<?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="2008-03-06 15:36:21"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04HBa0204I09-x3gqj/GenomeThreader_SGN_U_tomato/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-ukH9NU/lycopersicum_combined_unigene_seqs" 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/cxgn-bacpublish-resources-ukH9NU/lycopersicum_combined_unigene_seqs" ref_id="SGN-U312463" ref_strand="+" ref_description="SGN-U312463        Tomato 200607 #1 [2 ESTs aligned] arabidopsis/peptide: AT1G70490.1 | Symbol: None | Gene encoding ADP-ribosylation factor and similar to other ARFs and ARF-like proteins. Members of this family are known to be essential for vesicle coating and uncoating and functions in GTP-binding. The gene is shown to play a role in cell division, cell expansion and cellulose production using antisense construct. | chr1:26567590-26569471 REVERSE | Aliases: F24J13.6, F24J13_6 (evalue: 2e-82, score=301) genbank/nr: gi|47026845|gb|AAT08648.1| ADP-ribosylation factor [Hyacinthus orientalis] (evalue: 7e-82, score=305)">
      <seq>tcttctttcagtgctctttaacaaagggatcaccaacaagaaggagaaatggggctgtcattcaccaagcttttcagccggcttttcgccaagaaagaaatgcgaattctcatggttggacttgatgcagctggtaagaccaccatattgtacaagctcaagctgggcgagatcgttactactattcctaccattggtttcaatgtggagactgttgagtacaagaacatcagcttcactgtttgggatgtcgggggtcaggacaagattcgtccattatggaggcactatttccagaacactcagggtctcattttcgtggttgatagcaatgacagagatcgtgttgtggaggcaagagatgagttgcataggatgttaaatgaggaccagcttcgggatgctgtgcttcttgtttttgctaacaaacaagatcttcccaatgcaatgaatgctgccgaaataactgataagcttggactgcactctcttaggcagcgtcact</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0204I09-x3gqj/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0204I09.1" temp_strand="+" temp_description="C04HBa0204I09.1  CU457754.5 htgs_phase:3 submitted_to_sgn_as:C04HBa0204I09 sequenced_by:sanger upload_account_name:uk">
        <position start="38220" stop="42015"/>
      </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="38532" g_stop="38717" g_length="186"/>
          <reference_exon_boundary r_type="cDNA" r_start="12" r_stop="196" r_length="185" r_score="0.978"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="38718" i_stop="39610" i_length="893">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.996" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="39611" g_stop="39681" g_length="71"/>
          <reference_exon_boundary r_type="cDNA" r_start="197" r_stop="267" r_length="71" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="39682" i_stop="39870" i_length="189">
            <donor d_prob="0.999" d_score="1.00"/>
            <acceptor a_prob="0.955" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="39871" g_stop="39990" g_length="120"/>
          <reference_exon_boundary r_type="cDNA" r_start="268" r_stop="387" r_length="120" r_score="0.992"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="39991" i_stop="41597" i_length="1607">
