<?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="2009-07-24 23:37:22"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12SLe0032P11-SV6Lw/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C12SLe0032P11-SV6Lw/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-C12SLe0032P11-SV6Lw/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1447" ref_strand="+" ref_description="SGN-M1447 T0504 [cos_markers]">
      <seq>ttacaggaatggatgtgatcacaccaaatggtcaggatcccgatgtgttctatgaaaacttgcttcaaggtgtcagtggcataagtgagatagaatcttttgattgttcacaatttccaacaagaattgctggagagatcaagtctttctcaagtgatggctggatttcacctaaactttctaaacgaatggacaagttcatgctttacgctcta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12SLe0032P11-SV6Lw/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12SLe0032P11.1" temp_strand="-" temp_description="C12SLe0032P11.1  AC235099.2 htgs_phase:2 submitted_to_sgn_as:gi|237823119|gb|AC235099.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone SL_EcoRI-32P11, WORKING DRAFT SEQUENCE, 3 ordered pieces">
        <position start="11122" stop="10235"/>
      </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="10822" g_stop="10701" g_length="122"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="122" r_length="122" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="10700" i_stop="10628" i_length="73">
            <donor d_prob="0.985" d_score="1.00"/>
            <acceptor a_prob="0.955" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="10627" g_stop="10535" g_length="93"/>
          <reference_exon_boundary r_type="cDNA" r_start="123" r_stop="215" r_length="93" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12SLe0032P11.1" gen_strand="-" ref_id="SGN-M1447" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>215</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12SLe0032P11.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1447" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="10822" e_stop="10701"/>
          <exon e_start="10627" e_stop="10535"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTACAGGAATGGATGTGATCACACCAAATGGTCAGGATCCCGATGTGTTCTATGAAAACTTGCTTCAAGGTGTCAGTGGCATAAGTGAGATAGAATCTTTTGATTGTTCACAATTTCCAACAGTACGTCTTCTTCTTTGGTTAGTTTTTCTCTAAATGTAATATTTTAGATGTTAAAAAAGGGGTACAATTGCAGAGAATTGCTGGAGAGATCAAGTCTTTCTCAAGTGATGGCTGGATTTCACCTAAACTTTCTAAACGAATGGACAAGTTCATGCTTTACGCTCTA</genome_strand>
        <mrna_strand>TTACAGGAATGGATGTGATCACACCAAATGGTCAGGATCCCGATGTGTTCTATGAAAACTTGCTTCAAGGTGTCAGTGGCATAAGTGAGATAGAATCTTTTGATTGTTCACAATTTCCAACA.........................................................................AGAATTGCTGGAGAGATCAAGTCTTTCTCAAGTGATGGCTGGATTTCACCTAAACTTTCTAAACGAATGGACAAGTTCATGCTTTACGCTCTA</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-C12SLe0032P11-SV6Lw/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M6659-2" ref_strand="+" ref_description="SGN-M6659-2 C2_At1g19130-2 [cosii_markers]">
