<?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="2008-06-14 05:08:48"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C00HBa0291F09-aDabx/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/cxgn-bacpublish-resources-F27Lv5/sgn_marker_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-F27Lv5/sgn_marker_seqs" ref_id="SGN-M3970" ref_strand="+" ref_description="SGN-M3970 cLEY-15-N18 [est_clones]">
      <seq>gaagttacaatggactctctgaatgcttacgcatcgtcggcggcgatggcgcagcaaacctgggagttagagaacaacatcgtaacaatcgacgcgccgtcggggtcgaaaccggaaaactccgcgtcggacgctatattccactacgacgatgcggcacagacgaagtttcagcgggagaagccgtgggcgagtgaccctcactacttcaagcgtgtgaagatctctgctcttgctcttctcaagatggttgttcacgcgcgttccggaggtacaattgaggtcatgggactcatgcagggtaagactgacggcgatgccatcattgtaatggacgctattgccctccccgttgaaggcactgaaactagggttaatgctcaagctgatgcgtatgaatatatggtcgaatattcacagaccaacaagcaggctggtcg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0291F09-aDabx/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00HBa0291F09.1" temp_strand="-" temp_description="C00HBa0291F09.1  CU302231.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0291F09 sequenced_by:sanger upload_account_name:uk">
        <position start="122663" stop="121630"/>
      </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="122365" g_stop="121933" g_length="433"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="432" r_length="432" r_score="0.905"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0291F09.1" gen_strand="-" ref_id="SGN-M3970" ref_strand="+">
        <total_alignment_score>0.905</total_alignment_score>
        <cumulative_length_of_scored_exons>433</cumulative_length_of_scored_exons>
        <coverage percentage="0.984" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0291F09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M3970" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="122365" e_stop="121933"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>TCAGTTCCCAATGGACGCTCTGAATTCTTACGCATCGTCGGCGGCGATGGCGCAACAAACATGGGAGTTAGAAAACAACATCGTGACGACGGACGCGCCATCGGGGTCGGCACCGGAAAACTCTGCGTCGGATGCAATATTCCACTATGACGATGCGGCACAGACTAAGTTCCAGCGGGAGAAGCCGTGGACGAGTGACCCTCACTACTTCAAGCGCGTGAAGATCTCTGCTCTTGCTCTTCTAAAGATGGTTGTTCACGCGCGTTCTGGAGGTACAATTGAGGTAATGGGACTAATGCAAGGTAAGACGGATGGAGATGCTATTATTGTTATGGACGCTTTTGCCCTTCCAGTTGAAGGAACTGAAACTAGGGTTAATGCTCAAGCTGATGCGTATGAATACATGGTTGAATATTCACAGACCAACAAGCAG</genome_strand>
        <mrna_strand>GAAGTTAC-AATGGACTCTCTGAATGCTTACGCATCGTCGGCGGCGATGGCGCAGCAAACCTGGGAGTTAGAGAACAACATCGTAACAATCGACGCGCCGTCGGGGTCGAAACCGGAAAACTCCGCGTCGGACGCTATATTCCACTACGACGATGCGGCACAGACGAAGTTTCAGCGGGAGAAGCCGTGGGCGAGTGACCCTCACTACTTCAAGCGTGTGAAGATCTCTGCTCTTGCTCTTCTCAAGATGGTTGTTCACGCGCGTTCCGGAGGTACAATTGAGGTCATGGGACTCATGCAGGGTAAGACTGACGGCGATGCCATCATTGTAATGGACGCTATTGCCCTCCCCGTTGAAGGCACTGAAACTAGGGTTAATGCTCAAGCTGATGCGTATGAATATATGGTCGAATATTCACAGACCAACAAGCAG</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-F27Lv5/sgn_marker_seqs" ref_id="SGN-M4080" ref_strand="+" ref_description="SGN-M4080 cTOE-7-B4 [est_clones]">
