<?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 23:17:17"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12HBa0040O03-kixkX/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C12HBa0040O03-kixkX/gth_cdna_fileCXGN::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-C12HBa0040O03-kixkX/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U579503" ref_strand="+" ref_description="SGN-U579503 Tomato 200607#2 [26 ESTs aligned] (*GB) gi|147833320|emb|CAN64101.1| (e_value=3e-67) hypothetical; (*ATH) AT5G42000.1 (e_value=1e-67) | Symbol: None | ORMDL family protein, contains Pfam domain PF04061: ORMDL family | chr5:16816595-16818256 FORWARD | Aliases: MJC20.10, MJC20_10; (*SWP) sp|O42901|YBA9_SCHPO (e_value=1e-27) Uncharacterized protein C119.09c OS=Schizosaccharomyces pombe GN=SPBC119.09c; ">
      <seq>gagcggtcccaccacccctacccatagcagccacctatcccctcttcgttttcgtgagtctctgttttttcgttgatcaaatactcatactaatgcgatattaatcgccatatccaattgtttcttcttcaagttttgtattgataacttttttcgattgggttgaaagtattgttcaatccatttggatggcgaatttgtatgtgagggctgctccaaccacggatctgaatcggaatactgagtggttcacctatcctggagtttggactatttacatattcattctgctcttctcatggctcgttgtgctctctgtttttgggtcctcatccggcatggcatggactattgtcaatctcgctcatttccttgtcacatatcactgttttcactggaagaagggaacaccatttgctgaagaccagggtatctacaacagattgacatggtgggagcaaatggataatggcaagcagcttactcccaataggaagtttctgacagttgttcctgtggtgctgtacttgatagcttcccatacaactgactatcaacacccaatgctgttcttgaacacattcgcagttttcatactggtggttgctaaatttcccaacatgcacaaggttcgaatatttgggatcaatgcagatcaatgaagtacttcattcaatttgaaattttagttccaactttactctcagctatatagtaagtatttgattggttttaacaattttgagtaaacagggaactcctgtacaaatgcaacaacttcaaagggtgaaattatatatatagtaaaaagattaagagccgatgttgggtttgcttagctacgctcttttttataacctgttgat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0040O03-kixkX/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C12HBa0040O03.2" temp_strand="-" temp_description="C12HBa0040O03.2  AC235491.2 htgs_phase:2 submitted_to_sgn_as:gi|238550291|gb|AC235491.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone LE_HBa-40O3, WORKING DRAFT SEQUENCE, 3 ordered pieces">
        <position start="46288" stop="41384"/>
      </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="45989" g_stop="45616" g_length="374"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="374" r_length="374" r_score="0.997"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="45615" i_stop="44721" i_length="895">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="0.992" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="44720" g_stop="44572" g_length="149"/>
          <reference_exon_boundary r_type="cDNA" r_start="375" r_stop="523" r_length="149" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="44571" i_stop="42027" i_length="2545">
