<?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="2009-02-20 08:31:20"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0203K06-jCCww/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0203K06-jCCww/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-C04HBa0203K06-jCCww/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U330305" ref_strand="+" ref_description="SGN-U330305        Tomato 200607 #1 [2 ESTs aligned] arabidopsis/peptide: | Symbol: None | GRAM domain-containing protein / ABA-responsive protein-related, contains similarity to ABA-responsive protein in barley (GI:4103635) (Hordeum vulgare) (J. Exp. Bot. 50, 727-728 (1999); contains Pfam PF02893: GRAM domain | chr5:7863334-7864274 REVERSE | Aliases: MKD15.23, MKD15_23(evalue: 9e-08, score=52) genbank/nr: gi|56542469|gb|AAV92899.1| Avr9/Cf-9 rapidly elicited protein 140 [Nicotiana tabacum] (evalue: 6e-07, score=55.8)">
      <seq>tatggaaaagccatcacaaaagtatatacagttagttacagaggacgattacgagttctggtttatggggttctttaataatcaaaaaactctaagatatctgcagcaggcaatttcaactttcacaaacttcaatcagctaagacgatagttttttaattttattttgtttcctaatacacccattcatcaatgtaaaatgttgatgcaagatgcagatatgttcaaacttgtaactagctccattgctcaaaggaggttttagattttttaggctttaagcctaagttgttaatacgaatgtatagacttattgtaaaactaatcaaacaggaggctaattcatcttaaaaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0203K06-jCCww/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0203K06.1" temp_strand="+" temp_description="C04HBa0203K06.1  CU929467.5 htgs_phase:3 submitted_to_sgn_as:C04HBa0203K06 sequenced_by:sanger upload_account_name:uk">
        <position start="32833" stop="33781"/>
      </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="33133" g_stop="33481" g_length="349"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="349" r_length="349" r_score="0.997"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="350" polyA_stop="370"/>
      <MATCH_line gen_id="C04HBa0203K06.1" gen_strand="+" ref_id="SGN-U330305" ref_strand="+">
        <total_alignment_score>0.997</total_alignment_score>
        <cumulative_length_of_scored_exons>349</cumulative_length_of_scored_exons>
        <coverage percentage="0.943" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0203K06.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U330305" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="33133" e_stop="33481"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TATGGAAAAGCCATCACAGAAGTATATACAGTTAGTTACAGAGGACGATTACGAGTTCTGGTTTATGGGGTTCTTTAATAATCAAAAAACTCTAAGATATCTGCAGCAGGCAATTTCAACTTTCACAAACTTCAATCAGCTAAGACGATAGTTTTTTAATTTTATTTTGTTTCCTAATACACCCATTCATCAATGTAAAATGTTGATGCAAGATGCAGATATGTTCAAACTTGTAACTAGCTCCATTGCTCAAAGGAGGTTTTAGATTTTTTAGGCTTTAAGCCTAAGTTGTTAATACGAATGTATAGACTTATTGTAAAACTAATCAAACAGGAGGCTAATTCATCTT</genome_strand>
        <mrna_strand>TATGGAAAAGCCATCACAAAAGTATATACAGTTAGTTACAGAGGACGATTACGAGTTCTGGTTTATGGGGTTCTTTAATAATCAAAAAACTCTAAGATATCTGCAGCAGGCAATTTCAACTTTCACAAACTTCAATCAGCTAAGACGATAGTTTTTTAATTTTATTTTGTTTCCTAATACACCCATTCATCAATGTAAAATGTTGATGCAAGATGCAGATATGTTCAAACTTGTAACTAGCTCCATTGCTCAAAGGAGGTTTTAGATTTTTTAGGCTTTAAGCCTAAGTTGTTAATACGAATGTATAGACTTATTGTAAAACTAATCAAACAGGAGGCTAATTCATCTT</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-C04HBa0203K06-jCCww/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U325813" ref_strand="-" ref_description="SGN-U325813        