<?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="2008-03-07 09:31:23"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12SLm0103K08-CKkT8/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-4sU2W2/sgn_marker_seqs" 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/cxgn-bacpublish-resources-4sU2W2/sgn_marker_seqs" ref_id="SGN-M1804" ref_strand="+" ref_description="SGN-M1804 T1159 [cos_markers]">
      <seq>taataagaaaaaactttcacttgaactgccaagactcggtttttttgcgggaaggcccttctagggttccgacccttttgttcgaaatttcttcgtttgtactgaaccgcttgcagaatcaaatcctgttccacaagatcctatatcagctatacatcctccttgcatttatgccggaggggtccagaaggctaaaaggtgggggagaaagaagcctaacctcttatccacctggacacataaagaattctcggcgtccagagagatttgagactccctacgtaactcagtgagtgctttctaagaagggcttggcagaagattatatacataacaagattaaggatgagaagattgaaaactccacacaaaataacctgcccttactgtgctactcactgctacttataacaaactcacgctcattacactgnttccctgcaccacttgtcatgttcttttcatcgggcttcaatacaaaatctgccaaccttttatagggaatactcacgcgcttgctccttctaggctgagt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12SLm0103K08-CKkT8/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12SLm0103K08.1" temp_strand="+" temp_description="C12SLm0103K08.1  AC217334.1 htgs_phase:1 submitted_to_sgn_as:C12SLm0103K08 upload_account_name:italy *** WORKING DRAFT SEQUENCE ***">
        <position start="1706" stop="2840"/>
      </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="2006" g_stop="2540" g_length="535"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="535" r_length="535" r_score="0.970"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12SLm0103K08.1" gen_strand="+" ref_id="SGN-M1804" ref_strand="+">
        <total_alignment_score>0.970</total_alignment_score>
        <cumulative_length_of_scored_exons>535</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12SLm0103K08.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1804" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="2006" e_stop="2540"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TAATAAGAAAAAACTTTCACTTGAACTGCCAAGACTCGGTTTTTTTGCGGGAAGGCCCTTCTAGGGTTCCGACCCTTTTGTTCGAAATTTCTTCGTTTGTACTGAACCGCTTGCAGAATCAAATCCTGTTCCACAAGATCCTATATCAGCTATACATCCTCCTTGCATTTATGCCGGAGGGGTCCAGAAGGCTAAAAGGTGGGGGAGAAGGAAGCCGAACCTCTAATCGACCTGGACACATAAAGAATTCTCGGCGTCGAGAGAGATTTGAGATTCCGTAAGTAACTCAGTGAGTGCTTTCTAAGAAGGGCTTGGAAGAAGATTAGATACAGAAGAAGATAAAGGATGAGAAGATAGAAAACTCCACACAAAATAACCTGCCCTTACTGTGCTACTCACTGCTACTTATAACAAACTCACGCTCATTACACTGTTTCCCTGCACCACTTGTCATGTTCTTTTCATCGGGCTTCAATACAAAATCTGCCAACCTTTTAGAGGGAATACTCACGCGCTTGCTCCTTCTAGGCTGAGT</genome_strand>
        <mrna_strand>TAATAAGAAAAAACTTTCACTTGAACTGCCAAGACTCGGTTTTTTTGCGGGAAGGCCCTTCTAGGGTTCCGACCCTTTTGTTCGAAATTTCTTCGTTTGTACTGAACCGCTTGCAGAATCAAATCCTGTTCCACAAGATCCTATATCAGCTATACATCCTCCTTGCATTTATGCCGGAGGGGTCCAGAAGGCTAAAAGGTGGGGGAGAAAGAAGCCTAACCTCTTATCCACCTGGACACATAAAGAATTCTCGGCGTCCAGAGAGATTTGAGACTCCCTACGTAACTCAGTGAGTGCTTTCTAAGAAGGGCTTGGCAGAAGATTATATACATAACAAGATTAAGGATGAGAAGATTGAAAACTCCACACAAAATAACCTGCCCTTACTGTGCTACTCACTGCTACTTATAACAAACTCACGCTCATTACACTGNTTCCCTGCACCACTTGTCATGTTCTTTTCATCGGGCTTCAATACAAAATCTGCCAACCTTTTATAGGGAATACTCACGCGCTTGCTCCTTCTAGGCTGAGT</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/cxgn-bacpublish-resources-4sU2W2/sgn_marker_seqs" ref_id="SGN-M259-F" ref_strand="+" ref_description="SGN-M259-F TG367-F [rflp_markers_forward]">