            <donor d_prob="0.912" d_score="1.00"/>
            <acceptor a_prob="0.993" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="42026" g_stop="41684" g_length="343"/>
          <reference_exon_boundary r_type="cDNA" r_start="524" r_stop="866" r_length="343" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0040O03.2" gen_strand="-" ref_id="SGN-U579503" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>866</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0040O03.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U579503" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="45989" e_stop="45616"/>
          <exon e_start="44720" e_stop="44572"/>
          <exon e_start="42026" e_stop="41684"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAGCGGTCCCACCACCCCTACCCATAGCAGCCACCTATCCCCTCTTCGTTTTCGTGAGTCTCTGTTTTTTCGTTGATCAAATACTCATACTAATGCGATATTAATCGCCATATCCAATTGTTTCTTCTTCAAGTTTTGTATTGATAACTTTTTTCGATTGGGTTGAAAGTATTGTTCAATCCATTTGGATGGCGAATTTGTATGTGAGGGCTGCTCCAACCACGGATCTGAATCGGAATACTGAGTGGTTCACCTATCCTGGAGTTTGGACTATTTACATATTCATTCTGCTCTTCTCATGGCTCGTTGTGCTCTCTGTTTTTGGGTCCTCATCCGGCATGGCATGGACTATTGTCAATCTCGCTCATTTCCTTGTACGTATTCATTTTTCTTTTTTTGAAAGGATTTTTAGGTATTGATCTGGTTATGGAATATGCGATTTATGATTAATTGACTGTGTTATGGTTTTTGAGATCTGGGATATTGGGAGGCAATGGATCTTAGACTGGTTTTCTGTTGGAAGAGGTGTATGATAATATTGATAAACCTATATATGGCTACTTAAAGCCTGGATGTTTGTTTTCTGCTTCCAATTTGATTGAGTTATACTTCATTTTGGTAAAGTTGAGTTTGAGTTTCGAAGACAACATTTTATTTGTAAATGCAGGGTAAGACAGCGTATCATAGATTCTTTGTGGTCGTCTTTTTCCATGGACTTTGTATATAGCGGGAGCTTAGTACACCAGGCTGCCCCTTTATAGGTCATTCTGGGACATGTATACAGGAAATTAGTGAACGAGGCTGTCCTCATTATGGTACATGCATATGGTCCTTGTGATTTCTCAAATTTTACCAGTCTTGTGGTATGAGGAGTATATAGTGAATCAGTACCTTTATTATAGGGAATATTTTTCAAAAGAGATAATTTTTTTGGATAAATTAAAACTTCATCAGTGTATGAAATGTATCATCATCCATTATGGCATTAGTACCTTTCCCTTATTGTGGTTAAGCTTTTCTTGCTTCGCTTTTGTTAGGAATAGATTTCACTTCTGTACTCTGCTATATTCTTCTGGAAAATATTGAGATACTTAATACATAAGAAATGTAGTAGGCACTCATTTAATTTTCCTTTAAGATGTTAAATTTTGATATTTCTGTAAAATCCTGAAAACTACCAGATGACATAGCAGAGTTGGGAAGCTTGTTGTGCACCTAACAGGCTTTTCTATCTCATTTGTGCATAACTTCTCGTCTGTTTATCTTCAGGTCACATATCACTGTTTTCACTGGAAGAAGGGAACACCATTTGCTGAAGACCAGGGTATCTACAACAGATTGACATGGTGGGAGCAAATGGATAATGGCAAGCAGCTTACTCCCAATAGGAAGTTTCTGACAGTTGTTCCTGTGGTGCTGTAAGTATTCATTTCATTGTGTAAATCATTGGTTGCAGCTTTCAGCTGTGATGTCAGCAATAGTTTTGTGCTTGCGATGATAAGAATCCACGTGTTATCATTCATGGTATAACAATCTATGCATTATAGTTCCTCATGACAATCCCAAATTATAATCTCTGTATAAGTAATCAAAGAAGTAAGCAATTCCTTAATGTCGTGGAGTTAATAATGGGGTACTTATTTACAATCCTAGTGAACTAAGCGTATATTATTGAAAATATGTGTATGGAGGTTGTAGCAAAATGGACTTATGAGTGTCAACTAGAATAAAAGTTTTTCTAACACAAAATTGGTAATATGGCACCTCACAAGATTGAAGCCTGCTGTAAACCAATTTTGGTATCTAAGTGAGAAGAGTAGAAAGACAAGACAATTATCCACCAAGTACTTTCTAAATTCTGTTTTTTTTGTAGTTAATTAAGCCTGGATCCCTTGTAAACTTTTTGGTACCTTCTTGTACGATTTTGAAAATAAAGTACTCAGTCTTATCCATGGAAAACCCATTATTAACCGAGTATTGAAGTAGGAAACAATGGCTTTCTCAGTCATTGGAAAAGTTAGTTAGTCTTTGAGTTAAATAAGTGAACTTATTGACATTGGTTTAGCTGTATGAGAGACTGGGTTGCTTTTTTTTTTTAAATTGATTTCATACTCTTAGTTCCAGAAAAATTTGAGGTCTTTGGTGCCTTAATTTTGATGTTGACCTATATGTAAGTCAGATGTTCTAAAAAAAAGGATTTTCCAATAATATAAGCACAAAGGAGTTATATGTAAAGCTTCGACTATTGTGACACAGCGAGACTAATCAATAATGAGAGAGGATTGAATGCTGTGAAACAGCATAATGTCTGATGGCTAGTTTCTGTAGAGACAAGCAGTGAGTTCTACTGTAAAAGGAAGGAAGTGAAAAATGAAACAACATTGGATATTCATTGACATCTGCTTAAAAGGGGAAAAAAGAAGGAACCTAGAAAATCTGCAATAATGGACTGTAAGGGAAAATATTTTGGACCGTGATTGTGTTGGTTTCTATGATAACATTTTCCTGCTAAAGTTGAGATCACCTTAGACCTTTTAACACAAGCATTTTTGATCTAGGACTGGATAATATTGAACTAGAAAGGTACTAGCAAACCAAAAGTTTGGGACTGAGGCATAGTTGTTGTTGGTTAAACTATCAGTCCAACTGGTTCTATATGAATTGCCGGACTTGTTATCAAAGGTGAAAAGCGCAAAAAAGCTCTAAGGTCCTTTGGGGCTTTAAGCGTAAACTGCAAATAAATTGTGGACATTAATGAAAAAAGGTGCAAAGGGAGAAAAAAAGCAAATATATATGTTTAGTCCAAACCTTATTTTCTAAACATGAATGATAAATATATTAAGAAAGAAATTTGAAAAAAGATTAAGATAAAGTGAAATATTAATTGATTAGTGTCTTCTCTTCAGAAGAGGCTCATTGACATGGAAAATTATGCCGTAGAACCTTGATGACGGCACTGAAGCACACATAAAGCGAGGCGAAGTGCTCAATATGTTTTGAGCCTCGCTTCAAGGCTTAATCGCGCCTTTGACAACACCGTTACAGGAAAAAATGATGAGAAACTAGTAATTTTGTATATCTTCGTTGTAACACTCAAAAAGTGTATGCAATATAATTGTGCTGAAAGCATTTTTACAATAGATTCCTAGTAGTTTCTCCAACAATATTACCTTAATCTGGGGTAAATGGTAATCTTCGAGAGCTAATGCTATAAACATTTTTTGGTGGAAGCCGTATTAGAAACCATAATATTAAATTAAGTAATCCGATAAACTATCAGTTTAAAGAATGTATTTTGATTTGGTTGTTATGAGATCTTTTTAGCTTGATCTTTTATGACTTCAACACATTATCTATGTTAAAACAAGTGGTTTGTTCGATTTATGTACATGTTAGGAAACATAAATGTTGGTTCCAATCAACTTTATTATGTGGTGAATGTCAAAGTATAACATTTTAGCGAAGTGTTCTTGGCACATTATTGGACAAAACATGCTCTACTATCTTTATGTTCATCAATAATAACACACTCCTACGTTCAAATGTAGAAGTGCAATATGTTTCGGATTCAGATCTACTTATGCCTACACGAGTGTGGAATGGACTGGATTTCTAAATAGTGCTCATAATGTGTTTGCGTATTACTGATCTATGAGAAGAAAAAGAGCTTCATCATATTGCTTACTGGTTGTGCATGAAACTTTTTACCCGTCTTTACAATGAACTGGAGCTCTCGTGTGATAGCTTGTTCTCTGATAAAGTTAATATAGTTCTAATGGTGTTGATAGGAGATGATCGTTTGCCATTTGTCTTGTCTCTGCCAACAGATACATCACACTCCCTCTTTTTCTCATTTTCTGGAGAAAAGAGATGGAGTACTTCAATTTAAATGATTCGTGCTTGTTTAAGACGATTTCATCTTTTGCCTTTACAAATATGTTCTAAACTTGCTTCATTGAATAGGTACTTGATAGCTTCCCATACAACTGACTATCAACACCCAATGCTGTTCTTGAACACATTCGCAGTTTTCATACTGGTGGTTGCTAAATTTCCCAACATGCACAAGGTTCGAATATTTGGGATCAATGCAGATCAATGAAGTACTTCATTCAATTTGAAATTTTAGTTCCAACTTTACTCTCAGCTATATAGTAAGTATTTGATTGGTTTTAACAATTTTGAGTAAACAGGGAACTCCTGTACAAATGCAACAACTTCAAAGGGTGAAATTATATATATAGTAAAAAGATTAAGAGCCGATGTTGGGTTTGCTTAGCTACGCTCTTTTTTATAACCTGTTGAT</genome_strand>