Tomato 200607 #1 [4 ESTs aligned] arabidopsis/peptide: | Symbol: None | GRAM domain-containing protein / ABA-responsive protein-related, contains similarity to ABA-responsive protein in barley (GI:4103635) (Hordeum vulgare) (J. Exp. Bot. 50, 727-728 (1999); contains Pfam PF02893: GRAM domain | chr5:7863334-7864274 REVERSE | Aliases: MKD15.23, MKD15_23(evalue: 5e-53, score=204) genbank/nr: gi|50911012|ref|XP_466939.1| ABA-responsive protein-like [Oryza sativa (japonica cultivar-group)] >gi|49388696|dbj|BAD25877.1| ABA-responsive protein-like [Oryza sativa (japonica cultivar-group)] >gi|49387971|dbj|BAD25079.1| ABA-responsive protein-like [Oryza sativa (japonica cultivar-group)] (evalue: 6e-52, score=207)">
      <seq>tcccacataccttcaaaatacagtaatactccacctcaaaccagaatcacaatggacttactccgtggaaattcggtgggtattcccatgagttcatcagtaggttcacttgaaagccagccgaaaagactacttgccttacctgcttgcgaagaccatatcgttccatatgcaacttcaaagaacttgtctcaaattaagcagagaagatatgtcattggtaagatgaacaaattgggagaaagggtggattgtctagtaaaaagcatccgcgagcatgtgagcctaagcccgaaactaacagaaactttaaagggaaaattgagccttggagcaaaaatccttcaagtaggagggttggagaaaatattcaggcagaagttcagtgttagagatgatgaaaagctattgaatgtttctcaatgctatttatcaacgacagctggtccaatagcaggccttctcttcatctctaccgataagattgctttctgcagcgagagatcaataaagctcttatctccaactggaaagttgcttagaatctactataaggtaaccatcccaataagtaagataatgaaagcaaaagagagcaaaaatatgcaaaagccatcacagaagtatatacaagtaattacagaggatgattttgagttctggtttatgggattcctcaatcatcaaaagacactgagatatctgcagcaggcaatctccagctcaagcaagttatgaagacacatttttttttctaatgagctcgttcttcaatgtaaaacgttcatgcaaaaacgaattcagggatctgttaaaactttgtaactagatccattgctcaaaggaggcttaaggtttaacctttgtgcccttaagagttaatgggaatgtatagacttttttttctctaaaactggtagcttttgtatagacttattttgttttttgagatagcaagagatacgaatgtacaaatttattataaaacttgtggagatagat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0203K06-jCCww/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0203K06.1" temp_strand="+" temp_description="C04HBa0203K06.1  CU929467.5 htgs_phase:3 submitted_to_sgn_as:C04HBa0203K06 sequenced_by:sanger upload_account_name:uk">
        <position start="37643" stop="39818"/>
      </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="37943" g_stop="38147" g_length="205"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="205" r_length="205" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="38148" i_stop="38240" i_length="93">
            <donor d_prob="0.000" d_score="1.00"/>
            <acceptor a_prob="0.991" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="38241" g_stop="38315" g_length="75"/>
          <reference_exon_boundary r_type="cDNA" r_start="206" r_stop="280" r_length="75" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="38316" i_stop="38716" i_length="401">
            <donor d_prob="0.997" 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="38717" g_stop="38991" g_length="275"/>
          <reference_exon_boundary r_type="cDNA" r_start="281" r_stop="555" r_length="275" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="38992" i_stop="39071" i_length="80">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.981" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="39072" g_stop="39518" g_length="447"/>
