<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-07-24 22:27:22"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12HBa0216D15-ppy0V/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C12HBa0216D15-ppy0V/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-C12HBa0216D15-ppy0V/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M8297" ref_strand="+" ref_description="SGN-M8297 C2_At4g19070 [cosii_markers]">
      <seq>ctactatattaacaaaatttcaatttcaaataatttttccttcgagcttcgcgaacattacactgagcagcaccctttcatggtagagatgattataaagggtctgttcaggagatacgaaagatggaatccagtgcatcctacatatggagccttctggggcatgggaataggcgttggctgtggggtgggatggggtcctggatttggtcctgaggctattggttatgttggagctggatgtggtgttggattcagcgttggcttctctctgctcggcgttggcattggtctacctgccaattacatttacacaggtccttacaatgcattcacagctgccagaagtggtgctattgagatgtctcgatcaactgatattcgaagcatgagaaacattgtggaagagagtcggtgttacctcgattcaaatattgctggcttccaagaaagagtgattcagtctttttcaagcataaggttcaaagaatcagtagggaaggcggtagattcgtctgaaatgccaatcaaaatgtcttttccggatcaatgcatggatcgtctaaaacaaggcatcaatagcttatttcatccttgcaaaggttcaaaggattaagcaacatgttgaggagcacaatcccagaagggttaatatacattgcacacttcacagcattggccttagtttttttgccttcccacagatagtagggagcatataggtagaagaaaaaagagcatttacagttgcagttgttaacatgctttcatttcttttagtttggtaaacattgtttgaatgaaagtgagaatttgaattaatacggaaaagggtcaaaaatgtctctgaactatcgcgaaaggtcataatatacccttcgtctttgtccatctattatgctaataatacttttcggatttttaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0216D15-ppy0V/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0216D15.1" temp_strand="+" temp_description="C12HBa0216D15.1  AC235605.2 htgs_phase:2 submitted_to_sgn_as:gi|238909032|gb|AC235605.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone LE_HBa-216D15, WORKING DRAFT SEQUENCE, 5 ordered pieces">
        <position start="18022" stop="22163"/>
      </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="18322" g_stop="18403" g_length="82"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="82" r_length="82" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="18404" i_stop="19915" i_length="1512">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.983" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="19916" g_stop="20162" g_length="247"/>
          <reference_exon_boundary r_type="cDNA" r_start="83" r_stop="329" r_length="247" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="20163" i_stop="20319" i_length="157">
            <donor d_prob="0.996" d_score="1.00"/>
            <acceptor a_prob="0.951" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="20320" g_stop="20592" g_length="273"/>
          <reference_exon_boundary r_type="cDNA" r_start="330" r_stop="602" r_length="273" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="20593" i_stop="21541" i_length="949">
            <donor d_prob="0.982" d_score="1.00"/>
            <acceptor a_prob="0.985" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="21542" g_stop="21863" g_length="322"/>
          <reference_exon_boundary r_type="cDNA" r_start="603" r_stop="924" r_length="322" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="925" polyA_stop="935"/>
      <MATCH_line gen_id="C12HBa0216D15.1" gen_strand="+" ref_id="SGN-M8297" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>924</cumulative_length_of_scored_exons>
        <coverage percentage="0.988" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0216D15.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M8297" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="18322" e_stop="18403"/>
          <exon e_start="19916" e_stop="20162"/>
          <exon e_start="20320" e_stop="20592"/>
          <exon e_start="21542" e_stop="21863"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CTACTATATTAACAAAATTTCAATTTCAAATAATTTTTCCTTCGAGCTTCGCGAACATTACACTGAGCAGCACCCTTTCATGGTAGAAACTTAAATCTCTGTATTTTTTTTATTTTTTGTTTCATTTCTATGTGTTGATGCTTGTTTTCATATGATTTCATTATTTGTATAAAGGGTATTTTGTGCTATTTTGTTCTTGGATTTTTGGCTAATTTGTAAGTGCATAACTTGTGTGAATCAATTATATTGAAGTATCCATTTGGTTTCTTGTTGTTGTTGCTTACTTTGAAATTTCATTGTTTTAAAAAAAAGGGGGCTTTTTGGGCTATTTTGATCTTTTGGGTATTTTCTAGTTCCTTAAGAGCACAATTTTGTGTGATTTGTCCATTTCAATTCCAAGTGTTGTGTTTATTTTGAGGTTTCTTTGTATAAAAGAGGGCTATTTTGTTCTTGGGGTTTCTCTAAATTATTGTTTGTTTGGTTCTCCACACGGTATCTGGTACCCACATTAGAGCCCGATTATATCAGATTCGCTCCGGGAAGTCCCACATTGGGGTTAAAGCACTGCCTAACAAAGGCGACTCCGTACCCAAGGAGCTCGAACACGAGACCTCTTGGTTAAGATGGAGGAATACTTACCATGGGGGTTTCTCTAAATTTTAAGAGCATGACTTTGTGTGAATCAAGTATAGTGATTTATCCATTTCAATTCTAAAGTGTTGCTGCTTACTCTGAGATTTCATTGTTTACTCTGAGATTTCATTGTTTAAAAAGAAAGCTTTTTTACCCTCTTTTGTTCTTGGGGTTTTCTCAATTTCTCAAGTGCTTAACTTGTGTGAATGAAGTACAATATACTGAATTGTTCATTTCATTTCTAAGTGTTGCTGGTTACTTTGATGAGCTTTCATTGTTTAAAGTTTGCTAAATTTGCGCTGTTTTTGTTCTTGGGTTTTTTCTATTGTTTTTAAGAGGATAGCTTGTGTGAACCATGTATACTGAAATATTCCTTAGTGTTTCATTTGGTAAGGGAGTAGTTAGCAAAATCTTCTGGTTTGTGAACACAAATAGAACTAGGAATAAAGGGGTTAACTTTCTAGTTGAATTTTCAAGTTATTATAAAATAGCTCCTTTTTTTTCCACAACTTGATGGTTAACTGGGATGAGTGGGGAGAATTAGTACGAAAAGATAGAGAAGGAAAAAACTCATGATCCAACTTATGTGTCGTACTTGCCTTTTTGGCATGTTCAAAAAAGAAAGTCACGTTTATTTAGAAAAAAGAATCAACTTTGAACTTCTCATTGCACCCTTAATGTGATGATTTATAGTCACGTCTATGTCTTGTTATAGACCACAAGTTTTAGACAACTTTCTTGTGTCTTATCAAACACAACAACGTAAACTGGGATGGAGAGAGTAAGACACAGAACCCCTGTGGAAGTAAAATTTGCCTTCCAGACTAAACTGTTAGAAAACTTTGAGAGGACAACTTTCCAAAGGAGTTAAAATTTGCCCTCCGGACTTGGCATTTCCATTTTCGTTATCTTAGGGTATCTCTCAACAGAATTTGATAGACTTATGGGCTTGTGATTGTAGGTAGAGATGATTATAAAGGGTCTGTTCAGGAGATACGAAAGATGGAATCCAGTGCATCCTACATATGGAGCCTTCTGGGGCATGGGAATAGGCGTTGGCTGTGGGGTGGGATGGGGTCCTGGATTTGGTCCTGAGGCTATTGGTTATGTTGGAGCTGGATGTGGTGTTGGATTCAGCGTTGGCTTCTCTCTGCTCGGCGTTGGCATTGGTCTACCTGCCAATTACATTTACACAGGTCCTTACAATGGTAAAAATAACCAACTTTTCATATTCAGCTTCTTAATGAATTTGGACGTTACATTTCTGTTACTTTTCGTTTATATTTGATGATTATTGCCAACTTTCTGAGAGTCGAAACTACTGTTGAAGTTGATTTATTGATTTACCCGTATATCCTTTCGTAGCATTCACAGCTGCCAGAAGTGGTGCTATTGAGATGTCTCGATCAACTGATATTCGAAGCATGAGAAACATTGTGGAAGAGAGTCGGTGTTACCTCGATTCAAATATTGCTGGCTTCCAAGAAAGAGTGATTCAGTCTTTTTCAAGCATAAGGTTCAAAGAATCAGTAGGGAAGGCGGTAGATTCGTCTGAAATGCCAATCAAAATGTCTTTTCCGGATCAATGCATGGATCGTCTAAAACAAGGCATCAATAGCTTATTTCATCCTTGCAAAGGTATGCTACAGAGTGCTCACAAATGGAAGTAGTACTGTATTACAGTTAAACCATGATTAGACTTTTCATGCTACTTTGTTCTGATTCTTTAAACAGTGTAATATCGGTGTCATCAAATGTGATTATTGACGGGGAAGGAACTTGATCTACCCTTGGTCAAAATGGTTATTGGTTCGGATTGGTGTGCAATTTGCAACTAAGATTGCTTTTTCATTTTACAATCATATCAACCACTTTTTTCCAACATTGACCATCTCCGACTGTTTTATGTTACTATGATTGAAGAAGTACTCACCAATTATATTCGTTTTTCATGGAGCACAAAGTCAATTCAAGACGACATTTTGGTGATAAAAGTGGGAAGAAGTAAAGAGTGTGTGTTGTGTGGGGGTAGATGGCGGATTAGATAGGACGAGAAACAGGACATAACTCCTACTTTCCTATGTATGAATCTTTTATGTCAAGTTTGTTACATTTATTAGGTGTAATCTGAAGCTAGATAATGATATCGATGTTTTTGTCAACGTTTTAGATTGAACATGAGCACTGTTTCCTTCATGACTTGTTCGGGGATCGTTACTGTTTCCTTCTGGTTCACTGAAACTGTGTTATGTATAGTCTTATCTTGAATCTGTGTTGAACTGTTAAATGTTGTTGAATAACAAAGCCGGTACTCTATCTGCAATCATTTGTTCCCTTTACTGATACTTCCACGCTAATATACAACGCGTTGTCATCTGTGTAGTCTATCGTGCTGTCATTTATAACTGTTCTACAACCATGACATTGCCAGTGTTGAGTACCTCATATGGATACTTGCACACACTCATATATCTGATATATACCATAAATGAATCCGCGTAACGTACATGTATTCAGTATCCACCTCTTACTGCAATTCAGAGAACACAAATAACTTCTCACGTTGTCGTGTATCGATTTCTTGCAGGTTCAAAGGATTAAGCAACATGTTGAGGAGCACAATCCCAGAAGGGTTAATATACATTGCACACTTCACAGCATTGGCCTTAGTTTTTTTGCCTTCCCACAGATAGTAGGGAGCATATAGGTAGAAGAAAAAAGAGCATTTACAGTTGCAGTTGTTAACATGCTTTCATTTCTTTTAGTTTGGTAAACATTGTTTGAATGAAAGTGAGAATTTGAATTAATACGGAAAAGGGTCAAAAATGTCTCTGAACTATCGCGAAAGGTCATAATATACCCTTCGTCTTTGTCCATCTATTATGCTAATAATACTTTTCGGATTTTTA</genome_strand>
        <mrna_strand>CTACTATATTAACAAAATTTCAATTTCAAATAATTTTTCCTTCGAGCTTCGCGAACATTACACTGAGCAGCACCCTTTCATG........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTAGAGATGATTATAAAGGGTCTGTTCAGGAGATACGAAAGATGGAATCCAGTGCATCCTACATATGGAGCCTTCTGGGGCATGGGAATAGGCGTTGGCTGTGGGGTGGGATGGGGTCCTGGATTTGGTCCTGAGGCTATTGGTTATGTTGGAGCTGGATGTGGTGTTGGATTCAGCGTTGGCTTCTCTCTGCTCGGCGTTGGCATTGGTCTACCTGCCAATTACATTTACACAGGTCCTTACAATG.............................................................................................................................................................CATTCACAGCTGCCAGAAGTGGTGCTATTGAGATGTCTCGATCAACTGATATTCGAAGCATGAGAAACATTGTGGAAGAGAGTCGGTGTTACCTCGATTCAAATATTGCTGGCTTCCAAGAAAGAGTGATTCAGTCTTTTTCAAGCATAAGGTTCAAAGAATCAGTAGGGAAGGCGGTAGATTCGTCTGAAATGCCAATCAAAATGTCTTTTCCGGATCAATGCATGGATCGTCTAAAACAAGGCATCAATAGCTTATTTCATCCTTGCAAAG.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTCAAAGGATTAAGCAACATGTTGAGGAGCACAATCCCAGAAGGGTTAATATACATTGCACACTTCACAGCATTGGCCTTAGTTTTTTTGCCTTCCCACAGATAGTAGGGAGCATATAGGTAGAAGAAAAAAGAGCATTTACAGTTGCAGTTGTTAACATGCTTTCATTTCTTTTAGTTTGGTAAACATTGTTTGAATGAAAGTGAGAATTTGAATTAATACGGAAAAGGGTCAAAAATGTCTCTGAACTATCGCGAAAGGTCATAATATACCCTTCGTCTTTGTCCATCTATTATGCTAATAATACTTTTCGGATTTTTA</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-C12HBa0216D15-ppy0V/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M79-F" ref_strand="+" ref_description="SGN-M79-F TG296-F [rflp_markers_forward]">
