<?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="2009-01-03 15:23:07"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09SLm0143I09-nQeog/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09SLm0143I09-nQeog/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-C09SLm0143I09-nQeog/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M815" ref_strand="+" ref_description="SGN-M815 SSR142 [est_by_read_no_qc_info]">
      <seq>aaactttctaaaacattatgttaaaactaataaaaaataagttcacgtctgaaaggagtttagattgaaggttttggtacgaaatgttaaatagagatgatatcttctacacgatagaaaatatattaatataattttatagattctgattcgacactaaacatatatatatatatattaaggtggttgtgaggtagacaactgggattcgaaattatttaaagttgagcatattattattattattattatctcgaacagatgcatagatgaagacttcaaaaagaaaaaataataaacaaagacaagtaacatcatcatatttttttaaataatgaataaagtaagatgagtcatcacttatatatttgtttattaatggcatggccatatatatatatatatattatatatcttgttttggcatttctagacatacagatcttattcacatgagtccacaccgtgtgaaaactctaattccaacaacaattttttgaaattctattgaatttttgtgagtggtagcttntattggtaaaaataattagtgcgatta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0143I09-nQeog/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0143I09.1" temp_strand="+" temp_description="C09SLm0143I09.1  AC225330.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLm0143I09 upload_account_name:spain (1 - 120727)">
        <position start="47849" stop="49007"/>
      </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="48149" g_stop="48707" g_length="559"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="559" r_length="559" r_score="0.995"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLm0143I09.1" gen_strand="+" ref_id="SGN-M815" ref_strand="+">
        <total_alignment_score>0.995</total_alignment_score>
        <cumulative_length_of_scored_exons>559</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLm0143I09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M815" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="48149" e_stop="48707"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAACTTTCTAAAACATTATGTTAAAACTAATAAAAAATAAGTTCACGTCTGAAAGGAGTTTAGATTGAAGGTTTTGGTACGAAATGTTAAATAGAGATGATATCTTCTACACGATAGAAAATATATTAATATAATTTTATAGATTCTGATTCGACACTAAACATATATATATATATATTAAGGTGGTTGTGAGGTAGACAACTGGGATTCGAAATTATTTAAAGTTGAGCATATTATTATTATTATTATTATCTCGAACAGATGCATAGATGAAGACTTCAAAAAGAAAAAATAATAAACAAAGACAAGTAACATCATCATATTTTTTTAAATAATGAATAAAGTAAGATGAGTCATCACTTATATATTTGTTTATTAATGGCATGGCCATATATATATATATATATTATATATCTTGTTTTGGCATTTCTAGACATACAGATCTTATTCACATGAGTCCACACCGTGTGAAAACTCTAATTCCAACAACAATTTTTTGAAATTCTATTGAATTTTTGTGAGTGGTATCTTTAATTGGTAAAAATAATTAGTGCGATTA</genome_strand>
        <mrna_strand>AAACTTTCTAAAACATTATGTTAAAACTAATAAAAAATAAGTTCACGTCTGAAAGGAGTTTAGATTGAAGGTTTTGGTACGAAATGTTAAATAGAGATGATATCTTCTACACGATAGAAAATATATTAATATAATTTTATAGATTCTGATTCGACACTAAACATATATATATATATATTAAGGTGGTTGTGAGGTAGACAACTGGGATTCGAAATTATTTAAAGTTGAGCATATTATTATTATTATTATTATCTCGAACAGATGCATAGATGAAGACTTCAAAAAGAAAAAATAATAAACAAAGACAAGTAACATCATCATATTTTTTTAAATAATGAATAAAGTAAGATGAGTCATCACTTATATATTTGTTTATTAATGGCATGGCCATATATATATATATATATTATATATCTTGTTTTGGCATTTCTAGACATACAGATCTTATTCACATGAGTCCACACCGTGTGAAAACTCTAATTCCAACAACAATTTTTTGAAATTCTATTGAATTTTTGTGAGTGGTAGCTTNTATTGGTAAAAATAATTAGTGCGATTA</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-C09SLm0143I09-nQeog/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M815-2" ref_strand="+" ref_description="SGN-M815-2 SSR142-2 [est_by_read]">
