<?xml version="1.0" encoding="ISO-8859-1"?>
<GTH_output xmlns="http://www.genomethreader.org/GTH_output/" GTH_XML_version="1.1">
  <header xmlns="http://www.genomethreader.org/GTH_output/header/">
    <source program="GenomeThreader" version="0.9.54" build_date="2006-07-28 11:55:15" run_date="2009-12-01 06:07:56"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U592830" ref_strand="+" ref_description="SGN-U592830 Tomato 200607#2 [1 ESTs aligned] (*GB) gi|82623397|gb|ABB87113.1| (e_value=2e-28) unknown; (*ATH) AT2G31610.1 (e_value=1e-27) | Symbol: None | 40S ribosomal protein S3 (RPS3A) | chr2:13457390-13458999 FORWARD | Aliases: T9H9.13, T9H9_13; (*SWP) sp|P48152|RS3_CAEEL (e_value=5e-27) 40S ribosomal protein S3 OS=Caenorhabditis elegans GN=rps-3; ">
      <seq>gtgcttacaaaatagattggcggaggatggatactccggagttgaattacaggatactcccgtgcgaactgatgccttcataatggccactcgtactcagaacgttcttggtgaaaaaggtaggagaattagggagctgacttcagttgttcagaagcggtttaatttcaaggaaaacactgttgagctctatgcagagaaagtcaacaataggggtctctgtgccattgctca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="1927" stop="261"/>
      </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="1677" g_stop="1569" g_length="109"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="110" r_length="110" r_score="0.844"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884">
            <donor d_prob="0.997" d_score="0.88"/>
            <acceptor a_prob="1.000" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="684" g_stop="561" g_length="124"/>
          <reference_exon_boundary r_type="cDNA" r_start="111" r_stop="234" r_length="124" r_score="0.992"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-U592830" ref_strand="+">
        <total_alignment_score>0.923</total_alignment_score>
        <cumulative_length_of_scored_exons>233</cumulative_length_of_scored_exons>
        <coverage percentage="0.996" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U592830" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="1677" e_stop="1569"/>
          <exon e_start="684" e_stop="561"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTGCTTACAAGAGAG-TTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTGGTACATAAATATATATATAAGCTAATTTTTTCTTAATGAAATTCATCGACACACTTATAAGTGACTCCATCTGTAAGAGTTGCAGCCATCAGCTAGCAGACTAAATGTAATTAAACATTCTACAGAATAGCAACTGTATATATTTGCAAATGTACAGCAGACAAGTCTATCTTTCCATGAAAGAAGGCGTGTTTAATCTGTGTATATGAACTCTAGTAATCAATTATTAGTTTGGTGTAGTTCTGACTCTTTAATGGAGTTAGTTGAGGTGTATGCTGCTATAGCTCTGACACCACAATTATCATAACAAAATTATATACCCTTGATGAAGCTTATATTATGCATTTGTTAATTAAGGGTCTAAATTTTGTAGAATGTTGTAGAACTTAAGTAAAGATTCTGAATGCTGTAACATTACATTACTATTTTTTTTTAGAAAAAGATTCTGAATGCTGTGTCGTGCAATGCAGATTACTCTGTTTATCCCATTTATCTGCCTTAGTTGGACACGTTGCTCAAAATAAATGTCAGTAGTTTTTATTTAGATAGAATTGGGTTCCAAAATGGACGGAAGATGATACTTGCAGAGATTAAACTTCTCCCAGTGTGATGTTATGTCCTGGGGTACTTTTTTTAATCATAAAATACAAAATATCAAAGATGGTACATGAAAAAGGTATTTATGTAAAAAATTTATTCTAAAAAAAGGAAGCCTTTTATGTAGAAACGGGAGGTACTTTGGGATAACTTACTAAAATAGGATATTTGTTTGAATCGGAGGCAAATGAATCATCCTTGCTGATTATTGGATGAGCTGGAAGTAGGTGTGCTTTAACGGATTGATTGTAGTAGTAGTTGAATAATGTTGTGTGTGTATTTTCCAGGTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCA</genome_strand>