        <mrna_strand>GAGCGGTCCCACCACCCCTACCCATAGCAGCCACCTATCCCCTCTTCGTTTTCGTGAGTCTCTGTTTTTTCGTTGATCAAATACTCATACTAATGCGATATTAATCGCCATATCCAATTGTTTCTTCTTCAAGTTTTGTATTGATAACTTTTTTCGATTGGGTTGAAAGTATTGTTCAATCCATTTGGATGGCGAATTTGTATGTGAGGGCTGCTCCAACCACGGATCTGAATCGGAATACTGAGTGGTTCACCTATCCTGGAGTTTGGACTATTTACATATTCATTCTGCTCTTCTCATGGCTCGTTGTGCTCTCTGTTTTTGGGTCCTCATCCGGCATGGCATGGACTATTGTCAATCTCGCTCATTTCCTT...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTCACATATCACTGTTTTCACTGGAAGAAGGGAACACCATTTGCTGAAGACCAGGGTATCTACAACAGATTGACATGGTGGGAGCAAATGGATAATGGCAAGCAGCTTACTCCCAATAGGAAGTTTCTGACAGTTGTTCCTGTGGTGCT.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTACTTGATAGCTTCCCATACAACTGACTATCAACACCCAATGCTGTTCTTGAACACATTCGCAGTTTTCATACTGGTGGTTGCTAAATTTCCCAACATGCACAAGGTTCGAATATTTGGGATCAATGCAGATCAATGAAGTACTTCATTCAATTTGAAATTTTAGTTCCAACTTTACTCTCAGCTATATAGTAAGTATTTGATTGGTTTTAACAATTTTGAGTAAACAGGGAACTCCTGTACAAATGCAACAACTTCAAAGGGTGAAATTATATATATAGTAAAAAGATTAAGAGCCGATGTTGGGTTTGCTTAGCTACGCTCTTTTTTATAACCTGTTGAT</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-C12HBa0040O03-kixkX/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_U_tomato" ref_id="SGN-U600319" ref_strand="+" ref_description="SGN-U600319 Tomato 200607#2 [1 ESTs aligned] ">
      <seq>gatcttccttcgttccctttagctttgtcactgcctccaatatgttccttgctagttgatacggacaccatcttaatctgtcaggctagtaatttaaacaggattgctccccagttcaacacctatggaacttgtcaaaactcaaaaatggaatcatactgctttcatctagacaaacatttggatctcctacatgctgaaaataagattgataaacttgcgttagacagtatttggtgttctataatctcagtggtccttagctttgaacttaagccgtttgtgtgtcaagcgtattcaacttcgtttaaatcgtagtggattaaggcataagaaaaagaaacaagcaatcacacaatcctctagaaggtacatccttcttcaggagttgcttctgaaaattctattattttactttttcctaagatgatatttttgtagtagcactatacctctatatacttgagacaatttggatacaaagaaaagtagattacccttttttcttgaaactgagaaagaagagtagattattggaggggatagggcagtagtttagtcaattactatacttgtaagaaaactgtattgtgggcccgcttaac</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0040O03-kixkX/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C12HBa0040O03.2" temp_strand="-" temp_description="C12HBa0040O03.2  AC235491.2 htgs_phase:2 submitted_to_sgn_as:gi|238550291|gb|AC235491.2| upload_account_name:italy Solanum lycopersicum chromosome 12 clone LE_HBa-40O3, WORKING DRAFT SEQUENCE, 3 ordered pieces">
        <position start="49262" stop="48059"/>
      </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="48963" g_stop="48359" g_length="605"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="605" r_length="605" r_score="0.993"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0040O03.2" gen_strand="-" ref_id="SGN-U600319" ref_strand="+">
        <total_alignment_score>0.993</total_alignment_score>
