  G  L  I  I  *  I  I  Y  Q  P  K  W :   H  *  H  S  G  R  T  L  R  N  M  R  M  M  I  M  L  I  L  *  S  S  R :   G  L  V  V  L  F  L  L  V  E  T  Y  I  C  S  M  M  D  E  T  Q  :  G  I  L  A  L  N  V  F  I  E  C  I  G  F  A  T  T  F  I  L  T  R  N  R  I  L  L  L  F  M  E  C  Q  W  V  G  V  H  P  *  *  L  Q  *  N  S  L  S  S  L  R  K   </second_frame>
            <third_frame>   F  S  S  T  K  S  T  *  L  S  *  Y  G  N  N  I  Y  S  *  *  H  H  N  V  S  N  A  S  T  S  I  E  T  K  *  R   : G  C  Y  G  *  G  N  G  L  R  *  N  A  H  L  E  S  A  *  *  F  K  L  Y  I  S  Q  S   : G  I  S  T  R  A  E  L  *  E  I  *  E  *  *  *  C  *  F  C  N  H  Q   : G  G  W  S  Y  F  F  C  W  W  R  L  T  Y  V  L  *  W  T  K  H  K :   G  F  W  H  *  M  Y  L  *  N  V  L  A  L  L  P  H  S  Y  L  Q  E  T  A  Y  C  S  C  S  W  N  V  S  G  W  G  C  I  L  D  D  S  N  E  I  L  C  R  H  *  E  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="C07SLe0088K03.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="74323" stop="74243"/>
                    <exon start="74135" stop="74052"/>
                    <exon start="73951" stop="73883"/>
                    <exon start="73580" stop="73517"/>
                    <exon start="73393" stop="73236"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>456</number_coding_nucleotides>
                  <number_encoded_amino_acids>152</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VDMAIISIPSSTTMFPMPQQVLRRNKEVVMAEEMGCARMLTLNRPDNLNYISAKVALALGQNFEKYENDDNADFVIIKGAGRTFSAGGDLHMFYDGRNTRDSGIECIYRMYWLCYHIHTYKKPHIALVHGMSVGGGASLMTPMKFSVVTEKA</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 1 chain has been computed
$ 
$ memory statistics:
$ 2024 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2024 bytes was the average size of a spliced alignment
$ 5656 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5656 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 1 backtrace matrix has been allocated
$ 
$ date finished: 2009-07-24 21:32:44
-->