        <mrna_strand>GTGCTTACAAAATAGATTGGCGGAGGATGGATACTCCGGAGTTGAATTACAGGATACTCCCGTGCGAACTGATGCCTTCATAATGGCCACTCGTACTCAGAACGTTCTTG....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGGTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U582381" ref_strand="+" ref_description="SGN-U582381 Tomato 200607#2 [4 ESTs aligned] ">
      <seq>tatcgcaggaaagaattacaaaagagagaaaagaagagtgagacatcacagaggaaaataatctctaaggaaaaatagagagtgtgagcgatattgtagtgagatggaaaaatcaaaagagtgttatttcttttgaatgtgtagtgatctttagagttttactcaaacatacaagtgtaaaatccttactatagtgatattcgttgcttctcttgggtcgtggtttttctcttatttaggagggtttccacgt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="13414" stop="12568"/>
      </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="13119" g_stop="12870" g_length="250"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="251" r_length="251" r_score="0.912"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-U582381" ref_strand="+">
        <total_alignment_score>0.912</total_alignment_score>
        <cumulative_length_of_scored_exons>250</cumulative_length_of_scored_exons>
        <coverage percentage="0.988" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U582381" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="13119" e_stop="12870"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TGCACCAAAAAAGAATTACAAAGGAGAGAAAAGAAGACTGAGGCATCACAGAGGAAAATATTCTGTGAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGGTGGAAAAATC-AAAGACTGTTATTTCTTTTGAATGTGTAGTGGTCTTTGGAGTTTTACTCAGACATACAAGTGTAAAATCCTTGCTATAGTGATATTCGTTGCTCCTCTCGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</genome_strand>
        <mrna_strand>TATCGCAGGAAAGAATTACAAAAGAGAGAAAAGAAGAGTGAGACATCACAGAGGAAAATAATCTCTAAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGATGGAAAAATCAAAAGAGTGTTATTTCTTTTGAATGTGTAGTGATCTTTAGAGTTTTACTCAAACATACAAGTGTAAAATCCTTACTATAGTGATATTCGTTGCTTCTCTTGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U602841" ref_strand="+" ref_description="SGN-U602841 Tomato 200607#2 [1 ESTs aligned] (*GB) gi|13540823|gb|AAK29467.1| (e_value=3e-11) polyprotein-like [Lycopersicon chilense]; (*SWP) sp|P10978|POLX_TOBAC (e_value=6e-11) Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Nicotiana tabacum; ">
      <seq>aaagccatagtgctcctaaactcgttgccatcttcctacgatactttatcaacaaccattttacatggtaaggattctattgagttgaaggatgtcacatcagcccttttgcttaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="17524" stop="16809"/>
      </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="17224" g_stop="17109" g_length="116"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="116" r_length="116" r_score="0.948"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-U602841" ref_strand="+">
        <total_alignment_score>0.948</total_alignment_score>
        <cumulative_length_of_scored_exons>116</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U602841" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="17224" e_stop="17109"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAAGCCATAGTGCTCATAAACTCGTTGTCATCTTCCTACGATACTTTAGCAACAACCATTTTACATGGTAAGGACTCTGTTGAGTTGAAGGATGTCATATCAGCCCTTTTGCTTAA</genome_strand>
        <mrna_strand>AAAGCCATAGTGCTCCTAAACTCGTTGCCATCTTCCTACGATACTTTATCAACAACCATTTTACATGGTAAGGATTCTATTGAGTTGAAGGATGTCACATCAGCCCTTTTGCTTAA</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-C00SLf0138K20-YaNib/gth_cdna_fileCXGN::TomatoGenome::BACSubmission::Analysis::GenomeThreader::SGN_U_tomato" ref_id="SGN-U582156" ref_strand="+" ref_description="SGN-U582156 Tomato 200607#2 [2 ESTs aligned] ">