        <cumulative_length_of_scored_exons>605</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0040O03.2" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U600319" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="48963" e_stop="48359"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TATCTTCCTTCGTTCCCTTTAGCTTTGTCACTGCCTCCAATATGTTCCTTGCTAGTTGATACGGACACCATCTTAATCTGTCAGGCTAGTAATTTAAACAGGATTGCTCCCCAGTTCAACACCTATGGAACTTGTCAAAACTCAAAAATGGAATCATACTGCTTTCATCTAGACAAACATTTGGATCTCCTACATGCTGAAAATAAGATTGATAAACTTGCGTTAGACAGTATTTGGTGTTCTATAATCTCAGTGGTCCTTAGCTTTGAACTTAAGCCGTTTGTGTGTCAAGCGTATTCAACTTCGTTTAAATCGTAGTGGATTAAGGCATAAGAAAAAGAAACAAGCAATCACACAATCCTCTAGAAGGTACATCCTTCTTCAGGAGTTGCTTCTGAAAATTCTATTATTTTACTTTTTCCTAAGATGATATTTTTGTAGTAGCACTATACCTCTATATACTTGAGACAATTTGGATACAAAGAAAAGTAGATTACCCTTTTTTCTTGAAACTGAGAAAGAAGAGTAGATTATT-GAGGGGATAAGGGCAGTAGTTTAGTCAATTACTATACTTGTAAGAAAACTGTATTGTGGGCCCGCTTAAC</genome_strand>
        <mrna_strand>GATCTTCCTTCGTTCCCTTTAGCTTTGTCACTGCCTCCAATATGTTCCTTGCTAGTTGATACGGACACCATCTTAATCTGTCAGGCTAGTAATTTAAACAGGATTGCTCCCCAGTTCAACACCTATGGAACTTGTCAAAACTCAAAAATGGAATCATACTGCTTTCATCTAGACAAACATTTGGATCTCCTACATGCTGAAAATAAGATTGATAAACTTGCGTTAGACAGTATTTGGTGTTCTATAATCTCAGTGGTCCTTAGCTTTGAACTTAAGCCGTTTGTGTGTCAAGCGTATTCAACTTCGTTTAAATCGTAGTGGATTAAGGCATAAGAAAAAGAAACAAGCAATCACACAATCCTCTAGAAGGTACATCCTTCTTCAGGAGTTGCTTCTGAAAATTCTATTATTTTACTTTTTCCTAAGATGATATTTTTGTAGTAGCACTATACCTCTATATACTTGAGACAATTTGGATACAAAGAAAAGTAGATTACCCTTTTTTCTTGAAACTGAGAAAGAAGAGTAGATTATTGGAGGGGAT-AGGGCAGTAGTTTAGTCAATTACTATACTTGTAAGAAAACTGTATTGTGGGCCCGCTTAAC</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>2</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="45989" PGL_stop="41684"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="45989" e_stop="45616"/>
            <exon e_start="44720" e_stop="44572"/>
            <exon e_start="42026" e_stop="41684"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.995" acc_prob="0.992" e_score="0.997"/>
          <exon-intron don_prob="0.912" acc_prob="0.993" 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="0.997">
            <gDNA_exon_boundary e_start="45989" e_stop="45616" e_length="374"/>
          </exon>
          <intron i_serial="1" don_prob="0.995" acc_prob="0.992">
            <gDNA_intron_boundary i_start="45615" i_stop="44721" i_length="895"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="44720" e_stop="44572" e_length="149"/>
          </exon>
          <intron i_serial="2" don_prob="0.912" acc_prob="0.993">
            <gDNA_intron_boundary i_start="44571" i_stop="42027" i_length="2545"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="42026" e_stop="41684" e_length="343"/>
          </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="45989" stop="45616"/>
              <exon start="44720" stop="44572"/>
