<?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="2009-01-18 05:36:57"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12HBa0090D09-eZc9V/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C12HBa0090D09-eZc9V/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" type="ESTcDNA"/>
    </reference_files>
    <splice_site_parameters parameter_type="Bayesian" species="arabidopsis"/>
    <parameters>
      <parameter name="bssmfile" value="arabidopsis"/>
      <parameter name="scorematrixfile" value="BLOSUM62"/>
      <parameter name="searchmode" value="forward=True,reverse=True)"/>
      <parameter name="translationtable" value="1"/>
      <parameter name="frompos" value="0"/>
      <parameter name="topos" value="0"/>
      <parameter name="width" value="0"/>
      <parameter name="verbose" value="False"/>
      <parameter name="skipalignmentout" value="False"/>
      <parameter name="showintronmaxlen" value="120"/>
      <parameter name="minorflen" value="64"/>
      <parameter name="showseqnums" value="False"/>
      <parameter name="gs2out" value="False"/>
      <parameter name="maskpolyatails" value="False"/>
      <parameter name="noautoindex" value="False"/>
      <parameter name="minmatchlen" value="20"/>
      <parameter name="seedlength" value="16"/>
      <parameter name="exdrop" value="2"/>
      <parameter name="online" value="False"/>
      <parameter name="inverse" value="False"/>
      <parameter name="exact" value="False"/>
      <parameter name="chainwf" value="0.500000"/>
      <parameter name="gcmaxgapwidth" value="1000000"/>
      <parameter name="gcmincoverage" value="50"/>
      <parameter name="introncutout" value="False"/>
      <parameter name="autointroncutout" value="0"/>
      <parameter name="icinitialdelta" value="50"/>
      <parameter name="iciterations" value="2"/>
      <parameter name="icdeltaincrease" value="50"/>
      <parameter name="icminremintronlen" value="10"/>
      <parameter name="nou12intronmodel" value="False"/>
      <parameter name="u12donorprob" value="0.990000"/>
      <parameter name="u12donorprob1mism" value="0.900000"/>
      <parameter name="probies" value="0.500000"/>
      <parameter name="probdelgen" value="0.030000"/>
      <parameter name="identityweight" value="2.000000"/>
      <parameter name="mismatchweight" value="-2.000000"/>
      <parameter name="undetcharweight" value="0.000000"/>
      <parameter name="deletionweight" value="-4.000000"/>
      <parameter name="dpminexonlen" value="5"/>
      <parameter name="dpminintronlen" value="50"/>
      <parameter name="shortexonpenal" value="100"/>
      <parameter name="shortintronpenal" value="100"/>
      <parameter name="wzerotransition" value="80"/>
      <parameter name="wdecreasedoutput" value="80"/>
      <parameter name="leadcutoffsmode" value="RELAXED"/>
      <parameter name="termcutoffsmode" value="STRICT"/>
      <parameter name="cutoffsminexonlen" value="5"/>
      <parameter name="scoreminexonlen" value="50"/>
      <parameter name="minaveragessp" value="0.500000"/>
      <parameter name="minalignmentscore" value="0.900000"/>
      <parameter name="maxalignmentscore" value="1.000000"/>
      <parameter name="mincoverage" value="0.900000"/>
      <parameter name="maxcoverage" value="100.000000"/>
