<?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 17:52:50"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0006D20-RuISC/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0006D20-RuISC/gth_cdna_fileCXGN::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-C04HBa0006D20-RuISC/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U329457" ref_strand="+" ref_description="SGN-U329457        Tomato 200607 #1 [3 ESTs aligned]">
      <seq>gataagacgatagattcaagttctatctcaccaaaagggtaagacatcaattagagttttgatacaccgtgattgggttcaagttccatagaattatggcgtaacacgccttacatgggtaagacattgagtttgatccaatgcataaaatgatgactaagaaaaataatatatttttgatgaaatgtctttaaattcatcatattgaatttgctccatttcttgaaaagaatatggtagcaacatgtgataactctgaaatccacctgttgacttgctccattcaatcatatgaatgtggtagcagtgaatgattagtttgaaagatgacaaataattaatgatatagaataagggagtggagggaaagaattataatagtcatcattgtggtaatgataaaaggaagaacactatgagttcttcaaatagtccttcaaaatgtgaagacaacttttattatgaaaatggtatgaaaagtcattagacttgtgaatgttgtcaacccaataacttgacaagtttataaatcctctatcatgatataagaagataaagtgatggtacactttatctttcaaagtgatgttgaggtgtgtcatggaaatatgatgaattttaaagtcatgacaatgtgcttataatgcaaatttataaagtacatatgaataattagtccaatctttgaagagaatgtgacttgtaatgagtatcgtgaatgctcgaccattctataagagaatgggtccagatgtgataaaatcattatgggttggatatatgtcacaactcacctctatagaaggttttgaaaaaaaaaaaaaaaaaactcggactagttctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0006D20-RuISC/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0006D20.1" temp_strand="+" temp_description="C04HBa0006D20.1  CU468294.6 htgs_phase:3 submitted_to_sgn_as:C04HBa0006D20 sequenced_by:sanger upload_account_name:uk">
        <position start="125542" stop="126970"/>
      </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="125842" g_stop="126644" g_length="803"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="805" r_length="805" r_score="0.917"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="812" polyA_stop="830"/>
      <MATCH_line gen_id="C04HBa0006D20.1" gen_strand="+" ref_id="SGN-U329457" ref_strand="+">
        <total_alignment_score>0.917</total_alignment_score>
        <cumulative_length_of_scored_exons>803</cumulative_length_of_scored_exons>
        <coverage percentage="0.951" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0006D20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U329457" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="125842" e_stop="126644"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GATAAGACAATAGATTCAAGTTCTATTGCACCAAAAGGGTAAGACATCAATTTGAGTTTTGATGCACCGTGATTGGGTTCAAGTCCCATAGAATTATGGCGTAAAACGCCTTATATGGATAAGACATTGAGTTTGAGTCAATGCACCATAATGATGA-TATAATGATGACTAAGGCTTTGATGAAAAATCTTGAAATTCGTCCTATTGAATTTGCTTCGTTCCTTGAAAAGAATGTGGTAGCAACATGTAATAACTCTGAAATTCGCCTGTTAACTTGCTCCATTCAATCATATGAATGTGGTAGCAGTGAATG-TTAGACTGAAAGATGACAAATGATTAATGATAT-GAATAAGGGTGTGGAGGGACATAATTATAATAGTCATCATTGTGATAATGATAAAAGGAAGAACACTATGAGTTCTTCAAATAGTCCTTCAAAATGTGAAGGCAATATTTATTATCAAAATGGTATGAAAGGTCATTAGACTTGTGAATGTTGTCAACCCAACAATTTGACAAATTTATAAATCTTCTATCATGATACAAGAAGATAAAGTGACGGTACACTTAATCTTTCAAAGTGATGTTGAGGTGTGTCATGGAAATATGATGAATTTTAAAGCCATGACAATGTGCTTATAATGCAAATTTATAAAGTACATATAAATAATTAGTCCAATCCTTGAAGAGAATGTGACTTGTAATGAGTATCGTGAATGCTCGACCATTCTATAAGAGAATGGGTCCAGATGTGATAAAATCATTATGGGTTTGATATATGTCACAACTCACCTCTATAGAAG</genome_strand>
        <mrna_strand>GATAAGACGATAGATTCAAGTTCTATCTCACCAAAAGGGTAAGACATCAATTAGAGTTTTGATACACCGTGATTGGGTTCAAGTTCCATAGAATTATGGCGTAACACGCCTTACATGGGTAAGACATTGAGTTTGATCCAATGCA-TAAAATGATGACTAAGAAAAATAATATATTTTTGATGAAATGTCTTTAAATTCATCATATTGAATTTGCTCCATTTCTTGAAAAGAATATGGTAGCAACATGTGATAACTCTGAAATCCACCTGTTGACTTGCTCCATTCAATCATATGAATGTGGTAGCAGTGAATGATTAGTTTGAAAGATGACAAATAATTAATGATATAGAATAAGGGAGTGGAGGGAAAGAATTATAATAGTCATCATTGTGGTAATGATAAAAGGAAGAACACTATGAGTTCTTCAAATAGTCCTTCAAAATGTGAAGACAACTTTTATTATGAAAATGGTATGAAAAGTCATTAGACTTGTGAATGTTGTCAACCCAATAACTTGACAAGTTTATAAATCCTCTATCATGATATAAGAAGATAAAGTGATGGTACACTTTATCTTTCAAAGTGATGTTGAGGTGTGTCATGGAAATATGATGAATTTTAAAGTCATGACAATGTGCTTATAATGCAAATTTATAAAGTACATATGAATAATTAGTCCAATCTTTGAAGAGAATGTGACTTGTAATGAGTATCGTGAATGCTCGACCATTCTATAAGAGAATGGGTCCAGATGTGATAAAATCATTATGGGTTGGATATATGTCACAACTCACCTCTATAGAAG</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-C04HBa0006D20-RuISC/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U322792" ref_strand="+" ref_description="SGN-U322792        Tomato 200607 #1 [7 ESTs aligned] genbank/nr: gi|15144516|gb|AAK84483.1| putative copia-like polyprotein [Lycopersicon esculentum](evalue: 2e-16, score=90.1)">
      <seq>cagagtttatgatacgccgaaagcgtaatagaccaattgattccaaatataaaattccttaaagaaggaaggagcaaatgatcaatatggtcatgataatgaggcaagtgctataaaggagcacattgacataacacttcataaaatcttgaaaaaggttcaggtacctgaaataatgaaaaaaattgaagagatctcgataagttatgtcttgttggaatcgatatcaaataaccgtcgacggtatctttgatatgaggtagcgctcaatgatataaattgtgatgaggatcttgaattcaaatctgtcatatagtgtggacagattaatggttgaccaagtaaaatgcacaattcaagtatattttgtttcacttagaaaagtgacattttggactggtagtccataaatcaaggtataatgtcagtggggtacaaataaattattatgcaataatataaccgtaagatatcaaatacggtttgtgtcttggggcataaaggtttatcgcaaaaatcctgacattattggagatgttttctcctttggtggatgcaatgaggtttgttttgatctggcaacatatgaaaagcttgaatgcatgtaatgaataattgtaatgtctagctagacaatgaaggttatatgaaaatccttgaaacaatcgaggtgtctgaagcatacaagagtttgaaagaaactttttcaataaagcttcaagaatccttatatggattgaaatagtcaaggaagaaaagggtacaaaagaatgatcctaattgtccttgtatttttatgaaaaggtcttggtaagacaaaattttgtcttgacctacagattgttaatttgacaaataaaatatttgtctaacagtgcacatacactgaaaaattttgatgcaattttatgtgaataaatcgcattcattgagtaccccaatgattatgagattacttgacataaatgatgattcagtttgatctcaaaagaaggatgatgagtttcttggtgatgaaactctatcttggtgcaatcagggcactagtgcatcttactaacaatattattccagatatttgttttgcagtaaatttact</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0006D20-RuISC/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0006D20.1" temp_strand="+" temp_description="C04HBa0006D20.1  CU468294.6 htgs_phase:3 submitted_to_sgn_as:C04HBa0006D20 sequenced_by:sanger upload_account_name:uk">
        <position start="127784" stop="129478"/>
      </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="128083" g_stop="129178" g_length="1096"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="1099" r_length="1099" r_score="0.957"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0006D20.1" gen_strand="+" ref_id="SGN-U322792" ref_strand="+">
        <total_alignment_score>0.957</total_alignment_score>
        <cumulative_length_of_scored_exons>1096</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0006D20.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U322792" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="128083" e_stop="129178"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAGAGTCTATGGTACGCCGGAAGCGTAATAGACCAATCGATTTCAAATATAAAATTCCTTGTAGAAGGAAGGAGCAAATGATCAATATGGTCATGATAATGAGGCAAGTGCTATAAAAGAGCACATTGACATAACACTTCATAAAATCTTGAAAAAGGTTCAGGTACCTGAAATAATG--AAAAA-TGAAGAGATCTCGATAAGTTATGTCTTGTTGAAATCGATATCAAATAACTGTCGACGGTATCTTTGATATGAGGTAGCGCTCAATGATATAAATTGTGATGAGGATCTTGAATTCAAATCTGTCATATAGTGTGAACAGATAAATGGTTGACCAAGTAAAATGCACAATTCAAGTATATTTTGTTTCACTTAGAAAAGTGACATTTTGGACTGGTAGTCCATAAATCAAGATATAGTGTCAGTGGGGTACAAATAAATTATTATGCGATAGTATAACCGTAAGTTATCAAATACGATTTGTGCCTTGGGGCATAAAGGTTTATCGCAAAACTCCTGACATTAGTGGAGATGTTTTCTCCTTTGGTGGATGAAATGAGGTTTGTTTTGATCTGGCAACATATGAAAA-CTTGAATGCATGTAAACGAATAATTGTAATGTCTAGCTAGACAATGAAGGTTATATGAAAATCCTTGAAACAATCGAGGTGTCTGAAGCATATAAGAGTTTGAAAGAAACTTATCCAGTAAAGCTTCAAGAATTCTTATATGGATTGAAATAGTCAAGGAAGAAAAAGGGTACAAAAGAATGACCCTAATTGTCCTTGTATTTTTATGAAAAGGTCTTGGTAAGACAAAATTTTGTCTTGACCTACAGATTGTTAATTTGACAAATAAAATATTTGTCTAACGGTGCACATACACTGAAAAATTTTGATGCAATTTTATGTGGATATATCGCATTCATTGAGTACCCCAATGATTATGAGATCACTTGACATAAATGATGATTCAGTTTGATCTCAAAAGAAGGATGA-GAGTTTCTTGGTGATGAAACTCTATCTTGGTGTAATCAGGGCACTAGTGCATCTTACTAACAATATTATTCCAGATATTTGTTTTGCAGTAAATTTACT</genome_strand>
