<?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="2008-11-23 23:08:11"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C07SLm0093E04-gGJk3/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C07SLm0093E04-gGJk3/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-C07SLm0093E04-gGJk3/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M7169" ref_strand="+" ref_description="SGN-M7169 C2_At2g04842 [cosii_markers]">
      <seq>gaatatgtttgatcagatggagattgaggaagagctttttcagctacggccaatgaactgcccttatcatgtattgatctataagaggcagttacactcttatcgggattttccgatcagagttgcagagttgggaacagtgtataggtatgagttatctggaagcttacatgggcttttccgtgtaagaggttttactcaggatgatgcacacatcttctgtttagaggatcaaattanagatgaaatcaggggcgttttagatctgaccgaggaaatattacagcaatttggttttgacaagtatgaggtgaacctttcaacaaggccagaaaaagctgttggagatgatgagatttgggaaaaagcaacatttgcacttaaggatgctttacaagataagggttggagctatcaaatagatgatggtggtggggccttctatggtccaaagattgatctgaaaattgaggatgctcttggaaggaagtggcaatgctcaactatacaggttgatttcaatttaccccagcgctttgacattacatatgttgattcaaatcaagagaggaagcgacctatcatgatccatatagcagttcttggatctttggagcgcttttttggtgttctcatagagaattatgctggtgattttccactttggctttctcccatccaagctcgagttttaccagttactgatgcgcagctccagtactgcaatgaagtaggcaagaaactaaaagctag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07SLm0093E04-gGJk3/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07SLm0093E04.2" temp_strand="-" temp_description="C07SLm0093E04.2  AC212653.2 htgs_phase:2 submitted_to_sgn_as:gi|167744689|gb|AC212653.2| upload_account_name:france Solanum lycopersicum chromosome 7 clone C07SLm0093E04, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces">
        <position start="6066" stop="2275"/>
      </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="5766" g_stop="5565" g_length="202"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="202" r_length="202" r_score="0.985"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="5564" i_stop="3644" i_length="1921">
            <donor d_prob="0.968" d_score="0.98"/>
            <acceptor a_prob="0.997" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="3643" g_stop="3335" g_length="309"/>
          <reference_exon_boundary r_type="cDNA" r_start="203" r_stop="511" r_length="309" r_score="0.971"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="3334" i_stop="3107" i_length="228">
            <donor d_prob="0.774" d_score="1.00"/>
            <acceptor a_prob="0.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="3106" g_stop="2906" g_length="201"/>
          <reference_exon_boundary r_type="cDNA" r_start="512" r_stop="712" r_length="201" r_score="0.985"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="2905" i_stop="2616" i_length="290">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.865" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="2615" g_stop="2575" g_length="41"/>
          <reference_exon_boundary r_type="cDNA" r_start="713" r_stop="753" r_length="41" r_score="0.976"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07SLm0093E04.2" gen_strand="-" ref_id="SGN-M7169" ref_strand="+">
        <total_alignment_score>0.979</total_alignment_score>
        <cumulative_length_of_scored_exons>753</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07SLm0093E04.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M7169" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="5766" e_stop="5565"/>
          <exon e_start="3643" e_stop="3335"/>
          <exon e_start="3106" e_stop="2906"/>