      <parameter name="intermediate" value="False"/>
      <parameter name="sortags" value="False"/>
      <parameter name="sortagswf" value="1.000000"/>
      <parameter name="first" value="0"/>
      <parameter name="exondistri" value="False"/>
      <parameter name="introndistri" value="False"/>
      <parameter name="refseqcovdistri" value="False"/>
    </parameters>
    <overall_reference_type>ESTcDNA</overall_reference_type>
  </header>
  <alignment_module>
  <spliced_alignment xmlns="http://www.genomethreader.org/GTH_output/alignment_module/spliced_alignment/">
    <reference ref_file="/tmp/bac-submission-temp-C12HBa0090D09-eZc9V/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M9180" ref_strand="+" ref_description="SGN-M9180 C2_At5g63540 [cosii_markers]">
      <seq>aagtagctgctggaataaagaggtgtctgaaattgtccatgactgatggcattcagcgagtgtttgggatggagtacaggcctataaaagatctcgatgttctagctccttctggactgaaggttgctatctgtaatgttcatgttaggcatggaattctgatgttggtccctgaagttattgaagttctgggtgggatggtggaagacttagaagaagcaaggaagcggctagttaatgaaataaataagccaccaagggggaaaagaacaaggtctggtgtggttcctcctttggcaactagagctattgctgctgcatggccacgagaaggtgttactgttccagagcactctgatacttcctcaagacaaaatatgcaatttcaggttcatgaacgaggaacatctggcattgctactactgcaactgaagaaattcatcccgttacatctgggctaccatcttctacgtcattcatcactcctgtttatagaagagaggctcaatctaatatcccatctactccagctgtttctgtcccattcaataggaacgctgaacctaccttttcatctgatgcagctagtcatgcagaggatatccatatggctgacatgaccactgaaggcattgatgttccaattagaagggaacataatgacactgtcctttcatctttttcttccatggaagtggaggaacttttgtcagatattagaagtgaccctgccacacctgccagtagcaggagcagaggaagcattcgtgtctctagtgatagtttccattatgaagatgtaacaccagatacattgtctactgcagcaattgacgttgatgaaattgatttggttgatgaattggaccatccatatatactttctggagcaaaggaaaaccctttcacttacttagctagtctgtcagctaagcaggctggtatgcatggcagtgcttccactgttacaggaaaaattaagtgctttcttactggtgtgaagggatttcagtataaacagagtagtaaatacgagcttcgggtttatgttgatgatggcagcctaatctctgagatccttatagatcatgctctt</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0090D09-eZc9V/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0090D09.1" temp_strand="+" temp_description="C12HBa0090D09.1  AC212766.1 htgs_phase:3 submitted_to_sgn_as:C12HBa0090D09 upload_account_name:italy">
        <position start="17422" stop="20819"/>
      </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="17722" g_stop="17843" g_length="122"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="122" r_length="122" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="17844" i_stop="17997" i_length="154">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.994" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="17998" g_stop="18143" g_length="146"/>
          <reference_exon_boundary r_type="cDNA" r_start="123" r_stop="268" r_length="146" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="18144" i_stop="18671" i_length="528">
            <donor d_prob="0.615" d_score="1.00"/>
            <acceptor a_prob="0.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="18672" g_stop="18805" g_length="134"/>
          <reference_exon_boundary r_type="cDNA" r_start="269" r_stop="402" r_length="134" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="18806" i_stop="19296" i_length="491">