      <seq>ttaggtttttgtgtggttcaacgtttttggttttgatttttatgtgttttcttagttccttgcttcaccattttgatggtattttgagtttttgatgttctgtcggcataaagtagtgatttttcagacagtttggtattatggagtatgtttctttgctcttctctaatttggattggttctgatttgtatatgcttgttttagtttcgatggtttttgagtttttgatgattcattggcacaaagtagtgatttttcagactgttgggttttgtggggttcccgtgcttgctcttcactaatttggattggttctgatttgtatatgttttagttttgatggtttttgagtttttgatgattcatcggcacaaagtagtgatctttcagacagttgggttttgtggggttcacgtgcttattcttcactattctcggttggtttgatttgtaggtccgttttagcat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0216D15-ppy0V/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0216D15.1" temp_strand="+" temp_description="C12HBa0216D15.1  AC235605.2 htgs_phase:2 submitted_to_sgn_as:gi|238909032|gb|AC235605.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone LE_HBa-216D15, WORKING DRAFT SEQUENCE, 5 ordered pieces">
        <position start="94375" stop="95443"/>
      </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="94675" g_stop="95143" g_length="469"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="469" r_length="469" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0216D15.1" gen_strand="+" ref_id="SGN-M79-F" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>469</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0216D15.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M79-F" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="94675" e_stop="95143"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTAGGTTTTTGTGTGGTTCAACGTTTTTGGTTTTGATTTTTATGTGTTTTCTTAGTTCCTTGCTTCACCATTTTGATGGTATTTTGAGTTTTTGATGTTCTGTCGGCATAAAGTAGTGATTTTTCAGACAGTTTGGTATTATGGAGTATGTTTCTTTGCTCTTCTCTAATTTGGATTGGTTCTGATTTGTATATGCTTGTTTTAGTTTCGATGGTTTTTGAGTTTTTGATGATTCATTGGCACAAAGTAGTGATTTTTCAGACTGTTGGGTTTTGTGGGGTTCCCGTGCTTGCTCTTCACTAATTTGGATTGGTTCTGATTTGTATATGTTTTAGTTTTGATGGTTTTTGAGTTTTTGATGATTCATCGGCACAAAGTAGTGATCTTTCAGACAGTTGGGTTTTGTGGGGTTCACGTGCTTATTCTTCACTATTCTCGGTTGGTTTGATTTGTAGGTCCGTTTTAGCAT</genome_strand>
        <mrna_strand>TTAGGTTTTTGTGTGGTTCAACGTTTTTGGTTTTGATTTTTATGTGTTTTCTTAGTTCCTTGCTTCACCATTTTGATGGTATTTTGAGTTTTTGATGTTCTGTCGGCATAAAGTAGTGATTTTTCAGACAGTTTGGTATTATGGAGTATGTTTCTTTGCTCTTCTCTAATTTGGATTGGTTCTGATTTGTATATGCTTGTTTTAGTTTCGATGGTTTTTGAGTTTTTGATGATTCATTGGCACAAAGTAGTGATTTTTCAGACTGTTGGGTTTTGTGGGGTTCCCGTGCTTGCTCTTCACTAATTTGGATTGGTTCTGATTTGTATATGTTTTAGTTTTGATGGTTTTTGAGTTTTTGATGATTCATCGGCACAAAGTAGTGATCTTTCAGACAGTTGGGTTTTGTGGGGTTCACGTGCTTATTCTTCACTATTCTCGGTTGGTTTGATTTGTAGGTCCGTTTTAGCAT</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-C12HBa0216D15-ppy0V/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M79-R" ref_strand="+" ref_description="SGN-M79-R TG296-R [rflp_markers_reverse]">
      <seq>agaatataacaaaaaagcagataaatcagttaattatgcctcaatctcaacaagtgaataacaaatcctatcagaagatatagtagacgataaacagtgaaggtagaagcctaactctatgacattatcttgagacccaaaacacttcatcaaagactcaaaagaaataatttgttcaccaagtactattaactaattatcaaaactagaattctcaaaataaaaaataacaaatcttatcagtcacatggacattcattaaacatcatgaagaagacaacaagggaaggtcaaaactggactccatggcacataagataataacaaaaggtagtttaaggcctaaaacacttcaaaaataaaatttattcaccagatatcaataatattatctgttcttccttcattcatgaggggcatgcacaagagacaatatacatcatttctccttttactttttctttcctgaggaagtaaaaggagcagaaagcagatagaaaga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0216D15-ppy0V/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0216D15.1" temp_strand="-" temp_description="C12HBa0216D15.1  AC235605.2 htgs_phase:2 submitted_to_sgn_as:gi|238909032|gb|AC235605.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone LE_HBa-216D15, WORKING DRAFT SEQUENCE, 5 ordered pieces">
        <position start="96042" stop="94941"/>
      </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="95742" g_stop="95241" g_length="502"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="502" r_length="502" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0216D15.1" gen_strand="-" ref_id="SGN-M79-R" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>502</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0216D15.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M79-R" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="95742" e_stop="95241"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGAATATAACAAAAAAGCAGATAAATCAGTTAATTATGCCTCAATCTCAACAAGTGAATAACAAATCCTATCAGAAGATATAGTAGACGATAAACAGTGAAGGTAGAAGCCTAACTCTATGACATTATCTTGAGACCCAAAACACTTCATCAAAGACTCAAAAGAAATAATTTGTTCACCAAGTACTATTAACTAATTATCAAAACTAGAATTCTCAAAATAAAAAATAACAAATCTTATCAGTCACATGGACATTCATTAAACATCATGAAGAAGACAACAAGGGAAGGTCAAAACTGGACTCCATGGCACATAAGATAATAACAAAAGGTAGTTTAAGGCCTAAAACACTTCAAAAATAAAATTTATTCACCAGATATCAATAATATTATCTGTTCTTCCTTCATTCATGAGGGGCATGCACAAGAGACAATATACATCATTTCTCCTTTTACTTTTTCTTTCCTGAGGAAGTAAAAGGAGCAGAAAGCAGATAGAAAGA</genome_strand>