          <exon e_start="2615" e_stop="2575"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GAATATGTTTGATCAGATGGAGATTGAGGAAGAGCTTTTTCAGCTTCGGCCAATGAACTGCCCTTATCATGTATTGATCTATAAGAGGCAGTTACACTCTTATCGGGATTTTCCAATCAGAGTTGCAGAGTTGGGAACAGTGTATAGGTATGAGTTATCCGGAAGCTTACATGGGCTTTTCCGTGTAAGAGGTTTTACTCAGGTGCGTTCCAAGTATAAAATATTTATTTCCTCAAGTCTCAACATCTGTATCCTTGATTAGAACTATCATCCCTAAGAGGGAGCGGTTACTGATCAATTGTCTGAAAGAAGAAGGAGTGAAGGGTGGTACAAAATGGGTCTTGCATTTTATTTGTGTTTTCCTGTGCAGTAACCACAATGACCTATGTGTTATGCAACAATTAATTTGAGTAAATGAAGATGGATTTTCTAGAAGCCCATTGTTGTGGAGCACAAACATACTTGCTGTAGTTGATATAAGTGGTCTCTTTTCTCCTCTTGGAGGGCTAGGATTTTGTCTTGGTCTGCTTTGGGTTCTCTGGGACATAGAGAACATACCTAATGTGGTTGAACAAACCAGTATGTTCTCTCTTTAGGGGTTTTGTTTACCATTGAGTCTCAACATCTGAACTTTGTTATTGGCAGAAACATTTGGTATTTTCCAGTAAACATGAAAAGTTTCTCAATTAAGAGAACTGCAAATCATTTATATTGGTTTTAGTTTCTTTTTATTGTGAAATTTTTCATTGGGCATCCGACGGTAAAAAGAAAATGATTCAGTTCCAGAGCTAAAGATCATAGTTCTCGAACGAGCAATTGAAAAGATTCTGGATCATCTTCGGGATAAGGTATTATTCTCCCAATGATCGTAGTACCGTTTACGTCCTATCGAGCTCCAATATGATCCAATTTATAAGTAAGCATCTCTTGTAAAATGTGAGCAACCCCAAACCCTTCTAGATCCCAAACCTCAGTTTCTTGTCAGATCCCAGAGGAGTGGTGTTTATGACACCAGAAAGACTAGCAATTTCTTCCAGATGAAACATTAGTATGCCCCATAAAAGTTCCATCACCCGCGAAACATATACAAAGAACTGCCTGAGAAGGGAGAGAGGAAAACAACAAACACTAACCTGTACACATAAAAGTAGTGCCTGCTATAAATGAGGACAGTCGGACACTTCTTTAGATTACTTTAATTTTCTTTTTCTTGCCCCTATACTAATTCAGGGGCAGCCTGCTTCCGCCACAAGGCTACATGCATAAGCCAAGTAATCCTACTCACAGTGGCTGGAGTAGATCACATTAGATTTTAGAGTGTTGTAGTTGGGATAGGAACTTAAAATCTCTAGGTTGTACCATTGTACTCCTTTGCCTCCACCACTAGGCCGTCCTCTTAAAGACCAGACTACTTTGATTTGCTCACTTTTTTTGGTCATTATTGTTTAATGTTCCTTCCATCTTTTCCGGTCAGCACTTAACTTGGTCCAAAGATTTCCCCTTCTGCTTGTTGCTTGTCACACCTTCCTTGAGAATTATGCGCAATGCAGACATTCCTCATCGTCCCCAAAACTATATATCCAGAATTTCTGGAATGTTCATAATTCTGCAATCTGACTGTGGAGCCAACCCCCATTATCTCCTCTATTCATACCAAGGACTTTCCAAGAGGAGCACCTAAAAAATTAAAGAGATTTGACTGAGTGCATTGCTTGTGATGTTGTAGAGTTTCAGCTTTTTAACCTGCATAACTTAGATATCTTACATTATGTTATACTTCAGCCTTTTGTAAAAGACTTTTATTGTACTCTTTTACCCTGTATTACAGGTGGTGGTGGGGAGTTGTTAACTTGTTAACTTTTTTACCTTTTTGTTATCTTCTCCACTGCTGTAAGAGATTTTTGTTTCCACATTTATAATTATAATCATTAAAACATATTGCAATGTACAGTCGTCTTAGTAGTATGCTTGTCCTCTCTCAGAAAAGGACGAGAAATATTGAATAGTATGAGATAATTCAGATAAAATGTCTGCTTTCAAGTGTTGATTCTTTCATCCAGAAACTCTAAAGTAGTAGCAGCTTGCATTACTGTTATCTGATACCCCCTATATTGATTTTGCAGGATGATGCACACATCTTCTGTTTAGAAGATCAAATTAAAGATGAAATCAGGGGTGTTTTAGATCTGACAGAGGAAATATTACAGCAATTTGGTTTTGACAAGTATGAAGTGAACCTCTCAACAAGGCCAGAAAAAGCTGTTGGAGATGATGAGATCTGGGAAAAAGCAACATTTGCACTTAAGGATGCTTTAGAAGATAAAGGTTGGAGCTATCAAATAGATGATGGTGGTGGGGCCTTCTATGGTCCAAAGATTGATCTGAAAATTGAGGATGCTCTTGGAAGGAAGTGGCAATGCTCAACTATACAGGCATGTTTTGATCTTGGTCTCCTTTTCCATTGGCCTGTATGCTCCATGGGACCACTCTCCTCTGTCTTCTTGTCTTCTTGGTCCCTCTGCTCGCTTTTTTCTAAAGTCTAATCAAGTTTGCTTTAGTCTTGACCTCTCGCAAACTTGAAAGTGTTTTTTCTATTCATTTTATTTGTCCAAGCTCCTTAGCTTCTTTGTAATCCTTCATTGACACATGAGCTTCTACAGGTTGATTTCAATTTACCCCAGCGCTTTGACATTACATATGTCGATTCAAATCAAGAGAGGAAGCGACCTATCATGATCCATAGAGCAGTTCTTGGATCTTTGGAGCGCTTTTTTGGTGTTCTCATAGAGAATTATGCTGGTGATTTTCCACTTTGGCTTTCTCCCATCCAAGCTCGAGTTTTACCAGTTACTGATGCTCAGGTAATCAATACTCTTTTGACTAATTCTCGTCTCCATTTGCATAAATACATGTTTAGTATTTTACCCTGACGAGAGATGCTTACACTACACTAACTCCTGGAAGTCGCCCTTTAACATAATTTGTGGTTCTATTTGAGTGTAGAGTACATCTTGATCCATTTCATTTTCATCAAGTAAAAAACTAGCACAAGGCTTCATAATTTCTTCTATATTTTAATCTGTGAAATTTGCTTCTGGTGTTATATATATATGGTGTCTCATACTGACTTATGAGAGCATTATGTTCACAGCTCCAGTACTGCAATGAAGTAGTCAAGAAACTAAAAGCTAG</genome_strand>
