<?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 07:26:43"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C01HBa0216G16-sx9oh/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C01HBa0216G16-sx9oh/gth_cdna_fileCXGN::TomatoGenome::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-C01HBa0216G16-sx9oh/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="SSR414" ref_strand="+" ref_description="SSR414">
      <seq>agagagagagagagagagagagagcgagagagagagagagagagagagagagagagaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0216G16-sx9oh/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0216G16.2" temp_strand="-" temp_description="C01HBa0216G16.2  AC171728.2 htgs_phase:3 submitted_to_sgn_as:Contig49 sequenced_by:cornell upload_account_name:us">
        <position start="26247" stop="25589"/>
      </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="25947" g_stop="25888" g_length="60"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="60" r_length="60" r_score="0.933"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0216G16.2" gen_strand="-" ref_id="SSR414" ref_strand="+">
        <total_alignment_score>0.933</total_alignment_score>
        <cumulative_length_of_scored_exons>60</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0216G16.2" gen_strand="-"/>
        <rDNA rDNA_id="SSR414" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="25947" e_stop="25888"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAGAGAGAGAGAGACAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAT</genome_strand>
        <mrna_strand>AGAGAGAGAGAGAGAGAGAGAGAGCGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAA</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-C01HBa0216G16-sx9oh/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="SSR416" ref_strand="+" ref_description="SSR416">
      <seq>ctctctctctctctctctctctctctctctctctctctctctctctctctctctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0216G16-sx9oh/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0216G16.2" temp_strand="+" temp_description="C01HBa0216G16.2  AC171728.2 htgs_phase:3 submitted_to_sgn_as:Contig49 sequenced_by:cornell upload_account_name:us">
        <position start="25592" stop="26246"/>
      </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="25892" g_stop="25946" g_length="55"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="55" r_length="55" r_score="0.964"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0216G16.2" gen_strand="+" ref_id="SSR416" ref_strand="+">
        <total_alignment_score>0.964</total_alignment_score>
        <cumulative_length_of_scored_exons>55</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0216G16.2" gen_strand="+"/>
        <rDNA rDNA_id="SSR416" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="25892" e_stop="25946"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTGTCTCTCTCTCTCTC</genome_strand>
        <mrna_strand>CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC</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-C01HBa0216G16-sx9oh/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="SSR415" ref_strand="+" ref_description="SSR415">
      <seq>ctctctctctctctctctctctctctttctctctctctctctctctctctctc</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0216G16-sx9oh/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0216G16.2" temp_strand="+" temp_description="C01HBa0216G16.2  AC171728.2 htgs_phase:3 submitted_to_sgn_as:Contig49 sequenced_by:cornell upload_account_name:us">
        <position start="25592" stop="26244"/>
      </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="25894" g_stop="25946" g_length="53"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="53" r_length="53" r_score="0.943"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0216G16.2" gen_strand="+" ref_id="SSR415" ref_strand="+">