      <seq>aactttctaaaacattatgttaaaactaataaaaaataagttcacgtctgaaaggagtttagattgaaggttttggtacgaaatgttaaatagagatgatatcttctacacgatagaaaatatattaatataattttatagattctgattcgacactaaacatatatatatatatattaaggtggttgtgaggtagacaactgggattcgaaattatttaaagttgagcatattattattattattattatctcgaacagatgcatagatgaagacttcaaaaagaaaaaataataaacaaagacaagtaacatcatcatatttttttaaataatgaataaagtaagatgagtcatcacttatatatttgtttattaatggcatggccatatatatatatatatattatatatcttgttttggcatttctagacatacagatcttattcacatgagtccacaccgtgtgaaaactctaattccaacaacaattttttg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0143I09-nQeog/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0143I09.1" temp_strand="+" temp_description="C09SLm0143I09.1  AC225330.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLm0143I09 upload_account_name:spain (1 - 120727)">
        <position start="47850" stop="48947"/>
      </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="48150" g_stop="48647" g_length="498"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="498" r_length="498" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLm0143I09.1" gen_strand="+" ref_id="SGN-M815-2" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>498</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLm0143I09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M815-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="48150" e_stop="48647"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AACTTTCTAAAACATTATGTTAAAACTAATAAAAAATAAGTTCACGTCTGAAAGGAGTTTAGATTGAAGGTTTTGGTACGAAATGTTAAATAGAGATGATATCTTCTACACGATAGAAAATATATTAATATAATTTTATAGATTCTGATTCGACACTAAACATATATATATATATATTAAGGTGGTTGTGAGGTAGACAACTGGGATTCGAAATTATTTAAAGTTGAGCATATTATTATTATTATTATTATCTCGAACAGATGCATAGATGAAGACTTCAAAAAGAAAAAATAATAAACAAAGACAAGTAACATCATCATATTTTTTTAAATAATGAATAAAGTAAGATGAGTCATCACTTATATATTTGTTTATTAATGGCATGGCCATATATATATATATATATTATATATCTTGTTTTGGCATTTCTAGACATACAGATCTTATTCACATGAGTCCACACCGTGTGAAAACTCTAATTCCAACAACAATTTTTTG</genome_strand>
        <mrna_strand>AACTTTCTAAAACATTATGTTAAAACTAATAAAAAATAAGTTCACGTCTGAAAGGAGTTTAGATTGAAGGTTTTGGTACGAAATGTTAAATAGAGATGATATCTTCTACACGATAGAAAATATATTAATATAATTTTATAGATTCTGATTCGACACTAAACATATATATATATATATTAAGGTGGTTGTGAGGTAGACAACTGGGATTCGAAATTATTTAAAGTTGAGCATATTATTATTATTATTATTATCTCGAACAGATGCATAGATGAAGACTTCAAAAAGAAAAAATAATAAACAAAGACAAGTAACATCATCATATTTTTTTAAATAATGAATAAAGTAAGATGAGTCATCACTTATATATTTGTTTATTAATGGCATGGCCATATATATATATATATATTATATATCTTGTTTTGGCATTTCTAGACATACAGATCTTATTCACATGAGTCCACACCGTGTGAAAACTCTAATTCCAACAACAATTTTTTG</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-C09SLm0143I09-nQeog/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1470" ref_strand="+" ref_description="SGN-M1470 T0556 [cos_markers]">
      <seq>aagttagaagttgtgatcattctatctcactaatacagaaatggcaaccatcactgcttgcaccacaacttcttcggtggcgcgtgccgccctcgtgcaaaggggatctgtatctcgcacctcagttgttcttggattaccatcaatgagcaagggtggaaaagtgaaatgttcaatggaaggaaagggaaagggtgaatcaaagttgggaatgggagaatcattgatggcagcagcagtagcagcaagcgtgtcaagcccagttgcaatggctttggttgatgaaagaatgagcactgaaggaacagggctaccatttggactcagtaacagtcttcttggttggatccttttacgtgtatttggtttgatttggtctctctacactgtttacacttctggacttgatgaagatga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLm0143I09-nQeog/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLm0143I09.1" temp_strand="-" temp_description="C09SLm0143I09.1  AC225330.1 htgs_phase:2 submitted_to_sgn_as:gnl|gbrgsp|C09SLm0143I09 upload_account_name:spain (1 - 120727)">