        <mrna_strand>AGAATATAACAAAAAAGCAGATAAATCAGTTAATTATGCCTCAATCTCAACAAGTGAATAACAAATCCTATCAGAAGATATAGTAGACGATAAACAGTGAAGGTAGAAGCCTAACTCTATGACATTATCTTGAGACCCAAAACACTTCATCAAAGACTCAAAAGAAATAATTTGTTCACCAAGTACTATTAACTAATTATCAAAACTAGAATTCTCAAAATAAAAAATAACAAATCTTATCAGTCACATGGACATTCATTAAACATCATGAAGAAGACAACAAGGGAAGGTCAAAACTGGACTCCATGGCACATAAGATAATAACAAAAGGTAGTTTAAGGCCTAAAACACTTCAAAAATAAAATTTATTCACCAGATATCAATAATATTATCTGTTCTTCCTTCATTCATGAGGGGCATGCACAAGAGACAATATACATCATTTCTCCTTTTACTTTTTCTTTCCTGAGGAAGTAAAAGGAGCAGAAAGCAGATAGAAAGA</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-C12HBa0216D15-ppy0V/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1912" ref_strand="+" ref_description="SGN-M1912 T1305 [cos_markers]">
      <seq>gaaaaccctaccgccgctgctctccttgtacccccaaatctgagcaaatcgaaagcaacaatggcagaagaagcacagtacggagcaccagatgccggtaacaacaagaggaagtacgatgatcaaacggcaccgtctcctggtccacgtagacctactggattttctgctccgatcgcttccttatcttctcccgacggtgctgctcctccttcgtcttacaacaatgttccgccgcctatggatgatttccagttggctaagcagaaggctcaggagatcgctgctaggttgttgaatagtgctgaagcgaagaaacctagagttgataataacggcggtggtgccggtggatatgattcctatgaacacaagcccattgttactccttcagttacaagttcatatggttatccggggcagagcaagaagattgaaataccaaatggcagagttggtgtgattataggaaaaggtggggagaccatcaagtatcttcaactccagtctggagccaaaattcaggttactagagacatggatgctgatcctaattctcaaaacagagcagttgaactcatgggta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0216D15-ppy0V/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0216D15.1" temp_strand="+" temp_description="C12HBa0216D15.1  AC235605.2 htgs_phase:2 submitted_to_sgn_as:gi|238909032|gb|AC235605.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone LE_HBa-216D15, WORKING DRAFT SEQUENCE, 5 ordered pieces">
        <position start="108884" stop="110899"/>
      </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="109184" g_stop="109552" g_length="369"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="370" r_length="370" r_score="0.981"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="109553" i_stop="110383" i_length="831">
            <donor d_prob="0.994" d_score="1.00"/>
            <acceptor a_prob="0.972" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="110384" g_stop="110599" g_length="216"/>
          <reference_exon_boundary r_type="cDNA" r_start="371" r_stop="586" r_length="216" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0216D15.1" gen_strand="+" ref_id="SGN-M1912" ref_strand="+">
        <total_alignment_score>0.988</total_alignment_score>
        <cumulative_length_of_scored_exons>585</cumulative_length_of_scored_exons>
        <coverage percentage="0.998" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0216D15.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M1912" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="109184" e_stop="109552"/>
          <exon e_start="110384" e_stop="110599"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAAAACCCTACCGCCGCTGCTCTCCTTTTA-CCCCAAATCTGAGCAAATCGAAAGCAACAATGGCAGAAGAAGCACAGTACGGTGCACCAGATGCCGGTAACAACAAGAGGAAGTACGATGATCAAGCGGCACCGTCTCCTGGTCCTCGTAGACCTACTGGATTTTCTGCTCCGATCGCTTCCTTATCTTCTCCTGACGGTGCTGCTCCTCCTTCGTCTTACAACAATGTTCCGCCGCCTATGGATGATTTCCAGTTGGCTAAGCAGAAGGCTCAGGAGATCGCTGCTAGGTTGTTGAATAGTGCTGAAGCGAAGAAACCTAGAGTTGATAATAACGGCGGTGGTGCCGGTGGATATGATTCCTATGAACGTAAGGGTTCTGAGCTTTTTCTAACCTTTTGCTGTTATGGATTTTGTGTTTTCTTTAGTTTGTCTGTTTTTTTTTTCGGACACGAAGTTGAGATTTTTTTTTTAAAATGTAATTTTTTCTGTAATTCTTTGCTGTTAGATATACTGCTCTATTAAATCGAAGTTCATCTTTTACAGATATCGTTAAACCCAATATCGAAATTGTGTTTATATTTGCTTCGATTGATTTAATTAGTTTGTATGGTAGTCAAGTTTACAAGATTTATGAGTTTTCTGTCCTTTTCTGTTATTGATTTTGTGGTGCTGGTTTTTTGAGATGGAGGTGAGATGTTTTTTTTAAATAAAAAGATGTATTTTCTCACTGAAATTCTTTTCCATTTGGATACAAGTATTTTAATTTGTTATTTACAGGTATCCTTGTATCTTATACATCCCGTTGTAGTATTTTTTTATATATCCAAATGTTGTTGGTGGATTTGATTCCTCAAGGGTTTACTTTCTTTTGTTGTTGTTGATTTGTGTTTATGCCTTTTTTGCTGTGGGAGAACTATTTTCACGGATTGATTTTTTTTTATAATTAATGAAGTGTTGTTCTATTGCTTATTGTTATTGTAATTTTCACCTTCTTCTATACCTGACCAAAAATAATCTGTTCACAAAATATTGATGATGAAATACAATTATCCATACCGAATTCATGTTTGTAATTGGCTACCACTGATGTGATTAGTTGGCAAGGTAGTAGGGTTTTAGCTTTTACTATGATAGCAATTCTGGTTCGTTTTAAGATCTTGTTGAGATGTTAAATATTTGTGGCTTTTCTTGACCGCAGACAAGCCCATTGTTACTCCTTCAGTTACAAGTTCATATGGTTATCCGGGGCAGAGCAAGAAGATTGAAATACCAAATGGCAGAGTTGGTGTGATTATAGGAAAAGGTGGGGAGACCATCAAGTATCTTCAACTCCAGTCTGGAGCCAAAATTCAGGTTACTAGAGACATGGATGCTGATCCTAATTCTCAAAACAGAGCAGTTGAACTCATGGGTA</genome_strand>
