<?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 23:36:59"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0107D06-ANm83/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04HBa0107D06-ANm83/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C04HBa0107D06-ANm83/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1965" ref_strand="+" ref_description="SGN-M1965 T1380 [cos_markers]">
      <seq>acaatgatccatatcctttcttcttctactactacaagtacttttctcatactctttttggtccttttcactctgtctccatttccagtttcgattgccacttcatctaccgtacctttcaacatctcccacttcctttatccaagaatcaactacgaggaatatccccaatcttcacctaatcctccttcatttctagaggacgtgttaaagggaattgctgagcgagagaaatgggatttgcagcacttgagagtttccaagttggatgtgaagaaatcaaagtttgggactttgaggaggtatgagtttcgggtcagaattgggaagacggaattggtattcatgatggcagatgaagtatctcagtggaaaggccttcactttcctaacaagaatgaatccaacttcgagtctttggtcaaagagattggttccaaagccactcttgatgtcctaaaaatccaagggccattcgaattatatgctactggagatgattacctgtccttgaccttacccctga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0107D06-ANm83/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0107D06.1" temp_strand="-" temp_description="C04HBa0107D06.1  CU914524.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0107D06 sequenced_by:sanger upload_account_name:uk">
        <position start="63353" stop="61897"/>
      </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="63061" g_stop="62858" g_length="204"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="201" r_length="201" r_score="0.966"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="62857" i_stop="62520" i_length="338">
            <donor d_prob="0.991" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="62519" g_stop="62199" g_length="321"/>
          <reference_exon_boundary r_type="cDNA" r_start="202" r_stop="522" r_length="321" r_score="0.984"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0107D06.1" gen_strand="-" ref_id="SGN-M1965" ref_strand="+">
        <total_alignment_score>0.977</total_alignment_score>
        <cumulative_length_of_scored_exons>525</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0107D06.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1965" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="63061" e_stop="62858"/>
          <exon e_start="62519" e_stop="62199"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ACAATGATCCATATCCTTTCTTCTTCTTCTACTACTACTACTACTTTTCTCATACTCTTTTTGGTCCTTTTCACTCTATCTCCATTTCCAGTTTCGATTGCCACTTCATCTACCATACCTTTCAACATCTCCCACTTCCTTTATCCAAGAATCAACTACGAGGAATATCCCCAATCTTCACCTAATCCTCCTTCATTTCTAGAGGTTTTGTTCAATTTCCTAACTGGGTTTTTCCTAATTACTGTTATTGTTCTGATTCTCTAATGGGTTTTGCCTATTTTCTGTTATTTGCTCTGTTTCTCTAATGAGGTTGGCCTAATTACTGTTATTGGTTCTGATTCTCTGATTGGGTTTGCCTAATTCCTGTTATTTGTGCTGTTTCTCTAACGGGGTTTGCCTAATTGTTGTTAATTTTTCTGATTCTTCAATGAGTTTTGCTTTAATTACTGCTATTTGTTGTGTTTCTCTAATGGGTTTTGCTTAAAGTTCTGTTTTTTGTTCTGTTTCTCTTATTTATGGTTCTATTTGTTTATGTTGTCCAGGACGTGTTAAAGGGGATTGCTGAGCGAGAGAAATGGGATTTGCAGGACTTGAGAGTTTCCAAGTTGGATGTGAAGAAATCAAAGTTTGGGACTTTGAGGAGGTATGAGTTTCGGGTCAGAATTGGGAAGACGGAATTCGTATTCATGATGGCAGATGAAGTATCTCAGTGGAAAGGCCTTCACTTTCCTAACAAGAATGAATCCGACTTCGAGTCTTTGGTCAAAGAGATTGGTTCCAAAGCCACTCTTGATGTTCTAAAAATCCAAGGGCCATTCGAATTATATGCTACTGGAGATGATTACCTGTCCTTGACCTTACCC</genome_strand>