              <exon start="42026" stop="41684"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U579503" 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>CAGCGGTCCCACCACCCCTACCCATAGCAGCCACCTATCCCCTCTTCGTTTTCGTGAGTCTCTGTTTTTTCGTTGATCAAATACTCATACTAATGCGATATTAATCGCCATATCCAATTGTTTCTTCTTCAAGTTTTGTATTGATAACTTTTTTCGATTGGGTTGAAAGTATTGTTCAATCCATTTGGATGGCGAATTTGTATGTGAGGGCTGCTCCAACCACGGATCTGAATCGGAATACTGAGTGGTTCACCTATCCTGGAGTTTGGACTATTTACATATTCATTCTGCTCTTCTCATGGCTCGTTGTGCTCTCTGTTTTTGGGTCCTCATCCGGCATGGCATGGACTATTGTCAATCTCGCTCATTTCCTT : GTCACATATCACTGTTTTCACTGGAAGAAGGGAACACCATTTGCTGAAGACCAGGGTATCTACAACAGATTGACATGGTGGGAGCAAATGGATAATGGCAAGCAGCTTACTCCCAATAGGAAGTTTCTGACAGTTGTTCCTGTGGTGCT : GTACTTGATAGCTTCCCATACAACTGACTATCAACACCCAATGCTGTTCTTGAACACATTCGCAGTTTTCATACTGGTGGTTGCTAAATTTCCCAACATGCACAAGGTTCGAATATTTGGGATCAATGCAGATCAATGAAGTACTTCATTCAATTTGAAATTTTAGTTCCAACTTTACTCTCAGCTATATAGTAAGTATTTGATTGGTTTTAACAATTTTGAGTAAACAGGGAACTCCTGTACAAATGCAACAACTTCAAAGGGTGAAATTATATATATAGTAAAAAGATTAAGAGCCGATGTTGGGTTTGCTTAGCTACGCTCTTTTTTATAACCTGTTGAT</gDNA_template>
            <first_frame> Q  R  S  H  H  P  Y  P  *  Q  P  P  I  P  S  S  F  S  *  V  S  V  F  S  L  I  K  Y  S  Y  *  C  D  I  N  R  H  I  Q  L  F  L  L  Q  V  L  Y  *  *  L  F  S  I  G  L  K  V  L  F  N  P  F  G  W  R  I  C  M  *  G  L  L  Q  P  R  I  *  I  G  I  L  S  G  S  P  I  L  E  F  G  L  F  T  Y  S  F  C  S  S  H  G  S  L  C  S  L  F  L  G  P  H  P  A  W  H  G  L  L  S  I  S  L  I  S  L :   S  H  I  T  V  F  T  G  R  R  E  H  H  L  L  K  T  R  V  S  T  T  D  *  H  G  G  S  K  W  I  M  A  S  S  L  L  P  I  G  S  F  *  Q  L  F  L  W  C   : C  T  *  *  L  P  I  Q  L  T  I  N  T  Q  C  C  S  *  T  H  S  Q  F  S  Y  W  W  L  L  N  F  P  T  C  T  R  F  E  Y  L  G  S  M  Q  I  N  E  V  L  H  S  I  *  N  F  S  S  N  F  T  L  S  Y  I  V  S  I  *  L  V  L  T  I  L  S  K  Q  G  T  P  V  Q  M  Q  Q  L  Q  R  V  K  L  Y  I  *  *  K  D  *  E  P  M  L  G  L  L  S  Y  A  L  F  Y  N  L  L   </first_frame>
            <second_frame>  S  G  P  T  T  P  T  H  S  S  H  L  S  P  L  R  F  R  E  S  L  F  F  R  *  S  N  T  H  T  N  A  I  L  I  A  I  S  N  C  F  F  F  K  F  C  I  D  N  F  F  R  L  G  *  K  Y  C  S  I  H  L  D  G  E  F  V  C  E  G  C  S  N  H  G  S  E  S  E  Y  *  V  V  H  L  S  W  S  L  D  Y  L  H  I  H  S  A  L  L  M  A  R  C  A  L  C  F  W  V  L  I  R  H  G  M  D  Y  C  Q  S  R  S  F  P   : C  H  I  S  L  F  S  L  E  E  G  N  T  I  C  *  R  P  G  Y  L  Q  Q  I  D  M  V  G  A  N  G  *  W  Q  A  A  Y  S  Q  *  E  V  S  D  S  C  S  C  G  A  :  V  L  D  S  F  P  Y  N  *  L  S  T  P  N  A  V  L  E  H  I  R  S  F  H  T  G  G  C  *  I  S  Q  H  A  Q  G  S  N  I  W  D  Q  C  R  S  M  K  Y  F  I  Q  F  E  I  L  V  P  T  L  L  S  A  I  *  *  V  F  D  W  F  *  Q  F  *  V  N  R  E  L  L  Y  K  C  N  N  F  K  G  *  N  Y  I  Y  S  K  K  I  K  S  R  C  W  V  C  L  A  T  L  F  F  I  T  C  *  </second_frame>