        <mrna_strand>GAATATGTTTGATCAGATGGAGATTGAGGAAGAGCTTTTTCAGCTACGGCCAATGAACTGCCCTTATCATGTATTGATCTATAAGAGGCAGTTACACTCTTATCGGGATTTTCCGATCAGAGTTGCAGAGTTGGGAACAGTGTATAGGTATGAGTTATCTGGAAGCTTACATGGGCTTTTCCGTGTAAGAGGTTTTACTCAG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GATGATGCACACATCTTCTGTTTAGAGGATCAAATTANAGATGAAATCAGGGGCGTTTTAGATCTGACCGAGGAAATATTACAGCAATTTGGTTTTGACAAGTATGAGGTGAACCTTTCAACAAGGCCAGAAAAAGCTGTTGGAGATGATGAGATTTGGGAAAAAGCAACATTTGCACTTAAGGATGCTTTACAAGATAAGGGTTGGAGCTATCAAATAGATGATGGTGGTGGGGCCTTCTATGGTCCAAAGATTGATCTGAAAATTGAGGATGCTCTTGGAAGGAAGTGGCAATGCTCAACTATACAG....................................................................................................................................................................................................................................GTTGATTTCAATTTACCCCAGCGCTTTGACATTACATATGTTGATTCAAATCAAGAGAGGAAGCGACCTATCATGATCCATATAGCAGTTCTTGGATCTTTGGAGCGCTTTTTTGGTGTTCTCATAGAGAATTATGCTGGTGATTTTCCACTTTGGCTTTCTCCCATCCAAGCTCGAGTTTTACCAGTTACTGATGCGCAG..................................................................................................................................................................................................................................................................................................CTCCAGTACTGCAATGAAGTAGGCAAGAAACTAAAAGCTAG</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-C07SLm0093E04-gGJk3/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M821" ref_strand="+" ref_description="SGN-M821 SSR148 [est_by_read_no_qc_info]">
      <seq>gctcttcacttcctcttataaatccatttctcctctcagtagaaaccccttttcttccttcccaattcgtcagtatcgtattctttttgttcttgatccctctaacaacaacaacaacaacaaaactaaccggaacaagttgctgagacgtcgcacttctttctctacccatgcttccaccgccctacaagaagctcctgccccaaatgagaaaatggttctcccaactaacgagtcatcagatgggctacttcgaattcgccatacgtgtgctcatgttatggccatggcagtccaaaaactctacccgaatgcaaaagtgacaattgggccctggatcgataatggtttttattatgattttgatatggagcctttgactgacagtgacctgaagaggattaagaaggaaatggatcgaattatcagccgaaacttgcctcttgttagagaagaagttagccgggatgaagctcaaagaagaataatgtctatcaacgaaccttacaagatcgaaattttagagagcataaaggaggaaccaattaccatttatcatattggtgatgaat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07SLm0093E04-gGJk3/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07SLm0093E04.2" temp_strand="-" temp_description="C07SLm0093E04.2  AC212653.2 htgs_phase:2 submitted_to_sgn_as:gi|167744689|gb|AC212653.2| upload_account_name:france Solanum lycopersicum chromosome 7 clone C07SLm0093E04, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces">
        <position start="9606" stop="7699"/>
      </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="9307" g_stop="9040" g_length="268"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="268" r_length="268" r_score="0.996"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="9039" i_stop="8457" i_length="583">
            <donor d_prob="0.942" d_score="1.00"/>
            <acceptor a_prob="0.977" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="8456" g_stop="8310" g_length="147"/>
          <reference_exon_boundary r_type="cDNA" r_start="269" r_stop="415" r_length="147" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="8309" i_stop="8155" i_length="155">
            <donor d_prob="0.978" d_score="1.00"/>
            <acceptor a_prob="0.883" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="8154" g_stop="8007" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="416" r_stop="563" r_length="148" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07SLm0093E04.2" gen_strand="-" ref_id="SGN-M821" ref_strand="+">
        <total_alignment_score>0.998</total_alignment_score>
        <cumulative_length_of_scored_exons>563</cumulative_length_of_scored_exons>
        <coverage percentage="0.984" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07SLm0093E04.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M821" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="9307" e_stop="9040"/>
          <exon e_start="8456" e_stop="8310"/>