        <mrna_strand>ACAATGATCCATATCC--T-TTCTTCTTCTACTACTACAAGTACTTTTCTCATACTCTTTTTGGTCCTTTTCACTCTGTCTCCATTTCCAGTTTCGATTGCCACTTCATCTACCGTACCTTTCAACATCTCCCACTTCCTTTATCCAAGAATCAACTACGAGGAATATCCCCAATCTTCACCTAATCCTCCTTCATTTCTAGAG..................................................................................................................................................................................................................................................................................................................................................GACGTGTTAAAGGGAATTGCTGAGCGAGAGAAATGGGATTTGCAGCACTTGAGAGTTTCCAAGTTGGATGTGAAGAAATCAAAGTTTGGGACTTTGAGGAGGTATGAGTTTCGGGTCAGAATTGGGAAGACGGAATTGGTATTCATGATGGCAGATGAAGTATCTCAGTGGAAAGGCCTTCACTTTCCTAACAAGAATGAATCCAACTTCGAGTCTTTGGTCAAAGAGATTGGTTCCAAAGCCACTCTTGATGTCCTAAAAATCCAAGGGCCATTCGAATTATATGCTACTGGAGATGATTACCTGTCCTTGACCTTACCC</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-C04HBa0107D06-ANm83/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M8844" ref_strand="+" ref_description="SGN-M8844 C2_At5g25900 [cosii_markers]">
      <seq>aaattgggctgaaacttatggacctatttattccatcaaaaccggcgcaaatacaattgttgtactcagttctagtgaacttgcaaaggaggctatggtgactagatattcatccatctcaactagaaagctaacaaacgcattgagaatccttacttgtgataagagtatagtcgcgataagtgattacgatgagtttcacaagacagcgaagcgccacatactgaccagtgttctaggaccaactgctcagaaacgcttccgtatccacagggacaccttggtagaaaatgtgtcaaagcaactacatgatttggttaggactgatcctaacgaagcaattaatctaaggaagtcatttcagtcggaactttttggtttagcattgaaacaagctttggg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0107D06-ANm83/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04HBa0107D06.1" temp_strand="-" temp_description="C04HBa0107D06.1  CU914524.3 htgs_phase:3 submitted_to_sgn_as:C04HBa0107D06 sequenced_by:sanger upload_account_name:uk">
        <position start="92375" stop="90048"/>
      </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="92075" g_stop="91985" g_length="91"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="91" r_length="91" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="91984" i_stop="90744" i_length="1241">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.990" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="90743" g_stop="90582" g_length="162"/>
          <reference_exon_boundary r_type="cDNA" r_start="92" r_stop="253" r_length="162" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="90581" i_stop="90494" i_length="88">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.782" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="90493" g_stop="90353" g_length="141"/>
          <reference_exon_boundary r_type="cDNA" r_start="254" r_stop="394" r_length="141" r_score="0.993"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="90352" i_stop="90257" i_length="96">
            <donor d_prob="0.611" d_score="1.00"/>
            <acceptor a_prob="0.986" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="90256" g_stop="90249" g_length="8"/>
          <reference_exon_boundary r_type="cDNA" r_start="395" r_stop="402" r_length="8" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0107D06.1" gen_strand="-" ref_id="SGN-M8844" ref_strand="+">
        <total_alignment_score>0.997</total_alignment_score>
        <cumulative_length_of_scored_exons>402</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0107D06.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M8844" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="92075" e_stop="91985"/>
          <exon e_start="90743" e_stop="90582"/>
          <exon e_start="90493" e_stop="90353"/>