      <seq>aaaaatggcatcaaattctacagagcctacagcttcaaaaattgttgctaagctaaacttgaaggtacatccagaagggggattttactcagaaacatttagagataactcagttattctctccagatctcatcttccatctacatataaggttgatcgacctgtcagtacatgcatctacttcttgctaccttctggaagtgcgtctcatcttcaccggataccttgtgcagaaacatggcatttttatatgggagagccaatcactgtgatggagctaaacgaaactgatggcaaggtgaagttaacttgcgttggacccgatcccctcgtagatgatcaattcgtgcagtatacagtacctccaaatgtatggtttggcgcatttcccacgaaggattacaacatatcttccgatatgcaagtaacgaaagcacctacaagagatggtgagaaacatttctctctagttggatgcacttgtgctccagcattccagtttgaagattttgaattagcaaaacgttctgatcttgtctcgcgttttcctgcccacgaatcccttgtctctttgctagccttccctgatctgtgagagatatgtattcaatggcggatctagagcataatctacgggttttacataacctagtagctttttcgcggaccttgtaaaatatctatatatatttgattcttgtttccaaaaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12SLe0032P11-SV6Lw/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12SLe0032P11.1" temp_strand="+" temp_description="C12SLe0032P11.1  AC235099.2 htgs_phase:2 submitted_to_sgn_as:gi|237823119|gb|AC235099.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone SL_EcoRI-32P11, WORKING DRAFT SEQUENCE, 3 ordered pieces">
        <position start="70229" stop="73757"/>
      </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="70529" g_stop="70674" g_length="146"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="146" r_length="146" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="70675" i_stop="72192" i_length="1518">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.964" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="72193" g_stop="72314" g_length="122"/>
          <reference_exon_boundary r_type="cDNA" r_start="147" r_stop="268" r_length="122" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="72315" i_stop="73020" i_length="706">
            <donor d_prob="0.590" d_score="1.00"/>
            <acceptor a_prob="0.998" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="73021" g_stop="73458" g_length="438"/>
          <reference_exon_boundary r_type="cDNA" r_start="269" r_stop="706" r_length="438" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="707" polyA_stop="723"/>
      <MATCH_line gen_id="C12SLe0032P11.1" gen_strand="+" ref_id="SGN-M6659-2" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>706</cumulative_length_of_scored_exons>
        <coverage percentage="0.976" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12SLe0032P11.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6659-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="70529" e_stop="70674"/>
          <exon e_start="72193" e_stop="72314"/>
