<?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="2009-12-01 06:10:40"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0203K18-izrUJ/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00HBa0203K18-izrUJ/gth_cdna_fileCXGN::TomatoGenome::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-C00HBa0203K18-izrUJ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U569000" ref_strand="+" ref_description="SGN-U569000 Tomato 200607#2 [7 ESTs aligned] (*GB) gi|157339885|emb|CAO45562.1| (e_value=1e-52) unnamed; (*ATH) AT5G40990.1 (e_value=9e-49) | Symbol: None | GDSL-motif lipase/hydrolase family protein, similar to lipase (Arabidopsis thaliana) GI:1145627; contains Pfam profile PF00657: Lipase/Acylhydrolase with GDSL-like motif | chr5:16436148-16437628 FORWARD | Aliases: MEE6.6, MEE6_6; (*SWP) sp|P40603|APG_BRANA (e_value=4e-22) Anther-specific proline-rich protein APG (Fragment) OS=Brassica napus GN=APG; ">
      <seq>aagtatcaagtttcaaagattatttttccatgggaaatatattctttcatctctgcattttgatatccctagcttctttaaatttcctagttaattgttttgatatagaaaacaaagtgacaacaactgtttttgtgtttggagactccatgtttgatcctggaaacaataattacataacgaatccttcagcttataaagcaaattttgagccatatggaatatcatattttaagcatcccactggcagattttctgatggccgcctcctccctgattttattgcggaatttgcaaatttaccaatgattccatcattttaccaagctctacataaccattctattaatcatggagtgaactttgcttctgctggtgctggttgtctagatgaaacataccgtgaaaaggtgatccccttaaatactcaattaggcaattttaagataataagaaaaaagttgttggcacaactaggggaaaaaggttcaaaggcaatgttatccaatgcagtctacttgttcagcataggcaacaacgattatctacgcctttatgacattccagatataccttcagactcatcttgcttagcttatacaacagagcacgaatacatgaatatggtgatggatagcctcgttacagtcatgatggaaatatacaagttaggtgggagaaaatttgggatccaggatttgttgcctttgggttgtttaccaagatttaggggtcttgctttgct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0203K18-izrUJ/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0203K18.1" temp_strand="-" temp_description="C00HBa0203K18.1  CU927986.7 htgs_phase:3 submitted_to_sgn_as:C00HBa0203K18 sequenced_by:sanger upload_account_name:uk">
        <position start="104731" stop="101789"/>
      </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="104432" g_stop="104148" g_length="285"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="285" r_length="285" r_score="0.996"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="104147" i_stop="104033" i_length="115">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.541" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="104032" g_stop="103908" g_length="125"/>
          <reference_exon_boundary r_type="cDNA" r_start="286" r_stop="410" r_length="125" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="103907" i_stop="102501" i_length="1407">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.916" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="102500" g_stop="102255" g_length="246"/>
          <reference_exon_boundary r_type="cDNA" r_start="411" r_stop="656" r_length="246" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="102254" i_stop="102178" i_length="77">
            <donor d_prob="0.997" d_score="1.00"/>