          <exon e_start="8154" e_stop="8007"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTCTTCACTTCCTCTTATAAATCCATTTCTCCTCTCAGTAGAAACCCCTTTTCTTCCTTCCCAATTCGTCAGTATCGTATTCTTTTTGTTCTTGATCCCTCTAACAACAACAACAACAACAAAACTAACCGGAACAAGTTGCTGAGACGTCGCACTTCTTTCTCTACCCATGCTTCCACCGCCCTACAAGAAGCTCCTGCCCCAAATGAGAAAATGGTTCTCCCAACTAACGAGTCATCAGATGGGCTACTTCGAATTCGCCATACGGTAATGTTGATACTGGTTCCGTTTATGGGTATTCATGAAATTGAATTGTTTCCAGTTTTATCGTGTTTATAATTGAAAATATTAAGTGGGTCGATTACAGAAATTAGTATTGCTTAGTATATATACATTGTTGCTCAATATAGTTATCAGTAAAAAAATGCGTTTTTTATACTGTTTCCTAGATTACAGAAAGCTAATTTTCTTGTGAAGTAACTTGTTTAGTTTATAACTCATTGTATACTCCTTGTACATTTGTTGGATTTGGGAAGTTTGATTTTTTTTTAATAAGTGTGGTTTCCAACCCAGCTTGTGTGCACCTTTGACTAATTTCATAGGTAAATTTGTCTACCAAGGAAAAGAAATCATTTAATGTTGATTTGGGGAGTTTTTTTTCTTTTATTATACTCTATTAATGTTGTCGGATATGAGGTTTGTATTATCTGTTGCTTGTTTTTAGCGAGGATTGGTGTGTTTACTAGTTCATTATGTAGAATGCTGAGTTTTTATAGTTTAAATGTGACCAGTAGATTTTGGTAATATAAATTACCATTCTGAGGGTGGGTTGATGTGTTCTTTGCTGCAGTGTGCTCATGTTATGGCCATGGCAGTCCAAAAACTCTACCCGAATGCAAAAGTGACAATTGGGCCCTGGATCGATAATGGTTTTTATTATGATTTTGATATGGAGCCTTTGACTGACAGTGACCTGAAGAGGATTAAGAAGGAAATGGTAAGCTAACTTGTGCTTTTTAGTGATTGTTAGAAAGTTACTCCCTCTGCCTCCCCACAAGGGTCCACTCCCCCTAAAGAACTAAAAAATAGTTTGATCTTGTCAATGAAGCTTTGATTTTTGGTTAGAGAATTGACATCTTAAATTTTCTCTAGGATCGAATTATCAGCCGAAACTTGCCTCTTGTTAGAGAAGAAGTTAGCCGGGATGAAGCTCAAAGAAGAATAATGTCTATCAACGAACCTTACAAGATCGAAATTTTAGAGAGCATAAAGGAGGAACCAATTACCATTTATCATATTG</genome_strand>
        <mrna_strand>GCTCTTCACTTCCTCTTATAAATCCATTTCTCCTCTCAGTAGAAACCCCTTTTCTTCCTTCCCAATTCGTCAGTATCGTATTCTTTTTGTTCTTGATCCCTCTAACAACAACAACAACAACAAAACTAACCGGAACAAGTTGCTGAGACGTCGCACTTCTTTCTCTACCCATGCTTCCACCGCCCTACAAGAAGCTCCTGCCCCAAATGAGAAAATGGTTCTCCCAACTAACGAGTCATCAGATGGGCTACTTCGAATTCGCCATACG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGTGCTCATGTTATGGCCATGGCAGTCCAAAAACTCTACCCGAATGCAAAAGTGACAATTGGGCCCTGGATCGATAATGGTTTTTATTATGATTTTGATATGGAGCCTTTGACTGACAGTGACCTGAAGAGGATTAAGAAGGAAATG...........................................................................................................................................................GATCGAATTATCAGCCGAAACTTGCCTCTTGTTAGAGAAGAAGTTAGCCGGGATGAAGCTCAAAGAAGAATAATGTCTATCAACGAACCTTACAAGATCGAAATTTTAGAGAGCATAAAGGAGGAACCAATTACCATTTATCATATTG</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-C07SLm0093E04-gGJk3/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M821-2" ref_strand="+" ref_description="SGN-M821-2 SSR148-2 [est_by_read]">
      <seq>tcttcacttcctcttataaatccatttctcctctcagtagaaaccccttttcttccttcccaattcgtcagtatcgtattctttttgttcttgatccctctaacaacaacaacaacaacaaaactaaccggaacaagttgctgagacgtcgcacttctttctctacccatgcttccaccgccctacaagaagctcctgccccaaatgagaaaatggttctcccaactaacgagtcatcagatgggctacttcgaattcgccatacgtgtgctcatgttatggccatggcagtccaaaaactctacccgaatgcaaaagtgacaattgggccctggatcgataatggtttttattatgattttgatatggagcctttgactgacagtgacctgaagaggattaagaaggaaatggatcgaattatcagccgaaacttgcctcttgttagagaagaagttagccgggatgaagctcaaagaagaataatgtctatcaacgaaccttacaagatcgaaattttagagagcataaaggaggaaccaattaccatttatcatattggtgatgaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C07SLm0093E04-gGJk3/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C07SLm0093E04.2" temp_strand="-" temp_description="C07SLm0093E04.2  AC212653.2 htgs_phase:2 submitted_to_sgn_as:gi|167744689|gb|AC212653.2| upload_account_name:france Solanum lycopersicum chromosome 7 clone C07SLm0093E04, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces">
        <position start="9605" stop="7701"/>
      </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="9305" g_stop="9040" g_length="266"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="266" r_length="266" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="9039" i_stop="8457" i_length="583">