      <seq>ctgcgctttcagtgaaaactatacgcatcagttctgctattttggccgcacagagtccattcttttacaaggctaggagtttttaatgctctgtttttgatgaattagaaagtcttgattgcttgttttttgacgtcttcttgttttcttcatagctattctccaatggcatgagagagtcagagtcagagaagcagcttgttactgtacaaatctatgcctcgggttagtattaagattttttagttgtagtttggcatgttctcatttcattgtattgtcctttccgttactcctattacacagactagccacctcttgtgcacttgatttgacatttcaataacaagttttagatgtttaggatgtgcaattagagagcaatgtgtatcaatcactaattgaaaattcagttttttcggctgtttgaattcatagaattaaggggattcttgtacttccatcagatggatgtttaagaaagaagtatttttgaccaataagtt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12SLm0103K08-CKkT8/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12SLm0103K08.1" temp_strand="+" temp_description="C12SLm0103K08.1  AC217334.1 htgs_phase:1 submitted_to_sgn_as:C12SLm0103K08 upload_account_name:italy *** WORKING DRAFT SEQUENCE ***">
        <position start="76701" stop="77806"/>
      </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="77001" g_stop="77506" g_length="506"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="506" r_length="506" r_score="0.996"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12SLm0103K08.1" gen_strand="+" ref_id="SGN-M259-F" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>506</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12SLm0103K08.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M259-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="77001" e_stop="77506"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTGCGCTTTCAGTGAAAACTATACGCATCAGTTCTGCTATTTTGGCCGCACAGAGTCCATTCTTTTACAAGGCTAGGAGTTTTTAATGCTCTGTTTTTGATGAATTAGAAAGTCTTGATTGCTTGTTTTTTGACGTCTTCTTGTTTTCTTCATAGCTATTCTCCAATGGCATGAGAGAGTCAGAGTCAGAGAAGCAGCTTGTTACTGTACAAATCTATGCCTCGGGTTAGTATTAAGATTTTTTAGTTGTAGTTTGGCATGTTCTCATTTCATTGTATTGTCCTTTCCGTTACTCCTATTACACAGACTAGCCACCTCTTGTGCACTTGATTTGACATTTCAATAACAAGTTTTAGATGTTTAGGATGTGCAATTAGAGAGCAATGTGTATCAATCACTAATTGAAAATTCAGTTTTTTCGGCTGTTTGAATTCATAGAATTAAGGGGATTCTTGTACTTCCATCAGATGGTTGTTTAAGAAAGAAGTATTTTTGACAAATAAGTT</genome_strand>
        <mrna_strand>CTGCGCTTTCAGTGAAAACTATACGCATCAGTTCTGCTATTTTGGCCGCACAGAGTCCATTCTTTTACAAGGCTAGGAGTTTTTAATGCTCTGTTTTTGATGAATTAGAAAGTCTTGATTGCTTGTTTTTTGACGTCTTCTTGTTTTCTTCATAGCTATTCTCCAATGGCATGAGAGAGTCAGAGTCAGAGAAGCAGCTTGTTACTGTACAAATCTATGCCTCGGGTTAGTATTAAGATTTTTTAGTTGTAGTTTGGCATGTTCTCATTTCATTGTATTGTCCTTTCCGTTACTCCTATTACACAGACTAGCCACCTCTTGTGCACTTGATTTGACATTTCAATAACAAGTTTTAGATGTTTAGGATGTGCAATTAGAGAGCAATGTGTATCAATCACTAATTGAAAATTCAGTTTTTTCGGCTGTTTGAATTCATAGAATTAAGGGGATTCTTGTACTTCCATCAGATGGATGTTTAAGAAAGAAGTATTTTTGACCAATAAGTT</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/cxgn-bacpublish-resources-4sU2W2/sgn_marker_seqs" ref_id="SGN-M259-R" ref_strand="+" ref_description="SGN-M259-R TG367-R [rflp_markers_reverse]">
