<?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="2009-01-15 23:53:18"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C04SLm0124K05-Y7a1P/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C04SLm0124K05-Y7a1P/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-C04SLm0124K05-Y7a1P/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M6662" ref_strand="+" ref_description="SGN-M6662 C2_At1g19530 [cosii_markers]">
      <seq>gggctccaggattcggcatgaaattaattaactgtgtgttaagtttaattaagaagttaattagcaacaaaaagagataattatgggttctcttatggcaggttgggactctcctgtttctgatcctcaagctatgaaattacgaacaaataagtcattaacaaagaaagagatagatgcatattggagatcaaaaaaactaattgaagaagagcatcaaaaatatatctctacgttatcccctcgaagccaaaaacaggcgaatattgtatttgaggaggcaactaaaacagcggaagaaagtctttctaatttggaaaatgaggaaagtttggatcaactaatcaggaaaaatggatggtggataagtagcaattgggcacatttaaatgagccaccagtagaagtacgagaaggtccagcttacaaatacgtgtcacaatttcacgtagccaacatggctactgggtccaacactaaacccggtccagccggaatcaacgcttgaaccgtcgtttggctttagaccggtttgctaataagtactagtatagtactttttttaggttaattttaatttttttttatgacaaattacttttaattttatttgcgaaagtatttgtatttgagttgatatttagagtttgcgttaagagatgtcgatacttgtaatgttgggacatacatacatgtcgttgtaatatattttttgtgctttcttcgataaaagttaaagtatattaatattttgatgtgatatatttttttctgcaaattttataaaatttaatttgtagaaggtaaaaaaaaaaaaacaaaaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0124K05-Y7a1P/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0124K05.1" temp_strand="+" temp_description="C04SLm0124K05.1  CU468239.4 htgs_phase:3 submitted_to_sgn_as:C04SLm0124K05 sequenced_by:sanger upload_account_name:uk">
        <position start="103305" stop="105417"/>
      </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="103605" g_stop="103720" g_length="116"/>
          <reference_exon_boundary r_type="cDNA" r_start="19" r_stop="134" r_length="116" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="103721" i_stop="103825" i_length="105">
            <donor d_prob="1.000" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="103826" g_stop="103950" g_length="125"/>
          <reference_exon_boundary r_type="cDNA" r_start="135" r_stop="259" r_length="125" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="103951" i_stop="104054" i_length="104">
            <donor d_prob="0.994" d_score="1.00"/>
            <acceptor a_prob="0.999" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="104055" g_stop="104155" g_length="101"/>
          <reference_exon_boundary r_type="cDNA" r_start="260" r_stop="360" r_length="101" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="104156" i_stop="104669" i_length="514">
            <donor d_prob="0.962" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="104670" g_stop="105116" g_length="447"/>
          <reference_exon_boundary r_type="cDNA" r_start="361" r_stop="807" r_length="447" r_score="0.998"/>
        </exon>
      </exon-intron_info>
      <PPA_line polyA_start="808" polyA_stop="834"/>
      <MATCH_line gen_id="C04SLm0124K05.1" gen_strand="+" ref_id="SGN-M6662" ref_strand="+">
        <total_alignment_score>0.999</total_alignment_score>
        <cumulative_length_of_scored_exons>789</cumulative_length_of_scored_exons>
