<?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="2009-01-16 05:36:01"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C05SLe0028N03-1AJF1/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C05SLe0028N03-1AJF1/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-C05SLe0028N03-1AJF1/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M6575" ref_strand="+" ref_description="SGN-M6575 C2_At1g10580 [cosii_markers]">
      <seq>gtttttgacagctggatatgataagtacattaagtattgggatacagaaacaggacaagtaattcaaaccttcacgacaggtaagataccctatgtggtgaggcttaatcctgatgaggataagcagaatgtacttttggccggtatgagtgataagaagattgtgcagtgggatataaacagtggacagattacacaagagtacgatcaacatctgggggcagttaatacaattacctttgtggataataataggaggtttgtgacctctagtgatgataaatcactacgtgtttgggaatatggtattccggttgttatcaagtatataagtgaaccccatatgcattccatgccatctatttctccccatccaaatgggaattggattgcagcacaaagtttggataaccagattcttatttatagtacgcgagagagatttcagctgaataaaaagaaaagatttgctggacacattgtcgctggttatgcctgccaggtcaatttctcacctgatggacggtttgtcttctcaggagatggtgaaggcagatgctggttttgggaatggaaatcgtgtaaggcttcagaactctcagtgtcatgacggggtctgtattggtgcagagtggcatcctctggaacaaagtaaagttgctacttgtggttggga</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C05SLe0028N03-1AJF1/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C05SLe0028N03.1" temp_strand="+" temp_description="C05SLe0028N03.1  AC212305.1 htgs_phase:3 submitted_to_sgn_as:C05SLe0028N03 sequenced_by:iitg upload_account_name:india complete sequence">
        <position start="26486" stop="27761"/>
      </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="26786" g_stop="27461" g_length="676"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="676" r_length="676" r_score="0.942"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C05SLe0028N03.1" gen_strand="+" ref_id="SGN-M6575" ref_strand="+">
        <total_alignment_score>0.942</total_alignment_score>
        <cumulative_length_of_scored_exons>676</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C05SLe0028N03.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M6575" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="26786" e_stop="27461"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>GTTTTTGGCAGCTGGCTATGATAAGCACATTAAGTATTGGGATACAGAAACAGGACAAGTAATTCAAACATTCTCGACAAGTAATATACCCTATGTAGTGAGGCTTAATCCTGATGAGGATAAGCAGAATGAACTTTTGGCTGGAATGAGTGATAAGAAGATTGTGCAGTGGGATATAAACAGTGGACAGATTACACAAGAGTACGATCAACATCTGGGGGCAGTTAATACAATTACCTTTGTGGATAATAATAGGAGGATTGTGACTTATAGTGATGATAAATCACTACGTGTTTGGGAATATGGTATTCTGGTTGTTATTAAGTATATAAGTGAACCCCATATGCATTCCATGCCATCTATTTTGCCCCATCCAAATGGAAATTGGATTGCAGCACGAAGTCTGGATAACCAGATTCTTATTTGTAGTACGC--GAGAGATTTCAGCTGAATAAAAAGAAAAGATTTGCTGGACACATTGTTGCTGGTTATGCCTGCCAGTTCAATTTCTCACCAGATGGATGGTTTGTCTTGTCAGGAGATGGTGAAGGCAGATGCTGGTTTTGGGATTGGAAATCGTGTAGGGTCTTCAGAACTCCCAAGTGTCATGAAGGGGTCTGTATTGGTGCAGAGTGGCATCCTCCGGAACAAAGTAAAGTTGCTACATGTGGTTGGGA</genome_strand>