            <donor d_prob="0.999" d_score="0.98"/>
            <acceptor a_prob="0.935" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="41598" g_stop="41715" g_length="118"/>
          <reference_exon_boundary r_type="cDNA" r_start="388" r_stop="505" r_length="118" r_score="0.983"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0204I09.1" gen_strand="+" ref_id="SGN-U312463" ref_strand="+">
        <total_alignment_score>0.986</total_alignment_score>
        <cumulative_length_of_scored_exons>495</cumulative_length_of_scored_exons>
        <coverage percentage="0.980" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0204I09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-U312463" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="38532" e_stop="38717"/>
          <exon e_start="39611" e_stop="39681"/>
          <exon e_start="39871" e_stop="39990"/>
          <exon e_start="41598" e_stop="41715"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TGCTCTTTTAACATAGGGATCACCAACAAGAAGGAGAAATGGGGATGTCATTCACCAAGCTTTTCAGTCGGCTTTTCGCCAAGAAAGAAATGCGAATTCTCATGGTTGGACTTGATGCAGCTGGTAAGACCACCATATTGTACAAGCTCAAGCTGGGCGAGATCGTTACTACTATTCCTACCATTGGTACGTACTTCACTTATATGCATATCTGTACTTACAAATTAACTGTTCAAACTATAGTTTATAACTTTCAAAAAATGCATCTAATGTACCTGTGATGAATATAGTATTGGAAGATAACATTAGAAATCCATAAATGTAAGCTATGGTTGGATTTTCTTCCTCAGAAGAGAATTCATTATGGGTGAATTATGAGTCTGCTAAAATGCTAGAATTTTAGATAAAATAATGTATCGATTTGAAGCTTAATTGAATGTTAGCATTCATTTTTTTATTGTTTGACTGGTTACAAAGGACATTACAGAAGTTACTTTTGAATTAAAATTATACTATTATCTTTTATCATAATATGTTGCTGTATATCATAAAAAGGATATTCATGGACGTCTGATGCAATAGAGTAGGGGTATGTATATAATCCTTTTATCATCTAAAATTCTATAGGGGGCTATTCTACGGCTTGACTTTCTATATTAAAAACTAAGAAAGGGGCTTTGATATGAAAGATTAAATTACATTATGCTAATTAATCTCTATTCTCTGCTCGATCAACATTTTATAATAGAATTAGGTTGATTTTTTCGTTTTCTTTTGGGATTACATGGCAGTAGGAAATTGTTTATGCTTTTCTAAACCAATATTTTGGTTTTAAGATGAGTAAGTTTTTCATAATTCTTAAGAAAACATTTCTATGAATGCACCAAAAGAGAGCCTTTAAAGTGAACTAAAGAAAGGAAGTATGTTATGTTTTTTCTATGCGCTTTTTTTCACAACCTTGTTGGAACTGTTGCGATGAATAGATAATCAGCTCTGTCTGAAGCTTACTCTAATCTCTGTAATTGTATACTTATAATATTACTGCTTGGATGCTGTCAATAATAATTGATAATTTGTAGGTTTCAATGTGGAGACTGTTGAGTACAAGAACATCAGCTTCACTGTTTGGGATGTCGGGGGTCAGGACAAGGTATAATTTTTTTTAGTGTAAGGAATATAAGTTAATTTTGAGTTTGTTATTTGTTTATGATAAACCGGGAGCAAGTCTTTATCTATGTTTGCTGACCTTAACTTTCCCCTTTCCTCGACTTATGTGCTTCATAGAATTAGGCCTTTGATTTAACTGTTTAAAGCACAACCACCATTTATTTTTTTCCAGATTCGTCCATTATGGAGGCACTATTTCCAGAACACTCAGGGTCTCATTTTCGTGGTTGATAGCAATGACAGAGATCGCGTTGTGGAGGCAAGAGATGAGTTGCATAGGATGTTAAATGAGGTAATAATTTTCACACCTTTTTTATATTGTTTTTAGTTTTCACGAAATGAGATTCAACTTTTAAAGCTTTAAGCTGCATGGCAAAAAAAAAGTCTGTGACTATTTTAAGTGAACAGTACTGAAATCTGCATTGTATACTAATTAGCTCTTCAAGCTGATACCCGAGCCATTGAACTAATCACAAGCATTTGCAATAGTCGTTTTCATCTAGAGTGATTACAACTTGTGGTTATGACACTGTATATCTGTCTACCAAAAGTCTCTCTTTCTTAAACTCCTCATACTAAGTTAAACCATCCATATAATTTTAAATGTAGGAAGTACTTTTTTCCCTCCATCTTGTCACATAATGCTTGGAAGAAATTATTAAAACTAAAATATGAATTATTTTTCCATTTTTGTTTTGTTCTTTTTTAAACTACAAAGCGATGACTCTTAATTTGCTGAAAATCCCTGAACATGGACTAATAATAAATCAAAACCATGGATGAGAAAAACAAAATACTTTTATCCCTCCCAATAATCTTGGATATAACTTCATTTTCAGATAAAAACAAATTGGATATAACTTAATTTTATGTAATTCAGAGTTCCTAAATGGAGCCTTGAGCATATTGGCAAATTCTTATTTGAAATGAATTTTGGCTAATGTGTGCTAATTTTTAACTTCCTTTATTTTGAGTAGCCCTAATTCAAAATCTTAGTTTGGTAATTTTCTTATCTCATTTGCCATAGCCATAAGCTAAAGTAGTTTCCATTAGGAGGAGTTAATGAGTTAGATTTAAACCTTACTGTAATCCTCATTAAGGAGTATGCCAAATGTCTGATACCATACACGAATAATCTATGTTATGTTATCAATTTCTATAGCGAAGATTTACAGTCAACAACAATGTCAATGGTATCGCAGCTTGAATAAAGATAAAAGAACTGTGCTTGCAAAGTAAAAGAAAACTGTATAACTCTTGTATAACTCTTGACTGTACTGACTGCACTAATTTTATTCAATTTTTTGGAGCTTTAAGTGGAGCCAAAGATGATGTTTCAGTGATTCAAAATTGTCAAACATTTTTCCTTGAACTTATGGAGTGTGTCATATCGTCCAATCATTTTGTCCCTCCGTCTTTGAAATGCTATTTAGGATGTTATTGTTAGTAAGATGAATGTCATAATTGGAACTATTCATCAACTTTGATCCATTGTTGAATGGGACAGTTGGTTATTTATGGTTTAACCGTTAGTAGGTGAAGTACCTGTAGGAGTTCAGGGAGAATAGCTCAAAGAGGAGATTTTACCATCTGCTTGTCATTTAATTAAAATAGTAGAGAGAACTGGCAATACTTCACTTTATGTTTGCACAGGTCAACGTGTCCATATATTGTTTCTTAGGAAAAGAACACATAAAAATAGTGAACGGTGAGTAGGAGCAGGGAGCTTCTACACTGAACCACAGTACCCAAATGCTTTTTCTGCTCATAGCTCATGCTTAATATGCTCATAGTTACATTAATTGTTAAATGACAAAGTGAAAGGATTTTGTTCTTAAGTTTGACTTAAACTTTGCCGACTGACCTGTGGAGTTTAATAGTCTTTACTCTCTGTTCTAGGACGAGCTTCGGGATGTTGTGCTTCTTGTTTTTGCTAACAAACAAGATCTTCCCAATGCAATGAATGCTGCCGAAATAACTGATAAGCTTGGACTGCACTCTCTTAGGCAGCGTCACT</genome_strand>
        <mrna_strand>TGCTCTT-TAACAAAGGGATCACCAACAAGAAGGAGAAATGGGGCTGTCATTCACCAAGCTTTTCAGCCGGCTTTTCGCCAAGAAAGAAATGCGAATTCTCATGGTTGGACTTGATGCAGCTGGTAAGACCACCATATTGTACAAGCTCAAGCTGGGCGAGATCGTTACTACTATTCCTACCATTG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTTTCAATGTGGAGACTGTTGAGTACAAGAACATCAGCTTCACTGTTTGGGATGTCGGGGGTCAGGACAAG.............................................................................................................................................................................................ATTCGTCCATTATGGAGGCACTATTTCCAGAACACTCAGGGTCTCATTTTCGTGGTTGATAGCAATGACAGAGATCGTGTTGTGGAGGCAAGAGATGAGTTGCATAGGATGTTAAATGAG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GACCAGCTTCGGGATGCTGTGCTTCTTGTTTTTGCTAACAAACAAGATCTTCCCAATGCAATGAATGCTGCCGAAATAACTGATAAGCTTGGACTGCACTCTCTTAGGCAGCGTCACT</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/cxgn-bacpublish-resources-ukH9NU/lycopersicum_combined_unigene_seqs" ref_id="SGN-U340786" ref_strand="+" ref_description="SGN-U340786        Tomato 200607 #1 [1 ESTs aligned] genbank/nr: SJCHGC09205(evalue: 7e-05, score=50.8)">
      <seq>agtagccaggcgggttccttcccctctcccttatcctattatacgaaaattgtactcgaaggccccaggtcgaaatctccctttctctcttgtccttcctctaaaatgggatgtctcccttcgattttctgttgatgatcgtacaaggatagagttggaagcttatgctgaagaagggatttgaatttcgaaatcaaatcccatccattttccgcccaaaaattttcttcccatttttctctcctataaatatcagtgagagaaaagggaaaaaacttctttagcttgaaaaaatattacaaaaagtagaaagattttgagtccatttttgttagcaagaacttacaagaaaaggaattactaggttataatattcatataacaaacatgcgataatttatttttttttgttatttgttgcaaaatttgttggatttctgaatcttaaaggaagatattgaagtctatccaagctcattcctatctctggttctctatacgaagaaggtacaactcgtttctcgataacatactctccttttctcctccgttttctctgtgaaatagcactttgttgctggaaattttctgctgtttgttcatctatttaatgttaattcaatggagatattggtatgacttatatngttgttgattcatttaagtagatatggta</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04HBa0204I09-x3gqj/GenomeThreader_SGN_U_tomato/un_xed_seqs" temp_id="C04HBa0204I09.1" temp_strand="-" temp_description="C04HBa0204I09.1  