        <coverage percentage="0.946" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0124K05.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6662" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="103605" e_stop="103720"/>
          <exon e_start="103826" e_stop="103950"/>
          <exon e_start="104055" e_stop="104155"/>
          <exon e_start="104670" e_stop="105116"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TGAAATTAATTAACTGTGTGTTAAGTTTAATTAAGAAGTTAATTAGCAACAAAAAGAGATAATTATGGGTTCTCTTATGGCAGGTTGGGACTCTCCTGTTTCTGATCCTCAAGCTAGTAAGTTCATTTTAGTCTTAATTTCTTTAATTAATGACAAATAATATAAGTTCTTTTATAATTTGTTTAATTGTTTTTTTTTCTTTTTTTGGATTTAATTTACAGTGAAATTACGAACAAATAAGTCATTAACAAAGAAAGAGATAGATGCATATTGGAGATCAAAAAAACTAATTGAAGAAGAGCATCAAAAATATATCTCTACGTTATCCCCTCGAAGCCAAAAACAGGTATACATAGACGGATTTAGAATTTTAAATTATTATAATTATTAAGTTCCGTCGAATTCGTAATATTATGATAATTAATTTTTGATTGTTTTAATTGGAGACAGGCGAATATTGTATTTGAGGAGGCAACTAAAACAGCGGAAGAAAGTCTTTCTAATTTGGAAAATGAGGAAAGTTTGGATCAACTAATCAGGAAAAATGGATGGTAATTAATTTATGAAAAAAATAATTAAAGATATATTTTATTTTATCACAATTTCTAAATTTTTAATCATTTAAATAGAATTTCAAAAATCTTCTCTCGATTCATCCCTCTCTACCCCCAGTTACATCTTTCACCTATGTATCTAGGTGTATGCTAAAATATTTCGAATATCTTATACCGAGCTTTCTAGTGCATCCTCTCGAACGTATGTATCTTTATGTCTTCAACTGTATTCGTAAGTCCAGTAATATATCTGAAATTATAAATTTTAAGAAATTTTTTGTAATATGAAAAAGATTAGAAAAATACTGCAATTGGCTTTTAAAACTATGAAATTTAGACGAGTTAATGATCTTTATTAGTAGTAAGTAGCAAGTTTGACTCCTGGTTTAATTATAGAAAAGATCGGGTTTTTTTTTATAGTATATTTAATTAAATGAATTTATTTTAGTTGATTGATTAAAAAATAATAATATATTCATTTATTTATAAAAAAATATTTTTTTAATTGCAGGTGGATAAGTAGCAATTGGGCACATTTAAATGAGCCACCAGTAGAAGTACGAGAAGGTCCAGCTTACAAATACGTGTCACAATTTCACGTAGCCAACATGGCTACTGGGTCCAACACTAAACCCGGTCCAGCCGGAATCAACGCTTGAACCGTCGTTTGGCTTTAGACCGGTTTGCTAATAAGTACTAGTATAGTACTTTTTTTAGGTTAATTTTAATTTTTTTTTATGACAAATTACTTTTAATTTTATTTGCGAAAGTATTTGTATTTGAGTTGATATTTAGAGTTTGCGTTAAGAGATGTCGATACTTGTAATGTTGGGACATACATACATGTCGTTGTAATATATTTTTTGTGCTTTCTTCGATAAAAGTTAAAGTATATTAATATTTTGATGTGATATATTTTTTTCTGCAAATTTTATAAAATTTAATTTGTAGAATGTAA</genome_strand>
        <mrna_strand>TGAAATTAATTAACTGTGTGTTAAGTTTAATTAAGAAGTTAATTAGCAACAAAAAGAGATAATTATGGGTTCTCTTATGGCAGGTTGGGACTCTCCTGTTTCTGATCCTCAAGCTA.........................................................................................................TGAAATTACGAACAAATAAGTCATTAACAAAGAAAGAGATAGATGCATATTGGAGATCAAAAAAACTAATTGAAGAAGAGCATCAAAAATATATCTCTACGTTATCCCCTCGAAGCCAAAAACAG........................................................................................................GCGAATATTGTATTTGAGGAGGCAACTAAAACAGCGGAAGAAAGTCTTTCTAATTTGGAAAATGAGGAAAGTTTGGATCAACTAATCAGGAAAAATGGATG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGGATAAGTAGCAATTGGGCACATTTAAATGAGCCACCAGTAGAAGTACGAGAAGGTCCAGCTTACAAATACGTGTCACAATTTCACGTAGCCAACATGGCTACTGGGTCCAACACTAAACCCGGTCCAGCCGGAATCAACGCTTGAACCGTCGTTTGGCTTTAGACCGGTTTGCTAATAAGTACTAGTATAGTACTTTTTTTAGGTTAATTTTAATTTTTTTTTATGACAAATTACTTTTAATTTTATTTGCGAAAGTATTTGTATTTGAGTTGATATTTAGAGTTTGCGTTAAGAGATGTCGATACTTGTAATGTTGGGACATACATACATGTCGTTGTAATATATTTTTTGTGCTTTCTTCGATAAAAGTTAAAGTATATTAATATTTTGATGTGATATATTTTTTTCTGCAAATTTTATAAAATTTAATTTGTAGAAGGTAA</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-C04SLm0124K05-Y7a1P/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M2219" ref_strand="+" ref_description="SGN-M2219 T1716 [cos_markers]">
