<?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 07:19:04"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C01HBa0163B20-npMIl/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C01HBa0163B20-npMIl/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-C01HBa0163B20-npMIl/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="T1422" ref_strand="+" ref_description="T1422">
      <seq>atttgcattatttaccatgaataacgatgccccaagcatgattcatgatccattgattgattccacaggagatggaggctatgcattgagtggcaaaattatgctaagtgctattgttatcttattcactgttgttgttttcatggtgggtcttcatctatatgctcgttggtaccttctatctcagcgccgtcgtgaactccttcgccgccgtagggttaaccatagacggactcatattgttttctacgttgataatcctggttccggtttgtctgatgctaaccggggtttggaacaggcggttctcaattccttgccggtttttgtttattccgacaagactcacccggaaccgctggaatgtgctgtttgtttatcggaatttgaggagaatgaaaagggtcgggttttacccaagtgtaatcactcttttcattccgaatgtattgatatgtggtttcattcccattctacttgccctctatgtcgctctccggtagaagcagtacttatc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0163B20-npMIl/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0163B20.1" temp_strand="+" temp_description="C01HBa0163B20.1  AC171727.1 htgs_phase:3 submitted_to_sgn_as:092005.asm.C1 sequenced_by:cornell upload_account_name:us 092005.asm.assem.ace.1 from 335 to 134436">
        <position start="36219" stop="37335"/>
      </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="36519" g_stop="37035" g_length="517"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="517" r_length="517" r_score="0.967"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0163B20.1" gen_strand="+" ref_id="T1422" ref_strand="+">
        <total_alignment_score>0.967</total_alignment_score>
        <cumulative_length_of_scored_exons>517</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0163B20.1" gen_strand="+"/>
        <rDNA rDNA_id="T1422" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="36519" e_stop="37035"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATTGGCAGTATTTACCATGAATAACGATACCCCAAGCATGATTCATGATCCATTGATTGATTCCACAGGAGATGGAGGCTATGCATTGAGTGGAAAAATTATGCTAAGTGCTATTGTTATCTTATTCACTGTTGTTGTTTTCATGGTGGGTCTTCATTTATATGCTCGTTGGTACCTTGTGTCTCAGCGCCGCCGTGAACTCCTTCGCCGCCGTAGGGTCAACCATCGACGGACTCATATTGTTTTCTACGTTGATAATCCTGGTTCCGGTTTGTCTGATGCTAACCGGGGTTTGGAACAGGCGGTTCTCAGTTCCTTGCCGGTTTTTGTTTATTCCGACAAGACTCACCCGGAACCGCTGGAATGTGCTGTTTGTTTATCGGAATTTGAGGAGAATGAAAAGGGTCGGGTTTTACCCAAGTGTAATCACTCTTTTCATTCGGAATGTATTGATATGTGGTTTCATTCTCATTCTACGTGCCCTCTTTGTCGCTCTCCGGTGGAGGCAGTACTTATC</genome_strand>
        <mrna_strand>ATTTGCATTATTTACCATGAATAACGATGCCCCAAGCATGATTCATGATCCATTGATTGATTCCACAGGAGATGGAGGCTATGCATTGAGTGGCAAAATTATGCTAAGTGCTATTGTTATCTTATTCACTGTTGTTGTTTTCATGGTGGGTCTTCATCTATATGCTCGTTGGTACCTTCTATCTCAGCGCCGTCGTGAACTCCTTCGCCGCCGTAGGGTTAACCATAGACGGACTCATATTGTTTTCTACGTTGATAATCCTGGTTCCGGTTTGTCTGATGCTAACCGGGGTTTGGAACAGGCGGTTCTCAATTCCTTGCCGGTTTTTGTTTATTCCGACAAGACTCACCCGGAACCGCTGGAATGTGCTGTTTGTTTATCGGAATTTGAGGAGAATGAAAAGGGTCGGGTTTTACCCAAGTGTAATCACTCTTTTCATTCCGAATGTATTGATATGTGGTTTCATTCCCATTCTACTTGCCCTCTATGTCGCTCTCCGGTAGAAGCAGTACTTATC</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="36519" PGL_stop="37035"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="36519" e_stop="37035"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.967"/>
        </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="0.967">
