<?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 05:56:20"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0206I01-niivK/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0206I01-niivK/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" 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-C00HBa0206I01-niivK/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U579150" ref_strand="+" ref_description="SGN-U579150 Tomato 200607#2 [5 ESTs aligned] (*GB) gi|113205316|gb|ABI34339.1| (e_value=9e-121) Polyprotein,; (*ATH) ATMG00860.1 (e_value=3e-15) | Symbol: ORF158 | hypothetical protein | chrM:235916-236392 FORWARD | Aliases: ORF158; (*SWP) sp|Q99315|YG31B_YEAST (e_value=3e-49) Transposon Ty3-G Gag-Pol polyprotein OS=Saccharomyces cerevisiae GN=TY3B-G; ">
      <seq>gcggccgctctatattagntggacccgcgggctgcaggaattcggcacgaggagaatcccttgacaaatcggcggtagtagctagctaacccaacaaagctccttatttctgacacattagtaggtcttacccaattcttcactgtctcaatcttagaaggatccaccatcactccatccttagaaaccacgttccccaagaaggacactacatctagccaaaactcacacttagagaacttggcataaaactttttctccctcaacatttccaataccattctcaaatgctcttcatgttcctccttacttttagagtatatcagtatatcatcaataaatacgatcacaaagagatccaaatatggcttaaaaatcccttttattaaactcataaacgcagcaggggcattcataagaccaaaagacatcactacaaatttgtaatgcccatacctggttctaaaagcagtctttggcacatccgttgcccgtattttcaattgatgataaccggatctcaagtcaatcttagaaaagacacaagcaccttgtaactgatcgaacaagtcattaatgcgaggaagaggatacttgttctttatggttaccttgttcaactgccggtagcctatgcacatccgaaaactccaatccttcttctttacaaacaaaaccggagcaccccaaggagatgcagttggtctaatgaagactttgctcaaaaactcttgaaagtgggcctttaactctcttaactccgcgggagccattctataagggggtatagaaatggggcgagtgcccgtttcaagatcgaagcagaagtcaatatccctttctggtggcataccggggagatctg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0206I01-niivK/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0206I01.1" temp_strand="+" temp_description="C00HBa0206I01.1  CU927987.6 htgs_phase:3 submitted_to_sgn_as:C00HBa0206I01 sequenced_by:sanger upload_account_name:uk">
        <position start="1770" stop="3187"/>
      </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="2074" g_stop="2887" g_length="814"/>
          <reference_exon_boundary r_type="cDNA" r_start="53" r_stop="865" r_length="813" r_score="0.903"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0206I01.1" gen_strand="+" ref_id="SGN-U579150" ref_strand="+">
        <total_alignment_score>0.903</total_alignment_score>
        <cumulative_length_of_scored_exons>814</cumulative_length_of_scored_exons>
        <coverage percentage="0.941" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0206I01.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U579150" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="2074" e_stop="2887"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAATCCCTTGACAAATCGACGGTAGTAGCTGGCTAAACTAACAAAGCTCCTTATTTCTGACACATTAGTAGGTCTTACCCAATTTCTCACTGTTTCAATCTTAGAAGGATCCACCATCACTCCATCCTTAGAAACCACGTGCCCCAAAAAGGACACTGAATCTAGCCAAAACTCACACTTGGAGAATTTGGCATAAAGCCTTTTCTCCCTTAACACTTCCAACACAATTCTCAAATGCTCCTCATGTTCCTTCTTACTCTTGGAGTATATCAGTATATCATCAATAAATACGATCACAAAGAGATCCAGATATGGCTTAAAAATCCCGTTCATCAAGCCCATGAAAGCAGCAGGGGCATTCGTAAGACCAAAAGATATTACTACAAATTCGTAATGCCCATACCAGGTTCGAAAAGCAGTCTTTGGCACATCCGTTGCCCGTATTTTCAATTGATGATAACCGGATCTCAAGTCAATCTTAGAGAAGACACAATCACCTTGTAACTGATCGAACAAGTCATCAATGCGAGGAATGGGATAATTGTTCTTAATAGTTACCTTGTTCAACTGCCAGTAGTCTATGCACATCTGAAAACTCCCATCCTTCTTCTTTACAAATAACACCGGAGCACCCCAAGGGGGATGCACTTGGTCTAATGAAACCTTTACTTAACAACTCTTGAAGTTGGGCCTTCAACTCCCTTAACTCCGCTGGAGCCATCCTATAATGGGGTATGGAAATGGGGCGAGTGCCCGGCTCCAGATCTATACAGAAATCAATATCCCTATCCGGTGGCATACCAGGAAGGTCTG</genome_strand>
        <mrna_strand>AGAATCCCTTGACAAATCGGCGGTAGTAGCTAGCTAACCCAACAAAGCTCCTTATTTCTGACACATTAGTAGGTCTTACCCAATTCTTCACTGTCTCAATCTTAGAAGGATCCACCATCACTCCATCCTTAGAAACCACGTTCCCCAAGAAGGACACTACATCTAGCCAAAACTCACACTTAGAGAACTTGGCATAAAACTTTTTCTCCCTCAACATTTCCAATACCATTCTCAAATGCTCTTCATGTTCCTCCTTACTTTTAGAGTATATCAGTATATCATCAATAAATACGATCACAAAGAGATCCAAATATGGCTTAAAAATCCCTTTTATTAAACTCATAAACGCAGCAGGGGCATTCATAAGACCAAAAGACATCACTACAAATTTGTAATGCCCATACCTGGTTCTAAAAGCAGTCTTTGGCACATCCGTTGCCCGTATTTTCAATTGATGATAACCGGATCTCAAGTCAATCTTAGAAAAGACACAAGCACCTTGTAACTGATCGAACAAGTCATTAATGCGAGGAAGAGGATACTTGTTCTTTATGGTTACCTTGTTCAACTGCCGGTAGCCTATGCACATCCGAAAACTCCAATCCTTCTTCTTTACAAACAAAACCGGAGCACCCCAA-GGAGATGCAGTTGGTCTAATGAAGACTTTGCTCAAAAACTCTTGAAAGTGGGCCTTTAACTCTCTTAACTCCGCGGGAGCCATTCTATAAGGGGGTATAGAAATGGGGCGAGTGCCCGTTTCAAGATCGAAGCAGAAGTCAATATCCCTTTCTGGTGGCATACCGGGGAGATCTG</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-C00HBa0206I01-niivK/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U592023" ref_strand="+" ref_description="SGN-U592023 Tomato 200607#2 [1 ESTs aligned] (*GB) gi|113205363|gb|AAT66771.2| (e_value=2e-56) Putative; ">
      <seq>ttacttcggcacgaggatttgatcctgcctccacattttcatatgtatcttcctcatttgctactgttcttaatttacatagtgaatcgcttgacatacctattcgtgttctactccggtgggtgagtctgtgattgttgaaaaggtgtataggtcttgtcttgtgacatttgtgggagcaatactcatgtagacttggttatcctataaatggttgacttcgatgtaattctgggtatgacttggctgtctccaaattttgcaatcttggattgtaatgctaaaactgtaacgttggccaagcctgagatagatgcgttagtgtgggagggtgactacacttccactccagttcgtatcatctcctttctttgtgctaagagaatggttagtaaagggtgtttagctttcttggcacacctcagggatgatactacccaagtaccttcaattgagtcagtttcgatagtccgtgagtttctggatgtgtttcctgcagaccttcctggtatgccaccggatagggatattgacttttgcattgatctggagccgggtgatcaccccatttccatacccccttatagaatggctcccgctgagttgggggagttaaaggcccaacttcaagagttgttangtaagggcttcatt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0206I01-niivK/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0206I01.1" temp_strand="-" temp_description="C00HBa0206I01.1  CU927987.6 htgs_phase:3 submitted_to_sgn_as:C00HBa0206I01 sequenced_by:sanger upload_account_name:uk">
        <position start="3669" stop="2430"/>
      </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="3369" g_stop="2730" g_length="640"/>
          <reference_exon_boundary r_type="cDNA" r_start="17" r_stop="654" r_length="638" r_score="0.911"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0206I01.1" gen_strand="-" ref_id="SGN-U592023" ref_strand="+">
        <total_alignment_score>0.911</total_alignment_score>