      <seq>ttgactgcacagctctactgatcagaaagagggctaaaccgaaagaagaagaaggaggaggtcaaacatgggaaccctcgggaaagcaatttactccctgggatccatcgttcgagcgaccggcaaagctcttgatcgcgtcggaaatcgcctacaaggcagctcccacatagaggaacacctgtccaggcatcggactcttatgaacgtattcgataaagctccggtggtggataaggatgtatttgtagctccaggtgcctcagtcattggagatgtccatgtgggacgcaattcatctatttggtatggatgtgtactaagaggtgatgttaacagcatcagtgtcggatctggtaccaatatacaggacaactcccttgttcatgtggccaaatcaaatataagtcaaaaggtgctgcccaccatcatagggaacaatgttactgttggtcatagtgctgttgtacatggctgcaccat</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C04SLm0124K05-Y7a1P/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C04SLm0124K05.1" temp_strand="+" temp_description="C04SLm0124K05.1  CU468239.4 htgs_phase:3 submitted_to_sgn_as:C04SLm0124K05 sequenced_by:sanger upload_account_name:uk">
        <position start="116571" stop="121434"/>
      </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="116871" g_stop="117052" g_length="182"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="182" r_length="182" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="117053" i_stop="119247" i_length="2195">
            <donor d_prob="0.970" d_score="1.00"/>
            <acceptor a_prob="0.949" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="119248" g_stop="119391" g_length="144"/>
          <reference_exon_boundary r_type="cDNA" r_start="183" r_stop="326" r_length="144" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="119392" i_stop="120908" i_length="1517">
            <donor d_prob="0.995" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="120909" g_stop="121034" g_length="126"/>
          <reference_exon_boundary r_type="cDNA" r_start="327" r_stop="452" r_length="126" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="121035" i_stop="121103" i_length="69">
            <donor d_prob="0.887" d_score="1.00"/>
            <acceptor a_prob="0.935" a_score="0.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="121104" g_stop="121134" g_length="31"/>
          <reference_exon_boundary r_type="cDNA" r_start="453" r_stop="483" r_length="31" r_score="1.000"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C04SLm0124K05.1" gen_strand="+" ref_id="SGN-M2219" ref_strand="+">
        <total_alignment_score>1.000</total_alignment_score>
        <cumulative_length_of_scored_exons>483</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C04SLm0124K05.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M2219" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="116871" e_stop="117052"/>
          <exon e_start="119248" e_stop="119391"/>
          <exon e_start="120909" e_stop="121034"/>