      <seq>ctcactatagggagacagcttgcatgcctgcagtgtctcatgcatgatgcaacctcaaatttgtcagcagccataagcacatcaagcatagcagtagctggtatcgtagacaaagtattgctatacatgaattgtagtaactttacgaaggcagcttcttctgcgagaaaaagagataaagaaaggtggatgagaaaaaaagaaaatttgtgaacacaaattaaaggaactatatgttcactagttaaagtaactatctaagaactcttctttaaatatgcttagaagcaaaacgagcagtactagcacttggaacatgttattaaccttgcaaacatatgaatagacaatcaatgtttcacacaaatgtttcggaaagagacacaatttttgttctggtgtctaatccttctattattcatcaagatagataaagtactggatatttagaatgatgcttttctatatttgaagacttcttattacttcttaacatttctacttagccatgtgaacacgaggtcatgagttcaagctatgaaaacagcctcttgcaaaaatatagggta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12SLm0103K08-CKkT8/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12SLm0103K08.1" temp_strand="-" temp_description="C12SLm0103K08.1  AC217334.1 htgs_phase:1 submitted_to_sgn_as:C12SLm0103K08 upload_account_name:italy *** WORKING DRAFT SEQUENCE ***">
        <position start="78526" stop="77381"/>
      </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="78224" g_stop="77681" g_length="544"/>
          <reference_exon_boundary r_type="cDNA" r_start="26" r_stop="569" r_length="544" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12SLm0103K08.1" gen_strand="-" ref_id="SGN-M259-R" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>544</cumulative_length_of_scored_exons>
        <coverage percentage="0.956" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12SLm0103K08.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M259-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="78224" e_stop="77681"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GGCTGCAGTGTCTCATGCATGATGCAACCTCAAATTTGTCAGCAGCCATAAGCACATCAAGCATAGCAGTAGCTGGTATCGTAGACAAAGTATTGCTATACATGAATTGTAGTAACTTTACGAAGGCAGCTTCTTCTGCGAGAAAAAGAGATAAAGAAAGGTGGATGAGAAAAAAAGAAAATTTGTGAACACAAATTAAAGGAACTATATGTTCACTAGTTAAAGTAACTATCTAAGAACTCTTCTTTAAATATGCTTAGAAGCAAAACGAGCAGTACTAGCACTTGGAACATGTTATTAACCTTGCAAACATATGAATAGACAATCAATGTTTCACACAAATGTTTCGGAAAGAGACACAATTTTTGTTCTGGTGTCTAATCCTTCTATTATTCATCAAGATAGATAAAGTACTGGATATTTAGAATGATGCTTTTCTATATTTGAAGACTTCTTATTACTTCTTAACATTTCTACTTAGCCATGTGAACACGAGGTCATGAGTTCAAGCTATGAAAACAGCCTCTTGCAAAAATATAGGGTA</genome_strand>
        <mrna_strand>GCCTGCAGTGTCTCATGCATGATGCAACCTCAAATTTGTCAGCAGCCATAAGCACATCAAGCATAGCAGTAGCTGGTATCGTAGACAAAGTATTGCTATACATGAATTGTAGTAACTTTACGAAGGCAGCTTCTTCTGCGAGAAAAAGAGATAAAGAAAGGTGGATGAGAAAAAAAGAAAATTTGTGAACACAAATTAAAGGAACTATATGTTCACTAGTTAAAGTAACTATCTAAGAACTCTTCTTTAAATATGCTTAGAAGCAAAACGAGCAGTACTAGCACTTGGAACATGTTATTAACCTTGCAAACATATGAATAGACAATCAATGTTTCACACAAATGTTTCGGAAAGAGACACAATTTTTGTTCTGGTGTCTAATCCTTCTATTATTCATCAAGATAGATAAAGTACTGGATATTTAGAATGATGCTTTTCTATATTTGAAGACTTCTTATTACTTCTTAACATTTCTACTTAGCCATGTGAACACGAGGTCATGAGTTCAAGCTATGAAAACAGCCTCTTGCAAAAATATAGGGTA</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="2006" PGL_stop="2540"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="2006" e_stop="2540"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.970"/>
        </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="0.970">
            <gDNA_exon_boundary e_start="2006" e_stop="2540" e_length="535"/>