          <exon e_start="90256" e_stop="90249"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAATTGGGCTGAAACTTATGGACCTATTTATTCCATCAAAACCGGCGCAAATACAATTGTTGTACTCAGTTCTAGTGAACTTGCAAAGGAGGTAATCAAAATAATCACTCTCAAACCTCTTTTCTATGTTAATAAGTAAGAAACAAGCATTGGAGTTCTAAGTTCGTCGCAAAAAGTAAACCTTTTTGGTTGTAATCCATTTTCTAGTTGCTATGTAGCTTCTTCTGTCTTAATTTTTATGATGTCAAAAGGTTTTACGTCCTACTAATTGCTGGTTTTAAGTTGTGAAATGATTCAATCTGGTATTTCAAGTTTTTCTAGTTAGAAAGATACTAAAATATGAGATGGTACACTCGTAATAAAAGTTTAGTTAAAATGGTATGCAGAAAGAGGAGAGTGGCAACAGAGAAATGTAGACAAATTACGTGGTCCTTCAGCACCACACCATTTAGTAGAGGAATTGGATATGTTTCTTTAGTAATATGTACTGAGAGTCAGGAATATTTTACTTTAGTATGACTGGACCAGGGGATAAAACTTATAATCTGACTAATGCTGTATATGAGCCCCAGATTTTCCTGATAGCTGCAGTTGCATTGGTTTCAGTATTATATAGGATCGAACTTAAAGTACGTGTCCCTGCCTCTCGATGATCACTAAATGGATTGTATTGCCTAGTTCCTCTTTGTTGAGACTAGACCATACTACAAGGTGAAGCAGTTGGTGATTTAGACAACTGCTATCTCCATATTATATCCCTGGATTGTATGTTGGTTGTTCTCTGGTAAGACCTCAACTGTATAATTGGAAAATCTTCGGTTGTTGAGGTTCTGAATCACCGTACTAGATATGATAAAGTAGTGTCATGTACCACCTCAGTCGCGGCATATGTTGGCTGTGTATCAGCAAAGTTCCATTTTCACTATACAGTTGGTTTAGACTTTATAATTTTCTGATAAATATCTGAGAAAATACATAGAATATGAAGATCTTATAAACTAATGTTGAGGTAGAACGACTACTCGCACATTGTTGCACAGAGCTTAAAGTATTTACCTCCAGTTTCCTTGCAAGAGGAGAGCTTTTGCATTGTTTTAAGGTATTTAGTTCTTTATCACGTAGAATAAGCATCAACACCAAAGTAACGACTCAAATGTAACATTGACACTACTGGGGTGTCATCGATCACCAATAGCTTGAGTTATAAGCCAATATATAGAGGCATGTTTGGTGCTTATTTTTTAAATCACTGTTGTGTTATTTGTGTGCTTATCATATCTATACTCAAACACTTGATACAGATCTAAATATTGTCCTTTTTCGTCTTTTTAGGCTATGGTGACTAGATATTCATCCATCTCAACTAGAAAGCTAACAAACGCATTGAGAATCCTTACTTGTGATAAGAGTATAGTCGCGATAAGTGATTACGATGAGTTTCACAAGACAGCGAAGCGCCACATACTGACCAGTGTTCTAGGACCAACTGCTCAGGTTTGTCATTTACAAATCGACCTCCATAATTCTCTTCATTTGTTTCATCGACTCCATATCTAACAGGAAAGTGCTGCTTAATATGCAGAAACGCTTCCGTATCCACAGGGACACCTTGGTAGAAAATGTGTCAAAGCAACTACATGATTTGGTTAGGACTGATCCTAACGAAGCAGTTAATCTAAGGAAGTCATTTCAGTCGGAACTTTTTGGTTTAGCATTGAAACAAGTTAGTTTTTCAAAATTCAGTTTCATCAGTATGTTGTTATTTTGGGAACTCCTTTAATCTGCGCGATCATTTTAAAAGTTTTAACTTCATTTGCAGGCTTTGGG</genome_strand>
        <mrna_strand>AAATTGGGCTGAAACTTATGGACCTATTTATTCCATCAAAACCGGCGCAAATACAATTGTTGTACTCAGTTCTAGTGAACTTGCAAAGGAG.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GCTATGGTGACTAGATATTCATCCATCTCAACTAGAAAGCTAACAAACGCATTGAGAATCCTTACTTGTGATAAGAGTATAGTCGCGATAAGTGATTACGATGAGTTTCACAAGACAGCGAAGCGCCACATACTGACCAGTGTTCTAGGACCAACTGCTCAG........................................................................................AAACGCTTCCGTATCCACAGGGACACCTTGGTAGAAAATGTGTCAAAGCAACTACATGATTTGGTTAGGACTGATCCTAACGAAGCAATTAATCTAAGGAAGTCATTTCAGTCGGAACTTTTTGGTTTAGCATTGAAACAA................................................................................................GCTTTGGG</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="63061" PGL_stop="62199"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="63061" e_stop="62858"/>
            <exon e_start="62519" e_stop="62199"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.991" acc_prob="1.000" e_score="0.966"/>
          <exon-only e_score="0.984"/>
        </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="0.966">
            <gDNA_exon_boundary e_start="63061" e_stop="62858" e_length="204"/>
          </exon>
          <intron i_serial="1" don_prob="0.991" acc_prob="1.000">
            <gDNA_intron_boundary i_start="62857" i_stop="62520" i_length="338"/>
          </intron>
          <exon e_serial="2" e_score="0.984">
            <gDNA_exon_boundary e_start="62519" e_stop="62199" e_length="321"/>
          </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="63061" stop="62858"/>
              <exon start="62519" stop="62199"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1965" 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>ACAATGATCCATATCCTTTCTTCTTCTTCTACTACTACTACTACTTTTCTCATACTCTTTTTGGTCCTTTTCACTCTATCTCCATTTCCAGTTTCGATTGCCACTTCATCTACCATACCTTTCAACATCTCCCACTTCCTTTATCCAAGAATCAACTACGAGGAATATCCCCAATCTTCACCTAATCCTCCTTCATTTCTAGAG : GACGTGTTAAAGGGGATTGCTGAGCGAGAGAAATGGGATTTGCAGGACTTGAGAGTTTCCAAGTTGGATGTGAAGAAATCAAAGTTTGGGACTTTGAGGAGGTATGAGTTTCGGGTCAGAATTGGGAAGACGGAATTCGTATTCATGATGGCAGATGAAGTATCTCAGTGGAAAGGCCTTCACTTTCCTAACAAGAATGAATCCGACTTCGAGTCTTTGGTCAAAGAGATTGGTTCCAAAGCCACTCTTGATGTTCTAAAAATCCAAGGGCCATTCGAATTATATGCTACTGGAGATGATTACCTGTCCTTGACCTTACCC</gDNA_template>