        <position start="66573" stop="64894"/>
      </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="66273" g_stop="66140" g_length="134"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="134" r_length="134" r_score="0.993"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="66139" i_stop="65477" i_length="663">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="65476" g_stop="65194" g_length="283"/>
          <reference_exon_boundary r_type="cDNA" r_start="135" r_stop="417" r_length="283" r_score="0.982"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLm0143I09.1" gen_strand="-" ref_id="SGN-M1470" ref_strand="+">
        <total_alignment_score>0.986</total_alignment_score>
        <cumulative_length_of_scored_exons>417</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLm0143I09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1470" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="66273" e_stop="66140"/>
          <exon e_start="65476" e_stop="65194"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAGTTAGAAGTTGTGATCATTCTCTCTCACTAATACAGAAATGGCAACCATCACTGCTTGCACCACAACTTCTTCGGTGGCGCGTGCCGCCCTCGTGCAAAGGGGATCTGTATCTCGCACCTCAGTTGTTCTTGGTACGTTCATTTTCTAGTTTAATTTCATAAATTTCGAAGTATGATAGTTTTAGTTTATCGCAAGTTCAATCTCAAGAAGTTGAAAGTAAATTCGTTTCACATGTATAAGCATGTCTATCATTCATCGCTTAGGGTTAATAACAATGTTGAGTTCATACATCGATTTAGAGAGGCATTATTGATCGGTTTCTTTTATATAGTTTTCGATAATTTTCACTTATTTAGGGACTTTTGGACTTAAATTAAGTCCAAAATTCACGAGCATGGGTTCATCGATCTTTACATACGTATAACACACACATTCACCTAAAAGTTACTCTGTTTTATTTCAATTCATGTTATATTTTTATTTTTCAAAATTCAAAGTCTGCAAACATTGATCAATAATTTAAAAAATATATCTTTTTTACATTGAAAGAGAATTGCAAATTATAGTATAAACTTTGAATAGATGAATTTTAATCCATCAGTCAAATTGATTCTTAGAAAACACGAAGATTGAGACAAAATTAGAAAATAGTATATATATCAAAGTCAGAACTAGTTTGAACCTTGTACCTTCTTCAAAGATTAGTCAAATTGATTCTCAAAAATCAAAAAGCGCCACATATATTAGGACAGAGTAAATATTTAAATTTAAATTCTGAATCTGTGTTTATTCAGGATTACCATCAATGAGCAAGGGTGGAAAAGTGAAATGTTCAATGGAAGGAAAGGGAAAGGGTGAATCAAAGTTGGGAATGGGAGAATCATTGATGGCAGCAGCAGTAGCAGCAAGCATGTCAAGCCCAGTAGCAATGGCTTTGGTTGATGAAAGAATGAGCACTGAAGGAACAGGGCTACCATTTGGACTCAGCAACAATCTTCTTGGTTGGATCCTTTTAGGTGTATTTGGTTTGATTTGGTCTCTCTACACTGTTTACACTTCTGGACTTGATGAAGATGA</genome_strand>
        <mrna_strand>AAGTTAGAAGTTGTGATCATTCTATCTCACTAATACAGAAATGGCAACCATCACTGCTTGCACCACAACTTCTTCGGTGGCGCGTGCCGCCCTCGTGCAAAGGGGATCTGTATCTCGCACCTCAGTTGTTCTTG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATTACCATCAATGAGCAAGGGTGGAAAAGTGAAATGTTCAATGGAAGGAAAGGGAAAGGGTGAATCAAAGTTGGGAATGGGAGAATCATTGATGGCAGCAGCAGTAGCAGCAAGCGTGTCAAGCCCAGTTGCAATGGCTTTGGTTGATGAAAGAATGAGCACTGAAGGAACAGGGCTACCATTTGGACTCAGTAACAGTCTTCTTGGTTGGATCCTTTTACGTGTATTTGGTTTGATTTGGTCTCTCTACACTGTTTACACTTCTGGACTTGATGAAGATGA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>3</total_number_ESTs_reported>
    </alignment_module>
  <PGL_module xmlns="http://www.genomethreader.org/GTH_output/PGL_module/">
    <predicted_gene_location>
      <PGL_line PGL_serial="1" PGL_strand="+" PGL_start="48149" PGL_stop="48707"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="48149" e_stop="48707"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.995"/>