            <third_frame>   A  V  P  P  P  L  P  I  A  A  T  Y  P  L  F  V  F  V  S  L  C  F  F  V  D  Q  I  L  I  L  M  R  Y  *  S  P  Y  P  I  V  S  S  S  S  F  V  L  I  T  F  F  D  W  V  E  S  I  V  Q  S  I  W  M  A  N  L  Y  V  R  A  A  P  T  T  D  L  N  R  N  T  E  W  F  T  Y  P  G  V  W  T  I  Y  I  F  I  L  L  F  S  W  L  V  V  L  S  V  F  G  S  S  S  G  M  A  W  T  I  V  N  L  A  H  F  L  :  V  T  Y  H  C  F  H  W  K  K  G  T  P  F  A  E  D  Q  G  I  Y  N  R  L  T  W  W  E  Q  M  D  N  G  K  Q  L  T  P  N  R  K  F  L  T  V  V  P  V  V  L :   Y  L  I  A  S  H  T  T  D  Y  Q  H  P  M  L  F  L  N  T  F  A  V  F  I  L  V  V  A  K  F  P  N  M  H  K  V  R  I  F  G  I  N  A  D  Q  *  S  T  S  F  N  L  K  F  *  F  Q  L  Y  S  Q  L  Y  S  K  Y  L  I  G  F  N  N  F  E  *  T  G  N  S  C  T  N  A  T  T  S  K  G  E  I  I  Y  I  V  K  R  L  R  A  D  V  G  F  A  *  L  R  S  F  L  *  P  V  D </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="C12HBa0040O03.2" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="45885" stop="45616"/>
                    <exon start="44720" stop="44572"/>
                    <exon start="42026" stop="41888"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>555</number_coding_nucleotides>
                  <number_encoded_amino_acids>185</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>SPYPIVSSSSFVLITFFDWVESIVQSIWMANLYVRAAPTTDLNRNTEWFTYPGVWTIYIFILLFSWLVVLSVFGSSSGMAWTIVNLAHFLVTYHCFHWKKGTPFAEDQGIYNRLTWWEQMDNGKQLTPNRKFLTVVPVVLYLIASHTTDYQHPMLFLNTFAVFILVVAKFPNMHKVRIFGINADQ*</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="48963" PGL_stop="48359"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="48963" e_stop="48359"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.993"/>
        </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="0.993">
            <gDNA_exon_boundary e_start="48963" e_stop="48359" e_length="605"/>
          </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="48963" stop="48359"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U600319" 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>TATCTTCCTTCGTTCCCTTTAGCTTTGTCACTGCCTCCAATATGTTCCTTGCTAGTTGATACGGACACCATCTTAATCTGTCAGGCTAGTAATTTAAACAGGATTGCTCCCCAGTTCAACACCTATGGAACTTGTCAAAACTCAAAAATGGAATCATACTGCTTTCATCTAGACAAACATTTGGATCTCCTACATGCTGAAAATAAGATTGATAAACTTGCGTTAGACAGTATTTGGTGTTCTATAATCTCAGTGGTCCTTAGCTTTGAACTTAAGCCGTTTGTGTGTCAAGCGTATTCAACTTCGTTTAAATCGTAGTGGATTAAGGCATAAGAAAAAGAAACAAGCAATCACACAATCCTCTAGAAGGTACATCCTTCTTCAGGAGTTGCTTCTGAAAATTCTATTATTTTACTTTTTCCTAAGATGATATTTTTGTAGTAGCACTATACCTCTATATACTTGAGACAATTTGGATACAAAGAAAAGTAGATTACCCTTTTTTCTTGAAACTGAGAAAGAAGAGTAGATTATTGAGGGGATAAGGGCAGTAGTTTAGTCAATTACTATACTTGTAAGAAAACTGTATTGTGGGCCCGCTTAAC</gDNA_template>