          <exon e_start="73021" e_stop="73458"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAAAATGGCATCAAATTCTACAGAGCCTACAGCTTCAAAAATTGTTGCTAAGCTAAACTTGAAGGTACATCCAGAAGGGGGATTTTACTCAGAAACATTTAGAGATAACTCAGTTATTCTCTCCAGATCTCATCTTCCATCTACATGTAAGTTTTTTTTTTTTTTTTTGTATAAATTTAATTTACTTTTTGGATCTTGAATTTCTTAGATCCCTCATGAGATTTTTGGATCTTAGATCTGTTTTTCATCCATATGTTTTTAGGATGTTTACTTGGATATTGCTATATGAAGTGTGATGGATATGTGATTTGGACTTTTAGGATCTCAAATTGCCCCCAAAAACCATGATTTGGAAATGGTAGTAACAAAAGAAATTTAATATGTAAAAAATTAGACGTAATACGTAAATATACCCTTTATTTTAACTTCATTTTACATTTACGCCCTTTAATTTTGATTGTGCACAAATCGACACTTAAACTCTTATAAAGTTAAACAAATAGACACACGAGTCCTACATGTCACAATACACGTAGGACACAAATTTTCATGGGCATAATACATAAATATGCCCTTTAACTTGGCTTCGAATCACATATATGCCCTTCAATTTTTGGTTTACACAAGTAGACACTTAAACTTGTATAAAGTAGAACAAGTAGACACACACGTCCTACATGTCATTTTTTGTCCTATGTGGTGTCCTACGTGTATTTTGCAATGTAAGACTCATGTGTTTATTTATTAGTTGGATAGTTAAAGTGTCTGTTTGTGCATTATGAAAGTTAGAGGACAAAGTTAAAATTTGAAACCAAGTTTAGGGTCCATTATATGTATTATGCCTATATAGGATGTCATGCAGGACGTTTGTGTCTATTTGTTTAATTTTATACAAGTTTAAGTGTCTGCTTGTGCACACCCAAAGTTGGAGGGCATAAATCAGAGTGCATGTTAATTTTATGTATTATGCCTAAAAAAAATTAACATGCACTCTGATTTTGCTATTTTGGGTGTGTACAAGCAGTTAATTGAACTTTTATAAAATTGAACAGTAGACACATGAGCATTCTGTGACATAATACGCATAGGACACTACATAGAATTGTTCGTTTTTATACAAGTGTATACCTGTGCGCATTCAATGTTGAAGGGCATAAATGTGAAATGATGCTAAGTTAAAAGGGCATATTTATGTATTATGCCTATTTTAAATTTTGTAGAAAGATATTCGTGTTCGGTTGTTTGAATTATATACAAGGAATAACTAGTTACTACTTTTATTGATTTGTAGATCTTTATGACATTATGCGTACTTAGAAGTTCGTCATCACAAATATCTATTTATAAAAGAAACATGAAGATATGTAATTTATTTATGGGCTTAAGATATTTCGATATTCTGTTTCTTAATTTTACTATCTCATATGTATCACCAGCAACATTTGCAGTGGTGTAACCAGTATTTCATTAAGCAAATGAAAAGCATAAGGAGGTTCAATATCTGCTATATATATCTGCATAAACCGTATAACTTTCCGCGATCTGAACCCCTTGACCTCACCGACCTCACCTGGTTCCGTCCTTGAGCATTTGCTTCATAAGATAGAGTACTATCAAATTAGTTAGTTGTTTTTTCCCTGATGTTTCGGGTTTCACCATTGCAGATAAGGTTGATCGACCTGTCAGTACATGCATCTACTTCTTGCTACCTTCTGGAAGTGCGTCTCATCTTCACCGGATACCTTGTGCAGAAACATGGCATTTTTATATGGGAGAGCCAATCACTGTGAGATCATCTTTCCCGCAGTCTACTTTATGCACCAGATTAGGATTATCTCTGTGCTGTTCTGTATATTTATGTCATGCGTTGTGTGTTAAGGCTTAATACGTAAACAAACACTTAAACTTGGCCTCAGCTGGGAAGTAAACACTCCAACTTTGAGAGTGCACATCTACACGTGCACCTCAGACTCGTCTCCATTGTGTCATTTGAGCCACTCCAACTTACGAAATGATCATCTAGACACCCTCCAATATTTATATCTCACGTCAACTTGGATGTTCCATAAGACACGGTTATGACGAGTTTGAGTGATAAGTTATAAGTTGAAACCAAATTGAGGAATCTCTCTAAGTTGGAGTACTAAATTGTTAGCTGAGCCCGAGGCCAAGTTTGGATATATGTTTATGTATTATGCCTTGTGTTTTGGTGTGAACTGAAAGGGATTTGACTAACACTCAAAAGTGTTAATAAAACTTGTAAGGACTATAAGGGTCGTTAAGATTCGTTGCCTAAATAGGAAAGAGACCGCCTTTCTGAAACAGACTAAAAAGGAAAGTAATACAGGCAAATTGATACATTGGATCTTCATAATCATCTTGTTCTTTACGATAATTGAACATTTGTTGCTCCCCGGTAAGAGTGATGAACTAGTCATTCACCAATGTTTTCCTAGAAATGACGATAATGACAACACTTCTTGTGCTTTCAGGTGATGGAGCTAAACGAAACTGATGGCAAGGTGAAGTTAACTTGCGTTGGACCCGATCCCCTCGTAGATGATCAATTCGTGCAGTATACAGTACCTCCAAATGTATGGTTTGGCGCATTTCCCACGAAGGATTACAACATATCTTCCGATATGCAAGTAACGAAAGCACCTACAAGAGATGGTGAGAAACATTTCTCTCTAGTTGGATGCACTTGTGCTCCAGCATTCCAGTTTGAAGATTTTGAATTAGCAAAACGTTCTGATCTTGTCTCGCGTTTTCCTGCCCACGAATCCCTTGTCTCTTTGCTAGCCTTCCCTGATCTGTGAGAGATATGTATTCAATGGCGGATCTAGAGCATAATCTACGGGTTTTACATAACCTAGTAGCTTTTTCGCGGACCTTGTAAAATATCTATATATATTTGATTCTTGTTTCCT</genome_strand>