            <donor d_prob="0.942" d_score="1.00"/>
            <acceptor a_prob="0.977" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="8456" g_stop="8310" g_length="147"/>
          <reference_exon_boundary r_type="cDNA" r_start="267" r_stop="413" r_length="147" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="8309" i_stop="8155" i_length="155">
            <donor d_prob="0.978" d_score="1.00"/>
            <acceptor a_prob="0.883" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="8154" g_stop="8007" g_length="148"/>
          <reference_exon_boundary r_type="cDNA" r_start="414" r_stop="561" r_length="148" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C07SLm0093E04.2" gen_strand="-" ref_id="SGN-M821-2" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>561</cumulative_length_of_scored_exons>
        <coverage percentage="0.986" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C07SLm0093E04.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M821-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="9305" e_stop="9040"/>
          <exon e_start="8456" e_stop="8310"/>
          <exon e_start="8154" e_stop="8007"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCTTCACTTCCTCTTATAAATCCATTTCTCCTCTCAGTAGAAACCCCTTTTCTTCCTTCCCAATTCGTCAGTATCGTATTCTTTTTGTTCTTGATCCCTCTAACAACAACAACAACAACAAAACTAACCGGAACAAGTTGCTGAGACGTCGCACTTCTTTCTCTACCCATGCTTCCACCGCCCTACAAGAAGCTCCTGCCCCAAATGAGAAAATGGTTCTCCCAACTAACGAGTCATCAGATGGGCTACTTCGAATTCGCCATACGGTAATGTTGATACTGGTTCCGTTTATGGGTATTCATGAAATTGAATTGTTTCCAGTTTTATCGTGTTTATAATTGAAAATATTAAGTGGGTCGATTACAGAAATTAGTATTGCTTAGTATATATACATTGTTGCTCAATATAGTTATCAGTAAAAAAATGCGTTTTTTATACTGTTTCCTAGATTACAGAAAGCTAATTTTCTTGTGAAGTAACTTGTTTAGTTTATAACTCATTGTATACTCCTTGTACATTTGTTGGATTTGGGAAGTTTGATTTTTTTTTAATAAGTGTGGTTTCCAACCCAGCTTGTGTGCACCTTTGACTAATTTCATAGGTAAATTTGTCTACCAAGGAAAAGAAATCATTTAATGTTGATTTGGGGAGTTTTTTTTCTTTTATTATACTCTATTAATGTTGTCGGATATGAGGTTTGTATTATCTGTTGCTTGTTTTTAGCGAGGATTGGTGTGTTTACTAGTTCATTATGTAGAATGCTGAGTTTTTATAGTTTAAATGTGACCAGTAGATTTTGGTAATATAAATTACCATTCTGAGGGTGGGTTGATGTGTTCTTTGCTGCAGTGTGCTCATGTTATGGCCATGGCAGTCCAAAAACTCTACCCGAATGCAAAAGTGACAATTGGGCCCTGGATCGATAATGGTTTTTATTATGATTTTGATATGGAGCCTTTGACTGACAGTGACCTGAAGAGGATTAAGAAGGAAATGGTAAGCTAACTTGTGCTTTTTAGTGATTGTTAGAAAGTTACTCCCTCTGCCTCCCCACAAGGGTCCACTCCCCCTAAAGAACTAAAAAATAGTTTGATCTTGTCAATGAAGCTTTGATTTTTGGTTAGAGAATTGACATCTTAAATTTTCTCTAGGATCGAATTATCAGCCGAAACTTGCCTCTTGTTAGAGAAGAAGTTAGCCGGGATGAAGCTCAAAGAAGAATAATGTCTATCAACGAACCTTACAAGATCGAAATTTTAGAGAGCATAAAGGAGGAACCAATTACCATTTATCATATTG</genome_strand>
        <mrna_strand>TCTTCACTTCCTCTTATAAATCCATTTCTCCTCTCAGTAGAAACCCCTTTTCTTCCTTCCCAATTCGTCAGTATCGTATTCTTTTTGTTCTTGATCCCTCTAACAACAACAACAACAACAAAACTAACCGGAACAAGTTGCTGAGACGTCGCACTTCTTTCTCTACCCATGCTTCCACCGCCCTACAAGAAGCTCCTGCCCCAAATGAGAAAATGGTTCTCCCAACTAACGAGTCATCAGATGGGCTACTTCGAATTCGCCATACG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGTGCTCATGTTATGGCCATGGCAGTCCAAAAACTCTACCCGAATGCAAAAGTGACAATTGGGCCCTGGATCGATAATGGTTTTTATTATGATTTTGATATGGAGCCTTTGACTGACAGTGACCTGAAGAGGATTAAGAAGGAAATG...........................................................................................................................................................GATCGAATTATCAGCCGAAACTTGCCTCTTGTTAGAGAAGAAGTTAGCCGGGATGAAGCTCAAAGAAGAATAATGTCTATCAACGAACCTTACAAGATCGAAATTTTAGAGAGCATAAAGGAGGAACCAATTACCATTTATCATATTG</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="5766" PGL_stop="2575"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="5766" e_stop="5565"/>
            <exon e_start="3643" e_stop="3335"/>
            <exon e_start="3106" e_stop="2906"/>