          </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="2006" stop="2540"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1804" 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>TAATAAGAAAAAACTTTCACTTGAACTGCCAAGACTCGGTTTTTTTGCGGGAAGGCCCTTCTAGGGTTCCGACCCTTTTGTTCGAAATTTCTTCGTTTGTACTGAACCGCTTGCAGAATCAAATCCTGTTCCACAAGATCCTATATCAGCTATACATCCTCCTTGCATTTATGCCGGAGGGGTCCAGAAGGCTAAAAGGTGGGGGAGAAGGAAGCCGAACCTCTAATCGACCTGGACACATAAAGAATTCTCGGCGTCGAGAGAGATTTGAGATTCCGTAAGTAACTCAGTGAGTGCTTTCTAAGAAGGGCTTGGAAGAAGATTAGATACAGAAGAAGATAAAGGATGAGAAGATAGAAAACTCCACACAAAATAACCTGCCCTTACTGTGCTACTCACTGCTACTTATAACAAACTCACGCTCATTACACTGTTTCCCTGCACCACTTGTCATGTTCTTTTCATCGGGCTTCAATACAAAATCTGCCAACCTTTTAGAGGGAATACTCACGCGCTTGCTCCTTCTAGGCTGAGT</gDNA_template>
            <first_frame> *  *  E  K  T  F  T  *  T  A  K  T  R  F  F  C  G  K  A  L  L  G  F  R  P  F  C  S  K  F  L  R  L  Y  *  T  A  C  R  I  K  S  C  S  T  R  S  Y  I  S  Y  T  S  S  L  H  L  C  R  R  G  P  E  G  *  K  V  G  E  K  E  A  E  P  L  I  D  L  D  T  *  R  I  L  G  V  E  R  D  L  R  F  R  K  *  L  S  E  C  F  L  R  R  A  W  K  K  I  R  Y  R  R  R  *  R  M  R  R  *  K  T  P  H  K  I  T  C  P  Y  C  A  T  H  C  Y  L  *  Q  T  H  A  H  Y  T  V  S  L  H  H  L  S  C  S  F  H  R  A  S  I  Q  N  L  P  T  F  *  R  E  Y  S  R  A  C  S  F  *  A  E  </first_frame>
            <second_frame>  N  K  K  K  L  S  L  E  L  P  R  L  G  F  F  A  G  R  P  F  *  G  S  D  P  F  V  R  N  F  F  V  C  T  E  P  L  A  E  S  N  P  V  P  Q  D  P  I  S  A  I  H  P  P  C  I  Y  A  G  G  V  Q  K  A  K  R  W  G  R  R  K  P  N  L  *  S  T  W  T  H  K  E  F  S  A  S  R  E  I  *  D  S  V  S  N  S  V  S  A  F  *  E  G  L  G  R  R  L  D  T  E  E  D  K  G  *  E  D  R  K  L  H  T  K  *  P  A  L  T  V  L  L  T  A  T  Y  N  K  L  T  L  I  T  L  F  P  C  T  T  C  H  V  L  F  I  G  L  Q  Y  K  I  C  Q  P  F  R  G  N  T  H  A  L  A  P  S  R  L  S </second_frame>
            <third_frame>   I  R  K  N  F  H  L  N  C  Q  D  S  V  F  L  R  E  G  P  S  R  V  P  T  L  L  F  E  I  S  S  F  V  L  N  R  L  Q  N  Q  I  L  F  H  K  I  L  Y  Q  L  Y  I  L  L  A  F  M  P  E  G  S  R  R  L  K  G  G  G  E  G  S  R  T  S  N  R  P  G  H  I  K  N  S  R  R  R  E  R  F  E  I  P  *  V  T  Q  *  V  L  S  K  K  G  L  E  E  D  *  I  Q  K  K  I  K  D  E  K  I  E  N  S  T  Q  N  N  L  P  L  L  C  Y  S  L  L  L  I  T  N  S  R  S  L  H  C  F  P  A  P  L  V  M  F  F  S  S  G  F  N  T  K  S  A  N  L  L  E  G  I  L  T  R  L  L  L  L  G  *   </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="C12SLm0103K08.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="2008" stop="2286"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>276</number_coding_nucleotides>
                  <number_encoded_amino_acids>92</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IRKNFHLNCQDSVFLREGPSRVPTLLFEISSFVLNRLQNQILFHKILYQLYILLAFMPEGSRRLKGGGEGSRTSNRPGHIKNSRRRERFEIP*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C12SLm0103K08.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="2332" stop="2538"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>204</number_coding_nucleotides>
                  <number_encoded_amino_acids>68</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IQKKIKDEKIENSTQNNLPLLCYSLLLITNSRSLHCFPAPLVMFFSSGFNTKSANLLEGILTRLLLLG*</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="77001" PGL_stop="77506"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="77001" e_stop="77506"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.996"/>