CU457754.5 htgs_phase:3 submitted_to_sgn_as:C04HBa0204I09 sequenced_by:sanger upload_account_name:uk">
        <position start="139577" stop="138595"/>
      </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="139568" g_stop="138895" g_length="674"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="676" r_length="676" r_score="0.994"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04HBa0204I09.1" gen_strand="-" ref_id="SGN-U340786" ref_strand="+">
        <total_alignment_score>0.994</total_alignment_score>
        <cumulative_length_of_scored_exons>674</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04HBa0204I09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-U340786" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="139568" e_stop="138895"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AGTAGCCAGGCGGGTTCCTTCCCCTCTCCCTTATCCTATTATACGAAAATTGTACTCGAAGGCCCCAGGTCGAAATCTCCCTTTCTCTCTTGTCCTTCCTCTAAAATGGGATGTCTCCCTTCGATTTTCTGTTGATGATCGTACAAGGATAGAGTTGGAAGCTTATGCTGAAG-AGGGATTTGAATTTCGAAATCAAATCCCATCCATTTTCCGCCCAAAAATTTTCTTCCCATTTTTCTCTCCTATAAATATCAGTGAGAGAAAAGGGAAAAAACTTCTTTAGCTTGAAAAAATATTACAAAAAGTAGAAAGATTTTGAGTCCATTTTTGTTAGCAAGAACTTACAAGAAAAGGAATTACTAGGTTATAATATTCATATAACAAACATGCGATAATTTATTTTTTTTTGTTATTTGTTGCAAAATTTGTTGGATTTCTGAATCTTAAAGGAAGATATTGAAGTCTATCCAAGCTCATTCCTATCTCTGGTTCTCTATACGAAGAAGGTACAACTCGTTTCTCGATAACATACTCTCCTTTTCTCCTCCGTTTTCTCTGTGAAATAGCACTTTGTTGCTGGAAATTTTCTGCTGTTTGTTCATCTATTTAATGTTAATTCAATGGAGATATTGGTATGACTTATAT-GTTGTTGATTCATTTAAGTAGATATGGTA</genome_strand>
        <mrna_strand>AGTAGCCAGGCGGGTTCCTTCCCCTCTCCCTTATCCTATTATACGAAAATTGTACTCGAAGGCCCCAGGTCGAAATCTCCCTTTCTCTCTTGTCCTTCCTCTAAAATGGGATGTCTCCCTTCGATTTTCTGTTGATGATCGTACAAGGATAGAGTTGGAAGCTTATGCTGAAGAAGGGATTTGAATTTCGAAATCAAATCCCATCCATTTTCCGCCCAAAAATTTTCTTCCCATTTTTCTCTCCTATAAATATCAGTGAGAGAAAAGGGAAAAAACTTCTTTAGCTTGAAAAAATATTACAAAAAGTAGAAAGATTTTGAGTCCATTTTTGTTAGCAAGAACTTACAAGAAAAGGAATTACTAGGTTATAATATTCATATAACAAACATGCGATAATTTATTTTTTTTTGTTATTTGTTGCAAAATTTGTTGGATTTCTGAATCTTAAAGGAAGATATTGAAGTCTATCCAAGCTCATTCCTATCTCTGGTTCTCTATACGAAGAAGGTACAACTCGTTTCTCGATAACATACTCTCCTTTTCTCCTCCGTTTTCTCTGTGAAATAGCACTTTGTTGCTGGAAATTTTCTGCTGTTTGTTCATCTATTTAATGTTAATTCAATGGAGATATTGGTATGACTTATATNGTTGTTGATTCATTTAAGTAGATATGGTA</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="38532" PGL_stop="41715"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="38532" e_stop="38717"/>
            <exon e_start="39611" e_stop="39681"/>
            <exon e_start="39871" e_stop="39990"/>