          <reference_exon_boundary r_type="cDNA" r_start="556" r_stop="1002" r_length="447" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0203K06.1" gen_strand="+" ref_id="SGN-U325813" ref_strand="-">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>1002</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0203K06.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U325813" rDNA_strand="-"/>
        <gDNA_exon_coordinates>
          <exon e_start="37943" e_stop="38147"/>
          <exon e_start="38241" e_stop="38315"/>
          <exon e_start="38717" e_stop="38991"/>
          <exon e_start="39072" e_stop="39518"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCCCACATACCTTCAAAATACAGTAATACTCCACCTCAAACCAGAATCACAATGGACTTACTCCGTGGAAATTCGGTGGGTATTCCCATGAGTTCATCAGTAGGTTCACTTGAAAGCCAGCCGAAAAGACTACTTGCCTTACCTGCTTGCGAAGACCATATCGTTCCATATGCAACTTCAAAGAACTTGTCTCAAATTAAGCAGAGTGAGTATTTCCCTGGTCCCTTGATGAAGAATCAACTTGATCTAAACCTTGAATGAAGAGATCATAAAAATAACAATATTCTTGAATATGCAGGAAGATATGTCATTGGTAAGATGAACAAATTGGGAGAAAGGGTGGATTGTCTAGTAAAAAGCATCCGCGAGCATGGTAAGCGCTTAAAATTCTCTATAAAAGACTTAAATATATCTATTGAAAATATTACTGAGATAATAGTTTGTTTTAAGTCGAAAAATAAGTATTTGAACTTAAAGTTTGTGTCTGGACATGAACTCCATTTGAAAAAAAAAAGAAGGTTAAAGCGAAAACAATTATCTCACTCAAAAATGCTACTCAGACAAGTTAATTCCATACTATACCAGCCTTTCAAATGCTAAAATGTTCACCAATTGCGAATACTGATGGACAAACTTCACCTTTAAGTATTTGCAAGTGAAGTCATGACCAAACACTAGTGTAAATCTAAAGAACTCAGAGAAGTGAGTAATAAGTACAAAATTCATGTAAACATGACAGAAAATATTGATTCTAAATGTACTCTGATTGTGCAGTGAGCCTAAGCCCGAAACTAACAGAAACTTTAAAGGGAAAATTGAGCCTTGGAGCAAAAATCCTTCAAGTAGGAGGGTTGGAGAAAATATTCAGGCAGAAGTTCAGTGTTAGAGATGATGAAAAGCTATTGAATGTTTCTCAATGCTATTTATCAACGACAGCTGGTCCAATAGCAGGCCTTCTCTTCATCTCTACCGATAAGATTGCTTTCTGCAGCGAGAGATCAATAAAGCTCTTATCTCCAACTGGAAAGTTGCTTAGAATCTACTATAAGGTATAACTCTGCTCCATTTTTCTTCCAACTTTTCATTTTCTAACCACGTAAAGCATAATCTAACTGGTTCACAATGGCAGGTAACCATCCCAATAAGTAAGATAATGAAAGCAAAAGAGAGCAAAAATATGCAAAAGCCATCACAGAAGTATATACAAGTAATTACAGAGGATGATTTTGAGTTCTGGTTTATGGGATTCCTCAATCATCAAAAGACACTGAGATATCTGCAGCAGGCAATCTCCAGCTCAAGCAAGTTATGAAGACACATTTTTTTTTCTAATGAGCTCGTTCTTCAATGTAAAACGTTCATGCAAAAACGAATTCAGGGATCTGTTAAAACTTTGTAACTAGATCCATTGCTCAAAGGAGGCTTAAGGTTTAACCTTTGTGCCCTTAAGAGTTAATGGGAATGTATAGACTTTTTTTTCTCTAAAACTGGTAGCTTTTGTATAGACTTATTTTGTTTTTTGAGATAGCAAGAGATACGAATGTACAAATTTATTATAAAACTTGTGGAGATAGAT</genome_strand>
        <mrna_strand>TCCCACATACCTTCAAAATACAGTAATACTCCACCTCAAACCAGAATCACAATGGACTTACTCCGTGGAAATTCGGTGGGTATTCCCATGAGTTCATCAGTAGGTTCACTTGAAAGCCAGCCGAAAAGACTACTTGCCTTACCTGCTTGCGAAGACCATATCGTTCCATATGCAACTTCAAAGAACTTGTCTCAAATTAAGCAGA.............................................................................................GAAGATATGTCATTGGTAAGATGAACAAATTGGGAGAAAGGGTGGATTGTCTAGTAAAAAGCATCCGCGAGCATG.................................................................................................................................................................................................................................................................................................................................................................................................................TGAGCCTAAGCCCGAAACTAACAGAAACTTTAAAGGGAAAATTGAGCCTTGGAGCAAAAATCCTTCAAGTAGGAGGGTTGGAGAAAATATTCAGGCAGAAGTTCAGTGTTAGAGATGATGAAAAGCTATTGAATGTTTCTCAATGCTATTTATCAACGACAGCTGGTCCAATAGCAGGCCTTCTCTTCATCTCTACCGATAAGATTGCTTTCTGCAGCGAGAGATCAATAAAGCTCTTATCTCCAACTGGAAAGTTGCTTAGAATCTACTATAAG................................................................................GTAACCATCCCAATAAGTAAGATAATGAAAGCAAAAGAGAGCAAAAATATGCAAAAGCCATCACAGAAGTATATACAAGTAATTACAGAGGATGATTTTGAGTTCTGGTTTATGGGATTCCTCAATCATCAAAAGACACTGAGATATCTGCAGCAGGCAATCTCCAGCTCAAGCAAGTTATGAAGACACATTTTTTTTTCTAATGAGCTCGTTCTTCAATGTAAAACGTTCATGCAAAAACGAATTCAGGGATCTGTTAAAACTTTGTAACTAGATCCATTGCTCAAAGGAGGCTTAAGGTTTAACCTTTGTGCCCTTAAGAGTTAATGGGAATGTATAGACTTTTTTTTCTCTAAAACTGGTAGCTTTTGTATAGACTTATTTTGTTTTTTGAGATAGCAAGAGATACGAATGTACAAATTTATTATAAAACTTGTGGAGATAGAT</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="33133" PGL_stop="33481"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="33133" e_stop="33481"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.997"/>
        </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="0.997">
            <gDNA_exon_boundary e_start="33133" e_stop="33481" e_length="349"/>
          </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="33133" stop="33481"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U330305" 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>TATGGAAAAGCCATCACAGAAGTATATACAGTTAGTTACAGAGGACGATTACGAGTTCTGGTTTATGGGGTTCTTTAATAATCAAAAAACTCTAAGATATCTGCAGCAGGCAATTTCAACTTTCACAAACTTCAATCAGCTAAGACGATAGTTTTTTAATTTTATTTTGTTTCCTAATACACCCATTCATCAATGTAAAATGTTGATGCAAGATGCAGATATGTTCAAACTTGTAACTAGCTCCATTGCTCAAAGGAGGTTTTAGATTTTTTAGGCTTTAAGCCTAAGTTGTTAATACGAATGTATAGACTTATTGTAAAACTAATCAAACAGGAGGCTAATTCATCTT</gDNA_template>
            <first_frame> Y  G  K  A  I  T  E  V  Y  T  V  S  Y  R  G  R  L  R  V  L  V  Y  G  V  L  *  *  S  K  N  S  K  I  S  A  A  G  N  F  N  F  H  K  L  Q  S  A  K  T  I  V  F  *  F  Y  F  V  S  *  Y  T  H  S  S  M  *  N  V  D  A  R  C  R  Y  V  Q  T  C  N  *  L  H  C  S  K  E  V  L  D  F  L  G  F  K  P  K  L  L  I  R  M  Y  R  L  I  V  K  L  I  K  Q  E  A  N  S  S  </first_frame>
            <second_frame>  M  E  K  P  S  Q  K  Y  I  Q  L  V  T  E  D  D  Y  E  F  W  F  M  G  F  F  N  N  Q  K  T  L  R  Y  L  Q  Q  A  I  S  T  F  T  N  F  N  Q  L  R  R  *  F  F  N  F  I  L  F  P  N  T  P  I  H  Q  C  K  M  L  M  Q  D  A  D  M  F  K  L  V  T  S  S  I  A  Q  R  R  F  *  I  F  *  A  L  S  L  S  C  *  Y  E  C  I  D  L  L  *  N  *  S  N  R  R  L  I  H  L </second_frame>
            <third_frame>   W  K  S  H  H  R  S  I  Y  S  *  L  Q  R  T  I  T  S  S  G  L  W  G  S  L  I  I  K  K  L  *  D  I  C  S  R  Q  F  Q  L  S  Q  T  S  I  S  *  D  D  S  F  L  I  L  F  C  F  L  I  H  P  F  I  N  V  K  C  *  C  K  M  Q  I  C  S  N  L  *  L  A  P  L  L  K  G  G  F  R  F  F  R  L  *  A  *  V  V  N  T  N  V  *  T  Y  C  K  T  N  Q  T  G  G  *  F  I   </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="C04HBa0203K06.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="+" PGL_start="37943" PGL_stop="39518"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="37943" e_stop="38147"/>
            <exon e_start="38241" e_stop="38315"/>
            <exon e_start="38717" e_stop="38991"/>
            <exon e_start="39072" e_stop="39518"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.000" acc_prob="0.991" e_score="1.000"/>
          <exon-intron don_prob="0.997" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.996" acc_prob="0.981" 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="37943" e_stop="38147" e_length="205"/>