      <seq>cacgaggctcgtagtcagtcaatatgagggttcgcttggggaccctcaaatgttgatcacgttgagggtgtagattgggatcgtgataaaaggtaacaactcgatatatcctgaaagttcagtcactgttattgaagcacggaagagttggatgggtctcatgtattccatattagcaaaattatgtgtgctactcaaagttgaaaggataaatttgccaggtgcgcttaagatggtggcttgggaagaatgattttattcttgatcaaggtctttgagtgaaattggatggaatagtggaaccaactcaaaagatacacatttggtattggatacaagcctactcctaaagaagtctcatcgtctaatctcaaaaagaaaagtggcattcccttaccacaacctatcccactcttgaatcagtcatttcaagacattgcacaagaatattcagaggaaagtgttgagataacctcaaaaacttgttcattgaagaagttgaatgcaatatgagtttggaggattgcattgaggcctggaccacatgggatactatgcttggagatactttgaacaattggacttgtaacccgtccacggttcccacaaaatattggtagatgattgtattagaattaacaaaatagcatggtctaaatttgtggggtccattcccatgtaccaaactttgaataactctctgcaaatttcaaagtttggcaaatttggtgctgaattatttttcaactttacttaattttcaatagtaggtaagctatgaagaaaaacaattgtttttcttctatagcacatttggagggtagtgcatttgtttttcaataaatggag</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00SLf0138K20-YaNib/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C00SLf0138K20.2" temp_strand="-" temp_description="C00SLf0138K20.2  CU856534.4 htgs_phase:3 submitted_to_sgn_as:C04SLf0138K20 sequenced_by:sanger upload_account_name:uk">
        <position start="19262" stop="17820"/>
      </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="18954" g_stop="18120" g_length="835"/>
          <reference_exon_boundary r_type="cDNA" r_start="15" r_stop="849" r_length="835" r_score="0.995"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00SLf0138K20.2" gen_strand="-" ref_id="SGN-U582156" ref_strand="+">
        <total_alignment_score>0.995</total_alignment_score>
        <cumulative_length_of_scored_exons>835</cumulative_length_of_scored_exons>
        <coverage percentage="0.984" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00SLf0138K20.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U582156" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="18954" e_stop="18120"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCAGTCAATATGAGGGTTCGCTTGGGGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGCAAATTTCAAAGTTTGGCAAATTTGGTGCTGAATTATTTTTCAACTTTACTTAATTTTCAATAGTAGGTAAGCTATGAAGAAAAACAATTGTTTTTCTTCTATAGCACATTTGGAGGGTAGTGCATTTGTTTTCAATAAAATGGAG</genome_strand>
        <mrna_strand>TCAGTCAATATGAGGGTTCGCTTGGGGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGCAAATTTCAAAGTTTGGCAAATTTGGTGCTGAATTATTTTTCAACTTTACTTAATTTTCAATAGTAGGTAAGCTATGAAGAAAAACAATTGTTTTTCTTCTATAGCACATTTGGAGGGTAGTGCATTTGTTTTTCAATAAATGGAG</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="1677" PGL_stop="561"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="1677" e_stop="1569"/>
            <exon e_start="684" e_stop="561"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.997" acc_prob="1.000" e_score="0.844"/>
          <exon-only e_score="0.992"/>
        </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="0.844">
            <gDNA_exon_boundary e_start="1677" e_stop="1569" e_length="109"/>
          </exon>
          <intron i_serial="1" don_prob="0.997" acc_prob="1.000">
            <gDNA_intron_boundary i_start="1568" i_stop="685" i_length="884"/>
          </intron>
          <exon e_serial="2" e_score="0.992">
            <gDNA_exon_boundary e_start="684" e_stop="561" e_length="124"/>