            <donor d_prob="0.979" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="0.96"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="19297" g_stop="19877" g_length="581"/>
          <reference_exon_boundary r_type="cDNA" r_start="403" r_stop="983" r_length="581" r_score="0.966"/>
        </exon>
        <intron i_serial="4">
          <gDNA_intron_boundary i_start="19878" i_stop="20406" i_length="529">
            <donor d_prob="0.969" d_score="0.96"/>
            <acceptor a_prob="0.926" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="5">
          <gDNA_exon_boundary g_start="20407" g_stop="20517" g_length="111"/>
          <reference_exon_boundary r_type="cDNA" r_start="984" r_stop="1094" r_length="111" r_score="0.991"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0090D09.1" gen_strand="+" ref_id="SGN-M9180" ref_strand="+">
        <total_alignment_score>0.981</total_alignment_score>
        <cumulative_length_of_scored_exons>1094</cumulative_length_of_scored_exons>
        <coverage percentage="0.997" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0090D09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M9180" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="17722" e_stop="17843"/>
          <exon e_start="17998" e_stop="18143"/>
          <exon e_start="18672" e_stop="18805"/>
          <exon e_start="19297" e_stop="19877"/>
          <exon e_start="20407" e_stop="20517"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>AAGTAGCTGCTGGAATAAAGAGGTGTCTGAAATTGTCCATGACTGATGGCATTCAGCGAGTGTTTGGGATGGAGTACAGGCCTATAAAAGATCTCGATGTTCTAGCTCCTTCTGGACTGAAGGTATATCTATGGAGTACCAATTAGCAATTACTATGTTGTTTATTAGTTTGTCAAGTAGCTTTCAAAGTCTCATTTACAAGATGAGAATGGATAAGAATAATATCCGTCATAAAACTTTTTCCATATTCATATGGATTGTTGCTGCATTTTGCAGGTTGCTATCTGTAATGTTCATGTTAGGCATGGAATTCTGATGTTGGTCCCTGAAGTTATTGAAGTTCTGGGTGGGATGGTGGAAGACTTAGAAGAAGCAAGGAAGCGGCTAGTTAATGAAATAAATAAGCCACCAAGGGGGAAAAGGTATGACGAAGGACCAAGAAAACATTTACTGTTTGAACCTAATTACCAAATTCTGATATTGTTGGTAGATGCCTTATACAAGTGTTGAATTCACTTGAATGGCAGAGGTTGATGCTCAGTGCTAGCATTAGAGGACCCTGACTGACTGTATATTTGAATGTAATCAAATGAGGATTCTACTAGTCAACCCCAAGTCCCCAACTAACATGGATTATGGTGTAGTAGTTGATGTTCAAGTCTCTTCAGGGGTATTCTTAAGGGTCAAATAGATATTCTGATGGTCCTAACTTAAAGGTTAAAGTTAAGAGCTGTTTCTCTGAATCTTAGCAAAGTGGTACTTTGTACTCCTCCTTCCTTGTCCATTTTATTTCTTGACCTTCTAGTGAAGACTTAATATCTGTTGCTCAGTTATAGGCTTTGGTTTACAAATGAGCGAATAAGGCGTATTGTCATGATTTATTATTGTTATTCTAGAAACAACCTCATCACTTTTGGTTATTTAGTTACTTCGTCTATGCCCAATGCCAGAACAAGGTCTGGTGTGGTTCCTCCTTTGGCAACTAGAGCTATTGCTGCTGCATGGCCACGAGAAGGTGTTACTGTTCCAGAGCACTCTGATACTTCCTCAAGACAAAATATGCAATTTCAGGTTCATGAACGAGGTACTTTGACACCCTAAAGAGCTTCTTTGCAATTGGTTTAGGATATCTGTATATGTACTGCATGTTCATTTGTTTTTGGTGTAGCTTTCAGTGTGAAAAACAATGTGTGTGCTACTTTGGCTTATTTGGTTAAGCTGACCTTCTGACTATTAGTATGAGAGAGAAGATGATATTTTATCAGATTGCTCCCTTTTGATGGCTTCTCTCCACACAAGCTTGTGTTTGAAGCTTTAGTTTTTGGAATTTTTACTCTAGTTTGAGTGTTAGTTTGCAGAACATTTATCCCACAGTGATATAGCTAAGATAGTGCTACAAGATGAAAGATTGGTTCACATATTTAAATTGGAATAAGTTCTAGATATAGCCTCTTGTATCATCATGTGGTGAATGGTTATGTACCTGGTCTTGCTCGTTGGACCACATATCACCCGTTGGACATGTATTGTAATAACAGAGGTATCTATCTTTTAATTTCTCTCTTTGGGGTGCAGGAACATCTGGCATTGCTACTACTGCAAGTGAAGAAATTCATCCCGTTAGATCTGGGCTACCATCTTCTACGACATTCATCACTCCTGTTTATAGAAGAGAGGCTCAATCTAATATCCCATCTACTCCAGCTGTTTCTGTCCCATTCAATAGGAACGCTGAACCTACCTTTTCATCTGATGCAGCTAGTCATGCAGAGGATATCCATATGGCTGACATGACCACTGAAGACATTGATGTTGCAATTAGAAGGGAACATAATGACACTGTCCTTTCATCTTTGTCTTCCATGGATGTGGAGGAACTTTTGTCAGATGTTAGAAGTGACCCTACCACACCTGCCAGTAGCAGGACCAGAGGAAGCGTTTGTGTGTCTAGCGGTAGTTTCCATAATGAAGATGTAACACCAGATACATTGTCTACTGCAGCAATTGACGTTGATCAAATTGATTTGGTTGATGAATTGGACCATCCATATATACTTTCTGGAGCGAAGGAAAACCCTTTCACTTACTTAGCTAGTCTGTCAGCTAAGCAGGCTGGTGTGAATGGCAGTGCTTCCACTGTTACAGGAAAAATTAAGGTAACTTTTGCTCTCCCTCGTGATATCAACTTCTCTGATGCTTCCATGTAGAAAATTCACTGCGTCCTTTCTATCTTACCCTTGTTAATTGGGTCTTTTTCCACTTGGCTGTAATTTGTATGGGTCAATTGGAGATACTCGCAAGCAGAATAATCTCTATAAATTAATCTAATGAAAGTACAAGACTAAAATTCCAATGGCAAATTGCTCAAGTAGGAATGGATTTTTTCTTAAGCCAATGCAAATTGCAATCTATCAAGAAAAACCCCATAACTGGCATCCCTCTTCCTAGCAGCGTACTTTTATGCATATCTGGTTCATTTGCTATCATTCTGCCTTGTCTTGATTTTTGCGCATTTAGAGTTGGTAATTAGCCATTTCGATTAAGATTATTTTAATATCGTGTTTTGTCACTCAAAATACTAAACAGTGAACTCTATTTTTTTTACTTTTAGTGCAAAAAGTTGGGATTACGGAGTAGAATTATCTTCATGTTAATAAGAAACTGATATCTGCCTTAAATCTGCAGTGCTTTCTTACTGGTGTGAAGGGCTTTCAGTATAAACAGAGTAGTAAATACGAGCTTCGGGTTTATGTTGATGATGGCAGCCTAATCTCTGAGATCCTTATAGATCATGCT</genome_strand>
        <mrna_strand>AAGTAGCTGCTGGAATAAAGAGGTGTCTGAAATTGTCCATGACTGATGGCATTCAGCGAGTGTTTGGGATGGAGTACAGGCCTATAAAAGATCTCGATGTTCTAGCTCCTTCTGGACTGAAG..........................................................................................................................................................GTTGCTATCTGTAATGTTCATGTTAGGCATGGAATTCTGATGTTGGTCCCTGAAGTTATTGAAGTTCTGGGTGGGATGGTGGAAGACTTAGAAGAAGCAAGGAAGCGGCTAGTTAATGAAATAAATAAGCCACCAAGGGGGAAAAG................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AACAAGGTCTGGTGTGGTTCCTCCTTTGGCAACTAGAGCTATTGCTGCTGCATGGCCACGAGAAGGTGTTACTGTTCCAGAGCACTCTGATACTTCCTCAAGACAAAATATGCAATTTCAGGTTCATGAACGAG...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAACATCTGGCATTGCTACTACTGCAACTGAAGAAATTCATCCCGTTACATCTGGGCTACCATCTTCTACGTCATTCATCACTCCTGTTTATAGAAGAGAGGCTCAATCTAATATCCCATCTACTCCAGCTGTTTCTGTCCCATTCAATAGGAACGCTGAACCTACCTTTTCATCTGATGCAGCTAGTCATGCAGAGGATATCCATATGGCTGACATGACCACTGAAGGCATTGATGTTCCAATTAGAAGGGAACATAATGACACTGTCCTTTCATCTTTTTCTTCCATGGAAGTGGAGGAACTTTTGTCAGATATTAGAAGTGACCCTGCCACACCTGCCAGTAGCAGGAGCAGAGGAAGCATTCGTGTCTCTAGTGATAGTTTCCATTATGAAGATGTAACACCAGATACATTGTCTACTGCAGCAATTGACGTTGATGAAATTGATTTGGTTGATGAATTGGACCATCCATATATACTTTCTGGAGCAAAGGAAAACCCTTTCACTTACTTAGCTAGTCTGTCAGCTAAGCAGGCTGGTATGCATGGCAGTGCTTCCACTGTTACAGGAAAAATTAAG.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGCTTTCTTACTGGTGTGAAGGGATTTCAGTATAAACAGAGTAGTAAATACGAGCTTCGGGTTTATGTTGATGATGGCAGCCTAATCTCTGAGATCCTTATAGATCATGCT</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-C12HBa0090D09-eZc9V/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M9180-2" ref_strand="+" ref_description="SGN-M9180-2 C2_At5g63540-2 [cosii_markers]">
      <seq>gttaatgaaataaataagccaccaagggggaaaagaacaaggtctggagtggttcctcctttggcaactagagctactggtgctgcatggccacgagaaggtgttactgttccagagcactctgatacttcctcaagacaaagtatgcattttcaggttcatgaacgaggaacatctggtattgctacttctgcaactgaagaaattcatcccattacatctgggctaccatcttctacgacattcaccactcctgtttatagaagagaggctcaatctaattttccatctactccagctgtttctgtcccattcaataggaaggttactgggcataccttttcatctgatgcagctagtcatgcagatgatatccatatggctgacatgaccaccgaaggcattgatgttccaattagaagggaacataatgaccctgtcctttcatcttcttactccatggaagtggaggaacttctgtcagatgttagaagtgaccctgccacacctgccagtagcaggagcagaggaagcgtccgtgtctctggcggtagtgtccataatgaggatgtaacaccagatacattgtctactgcagcaattgacattgatgaaattgatttggttgatgaattgga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0090D09-eZc9V/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0090D09.1" temp_strand="+" temp_description="C12HBa0090D09.1  AC212766.1 htgs_phase:3 submitted_to_sgn_as:C12HBa0090D09 upload_account_name:italy">