          </exon>
          <intron i_serial="1" don_prob="0.000" acc_prob="0.991">
            <gDNA_intron_boundary i_start="38148" i_stop="38240" i_length="93"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="38241" e_stop="38315" e_length="75"/>
          </exon>
          <intron i_serial="2" don_prob="0.997" acc_prob="0.999">
            <gDNA_intron_boundary i_start="38316" i_stop="38716" i_length="401"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="38717" e_stop="38991" e_length="275"/>
          </exon>
          <intron i_serial="3" don_prob="0.996" acc_prob="0.981">
            <gDNA_intron_boundary i_start="38992" i_stop="39071" i_length="80"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="39072" e_stop="39518" e_length="447"/>
          </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="37943" stop="38147"/>
              <exon start="38241" stop="38315"/>
              <exon start="38717" stop="38991"/>
              <exon start="39072" stop="39518"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U325813" 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>TCCCACATACCTTCAAAATACAGTAATACTCCACCTCAAACCAGAATCACAATGGACTTACTCCGTGGAAATTCGGTGGGTATTCCCATGAGTTCATCAGTAGGTTCACTTGAAAGCCAGCCGAAAAGACTACTTGCCTTACCTGCTTGCGAAGACCATATCGTTCCATATGCAACTTCAAAGAACTTGTCTCAAATTAAGCAGA : GAAGATATGTCATTGGTAAGATGAACAAATTGGGAGAAAGGGTGGATTGTCTAGTAAAAAGCATCCGCGAGCATG : TGAGCCTAAGCCCGAAACTAACAGAAACTTTAAAGGGAAAATTGAGCCTTGGAGCAAAAATCCTTCAAGTAGGAGGGTTGGAGAAAATATTCAGGCAGAAGTTCAGTGTTAGAGATGATGAAAAGCTATTGAATGTTTCTCAATGCTATTTATCAACGACAGCTGGTCCAATAGCAGGCCTTCTCTTCATCTCTACCGATAAGATTGCTTTCTGCAGCGAGAGATCAATAAAGCTCTTATCTCCAACTGGAAAGTTGCTTAGAATCTACTATAAG : GTAACCATCCCAATAAGTAAGATAATGAAAGCAAAAGAGAGCAAAAATATGCAAAAGCCATCACAGAAGTATATACAAGTAATTACAGAGGATGATTTTGAGTTCTGGTTTATGGGATTCCTCAATCATCAAAAGACACTGAGATATCTGCAGCAGGCAATCTCCAGCTCAAGCAAGTTATGAAGACACATTTTTTTTTCTAATGAGCTCGTTCTTCAATGTAAAACGTTCATGCAAAAACGAATTCAGGGATCTGTTAAAACTTTGTAACTAGATCCATTGCTCAAAGGAGGCTTAAGGTTTAACCTTTGTGCCCTTAAGAGTTAATGGGAATGTATAGACTTTTTTTTCTCTAAAACTGGTAGCTTTTGTATAGACTTATTTTGTTTTTTGAGATAGCAAGAGATACGAATGTACAAATTTATTATAAAACTTGTGGAGATAGAT</gDNA_template>
            <first_frame> S  H  I  P  S  K  Y  S  N  T  P  P  Q  T  R  I  T  M  D  L  L  R  G  N  S  V  G  I  P  M  S  S  S  V  G  S  L  E  S  Q  P  K  R  L  L  A  L  P  A  C  E  D  H  I  V  P  Y  A  T  S  K  N  L  S  Q  I  K  Q   : R  R  Y  V  I  G  K  M  N  K  L  G  E  R  V  D  C  L  V  K  S  I  R  E  H   : V  S  L  S  P  K  L  T  E  T  L  K  G  K  L  S  L  G  A  K  I  L  Q  V  G  G  L  E  K  I  F  R  Q  K  F  S  V  R  D  D  E  K  L  L  N  V  S  Q  C  Y  L  S  T  T  A  G  P  I  A  G  L  L  F  I  S  T  D  K  I  A  F  C  S  E  R  S  I  K  L  L  S  P  T  G  K  L  L  R  I  Y  Y  K  :  V  T  I  P  I  S  K  I  M  K  A  K  E  S  K  N  M  Q  K  P  S  Q  K  Y  I  Q  V  I  T  E  D  D  F  E  F  W  F  M  G  F  L  N  H  Q  K  T  L  R  Y  L  Q  Q  A  I  S  S  S  S  K  L  *  R  H  I  F  F  S  N  E  L  V  L  Q  C  K  T  F  M  Q  K  R  I  Q  G  S  V  K  T  L  *  L  D  P  L  L  K  G  G  L  R  F  N  L  C  A  L  K  S  *  W  E  C  I  D  F  F  F  S  K  T  G  S  F  C  I  D  L  F  C  F  L  R  *  Q  E  I  R  M  Y  K  F  I  I  K  L  V  E  I  D </first_frame>