        <cumulative_length_of_scored_exons>640</cumulative_length_of_scored_exons>
        <coverage percentage="0.979" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0206I01.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U592023" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="3369" e_stop="2730"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATTTGACCCTGGCTCCACATTTTCATATGTATCTTTCGCATTTGCTACTGGCCTTAATTTAAATTGTGAATTGCTTGACATGCCTATTCGTGTTTCTTCTCCGGTGGGTGAGTCTGTGATAGTGGAAAAGGTATATAGGTCTTGTCTGGTGACTTTTGTGGGAAGCAATACTCATGTAGACTTGGTTATCTTAGAAATGGTTGACTTCGATGTAATTCTGGGTATGACTTGGCTTTCTCCAAACTTTGCAATCTTAGATTGTAATGCTAAAACTGTAACATTGGCCAAGCCTGGGACAGAGCCGTTAGTGTGGGAGGGTGACTACACTTCCACTCTAGTTCGTATCATCTCCTTCCTTCGTGCTAAGAGAATGGTTAGAAAAGGGTTGTTTAGCTTTCTTGGCACACC-CAGGGATGATACTACCCAAGTACCTTCAATTGAGTCGGTTCCGGTAGTCTGTGAGTTTCTGGATGTGTTTCCTGCAGACCTTCCTGGTATGCCACCGGATAGGGATATTGATTTCTGTATAGATCTGGAGCCGGGCACTCGCCCCATTTCCATACCCCATTATAGGATGGCTCCAGCGGAGTTAAGGGAGTTGAAGGCCCAACTTCAAGAGTTGTTAAGTAAAGGTTTCATT</genome_strand>
        <mrna_strand>ATTTGATCCTGCCTCCACATTTTCATATGTATCTTCCTCATTTGCTACTGTTCTTAATTTACATAGTGAATCGCTTGACATACCTATTCGTG-TTCTACTCCGGTGGGTGAGTCTGTGATTGTTGAAAAGGTGTATAGGTCTTGTCTTGTGACATTTGTGGG-AGCAATACTCATGTAGACTTGGTTATCCTATAAATGGTTGACTTCGATGTAATTCTGGGTATGACTTGGCTGTCTCCAAATTTTGCAATCTTGGATTGTAATGCTAAAACTGTAACGTTGGCCAAGCCTGAGATAGATGCGTTAGTGTGGGAGGGTGACTACACTTCCACTCCAGTTCGTATCATCTCCTTTCTTTGTGCTAAGAGAATGGTTAGTAAAGGG-TGTTTAGCTTTCTTGGCACACCTCAGGGATGATACTACCCAAGTACCTTCAATTGAGTCAGTTTCGATAGTCCGTGAGTTTCTGGATGTGTTTCCTGCAGACCTTCCTGGTATGCCACCGGATAGGGATATTGACTTTTGCATTGATCTGGAGCCGGGTGATCACCCCATTTCCATACCCCCTTATAGAATGGCTCCCGCTGAGTTGGGGGAGTTAAAGGCCCAACTTCAAGAGTTGTTANGTAAGGGCTTCATT</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-C00HBa0206I01-niivK/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U591718" ref_strand="+" ref_description="SGN-U591718 Tomato 200607#2 [1 ESTs aligned] (*GB) gi|48057631|gb|AAT39954.1| (e_value=1e-28) putative integrase [Solanum demissum]; ">
      <seq>gggatctgtcccaggcttggctaacgtcacagttttagcattacaatccaagattgcaaaatttggagaaagccaagtcatacccagaattacatcaaaatcaaccatttctaagataaccaagtctacataagtattgctccccacaaaagtcaccagaccagacctatatactttttcaactatcacagactcacccaccggagtagaaacacgaataggcatgtcaagcaattcataatttaatttaagaccagtagcaaatgaggaagatacatatgaaaatgtggatccagggtcaaataatacaaaagccatgcaatcac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0206I01-niivK/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0206I01.1" temp_strand="+" temp_description="C00HBa0206I01.1  CU927987.6 htgs_phase:3 submitted_to_sgn_as:C00HBa0206I01 sequenced_by:sanger upload_account_name:uk">
        <position start="2767" stop="3691"/>
      </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="3066" g_stop="3391" g_length="326"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="326" r_length="326" r_score="0.929"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0206I01.1" gen_strand="+" ref_id="SGN-U591718" ref_strand="+">
        <total_alignment_score>0.929</total_alignment_score>