            <exon e_start="41598" e_stop="41715"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.996" e_score="0.978"/>
          <exon-intron don_prob="0.999" acc_prob="0.955" e_score="1.000"/>
          <exon-intron don_prob="0.999" acc_prob="0.935" e_score="0.992"/>
          <exon-only e_score="0.983"/>
        </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="0.978">
            <gDNA_exon_boundary e_start="38532" e_stop="38717" e_length="186"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.996">
            <gDNA_intron_boundary i_start="38718" i_stop="39610" i_length="893"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="39611" e_stop="39681" e_length="71"/>
          </exon>
          <intron i_serial="2" don_prob="0.999" acc_prob="0.955">
            <gDNA_intron_boundary i_start="39682" i_stop="39870" i_length="189"/>
          </intron>
          <exon e_serial="3" e_score="0.992">
            <gDNA_exon_boundary e_start="39871" e_stop="39990" e_length="120"/>
          </exon>
          <intron i_serial="3" don_prob="0.999" acc_prob="0.935">
            <gDNA_intron_boundary i_start="39991" i_stop="41597" i_length="1607"/>
          </intron>
          <exon e_serial="4" e_score="0.983">
            <gDNA_exon_boundary e_start="41598" e_stop="41715" e_length="118"/>
          </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="38532" stop="38717"/>
              <exon start="39611" stop="39681"/>
              <exon start="39871" stop="39990"/>
              <exon start="41598" stop="41715"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U312463" 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>TGCTCTTTTAACATAGGGATCACCAACAAGAAGGAGAAATGGGGATGTCATTCACCAAGCTTTTCAGTCGGCTTTTCGCCAAGAAAGAAATGCGAATTCTCATGGTTGGACTTGATGCAGCTGGTAAGACCACCATATTGTACAAGCTCAAGCTGGGCGAGATCGTTACTACTATTCCTACCATTG : GTTTCAATGTGGAGACTGTTGAGTACAAGAACATCAGCTTCACTGTTTGGGATGTCGGGGGTCAGGACAAG : ATTCGTCCATTATGGAGGCACTATTTCCAGAACACTCAGGGTCTCATTTTCGTGGTTGATAGCAATGACAGAGATCGCGTTGTGGAGGCAAGAGATGAGTTGCATAGGATGTTAAATGAG : GACGAGCTTCGGGATGTTGTGCTTCTTGTTTTTGCTAACAAACAAGATCTTCCCAATGCAATGAATGCTGCCGAAATAACTGATAAGCTTGGACTGCACTCTCTTAGGCAGCGTCACT</gDNA_template>
            <first_frame> C  S  F  N  I  G  I  T  N  K  K  E  K  W  G  C  H  S  P  S  F  S  V  G  F  S  P  R  K  K  C  E  F  S  W  L  D  L  M  Q  L  V  R  P  P  Y  C  T  S  S  S  W  A  R  S  L  L  L  F  L  P  L  :  V  S  M  W  R  L  L  S  T  R  T  S  A  S  L  F  G  M  S  G  V  R  T  R :   F  V  H  Y  G  G  T  I  S  R  T  L  R  V  S  F  S  W  L  I  A  M  T  E  I  A  L  W  R  Q  E  M  S  C  I  G  C  *  M  R :   T  S  F  G  M  L  C  F  L  F  L  L  T  N  K  I  F  P  M  Q  *  M  L  P  K  *  L  I  S  L  D  C  T  L  L  G  S  V  T </first_frame>