            <first_frame> Y  L  P  S  F  P  L  A  L  S  L  P  P  I  C  S  L  L  V  D  T  D  T  I  L  I  C  Q  A  S  N  L  N  R  I  A  P  Q  F  N  T  Y  G  T  C  Q  N  S  K  M  E  S  Y  C  F  H  L  D  K  H  L  D  L  L  H  A  E  N  K  I  D  K  L  A  L  D  S  I  W  C  S  I  I  S  V  V  L  S  F  E  L  K  P  F  V  C  Q  A  Y  S  T  S  F  K  S  *  W  I  K  A  *  E  K  E  T  S  N  H  T  I  L  *  K  V  H  P  S  S  G  V  A  S  E  N  S  I  I  L  L  F  P  K  M  I  F  L  *  *  H  Y  T  S  I  Y  L  R  Q  F  G  Y  K  E  K  *  I  T  L  F  S  *  N  *  E  R  R  V  D  Y  *  G  D  K  G  S  S  L  V  N  Y  Y  T  C  K  K  T  V  L  W  A  R  L   </first_frame>
            <second_frame>  I  F  L  R  S  L  *  L  C  H  C  L  Q  Y  V  P  C  *  L  I  R  T  P  S  *  S  V  R  L  V  I  *  T  G  L  L  P  S  S  T  P  M  E  L  V  K  T  Q  K  W  N  H  T  A  F  I  *  T  N  I  W  I  S  Y  M  L  K  I  R  L  I  N  L  R  *  T  V  F  G  V  L  *  S  Q  W  S  L  A  L  N  L  S  R  L  C  V  K  R  I  Q  L  R  L  N  R  S  G  L  R  H  K  K  K  K  Q  A  I  T  Q  S  S  R  R  Y  I  L  L  Q  E  L  L  L  K  I  L  L  F  Y  F  F  L  R  *  Y  F  C  S  S  T  I  P  L  Y  T  *  D  N  L  D  T  K  K  S  R  L  P  F  F  L  E  T  E  K  E  E  *  I  I  E  G  I  R  A  V  V  *  S  I  T  I  L  V  R  K  L  Y  C  G  P  A  *  </second_frame>
            <third_frame>   S  S  F  V  P  F  S  F  V  T  A  S  N  M  F  L  A  S  *  Y  G  H  H  L  N  L  S  G  *  *  F  K  Q  D  C  S  P  V  Q  H  L  W  N  L  S  K  L  K  N  G  I  I  L  L  S  S  R  Q  T  F  G  S  P  T  C  *  K  *  D  *  *  T  C  V  R  Q  Y  L  V  F  Y  N  L  S  G  P  *  L  *  T  *  A  V  C  V  S  S  V  F  N  F  V  *  I  V  V  D  *  G  I  R  K  R  N  K  Q  S  H  N  P  L  E  G  T  S  F  F  R  S  C  F  *  K  F  Y  Y  F  T  F  S  *  D  D  I  F  V  V  A  L  Y  L  Y  I  L  E  T  I  W  I  Q  R  K  V  D  Y  P  F  F  L  K  L  R  K  K  S  R  L  L  R  G  *  G  Q  *  F  S  Q  L  L  Y  L  *  E  N  C  I  V  G  P  L  N </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="C12HBa0040O03.2" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="48963" stop="48646"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>315</number_coding_nucleotides>
                  <number_encoded_amino_acids>105</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>YLPSFPLALSLPPICSLLVDTDTILICQASNLNRIAPQFNTYGTCQNSKMESYCFHLDKHLDLLHAENKIDKLALDSIWCSIISVVLSFELKPFVCQAYSTSFKS*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 13 chains have been computed
$ 
$ memory statistics:
$ 4320 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2160 bytes was the average size of a spliced alignment
$ 6768 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3384 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: 2009-07-24 23:17:32
-->