        <position start="17809" stop="20062"/>
      </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="18109" g_stop="18143" g_length="35"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="35" r_length="35" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="18144" i_stop="18671" i_length="528">
            <donor d_prob="0.615" d_score="0.00"/>
            <acceptor a_prob="0.000" a_score="0.94"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="18672" g_stop="18805" g_length="134"/>
          <reference_exon_boundary r_type="cDNA" r_start="36" r_stop="169" r_length="134" r_score="0.963"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="18806" i_stop="19296" i_length="491">
            <donor d_prob="0.979" d_score="0.96"/>
            <acceptor a_prob="1.000" a_score="0.90"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="19297" g_stop="19762" g_length="466"/>
          <reference_exon_boundary r_type="cDNA" r_start="170" r_stop="638" r_length="469" r_score="0.916"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0090D09.1" gen_strand="+" ref_id="SGN-M9180-2" ref_strand="+">
        <total_alignment_score>0.927</total_alignment_score>
        <cumulative_length_of_scored_exons>635</cumulative_length_of_scored_exons>
        <coverage percentage="0.995" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0090D09.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M9180-2" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="18109" e_stop="18143"/>
          <exon e_start="18672" e_stop="18805"/>
          <exon e_start="19297" e_stop="19762"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTTAATGAAATAAATAAGCCACCAAGGGGGAAAAGGTATGACGAAGGACCAAGAAAACATTTACTGTTTGAACCTAATTACCAAATTCTGATATTGTTGGTAGATGCCTTATACAAGTGTTGAATTCACTTGAATGGCAGAGGTTGATGCTCAGTGCTAGCATTAGAGGACCCTGACTGACTGTATATTTGAATGTAATCAAATGAGGATTCTACTAGTCAACCCCAAGTCCCCAACTAACATGGATTATGGTGTAGTAGTTGATGTTCAAGTCTCTTCAGGGGTATTCTTAAGGGTCAAATAGATATTCTGATGGTCCTAACTTAAAGGTTAAAGTTAAGAGCTGTTTCTCTGAATCTTAGCAAAGTGGTACTTTGTACTCCTCCTTCCTTGTCCATTTTATTTCTTGACCTTCTAGTGAAGACTTAATATCTGTTGCTCAGTTATAGGCTTTGGTTTACAAATGAGCGAATAAGGCGTATTGTCATGATTTATTATTGTTATTCTAGAAACAACCTCATCACTTTTGGTTATTTAGTTACTTCGTCTATGCCCAATGCCAGAACAAGGTCTGGTGTGGTTCCTCCTTTGGCAACTAGAGCTATTGCTGCTGCATGGCCACGAGAAGGTGTTACTGTTCCAGAGCACTCTGATACTTCCTCAAGACAAAATATGCAATTTCAGGTTCATGAACGAGGTACTTTGACACCCTAAAGAGCTTCTTTGCAATTGGTTTAGGATATCTGTATATGTACTGCATGTTCATTTGTTTTTGGTGTAGCTTTCAGTGTGAAAAACAATGTGTGTGCTACTTTGGCTTATTTGGTTAAGCTGACCTTCTGACTATTAGTATGAGAGAGAAGATGATATTTTATCAGATTGCTCCCTTTTGATGGCTTCTCTCCACACAAGCTTGTGTTTGAAGCTTTAGTTTTTGGAATTTTTACTCTAGTTTGAGTGTTAGTTTGCAGAACATTTATCCCACAGTGATATAGCTAAGATAGTGCTACAAGATGAAAGATTGGTTCACATATTTAAATTGGAATAAGTTCTAGATATAGCCTCTTGTATCATCATGTGGTGAATGGTTATGTACCTGGTCTTGCTCGTTGGACCACATATCACCCGTTGGACATGTATTGTAATAACAGAGGTATCTATCTTTTAATTTCTCTCTTTGGGGTGCAGGAACATCTGGCATTGCTACTACTGCAAGTGAAGAAATTCATCCCGTTAGATCTGGGCTACCATCTTCTACGACATTCATCACTCCTGTTTATAGAAGAGAGGCTCAATCTAATATCCCATCTACTCCAGCTGTTTCTGTCCCATTCAATAGGAACG---CTGAACCTACCTTTTCATCTGATGCAGCTAGTCATGCAGAGGATATCCATATGGCTGACATGACCACTGAAGACATTGATGTTGCAATTAGAAGGGAACATAATGACACTGTCCTTTCATCTTTGTCTTCCATGGATGTGGAGGAACTTTTGTCAGATGTTAGAAGTGACCCTACCACACCTGCCAGTAGCAGGACCAGAGGAAGCGTTTGTGTGTCTAGCGGTAGTTTCCATAATGAAGATGTAACACCAGATACATTGTCTACTGCAGCAATTGACGTTGATCAAATTGATTTGGTTGATGAATTGGA</genome_strand>