        <mrna_strand>CAGAGTTTATGATACGCCGAAAGCGTAATAGACCAATTGATTCCAAATATAAAATTCCTTAAAGAAGGAAGGAGCAAATGATCAATATGGTCATGATAATGAGGCAAGTGCTATAAAGGAGCACATTGACATAACACTTCATAAAATCTTGAAAAAGGTTCAGGTACCTGAAATAATGAAAAAAATTGAAGAGATCTCGATAAGTTATGTCTTGTTGGAATCGATATCAAATAACCGTCGACGGTATCTTTGATATGAGGTAGCGCTCAATGATATAAATTGTGATGAGGATCTTGAATTCAAATCTGTCATATAGTGTGGACAGATTAATGGTTGACCAAGTAAAATGCACAATTCAAGTATATTTTGTTTCACTTAGAAAAGTGACATTTTGGACTGGTAGTCCATAAATCAAGGTATAATGTCAGTGGGGTACAAATAAATTATTATGCAATAATATAACCGTAAGATATCAAATACGGTTTGTGTCTTGGGGCATAAAGGTTTATCGCAAAAATCCTGACATTATTGGAGATGTTTTCTCCTTTGGTGGATGCAATGAGGTTTGTTTTGATCTGGCAACATATGAAAAGCTTGAATGCATGT-AATGAATAATTGTAATGTCTAGCTAGACAATGAAGGTTATATGAAAATCCTTGAAACAATCGAGGTGTCTGAAGCATACAAGAGTTTGAAAGAAACTTTTTCAATAAAGCTTCAAGAATCCTTATATGGATTGAAATAGTCAAGGAAG-AAAAGGGTACAAAAGAATGATCCTAATTGTCCTTGTATTTTTATGAAAAGGTCTTGGTAAGACAAAATTTTGTCTTGACCTACAGATTGTTAATTTGACAAATAAAATATTTGTCTAACAGTGCACATACACTGAAAAATTTTGATGCAATTTTATGTGAATAAATCGCATTCATTGAGTACCCCAATGATTATGAGATTACTTGACATAAATGATGATTCAGTTTGATCTCAAAAGAAGGATGATGAGTTTCTTGGTGATGAAACTCTATCTTGGTGCAATCAGGGCACTAGTGCATCTTACTAACAATATTATTCCAGATATTTGTTTTGCAGTAAATTTACT</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="125842" PGL_stop="126644"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="125842" e_stop="126644"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.917"/>
        </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="0.917">
            <gDNA_exon_boundary e_start="125842" e_stop="126644" e_length="803"/>
          </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="125842" stop="126644"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U329457" 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>GATAAGACAATAGATTCAAGTTCTATTGCACCAAAAGGGTAAGACATCAATTTGAGTTTTGATGCACCGTGATTGGGTTCAAGTCCCATAGAATTATGGCGTAAAACGCCTTATATGGATAAGACATTGAGTTTGAGTCAATGCACCATAATGATGATATAATGATGACTAAGGCTTTGATGAAAAATCTTGAAATTCGTCCTATTGAATTTGCTTCGTTCCTTGAAAAGAATGTGGTAGCAACATGTAATAACTCTGAAATTCGCCTGTTAACTTGCTCCATTCAATCATATGAATGTGGTAGCAGTGAATGTTAGACTGAAAGATGACAAATGATTAATGATATGAATAAGGGTGTGGAGGGACATAATTATAATAGTCATCATTGTGATAATGATAAAAGGAAGAACACTATGAGTTCTTCAAATAGTCCTTCAAAATGTGAAGGCAATATTTATTATCAAAATGGTATGAAAGGTCATTAGACTTGTGAATGTTGTCAACCCAACAATTTGACAAATTTATAAATCTTCTATCATGATACAAGAAGATAAAGTGACGGTACACTTAATCTTTCAAAGTGATGTTGAGGTGTGTCATGGAAATATGATGAATTTTAAAGCCATGACAATGTGCTTATAATGCAAATTTATAAAGTACATATAAATAATTAGTCCAATCCTTGAAGAGAATGTGACTTGTAATGAGTATCGTGAATGCTCGACCATTCTATAAGAGAATGGGTCCAGATGTGATAAAATCATTATGGGTTTGATATATGTCACAACTCACCTCTATAGAAG</gDNA_template>
            <first_frame> D  K  T  I  D  S  S  S  I  A  P  K  G  *  D  I  N  L  S  F  D  A  P  *  L  G  S  S  P  I  E  L  W  R  K  T  P  Y  M  D  K  T  L  S  L  S  Q  C  T  I  M  M  I  *  *  *  L  R  L  *  *  K  I  L  K  F  V  L  L  N  L  L  R  S  L  K  R  M  W  *  Q  H  V  I  T  L  K  F  A  C  *  L  A  P  F  N  H  M  N  V  V  A  V  N  V  R  L  K  D  D  K  *  L  M  I  *  I  R  V  W  R  D  I  I  I  I  V  I  I  V  I  M  I  K  G  R  T  L  *  