        </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="0.995">
            <gDNA_exon_boundary e_start="48149" e_stop="48707" e_length="559"/>
          </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="48149" stop="48707"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M815" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="48150" stop="48647"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M815-2" 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="1" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>AAACTTTCTAAAACATTATGTTAAAACTAATAAAAAATAAGTTCACGTCTGAAAGGAGTTTAGATTGAAGGTTTTGGTACGAAATGTTAAATAGAGATGATATCTTCTACACGATAGAAAATATATTAATATAATTTTATAGATTCTGATTCGACACTAAACATATATATATATATATTAAGGTGGTTGTGAGGTAGACAACTGGGATTCGAAATTATTTAAAGTTGAGCATATTATTATTATTATTATTATCTCGAACAGATGCATAGATGAAGACTTCAAAAAGAAAAAATAATAAACAAAGACAAGTAACATCATCATATTTTTTTAAATAATGAATAAAGTAAGATGAGTCATCACTTATATATTTGTTTATTAATGGCATGGCCATATATATATATATATATTATATATCTTGTTTTGGCATTTCTAGACATACAGATCTTATTCACATGAGTCCACACCGTGTGAAAACTCTAATTCCAACAACAATTTTTTGAAATTCTATTGAATTTTTGTGAGTGGTATCTTTAATTGGTAAAAATAATTAGTGCGATTA</gDNA_template>
            <first_frame> K  L  S  K  T  L  C  *  N  *  *  K  I  S  S  R  L  K  G  V  *  I  E  G  F  G  T  K  C  *  I  E  M  I  S  S  T  R  *  K  I  Y  *  Y  N  F  I  D  S  D  S  T  L  N  I  Y  I  Y  I  L  R  W  L  *  G  R  Q  L  G  F  E  I  I  *  S  *  A  Y  Y  Y  Y  Y  Y  Y  L  E  Q  M  H  R  *  R  L  Q  K  E  K  I  I  N  K  D  K  *  H  H  H  I  F  L  N  N  E  *  S  K  M  S  H  H  L  Y  I  C  L  L  M  A  W  P  Y  I  Y  I  Y  I  I  Y  L  V  L  A  F  L  D  I  Q  I  L  F  T  *  V  H  T  V  *  K  L  *  F  Q  Q  Q  F  F  E  I  L  L  N  F  C  E  W  Y  L  *  L  V  K  I  I  S  A  I  </first_frame>
            <second_frame>  N  F  L  K  H  Y  V  K  T  N  K  K  *  V  H  V  *  K  E  F  R  L  K  V  L  V  R  N  V  K  *  R  *  Y  L  L  H  D  R  K  Y  I  N  I  I  L  *  I  L  I  R  H  *  T  Y  I  Y  I  Y  *  G  G  C  E  V  D  N  W  D  S  K  L  F  K  V  E  H  I  I  I  I  I  I  I  S  N  R  C  I  D  E  D  F  K  K  K  K  *  *  T  K  T  S  N  I  I  I  F  F  *  I  M  N  K  V  R  *  V  I  T  Y  I  F  V  Y  *  W  H  G  H  I  Y  I  Y  I  L  Y  I  L  F  W  H  F  *  T  Y  R  S  Y  S  H  E  S  T  P  C  E  N  S  N  S  N  N  N  F  L  K  F  Y  *  I  F  V  S  G  I  F  N  W  *  K  *  L  V  R  L </second_frame>
            <third_frame>   T  F  *  N  I  M  L  K  L  I  K  N  K  F  T  S  E  R  S  L  D  *  R  F  W  Y  E  M  L  N  R  D  D  I  F  Y  T  I  E  N  I  L  I  *  F  Y  R  F  *  F  D  T  K  H  I  Y  I  Y  I  K  V  V  V  R  *  T  T  G  I  R  N  Y  L  K  L  S  I  L  L  L  L  L  L  S  R  T  D  A  *  M  K  T  S  K  R  K  N  N  K  Q  R  Q  V  T  S  S  Y  F  F  K  *  *  I  K  *  D  E  S  S  L  I  Y  L  F  I  N  G  M  A  I  Y  I  Y  I  Y  Y  I  S  C  F  G  I  S  R  H  T  D  L  I  H  M  S  P  H  R  V  K  T  L  I  P  T  T  I  F  *  N  S  I  E  F  L  *  V  V  S  L  I  G  K  N  N  *  C  D   </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="C09SLm0143I09.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="-" PGL_start="66273" PGL_stop="65194"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="66273" e_stop="66140"/>
            <exon e_start="65476" e_stop="65194"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.999" e_score="0.993"/>