        <cumulative_length_of_scored_exons>326</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0206I01.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U591718" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="3066" e_stop="3391"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CGGCTCTGTCCCAGGCTTGGCCAATGTTACAGTTTTAGCATTACAATCTAAGATTGCAAAGTTTGGAGAAAGCCAAGTCATACCCAGAATTACATCGAAGTCAACCATTTCTAAGATAACCAAGTCTACATGAGTATTGCTTCCCACAAAAGTCACCAGACAAGACCTATATACCTTTTCCACTATCACAGACTCACCCACCGGAGAAGAAACACGAATAGGCATGTCAAGCAATTCACAATTTAAATTAAGGCCAGTAGCAAATGCGAAAGATACATATGAAAATGTGGAGCCAGGGTCAAATAATACAGAAGCCATACAATCAC</genome_strand>
        <mrna_strand>GGGATCTGTCCCAGGCTTGGCTAACGTCACAGTTTTAGCATTACAATCCAAGATTGCAAAATTTGGAGAAAGCCAAGTCATACCCAGAATTACATCAAAATCAACCATTTCTAAGATAACCAAGTCTACATAAGTATTGCTCCCCACAAAAGTCACCAGACCAGACCTATATACTTTTTCAACTATCACAGACTCACCCACCGGAGTAGAAACACGAATAGGCATGTCAAGCAATTCATAATTTAATTTAAGACCAGTAGCAAATGAGGAAGATACATATGAAAATGTGGATCCAGGGTCAAATAATACAAAAGCCATGCAATCAC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>3</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="2074" PGL_stop="2887"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="2074" e_stop="2887"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.903"/>
        </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="0.903">
            <gDNA_exon_boundary e_start="2074" e_stop="2887" e_length="814"/>
          </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="2074" stop="2887"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U579150" 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>AGAATCCCTTGACAAATCGACGGTAGTAGCTGGCTAAACTAACAAAGCTCCTTATTTCTGACACATTAGTAGGTCTTACCCAATTTCTCACTGTTTCAATCTTAGAAGGATCCACCATCACTCCATCCTTAGAAACCACGTGCCCCAAAAAGGACACTGAATCTAGCCAAAACTCACACTTGGAGAATTTGGCATAAAGCCTTTTCTCCCTTAACACTTCCAACACAATTCTCAAATGCTCCTCATGTTCCTTCTTACTCTTGGAGTATATCAGTATATCATCAATAAATACGATCACAAAGAGATCCAGATATGGCTTAAAAATCCCGTTCATCAAGCCCATGAAAGCAGCAGGGGCATTCGTAAGACCAAAAGATATTACTACAAATTCGTAATGCCCATACCAGGTTCGAAAAGCAGTCTTTGGCACATCCGTTGCCCGTATTTTCAATTGATGATAACCGGATCTCAAGTCAATCTTAGAGAAGACACAATCACCTTGTAACTGATCGAACAAGTCATCAATGCGAGGAATGGGATAATTGTTCTTAATAGTTACCTTGTTCAACTGCCAGTAGTCTATGCACATCTGAAAACTCCCATCCTTCTTCTTTACAAATAACACCGGAGCACCCCAAGGGGGATGCACTTGGTCTAATGAAACCTTTACTTAACAACTCTTGAAGTTGGGCCTTCAACTCCCTTAACTCCGCTGGAGCCATCCTATAATGGGGTATGGAAATGGGGCGAGTGCCCGGCTCCAGATCTATACAGAAATCAATATCCCTATCCGGTGGCATACCAGGAAGGTCTG</gDNA_template>
            <first_frame> R  I  P  *  Q  I  D  G  S  S  W  L  N  *  Q  S  S  L  F  L  T  H  *  *  V  L  P  N  F  S  L  F  Q  S  *  K  D  P  P  S  L  H  P  *  K  P  R  A  P  K  R  T  L  N  L  A  K  T  H  T  W  R  I  W  H  K  A  F  S  P  L  T  L  P  T  Q  F  S  N  A  P  H  V  P  S  Y  S  W  S  I  S  V  Y  H  Q  *  I  R  S  Q  R  D  P  D  M  A  *  K  S  R  S  S  S  P  *  K  Q  Q  G  H  S  *  D  Q  K  I  L  L  Q  I  R  N  A  H  T  R  F  E  K  Q  S  L  A  H  P  L  P  V  F  S  I  D  D  N  R  I  S  S  Q  S  *  R  R  H  N  H  L  V  T  D  R  T  S  H  Q  C  E  E  W  D  N  C  S  *  *  L  P  C  S  T  A  S  S  L  C  T  S  E  N  S  H  P  S  S  L  Q  I  T  P  E  H  P  K  G  D  A  L  G  L  M  K  P  L  L  N  N  S  *  S  W  A  F  N  S  L  N  S  A  G  A  I  L  *  W  G  M  E  M  G  R  V  P  G  S  R  S  I  Q  K  S  I  S  L  S  G  G  I  P  G  R  S  </first_frame>