            <second_frame>  A  L  L  T  *  G  S  P  T  R  R  R  N  G  D  V  I  H  Q  A  F  Q  S  A  F  R  Q  E  R  N  A  N  S  H  G  W  T  *  C  S  W  *  D  H  H  I  V  Q  A  Q  A  G  R  D  R  Y  Y  Y  S  Y  H  W :   F  Q  C  G  D  C  *  V  Q  E  H  Q  L  H  C  L  G  C  R  G  S  G  Q   : D  S  S  I  M  E  A  L  F  P  E  H  S  G  S  H  F  R  G  *  *  Q  *  Q  R  S  R  C  G  G  K  R  *  V  A  *  D  V  K  *   : G  R  A  S  G  C  C  A  S  C  F  C  *  Q  T  R  S  S  Q  C  N  E  C  C  R  N  N  *  *  A  W  T  A  L  S  *  A  A  S   </second_frame>
            <third_frame>   L  F  *  H  R  D  H  Q  Q  E  G  E  M  G  M  S  F  T  K  L  F  S  R  L  F  A  K  K  E  M  R  I  L  M  V  G  L  D  A  A  G  K  T  T  I  L  Y  K  L  K  L  G  E  I  V  T  T  I  P  T  I   : G  F  N  V  E  T  V  E  Y  K  N  I  S  F  T  V  W  D  V  G  G  Q  D  K  :  I  R  P  L  W  R  H  Y  F  Q  N  T  Q  G  L  I  F  V  V  D  S  N  D  R  D  R  V  V  E  A  R  D  E  L  H  R  M  L  N  E  :  D  E  L  R  D  V  V  L  L  V  F  A  N  K  Q  D  L  P  N  A  M  N  A  A  E  I  T  D  K  L  G  L  H  S  L  R  Q  R  H  </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="C04HBa0204I09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="38543" stop="38717"/>
                    <exon start="39611" stop="39681"/>
                    <exon start="39871" stop="39990"/>
                    <exon start="41598" stop="41714"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>483</number_coding_nucleotides>
                  <number_encoded_amino_acids>161</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>HRDHQQEGEMGMSFTKLFSRLFAKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDVVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRH</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="139568" PGL_stop="138895"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="139568" e_stop="138895"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.994"/>
        </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="0.994">
            <gDNA_exon_boundary e_start="139568" e_stop="138895" e_length="674"/>
          </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="139568" stop="138895"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-U340786" 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>AGTAGCCAGGCGGGTTCCTTCCCCTCTCCCTTATCCTATTATACGAAAATTGTACTCGAAGGCCCCAGGTCGAAATCTCCCTTTCTCTCTTGTCCTTCCTCTAAAATGGGATGTCTCCCTTCGATTTTCTGTTGATGATCGTACAAGGATAGAGTTGGAAGCTTATGCTGAAGAGGGATTTGAATTTCGAAATCAAATCCCATCCATTTTCCGCCCAAAAATTTTCTTCCCATTTTTCTCTCCTATAAATATCAGTGAGAGAAAAGGGAAAAAACTTCTTTAGCTTGAAAAAATATTACAAAAAGTAGAAAGATTTTGAGTCCATTTTTGTTAGCAAGAACTTACAAGAAAAGGAATTACTAGGTTATAATATTCATATAACAAACATGCGATAATTTATTTTTTTTTGTTATTTGTTGCAAAATTTGTTGGATTTCTGAATCTTAAAGGAAGATATTGAAGTCTATCCAAGCTCATTCCTATCTCTGGTTCTCTATACGAAGAAGGTACAACTCGTTTCTCGATAACATACTCTCCTTTTCTCCTCCGTTTTCTCTGTGAAATAGCACTTTGTTGCTGGAAATTTTCTGCTGTTTGTTCATCTATTTAATGTTAATTCAATGGAGATATTGGTATGACTTATATGTTGTTGATTCATTTAAGTAGATATGGTA</gDNA_template>