            <acceptor a_prob="0.970" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="102177" g_stop="102089" g_length="89"/>
          <reference_exon_boundary r_type="cDNA" r_start="657" r_stop="745" r_length="89" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0203K18.1" gen_strand="-" ref_id="SGN-U569000" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>745</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0203K18.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U569000" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="104432" e_stop="104148"/>
          <exon e_start="104032" e_stop="103908"/>
          <exon e_start="102500" e_stop="102255"/>
          <exon e_start="102177" e_stop="102089"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAGTATCAAGTTTCAAAGATTATTTTTCCATGGGAAATATATTCTTTCATCTCTGCATTTTGATATCCCTAGCTTCTTTAAATTTCCTAGTTAATTGTTTTGATATAGAAAACAAAGTGACAACAACTGTTTTTGTGTTTGGAGACTCCATGTTTGATCCTGGAAACAATAATTACATAACGAATCCTTCAGCTTATAAAGCAAATTTTGAGCCATATGGAATATCATATTTTAAGCATCCCACTGGCAGATTTTCTGATGGCCGCCTCCTCCCTGATTTTATTGGTACTTTCACACCTCTATAATTTCTTATTTTGAGTTCAATACAAGTTTTATGTACTAATTTTTTGAATTTAACACAAATTTTATGTACTGGCGGTATTTTTTTATTCGCTGTTAGCGGAATTTGCAAATTTACCAATGATTCCATCATTTTACCAAGCTCTACATAACCATTCTATTAATCATGGAGTGAACTTTGCTTCTGCTGGTGCTGGTTGTCTAGATGAAACATACCGTGAAAAGGTTGGTAAAGCTAAATAGTTCTACTTCTGTAATATAAAATAGAATGTTACAAACTGTTTGTAGTTTATTTCTCCCGGAGACGTAGAGGGTTTGACATGTTTCTCAAATTTGTTTTGATATGAAAGTGACTTATATATAATTTTATTATTTTATAATATATTTAATAAAATTATTAGAATATTATTTTGTGTCAATAAAATCACATGCTCTATATTCTTGCTCAACTTATAATCCCAAAATAAAGCTCTAGATTGAGTGTGCATTTATATGTTAATTGTATTAATCTTTGCTGACTGAATCTTCCGTGATTAATTTTTGAGGAGTCAATTTATCATAATAAATTTCATTAATTGAATTTTAATGTAATTTAAAAGTCAACATGCTGCCATTTCCGTAGATACTATGTTTTGCTCTCTACCCGCTCTAGTTGTAGGATTAATAACTTAACTGCTCCTATTATCATGTTATTGAACCATTCTCCTTCTCGTTATAAGCCAATGAAAATGCTATACGATGATGAATCAAATTTATTATTTTGATTGTCAAGTTTATTTATGTTTTATTAATTTAAATTTATATTTTTTGATAATCAAATTTATTTATATTTCACTAATTATCATGTAAAATTTAGATGCCCCATTTTTTTTAATTTATACAAATGCAAAAACTAAATTACTGGTATAGCTGCAAAAAAAATTAATTTTAAAATTTTCTTTGCACTAAAGAATGAAAAGAAAAATAAAAAAGAAACACAAGTAGTGATAATCAAAGAATTCAAAATAATTATTTTTATCCGAATTTTCCGCTAGAAGGATCATATATATGTATATATATACTCCTATATGAATTTTTAAAAAAATTTAGAGTAAAAAAAAATTAAAACTAATTTTTTTTTACTTTGTTAGATAAAGGGTATATGTGAGCTCATTTTGTAACGGTAAGGGTATATGTGAGTCATTTGTAATCGTAAGGATATATATGAGTAACTTTTATAACAATAGGTATGTCAATTCTAAATGACAAATTTAAAGGCATAATACTCTTTTCCCTTTCTACGTGATCACTTAGCTAATTATTGAGTATCTATTGTATTTTACGTAACATTGTTTTTGTGATCTAATATAATTCTTAGATATTTGTGTGGCAAATCTTATTTTATCAATAGTAAAAGAAATTTTTTAAGAATATAATTATTTCTAATTATAATAAGATGACACTTTTTTTTGAAACAACTAAAAAAAAATGTCTCCTGAAATGAAACAAAGAAAATATATCAAAAAATCACTTTTTCTTATAGAAAAATATTGGATTAAGAAGTAAAGTAATTAGCTGGGTGATCATTTTAGATACAACTTTTGCCAAATCAACAAATATTGTTTTCTCTTACAATCTTAATTGACCTTACAGGTGATCCCCTTAAATACTCAATTAGGCAATTTTAAGATAATAAGAAAAAAGTTGTTGGCACAACTAGGGGAAAAAGGTTCAAAGGCAATGTTATCCAATGCAGTCTACTTGTTCAGCATAGGCAACAACGATTATCTACGCCTTTATGACATTCCAGATATACCTTCAGACTCATCTTGCTTAGCTTATACAACAGAGCACGAATACATGAATATGGTGATGGATAGCCTCGTTACAGTCATGATGGTAACCAAATACATATTTTTAATTCCTACATTTAACATGTTTATATAAGTAATTTGTTGCGTTTTTTTTAAAACTAGGAAATATACAAGTTAGGTGGGAGAAAATTTGGGATCCAGGATTTGTTGCCTTTGGGTTGTTTACCAAGATTTAGGGGTCTTGCTTTGCT</genome_strand>