        <mrna_strand>GTTAATGAAATAAATAAGCCACCAAGGGGGAAAAG................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AACAAGGTCTGGAGTGGTTCCTCCTTTGGCAACTAGAGCTACTGGTGCTGCATGGCCACGAGAAGGTGTTACTGTTCCAGAGCACTCTGATACTTCCTCAAGACAAAGTATGCATTTTCAGGTTCATGAACGAG...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAACATCTGGTATTGCTACTTCTGCAACTGAAGAAATTCATCCCATTACATCTGGGCTACCATCTTCTACGACATTCACCACTCCTGTTTATAGAAGAGAGGCTCAATCTAATTTTCCATCTACTCCAGCTGTTTCTGTCCCATTCAATAGGAAGGTTACTGGGCATACCTTTTCATCTGATGCAGCTAGTCATGCAGATGATATCCATATGGCTGACATGACCACCGAAGGCATTGATGTTCCAATTAGAAGGGAACATAATGACCCTGTCCTTTCATCTTCTTACTCCATGGAAGTGGAGGAACTTCTGTCAGATGTTAGAAGTGACCCTGCCACACCTGCCAGTAGCAGGAGCAGAGGAAGCGTCCGTGTCTCTGGCGGTAGTGTCCATAATGAGGATGTAACACCAGATACATTGTCTACTGCAGCAATTGACATTGATGAAATTGATTTGGTTGATGAATTGGA</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="17722" PGL_stop="20517"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="17722" e_stop="17843"/>
            <exon e_start="17998" e_stop="18143"/>
            <exon e_start="18672" e_stop="18805"/>
            <exon e_start="19297" e_stop="19877"/>
            <exon e_start="20407" e_stop="20517"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.998" acc_prob="0.994" e_score="1.000"/>
          <exon-intron don_prob="0.615" acc_prob="0.000" e_score="1.000"/>
          <exon-intron don_prob="0.979" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.969" acc_prob="0.926" e_score="0.966"/>
          <exon-only e_score="0.991"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="17722" e_stop="17843" e_length="122"/>
          </exon>
          <intron i_serial="1" don_prob="0.998" acc_prob="0.994">
            <gDNA_intron_boundary i_start="17844" i_stop="17997" i_length="154"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="17998" e_stop="18143" e_length="146"/>
          </exon>
          <intron i_serial="2" don_prob="0.615" acc_prob="0.000">
            <gDNA_intron_boundary i_start="18144" i_stop="18671" i_length="528"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="18672" e_stop="18805" e_length="134"/>
          </exon>
          <intron i_serial="3" don_prob="0.979" acc_prob="1.000">
            <gDNA_intron_boundary i_start="18806" i_stop="19296" i_length="491"/>
          </intron>
          <exon e_serial="4" e_score="0.966">
            <gDNA_exon_boundary e_start="19297" e_stop="19877" e_length="581"/>
          </exon>
          <intron i_serial="4" don_prob="0.969" acc_prob="0.926">
            <gDNA_intron_boundary i_start="19878" i_stop="20406" i_length="529"/>
          </intron>
          <exon e_serial="5" e_score="0.991">
            <gDNA_exon_boundary e_start="20407" e_stop="20517" e_length="111"/>
          </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="17722" stop="17843"/>
              <exon start="17998" stop="18143"/>
              <exon start="18672" stop="18805"/>
              <exon start="19297" stop="19877"/>