        </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="77001" e_stop="77506" e_length="506"/>
          </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="77001" stop="77506"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M259-F" 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>CTGCGCTTTCAGTGAAAACTATACGCATCAGTTCTGCTATTTTGGCCGCACAGAGTCCATTCTTTTACAAGGCTAGGAGTTTTTAATGCTCTGTTTTTGATGAATTAGAAAGTCTTGATTGCTTGTTTTTTGACGTCTTCTTGTTTTCTTCATAGCTATTCTCCAATGGCATGAGAGAGTCAGAGTCAGAGAAGCAGCTTGTTACTGTACAAATCTATGCCTCGGGTTAGTATTAAGATTTTTTAGTTGTAGTTTGGCATGTTCTCATTTCATTGTATTGTCCTTTCCGTTACTCCTATTACACAGACTAGCCACCTCTTGTGCACTTGATTTGACATTTCAATAACAAGTTTTAGATGTTTAGGATGTGCAATTAGAGAGCAATGTGTATCAATCACTAATTGAAAATTCAGTTTTTTCGGCTGTTTGAATTCATAGAATTAAGGGGATTCTTGTACTTCCATCAGATGGTTGTTTAAGAAAGAAGTATTTTTGACAAATAAGTT</gDNA_template>
            <first_frame> L  R  F  Q  *  K  L  Y  A  S  V  L  L  F  W  P  H  R  V  H  S  F  T  R  L  G  V  F  N  A  L  F  L  M  N  *  K  V  L  I  A  C  F  L  T  S  S  C  F  L  H  S  Y  S  P  M  A  *  E  S  Q  S  Q  R  S  S  L  L  L  Y  K  S  M  P  R  V  S  I  K  I  F  *  L  *  F  G  M  F  S  F  H  C  I  V  L  S  V  T  P  I  T  Q  T  S  H  L  L  C  T  *  F  D  I  S  I  T  S  F  R  C  L  G  C  A  I  R  E  Q  C  V  S  I  T  N  *  K  F  S  F  F  G  C  L  N  S  *  N  *  G  D  S  C  T  S  I  R  W  L  F  K  K  E  V  F  L  T  N  K   </first_frame>
            <second_frame>  C  A  F  S  E  N  Y  T  H  Q  F  C  Y  F  G  R  T  E  S  I  L  L  Q  G  *  E  F  L  M  L  C  F  *  *  I  R  K  S  *  L  L  V  F  *  R  L  L  V  F  F  I  A  I  L  Q  W  H  E  R  V  R  V  R  E  A  A  C  Y  C  T  N  L  C  L  G  L  V  L  R  F  F  S  C  S  L  A  C  S  H  F  I  V  L  S  F  P  L  L  L  L  H  R  L  A  T  S  C  A  L  D  L  T  F  Q  *  Q  V  L  D  V  *  D  V  Q  L  E  S  N  V  Y  Q  S  L  I  E  N  S  V  F  S  A  V  *  I  H  R  I  K  G  I  L  V  L  P  S  D  G  C  L  R  K  K  Y  F  *  Q  I  S  </second_frame>
            <third_frame>   A  L  S  V  K  T  I  R  I  S  S  A  I  L  A  A  Q  S  P  F  F  Y  K  A  R  S  F  *  C  S  V  F  D  E  L  E  S  L  D  C  L  F  F  D  V  F  L  F  S  S  *  L  F  S  N  G  M  R  E  S  E  S  E  K  Q  L  V  T  V  Q  I  Y  A  S  G  *  Y  *  D  F  L  V  V  V  W  H  V  L  I  S  L  Y  C  P  F  R  Y  S  Y  Y  T  D  *  P  P  L  V  H  L  I  *  H  F  N  N  K  F  *  M  F  R  M  C  N  *  R  A  M  C  I  N  H  *  L  K  I  Q  F  F  R  L  F  E  F  I  E  L  R  G  F  L  Y  F  H  Q  M  V  V  *  E  R  S  I  F  D  K  *  V </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="C12SLm0103K08.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="77134" stop="77346"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>210</number_coding_nucleotides>
                  <number_encoded_amino_acids>70</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>RLLVFFIAILQWHERVRVREAACYCTNLCLGLVLRFFSCSLACSHFIVLSFPLLLLHRLATSCALDLTFQ*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="78224" PGL_stop="77681"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="78224" e_stop="77681"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="0.998">