        <mrna_strand>AAGTATCAAGTTTCAAAGATTATTTTTCCATGGGAAATATATTCTTTCATCTCTGCATTTTGATATCCCTAGCTTCTTTAAATTTCCTAGTTAATTGTTTTGATATAGAAAACAAAGTGACAACAACTGTTTTTGTGTTTGGAGACTCCATGTTTGATCCTGGAAACAATAATTACATAACGAATCCTTCAGCTTATAAAGCAAATTTTGAGCCATATGGAATATCATATTTTAAGCATCCCACTGGCAGATTTTCTGATGGCCGCCTCCTCCCTGATTTTATTG...................................................................................................................CGGAATTTGCAAATTTACCAATGATTCCATCATTTTACCAAGCTCTACATAACCATTCTATTAATCATGGAGTGAACTTTGCTTCTGCTGGTGCTGGTTGTCTAGATGAAACATACCGTGAAAAG...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGATCCCCTTAAATACTCAATTAGGCAATTTTAAGATAATAAGAAAAAAGTTGTTGGCACAACTAGGGGAAAAAGGTTCAAAGGCAATGTTATCCAATGCAGTCTACTTGTTCAGCATAGGCAACAACGATTATCTACGCCTTTATGACATTCCAGATATACCTTCAGACTCATCTTGCTTAGCTTATACAACAGAGCACGAATACATGAATATGGTGATGGATAGCCTCGTTACAGTCATGATG.............................................................................GAAATATACAAGTTAGGTGGGAGAAAATTTGGGATCCAGGATTTGTTGCCTTTGGGTTGTTTACCAAGATTTAGGGGTCTTGCTTTGCT</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-C00HBa0203K18-izrUJ/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U591120" ref_strand="+" ref_description="SGN-U591120 Tomato 200607#2 [1 ESTs aligned] ">
      <seq>cttattgtagatgaccaattttttcttcgaatacgaaattaaattacaatacacacaaaaaaaatatttgaattttttttatttaaactaaggaatgaaagaaaaaaacaaaataagaataagaaactcaaattattataataaaagaagtcaaaaaataatttttgtatgaaaaaattaaaatataccttgaactttgatagaagaatcatatatatccctaaatattttttttaaaaaaaaattagaagtaacaaatataaatttaaaactaattttttaactttcgttaaatgaagggtatatgtgagccattttctaacggcaggggtatatgtgagccgtttgtataacgataagggcatatatgaaccacttttattacgagggatatatcagctctaaatgacaaagttgagaggtatatcagacccttttccctattttttaaaatttcatac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0203K18-izrUJ/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00HBa0203K18.1" temp_strand="+" temp_description="C00HBa0203K18.1  CU927986.7 htgs_phase:3 submitted_to_sgn_as:C00HBa0203K18 sequenced_by:sanger upload_account_name:uk">
        <position start="116011" stop="117072"/>
      </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="116311" g_stop="116772" g_length="462"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="461" r_length="461" r_score="0.903"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0203K18.1" gen_strand="+" ref_id="SGN-U591120" ref_strand="+">
        <total_alignment_score>0.903</total_alignment_score>
        <cumulative_length_of_scored_exons>462</cumulative_length_of_scored_exons>
        <coverage percentage="1.002" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0203K18.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U591120" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="116311" e_stop="116772"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTTATTATAGATGACCAAATTTTTTCTTCGAGTACGAAATTAAATTACAATACACACAAAAAATA-GTTTAATTTTTTTTTCTTTAAACTAAGGAATGAAAGAAAAAAACAAAATAAGAATAAGAAACTCAAATAATTATAATAGAAGAAGTCAAAAAATAATTTATGTATGAAAAAAATTAAAATATACCTTGAACTTTGATAAAAGAATTATATATACCCCTAAATA--ATTTTTAAAAAAAAATTAGAAGTAACAAAAATAACTTTAAAACTAATTTTTTAATTTCCGTTAAATAAAGGGTATATGTGAGCCATTTTGTAACGGCAGGGGTATATGTGAGTCGTTTGTATAATGGTAAGGGCATATATGAGCCACTTTGATAACGAGGGGTATATCAGCTCTAAATGACAAAGTTGAGGGGTATATCAGACCTTTTTCCCATATTTTTATACTATCTCCAAA</genome_strand>