      <seq>ccaatggacgctctgaattcttacgcatcgtcggcggcgatggcgcaacaaacatgggagttagaaaacaacatcgtgacgacggacgcgccatcggggtcggcaccggaaaactctgcgtcggatgcaatattccactatgacgatgcggcacagactaagttccagcgggagaagccgtggacgagtgaccctcactactgcaagcgcgtgaagatctgtgctcttgctcttctaaagatggttgttcacgcgcgttctggaggtacaattgaggtaatgggactaatgcaaggtaagacggatggagatgctattattgttatggacgctttagcccttccagttgaaggaactgaaactagggttaatgctcaagctgatgcgtatgaatacatggttgaatattcacagaccaacaagcatgctggtcg</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C00HBa0291F09-aDabx/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C00HBa0291F09.1" temp_strand="-" temp_description="C00HBa0291F09.1  CU302231.4 htgs_phase:3 submitted_to_sgn_as:C04HBa0291F09 sequenced_by:sanger upload_account_name:uk">
        <position start="122658" stop="121630"/>
      </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="122358" g_stop="121933" g_length="426"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="426" r_length="426" r_score="0.991"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C00HBa0291F09.1" gen_strand="-" ref_id="SGN-M4080" ref_strand="+">
        <total_alignment_score>0.991</total_alignment_score>
        <cumulative_length_of_scored_exons>426</cumulative_length_of_scored_exons>
        <coverage percentage="0.982" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C00HBa0291F09.1" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M4080" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="122358" e_stop="121933"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CCAATGGACGCTCTGAATTCTTACGCATCGTCGGCGGCGATGGCGCAACAAACATGGGAGTTAGAAAACAACATCGTGACGACGGACGCGCCATCGGGGTCGGCACCGGAAAACTCTGCGTCGGATGCAATATTCCACTATGACGATGCGGCACAGACTAAGTTCCAGCGGGAGAAGCCGTGGACGAGTGACCCTCACTACTTCAAGCGCGTGAAGATCTCTGCTCTTGCTCTTCTAAAGATGGTTGTTCACGCGCGTTCTGGAGGTACAATTGAGGTAATGGGACTAATGCAAGGTAAGACGGATGGAGATGCTATTATTGTTATGGACGCTTTTGCCCTTCCAGTTGAAGGAACTGAAACTAGGGTTAATGCTCAAGCTGATGCGTATGAATACATGGTTGAATATTCACAGACCAACAAGCAG</genome_strand>
        <mrna_strand>CCAATGGACGCTCTGAATTCTTACGCATCGTCGGCGGCGATGGCGCAACAAACATGGGAGTTAGAAAACAACATCGTGACGACGGACGCGCCATCGGGGTCGGCACCGGAAAACTCTGCGTCGGATGCAATATTCCACTATGACGATGCGGCACAGACTAAGTTCCAGCGGGAGAAGCCGTGGACGAGTGACCCTCACTACTGCAAGCGCGTGAAGATCTGTGCTCTTGCTCTTCTAAAGATGGTTGTTCACGCGCGTTCTGGAGGTACAATTGAGGTAATGGGACTAATGCAAGGTAAGACGGATGGAGATGCTATTATTGTTATGGACGCTTTAGCCCTTCCAGTTGAAGGAACTGAAACTAGGGTTAATGCTCAAGCTGATGCGTATGAATACATGGTTGAATATTCACAGACCAACAAGCAT</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="122365" PGL_stop="121933"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="122365" e_stop="121933"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <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="0.991">
            <gDNA_exon_boundary e_start="122365" e_stop="121933" e_length="433"/>
          </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="122365" stop="121933"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M3970" strand="+"/>