          </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="1677" stop="1569"/>
              <exon start="684" stop="561"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U592830" 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>GTGCTTACAAGAGAGTTGGCGGAGGATGGTTACTCGGGAGTTGAAGTTAGGGTTACTCCCGTGCGAACTGAAATCATCATTAGGGCCACTCGTACTCAGAACGTTCTTG : GTGAAAAAGGTAGGAGAATTAGGGAGCTGACTTCAGTTGTTCAGAAGCGTTTTAATTTCAAGGAAAACACTGTTGAGCTCTATGCAGAGAAAGTCAACAATAGGGGTCTCTGTGCCATTGCTCA</gDNA_template>
            <first_frame> V  L  T  R  E  L  A  E  D  G  Y  S  G  V  E  V  R  V  T  P  V  R  T  E  I  I  I  R  A  T  R  T  Q  N  V  L   : G  E  K  G  R  R  I  R  E  L  T  S  V  V  Q  K  R  F  N  F  K  E  N  T  V  E  L  Y  A  E  K  V  N  N  R  G  L  C  A  I  A   </first_frame>
            <second_frame>  C  L  Q  E  S  W  R  R  M  V  T  R  E  L  K  L  G  L  L  P  C  E  L  K  S  S  L  G  P  L  V  L  R  T  F  L  :  V  K  K  V  G  E  L  G  S  *  L  Q  L  F  R  S  V  L  I  S  R  K  T  L  L  S  S  M  Q  R  K  S  T  I  G  V  S  V  P  L  L  </second_frame>
            <third_frame>   A  Y  K  R  V  G  G  G  W  L  L  G  S  *  S  *  G  Y  S  R  A  N  *  N  H  H  *  G  H  S  Y  S  E  R  S  W :   *  K  R  *  E  N  *  G  A  D  F  S  C  S  E  A  F  *  F  Q  G  K  H  C  *  A  L  C  R  E  S  Q  Q  *  G  S  L  C  H  C  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/">
            <orf_entry>
              <id_line>
                <gDNA id="C00SLf0138K20.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="1677" stop="1569"/>
                    <exon start="684" stop="563"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>231</number_coding_nucleotides>
                  <number_encoded_amino_acids>77</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFNFKENTVELYAEKVNNRGLCAIA</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="13119" PGL_stop="12870"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="13119" e_stop="12870"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.912"/>
        </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="0.912">
            <gDNA_exon_boundary e_start="13119" e_stop="12870" e_length="250"/>
          </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="13119" stop="12870"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U582381" 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>TGCACCAAAAAAGAATTACAAAGGAGAGAAAAGAAGACTGAGGCATCACAGAGGAAAATATTCTGTGAGGAAAAATAGAGAGTGTGAGCGATATTGTAGTGAGGTGGAAAAATCAAAGACTGTTATTTCTTTTGAATGTGTAGTGGTCTTTGGAGTTTTACTCAGACATACAAGTGTAAAATCCTTGCTATAGTGATATTCGTTGCTCCTCTCGGGTCGTGGTTTTTCTCTTATTTAGGAGGGTTTCCAC</gDNA_template>
            <first_frame> C  T  K  K  E  L  Q  R  R  E  K  K  T  E  A  S  Q  R  K  I  F  C  E  E  K  *  R  V  *  A  I  L  *  *  G  G  K  I  K  D  C  Y  F  F  *  M  C  S  G  L  W  S  F  T  Q  T  Y  K  C  K  I  L  A  I  V  I  F  V  A  P  L  G  S  W  F  F  S  Y  L  G  G  F  P  </first_frame>
            <second_frame>  A  P  K  K  N  Y  K  G  E  K  R  R  L  R  H  H  R  G  K  Y  S  V  R  K  N  R  E  C  E  R  Y  C  S  E  V  E  K  S  K  T  V  I  S  F  E  C  V  V  V  F  G  V  L  L  R  H  T  S  V  K  S  L  L  *  *  Y  S  L  L  L  S  G  R  G  F  S  L  I  *  E  G  F  H </second_frame>