            <exon e_start="2615" e_stop="2575"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.968" acc_prob="0.997" e_score="0.985"/>
          <exon-intron don_prob="0.774" acc_prob="0.000" e_score="0.971"/>
          <exon-intron don_prob="0.999" acc_prob="0.865" e_score="0.985"/>
          <exon-only e_score="0.976"/>
        </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="0.985">
            <gDNA_exon_boundary e_start="5766" e_stop="5565" e_length="202"/>
          </exon>
          <intron i_serial="1" don_prob="0.968" acc_prob="0.997">
            <gDNA_intron_boundary i_start="5564" i_stop="3644" i_length="1921"/>
          </intron>
          <exon e_serial="2" e_score="0.971">
            <gDNA_exon_boundary e_start="3643" e_stop="3335" e_length="309"/>
          </exon>
          <intron i_serial="2" don_prob="0.774" acc_prob="0.000">
            <gDNA_intron_boundary i_start="3334" i_stop="3107" i_length="228"/>
          </intron>
          <exon e_serial="3" e_score="0.985">
            <gDNA_exon_boundary e_start="3106" e_stop="2906" e_length="201"/>
          </exon>
          <intron i_serial="3" don_prob="0.999" acc_prob="0.865">
            <gDNA_intron_boundary i_start="2905" i_stop="2616" i_length="290"/>
          </intron>
          <exon e_serial="4" e_score="0.976">
            <gDNA_exon_boundary e_start="2615" e_stop="2575" e_length="41"/>
          </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="5766" stop="5565"/>
              <exon start="3643" stop="3335"/>
              <exon start="3106" stop="2906"/>
              <exon start="2615" stop="2575"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M7169" 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>GAATATGTTTGATCAGATGGAGATTGAGGAAGAGCTTTTTCAGCTTCGGCCAATGAACTGCCCTTATCATGTATTGATCTATAAGAGGCAGTTACACTCTTATCGGGATTTTCCAATCAGAGTTGCAGAGTTGGGAACAGTGTATAGGTATGAGTTATCCGGAAGCTTACATGGGCTTTTCCGTGTAAGAGGTTTTACTCAG : GATGATGCACACATCTTCTGTTTAGAAGATCAAATTAAAGATGAAATCAGGGGTGTTTTAGATCTGACAGAGGAAATATTACAGCAATTTGGTTTTGACAAGTATGAAGTGAACCTCTCAACAAGGCCAGAAAAAGCTGTTGGAGATGATGAGATCTGGGAAAAAGCAACATTTGCACTTAAGGATGCTTTAGAAGATAAAGGTTGGAGCTATCAAATAGATGATGGTGGTGGGGCCTTCTATGGTCCAAAGATTGATCTGAAAATTGAGGATGCTCTTGGAAGGAAGTGGCAATGCTCAACTATACAG : GTTGATTTCAATTTACCCCAGCGCTTTGACATTACATATGTCGATTCAAATCAAGAGAGGAAGCGACCTATCATGATCCATAGAGCAGTTCTTGGATCTTTGGAGCGCTTTTTTGGTGTTCTCATAGAGAATTATGCTGGTGATTTTCCACTTTGGCTTTCTCCCATCCAAGCTCGAGTTTTACCAGTTACTGATGCTCAG : CTCCAGTACTGCAATGAAGTAGTCAAGAAACTAAAAGCTAG</gDNA_template>
            <first_frame> E  Y  V  *  S  D  G  D  *  G  R  A  F  S  A  S  A  N  E  L  P  L  S  C  I  D  L  *  E  A  V  T  L  L  S  G  F  S  N  Q  S  C  R  V  G  N  S  V  *  V  *  V  I  R  K  L  T  W  A  F  P  C  K  R  F  Y  S   : G  *  C  T  H  L  L  F  R  R  S  N  *  R  *  N  Q  G  C  F  R  S  D  R  G  N  I  T  A  I  W  F  *  Q  V  *  S  E  P  L  N  K  A  R  K  S  C  W  R  *  *  D  L  G  K  S  N  I  C  T  *  G  C  F  R  R  *  R  L  E  L  S  N  R  *  W  W  W  G  L  L  W  S  K  D  *  S  E  N  *  G  C  S  W  K  E  V  A  M  L  N  Y  T   : G  *  F  Q  F  T  P  A  L  *  H  Y  I  C  R  F  K  S  R  E  E  A  T  Y  H  D  P  *  S  S  S  W  I  F  G  A  L  F  W  C  S  H  R  E  L  C  W  *  F  S  T  L  A  F  S  H  P  S  S  S  F  T  S  Y  *  C  S   : A  P  V  L  Q  *  S  S  Q  E  T  K  S  * </first_frame>