        <total_alignment_score>0.943</total_alignment_score>
        <cumulative_length_of_scored_exons>53</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0216G16.2" gen_strand="+"/>
        <rDNA rDNA_id="SSR415" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="25894" e_stop="25946"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTGTCTCTCTCTCTCTC</genome_strand>
        <mrna_strand>CTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTC</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-C01HBa0216G16-sx9oh/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="TG125-R" ref_strand="+" ref_description="TG125-R">
      <seq>catccctggcctcctctttgattttgcccctctgaaaattgaagggtgtccttcttttctgtagtctgtcatcttagtaatgttgagataaacaactggtgtcttcatttctgatattactgattcaagaactctcatcatccatggatatggacctaattgagtctcgtttgttatcggtttcgtctccccatcacagtttcctcctgagttccattgaccacctctgcaaaaaagggaattcccctcattagcctatcaaacaacaaggggtctggagaaggtagggcgtacgcaaatgagagattgtttccgaaagatcctcaaaaattataagaatgaagaaagcatagcggttaaaaggagtcagtagactatcgaaaaaagagaagttttacttgaaatgagaagctgaatatcccctaaaaaacactctagttttggtgctgttgatagttgtatcaacccaatgtgcccatgtcttcaatgcctta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0216G16-sx9oh/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0216G16.2" temp_strand="+" temp_description="C01HBa0216G16.2  AC171728.2 htgs_phase:3 submitted_to_sgn_as:Contig49 sequenced_by:cornell upload_account_name:us">
        <position start="61722" stop="62815"/>
      </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="62022" g_stop="62515" g_length="494"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="494" r_length="494" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0216G16.2" gen_strand="+" ref_id="TG125-R" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>494</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0216G16.2" gen_strand="+"/>
        <rDNA rDNA_id="TG125-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="62022" e_stop="62515"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CATCCCTGGCCTCCTCTTTGATTTTGCCCCTCTGAAAATTGAAGGGTGTCCTTCTTTTCTGTAGTCTGTCATCTTAGTAATGTTGAGATAAACAACTGGTGTCTTCATTTCTGATATTACTGATTCAAGAACTCTCATCATCCATGGATATGGACCTAATTGAGTCTCGTTTGTTATCGGTTTCGTCTCCCCATCACAGTTTCCTCCTGAGTTCCATTGACCACCTCTGCAAAAAAGGGAATTCCCCTCATTAGCCTATCAAACAACAAGGGGTCTGGAGAAGGTAGGGCGTACGCAAATGAGAGATTGTTTCCGAAAGATCCTCAAAAATTATAAGAATGAAGAAAGCATAGCGGTTAAAAGGAGTCAGTAGACTATCGAAAAAAGAGAAGTTTTACTTGAAATGAGAAGCTGAATATCCCCTAAAAAACACTCTAGTTTTGGTGCTGTTGATAGTTGTATCAACCCAATGTGCCCATGTCTTCAATGCCTTA</genome_strand>
        <mrna_strand>CATCCCTGGCCTCCTCTTTGATTTTGCCCCTCTGAAAATTGAAGGGTGTCCTTCTTTTCTGTAGTCTGTCATCTTAGTAATGTTGAGATAAACAACTGGTGTCTTCATTTCTGATATTACTGATTCAAGAACTCTCATCATCCATGGATATGGACCTAATTGAGTCTCGTTTGTTATCGGTTTCGTCTCCCCATCACAGTTTCCTCCTGAGTTCCATTGACCACCTCTGCAAAAAAGGGAATTCCCCTCATTAGCCTATCAAACAACAAGGGGTCTGGAGAAGGTAGGGCGTACGCAAATGAGAGATTGTTTCCGAAAGATCCTCAAAAATTATAAGAATGAAGAAAGCATAGCGGTTAAAAGGAGTCAGTAGACTATCGAAAAAAGAGAAGTTTTACTTGAAATGAGAAGCTGAATATCCCCTAAAAAACACTCTAGTTTTGGTGCTGTTGATAGTTGTATCAACCCAATGTGCCCATGTCTTCAATGCCTTA</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-C01HBa0216G16-sx9oh/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_markers" ref_id="TG125-F" ref_strand="+" ref_description="TG125-F">