V  L  Q  I  V  L  Q  N  V  K  A  I  F  I  I  K  M  V  *  K  V  I  R  L  V  N  V  V  N  P  T  I  *  Q  I  Y  K  S  S  I  M  I  Q  E  D  K  V  T  V  H  L  I  F  Q  S  D  V  E  V  C  H  G  N  M  M  N  F  K  A  M  T  M  C  L  *  C  K  F  I  K  Y  I  *  I  I  S  P  I  L  E  E  N  V  T  C  N  E  Y  R  E  C  S  T  I  L  *  E  N  G  S  R  C  D  K  I  I  M  G  L  I  Y  V  T  T  H  L  Y  R   </first_frame>
            <second_frame>  I  R  Q  *  I  Q  V  L  L  H  Q  K  G  K  T  S  I  *  V  L  M  H  R  D  W  V  Q  V  P  *  N  Y  G  V  K  R  L  I  W  I  R  H  *  V  *  V  N  A  P  *  *  *  Y  N  D  D  *  G  F  D  E  K  S  *  N  S  S  Y  *  I  C  F  V  P  *  K  E  C  G  S  N  M  *  *  L  *  N  S  P  V  N  L  L  H  S  I  I  *  M  W  *  Q  *  M  L  D  *  K  M  T  N  D  *  *  Y  E  *  G  C  G  G  T  *  L  *  *  S  S  L  *  *  *  *  K  E  E  H  Y  E  F  F  K  *  S  F  K  M  *  R  Q  Y  L  L  S  K  W  Y  E  R  S  L  D  L  *  M  L  S  T  Q  Q  F  D  K  F  I  N  L  L  S  *  Y  K  K  I  K  *  R  Y  T  *  S  F  K  V  M  L  R  C  V  M  E  I  *  *  I  L  K  P  *  Q  C  A  Y  N  A  N  L  *  S  T  Y  K  *  L  V  Q  S  L  K  R  M  *  L  V  M  S  I  V  N  A  R  P  F  Y  K  R  M  G  P  D  V  I  K  S  L  W  V  *  Y  M  S  Q  L  T  S  I  E  </second_frame>
            <third_frame>   *  D  N  R  F  K  F  Y  C  T  K  R  V  R  H  Q  F  E  F  *  C  T  V  I  G  F  K  S  H  R  I  M  A  *  N  A  L  Y  G  *  D  I  E  F  E  S  M  H  H  N  D  D  I  M  M  T  K  A  L  M  K  N  L  E  I  R  P  I  E  F  A  S  F  L  E  K  N  V  V  A  T  C  N  N  S  E  I  R  L  L  T  C  S  I  Q  S  Y  E  C  G  S  S  E  C  *  T  E  R  *  Q  M  I  N  D  M  N  K  G  V  E  G  H  N  Y  N  S  H  H  C  D  N  D  K  R  K  N  T  M  S  S  S  N  S  P  S  K  C  E  G  N  I  Y  Y  Q  N  G  M  K  G  H  *  T  C  E  C  C  Q  P  N  N  L  T  N  L  *  I  F  Y  H  D  T  R  R  *  S  D  G  T  L  N  L  S  K  *  C  *  G  V  S  W  K  Y  D  E  F  *  S  H  D  N  V  L  I  M  Q  I  Y  K  V  H  I  N  N  *  S  N  P  *  R  E  C  D  L  *  *  V  S  *  M  L  D  H  S  I  R  E  W  V  Q  M  *  *  N  H  Y  G  F  D  I  C  H  N  S  P  L  *  K </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="C04HBa0006D20.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="125964" stop="126158"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>192</number_coding_nucleotides>
                  <number_encoded_amino_acids>64</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>DIEFESMHHNDDIMMTKALMKNLEIRPIEFASFLEKNVVATCNNSEIRLLTCSIQSYECGSSEC*</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="128083" PGL_stop="129178"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="128083" e_stop="129178"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.957"/>