            <second_frame>  E  S  L  D  K  S  T  V  V  A  G  *  T  N  K  A  P  Y  F  *  H  I  S  R  S  Y  P  I  S  H  C  F  N  L  R  R  I  H  H  H  S  I  L  R  N  H  V  P  Q  K  G  H  *  I  *  P  K  L  T  L  G  E  F  G  I  K  P  F  L  P  *  H  F  Q  H  N  S  Q  M  L  L  M  F  L  L  T  L  G  V  Y  Q  Y  I  I  N  K  Y  D  H  K  E  I  Q  I  W  L  K  N  P  V  H  Q  A  H  E  S  S  R  G  I  R  K  T  K  R  Y  Y  Y  K  F  V  M  P  I  P  G  S  K  S  S  L  W  H  I  R  C  P  Y  F  Q  L  M  I  T  G  S  Q  V  N  L  R  E  D  T  I  T  L  *  L  I  E  Q  V  I  N  A  R  N  G  I  I  V  L  N  S  Y  L  V  Q  L  P  V  V  Y  A  H  L  K  T  P  I  L  L  L  Y  K  *  H  R  S  T  P  R  G  M  H  L  V  *  *  N  L  Y  L  T  T  L  E  V  G  P  S  T  P  L  T  P  L  E  P  S  Y  N  G  V  W  K  W  G  E  C  P  A  P  D  L  Y  R  N  Q  Y  P  Y  P  V  A  Y  Q  E  G  L </second_frame>
            <third_frame>   N  P  L  T  N  R  R  *  *  L  A  K  L  T  K  L  L  I  S  D  T  L  V  G  L  T  Q  F  L  T  V  S  I  L  E  G  S  T  I  T  P  S  L  E  T  T  C  P  K  K  D  T  E  S  S  Q  N  S  H  L  E  N  L  A  *  S  L  F  S  L  N  T  S  N  T  I  L  K  C  S  S  C  S  F  L  L  L  E  Y  I  S  I  S  S  I  N  T  I  T  K  R  S  R  Y  G  L  K  I  P  F  I  K  P  M  K  A  A  G  A  F  V  R  P  K  D  I  T  T  N  S  *  C  P  Y  Q  V  R  K  A  V  F  G  T  S  V  A  R  I  F  N  *  *  *  P  D  L  K  S  I  L  E  K  T  Q  S  P  C  N  *  S  N  K  S  S  M  R  G  M  G  *  L  F  L  I  V  T  L  F  N  C  Q  *  S  M  H  I  *  K  L  P  S  F  F  F  T  N  N  T  G  A  P  Q  G  G  C  T  W  S  N  E  T  F  T  *  Q  L  L  K  L  G  L  Q  L  P  *  L  R  W  S  H  P  I  M  G  Y  G  N  G  A  S  A  R  L  Q  I  Y  T  E  I  N  I  P  I  R  W  H  T  R  K  V   </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="C00HBa0206I01.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="2288" stop="2578"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>288</number_coding_nucleotides>
                  <number_encoded_amino_acids>96</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>HFQHNSQMLLMFLLTLGVYQYIINKYDHKEIQIWLKNPVHQAHESSRGIRKTKRYYYKFVMPIPGSKSSLWHIRCPYFQLMITGSQVNLREDTITL*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="3369" PGL_stop="2730"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="3369" e_stop="2730"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.911"/>
        </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="0.911">
            <gDNA_exon_boundary e_start="3369" e_stop="2730" e_length="640"/>