      <seq>cattacagtagttgtgaagagtcttacagattgactgagacaggggagctccatgtaccacctgaatataccgatcaatactgcaaaggaccctgcttggaggagactcaccatgtgcttaattgtcttggaagcatactgtcgcagttcagattttataataaagccaccgtcagagcagtcgaagagactatcaaggagggatgtagctatggccctgaaagaggttaaactttctccacttcactatacaaaactgtccagtatatttgttctgttgataaacttattggatatgattaatttgtttcgagttgggagtacgtttaaagaaacaaatctttaatttatatacattgacagtacactattcaatgtgtttggatcttcttgtctctttatcgaaactgaactcattctgaaatatgtcaacaggtcttttcaatgttgctgagcacatcctagcttatgacaacactgcttttcgtgcttcaaaatcgtccatgct</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C01HBa0216G16-sx9oh/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C01HBa0216G16.2" temp_strand="-" temp_description="C01HBa0216G16.2  AC171728.2 htgs_phase:3 submitted_to_sgn_as:Contig49 sequenced_by:cornell upload_account_name:us">
        <position start="65135" stop="64030"/>
      </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="64837" g_stop="64330" g_length="508"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="508" r_length="508" r_score="0.996"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C01HBa0216G16.2" gen_strand="-" ref_id="TG125-F" ref_strand="+">
        <total_alignment_score>0.996</total_alignment_score>
        <cumulative_length_of_scored_exons>508</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C01HBa0216G16.2" gen_strand="-"/>
        <rDNA rDNA_id="TG125-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="64837" e_stop="64330"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATTTACAGTAGTTGTGAAGAGTCTTACAGATTGACTGAGACAGGGGAGCTCCATGTACCACCTGAATATACCGATCAATACTGCAAAGGACCCTGCTTGGAGGAGACTCACCATGTGCTTAATTGTCTTGGAAGCATACTGTCGCAGTTCAGATTTTATAATAAAGCCACCGTCAGAGCAGTCGAAGAGACTATCAAGGAGGGATGTAGCTATGGCCCTGAAAGAGGTTAAACTTTCTCCACTTCACTATACAAAACTGTCCAGTATATTTGTTCTGTTGATAAACTTATTGGATATGATTAATTTGTTTCGAGTTGGGAGTACGTTTAAAGAAACAAATCTTTAATTTATATACATTGACAGTACACTATTCAATGTGTTTGGATCTTCTTGTCTCTTTATCGAAACTGAACTCATTCTGAAATATGTCAACAGGTCTTTTCAATGTTGCTGAGCACATCCTAGCTTATGACAACACTGCTTTTCGTGCTTCAAAATCGTCCATGCT</genome_strand>
        <mrna_strand>CATTACAGTAGTTGTGAAGAGTCTTACAGATTGACTGAGACAGGGGAGCTCCATGTACCACCTGAATATACCGATCAATACTGCAAAGGACCCTGCTTGGAGGAGACTCACCATGTGCTTAATTGTCTTGGAAGCATACTGTCGCAGTTCAGATTTTATAATAAAGCCACCGTCAGAGCAGTCGAAGAGACTATCAAGGAGGGATGTAGCTATGGCCCTGAAAGAGGTTAAACTTTCTCCACTTCACTATACAAAACTGTCCAGTATATTTGTTCTGTTGATAAACTTATTGGATATGATTAATTTGTTTCGAGTTGGGAGTACGTTTAAAGAAACAAATCTTTAATTTATATACATTGACAGTACACTATTCAATGTGTTTGGATCTTCTTGTCTCTTTATCGAAACTGAACTCATTCTGAAATATGTCAACAGGTCTTTTCAATGTTGCTGAGCACATCCTAGCTTATGACAACACTGCTTTTCGTGCTTCAAAATCGTCCATGCT</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>5</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="25947" PGL_stop="25888"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="25947" e_stop="25888"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.933"/>
        </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="0.933">
            <gDNA_exon_boundary e_start="25947" e_stop="25888" e_length="60"/>
          </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="25947" stop="25888"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SSR414" 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>AGAGAGAGAGAGAGACAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAT</gDNA_template>
            <first_frame> R  E  R  E  R  Q  R  Q  R  E  R  E  R  E  R  E  R  E  R  N </first_frame>
            <second_frame>  E  R  E  R  D  R  D  R  E  R  E  R  E  R  E  R  E  R  E   </second_frame>
            <third_frame>   R  E  R  E  T  E  T  E  R  E  R  E  R  E  R  E  R  E  K  </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="C01HBa0216G16.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="2" PGL_strand="+" PGL_start="25892" PGL_stop="25946"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="25892" e_stop="25946"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.964"/>
        </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="0.964">
            <gDNA_exon_boundary e_start="25892" e_stop="25946" e_length="55"/>