        </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="128083" e_stop="129178" e_length="1096"/>
          </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="128083" stop="129178"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U322792" 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>TAGAGTCTATGGTACGCCGGAAGCGTAATAGACCAATCGATTTCAAATATAAAATTCCTTGTAGAAGGAAGGAGCAAATGATCAATATGGTCATGATAATGAGGCAAGTGCTATAAAAGAGCACATTGACATAACACTTCATAAAATCTTGAAAAAGGTTCAGGTACCTGAAATAATGAAAAATGAAGAGATCTCGATAAGTTATGTCTTGTTGAAATCGATATCAAATAACTGTCGACGGTATCTTTGATATGAGGTAGCGCTCAATGATATAAATTGTGATGAGGATCTTGAATTCAAATCTGTCATATAGTGTGAACAGATAAATGGTTGACCAAGTAAAATGCACAATTCAAGTATATTTTGTTTCACTTAGAAAAGTGACATTTTGGACTGGTAGTCCATAAATCAAGATATAGTGTCAGTGGGGTACAAATAAATTATTATGCGATAGTATAACCGTAAGTTATCAAATACGATTTGTGCCTTGGGGCATAAAGGTTTATCGCAAAACTCCTGACATTAGTGGAGATGTTTTCTCCTTTGGTGGATGAAATGAGGTTTGTTTTGATCTGGCAACATATGAAAACTTGAATGCATGTAAACGAATAATTGTAATGTCTAGCTAGACAATGAAGGTTATATGAAAATCCTTGAAACAATCGAGGTGTCTGAAGCATATAAGAGTTTGAAAGAAACTTATCCAGTAAAGCTTCAAGAATTCTTATATGGATTGAAATAGTCAAGGAAGAAAAAGGGTACAAAAGAATGACCCTAATTGTCCTTGTATTTTTATGAAAAGGTCTTGGTAAGACAAAATTTTGTCTTGACCTACAGATTGTTAATTTGACAAATAAAATATTTGTCTAACGGTGCACATACACTGAAAAATTTTGATGCAATTTTATGTGGATATATCGCATTCATTGAGTACCCCAATGATTATGAGATCACTTGACATAAATGATGATTCAGTTTGATCTCAAAAGAAGGATGAGAGTTTCTTGGTGATGAAACTCTATCTTGGTGTAATCAGGGCACTAGTGCATCTTACTAACAATATTATTCCAGATATTTGTTTTGCAGTAAATTTACT</gDNA_template>
            <first_frame> *  S  L  W  Y  A  G  S  V  I  D  Q  S  I  S  N  I  K  F  L  V  E  G  R  S  K  *  S  I  W  S  *  *  *  G  K  C  Y  K  R  A  H  *  H  N  T  S  *  N  L  E  K  G  S  G  T  *  N  N  E  K  *  R  D  L  D  K  L  C  L  V  E  I  D  I  K  *  L  S  T  V  S  L  I  *  G  S  A  Q  *  Y  K  L  *  *  G  S  *  I  Q  I  C  H  I  V  *  T  D  K  W  L  T  K  *  N  A  Q  F  K  Y  I  L  F  H  L  E  K  *  H  F  G  L  V  V  H  K  S  R  Y  S  V  S  G  V  Q  I  N  Y  Y  A  I  V  *  P  *  V  I  K  Y  D  L  C  L  G  A  *  R  F  I  A  K  L  L  T  L  V  E  M  F  S  P  L  V  D  E  M  R  F  V  L  I  W  Q  H  M  K  T  *  M  H  V  N  E  *  L  *  C  L  A  R  Q  *  R  L  Y  E  N  P  *  N  N  R  G  V  *  S  I  *  E  F  E  R  N  L  S  S  K  A  S  R  I  L  I  W  I  E  I  V  K  E  E  K  G  Y  K  R  M  T  L  I  V  L  V  F  L  *  K  G  L  G  K  T  K  F  C  L  D  L  Q  I  V  N  L  T  N  K  I  F  V  *  R  C  T  Y  T  E  K  F  *  C  N  F  M  W  I  Y  R  I  H  *  V  P  Q  *  L  *  D  H  L  T  *  M  M  I  Q  F  D  L  K  R  R  M  R  V  S  W  *  *  N  S  I  L  V  *  S  G  H  *  C  I  L  L  T  I  L  F  Q  I  F  V  L  Q  *  I  Y  </first_frame>