        <mrna_strand>AAAAATGGCATCAAATTCTACAGAGCCTACAGCTTCAAAAATTGTTGCTAAGCTAAACTTGAAGGTACATCCAGAAGGGGGATTTTACTCAGAAACATTTAGAGATAACTCAGTTATTCTCTCCAGATCTCATCTTCCATCTACAT..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATAAGGTTGATCGACCTGTCAGTACATGCATCTACTTCTTGCTACCTTCTGGAAGTGCGTCTCATCTTCACCGGATACCTTGTGCAGAAACATGGCATTTTTATATGGGAGAGCCAATCACT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGATGGAGCTAAACGAAACTGATGGCAAGGTGAAGTTAACTTGCGTTGGACCCGATCCCCTCGTAGATGATCAATTCGTGCAGTATACAGTACCTCCAAATGTATGGTTTGGCGCATTTCCCACGAAGGATTACAACATATCTTCCGATATGCAAGTAACGAAAGCACCTACAAGAGATGGTGAGAAACATTTCTCTCTAGTTGGATGCACTTGTGCTCCAGCATTCCAGTTTGAAGATTTTGAATTAGCAAAACGTTCTGATCTTGTCTCGCGTTTTCCTGCCCACGAATCCCTTGTCTCTTTGCTAGCCTTCCCTGATCTGTGAGAGATATGTATTCAATGGCGGATCTAGAGCATAATCTACGGGTTTTACATAACCTAGTAGCTTTTTCGCGGACCTTGTAAAATATCTATATATATTTGATTCTTGTTTCCA</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="10822" PGL_stop="10535"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="10822" e_stop="10701"/>
            <exon e_start="10627" e_stop="10535"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.985" acc_prob="0.955" 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="10822" e_stop="10701" e_length="122"/>
          </exon>
          <intron i_serial="1" don_prob="0.985" acc_prob="0.955">
            <gDNA_intron_boundary i_start="10700" i_stop="10628" i_length="73"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="10627" e_stop="10535" e_length="93"/>
          </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="10822" stop="10701"/>
              <exon start="10627" stop="10535"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1447" 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>TTACAGGAATGGATGTGATCACACCAAATGGTCAGGATCCCGATGTGTTCTATGAAAACTTGCTTCAAGGTGTCAGTGGCATAAGTGAGATAGAATCTTTTGATTGTTCACAATTTCCAACA : AGAATTGCTGGAGAGATCAAGTCTTTCTCAAGTGATGGCTGGATTTCACCTAAACTTTCTAAACGAATGGACAAGTTCATGCTTTACGCTCTA</gDNA_template>
            <first_frame> L  Q  E  W  M  *  S  H  Q  M  V  R  I  P  M  C  S  M  K  T  C  F  K  V  S  V  A  *  V  R  *  N  L  L  I  V  H  N  F  Q  Q :   E  L  L  E  R  S  S  L  S  Q  V  M  A  G  F  H  L  N  F  L  N  E  W  T  S  S  C  F  T  L   </first_frame>
            <second_frame>  Y  R  N  G  C  D  H  T  K  W  S  G  S  R  C  V  L  *  K  L  A  S  R  C  Q  W  H  K  *  D  R  I  F  *  L  F  T  I  S  N   : K  N  C  W  R  D  Q  V  F  L  K  *  W  L  D  F  T  *  T  F  *  T  N  G  Q  V  H  A  L  R  S  </second_frame>
            <third_frame>   T  G  M  D  V  I  T  P  N  G  Q  D  P  D  V  F  Y  E  N  L  L  Q  G  V  S  G  I  S  E  I  E  S  F  D  C  S  Q  F  P  T  :  R  I  A  G  E  I  K  S  F  S  S  D  G  W  I  S  P  K  L  S  K  R  M  D  K  F  M  L  Y  A  L </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C12SLe0032P11.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="10820" stop="10701"/>