          <exon-only e_score="0.982"/>
        </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="0.993">
            <gDNA_exon_boundary e_start="66273" e_stop="66140" e_length="134"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.999">
            <gDNA_intron_boundary i_start="66139" i_stop="65477" i_length="663"/>
          </intron>
          <exon e_serial="2" e_score="0.982">
            <gDNA_exon_boundary e_start="65476" e_stop="65194" e_length="283"/>
          </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="66273" stop="66140"/>
              <exon start="65476" stop="65194"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1470" 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>AAGTTAGAAGTTGTGATCATTCTCTCTCACTAATACAGAAATGGCAACCATCACTGCTTGCACCACAACTTCTTCGGTGGCGCGTGCCGCCCTCGTGCAAAGGGGATCTGTATCTCGCACCTCAGTTGTTCTTG : GATTACCATCAATGAGCAAGGGTGGAAAAGTGAAATGTTCAATGGAAGGAAAGGGAAAGGGTGAATCAAAGTTGGGAATGGGAGAATCATTGATGGCAGCAGCAGTAGCAGCAAGCATGTCAAGCCCAGTAGCAATGGCTTTGGTTGATGAAAGAATGAGCACTGAAGGAACAGGGCTACCATTTGGACTCAGCAACAATCTTCTTGGTTGGATCCTTTTAGGTGTATTTGGTTTGATTTGGTCTCTCTACACTGTTTACACTTCTGGACTTGATGAAGATGA</gDNA_template>
            <first_frame> K  L  E  V  V  I  I  L  S  H  *  Y  R  N  G  N  H  H  C  L  H  H  N  F  F  G  G  A  C  R  P  R  A  K  G  I  C  I  S  H  L  S  C  S  W :   I  T  I  N  E  Q  G  W  K  S  E  M  F  N  G  R  K  G  K  G  *  I  K  V  G  N  G  R  I  I  D  G  S  S  S  S  S  K  H  V  K  P  S  S  N  G  F  G  *  *  K  N  E  H  *  R  N  R  A  T  I  W  T  Q  Q  Q  S  S  W  L  D  P  F  R  C  I  W  F  D  L  V  S  L  H  C  L  H  F  W  T  *  *  R  * </first_frame>
            <second_frame>  S  *  K  L  *  S  F  S  L  T  N  T  E  M  A  T  I  T  A  C  T  T  T  S  S  V  A  R  A  A  L  V  Q  R  G  S  V  S  R  T  S  V  V  L   : G  L  P  S  M  S  K  G  G  K  V  K  C  S  M  E  G  K  G  K  G  E  S  K  L  G  M  G  E  S  L  M  A  A  A  V  A  A  S  M  S  S  P  V  A  M  A  L  V  D  E  R  M  S  T  E  G  T  G  L  P  F  G  L  S  N  N  L  L  G  W  I  L  L  G  V  F  G  L  I  W  S  L  Y  T  V  Y  T  S  G  L  D  E  D   </second_frame>
            <third_frame>   V  R  S  C  D  H  S  L  S  L  I  Q  K  W  Q  P  S  L  L  A  P  Q  L  L  R  W  R  V  P  P  S  C  K  G  D  L  Y  L  A  P  Q  L  F  L  :  D  Y  H  Q  *  A  R  V  E  K  *  N  V  Q  W  K  E  R  E  R  V  N  Q  S  W  E  W  E  N  H  *  W  Q  Q  Q  *  Q  Q  A  C  Q  A  Q  *  Q  W  L  W  L  M  K  E  *  A  L  K  E  Q  G  Y  H  L  D  S  A  T  I  F  L  V  G  S  F  *  V  Y  L  V  *  F  G  L  S  T  L  F  T  L  L  D  L  M  K  M  </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="C09SLm0143I09.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="66257" stop="66140"/>
                    <exon start="65476" stop="65196"/>
                  </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>SFSLTNTEMATITACTTTSSVARAALVQRGSVSRTSVVLGLPSMSKGGKVKCSMEGKGKGESKLGMGESLMAAAVAASMSSPVAMALVDERMSTEGTGLPFGLSNNLLGWILLGVFGLIWSLYTVYTSGLDED</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:
$ 6360 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 2120 bytes was the average size of a spliced alignment
$ 6736 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3368 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: 2009-01-03 15:23:11
-->