            <first_frame> T  M  I  H  I  L  S  S  S  S  T  T  T  T  T  F  L  I  L  F  L  V  L  F  T  L  S  P  F  P  V  S  I  A  T  S  S  T  I  P  F  N  I  S  H  F  L  Y  P  R  I  N  Y  E  E  Y  P  Q  S  S  P  N  P  P  S  F  L  E  :  D  V  L  K  G  I  A  E  R  E  K  W  D  L  Q  D  L  R  V  S  K  L  D  V  K  K  S  K  F  G  T  L  R  R  Y  E  F  R  V  R  I  G  K  T  E  F  V  F  M  M  A  D  E  V  S  Q  W  K  G  L  H  F  P  N  K  N  E  S  D  F  E  S  L  V  K  E  I  G  S  K  A  T  L  D  V  L  K  I  Q  G  P  F  E  L  Y  A  T  G  D  D  Y  L  S  L  T  L  P </first_frame>
            <second_frame>  Q  *  S  I  S  F  L  L  L  L  L  L  L  L  L  F  S  Y  S  F  W  S  F  S  L  Y  L  H  F  Q  F  R  L  P  L  H  L  P  Y  L  S  T  S  P  T  S  F  I  Q  E  S  T  T  R  N  I  P  N  L  H  L  I  L  L  H  F  *  R :   T  C  *  R  G  L  L  S  E  R  N  G  I  C  R  T  *  E  F  P  S  W  M  *  R  N  Q  S  L  G  L  *  G  G  M  S  F  G  S  E  L  G  R  R  N  S  Y  S  *  W  Q  M  K  Y  L  S  G  K  A  F  T  F  L  T  R  M  N  P  T  S  S  L  W  S  K  R  L  V  P  K  P  L  L  M  F  *  K  S  K  G  H  S  N  Y  M  L  L  E  M  I  T  C  P  *  P  Y   </second_frame>
            <third_frame>   N  D  P  Y  P  F  F  F  F  Y  Y  Y  Y  Y  F  S  H  T  L  F  G  P  F  H  S  I  S  I  S  S  F  D  C  H  F  I  Y  H  T  F  Q  H  L  P  L  P  L  S  K  N  Q  L  R  G  I  S  P  I  F  T  *  S  S  F  I  S  R   : G  R  V  K  G  D  C  *  A  R  E  M  G  F  A  G  L  E  S  F  Q  V  G  C  E  E  I  K  V  W  D  F  E  E  V  *  V  S  G  Q  N  W  E  D  G  I  R  I  H  D  G  R  *  S  I  S  V  E  R  P  S  L  S  *  Q  E  *  I  R  L  R  V  F  G  Q  R  D  W  F  Q  S  H  S  *  C  S  K  N  P  R  A  I  R  I  I  C  Y  W  R  *  L  P  V  L  D  L  T  </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="C04HBa0107D06.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="63061" stop="62858"/>
                    <exon start="62519" stop="62199"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>525</number_coding_nucleotides>
                  <number_encoded_amino_acids>175</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>TMIHILSSSSTTTTTFLILFLVLFTLSPFPVSIATSSTIPFNISHFLYPRINYEEYPQSSPNPPSFLEDVLKGIAEREKWDLQDLRVSKLDVKKSKFGTLRRYEFRVRIGKTEFVFMMADEVSQWKGLHFPNKNESDFESLVKEIGSKATLDVLKIQGPFELYATGDDYLSLTLP</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="92075" PGL_stop="90249"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="92075" e_stop="91985"/>
            <exon e_start="90743" e_stop="90582"/>
            <exon e_start="90493" e_stop="90353"/>
            <exon e_start="90256" e_stop="90249"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.990" e_score="1.000"/>
          <exon-intron don_prob="0.996" acc_prob="0.782" e_score="1.000"/>
          <exon-intron don_prob="0.611" acc_prob="0.986" e_score="0.993"/>
          <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="92075" e_stop="91985" e_length="91"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.990">
            <gDNA_intron_boundary i_start="91984" i_stop="90744" i_length="1241"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="90743" e_stop="90582" e_length="162"/>
          </exon>
          <intron i_serial="2" don_prob="0.996" acc_prob="0.782">
            <gDNA_intron_boundary i_start="90581" i_stop="90494" i_length="88"/>