            <third_frame>   H  Q  K  R  I  T  K  E  R  K  E  D  *  G  I  T  E  E  N  I  L  *  G  K  I  E  S  V  S  D  I  V  V  R  W  K  N  Q  R  L  L  F  L  L  N  V  *  W  S  L  E  F  Y  S  D  I  Q  V  *  N  P  C  Y  S  D  I  R  C  S  S  R  V  V  V  F  L  L  F  R  R  V  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="C00SLf0138K20.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="3" PGL_strand="-" PGL_start="17224" PGL_stop="17109"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="17224" e_stop="17109"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.948"/>
        </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="0.948">
            <gDNA_exon_boundary e_start="17224" e_stop="17109" e_length="116"/>
          </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="17224" stop="17109"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U602841" 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>AAAGCCATAGTGCTCATAAACTCGTTGTCATCTTCCTACGATACTTTAGCAACAACCATTTTACATGGTAAGGACTCTGTTGAGTTGAAGGATGTCATATCAGCCCTTTTGCTTAA</gDNA_template>
            <first_frame> K  A  I  V  L  I  N  S  L  S  S  S  Y  D  T  L  A  T  T  I  L  H  G  K  D  S  V  E  L  K  D  V  I  S  A  L  L  L   </first_frame>
            <second_frame>  K  P  *  C  S  *  T  R  C  H  L  P  T  I  L  *  Q  Q  P  F  Y  M  V  R  T  L  L  S  *  R  M  S  Y  Q  P  F  C  L  </second_frame>
            <third_frame>   S  H  S  A  H  K  L  V  V  I  F  L  R  Y  F  S  N  N  H  F  T  W  *  G  L  C  *  V  E  G  C  H  I  S  P  F  A  * </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="C00SLf0138K20.2"/>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
    <predicted_gene_location>
      <PGL_line PGL_serial="4" PGL_strand="-" PGL_start="18954" PGL_stop="18120"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="18954" e_stop="18120"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.995"/>
        </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="0.995">
            <gDNA_exon_boundary e_start="18954" e_stop="18120" e_length="835"/>
          </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="18954" stop="18120"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U582156" 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>TCAGTCAATATGAGGGTTCGCTTGGGGACCCTCAAATGTTGATCACGTTGAGGGTGTAGATTGGGATCGTGATAAAAGGTAACAACTCGATATATCCTGAAAGTTCAGTCACTGTTATTGAAGCACGGAAGAGTTGGATGGGTCTCATGTATTCCATATTAGCAAAATTATGTGTGCTACTCAAAGTTGAAAGGATAAATTTGCCAGGTGCGCTTAAGATGGTGGCTTGGGAAGAATGATTTTATTCTTGATCAAGGTCTTTGAGTGAAATTGGATGGAATAGTGGAACCAACTCAAAAGATACACATTTGGTATTGGATACAAGCCTACTCCTAAAGAAGTCTCATCGTCTAATCTCAAAAAGAAAAGTGGCATTCCCTTACCACAACCTATCCCACTCTTGAATCAGTCATTTCAAGACATTGCACAAGAATATTCAGAGGAAAGTGTTGAGATAACCTCAAAAACTTGTTCATTGAAGAAGTTGAATGCAATATGAGTTTGGAGGATTGCATTGAGGCCTGGACCACATGGGATACTATGCTTGGAGATACTTTGAACAATTGGACTTGTAACCCGTCCACGGTTCCCACAAAATATTGGTAGATGATTGTATTAGAATTAACAAAATAGCATGGTCTAAATTTGTGGGGTCCATTCCCATGTACCAAACTTTGAATAACTCTCTGCAAATTTCAAAGTTTGGCAAATTTGGTGCTGAATTATTTTTCAACTTTACTTAATTTTCAATAGTAGGTAAGCTATGAAGAAAAACAATTGTTTTTCTTCTATAGCACATTTGGAGGGTAGTGCATTTGTTTTCAATAAAATGGAG</gDNA_template>