            <second_frame>  N  M  F  D  Q  M  E  I  E  E  E  L  F  Q  L  R  P  M  N  C  P  Y  H  V  L  I  Y  K  R  Q  L  H  S  Y  R  D  F  P  I  R  V  A  E  L  G  T  V  Y  R  Y  E  L  S  G  S  L  H  G  L  F  R  V  R  G  F  T  Q  :  D  D  A  H  I  F  C  L  E  D  Q  I  K  D  E  I  R  G  V  L  D  L  T  E  E  I  L  Q  Q  F  G  F  D  K  Y  E  V  N  L  S  T  R  P  E  K  A  V  G  D  D  E  I  W  E  K  A  T  F  A  L  K  D  A  L  E  D  K  G  W  S  Y  Q  I  D  D  G  G  G  A  F  Y  G  P  K  I  D  L  K  I  E  D  A  L  G  R  K  W  Q  C  S  T  I  Q  :  V  D  F  N  L  P  Q  R  F  D  I  T  Y  V  D  S  N  Q  E  R  K  R  P  I  M  I  H  R  A  V  L  G  S  L  E  R  F  F  G  V  L  I  E  N  Y  A  G  D  F  P  L  W  L  S  P  I  Q  A  R  V  L  P  V  T  D  A  Q  :  L  Q  Y  C  N  E  V  V  K  K  L  K  A   </second_frame>
            <third_frame>   I  C  L  I  R  W  R  L  R  K  S  F  F  S  F  G  Q  *  T  A  L  I  M  Y  *  S  I  R  G  S  Y  T  L  I  G  I  F  Q  S  E  L  Q  S  W  E  Q  C  I  G  M  S  Y  P  E  A  Y  M  G  F  S  V  *  E  V  L  L  R :   M  M  H  T  S  S  V  *  K  I  K  L  K  M  K  S  G  V  F  *  I  *  Q  R  K  Y  Y  S  N  L  V  L  T  S  M  K  *  T  S  Q  Q  G  Q  K  K  L  L  E  M  M  R  S  G  K  K  Q  H  L  H  L  R  M  L  *  K  I  K  V  G  A  I  K  *  M  M  V  V  G  P  S  M  V  Q  R  L  I  *  K  L  R  M  L  L  E  G  S  G  N  A  Q  L  Y  R :   L  I  S  I  Y  P  S  A  L  T  L  H  M  S  I  Q  I  K  R  G  S  D  L  S  *  S  I  E  Q  F  L  D  L  W  S  A  F  L  V  F  S  *  R  I  M  L  V  I  F  H  F  G  F  L  P  S  K  L  E  F  Y  Q  L  L  M  L  S :   S  S  T  A  M  K  *  S  R  N  *  K  L  </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07SLm0093E04.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="5765" stop="5565"/>
                    <exon start="3643" stop="3335"/>
                    <exon start="3106" stop="2906"/>
                    <exon start="2615" stop="2577"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>750</number_coding_nucleotides>
                  <number_encoded_amino_acids>250</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>NMFDQMEIEEELFQLRPMNCPYHVLIYKRQLHSYRDFPIRVAELGTVYRYELSGSLHGLFRVRGFTQDDAHIFCLEDQIKDEIRGVLDLTEEILQQFGFDKYEVNLSTRPEKAVGDDEIWEKATFALKDALEDKGWSYQIDDGGGAFYGPKIDLKIEDALGRKWQCSTIQVDFNLPQRFDITYVDSNQERKRPIMIHRAVLGSLERFFGVLIENYAGDFPLWLSPIQARVLPVTDAQLQYCNEVVKKLKA</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="9307" PGL_stop="8007"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="9307" e_stop="9040"/>
            <exon e_start="8456" e_stop="8310"/>
            <exon e_start="8154" e_stop="8007"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.942" acc_prob="0.977" e_score="1.000"/>
          <exon-intron don_prob="0.978" acc_prob="0.883" 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="9307" e_stop="9040" e_length="268"/>
          </exon>
          <intron i_serial="1" don_prob="0.942" acc_prob="0.977">
            <gDNA_intron_boundary i_start="9039" i_stop="8457" i_length="583"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="8456" e_stop="8310" e_length="147"/>
          </exon>
          <intron i_serial="2" don_prob="0.978" acc_prob="0.883">
            <gDNA_intron_boundary i_start="8309" i_stop="8155" i_length="155"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="8154" e_stop="8007" e_length="148"/>
          </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="9307" stop="9040"/>
              <exon start="8456" stop="8310"/>
              <exon start="8154" stop="8007"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M821" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="9305" stop="9040"/>
              <exon start="8456" stop="8310"/>
              <exon start="8154" stop="8007"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M821-2" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="2" AGS_serial="1" gDNA_strand="-"/>