        <mrna_strand>GAAAACCCTACCGCCGCTGCTCTCCTTGTACCCCCAAATCTGAGCAAATCGAAAGCAACAATGGCAGAAGAAGCACAGTACGGAGCACCAGATGCCGGTAACAACAAGAGGAAGTACGATGATCAAACGGCACCGTCTCCTGGTCCACGTAGACCTACTGGATTTTCTGCTCCGATCGCTTCCTTATCTTCTCCCGACGGTGCTGCTCCTCCTTCGTCTTACAACAATGTTCCGCCGCCTATGGATGATTTCCAGTTGGCTAAGCAGAAGGCTCAGGAGATCGCTGCTAGGTTGTTGAATAGTGCTGAAGCGAAGAAACCTAGAGTTGATAATAACGGCGGTGGTGCCGGTGGATATGATTCCTATGAAC...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACAAGCCCATTGTTACTCCTTCAGTTACAAGTTCATATGGTTATCCGGGGCAGAGCAAGAAGATTGAAATACCAAATGGCAGAGTTGGTGTGATTATAGGAAAAGGTGGGGAGACCATCAAGTATCTTCAACTCCAGTCTGGAGCCAAAATTCAGGTTACTAGAGACATGGATGCTGATCCTAATTCTCAAAACAGAGCAGTTGAACTCATGGGTA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>4</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="18322" PGL_stop="21863"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="18322" e_stop="18403"/>
            <exon e_start="19916" e_stop="20162"/>
            <exon e_start="20320" e_stop="20592"/>
            <exon e_start="21542" e_stop="21863"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.999" acc_prob="0.983" e_score="1.000"/>
          <exon-intron don_prob="0.996" acc_prob="0.951" e_score="1.000"/>
          <exon-intron don_prob="0.982" acc_prob="0.985" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="18322" e_stop="18403" e_length="82"/>
          </exon>
          <intron i_serial="1" don_prob="0.999" acc_prob="0.983">
            <gDNA_intron_boundary i_start="18404" i_stop="19915" i_length="1512"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="19916" e_stop="20162" e_length="247"/>
          </exon>
          <intron i_serial="2" don_prob="0.996" acc_prob="0.951">
            <gDNA_intron_boundary i_start="20163" i_stop="20319" i_length="157"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="20320" e_stop="20592" e_length="273"/>
          </exon>
          <intron i_serial="3" don_prob="0.982" acc_prob="0.985">
            <gDNA_intron_boundary i_start="20593" i_stop="21541" i_length="949"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="21542" e_stop="21863" e_length="322"/>
          </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="18322" stop="18403"/>
              <exon start="19916" stop="20162"/>
              <exon start="20320" stop="20592"/>
              <exon start="21542" stop="21863"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M8297" 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>CTACTATATTAACAAAATTTCAATTTCAAATAATTTTTCCTTCGAGCTTCGCGAACATTACACTGAGCAGCACCCTTTCATG : GTAGAGATGATTATAAAGGGTCTGTTCAGGAGATACGAAAGATGGAATCCAGTGCATCCTACATATGGAGCCTTCTGGGGCATGGGAATAGGCGTTGGCTGTGGGGTGGGATGGGGTCCTGGATTTGGTCCTGAGGCTATTGGTTATGTTGGAGCTGGATGTGGTGTTGGATTCAGCGTTGGCTTCTCTCTGCTCGGCGTTGGCATTGGTCTACCTGCCAATTACATTTACACAGGTCCTTACAATG : CATTCACAGCTGCCAGAAGTGGTGCTATTGAGATGTCTCGATCAACTGATATTCGAAGCATGAGAAACATTGTGGAAGAGAGTCGGTGTTACCTCGATTCAAATATTGCTGGCTTCCAAGAAAGAGTGATTCAGTCTTTTTCAAGCATAAGGTTCAAAGAATCAGTAGGGAAGGCGGTAGATTCGTCTGAAATGCCAATCAAAATGTCTTTTCCGGATCAATGCATGGATCGTCTAAAACAAGGCATCAATAGCTTATTTCATCCTTGCAAAG : GTTCAAAGGATTAAGCAACATGTTGAGGAGCACAATCCCAGAAGGGTTAATATACATTGCACACTTCACAGCATTGGCCTTAGTTTTTTTGCCTTCCCACAGATAGTAGGGAGCATATAGGTAGAAGAAAAAAGAGCATTTACAGTTGCAGTTGTTAACATGCTTTCATTTCTTTTAGTTTGGTAAACATTGTTTGAATGAAAGTGAGAATTTGAATTAATACGGAAAAGGGTCAAAAATGTCTCTGAACTATCGCGAAAGGTCATAATATACCCTTCGTCTTTGTCCATCTATTATGCTAATAATACTTTTCGGATTTTTA</gDNA_template>