            <first_frame> S  S  Q  A  G  S  F  P  S  P  L  S  Y  Y  T  K  I  V  L  E  G  P  R  S  K  S  P  F  L  S  C  P  S  S  K  M  G  C  L  P  S  I  F  C  *  *  S  Y  K  D  R  V  G  S  L  C  *  R  G  I  *  I  S  K  S  N  P  I  H  F  P  P  K  N  F  L  P  I  F  L  S  Y  K  Y  Q  *  E  K  R  E  K  T  S  L  A  *  K  N  I  T  K  S  R  K  I  L  S  P  F  L  L  A  R  T  Y  K  K  R  N  Y  *  V  I  I  F  I  *  Q  T  C  D  N  L  F  F  F  V  I  C  C  K  I  C  W  I  S  E  S  *  R  K  I  L  K  S  I  Q  A  H  S  Y  L  W  F  S  I  R  R  R  Y  N  S  F  L  D  N  I  L  S  F  S  P  P  F  S  L  *  N  S  T  L  L  L  E  I  F  C  C  L  F  I  Y  L  M  L  I  Q  W  R  Y  W  Y  D  L  Y  V  V  D  S  F  K  *  I  W   </first_frame>
            <second_frame>  V  A  R  R  V  P  S  P  L  P  Y  P  I  I  R  K  L  Y  S  K  A  P  G  R  N  L  P  F  S  L  V  L  P  L  K  W  D  V  S  L  R  F  S  V  D  D  R  T  R  I  E  L  E  A  Y  A  E  E  G  F  E  F  R  N  Q  I  P  S  I  F  R  P  K  I  F  F  P  F  F  S  P  I  N  I  S  E  R  K  G  K  K  L  L  *  L  E  K  I  L  Q  K  V  E  R  F  *  V  H  F  C  *  Q  E  L  T  R  K  G  I  T  R  L  *  Y  S  Y  N  K  H  A  I  I  Y  F  F  L  L  F  V  A  K  F  V  G  F  L  N  L  K  G  R  Y  *  S  L  S  K  L  I  P  I  S  G  S  L  Y  E  E  G  T  T  R  F  S  I  T  Y  S  P  F  L  L  R  F  L  C  E  I  A  L  C  C  W  K  F  S  A  V  C  S  S  I  *  C  *  F  N  G  D  I  G  M  T  Y  M  L  L  I  H  L  S  R  Y  G  </second_frame>
            <third_frame>   *  P  G  G  F  L  P  L  S  L  I  L  L  Y  E  N  C  T  R  R  P  Q  V  E  I  S  L  S  L  L  S  F  L  *  N  G  M  S  P  F  D  F  L  L  M  I  V  Q  G  *  S  W  K  L  M  L  K  R  D  L  N  F  E  I  K  S  H  P  F  S  A  Q  K  F  S  S  H  F  S  L  L  *  I  S  V  R  E  K  G  K  N  F  F  S  L  K  K  Y  Y  K  K  *  K  D  F  E  S  I  F  V  S  K  N  L  Q  E  K  E  L  L  G  Y  N  I  H  I  T  N  M  R  *  F  I  F  F  C  Y  L  L  Q  N  L  L  D  F  *  I  L  K  E  D  I  E  V  Y  P  S  S  F  L  S  L  V  L  Y  T  K  K  V  Q  L  V  S  R  *  H  T  L  L  F  S  S  V  F  S  V  K  *  H  F  V  A  G  N  F  L  L  F  V  H  L  F  N  V  N  S  M  E  I  L  V  *  L  I  C  C  *  F  I  *  V  D  M  V </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="C04HBa0204I09.1" strand="-"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="139567" stop="139286"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>279</number_coding_nucleotides>
                  <number_encoded_amino_acids>93</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VARRVPSPLPYPIIRKLYSKAPGRNLPFSLVLPLKWDVSLRFSVDDRTRIELEAYAEEGFEFRNQIPSIFRPKIFFPFFSPINISERKGKKLL*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 72 chains have been computed
$ 
$ memory statistics:
$ 3296 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 1648 bytes was the average size of a spliced alignment
$ 6800 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3400 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 89 backtrace matrices have been allocated
$ 
$ date finished: 2008-03-06 15:37:25
-->