        <mrna_strand>CTTATTGTAGATGACC-AATTTTTTCTTCGAATACGAAATTAAATTACAATACACACAAAAAAAATATTTGAATTTTTTTTATTTAAACTAAGGAATGAAAGAAAAAAACAAAATAAGAATAAGAAACTCAAATTATTATAATAAAAGAAGTCAAAAAATAATTTTTGTATG-AAAAAATTAAAATATACCTTGAACTTTGATAGAAGAATCATATATATCCCTAAATATTTTTTTTAAAAAAAAATTAGAAGTAACAAATATAAATTTAAAACTAATTTTTTAACTTTCGTTAAATGAAGGGTATATGTGAGCCATTTTCTAACGGCAGGGGTATATGTGAGCCGTTTGTATAACGATAAGGGCATATATGAACCACTTTTATTACGAGGGATATATCAGCTCTAAATGACAAAGTTGAGAGGTATATCAGACCCTTTTCCC-TATTTTT-TAAAATTTCATAC</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="104432" PGL_stop="102089"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="104432" e_stop="104148"/>
            <exon e_start="104032" e_stop="103908"/>
            <exon e_start="102500" e_stop="102255"/>
            <exon e_start="102177" e_stop="102089"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.541" e_score="0.996"/>
          <exon-intron don_prob="0.999" acc_prob="0.916" e_score="1.000"/>
          <exon-intron don_prob="0.997" acc_prob="0.970" 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="0.996">
            <gDNA_exon_boundary e_start="104432" e_stop="104148" e_length="285"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.541">
            <gDNA_intron_boundary i_start="104147" i_stop="104033" i_length="115"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="104032" e_stop="103908" e_length="125"/>
          </exon>
          <intron i_serial="2" don_prob="0.999" acc_prob="0.916">
            <gDNA_intron_boundary i_start="103907" i_stop="102501" i_length="1407"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="102500" e_stop="102255" e_length="246"/>
          </exon>
          <intron i_serial="3" don_prob="0.997" acc_prob="0.970">
            <gDNA_intron_boundary i_start="102254" i_stop="102178" i_length="77"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="102177" e_stop="102089" e_length="89"/>
          </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="104432" stop="104148"/>
              <exon start="104032" stop="103908"/>
              <exon start="102500" stop="102255"/>
              <exon start="102177" stop="102089"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U569000" 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>GAGTATCAAGTTTCAAAGATTATTTTTCCATGGGAAATATATTCTTTCATCTCTGCATTTTGATATCCCTAGCTTCTTTAAATTTCCTAGTTAATTGTTTTGATATAGAAAACAAAGTGACAACAACTGTTTTTGTGTTTGGAGACTCCATGTTTGATCCTGGAAACAATAATTACATAACGAATCCTTCAGCTTATAAAGCAAATTTTGAGCCATATGGAATATCATATTTTAAGCATCCCACTGGCAGATTTTCTGATGGCCGCCTCCTCCCTGATTTTATTG : CGGAATTTGCAAATTTACCAATGATTCCATCATTTTACCAAGCTCTACATAACCATTCTATTAATCATGGAGTGAACTTTGCTTCTGCTGGTGCTGGTTGTCTAGATGAAACATACCGTGAAAAG : GTGATCCCCTTAAATACTCAATTAGGCAATTTTAAGATAATAAGAAAAAAGTTGTTGGCACAACTAGGGGAAAAAGGTTCAAAGGCAATGTTATCCAATGCAGTCTACTTGTTCAGCATAGGCAACAACGATTATCTACGCCTTTATGACATTCCAGATATACCTTCAGACTCATCTTGCTTAGCTTATACAACAGAGCACGAATACATGAATATGGTGATGGATAGCCTCGTTACAGTCATGATG : GAAATATACAAGTTAGGTGGGAGAAAATTTGGGATCCAGGATTTGTTGCCTTTGGGTTGTTTACCAAGATTTAGGGGTCTTGCTTTGCT</gDNA_template>