              <exon start="20407" stop="20517"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M9180" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="18109" stop="18143"/>
              <exon start="18672" stop="18805"/>
              <exon start="19297" stop="19762"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M9180-2" strand="+"/>
          </PGS_line>
        </supporting_evidence>
        <three_phase_translation xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/">
          <description PGL_serial="1" AGS_serial="1" gDNA_strand="+"/>
          <translation>
            <gDNA_template>AAGTAGCTGCTGGAATAAAGAGGTGTCTGAAATTGTCCATGACTGATGGCATTCAGCGAGTGTTTGGGATGGAGTACAGGCCTATAAAAGATCTCGATGTTCTAGCTCCTTCTGGACTGAAG : GTTGCTATCTGTAATGTTCATGTTAGGCATGGAATTCTGATGTTGGTCCCTGAAGTTATTGAAGTTCTGGGTGGGATGGTGGAAGACTTAGAAGAAGCAAGGAAGCGGCTAGTTAATGAAATAAATAAGCCACCAAGGGGGAAAAG : AACAAGGTCTGGTGTGGTTCCTCCTTTGGCAACTAGAGCTATTGCTGCTGCATGGCCACGAGAAGGTGTTACTGTTCCAGAGCACTCTGATACTTCCTCAAGACAAAATATGCAATTTCAGGTTCATGAACGAG : GAACATCTGGCATTGCTACTACTGCAAGTGAAGAAATTCATCCCGTTAGATCTGGGCTACCATCTTCTACGACATTCATCACTCCTGTTTATAGAAGAGAGGCTCAATCTAATATCCCATCTACTCCAGCTGTTTCTGTCCCATTCAATAGGAACGCTGAACCTACCTTTTCATCTGATGCAGCTAGTCATGCAGAGGATATCCATATGGCTGACATGACCACTGAAGACATTGATGTTGCAATTAGAAGGGAACATAATGACACTGTCCTTTCATCTTTGTCTTCCATGGATGTGGAGGAACTTTTGTCAGATGTTAGAAGTGACCCTACCACACCTGCCAGTAGCAGGACCAGAGGAAGCGTTTGTGTGTCTAGCGGTAGTTTCCATAATGAAGATGTAACACCAGATACATTGTCTACTGCAGCAATTGACGTTGATCAAATTGATTTGGTTGATGAATTGGACCATCCATATATACTTTCTGGAGCGAAGGAAAACCCTTTCACTTACTTAGCTAGTCTGTCAGCTAAGCAGGCTGGTGTGAATGGCAGTGCTTCCACTGTTACAGGAAAAATTAAG : TGCTTTCTTACTGGTGTGAAGGGCTTTCAGTATAAACAGAGTAGTAAATACGAGCTTCGGGTTTATGTTGATGATGGCAGCCTAATCTCTGAGATCCTTATAGATCATGCT</gDNA_template>
            <first_frame> K  *  L  L  E  *  R  G  V  *  N  C  P  *  L  M  A  F  S  E  C  L  G  W  S  T  G  L  *  K  I  S  M  F  *  L  L  L  D  *  R :   L  L  S  V  M  F  M  L  G  M  E  F  *  C  W  S  L  K  L  L  K  F  W  V  G  W  W  K  T  *  K  K  Q  G  S  G  *  L  M  K  *  I  S  H  Q  G  G  K   : E  Q  G  L  V  W  F  L  L  W  Q  L  E  L  L  L  L  H  G  H  E  K  V  L  L  F  Q  S  T  L  I  L  P  Q  D  K  I  C  N  F  R  F  M  N  E  :  E  H  L  A  L  L  L  L  Q  V  K  K  F  I  P  L  D  L  G  Y  H  L  L  R  H  S  S  L  L  F  I  E  E  R  L  N  L  I  S  H  L  L  Q  L  F  L  S  H  S  I  G  T  L  N  L  P  F  H  L  M  Q  L  V  M  Q  R  I  S  I  W  L  T  *  P  L  K  T  L  M  L  Q  L  E  G  N  I  M  T  L  S  F  H  L  C  L  P  W  M  W  R  N  F  C  Q  M  L  E  V  T  L  P  H  L  P  V  A  G  P  E  E  A  F  V  C  L  A  V  V  S  I  M  K  M  *  H  Q  I  H  C  L  L  Q  Q  L  T  L  I  K  L  I  W  L  M  N  W  T  I  H  I  Y  F  L  E  R  R  K  T  L  S  L  T  *  L  V  C  Q  L  S  R  L  V  *  M  A  V  L  P  L  L  Q  E  K  L  S :   A  F  L  L  V  *  R  A  F  S  I  N  R  V  V  N  T  S  F  G  F  M  L  M  M  A  A  *  S  L  R  S  L  *  I  M   </first_frame>