                    <exon start="10627" stop="10535"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>213</number_coding_nucleotides>
                  <number_encoded_amino_acids>71</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>TGMDVITPNGQDPDVFYENLLQGVSGISEIESFDCSQFPTRIAGEIKSFSSDGWISPKLSKRMDKFMLYAL</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="70529" PGL_stop="73458"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="70529" e_stop="70674"/>
            <exon e_start="72193" e_stop="72314"/>
            <exon e_start="73021" e_stop="73458"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.997" acc_prob="0.964" e_score="1.000"/>
          <exon-intron don_prob="0.590" acc_prob="0.998" e_score="1.000"/>
          <exon-only e_score="0.998"/>
        </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="70529" e_stop="70674" e_length="146"/>
          </exon>
          <intron i_serial="1" don_prob="0.997" acc_prob="0.964">
            <gDNA_intron_boundary i_start="70675" i_stop="72192" i_length="1518"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="72193" e_stop="72314" e_length="122"/>
          </exon>
          <intron i_serial="2" don_prob="0.590" acc_prob="0.998">
            <gDNA_intron_boundary i_start="72315" i_stop="73020" i_length="706"/>
          </intron>
          <exon e_serial="3" e_score="0.998">
            <gDNA_exon_boundary e_start="73021" e_stop="73458" e_length="438"/>
          </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="70529" stop="70674"/>
              <exon start="72193" stop="72314"/>
              <exon start="73021" stop="73458"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6659-2" 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>AAAAATGGCATCAAATTCTACAGAGCCTACAGCTTCAAAAATTGTTGCTAAGCTAAACTTGAAGGTACATCCAGAAGGGGGATTTTACTCAGAAACATTTAGAGATAACTCAGTTATTCTCTCCAGATCTCATCTTCCATCTACAT : ATAAGGTTGATCGACCTGTCAGTACATGCATCTACTTCTTGCTACCTTCTGGAAGTGCGTCTCATCTTCACCGGATACCTTGTGCAGAAACATGGCATTTTTATATGGGAGAGCCAATCACT : GTGATGGAGCTAAACGAAACTGATGGCAAGGTGAAGTTAACTTGCGTTGGACCCGATCCCCTCGTAGATGATCAATTCGTGCAGTATACAGTACCTCCAAATGTATGGTTTGGCGCATTTCCCACGAAGGATTACAACATATCTTCCGATATGCAAGTAACGAAAGCACCTACAAGAGATGGTGAGAAACATTTCTCTCTAGTTGGATGCACTTGTGCTCCAGCATTCCAGTTTGAAGATTTTGAATTAGCAAAACGTTCTGATCTTGTCTCGCGTTTTCCTGCCCACGAATCCCTTGTCTCTTTGCTAGCCTTCCCTGATCTGTGAGAGATATGTATTCAATGGCGGATCTAGAGCATAATCTACGGGTTTTACATAACCTAGTAGCTTTTTCGCGGACCTTGTAAAATATCTATATATATTTGATTCTTGTTTCCT</gDNA_template>
            <first_frame> K  N  G  I  K  F  Y  R  A  Y  S  F  K  N  C  C  *  A  K  L  E  G  T  S  R  R  G  I  L  L  R  N  I  *  R  *  L  S  Y  S  L  Q  I  S  S  S  I  Y  I :   *  G  *  S  T  C  Q  Y  M  H  L  L  L  A  T  F  W  K  C  V  S  S  S  P  D  T  L  C  R  N  M  A  F  L  Y  G  R  A  N  H   : C  D  G  A  K  R  N  *  W  Q  G  E  V  N  L  R  W  T  R  S  P  R  R  *  S  I  R  A  V  Y  S  T  S  K  C  M  V  W  R  I  S  H  E  G  L  Q  H  I  F  R  Y  A  S  N  E  S  T  Y  K  R  W  *  E  T  F  L  S  S  W  M  H  L  C  S  S  I  P  V  *  R  F  *  I  S  K  T  F  *  S  C  L  A  F  S  C  P  R  I  P  C  L  F  A  S  L  P  *  S  V  R  D  M  Y  S  M  A  D  L  E  H  N  L  R  V  L  H  N  L  V  A  F  S  R  T  L  *  N  I  Y  I  Y  L  I  L  V  S  </first_frame>