            <second_frame>  R  V  Y  G  T  P  E  A  *  *  T  N  R  F  Q  I  *  N  S  L  *  K  E  G  A  N  D  Q  Y  G  H  D  N  E  A  S  A  I  K  E  H  I  D  I  T  L  H  K  I  L  K  K  V  Q  V  P  E  I  M  K  N  E  E  I  S  I  S  Y  V  L  L  K  S  I  S  N  N  C  R  R  Y  L  *  Y  E  V  A  L  N  D  I  N  C  D  E  D  L  E  F  K  S  V  I  *  C  E  Q  I  N  G  *  P  S  K  M  H  N  S  S  I  F  C  F  T  *  K  S  D  I  L  D  W  *  S  I  N  Q  D  I  V  S  V  G  Y  K  *  I  I  M  R  *  Y  N  R  K  L  S  N  T  I  C  A  L  G  H  K  G  L  S  Q  N  S  *  H  *  W  R  C  F  L  L  W  W  M  K  *  G  L  F  *  S  G  N  I  *  K  L  E  C  M  *  T  N  N  C  N  V  *  L  D  N  E  G  Y  M  K  I  L  E  T  I  E  V  S  E  A  Y  K  S  L  K  E  T  Y  P  V  K  L  Q  E  F  L  Y  G  L  K  *  S  R  K  K  K  G  T  K  E  *  P  *  L  S  L  Y  F  Y  E  K  V  L  V  R  Q  N  F  V  L  T  Y  R  L  L  I  *  Q  I  K  Y  L  S  N  G  A  H  T  L  K  N  F  D  A  I  L  C  G  Y  I  A  F  I  E  Y  P  N  D  Y  E  I  T  *  H  K  *  *  F  S  L  I  S  K  E  G  *  E  F  L  G  D  E  T  L  S  W  C  N  Q  G  T  S  A  S  Y  *  Q  Y  Y  S  R  Y  L  F  C  S  K  F  T </second_frame>
            <third_frame>   E  S  M  V  R  R  K  R  N  R  P  I  D  F  K  Y  K  I  P  C  R  R  K  E  Q  M  I  N  M  V  M  I  M  R  Q  V  L  *  K  S  T  L  T  *  H  F  I  K  S  *  K  R  F  R  Y  L  K  *  *  K  M  K  R  S  R  *  V  M  S  C  *  N  R  Y  Q  I  T  V  D  G  I  F  D  M  R  *  R  S  M  I  *  I  V  M  R  I  L  N  S  N  L  S  Y  S  V  N  R  *  M  V  D  Q  V  K  C  T  I  Q  V  Y  F  V  S  L  R  K  V  T  F  W  T  G  S  P  *  I  K  I  *  C  Q  W  G  T  N  K  L  L  C  D  S  I  T  V  S  Y  Q  I  R  F  V  P  W  G  I  K  V  Y  R  K  T  P  D  I  S  G  D  V  F  S  F  G  G  *  N  E  V  C  F  D  L  A  T  Y  E  N  L  N  A  C  K  R  I  I  V  M  S  S  *  T  M  K  V  I  *  K  S  L  K  Q  S  R  C  L  K  H  I  R  V  *  K  K  L  I  Q  *  S  F  K  N  S  Y  M  D  *  N  S  Q  G  R  K  R  V  Q  K  N  D  P  N  C  P  C  I  F  M  K  R  S  W  *  D  K  I  L  S  *  P  T  D  C  *  F  D  K  *  N  I  C  L  T  V  H  I  H  *  K  I  L  M  Q  F  Y  V  D  I  S  H  S  L  S  T  P  M  I  M  R  S  L  D  I  N  D  D  S  V  *  S  Q  K  K  D  E  S  F  L  V  M  K  L  Y  L  G  V  I  R  A  L  V  H  L  T  N  N  I  I  P  D  I  C  F  A  V  N  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/">
            <none gDNA_id="C04HBa0006D20.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 33 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
$ 6704 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3352 bytes was the average size of a predicted gene location
$ 3 megabytes was the average size of the backtrace matrix
$ 45 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 17:53:56
-->