          <exon e_start="121104" e_stop="121134"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TTGACTGCACAGCTCTACTGATCAGAAAGAGGGCTAAACCGAAAGAAGAAGAAGGAGGAGGTCAAACATGGGAACCCTCGGGAAAGCAATTTACTCCCTGGGATCCATCGTTCGAGCGACCGGCAAAGCTCTTGATCGCGTCGGAAATCGCCTACAAGGCAGCTCCCACATAGAGGAACACCGTAATTTCCTTATTCTTAACCCTAGATCTCACCTCCACAATGTTTAATTTACCGATGTTTGAATATGATATTGTGTCGCGGATGCATCTATGCTTGTTTATGTTATTGCATTTTATCCTAATTTGTTAATACTTTTTGTCCGGGGATAAAATTGGTAGAGTTTGGAGTGTGGAGGTTAGAGCATTTAGAAATTGTTATTAATTTAGAAGTTGCCGTTAGTTAATAAGCTTATTTACCTTTTATCTTTATTGCTACTATGCTTGTTAATGTTATTGCATTTGAGCTTTGTTAGTACTCTTTGATTAGAAAAAAATGGTAAAATTTGGAGTGTGGAGGTCAGAACATCTGATTTTCAATGTGAGGGCATTAAGGAATTGATCCTAATTTTGAAGTTTTTGTGAGTTAATACGTTTATTTACCAATGTTTTAATATGATATTGGTGTCTCTTCTGCATCTACAATTGTATATGTTATTGCATTGAATCCTTTGGGCTTATTTAATACTCATTTGGGGGGGAATGGTATATTTTGGAGTGTGGAAGTTAGAACATCTGATTTTCAGTGTGAGGGAGGACATTTAGAAACAACATAAATATTTTATACATCAAACAAAAATAGACTGTAAATCACAACTTCTGTAGAAAAAATTTAGTGGAAGAAACATTCTGTGACTCCTCAATTAGTGCAAGTAGTATTCTTCTTGAGAATGTGAAACAAAGTCCTGTGAATGCGCAGTTCTCCTGTCTTCTTCAGGTCGTTATTGGAGTTCTTAGATTTGCACCTTTGAAATAGGTGTCCAGTCTCTATGAAGTTGTGCCTTAGGAAAAAGAACTAGGAAAGGGTGGAAAAGGCATTTTGGAGTGGGTTCTAATGCGTATTCATAGTCTTATGCTTATTTGAATTTTATGTTCAGTAATTTTAGGTAACTGATTCTGAGCGCAAATGAAGTACAAGAGAATGAAAGATGTAATATGTTATAATTGTCCTTGTAAGCATAAGAGATGCAGGCAATAACCTTAAGACTGGTATCTTATCAGAACTTTCCTTACGTCAAAACCTGTTTGCCTGGTCCTTTTGATTAATCCTTTTACTCATGTTAGGATTTTGATTCGCCGATTTGGTTGTTGTTAAGACACCAAAGACCCTTCTATTCTTAAAATTTGTTTGGTTGTATAAGAGAATCCCGGGAGAAAGCAAGTTAGATCTTAGGGCGAAAGCTCCATTGGATGGTTCATTCCAGTCTGAATAGCACCACTTATGCTTATAAAAGTGGTGCTATGTTTTGTCAATGCAGGAACCTGTCAAATAATGTGAGTAGAGTTAGCTACTTGCCTTAGAACCTATTTGCTTAATGATATTAGCTAAACCTATTCTAGCTGCATATTTAGCAGATTATCAAGGACTATTGGTGCTTATTTGAAGACTTTAGGCAGTTCATATGCCCACCAAGTATTTTGCTAATTAAAATAGTTGTGCCTTCAAATGGAGGAAGGATCACAAAGTTGGTTTTAGTTATTCCACAATTTTGTGGGATGTGGAATTGATCTCCCTATATCTTGGACAATTCTCACATCATGGCTAGATTTTGGGGTTGAGCTAAGTGTGAGATGCACTCCTTATCATGATTTTAGGGCCAAACACATCCCAATTTTGGTTAACCCGTTATTCATCCCCCATATTATGGTGTCCATACTCCAGTTGGCAAGCTCAGGCTTGTAGGGGTGTTAAGTTGTCCCATATCAGTTGTGAGATGTAGAACTGATCTCCTTATATAGTAATTGGACAACCCTCTCCTTGGGAGCTAACTTTTAGGGTTGAGTTAGGCCCAAGGTCCATTTCTTATTGGTTGGTTGTTGATTTAAGAGGGACCTGAAGTGGAATTTGTGTGGATTTCTTGCTAGTCTCCATTATGTATTGAGAACTTGATTGTTGTGCAAGTTGCTTCATTCTCCCTTCTAAAACATTGTACATTATCATTTTTATTTTAAAAATAAATGACATTAAGTGATGCTTTGTTGTCATATTTATTTACTCTCAAATGAATTGCTCCAGTTAGATACCTTCTCAAACCCCATCTACCTCATTAACAGAAAAATAAATGTCTGTTATTTAGCCTTCCTTCTAGTAATTAGACTCCTTTTTAAGTGGTCAATCTTTGATCTTAAACGTGGTTAGTTACTCCTTCTATGTTTCAGTGTCCAGGCATCGGACTCTTATGAACGTATTCGATAAAGCTCCGGTGGTGGATAAGGATGTATTTGTAGCTCCAGGTGCCTCAGTCATTGGAGATGTCCATGTGGGACGCAATTCATCTATTTGGTATGGATGTGTACTAAGAGGTAAGTATCTTATCACAGCATTGTTGTTGTTGGATGGTATGTTCAAGTGTTACATGTCAGTTTTGATTCTTAAGTAATAGCAGTTTTAACCTTGTTTCCTTGACTCATCCATTGTTCTAGTGAATAAAATTGTGAAGTTGGTATGATGCACGCTATCCATTAGCAAATAAGAGTTAGTCTTTTGTTGCTTGCTGGCCTTCTATATTTGTCCCTCAGTTTCTCCATATGGCAGTTAACATAGAGTACTAAAGTTGTGGTATGTGCAGTTTTCTTTGAATAGTGTAGCTCTTAATTTAGAACAAACTATTTGAAAATTGATCAGCAAATGAATGTTATTTTGGGGGCTTCTTGGCTAAGTTGCTCGGGTGCAGATCTAGAGATCCTTCATGATCTAATTTTTAATTTTTAAGGTTCAGGGATATAGATCCATGTATGGATTGGGGATTTGCCTAAAAATAATTAAAATATCTAAAAATAGAATTATAAAACCTAAATTATGAGATATTATGTGGAGAACTTGAGGAGAATCCTAGAAGGTGATTAAAGGAAAAAGAGTGATATGGAAATTTATATATAAAAGGTATTCCATTTTCTTCAATTTCACCTTAGCTTTTGTATCGATTACATAAATCATTAAAATTATTCCGACTTTCCCCATCAATTTTGGTCAAAGTACCTAAAATGAGTTGACCAAATCGTACACAGATCTCACACCCACACCTATGTCGTGTCGACACGGGTGCGGCACCAAAAGGGAAGAGTCCGAGCAACTTATTTTCTTCGAACTTGAACAGTTGTTTGTTTGAGTCACTAGTTTCAGATAAAAAAAACATTTTTTGTAGATCTTTTCCATCTTTTGGTTGTCGAACAGCAATTGCAACGGTCCGATTGACACTTCATTGGAATAGATGTTGGAAATCTCTTCTCCTCTTCCCTTCTCCTAGATATATTGTTCTTTCAGTCCCACAAGACACTTTAGAATGTAAAGTACTTTGAATAAATGCACAAAATACCATTTATATGGTTTTTGTTTTAAATTGTACATAAGGACCCTAAAACCCTGTCTTACACATGCCTATGTAGTCTGTTAGTACATATCCCTTCTCTTATCACATAAGCAATCAGCGAAAATGTGAGGTGTGTTTTAAGGGTGTTCTCATCCCAGTCCAACCTGTTAGGGGAAATTTTAAACTTCTCATACATGACCCATTCCAACAGGTAGGCTTCCCTTTCCCCTTGTATATGAGCTCTTGTAACTAATGAGTTAGGTGAAATTCAACTTTCATTTGAGTTATTTGTTTCTTTGTTTACCTATTCCTCCCTTCTCAATCCTTTTTCCCTTTCATGTATTACAAATATGATTGTCCATGGGAGTGTATTTAATCATTTCTAATAATTATTGATAACACCACTTCAGCATTTTTTTTGTGTGTTATGATTATTAATTGGCAAGAAATTTTCCGTATTTGCATGCTATATTGCAGTTTTATAAGTTTTATGTGCCTTCTCTTTTACAGGTGATGTTAACAGCATCAGTGTCGGATCTGGTACCAATATACAGGACAACTCCCTTGTTCATGTGGCCAAATCAAATATAAGTCAAAAGGTGCTGCCCACCATCATAGGGAACAATGTTACTGTTGGTAAGCATGCAAGTCAACCTTAGCATCAGTTATCTTGGTTTGATGGATAGTGACTTAGGCTTTCTGTAGGTCATAGTGCTGTTGTACATGGCTGCACCAT</genome_strand>
        <mrna_strand>TTGACTGCACAGCTCTACTGATCAGAAAGAGGGCTAAACCGAAAGAAGAAGAAGGAGGAGGTCAAACATGGGAACCCTCGGGAAAGCAATTTACTCCCTGGGATCCATCGTTCGAGCGACCGGCAAAGCTCTTGATCGCGTCGGAAATCGCCTACAAGGCAGCTCCCACATAGAGGAACACC...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGTCCAGGCATCGGACTCTTATGAACGTATTCGATAAAGCTCCGGTGGTGGATAAGGATGTATTTGTAGCTCCAGGTGCCTCAGTCATTGGAGATGTCCATGTGGGACGCAATTCATCTATTTGGTATGGATGTGTACTAAGAG.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGATGTTAACAGCATCAGTGTCGGATCTGGTACCAATATACAGGACAACTCCCTTGTTCATGTGGCCAAATCAAATATAAGTCAAAAGGTGCTGCCCACCATCATAGGGAACAATGTTACTGTTG.....................................................................GTCATAGTGCTGTTGTACATGGCTGCACCAT</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="103605" PGL_stop="105116"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="103605" e_stop="103720"/>
            <exon e_start="103826" e_stop="103950"/>
            <exon e_start="104055" e_stop="104155"/>
            <exon e_start="104670" e_stop="105116"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="1.000" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.994" acc_prob="0.999" e_score="1.000"/>
          <exon-intron don_prob="0.962" acc_prob="1.000" e_score="1.000"/>
          <exon-only e_score="0.998"/>
        </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="103605" e_stop="103720" e_length="116"/>
          </exon>
          <intron i_serial="1" don_prob="1.000" acc_prob="0.999">
            <gDNA_intron_boundary i_start="103721" i_stop="103825" i_length="105"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="103826" e_stop="103950" e_length="125"/>
          </exon>
          <intron i_serial="2" don_prob="0.994" acc_prob="0.999">
            <gDNA_intron_boundary i_start="103951" i_stop="104054" i_length="104"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="104055" e_stop="104155" e_length="101"/>
          </exon>
          <intron i_serial="3" don_prob="0.962" acc_prob="1.000">
            <gDNA_intron_boundary i_start="104156" i_stop="104669" i_length="514"/>
          </intron>
          <exon e_serial="4" e_score="0.998">
            <gDNA_exon_boundary e_start="104670" e_stop="105116" e_length="447"/>
          </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="103605" stop="103720"/>
              <exon start="103826" stop="103950"/>