            <gDNA_exon_boundary e_start="78224" e_stop="77681" e_length="544"/>
          </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="78224" stop="77681"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M259-R" 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="3" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>GGCTGCAGTGTCTCATGCATGATGCAACCTCAAATTTGTCAGCAGCCATAAGCACATCAAGCATAGCAGTAGCTGGTATCGTAGACAAAGTATTGCTATACATGAATTGTAGTAACTTTACGAAGGCAGCTTCTTCTGCGAGAAAAAGAGATAAAGAAAGGTGGATGAGAAAAAAAGAAAATTTGTGAACACAAATTAAAGGAACTATATGTTCACTAGTTAAAGTAACTATCTAAGAACTCTTCTTTAAATATGCTTAGAAGCAAAACGAGCAGTACTAGCACTTGGAACATGTTATTAACCTTGCAAACATATGAATAGACAATCAATGTTTCACACAAATGTTTCGGAAAGAGACACAATTTTTGTTCTGGTGTCTAATCCTTCTATTATTCATCAAGATAGATAAAGTACTGGATATTTAGAATGATGCTTTTCTATATTTGAAGACTTCTTATTACTTCTTAACATTTCTACTTAGCCATGTGAACACGAGGTCATGAGTTCAAGCTATGAAAACAGCCTCTTGCAAAAATATAGGGTA</gDNA_template>
            <first_frame> G  C  S  V  S  C  M  M  Q  P  Q  I  C  Q  Q  P  *  A  H  Q  A  *  Q  *  L  V  S  *  T  K  Y  C  Y  T  *  I  V  V  T  L  R  R  Q  L  L  L  R  E  K  E  I  K  K  G  G  *  E  K  K  K  I  C  E  H  K  L  K  E  L  Y  V  H  *  L  K  *  L  S  K  N  S  S  L  N  M  L  R  S  K  T  S  S  T  S  T  W  N  M  L  L  T  L  Q  T  Y  E  *  T  I  N  V  S  H  K  C  F  G  K  R  H  N  F  C  S  G  V  *  S  F  Y  Y  S  S  R  *  I  K  Y  W  I  F  R  M  M  L  F  Y  I  *  R  L  L  I  T  S  *  H  F  Y  L  A  M  *  T  R  G  H  E  F  K  L  *  K  Q  P  L  A  K  I  *  G  </first_frame>
            <second_frame>  A  A  V  S  H  A  *  C  N  L  K  F  V  S  S  H  K  H  I  K  H  S  S  S  W  Y  R  R  Q  S  I  A  I  H  E  L  *  *  L  Y  E  G  S  F  F  C  E  K  K  R  *  R  K  V  D  E  K  K  R  K  F  V  N  T  N  *  R  N  Y  M  F  T  S  *  S  N  Y  L  R  T  L  L  *  I  C  L  E  A  K  R  A  V  L  A  L  G  T  C  Y  *  P  C  K  H  M  N  R  Q  S  M  F  H  T  N  V  S  E  R  D  T  I  F  V  L  V  S  N  P  S  I  I  H  Q  D  R  *  S  T  G  Y  L  E  *  C  F  S  I  F  E  D  F  L  L  L  L  N  I  S  T  *  P  C  E  H  E  V  M  S  S  S  Y  E  N  S  L  L  Q  K  Y  R  V </second_frame>
            <third_frame>   L  Q  C  L  M  H  D  A  T  S  N  L  S  A  A  I  S  T  S  S  I  A  V  A  G  I  V  D  K  V  L  L  Y  M  N  C  S  N  F  T  K  A  A  S  S  A  R  K  R  D  K  E  R  W  M  R  K  K  E  N  L  *  T  Q  I  K  G  T  I  C  S  L  V  K  V  T  I  *  E  L  F  F  K  Y  A  *  K  Q  N  E  Q  Y  *  H  L  E  H  V  I  N  L  A  N  I  *  I  D  N  Q  C  F  T  Q  M  F  R  K  E  T  Q  F  L  F  W  C  L  I  L  L  L  F  I  K  I  D  K  V  L  D  I  *  N  D  A  F  L  Y  L  K  T  S  Y  Y  F  L  T  F  L  L  S  H  V  N  T  R  S  *  V  Q  A  M  K  T  A  S  C  K  N  I  G   </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="C12SLm0103K08.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 8 chains have been computed
$ 
$ memory statistics:
$ 5608 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 1869 bytes was the average size of a spliced alignment
$ 7880 bytes predicted gene locations in total
$ 3 predicted gene locations have been stored
$ 2626 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: 2008-03-07 09:31:28
-->