            <second_frame>  P  T  Y  L  Q  N  T  V  I  L  H  L  K  P  E  S  Q  W  T  Y  S  V  E  I  R  W  V  F  P  *  V  H  Q  *  V  H  L  K  A  S  R  K  D  Y  L  P  Y  L  L  A  K  T  I  S  F  H  M  Q  L  Q  R  T  C  L  K  L  S  R  :  E  D  M  S  L  V  R  *  T  N  W  E  K  G  W  I  V  *  *  K  A  S  A  S  M  :  *  A  *  A  R  N  *  Q  K  L  *  R  E  N  *  A  L  E  Q  K  S  F  K  *  E  G  W  R  K  Y  S  G  R  S  S  V  L  E  M  M  K  S  Y  *  M  F  L  N  A  I  Y  Q  R  Q  L  V  Q  *  Q  A  F  S  S  S  L  P  I  R  L  L  S  A  A  R  D  Q  *  S  S  Y  L  Q  L  E  S  C  L  E  S  T  I  R :   *  P  S  Q  *  V  R  *  *  K  Q  K  R  A  K  I  C  K  S  H  H  R  S  I  Y  K  *  L  Q  R  M  I  L  S  S  G  L  W  D  S  S  I  I  K  R  H  *  D  I  C  S  R  Q  S  P  A  Q  A  S  Y  E  D  T  F  F  F  L  M  S  S  F  F  N  V  K  R  S  C  K  N  E  F  R  D  L  L  K  L  C  N  *  I  H  C  S  K  E  A  *  G  L  T  F  V  P  L  R  V  N  G  N  V  *  T  F  F  S  L  K  L  V  A  F  V  *  T  Y  F  V  F  *  D  S  K  R  Y  E  C  T  N  L  L  *  N  L  W  R  *   </second_frame>
            <third_frame>   P  H  T  F  K  I  Q  *  Y  S  T  S  N  Q  N  H  N  G  L  T  P  W  K  F  G  G  Y  S  H  E  F  I  S  R  F  T  *  K  P  A  E  K  T  T  C  L  T  C  L  R  R  P  Y  R  S  I  C  N  F  K  E  L  V  S  N  *  A  E :   K  I  C  H  W  *  D  E  Q  I  G  R  K  G  G  L  S  S  K  K  H  P  R  A  C :   E  P  K  P  E  T  N  R  N  F  K  G  K  I  E  P  W  S  K  N  P  S  S  R  R  V  G  E  N  I  Q  A  E  V  Q  C  *  R  *  *  K  A  I  E  C  F  S  M  L  F  I  N  D  S  W  S  N  S  R  P  S  L  H  L  Y  R  *  D  C  F  L  Q  R  E  I  N  K  A  L  I  S  N  W  K  V  A  *  N  L  L  *   : G  N  H  P  N  K  *  D  N  E  S  K  R  E  Q  K  Y  A  K  A  I  T  E  V  Y  T  S  N  Y  R  G  *  F  *  V  L  V  Y  G  I  P  Q  S  S  K  D  T  E  I  S  A  A  G  N  L  Q  L  K  Q  V  M  K  T  H  F  F  F  *  *  A  R  S  S  M  *  N  V  H  A  K  T  N  S  G  I  C  *  N  F  V  T  R  S  I  A  Q  R  R  L  K  V  *  P  L  C  P  *  E  L  M  G  M  Y  R  L  F  F  L  *  N  W  *  L  L  Y  R  L  I  L  F  F  E  I  A  R  D  T  N  V  Q  I  Y  Y  K  T  C  G  D  R  </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="C04HBa0203K06.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="37943" stop="38147"/>
                    <exon start="38241" stop="38315"/>
                    <exon start="38717" stop="38991"/>
                    <exon start="39072" stop="39254"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>735</number_coding_nucleotides>
                  <number_encoded_amino_acids>245</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SHIPSKYSNTPPQTRITMDLLRGNSVGIPMSSSVGSLESQPKRLLALPACEDHIVPYATSKNLSQIKQRRYVIGKMNKLGERVDCLVKSIREHVSLSPKLTETLKGKLSLGAKILQVGGLEKIFRQKFSVRDDEKLLNVSQCYLSTTAGPIAGLLFISTDKIAFCSERSIKLLSPTGKLLRIYYKVTIPISKIMKAKESKNMQKPSQKYIQVITEDDFEFWFMGFLNHQKTLRYLQQAISSSSKL*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 9 chains have been computed
$ 
$ memory statistics:
$ 3808 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 1904 bytes was the average size of a spliced alignment
$ 6800 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3400 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 14 backtrace matrices have been allocated
$ 
$ date finished: 2009-02-20 08:31:38
-->