              <exon start="104055" stop="104155"/>
              <exon start="104670" stop="105116"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6662" 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>TGAAATTAATTAACTGTGTGTTAAGTTTAATTAAGAAGTTAATTAGCAACAAAAAGAGATAATTATGGGTTCTCTTATGGCAGGTTGGGACTCTCCTGTTTCTGATCCTCAAGCTA : TGAAATTACGAACAAATAAGTCATTAACAAAGAAAGAGATAGATGCATATTGGAGATCAAAAAAACTAATTGAAGAAGAGCATCAAAAATATATCTCTACGTTATCCCCTCGAAGCCAAAAACAG : GCGAATATTGTATTTGAGGAGGCAACTAAAACAGCGGAAGAAAGTCTTTCTAATTTGGAAAATGAGGAAAGTTTGGATCAACTAATCAGGAAAAATGGATG : GTGGATAAGTAGCAATTGGGCACATTTAAATGAGCCACCAGTAGAAGTACGAGAAGGTCCAGCTTACAAATACGTGTCACAATTTCACGTAGCCAACATGGCTACTGGGTCCAACACTAAACCCGGTCCAGCCGGAATCAACGCTTGAACCGTCGTTTGGCTTTAGACCGGTTTGCTAATAAGTACTAGTATAGTACTTTTTTTAGGTTAATTTTAATTTTTTTTTATGACAAATTACTTTTAATTTTATTTGCGAAAGTATTTGTATTTGAGTTGATATTTAGAGTTTGCGTTAAGAGATGTCGATACTTGTAATGTTGGGACATACATACATGTCGTTGTAATATATTTTTTGTGCTTTCTTCGATAAAAGTTAAAGTATATTAATATTTTGATGTGATATATTTTTTTCTGCAAATTTTATAAAATTTAATTTGTAGAATGTAA</gDNA_template>
            <first_frame> *  N  *  L  T  V  C  *  V  *  L  R  S  *  L  A  T  K  R  D  N  Y  G  F  S  Y  G  R  L  G  L  S  C  F  *  S  S  S  Y :   E  I  T  N  K  *  V  I  N  K  E  R  D  R  C  I  L  E  I  K  K  T  N  *  R  R  A  S  K  I  Y  L  Y  V  I  P  S  K  P  K  T   : G  E  Y  C  I  *  G  G  N  *  N  S  G  R  K  S  F  *  F  G  K  *  G  K  F  G  S  T  N  Q  E  K  W  M  :  V  D  K  *  Q  L  G  T  F  K  *  A  T  S  R  S  T  R  R  S  S  L  Q  I  R  V  T  I  S  R  S  Q  H  G  Y  W  V  Q  H  *  T  R  S  S  R  N  Q  R  L  N  R  R  L  A  L  D  R  F  A  N  K  Y  *  Y  S  T  F  F  R  L  I  L  I  F  F  Y  D  K  L  L  L  I  L  F  A  K  V  F  V  F  E  L  I  F  R  V  C  V  K  R  C  R  Y  L  *  C  W  D  I  H  T  C  R  C  N  I  F  F  V  L  S  S  I  K  V  K  V  Y  *  Y  F  D  V  I  Y  F  F  L  Q  I  L  *  N  L  I  C  R  M  * </first_frame>
            <second_frame>  E  I  N  *  L  C  V  K  F  N  *  E  V  N  *  Q  Q  K  E  I  I  M  G  S  L  M  A  G  W  D  S  P  V  S  D  P  Q  A   : M  K  L  R  T  N  K  S  L  T  K  K  E  I  D  A  Y  W  R  S  K  K  L  I  E  E  E  H  Q  K  Y  I  S  T  L  S  P  R  S  Q  K  Q  :  A  N  I  V  F  E  E  A  T  K  T  A  E  E  S  L  S  N  L  E  N  E  E  S  L  D  Q  L  I  R  K  N  G  W :   W  I  S  S  N  W  A  H  L  N  E  P  P  V  E  V  R  E  G  P  A  Y  K  Y  V  S  Q  F  H  V  A  N  M  A  T  G  S  N  T  K  P  G  P  A  G  I  N  A  *  T  V  V  W  L  *  T  G  L  L  I  S  T  S  I  V  L  F  L  G  *  F  *  F  F  F  M  T  N  Y  F  *  F  Y  L  R  K  Y  L  Y  L  S  *  Y  L  E  F  A  L  R  D  V  D  T  C  N  V  G  T  Y  I  H  V  V  V  I  Y  F  L  C  F  L  R  *  K  L  K  Y  I  N  I  L  M  *  Y  I  F  F  C  K  F  Y  K  I  *  F  V  E  C   </second_frame>