          </PGS_line>
          <PGS_line>
            <gDNA_exon_coordinates>
              <exon start="122358" stop="121933"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M4080" 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>TCAGTTCCCAATGGACGCTCTGAATTCTTACGCATCGTCGGCGGCGATGGCGCAACAAACATGGGAGTTAGAAAACAACATCGTGACGACGGACGCGCCATCGGGGTCGGCACCGGAAAACTCTGCGTCGGATGCAATATTCCACTATGACGATGCGGCACAGACTAAGTTCCAGCGGGAGAAGCCGTGGACGAGTGACCCTCACTACTTCAAGCGCGTGAAGATCTCTGCTCTTGCTCTTCTAAAGATGGTTGTTCACGCGCGTTCTGGAGGTACAATTGAGGTAATGGGACTAATGCAAGGTAAGACGGATGGAGATGCTATTATTGTTATGGACGCTTTTGCCCTTCCAGTTGAAGGAACTGAAACTAGGGTTAATGCTCAAGCTGATGCGTATGAATACATGGTTGAATATTCACAGACCAACAAGCAG</gDNA_template>
            <first_frame> S  V  P  N  G  R  S  E  F  L  R  I  V  G  G  D  G  A  T  N  M  G  V  R  K  Q  H  R  D  D  G  R  A  I  G  V  G  T  G  K  L  C  V  G  C  N  I  P  L  *  R  C  G  T  D  *  V  P  A  G  E  A  V  D  E  *  P  S  L  L  Q  A  R  E  D  L  C  S  C  S  S  K  D  G  C  S  R  A  F  W  R  Y  N  *  G  N  G  T  N  A  R  *  D  G  W  R  C  Y  Y  C  Y  G  R  F  C  P  S  S  *  R  N  *  N  *  G  *  C  S  S  *  C  V  *  I  H  G  *  I  F  T  D  Q  Q  A  </first_frame>
            <second_frame>  Q  F  P  M  D  A  L  N  S  Y  A  S  S  A  A  M  A  Q  Q  T  W  E  L  E  N  N  I  V  T  T  D  A  P  S  G  S  A  P  E  N  S  A  S  D  A  I  F  H  Y  D  D  A  A  Q  T  K  F  Q  R  E  K  P  W  T  S  D  P  H  Y  F  K  R  V  K  I  S  A  L  A  L  L  K  M  V  V  H  A  R  S  G  G  T  I  E  V  M  G  L  M  Q  G  K  T  D  G  D  A  I  I  V  M  D  A  F  A  L  P  V  E  G  T  E  T  R  V  N  A  Q  A  D  A  Y  E  Y  M  V  E  Y  S  Q  T  N  K  Q </second_frame>
            <third_frame>   S  S  Q  W  T  L  *  I  L  T  H  R  R  R  R  W  R  N  K  H  G  S  *  K  T  T  S  *  R  R  T  R  H  R  G  R  H  R  K  T  L  R  R  M  Q  Y  S  T  M  T  M  R  H  R  L  S  S  S  G  R  S  R  G  R  V  T  L  T  T  S  S  A  *  R  S  L  L  L  L  F  *  R  W  L  F  T  R  V  L  E  V  Q  L  R  *  W  D  *  C  K  V  R  R  M  E  M  L  L  L  L  W  T  L  L  P  F  Q  L  K  E  L  K  L  G  L  M  L  K  L  M  R  M  N  T  W  L  N  I  H  R  P  T  S   </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="C00HBa0291F09.1" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="122364" stop="121933"/>
                  </exon_boundaries>
                  <frame>1</frame>
                  <number_coding_nucleotides>432</number_coding_nucleotides>
                  <number_encoded_amino_acids>144</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>QFPMDALNSYASSAAMAQQTWELENNIVTTDAPSGSAPENSASDAIFHYDDAAQTKFQREKPWTSDPHYFKRVKISALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYMVEYSQTNKQ</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 12 chains have been computed
$ 
$ memory statistics:
$ 3312 bytes spliced alignments in total
$ 2 spliced alignments have been stored
$ 1656 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
$ 12 backtrace matrices have been allocated
$ 
$ date finished: 2008-06-14 05:08:52
-->