          </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="25892" stop="25946"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SSR416" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="25894" stop="25946"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SSR415" 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>CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTCTCTGTCTCTCTCTCTCTC</gDNA_template>
            <first_frame> L  S  L  S  L  S  L  S  L  S  L  C  L  C  L  S  L  S  </first_frame>
            <second_frame>  S  L  S  L  S  L  S  L  S  L  S  V  S  V  S  L  S  L </second_frame>
            <third_frame>   L  S  L  S  L  S  L  S  L  S  L  S  L  S  L  S  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/">
            <none gDNA_id="C01HBa0216G16.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="+" PGL_start="62022" PGL_stop="62515"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="62022" e_stop="62515"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="62022" e_stop="62515" e_length="494"/>
          </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="62022" stop="62515"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="TG125-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>CATCCCTGGCCTCCTCTTTGATTTTGCCCCTCTGAAAATTGAAGGGTGTCCTTCTTTTCTGTAGTCTGTCATCTTAGTAATGTTGAGATAAACAACTGGTGTCTTCATTTCTGATATTACTGATTCAAGAACTCTCATCATCCATGGATATGGACCTAATTGAGTCTCGTTTGTTATCGGTTTCGTCTCCCCATCACAGTTTCCTCCTGAGTTCCATTGACCACCTCTGCAAAAAAGGGAATTCCCCTCATTAGCCTATCAAACAACAAGGGGTCTGGAGAAGGTAGGGCGTACGCAAATGAGAGATTGTTTCCGAAAGATCCTCAAAAATTATAAGAATGAAGAAAGCATAGCGGTTAAAAGGAGTCAGTAGACTATCGAAAAAAGAGAAGTTTTACTTGAAATGAGAAGCTGAATATCCCCTAAAAAACACTCTAGTTTTGGTGCTGTTGATAGTTGTATCAACCCAATGTGCCCATGTCTTCAATGCCTTA</gDNA_template>
            <first_frame> H  P  W  P  P  L  *  F  C  P  S  E  N  *  R  V  S  F  F  S  V  V  C  H  L  S  N  V  E  I  N  N  W  C  L  H  F  *  Y  Y  *  F  K  N  S  H  H  P  W  I  W  T  *  L  S  L  V  C  Y  R  F  R  L  P  I  T  V  S  S  *  V  P  L  T  T  S  A  K  K  G  I  P  L  I  S  L  S  N  N  K  G  S  G  E  G  R  A  Y  A  N  E  R  L  F  P  K  D  P  Q  K  L  *  E  *  R  K  H  S  G  *  K  E  S  V  D  Y  R  K  K  R  S  F  T  *  N  E  K  L  N  I  P  *  K  T  L  *  F  W  C  C  *  *  L  Y  Q  P  N  V  P  M  S  S  M  P   </first_frame>
            <second_frame>  I  P  G  L  L  F  D  F  A  P  L  K  I  E  G  C  P  S  F  L  *  S  V  I  L  V  M  L  R  *  T  T  G  V  F  I  S  D  I  T  D  S  R  T  L  I  I  H  G  Y  G  P  N  *  V  S  F  V  I  G  F  V  S  P  S  Q  F  P  P  E  F  H  *  P  P  L  Q  K  R  E  F  P  S  L  A  Y  Q  T  T  R  G  L  E  K  V  G  R  T  Q  M  R  D  C  F  R  K  I  L  K  N  Y  K  N  E  E  S  I  A  V  K  R  S  Q  *  T  I  E  K  R  E  V  L  L  E  M  R  S  *  I  S  P  K  K  H  S  S  F  G  A  V  D  S  C  I  N  P  M  C  P  C  L  Q  C  L  </second_frame>
            <third_frame>   S  L  A  S  S  L  I  L  P  L  *  K  L  K  G  V  L  L  F  C  S  L  S  S  *  *  C  *  D  K  Q  L  V  S  S  F  L  I  L  L  I  Q  E  L  S  S  S  M  D  M  D  L  I  E  S  R  L  L  S  V  S  S  P  H  H  S  F  L  L  S  S  I  D  H  L  C  K  K  G  N  S  P  H  *  P  I  K  Q  Q  G  V  W  R  R  *  G  V  R  K  *  E  I  V  S  E  R  S  S  K  I  I  R  M  K  K  A  *  R  L  K  G  V  S  R  L  S  K  K  E  K  F  Y  L  K  *  E  A  E  Y  P  L  K  N  T  L  V  L  V  L  L  I  V  V  S  T  Q  C  A  H  V  F  N  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/">
            <none gDNA_id="C01HBa0216G16.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="4" PGL_strand="-" PGL_start="64837" PGL_stop="64330"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="64837" e_stop="64330"/>
          </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="64837" e_stop="64330" e_length="508"/>