            <third_frame>   K  L  I  N  C  V  L  S  L  I  K  K  L  I  S  N  K  K  R  *  L  W  V  L  L  W  Q  V  G  T  L  L  F  L  I  L  K  L  :  *  N  Y  E  Q  I  S  H  *  Q  R  K  R  *  M  H  I  G  D  Q  K  N  *  L  K  K  S  I  K  N  I  S  L  R  Y  P  L  E  A  K  N  R :   R  I  L  Y  L  R  R  Q  L  K  Q  R  K  K  V  F  L  I  W  K  M  R  K  V  W  I  N  *  S  G  K  M  D   : G  G  *  V  A  I  G  H  I  *  M  S  H  Q  *  K  Y  E  K  V  Q  L  T  N  T  C  H  N  F  T  *  P  T  W  L  L  G  P  T  L  N  P  V  Q  P  E  S  T  L  E  P  S  F  G  F  R  P  V  C  *  *  V  L  V  *  Y  F  F  *  V  N  F  N  F  F  L  *  Q  I  T  F  N  F  I  C  E  S  I  C  I  *  V  D  I  *  S  L  R  *  E  M  S  I  L  V  M  L  G  H  T  Y  M  S  L  *  Y  I  F  C  A  F  F  D  K  S  *  S  I  L  I  F  *  C  D  I  F  F  S  A  N  F  I  K  F  N  L  *  N  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="C04SLm0124K05.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="103651" stop="103720"/>
                    <exon start="103826" stop="103950"/>
                    <exon start="104055" stop="104155"/>
                    <exon start="104670" stop="104817"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>441</number_coding_nucleotides>
                  <number_encoded_amino_acids>147</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>QQKEIIMGSLMAGWDSPVSDPQAMKLRTNKSLTKKEIDAYWRSKKLIEEEHQKYISTLSPRSQKQANIVFEEATKTAEESLSNLENEESLDQLIRKNGWWISSNWAHLNEPPVEVREGPAYKYVSQFHVANMATGSNTKPGPAGINA*</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="116871" PGL_stop="121134"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="116871" e_stop="117052"/>
            <exon e_start="119248" e_stop="119391"/>
            <exon e_start="120909" e_stop="121034"/>
            <exon e_start="121104" e_stop="121134"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.970" acc_prob="0.949" e_score="1.000"/>
          <exon-intron don_prob="0.995" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.887" acc_prob="0.935" e_score="1.000"/>
          <exon-only e_score="1.000"/>
        </SCR_line>
        <exon-intron_info xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/exon-intron_info/">
          <exon e_serial="1" e_score="1.000">
            <gDNA_exon_boundary e_start="116871" e_stop="117052" e_length="182"/>
          </exon>
          <intron i_serial="1" don_prob="0.970" acc_prob="0.949">
            <gDNA_intron_boundary i_start="117053" i_stop="119247" i_length="2195"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="119248" e_stop="119391" e_length="144"/>
          </exon>
          <intron i_serial="2" don_prob="0.995" acc_prob="1.000">
            <gDNA_intron_boundary i_start="119392" i_stop="120908" i_length="1517"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="120909" e_stop="121034" e_length="126"/>
          </exon>
          <intron i_serial="3" don_prob="0.887" acc_prob="0.935">
            <gDNA_intron_boundary i_start="121035" i_stop="121103" i_length="69"/>
          </intron>
          <exon e_serial="4" e_score="1.000">
            <gDNA_exon_boundary e_start="121104" e_stop="121134" e_length="31"/>
          </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="116871" stop="117052"/>
              <exon start="119248" stop="119391"/>
              <exon start="120909" stop="121034"/>