          <translation>
            <gDNA_template>TCTCTTCACTTCCTCTTATAAATCCATTTCTCCTCTCAGTAGAAACCCCTTTTCTTCCTTCCCAATTCGTCAGTATCGTATTCTTTTTGTTCTTGATCCCTCTAACAACAACAACAACAACAAAACTAACCGGAACAAGTTGCTGAGACGTCGCACTTCTTTCTCTACCCATGCTTCCACCGCCCTACAAGAAGCTCCTGCCCCAAATGAGAAAATGGTTCTCCCAACTAACGAGTCATCAGATGGGCTACTTCGAATTCGCCATACG : TGTGCTCATGTTATGGCCATGGCAGTCCAAAAACTCTACCCGAATGCAAAAGTGACAATTGGGCCCTGGATCGATAATGGTTTTTATTATGATTTTGATATGGAGCCTTTGACTGACAGTGACCTGAAGAGGATTAAGAAGGAAATG : GATCGAATTATCAGCCGAAACTTGCCTCTTGTTAGAGAAGAAGTTAGCCGGGATGAAGCTCAAAGAAGAATAATGTCTATCAACGAACCTTACAAGATCGAAATTTTAGAGAGCATAAAGGAGGAACCAATTACCATTTATCATATTG</gDNA_template>
            <first_frame> S  L  H  F  L  L  *  I  H  F  S  S  Q  *  K  P  L  F  F  L  P  N  S  S  V  S  Y  S  F  C  S  *  S  L  *  Q  Q  Q  Q  Q  Q  N  *  P  E  Q  V  A  E  T  S  H  F  F  L  Y  P  C  F  H  R  P  T  R  S  S  C  P  K  *  E  N  G  S  P  N  *  R  V  I  R  W  A  T  S  N  S  P  Y   : V  C  S  C  Y  G  H  G  S  P  K  T  L  P  E  C  K  S  D  N  W  A  L  D  R  *  W  F  L  L  *  F  *  Y  G  A  F  D  *  Q  *  P  E  E  D  *  E  G  N   : G  S  N  Y  Q  P  K  L  A  S  C  *  R  R  S  *  P  G  *  S  S  K  K  N  N  V  Y  Q  R  T  L  Q  D  R  N  F  R  E  H  K  G  G  T  N  Y  H  L  S  Y   </first_frame>
            <second_frame>  L  F  T  S  S  Y  K  S  I  S  P  L  S  R  N  P  F  S  S  F  P  I  R  Q  Y  R  I  L  F  V  L  D  P  S  N  N  N  N  N  N  K  T  N  R  N  K  L  L  R  R  R  T  S  F  S  T  H  A  S  T  A  L  Q  E  A  P  A  P  N  E  K  M  V  L  P  T  N  E  S  S  D  G  L  L  R  I  R  H  T  :  C  A  H  V  M  A  M  A  V  Q  K  L  Y  P  N  A  K  V  T  I  G  P  W  I  D  N  G  F  Y  Y  D  F  D  M  E  P  L  T  D  S  D  L  K  R  I  K  K  E  M  :  D  R  I  I  S  R  N  L  P  L  V  R  E  E  V  S  R  D  E  A  Q  R  R  I  M  S  I  N  E  P  Y  K  I  E  I  L  E  S  I  K  E  E  P  I  T  I  Y  H  I  </second_frame>
            <third_frame>   S  S  L  P  L  I  N  P  F  L  L  S  V  E  T  P  F  L  P  S  Q  F  V  S  I  V  F  F  L  F  L  I  P  L  T  T  T  T  T  T  K  L  T  G  T  S  C  *  D  V  A  L  L  S  L  P  M  L  P  P  P  Y  K  K  L  L  P  Q  M  R  K  W  F  S  Q  L  T  S  H  Q  M  G  Y  F  E  F  A  I  R :   V  L  M  L  W  P  W  Q  S  K  N  S  T  R  M  Q  K  *  Q  L  G  P  G  S  I  M  V  F  I  M  I  L  I  W  S  L  *  L  T  V  T  *  R  G  L  R  R  K  W :   I  E  L  S  A  E  T  C  L  L  L  E  K  K  L  A  G  M  K  L  K  E  E  *  C  L  S  T  N  L  T  R  S  K  F  *  R  A  *  R  R  N  Q  L  P  F  I  I  L </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C07SLm0093E04.2" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="9306" stop="9040"/>
                    <exon start="8456" stop="8310"/>
                    <exon start="8154" stop="8008"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>561</number_coding_nucleotides>
                  <number_encoded_amino_acids>187</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>LFTSSYKSISPLSRNPFSSFPIRQYRILFVLDPSNNNNNNKTNRNKLLRRRTSFSTHASTALQEAPAPNEKMVLPTNESSDGLLRIRHTCAHVMAMAVQKLYPNAKVTIGPWIDNGFYYDFDMEPLTDSDLKRIKKEMDRIISRNLPLVREEVSRDEAQRRIMSINEPYKIEILESIKEEPITIYHI</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 11 chains have been computed
$ 
$ memory statistics:
$ 5816 bytes spliced alignments in total
$ 3 spliced alignments have been stored
$ 1938 bytes was the average size of a spliced alignment
$ 6864 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3432 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 12 backtrace matrices have been allocated
$ 
$ date finished: 2008-11-23 23:08:16
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