            <first_frame> L  L  Y  *  Q  N  F  N  F  K  *  F  F  L  R  A  S  R  T  L  H  *  A  A  P  F  H   : G  R  D  D  Y  K  G  S  V  Q  E  I  R  K  M  E  S  S  A  S  Y  I  W  S  L  L  G  H  G  N  R  R  W  L  W  G  G  M  G  S  W  I  W  S  *  G  Y  W  L  C  W  S  W  M  W  C  W  I  Q  R  W  L  L  S  A  R  R  W  H  W  S  T  C  Q  L  H  L  H  R  S  L  Q  C :   I  H  S  C  Q  K  W  C  Y  *  D  V  S  I  N  *  Y  S  K  H  E  K  H  C  G  R  E  S  V  L  P  R  F  K  Y  C  W  L  P  R  K  S  D  S  V  F  F  K  H  K  V  Q  R  I  S  R  E  G  G  R  F  V  *  N  A  N  Q  N  V  F  S  G  S  M  H  G  S  S  K  T  R  H  Q  *  L  I  S  S  L  Q  R :   F  K  G  L  S  N  M  L  R  S  T  I  P  E  G  L  I  Y  I  A  H  F  T  A  L  A  L  V  F  L  P  S  H  R  *  *  G  A  Y  R  *  K  K  K  E  H  L  Q  L  Q  L  L  T  C  F  H  F  F  *  F  G  K  H  C  L  N  E  S  E  N  L  N  *  Y  G  K  G  S  K  M  S  L  N  Y  R  E  R  S  *  Y  T  L  R  L  C  P  S  I  M  L  I  I  L  F  G  F  L </first_frame>
            <second_frame>  Y  Y  I  N  K  I  S  I  S  N  N  F  S  F  E  L  R  E  H  Y  T  E  Q  H  P  F  M  :  V  E  M  I  I  K  G  L  F  R  R  Y  E  R  W  N  P  V  H  P  T  Y  G  A  F  W  G  M  G  I  G  V  G  C  G  V  G  W  G  P  G  F  G  P  E  A  I  G  Y  V  G  A  G  C  G  V  G  F  S  V  G  F  S  L  L  G  V  G  I  G  L  P  A  N  Y  I  Y  T  G  P  Y  N   : A  F  T  A  A  R  S  G  A  I  E  M  S  R  S  T  D  I  R  S  M  R  N  I  V  E  E  S  R  C  Y  L  D  S  N  I  A  G  F  Q  E  R  V  I  Q  S  F  S  S  I  R  F  K  E  S  V  G  K  A  V  D  S  S  E  M  P  I  K  M  S  F  P  D  Q  C  M  D  R  L  K  Q  G  I  N  S  L  F  H  P  C  K   : G  S  K  D  *  A  T  C  *  G  A  Q  S  Q  K  G  *  Y  T  L  H  T  S  Q  H  W  P  *  F  F  C  L  P  T  D  S  R  E  H  I  G  R  R  K  K  S  I  Y  S  C  S  C  *  H  A  F  I  S  F  S  L  V  N  I  V  *  M  K  V  R  I  *  I  N  T  E  K  G  Q  K  C  L  *  T  I  A  K  G  H  N  I  P  F  V  F  V  H  L  L  C  *  *  Y  F  S  D  F   </second_frame>
            <third_frame>   T  I  L  T  K  F  Q  F  Q  I  I  F  P  S  S  F  A  N  I  T  L  S  S  T  L  S  W :   *  R  *  L  *  R  V  C  S  G  D  T  K  D  G  I  Q  C  I  L  H  M  E  P  S  G  A  W  E  *  A  L  A  V  G  W  D  G  V  L  D  L  V  L  R  L  L  V  M  L  E  L  D  V  V  L  D  S  A  L  A  S  L  C  S  A  L  A  L  V  Y  L  P  I  T  F  T  Q  V  L  T  M  :  H  S  Q  L  P  E  V  V  L  L  R  C  L  D  Q  L  I  F  E  A  *  E  T  L  W  K  R  V  G  V  T  S  I  Q  I  L  L  A  S  K  K  E  *  F  S  L  F  Q  A  *  G  S  K  N  Q  *  G  R  R  *  I  R  L  K  C  Q  S  K  C  L  F  R  I  N  A  W  I  V  *  N  K  A  S  I  A  Y  F  I  L  A  K  :  V  Q  R  I  K  Q  H  V  E  E  H  N  P  R  R  V  N  I  H  C  T  L  H  S  I  G  L  S  F  F  A  F  P  Q  I  V  G  S  I  *  V  E  E  K  R  A  F  T  V  A  V  V  N  M  L  S  F  L  L  V  W  *  T  L  F  E  *  K  *  E  F  E  L  I  R  K  R  V  K  N  V  S  E  L  S  R  K  V  I  I  Y  P  S  S  L  S  I  Y  Y  A  N  N  T  F  R  I  F  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C12HBa0216D15.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="18323" stop="18403"/>
                    <exon start="19916" stop="20162"/>
                    <exon start="20320" stop="20592"/>
                    <exon start="21542" stop="21555"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>612</number_coding_nucleotides>
                  <number_encoded_amino_acids>204</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>YYINKISISNNFSFELREHYTEQHPFMVEMIIKGLFRRYERWNPVHPTYGAFWGMGIGVGCGVGWGPGFGPEAIGYVGAGCGVGFSVGFSLLGVGIGLPANYIYTGPYNAFTAARSGAIEMSRSTDIRSMRNIVEESRCYLDSNIAGFQERVIQSFSSIRFKESVGKAVDSSEMPIKMSFPDQCMDRLKQGINSLFHPCKGSKD*</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="94675" PGL_stop="95143"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="94675" e_stop="95143"/>
          </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="94675" e_stop="95143" e_length="469"/>
          </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="94675" stop="95143"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M79-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>TTAGGTTTTTGTGTGGTTCAACGTTTTTGGTTTTGATTTTTATGTGTTTTCTTAGTTCCTTGCTTCACCATTTTGATGGTATTTTGAGTTTTTGATGTTCTGTCGGCATAAAGTAGTGATTTTTCAGACAGTTTGGTATTATGGAGTATGTTTCTTTGCTCTTCTCTAATTTGGATTGGTTCTGATTTGTATATGCTTGTTTTAGTTTCGATGGTTTTTGAGTTTTTGATGATTCATTGGCACAAAGTAGTGATTTTTCAGACTGTTGGGTTTTGTGGGGTTCCCGTGCTTGCTCTTCACTAATTTGGATTGGTTCTGATTTGTATATGTTTTAGTTTTGATGGTTTTTGAGTTTTTGATGATTCATCGGCACAAAGTAGTGATCTTTCAGACAGTTGGGTTTTGTGGGGTTCACGTGCTTATTCTTCACTATTCTCGGTTGGTTTGATTTGTAGGTCCGTTTTAGCAT</gDNA_template>