            <gDNA_exon_boundary e_start="36519" e_stop="37035" e_length="517"/>
          </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="36519" stop="37035"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="T1422" 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>ATTGGCAGTATTTACCATGAATAACGATACCCCAAGCATGATTCATGATCCATTGATTGATTCCACAGGAGATGGAGGCTATGCATTGAGTGGAAAAATTATGCTAAGTGCTATTGTTATCTTATTCACTGTTGTTGTTTTCATGGTGGGTCTTCATTTATATGCTCGTTGGTACCTTGTGTCTCAGCGCCGCCGTGAACTCCTTCGCCGCCGTAGGGTCAACCATCGACGGACTCATATTGTTTTCTACGTTGATAATCCTGGTTCCGGTTTGTCTGATGCTAACCGGGGTTTGGAACAGGCGGTTCTCAGTTCCTTGCCGGTTTTTGTTTATTCCGACAAGACTCACCCGGAACCGCTGGAATGTGCTGTTTGTTTATCGGAATTTGAGGAGAATGAAAAGGGTCGGGTTTTACCCAAGTGTAATCACTCTTTTCATTCGGAATGTATTGATATGTGGTTTCATTCTCATTCTACGTGCCCTCTTTGTCGCTCTCCGGTGGAGGCAGTACTTATC</gDNA_template>
            <first_frame> I  G  S  I  Y  H  E  *  R  Y  P  K  H  D  S  *  S  I  D  *  F  H  R  R  W  R  L  C  I  E  W  K  N  Y  A  K  C  Y  C  Y  L  I  H  C  C  C  F  H  G  G  S  S  F  I  C  S  L  V  P  C  V  S  A  P  P  *  T  P  S  P  P  *  G  Q  P  S  T  D  S  Y  C  F  L  R  *  *  S  W  F  R  F  V  *  C  *  P  G  F  G  T  G  G  S  Q  F  L  A  G  F  C  L  F  R  Q  D  S  P  G  T  A  G  M  C  C  L  F  I  G  I  *  G  E  *  K  G  S  G  F  T  Q  V  *  S  L  F  S  F  G  M  Y  *  Y  V  V  S  F  S  F  Y  V  P  S  L  S  L  S  G  G  G  S  T  Y  </first_frame>
            <second_frame>  L  A  V  F  T  M  N  N  D  T  P  S  M  I  H  D  P  L  I  D  S  T  G  D  G  G  Y  A  L  S  G  K  I  M  L  S  A  I  V  I  L  F  T  V  V  V  F  M  V  G  L  H  L  Y  A  R  W  Y  L  V  S  Q  R  R  R  E  L  L  R  R  R  R  V  N  H  R  R  T  H  I  V  F  Y  V  D  N  P  G  S  G  L  S  D  A  N  R  G  L  E  Q  A  V  L  S  S  L  P  V  F  V  Y  S  D  K  T  H  P  E  P  L  E  C  A  V  C  L  S  E  F  E  E  N  E  K  G  R  V  L  P  K  C  N  H  S  F  H  S  E  C  I  D  M  W  F  H  S  H  S  T  C  P  L  C  R  S  P  V  E  A  V  L  I </second_frame>
            <third_frame>   W  Q  Y  L  P  *  I  T  I  P  Q  A  *  F  M  I  H  *  L  I  P  Q  E  M  E  A  M  H  *  V  E  K  L  C  *  V  L  L  L  S  Y  S  L  L  L  F  S  W  W  V  F  I  Y  M  L  V  G  T  L  C  L  S  A  A  V  N  S  F  A  A  V  G  S  T  I  D  G  L  I  L  F  S  T  L  I  I  L  V  P  V  C  L  M  L  T  G  V  W  N  R  R  F  S  V  P  C  R  F  L  F  I  P  T  R  L  T  R  N  R  W  N  V  L  F  V  Y  R  N  L  R  R  M  K  R  V  G  F  Y  P  S  V  I  T  L  F  I  R  N  V  L  I  C  G  F  I  L  I  L  R  A  L  F  V  A  L  R  W  R  Q  Y  L   </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="C01HBa0163B20.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="36520" stop="37035"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>516</number_coding_nucleotides>
                  <number_encoded_amino_acids>172</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LAVFTMNNDTPSMIHDPLIDSTGDGGYALSGKIMLSAIVILFTVVVFMVGLHLYARWYLVSQRRRELLRRRRVNHRRTHIVFYVDNPGSGLSDANRGLEQAVLSSLPVFVYSDKTHPEPLECAVCLSEFEENEKGRVLPKCNHSFHSECIDMWFHSHSTCPLCRSPVEAVLI</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 165 chains have been computed
$ 
$ memory statistics:
$ 2040 bytes spliced alignments in total
$ 1 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
$ 165 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 07:19:07
-->