            <first_frame> E  Y  Q  V  S  K  I  I  F  P  W  E  I  Y  S  F  I  S  A  F  *  Y  P  *  L  L  *  I  S  *  L  I  V  L  I  *  K  T  K  *  Q  Q  L  F  L  C  L  E  T  P  C  L  I  L  E  T  I  I  T  *  R  I  L  Q  L  I  K  Q  I  L  S  H  M  E  Y  H  I  L  S  I  P  L  A  D  F  L  M  A  A  S  S  L  I  L  L  :  R  N  L  Q  I  Y  Q  *  F  H  H  F  T  K  L  Y  I  T  I  L  L  I  M  E  *  T  L  L  L  L  V  L  V  V  *  M  K  H  T  V  K  R :   *  S  P  *  I  L  N  *  A  I  L  R  *  *  E  K  S  C  W  H  N  *  G  K  K  V  Q  R  Q  C  Y  P  M  Q  S  T  C  S  A  *  A  T  T  I  I  Y  A  F  M  T  F  Q  I  Y  L  Q  T  H  L  A  *  L  I  Q  Q  S  T  N  T  *  I  W  *  W  I  A  S  L  Q  S  *  W :   K  Y  T  S  *  V  G  E  N  L  G  S  R  I  C  C  L  W  V  V  Y  Q  D  L  G  V  L  L  C  </first_frame>
            <second_frame>  S  I  K  F  Q  R  L  F  F  H  G  K  Y  I  L  S  S  L  H  F  D  I  P  S  F  F  K  F  P  S  *  L  F  *  Y  R  K  Q  S  D  N  N  C  F  C  V  W  R  L  H  V  *  S  W  K  Q  *  L  H  N  E  S  F  S  L  *  S  K  F  *  A  I  W  N  I  I  F  *  A  S  H  W  Q  I  F  *  W  P  P  P  P  *  F  Y  C :   G  I  C  K  F  T  N  D  S  I  I  L  P  S  S  T  *  P  F  Y  *  S  W  S  E  L  C  F  C  W  C  W  L  S  R  *  N  I  P  *  K   : G  D  P  L  K  Y  S  I  R  Q  F  *  D  N  K  K  K  V  V  G  T  T  R  G  K  R  F  K  G  N  V  I  Q  C  S  L  L  V  Q  H  R  Q  Q  R  L  S  T  P  L  *  H  S  R  Y  T  F  R  L  I  L  L  S  L  Y  N  R  A  R  I  H  E  Y  G  D  G  *  P  R  Y  S  H  D   : G  N  I  Q  V  R  W  E  K  I  W  D  P  G  F  V  A  F  G  L  F  T  K  I  *  G  S  C  F  A </second_frame>
            <third_frame>   V  S  S  F  K  D  Y  F  S  M  G  N  I  F  F  H  L  C  I  L  I  S  L  A  S  L  N  F  L  V  N  C  F  D  I  E  N  K  V  T  T  T  V  F  V  F  G  D  S  M  F  D  P  G  N  N  N  Y  I  T  N  P  S  A  Y  K  A  N  F  E  P  Y  G  I  S  Y  F  K  H  P  T  G  R  F  S  D  G  R  L  L  P  D  F  I   : A  E  F  A  N  L  P  M  I  P  S  F  Y  Q  A  L  H  N  H  S  I  N  H  G  V  N  F  A  S  A  G  A  G  C  L  D  E  T  Y  R  E  K  :  V  I  P  L  N  T  Q  L  G  N  F  K  I  I  R  K  K  L  L  A  Q  L  G  E  K  G  S  K  A  M  L  S  N  A  V  Y  L  F  S  I  G  N  N  D  Y  L  R  L  Y  D  I  P  D  I  P  S  D  S  S  C  L  A  Y  T  T  E  H  E  Y  M  N  M  V  M  D  S  L  V  T  V  M  M  :  E  I  Y  K  L  G  G  R  K  F  G  I  Q  D  L  L  P  L  G  C  L  P  R  F  R  G  L  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="C00HBa0203K18.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="104430" stop="104148"/>
                    <exon start="104032" stop="103908"/>
                    <exon start="102500" stop="102255"/>
                    <exon start="102177" stop="102091"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>741</number_coding_nucleotides>