            <first_frame> L  G  F  C  V  V  Q  R  F  W  F  *  F  L  C  V  F  L  V  P  C  F  T  I  L  M  V  F  *  V  F  D  V  L  S  A  *  S  S  D  F  S  D  S  L  V  L  W  S  M  F  L  C  S  S  L  I  W  I  G  S  D  L  Y  M  L  V  L  V  S  M  V  F  E  F  L  M  I  H  W  H  K  V  V  I  F  Q  T  V  G  F  C  G  V  P  V  L  A  L  H  *  F  G  L  V  L  I  C  I  C  F  S  F  D  G  F  *  V  F  D  D  S  S  A  Q  S  S  D  L  S  D  S  W  V  L  W  G  S  R  A  Y  S  S  L  F  S  V  G  L  I  C  R  S  V  L  A  </first_frame>
            <second_frame>  *  V  F  V  W  F  N  V  F  G  F  D  F  Y  V  F  S  *  F  L  A  S  P  F  *  W  Y  F  E  F  L  M  F  C  R  H  K  V  V  I  F  Q  T  V  W  Y  Y  G  V  C  F  F  A  L  L  *  F  G  L  V  L  I  C  I  C  L  F  *  F  R  W  F  L  S  F  *  *  F  I  G  T  K  *  *  F  F  R  L  L  G  F  V  G  F  P  C  L  L  F  T  N  L  D  W  F  *  F  V  Y  V  L  V  L  M  V  F  E  F  L  M  I  H  R  H  K  V  V  I  F  Q  T  V  G  F  C  G  V  H  V  L  I  L  H  Y  S  R  L  V  *  F  V  G  P  F  *  H </second_frame>
            <third_frame>   R  F  L  C  G  S  T  F  L  V  L  I  F  M  C  F  L  S  S  L  L  H  H  F  D  G  I  L  S  F  *  C  S  V  G  I  K  *  *  F  F  R  Q  F  G  I  M  E  Y  V  S  L  L  F  S  N  L  D  W  F  *  F  V  Y  A  C  F  S  F  D  G  F  *  V  F  D  D  S  L  A  Q  S  S  D  F  S  D  C  W  V  L  W  G  S  R  A  C  S  S  L  I  W  I  G  S  D  L  Y  M  F  *  F  *  W  F  L  S  F  *  *  F  I  G  T  K  *  *  S  F  R  Q  L  G  F  V  G  F  T  C  L  F  F  T  I  L  G  W  F  D  L  *  V  R  F  S   </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="C12HBa0216D15.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="95742" PGL_stop="95241"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="95742" e_stop="95241"/>
          </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="95742" e_stop="95241" e_length="502"/>
          </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="95742" stop="95241"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M79-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>AGAATATAACAAAAAAGCAGATAAATCAGTTAATTATGCCTCAATCTCAACAAGTGAATAACAAATCCTATCAGAAGATATAGTAGACGATAAACAGTGAAGGTAGAAGCCTAACTCTATGACATTATCTTGAGACCCAAAACACTTCATCAAAGACTCAAAAGAAATAATTTGTTCACCAAGTACTATTAACTAATTATCAAAACTAGAATTCTCAAAATAAAAAATAACAAATCTTATCAGTCACATGGACATTCATTAAACATCATGAAGAAGACAACAAGGGAAGGTCAAAACTGGACTCCATGGCACATAAGATAATAACAAAAGGTAGTTTAAGGCCTAAAACACTTCAAAAATAAAATTTATTCACCAGATATCAATAATATTATCTGTTCTTCCTTCATTCATGAGGGGCATGCACAAGAGACAATATACATCATTTCTCCTTTTACTTTTTCTTTCCTGAGGAAGTAAAAGGAGCAGAAAGCAGATAGAAAGA</gDNA_template>
            <first_frame> R  I  *  Q  K  S  R  *  I  S  *  L  C  L  N  L  N  K  *  I  T  N  P  I  R  R  Y  S  R  R  *  T  V  K  V  E  A  *  L  Y  D  I  I  L  R  P  K  T  L  H  Q  R  L  K  R  N  N  L  F  T  K  Y  Y  *  L  I  I  K  T  R  I  L  K  I  K  N  N  K  S  Y  Q  S  H  G  H  S  L  N  I  M  K  K  T  T  R  E  G  Q  N  W  T  P  W  H  I  R  *  *  Q  K  V  V  *  G  L  K  H  F  K  N  K  I  Y  S  P  D  I  N  N  I  I  C  S  S  F  I  H  E  G  H  A  Q  E  T  I  Y  I  I  S  P  F  T  F  S  F  L  R  K  *  K  E  Q  K  A  D  R  K  </first_frame>
            <second_frame>  E  Y  N  K  K  A  D  K  S  V  N  Y  A  S  I  S  T  S  E  *  Q  I  L  S  E  D  I  V  D  D  K  Q  *  R  *  K  P  N  S  M  T  L  S  *  D  P  K  H  F  I  K  D  S  K  E  I  I  C  S  P  S  T  I  N  *  L  S  K  L  E  F  S  K  *  K  I  T  N  L  I  S  H  M  D  I  H  *  T  S  *  R  R  Q  Q  G  K  V  K  T  G  L  H  G  T  *  D  N  N  K  R  *  F  K  A  *  N  T  S  K  I  K  F  I  H  Q  I  S  I  I  L  S  V  L  P  S  F  M  R  G  M  H  K  R  Q  Y  T  S  F  L  L  L  L  F  L  S  *  G  S  K  R  S  R  K  Q  I  E  R </second_frame>
            <third_frame>   N  I  T  K  K  Q  I  N  Q  L  I  M  P  Q  S  Q  Q  V  N  N  K  S  Y  Q  K  I  *  *  T  I  N  S  E  G  R  S  L  T  L  *  H  Y  L  E  T  Q  N  T  S  S  K  T  Q  K  K  *  F  V  H  Q  V  L  L  T  N  Y  Q  N  *  N  S  Q  N  K  K  *  Q  I  L  S  V  T  W  T  F  I  K  H  H  E  E  D  N  K  G  R  S  K  L  D  S  M  A  H  K  I  I  T  K  G  S  L  R  P  K  T  L  Q  K  *  N  L  F  T  R  Y  Q  *  Y  Y  L  F  F  L  H  S  *  G  A  C  T  R  D  N  I  H  H  F  S  F  Y  F  F  F  P  E  E  V  K  G  A  E  S  R  *  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="C12HBa0216D15.1"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="4" PGL_strand="+" PGL_start="109184" PGL_stop="110599"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="109184" e_stop="109552"/>