        <mrna_strand>GTTTTTGACAGCTGGATATGATAAGTACATTAAGTATTGGGATACAGAAACAGGACAAGTAATTCAAACCTTCACGACAGGTAAGATACCCTATGTGGTGAGGCTTAATCCTGATGAGGATAAGCAGAATGTACTTTTGGCCGGTATGAGTGATAAGAAGATTGTGCAGTGGGATATAAACAGTGGACAGATTACACAAGAGTACGATCAACATCTGGGGGCAGTTAATACAATTACCTTTGTGGATAATAATAGGAGGTTTGTGACCTCTAGTGATGATAAATCACTACGTGTTTGGGAATATGGTATTCCGGTTGTTATCAAGTATATAAGTGAACCCCATATGCATTCCATGCCATCTATTTCTCCCCATCCAAATGGGAATTGGATTGCAGCACAAAGTTTGGATAACCAGATTCTTATTTATAGTACGCGAGAGAGATTTCAGCTGAATAAAAAGAAAAGATTTGCTGGACACATTGTCGCTGGTTATGCCTGCCAGGTCAATTTCTCACCTGATGGACGGTTTGTCTTCTCAGGAGATGGTGAAGGCAGATGCTGGTTTTGGGAATGGAAATCGTGTAAGG-CTTCAGAACTCTC-AGTGTCATGACGGGGTCTGTATTGGTGCAGAGTGGCATCCTCTGGAACAAAGTAAAGTTGCTACTTGTGGTTGGGA</mrna_strand>
      </alignment>
    </predicted_gene_structure>
  </spliced_alignment>
    <total_number_ESTs_reported>1</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="26786" PGL_stop="27461"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="26786" e_stop="27461"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-only e_score="0.942"/>
        </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="0.942">
            <gDNA_exon_boundary e_start="26786" e_stop="27461" e_length="676"/>
          </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="26786" stop="27461"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M6575" 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>GTTTTTGGCAGCTGGCTATGATAAGCACATTAAGTATTGGGATACAGAAACAGGACAAGTAATTCAAACATTCTCGACAAGTAATATACCCTATGTAGTGAGGCTTAATCCTGATGAGGATAAGCAGAATGAACTTTTGGCTGGAATGAGTGATAAGAAGATTGTGCAGTGGGATATAAACAGTGGACAGATTACACAAGAGTACGATCAACATCTGGGGGCAGTTAATACAATTACCTTTGTGGATAATAATAGGAGGATTGTGACTTATAGTGATGATAAATCACTACGTGTTTGGGAATATGGTATTCTGGTTGTTATTAAGTATATAAGTGAACCCCATATGCATTCCATGCCATCTATTTTGCCCCATCCAAATGGAAATTGGATTGCAGCACGAAGTCTGGATAACCAGATTCTTATTTGTAGTACGCGAGAGATTTCAGCTGAATAAAAAGAAAAGATTTGCTGGACACATTGTTGCTGGTTATGCCTGCCAGTTCAATTTCTCACCAGATGGATGGTTTGTCTTGTCAGGAGATGGTGAAGGCAGATGCTGGTTTTGGGATTGGAAATCGTGTAGGGTCTTCAGAACTCCCAAGTGTCATGAAGGGGTCTGTATTGGTGCAGAGTGGCATCCTCCGGAACAAAGTAAAGTTGCTACATGTGGTTGGGA</gDNA_template>
            <first_frame> V  F  G  S  W  L  *  *  A  H  *  V  L  G  Y  R  N  R  T  S  N  S  N  I  L  D  K  *  Y  T  L  C  S  E  A  *  S  *  *  G  *  A  E  *  T  F  G  W  N  E  *  *  E  D  C  A  V  G  Y  K  Q  W  T  D  Y  T  R  V  R  S  T  S  G  G  S  *  Y  N  Y  L  C  G  *  *  *  E  D  C  D  L  *  *  *  *  I  T  T  C  L  G  I  W  Y  S  G  C  Y  *  V  Y  K  *  T  P  Y  A  F  H  A  I  Y  F  A  P  S  K  W  K  L  D  C  S  T  K  S  G  *  P  D  S  Y  L  *  Y  A  R  D  F  S  *  I  K  R  K  D  L  L  D  T  L  L  L  V  M  P  A  S  S  I  S  H  Q  M  D  G  L  S  C  Q  E  M  V  K  A  D  A  G  F  G  I  G  N  R  V  G  S  S  E  L  P  S  V  M  K  G  S  V  L  V  Q  S  G  I  L  R  N  K  V  K  L  L  H  V  V  G  </first_frame>