                  <number_encoded_amino_acids>247</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VSSFKDYFSMGNIFFHLCILISLASLNFLVNCFDIENKVTTTVFVFGDSMFDPGNNNYITNPSAYKANFEPYGISYFKHPTGRFSDGRLLPDFIAEFANLPMIPSFYQALHNHSINHGVNFASAGAGCLDETYREKVIPLNTQLGNFKIIRKKLLAQLGEKGSKAMLSNAVYLFSIGNNDYLRLYDIPDIPSDSSCLAYTTEHEYMNMVMDSLVTVMMEIYKLGGRKFGIQDLLPLGCLPRFRGLAL</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="116311" PGL_stop="116772"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="116311" e_stop="116772"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.903"/>
        </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="0.903">
            <gDNA_exon_boundary e_start="116311" e_stop="116772" e_length="462"/>
          </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="116311" stop="116772"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U591120" 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>CTTATTATAGATGACCAAATTTTTTCTTCGAGTACGAAATTAAATTACAATACACACAAAAAATAGTTTAATTTTTTTTTCTTTAAACTAAGGAATGAAAGAAAAAAACAAAATAAGAATAAGAAACTCAAATAATTATAATAGAAGAAGTCAAAAAATAATTTATGTATGAAAAAAATTAAAATATACCTTGAACTTTGATAAAAGAATTATATATACCCCTAAATAATTTTTAAAAAAAAATTAGAAGTAACAAAAATAACTTTAAAACTAATTTTTTAATTTCCGTTAAATAAAGGGTATATGTGAGCCATTTTGTAACGGCAGGGGTATATGTGAGTCGTTTGTATAATGGTAAGGGCATATATGAGCCACTTTGATAACGAGGGGTATATCAGCTCTAAATGACAAAGTTGAGGGGTATATCAGACCTTTTTCCCATATTTTTATACTATCTCCAAA</gDNA_template>
            <first_frame> L  I  I  D  D  Q  I  F  S  S  S  T  K  L  N  Y  N  T  H  K  K  *  F  N  F  F  F  F  K  L  R  N  E  R  K  K  Q  N  K  N  K  K  L  K  *  L  *  *  K  K  S  K  N  N  L  C  M  K  K  I  K  I  Y  L  E  L  *  *  K  N  Y  I  Y  P  *  I  I  F  K  K  K  L  E  V  T  K  I  T  L  K  L  I  F  *  F  P  L  N  K  G  Y  M  *  A  I  L  *  R  Q  G  Y  M  *  V  V  C  I  M  V  R  A  Y  M  S  H  F  D  N  E  G  Y  I  S  S  K  *  Q  S  *  G  V  Y  Q  T  F  F  P  Y  F  Y  T  I  S  K </first_frame>
            <second_frame>  L  L  *  M  T  K  F  F  L  R  V  R  N  *  I  T  I  H  T  K  N  S  L  I  F  F  S  L  N  *  G  M  K  E  K  N  K  I  R  I  R  N  S  N  N  Y  N  R  R  S  Q  K  I  I  Y  V  *  K  K  L  K  Y  T  L  N  F  D  K  R  I  I  Y  T  P  K  *  F  L  K  K  N  *  K  *  Q  K  *  L  *  N  *  F  F  N  F  R  *  I  K  G  I  C  E  P  F  C  N  G  R  G  I  C  E  S  F  V  *  W  *  G  H  I  *  A  T  L  I  T  R  G  I  S  A  L  N  D  K  V  E  G  Y  I  R  P  F  S  H  I  F  I  L  S  P   </second_frame>
            <third_frame>   Y  Y  R  *  P  N  F  F  F  E  Y  E  I  K  L  Q  Y  T  Q  K  I  V  *  F  F  F  L  *  T  K  E  *  K  K  K  T  K  *  E  *  E  T  Q  I  I  I  I  E  E  V  K  K  *  F  M  Y  E  K  N  *  N  I  P  *  T  L  I  K  E  L  Y  I  P  L  N  N  F  *  K  K  I  R  S  N  K  N  N  F  K  T  N  F  L  I  S  V  K  *  R  V  Y  V  S  H  F  V  T  A  G  V  Y  V  S  R  L  Y  N  G  K  G  I  Y  E  P  L  *  *  R  G  V  Y  Q  L  *  M  T  K  L  R  G  I  S  D  L  F  P  I  F  L  Y  Y  L  Q  </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="C00HBa0203K18.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 66 chains have been computed
$ 
$ memory statistics:
$ 4576 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2288 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
$ 76 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 06:11:13
-->