            <exon e_start="110384" e_stop="110599"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.994" acc_prob="0.972" e_score="0.981"/>
          <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="0.981">
            <gDNA_exon_boundary e_start="109184" e_stop="109552" e_length="369"/>
          </exon>
          <intron i_serial="1" don_prob="0.994" acc_prob="0.972">
            <gDNA_intron_boundary i_start="109553" i_stop="110383" i_length="831"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="110384" e_stop="110599" e_length="216"/>
          </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="109184" stop="109552"/>
              <exon start="110384" stop="110599"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1912" 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>GAAAACCCTACCGCCGCTGCTCTCCTTTTACCCCAAATCTGAGCAAATCGAAAGCAACAATGGCAGAAGAAGCACAGTACGGTGCACCAGATGCCGGTAACAACAAGAGGAAGTACGATGATCAAGCGGCACCGTCTCCTGGTCCTCGTAGACCTACTGGATTTTCTGCTCCGATCGCTTCCTTATCTTCTCCTGACGGTGCTGCTCCTCCTTCGTCTTACAACAATGTTCCGCCGCCTATGGATGATTTCCAGTTGGCTAAGCAGAAGGCTCAGGAGATCGCTGCTAGGTTGTTGAATAGTGCTGAAGCGAAGAAACCTAGAGTTGATAATAACGGCGGTGGTGCCGGTGGATATGATTCCTATGAAC : ACAAGCCCATTGTTACTCCTTCAGTTACAAGTTCATATGGTTATCCGGGGCAGAGCAAGAAGATTGAAATACCAAATGGCAGAGTTGGTGTGATTATAGGAAAAGGTGGGGAGACCATCAAGTATCTTCAACTCCAGTCTGGAGCCAAAATTCAGGTTACTAGAGACATGGATGCTGATCCTAATTCTCAAAACAGAGCAGTTGAACTCATGGGTA</gDNA_template>
            <first_frame> E  N  P  T  A  A  A  L  L  L  P  Q  I  *  A  N  R  K  Q  Q  W  Q  K  K  H  S  T  V  H  Q  M  P  V  T  T  R  G  S  T  M  I  K  R  H  R  L  L  V  L  V  D  L  L  D  F  L  L  R  S  L  P  Y  L  L  L  T  V  L  L  L  L  R  L  T  T  M  F  R  R  L  W  M  I  S  S  W  L  S  R  R  L  R  R  S  L  L  G  C  *  I  V  L  K  R  R  N  L  E  L  I  I  T  A  V  V  P  V  D  M  I  P  M  N  :  T  S  P  L  L  L  L  Q  L  Q  V  H  M  V  I  R  G  R  A  R  R  L  K  Y  Q  M  A  E  L  V  *  L  *  E  K  V  G  R  P  S  S  I  F  N  S  S  L  E  P  K  F  R  L  L  E  T  W  M  L  I  L  I  L  K  T  E  Q  L  N  S  W  V </first_frame>
            <second_frame>  K  T  L  P  P  L  L  S  F  Y  P  K  S  E  Q  I  E  S  N  N  G  R  R  S  T  V  R  C  T  R  C  R  *  Q  Q  E  E  V  R  *  S  S  G  T  V  S  W  S  S  *  T  Y  W  I  F  C  S  D  R  F  L  I  F  S  *  R  C  C  S  S  F  V  L  Q  Q  C  S  A  A  Y  G  *  F  P  V  G  *  A  E  G  S  G  D  R  C  *  V  V  E  *  C  *  S  E  E  T  *  S  *  *  *  R  R  W  C  R  W  I  *  F  L  *  T :   Q  A  H  C  Y  S  F  S  Y  K  F  I  W  L  S  G  A  E  Q  E  D  *  N  T  K  W  Q  S  W  C  D  Y  R  K  R  W  G  D  H  Q  V  S  S  T  P  V  W  S  Q  N  S  G  Y  *  R  H  G  C  *  S  *  F  S  K  Q  S  S  *  T  H  G   </second_frame>
            <third_frame>   K  P  Y  R  R  C  S  P  F  T  P  N  L  S  K  S  K  A  T  M  A  E  E  A  Q  Y  G  A  P  D  A  G  N  N  K  R  K  Y  D  D  Q  A  A  P  S  P  G  P  R  R  P  T  G  F  S  A  P  I  A  S  L  S  S  P  D  G  A  A  P  P  S  S  Y  N  N  V  P  P  P  M  D  D  F  Q  L  A  K  Q  K  A  Q  E  I  A  A  R  L  L  N  S  A  E  A  K  K  P  R  V  D  N  N  G  G  G  A  G  G  Y  D  S  Y  E   : H  K  P  I  V  T  P  S  V  T  S  S  Y  G  Y  P  G  Q  S  K  K  I  E  I  P  N  G  R  V  G  V  I  I  G  K  G  G  E  T  I  K  Y  L  Q  L  Q  S  G  A  K  I  Q  V  T  R  D  M  D  A  D  P  N  S  Q  N  R  A  V  E  L  M  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="C12HBa0216D15.1" strand="+"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="109186" stop="109552"/>
                    <exon start="110384" stop="110598"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>582</number_coding_nucleotides>
                  <number_encoded_amino_acids>194</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KPYRRCSPFTPNLSKSKATMAEEAQYGAPDAGNNKRKYDDQAAPSPGPRRPTGFSAPIASLSSPDGAAPPSSYNNVPPPMDDFQLAKQKAQEIAARLLNSAEAKKPRVDNNGGGAGGYDSYEHKPIVTPSVTSSYGYPGQSKKIEIPNGRVGVIIGKGGETIKYLQLQSGAKIQVTRDMDADPNSQNRAVELMG</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 5 chains have been computed
$ 
$ memory statistics:
$ 8128 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 2032 bytes was the average size of a spliced alignment
$ 9184 bytes predicted gene locations in total
$ 4 predicted gene locations have been stored
$ 2296 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 5 backtrace matrices have been allocated
$ 
$ date finished: 2009-07-24 22:27:25
-->