          </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="3369" stop="2730"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U592023" 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="2" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>ATTTGACCCTGGCTCCACATTTTCATATGTATCTTTCGCATTTGCTACTGGCCTTAATTTAAATTGTGAATTGCTTGACATGCCTATTCGTGTTTCTTCTCCGGTGGGTGAGTCTGTGATAGTGGAAAAGGTATATAGGTCTTGTCTGGTGACTTTTGTGGGAAGCAATACTCATGTAGACTTGGTTATCTTAGAAATGGTTGACTTCGATGTAATTCTGGGTATGACTTGGCTTTCTCCAAACTTTGCAATCTTAGATTGTAATGCTAAAACTGTAACATTGGCCAAGCCTGGGACAGAGCCGTTAGTGTGGGAGGGTGACTACACTTCCACTCTAGTTCGTATCATCTCCTTCCTTCGTGCTAAGAGAATGGTTAGAAAAGGGTTGTTTAGCTTTCTTGGCACACCCAGGGATGATACTACCCAAGTACCTTCAATTGAGTCGGTTCCGGTAGTCTGTGAGTTTCTGGATGTGTTTCCTGCAGACCTTCCTGGTATGCCACCGGATAGGGATATTGATTTCTGTATAGATCTGGAGCCGGGCACTCGCCCCATTTCCATACCCCATTATAGGATGGCTCCAGCGGAGTTAAGGGAGTTGAAGGCCCAACTTCAAGAGTTGTTAAGTAAAGGTTTCATT</gDNA_template>
            <first_frame> I  *  P  W  L  H  I  F  I  C  I  F  R  I  C  Y  W  P  *  F  K  L  *  I  A  *  H  A  Y  S  C  F  F  S  G  G  *  V  C  D  S  G  K  G  I  *  V  L  S  G  D  F  C  G  K  Q  Y  S  C  R  L  G  Y  L  R  N  G  *  L  R  C  N  S  G  Y  D  L  A  F  S  K  L  C  N  L  R  L  *  C  *  N  C  N  I  G  Q  A  W  D  R  A  V  S  V  G  G  *  L  H  F  H  S  S  S  Y  H  L  L  P  S  C  *  E  N  G  *  K  R  V  V  *  L  S  W  H  T  Q  G  *  Y  Y  P  S  T  F  N  *  V  G  S  G  S  L  *  V  S  G  C  V  S  C  R  P  S  W  Y  A  T  G  *  G  Y  *  F  L  Y  R  S  G  A  G  H  S  P  H  F  H  T  P  L  *  D  G  S  S  G  V  K  G  V  E  G  P  T  S  R  V  V  K  *  R  F  H  </first_frame>
            <second_frame>  F  D  P  G  S  T  F  S  Y  V  S  F  A  F  A  T  G  L  N  L  N  C  E  L  L  D  M  P  I  R  V  S  S  P  V  G  E  S  V  I  V  E  K  V  Y  R  S  C  L  V  T  F  V  G  S  N  T  H  V  D  L  V  I  L  E  M  V  D  F  D  V  I  L  G  M  T  W  L  S  P  N  F  A  I  L  D  C  N  A  K  T  V  T  L  A  K  P  G  T  E  P  L  V  W  E  G  D  Y  T  S  T  L  V  R  I  I  S  F  L  R  A  K  R  M  V  R  K  G  L  F  S  F  L  G  T  P  R  D  D  T  T  Q  V  P  S  I  E  S  V  P  V  V  C  E  F  L  D  V  F  P  A  D  L  P  G  M  P  P  D  R  D  I  D  F  C  I  D  L  E  P  G  T  R  P  I  S  I  P  H  Y  R  M  A  P  A  E  L  R  E  L  K  A  Q  L  Q  E  L  L  S  K  G  F  I </second_frame>
            <third_frame>   L  T  L  A  P  H  F  H  M  Y  L  S  H  L  L  L  A  L  I  *  I  V  N  C  L  T  C  L  F  V  F  L  L  R  W  V  S  L  *  *  W  K  R  Y  I  G  L  V  W  *  L  L  W  E  A  I  L  M  *  T  W  L  S  *  K  W  L  T  S  M  *  F  W  V  *  L  G  F  L  Q  T  L  Q  S  *  I  V  M  L  K  L  *  H  W  P  S  L  G  Q  S  R  *  C  G  R  V  T  T  L  P  L  *  F  V  S  S  P  S  F  V  L  R  E  W  L  E  K  G  C  L  A  F  L  A  H  P  G  M  I  L  P  K  Y  L  Q  L  S  R  F  R  *  S  V  S  F  W  M  C  F  L  Q  T  F  L  V  C  H  R  I  G  I  L  I  S  V  *  I  W  S  R  A  L  A  P  F  P  Y  P  I  I  G  W  L  Q  R  S  *  G  S  *  R  P  N  F  K  S  C  *  V  K  V  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="C00HBa0206I01.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="3368" stop="2730"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>639</number_coding_nucleotides>