            <second_frame>  S  S  C  W  N  K  E  V  S  E  I  V  H  D  *  W  H  S  A  S  V  W  D  G  V  Q  A  Y  K  R  S  R  C  S  S  S  F  W  T  E   : G  C  Y  L  *  C  S  C  *  A  W  N  S  D  V  G  P  *  S  Y  *  S  S  G  W  D  G  G  R  L  R  R  S  K  E  A  A  S  *  *  N  K  *  A  T  K  G  E  K  :  N  K  V  W  C  G  S  S  F  G  N  *  S  Y  C  C  C  M  A  T  R  R  C  Y  C  S  R  A  L  *  Y  F  L  K  T  K  Y  A  I  S  G  S  *  T  R :   N  I  W  H  C  Y  Y  C  K  *  R  N  S  S  R  *  I  W  A  T  I  F  Y  D  I  H  H  S  C  L  *  K  R  G  S  I  *  Y  P  I  Y  S  S  C  F  C  P  I  Q  *  E  R  *  T  Y  L  F  I  *  C  S  *  S  C  R  G  Y  P  Y  G  *  H  D  H  *  R  H  *  C  C  N  *  K  G  T  *  *  H  C  P  F  I  F  V  F  H  G  C  G  G  T  F  V  R  C  *  K  *  P  Y  H  T  C  Q  *  Q  D  Q  R  K  R  L  C  V  *  R  *  F  P  *  *  R  C  N  T  R  Y  I  V  Y  C  S  N  *  R  *  S  N  *  F  G  *  *  I  G  P  S  I  Y  T  F  W  S  E  G  K  P  F  H  L  L  S  *  S  V  S  *  A  G  W  C  E  W  Q  C  F  H  C  Y  R  K  N  *   : V  L  S  Y  W  C  E  G  L  S  V  *  T  E  *  *  I  R  A  S  G  L  C  *  *  W  Q  P  N  L  *  D  P  Y  R  S  C  </second_frame>
            <third_frame>   V  A  A  G  I  K  R  C  L  K  L  S  M  T  D  G  I  Q  R  V  F  G  M  E  Y  R  P  I  K  D  L  D  V  L  A  P  S  G  L  K  :  V  A  I  C  N  V  H  V  R  H  G  I  L  M  L  V  P  E  V  I  E  V  L  G  G  M  V  E  D  L  E  E  A  R  K  R  L  V  N  E  I  N  K  P  P  R  G  K  R :   T  R  S  G  V  V  P  P  L  A  T  R  A  I  A  A  A  W  P  R  E  G  V  T  V  P  E  H  S  D  T  S  S  R  Q  N  M  Q  F  Q  V  H  E  R   : G  T  S  G  I  A  T  T  A  S  E  E  I  H  P  V  R  S  G  L  P  S  S  T  T  F  I  T  P  V  Y  R  R  E  A  Q  S  N  I  P  S  T  P  A  V  S  V  P  F  N  R  N  A  E  P  T  F  S  S  D  A  A  S  H  A  E  D  I  H  M  A  D  M  T  T  E  D  I  D  V  A  I  R  R  E  H  N  D  T  V  L  S  S  L  S  S  M  D  V  E  E  L  L  S  D  V  R  S  D  P  T  T  P  A  S  S  R  T  R  G  S  V  C  V  S  S  G  S  F  H  N  E  D  V  T  P  D  T  L  S  T  A  A  I  D  V  D  Q  I  D  L  V  D  E  L  D  H  P  Y  I  L  S  G  A  K  E  N  P  F  T  Y  L  A  S  L  S  A  K  Q  A  G  V  N  G  S  A  S  T  V  T  G  K  I  K  :  C  F  L  T  G  V  K  G  F  Q  Y  K  Q  S  S  K  Y  E  L  R  V  Y  V  D  D  G  S  L  I  S  E  I  L  I  D  H  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/">
            <orf_entry>
              <id_line>
                <gDNA id="C12HBa0090D09.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="17724" stop="17843"/>
                    <exon start="17998" stop="18143"/>
                    <exon start="18672" stop="18805"/>
                    <exon start="19297" stop="19877"/>
                    <exon start="20407" stop="20517"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>1092</number_coding_nucleotides>
                  <number_encoded_amino_acids>364</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>VAAGIKRCLKLSMTDGIQRVFGMEYRPIKDLDVLAPSGLKVAICNVHVRHGILMLVPEVIEVLGGMVEDLEEARKRLVNEINKPPRGKRTRSGVVPPLATRAIAAAWPREGVTVPEHSDTSSRQNMQFQVHERGTSGIATTASEEIHPVRSGLPSSTTFITPVYRREAQSNIPSTPAVSVPFNRNAEPTFSSDAASHAEDIHMADMTTEDIDVAIRREHNDTVLSSLSSMDVEELLSDVRSDPTTPASSRTRGSVCVSSGSFHNEDVTPDTLSTAAIDVDQIDLVDELDHPYILSGAKENPFTYLASLSAKQAGVNGSASTVTGKIKCFLTGVKGFQYKQSSKYELRVYVDDGSLISEILIDHA</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 5 chains have been computed
$ 
$ memory statistics:
$ 4816 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 2408 bytes was the average size of a spliced alignment
$ 5656 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5656 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 5 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-18 05:37:01
-->