          </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="64837" stop="64330"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="TG125-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="4" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>ATTTACAGTAGTTGTGAAGAGTCTTACAGATTGACTGAGACAGGGGAGCTCCATGTACCACCTGAATATACCGATCAATACTGCAAAGGACCCTGCTTGGAGGAGACTCACCATGTGCTTAATTGTCTTGGAAGCATACTGTCGCAGTTCAGATTTTATAATAAAGCCACCGTCAGAGCAGTCGAAGAGACTATCAAGGAGGGATGTAGCTATGGCCCTGAAAGAGGTTAAACTTTCTCCACTTCACTATACAAAACTGTCCAGTATATTTGTTCTGTTGATAAACTTATTGGATATGATTAATTTGTTTCGAGTTGGGAGTACGTTTAAAGAAACAAATCTTTAATTTATATACATTGACAGTACACTATTCAATGTGTTTGGATCTTCTTGTCTCTTTATCGAAACTGAACTCATTCTGAAATATGTCAACAGGTCTTTTCAATGTTGCTGAGCACATCCTAGCTTATGACAACACTGCTTTTCGTGCTTCAAAATCGTCCATGCT</gDNA_template>
            <first_frame> I  Y  S  S  C  E  E  S  Y  R  L  T  E  T  G  E  L  H  V  P  P  E  Y  T  D  Q  Y  C  K  G  P  C  L  E  E  T  H  H  V  L  N  C  L  G  S  I  L  S  Q  F  R  F  Y  N  K  A  T  V  R  A  V  E  E  T  I  K  E  G  C  S  Y  G  P  E  R  G  *  T  F  S  T  S  L  Y  K  T  V  Q  Y  I  C  S  V  D  K  L  I  G  Y  D  *  F  V  S  S  W  E  Y  V  *  R  N  K  S  L  I  Y  I  H  *  Q  Y  T  I  Q  C  V  W  I  F  L  S  L  Y  R  N  *  T  H  S  E  I  C  Q  Q  V  F  S  M  L  L  S  T  S  *  L  M  T  T  L  L  F  V  L  Q  N  R  P  C  </first_frame>
            <second_frame>  F  T  V  V  V  K  S  L  T  D  *  L  R  Q  G  S  S  M  Y  H  L  N  I  P  I  N  T  A  K  D  P  A  W  R  R  L  T  M  C  L  I  V  L  E  A  Y  C  R  S  S  D  F  I  I  K  P  P  S  E  Q  S  K  R  L  S  R  R  D  V  A  M  A  L  K  E  V  K  L  S  P  L  H  Y  T  K  L  S  S  I  F  V  L  L  I  N  L  L  D  M  I  N  L  F  R  V  G  S  T  F  K  E  T  N  L  *  F  I  Y  I  D  S  T  L  F  N  V  F  G  S  S  C  L  F  I  E  T  E  L  I  L  K  Y  V  N  R  S  F  Q  C  C  *  A  H  P  S  L  *  Q  H  C  F  S  C  F  K  I  V  H  A </second_frame>
            <third_frame>   L  Q  *  L  *  R  V  L  Q  I  D  *  D  R  G  A  P  C  T  T  *  I  Y  R  S  I  L  Q  R  T  L  L  G  G  D  S  P  C  A  *  L  S  W  K  H  T  V  A  V  Q  I  L  *  *  S  H  R  Q  S  S  R  R  D  Y  Q  G  G  M  *  L  W  P  *  K  R  L  N  F  L  H  F  T  I  Q  N  C  P  V  Y  L  F  C  *  *  T  Y  W  I  *  L  I  C  F  E  L  G  V  R  L  K  K  Q  I  F  N  L  Y  T  L  T  V  H  Y  S  M  C  L  D  L  L  V  S  L  S  K  L  N  S  F  *  N  M  S  T  G  L  F  N  V  A  E  H  I  L  A  Y  D  N  T  A  F  R  A  S  K  S  S  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="C01HBa0216G16.2" strand="-"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="64803" stop="64492"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>309</number_coding_nucleotides>
                  <number_encoded_amino_acids>103</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LRQGSSMYHLNIPINTAKDPAWRRLTMCLIVLEAYCRSSDFIIKPPSEQSKRLSRRDVAMALKEVKLSPLHYTKLSSIFVLLINLLDMINLFRVGSTFKETNL*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C01HBa0216G16.2" strand="-"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="64837" stop="64607"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>228</number_coding_nucleotides>
                  <number_encoded_amino_acids>76</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IYSSCEESYRLTETGELHVPPEYTDQYCKGPCLEETHHVLNCLGSILSQFRFYNKATVRAVEETIKEGCSYGPERG*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 217 chains have been computed
$ 
$ memory statistics:
$ 10200 bytes spliced alignments in total
$ 5 spliced alignments have been stored
$ 2040 bytes was the average size of a spliced alignment
$ 9056 bytes predicted gene locations in total
$ 4 predicted gene locations have been stored
$ 2264 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 219 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 07:26:55
-->