            <first_frame> S  V  N  M  R  V  R  L  G  T  L  K  C  *  S  R  *  G  C  R  L  G  S  *  *  K  V  T  T  R  Y  I  L  K  V  Q  S  L  L  L  K  H  G  R  V  G  W  V  S  C  I  P  Y  *  Q  N  Y  V  C  Y  S  K  L  K  G  *  I  C  Q  V  R  L  R  W  W  L  G  K  N  D  F  I  L  D  Q  G  L  *  V  K  L  D  G  I  V  E  P  T  Q  K  I  H  I  W  Y  W  I  Q  A  Y  S  *  R  S  L  I  V  *  S  Q  K  E  K  W  H  S  L  T  T  T  Y  P  T  L  E  S  V  I  S  R  H  C  T  R  I  F  R  G  K  C  *  D  N  L  K  N  L  F  I  E  E  V  E  C  N  M  S  L  E  D  C  I  E  A  W  T  T  W  D  T  M  L  G  D  T  L  N  N  W  T  C  N  P  S  T  V  P  T  K  Y  W  *  M  I  V  L  E  L  T  K  *  H  G  L  N  L  W  G  P  F  P  C  T  K  L  *  I  T  L  C  K  F  Q  S  L  A  N  L  V  L  N  Y  F  S  T  L  L  N  F  Q  *  *  V  S  Y  E  E  K  Q  L  F  F  F  Y  S  T  F  G  G  *  C  I  C  F  Q  *  N  G  </first_frame>
            <second_frame>  Q  S  I  *  G  F  A  W  G  P  S  N  V  D  H  V  E  G  V  D  W  D  R  D  K  R  *  Q  L  D  I  S  *  K  F  S  H  C  Y  *  S  T  E  E  L  D  G  S  H  V  F  H  I  S  K  I  M  C  A  T  Q  S  *  K  D  K  F  A  R  C  A  *  D  G  G  L  G  R  M  I  L  F  L  I  K  V  F  E  *  N  W  M  E  *  W  N  Q  L  K  R  Y  T  F  G  I  G  Y  K  P  T  P  K  E  V  S  S  S  N  L  K  K  K  S  G  I  P  L  P  Q  P  I  P  L  L  N  Q  S  F  Q  D  I  A  Q  E  Y  S  E  E  S  V  E  I  T  S  K  T  C  S  L  K  K  L  N  A  I  *  V  W  R  I  A  L  R  P  G  P  H  G  I  L  C  L  E  I  L  *  T  I  G  L  V  T  R  P  R  F  P  Q  N  I  G  R  *  L  Y  *  N  *  Q  N  S  M  V  *  I  C  G  V  H  S  H  V  P  N  F  E  *  L  S  A  N  F  K  V  W  Q  I  W  C  *  I  I  F  Q  L  Y  L  I  F  N  S  R  *  A  M  K  K  N  N  C  F  S  S  I  A  H  L  E  G  S  A  F  V  F  N  K  M  E </second_frame>
            <third_frame>   S  Q  Y  E  G  S  L  G  D  P  Q  M  L  I  T  L  R  V  *  I  G  I  V  I  K  G  N  N  S  I  Y  P  E  S  S  V  T  V  I  E  A  R  K  S  W  M  G  L  M  Y  S  I  L  A  K  L  C  V  L  L  K  V  E  R  I  N  L  P  G  A  L  K  M  V  A  W  E  E  *  F  Y  S  *  S  R  S  L  S  E  I  G  W  N  S  G  T  N  S  K  D  T  H  L  V  L  D  T  S  L  L  L  K  K  S  H  R  L  I  S  K  R  K  V  A  F  P  Y  H  N  L  S  H  S  *  I  S  H  F  K  T  L  H  K  N  I  Q  R  K  V  L  R  *  P  Q  K  L  V  H  *  R  S  *  M  Q  Y  E  F  G  G  L  H  *  G  L  D  H  M  G  Y  Y  A  W  R  Y  F  E  Q  L  D  L  *  P  V  H  G  S  H  K  I  L  V  D  D  C  I  R  I  N  K  I  A  W  S  K  F  V  G  S  I  P  M  Y  Q  T  L  N  N  S  L  Q  I  S  K  F  G  K  F  G  A  E  L  F  F  N  F  T  *  F  S  I  V  G  K  L  *  R  K  T  I  V  F  L  L  *  H  I  W  R  V  V  H  L  F  S  I  K  W   </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="C00SLf0138K20.2" strand="-"/>
                <serials PGL_serial="4" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="18671" stop="18456"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>213</number_coding_nucleotides>
                  <number_encoded_amino_acids>71</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>WNQLKRYTFGIGYKPTPKEVSSSNLKKKSGIPLPQPIPLLNQSFQDIAQEYSEESVEITSKTCSLKKLNAI*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 14 chains have been computed
$ 
$ memory statistics:
$ 7376 bytes spliced alignments in total
$ 4 spliced alignments have been stored
$ 1844 bytes was the average size of a spliced alignment
$ 9088 bytes predicted gene locations in total
$ 4 predicted gene locations have been stored
$ 2272 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 14 backtrace matrices have been allocated
$ 
$ date finished: 2009-12-01 06:08:09
-->