          </intron>
          <exon e_serial="3" e_score="0.993">
            <gDNA_exon_boundary e_start="90493" e_stop="90353" e_length="141"/>
          </exon>
          <intron i_serial="3" don_prob="0.611" acc_prob="0.986">
            <gDNA_intron_boundary i_start="90352" i_stop="90257" i_length="96"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="90256" e_stop="90249" e_length="8"/>
          </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="92075" stop="91985"/>
              <exon start="90743" stop="90582"/>
              <exon start="90493" stop="90353"/>
              <exon start="90256" stop="90249"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M8844" 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>AAATTGGGCTGAAACTTATGGACCTATTTATTCCATCAAAACCGGCGCAAATACAATTGTTGTACTCAGTTCTAGTGAACTTGCAAAGGAG : GCTATGGTGACTAGATATTCATCCATCTCAACTAGAAAGCTAACAAACGCATTGAGAATCCTTACTTGTGATAAGAGTATAGTCGCGATAAGTGATTACGATGAGTTTCACAAGACAGCGAAGCGCCACATACTGACCAGTGTTCTAGGACCAACTGCTCAG : AAACGCTTCCGTATCCACAGGGACACCTTGGTAGAAAATGTGTCAAAGCAACTACATGATTTGGTTAGGACTGATCCTAACGAAGCAGTTAATCTAAGGAAGTCATTTCAGTCGGAACTTTTTGGTTTAGCATTGAAACAA : GCTTTGGG</gDNA_template>
            <first_frame> K  L  G  *  N  L  W  T  Y  L  F  H  Q  N  R  R  K  Y  N  C  C  T  Q  F  *  *  T  C  K  G   : G  Y  G  D  *  I  F  I  H  L  N  *  K  A  N  K  R  I  E  N  P  Y  L  *  *  E  Y  S  R  D  K  *  L  R  *  V  S  Q  D  S  E  A  P  H  T  D  Q  C  S  R  T  N  C  S   : E  T  L  P  Y  P  Q  G  H  L  G  R  K  C  V  K  A  T  T  *  F  G  *  D  *  S  *  R  S  S  *  S  K  E  V  I  S  V  G  T  F  W  F  S  I  E  T   : S  F  G </first_frame>
            <second_frame>  N  W  A  E  T  Y  G  P  I  Y  S  I  K  T  G  A  N  T  I  V  V  L  S  S  S  E  L  A  K  E  :  A  M  V  T  R  Y  S  S  I  S  T  R  K  L  T  N  A  L  R  I  L  T  C  D  K  S  I  V  A  I  S  D  Y  D  E  F  H  K  T  A  K  R  H  I  L  T  S  V  L  G  P  T  A  Q  :  K  R  F  R  I  H  R  D  T  L  V  E  N  V  S  K  Q  L  H  D  L  V  R  T  D  P  N  E  A  V  N  L  R  K  S  F  Q  S  E  L  F  G  L  A  L  K  Q  :  A  L   </second_frame>
            <third_frame>   I  G  L  K  L  M  D  L  F  I  P  S  K  P  A  Q  I  Q  L  L  Y  S  V  L  V  N  L  Q  R  R :   L  W  *  L  D  I  H  P  S  Q  L  E  S  *  Q  T  H  *  E  S  L  L  V  I  R  V  *  S  R  *  V  I  T  M  S  F  T  R  Q  R  S  A  T  Y  *  P  V  F  *  D  Q  L  L  R :   N  A  S  V  S  T  G  T  P  W  *  K  M  C  Q  S  N  Y  M  I  W  L  G  L  I  L  T  K  Q  L  I  *  G  S  H  F  S  R  N  F  L  V  *  H  *  N  K :   L  W  </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="C04HBa0107D06.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="92074" stop="91985"/>
                    <exon start="90743" stop="90582"/>
                    <exon start="90493" stop="90353"/>
                    <exon start="90256" stop="90251"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>399</number_coding_nucleotides>
                  <number_encoded_amino_acids>133</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>NWAETYGPIYSIKTGANTIVVLSSSELAKEAMVTRYSSISTRKLTNALRILTCDKSIVAISDYDEFHKTAKRHILTSVLGPTAQKRFRIHRDTLVENVSKQLHDLVRTDPNEAVNLRKSFQSELFGLALKQAL</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 14 chains have been computed
$ 
$ memory statistics:
$ 3792 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 1896 bytes was the average size of a spliced alignment
$ 6832 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3416 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 14 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 23:37:04
-->