              <exon start="121104" stop="121134"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M2219" 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>TTGACTGCACAGCTCTACTGATCAGAAAGAGGGCTAAACCGAAAGAAGAAGAAGGAGGAGGTCAAACATGGGAACCCTCGGGAAAGCAATTTACTCCCTGGGATCCATCGTTCGAGCGACCGGCAAAGCTCTTGATCGCGTCGGAAATCGCCTACAAGGCAGCTCCCACATAGAGGAACACC : TGTCCAGGCATCGGACTCTTATGAACGTATTCGATAAAGCTCCGGTGGTGGATAAGGATGTATTTGTAGCTCCAGGTGCCTCAGTCATTGGAGATGTCCATGTGGGACGCAATTCATCTATTTGGTATGGATGTGTACTAAGAG : GTGATGTTAACAGCATCAGTGTCGGATCTGGTACCAATATACAGGACAACTCCCTTGTTCATGTGGCCAAATCAAATATAAGTCAAAAGGTGCTGCCCACCATCATAGGGAACAATGTTACTGTTG : GTCATAGTGCTGTTGTACATGGCTGCACCAT</gDNA_template>
            <first_frame> L  T  A  Q  L  Y  *  S  E  R  G  L  N  R  K  K  K  K  E  E  V  K  H  G  N  P  R  E  S  N  L  L  P  G  I  H  R  S  S  D  R  Q  S  S  *  S  R  R  K  S  P  T  R  Q  L  P  H  R  G  T  P :   V  Q  A  S  D  S  Y  E  R  I  R  *  S  S  G  G  G  *  G  C  I  C  S  S  R  C  L  S  H  W  R  C  P  C  G  T  Q  F  I  Y  L  V  W  M  C  T  K  R :   *  C  *  Q  H  Q  C  R  I  W  Y  Q  Y  T  G  Q  L  P  C  S  C  G  Q  I  K  Y  K  S  K  G  A  A  H  H  H  R  E  Q  C  Y  C  W :   S  *  C  C  C  T  W  L  H  H </first_frame>
            <second_frame>  *  L  H  S  S  T  D  Q  K  E  G  *  T  E  R  R  R  R  R  R  S  N  M  G  T  L  G  K  A  I  Y  S  L  G  S  I  V  R  A  T  G  K  A  L  D  R  V  G  N  R  L  Q  G  S  S  H  I  E  E  H   : L  S  R  H  R  T  L  M  N  V  F  D  K  A  P  V  V  D  K  D  V  F  V  A  P  G  A  S  V  I  G  D  V  H  V  G  R  N  S  S  I  W  Y  G  C  V  L  R   : G  D  V  N  S  I  S  V  G  S  G  T  N  I  Q  D  N  S  L  V  H  V  A  K  S  N  I  S  Q  K  V  L  P  T  I  I  G  N  N  V  T  V   : G  H  S  A  V  V  H  G  C  T   </second_frame>
            <third_frame>   D  C  T  A  L  L  I  R  K  R  A  K  P  K  E  E  E  G  G  G  Q  T  W  E  P  S  G  K  Q  F  T  P  W  D  P  S  F  E  R  P  A  K  L  L  I  A  S  E  I  A  Y  K  A  A  P  T  *  R  N  T  :  C  P  G  I  G  L  L  *  T  Y  S  I  K  L  R  W  W  I  R  M  Y  L  *  L  Q  V  P  Q  S  L  E  M  S  M  W  D  A  I  H  L  F  G  M  D  V  Y  *  E  :  V  M  L  T  A  S  V  S  D  L  V  P  I  Y  R  T  T  P  L  F  M  W  P  N  Q  I  *  V  K  R  C  C  P  P  S  *  G  T  M  L  L  L  :  V  I  V  L  L  Y  M  A  A  P  </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="C04SLm0124K05.1" strand="+"/>
                <serials PGL_serial="2" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="116908" stop="117052"/>
                    <exon start="119248" stop="119391"/>
                    <exon start="120909" stop="121034"/>
                    <exon start="121104" stop="121132"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>444</number_coding_nucleotides>
                  <number_encoded_amino_acids>148</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>TERRRRRRSNMGTLGKAIYSLGSIVRATGKALDRVGNRLQGSSHIEEHLSRHRTLMNVFDKAPVVDKDVFVAPGASVIGDVHVGRNSSIWYGCVLRGDVNSISVGSGTNIQDNSLVHVAKSNISQKVLPTIIGNNVTVGHSAVVHGCT</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 15 chains have been computed
$ 
$ memory statistics:
$ 3536 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 1768 bytes was the average size of a spliced alignment
$ 6896 bytes predicted gene locations in total
$ 2 predicted gene locations have been stored
$ 3448 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 15 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-15 23:53:22
-->