                  <number_encoded_amino_acids>213</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FDPGSTFSYVSFAFATGLNLNCELLDMPIRVSSPVGESVIVEKVYRSCLVTFVGSNTHVDLVILEMVDFDVILGMTWLSPNFAILDCNAKTVTLAKPGTEPLVWEGDYTSTLVRIISFLRAKRMVRKGLFSFLGTPRDDTTQVPSIESVPVVCEFLDVFPADLPGMPPDRDIDFCIDLEPGTRPISIPHYRMAPAELRELKAQLQELLSKGFI</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="+" PGL_start="3066" PGL_stop="3391"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="3066" e_stop="3391"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.929"/>
        </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="0.929">
            <gDNA_exon_boundary e_start="3066" e_stop="3391" e_length="326"/>
          </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="3066" stop="3391"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U591718" 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="3" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>CGGCTCTGTCCCAGGCTTGGCCAATGTTACAGTTTTAGCATTACAATCTAAGATTGCAAAGTTTGGAGAAAGCCAAGTCATACCCAGAATTACATCGAAGTCAACCATTTCTAAGATAACCAAGTCTACATGAGTATTGCTTCCCACAAAAGTCACCAGACAAGACCTATATACCTTTTCCACTATCACAGACTCACCCACCGGAGAAGAAACACGAATAGGCATGTCAAGCAATTCACAATTTAAATTAAGGCCAGTAGCAAATGCGAAAGATACATATGAAAATGTGGAGCCAGGGTCAAATAATACAGAAGCCATACAATCAC</gDNA_template>
            <first_frame> R  L  C  P  R  L  G  Q  C  Y  S  F  S  I  T  I  *  D  C  K  V  W  R  K  P  S  H  T  Q  N  Y  I  E  V  N  H  F  *  D  N  Q  V  Y  M  S  I  A  S  H  K  S  H  Q  T  R  P  I  Y  L  F  H  Y  H  R  L  T  H  R  R  R  N  T  N  R  H  V  K  Q  F  T  I  *  I  K  A  S  S  K  C  E  R  Y  I  *  K  C  G  A  R  V  K  *  Y  R  S  H  T  I   </first_frame>
            <second_frame>  G  S  V  P  G  L  A  N  V  T  V  L  A  L  Q  S  K  I  A  K  F  G  E  S  Q  V  I  P  R  I  T  S  K  S  T  I  S  K  I  T  K  S  T  *  V  L  L  P  T  K  V  T  R  Q  D  L  Y  T  F  S  T  I  T  D  S  P  T  G  E  E  T  R  I  G  M  S  S  N  S  Q  F  K  L  R  P  V  A  N  A  K  D  T  Y  E  N  V  E  P  G  S  N  N  T  E  A  I  Q  S  </second_frame>
            <third_frame>   A  L  S  Q  A  W  P  M  L  Q  F  *  H  Y  N  L  R  L  Q  S  L  E  K  A  K  S  Y  P  E  L  H  R  S  Q  P  F  L  R  *  P  S  L  H  E  Y  C  F  P  Q  K  S  P  D  K  T  Y  I  P  F  P  L  S  Q  T  H  P  P  E  K  K  H  E  *  A  C  Q  A  I  H  N  L  N  *  G  Q  *  Q  M  R  K  I  H  M  K  M  W  S  Q  G  Q  I  I  Q  K  P  Y  N  H </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="C00HBa0206I01.1" strand="+"/>
                <serials PGL_serial="3" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="3199" stop="3390"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>192</number_coding_nucleotides>
                  <number_encoded_amino_acids>64</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VLLPTKVTRQDLYTFSTITDSPTGEETRIGMSSNSQFKLRPVANAKDTYENVEPGSNNTEAIQS</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 40 chains have been computed
$ 
$ memory statistics:
$ 5864 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 1954 bytes was the average size of a spliced alignment
$ 7880 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2626 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 48 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 05:56:41
-->