            <second_frame>  K  M  A  S  N  S  T  E  P  T  A  S  K  I  V  A  K  L  N  L  K  V  H  P  E  G  G  F  Y  S  E  T  F  R  D  N  S  V  I  L  S  R  S  H  L  P  S  T   : Y  K  V  D  R  P  V  S  T  C  I  Y  F  L  L  P  S  G  S  A  S  H  L  H  R  I  P  C  A  E  T  W  H  F  Y  M  G  E  P  I  T  :  V  M  E  L  N  E  T  D  G  K  V  K  L  T  C  V  G  P  D  P  L  V  D  D  Q  F  V  Q  Y  T  V  P  P  N  V  W  F  G  A  F  P  T  K  D  Y  N  I  S  S  D  M  Q  V  T  K  A  P  T  R  D  G  E  K  H  F  S  L  V  G  C  T  C  A  P  A  F  Q  F  E  D  F  E  L  A  K  R  S  D  L  V  S  R  F  P  A  H  E  S  L  V  S  L  L  A  F  P  D  L  *  E  I  C  I  Q  W  R  I  *  S  I  I  Y  G  F  Y  I  T  *  *  L  F  R  G  P  C  K  I  S  I  Y  I  *  F  L  F  P </second_frame>
            <third_frame>   K  W  H  Q  I  L  Q  S  L  Q  L  Q  K  L  L  L  S  *  T  *  R  Y  I  Q  K  G  D  F  T  Q  K  H  L  E  I  T  Q  L  F  S  P  D  L  I  F  H  L  H  :  I  R  L  I  D  L  S  V  H  A  S  T  S  C  Y  L  L  E  V  R  L  I  F  T  G  Y  L  V  Q  K  H  G  I  F  I  W  E  S  Q  S  L :   *  W  S  *  T  K  L  M  A  R  *  S  *  L  A  L  D  P  I  P  S  *  M  I  N  S  C  S  I  Q  Y  L  Q  M  Y  G  L  A  H  F  P  R  R  I  T  T  Y  L  P  I  C  K  *  R  K  H  L  Q  E  M  V  R  N  I  S  L  *  L  D  A  L  V  L  Q  H  S  S  L  K  I  L  N  *  Q  N  V  L  I  L  S  R  V  F  L  P  T  N  P  L  S  L  C  *  P  S  L  I  C  E  R  Y  V  F  N  G  G  S  R  A  *  S  T  G  F  T  *  P  S  S  F  F  A  D  L  V  K  Y  L  Y  I  F  D  S  C  F   </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="C12SLe0032P11.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="70530" stop="70674"/>
                    <exon start="72193" stop="72314"/>
                    <exon start="73021" stop="73347"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>591</number_coding_nucleotides>
                  <number_encoded_amino_acids>197</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KMASNSTEPTASKIVAKLNLKVHPEGGFYSETFRDNSVILSRSHLPSTYKVDRPVSTCIYFLLPSGSASHLHRIPCAETWHFYMGEPITVMELNETDGKVKLTCVGPDPLVDDQFVQYTVPPNVWFGAFPTKDYNISSDMQVTKAPTRDGEKHFSLVGCTCAPAFQFEDFELAKRSDLVSRFPAHESLVSLLAFPDL*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 8 chains have been computed
$ 
$ memory statistics:
$ 4048 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2024 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
$ 0 megabytes was the average size of the backtrace matrix
$ 8 backtrace matrices have been allocated
$ 
$ date finished: 2009-07-24 23:37:26
-->