            <second_frame>  F  L  A  A  G  Y  D  K  H  I  K  Y  W  D  T  E  T  G  Q  V  I  Q  T  F  S  T  S  N  I  P  Y  V  V  R  L  N  P  D  E  D  K  Q  N  E  L  L  A  G  M  S  D  K  K  I  V  Q  W  D  I  N  S  G  Q  I  T  Q  E  Y  D  Q  H  L  G  A  V  N  T  I  T  F  V  D  N  N  R  R  I  V  T  Y  S  D  D  K  S  L  R  V  W  E  Y  G  I  L  V  V  I  K  Y  I  S  E  P  H  M  H  S  M  P  S  I  L  P  H  P  N  G  N  W  I  A  A  R  S  L  D  N  Q  I  L  I  C  S  T  R  E  I  S  A  E  *  K  E  K  I  C  W  T  H  C  C  W  L  C  L  P  V  Q  F  L  T  R  W  M  V  C  L  V  R  R  W  *  R  Q  M  L  V  L  G  L  E  I  V  *  G  L  Q  N  S  Q  V  S  *  R  G  L  Y  W  C  R  V  A  S  S  G  T  K  *  S  C  Y  M  W  L  G </second_frame>
            <third_frame>   F  W  Q  L  A  M  I  S  T  L  S  I  G  I  Q  K  Q  D  K  *  F  K  H  S  R  Q  V  I  Y  P  M  *  *  G  L  I  L  M  R  I  S  R  M  N  F  W  L  E  *  V  I  R  R  L  C  S  G  I  *  T  V  D  R  L  H  K  S  T  I  N  I  W  G  Q  L  I  Q  L  P  L  W  I  I  I  G  G  L  *  L  I  V  M  I  N  H  Y  V  F  G  N  M  V  F  W  L  L  L  S  I  *  V  N  P  I  C  I  P  C  H  L  F  C  P  I  Q  M  E  I  G  L  Q  H  E  V  W  I  T  R  F  L  F  V  V  R  E  R  F  Q  L  N  K  K  K  R  F  A  G  H  I  V  A  G  Y  A  C  Q  F  N  F  S  P  D  G  W  F  V  L  S  G  D  G  E  G  R  C  W  F  W  D  W  K  S  C  R  V  F  R  T  P  K  C  H  E  G  V  C  I  G  A  E  W  H  P  P  E  Q  S  K  V  A  T  C  G  W   </third_frame>
          </translation>
          <probable_ORFs xmlns="http://www.genomethreader.org/GTH_output/PGL_module/predicted_gene_location/AGS_information/three_phase_translation/probable_ORFs/">
            <orf_entry>
              <id_line>
                <gDNA id="C05SLe0028N03.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="26787" stop="27239"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>450</number_coding_nucleotides>
                  <number_encoded_amino_acids>150</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>FLAAGYDKHIKYWDTETGQVIQTFSTSNIPYVVRLNPDEDKQNELLAGMSDKKIVQWDINSGQITQEYDQHLGAVNTITFVDNNRRIVTYSDDKSLRVWEYGILVVIKYISEPHMHSMPSILPHPNGNWIAARSLDNQILICSTREISAE*</predicted_protein_sequence>
            </orf_entry>
            <orf_entry>
              <id_line>
                <gDNA id="C05SLe0028N03.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="2"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="27236" stop="27460"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>225</number_coding_nucleotides>
                  <number_encoded_amino_acids>75</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>IKRKDLLDTLLLVMPASSISHQMDGLSCQEMVKADAGFGIGNRVGSSELPSVMKGSVLVQSGILRNKVKLLHVVG</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:
$ 2296 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2296 bytes was the average size of a spliced alignment
$ 5528 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5528 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: 2009-01-16 05:36:04
-->
