<?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="2009-01-19 12:02:15"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C09SLe0004D19-8gOjI/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C09SLe0004D19-8gOjI/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-C09SLe0004D19-8gOjI/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M1795" ref_strand="+" ref_description="SGN-M1795 T1148 [cos_markers]">
      <seq>atgtcaaatcctgccgtctttgtcaatgctgagttcctcaaggagcatgtaggacggaaggttcgaacagtggttcaggttatgcaatctgatggtgataaagtcattggaaaatccacggatgaaaaagaattagttgtgaaaggaaatccacctaatgctctttcaacttttgttgaagtaattggtatagctgacactatccagtctattgaagcagaaatttggaccaattttggtgatacatttgatgttaatagctatgacaaggtgtgcagactagcaaatggtgacagtgagcacttgtttatctgagaaatgatttataaaagaggacatatatcctcttatttctgctgcattgttccagagtgtcaatgtattataagtagtttgaagtactcctgaaaactttggattttcagcttctatttagggtttcatcaacagaaggtaagctctgtgcttagatgtaaacttgattttcttcaactgatgctatttggtattttgaacactaatatttgtggttccactagttagtcaacttggcattaaactagctgtgttacataca</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C09SLe0004D19-8gOjI/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C09SLe0004D19.3" temp_strand="-" temp_description="C09SLe0004D19.3  EF576815.2 htgs_phase:2 submitted_to_sgn_as:gb|EF576815| upload_account_name:spain (1 - 92010)">
        <position start="5297" stop="3026"/>
      </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="4997" g_stop="4748" g_length="250"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="250" r_length="250" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="4747" i_stop="3653" i_length="1095">
            <donor d_prob="0.976" d_score="1.00"/>
            <acceptor a_prob="0.989" a_score="0.98"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="3652" g_stop="3326" g_length="327"/>
          <reference_exon_boundary r_type="cDNA" r_start="251" r_stop="577" r_length="327" r_score="0.985"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C09SLe0004D19.3" gen_strand="-" ref_id="SGN-M1795" ref_strand="+">
        <total_alignment_score>0.991</total_alignment_score>
        <cumulative_length_of_scored_exons>577</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C09SLe0004D19.3" gen_strand="-"/>
        <rDNA rDNA_id="SGN-M1795" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="4997" e_stop="4748"/>
          <exon e_start="3652" e_stop="3326"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>ATGTCAAATCCTGCCGTCTTTGTCAATGCTGAGTTCCTCAAGGAGCATGTAGGACGGAAGGTTCGAACAGTGGTTCAGGTTATGCAATCTGATGGTGATAAAGTCATTGGAAAATCCACGGATGAAAAAGAATTAGTTGTGAAAGGAAATCCACCTAATGCTCTTTCAACTTTTGTTGAAGTAATTGGTATAGCTGACACTATCCAGTCTATTGAAGCAGAAATTTGGACCAATTTTGGTGATACATTTGGTATGTCTTGCTTATGTTATTCATATATATACACTTGGCTTCTCCTATATCCGTTAATGCATTTGAATGTCAATTTGTACCAAATTTGTTTCACTGGCAATCAAATCCATGATTTTATTACTTGTTGTTTCTTTTGCTTCATTTACGTCTTTTTTGTCGTTTTGCTACTGTTCTTCTCCTTTATCTTTAGCATTATTTTCTCATTACTGTATTTTCTTCCATACTTGAGTTTGATATGTTATACTTGAACCGAGGGTCTATCACAAATAGTCACTCTATCTTCACAAGGTAGTAAGACTATATACACACCACCCTCCCCAAACTCCACTCGTGGAATTACACTGGGTTTGTTATTGTTGTTTTGCCCTTCTTTATGTCTTGTTCTGCGTATTTTTTCAAGGTCATTTTGTAAGTTGCGAATATAGAACTGCCTAAGGCCAATGAACCATATAGTCTTCATACTCATCACTGAAAAGGAAAAGGATGGTGTTCTTTGATAAAGTTCATAACCCTATAATTGATGATAACACTATGAATATGCAAACTTTATGGTTATCATCTACCAGAAACCTTAAGATCTATAGATATTCAACAGATGAGTGGGTTGTAGTCAATTAAGTGAACTGAATAATAGATTGTAGAGTTAAACATTATTGTCCTTCCCAACTCGGCCAATTTTATCTTCATTCCTTCACTTCTCTGAAATGTTTCTATACAAATGGTGACTGGGGAGGGTAAAGTTTACGATGTCCCTGTTCTATATGAAATTCAAGGATTAAAACAAAGGGAGATTTGGTTAGTGCGACTTTTCAGGTTATGATATCTATATTTACGGTAGTGTTCTACTTTGTTTACAATCCTATCATCATGCGATAGCTGTTTTTATACTTGCTCTGTCAAACATATTCAAGACCAATGTAGTCATCAATTATGTCCAAACTGCATTTATTTTTGACACATTGTATAAGCATTTCATGTTGCTTGTTAAACTTCTACTCATGACTTAAGGTTTATAGAAACTTTATGATGTGTATCTAGTGCTTGTCTCTTGATGATATATACTTGCTAATCTACAAGTTCTTCAATATGTGACAGATGTTAATAGCTATGACAAGGTGTGCAGACTAGCAAATGGTGACAGTAAGCACTTGTTTATCTGAGAAATGATTTATAAAAGAGGACATATATCCTCTTATTTCTGCTGCATTGTTCCAGAGTTTCAATGTATTATAAGTAGTTTGAAGTACTCCTGAAAACTTTGGATTTTCAGCTTCTATTTAGGGTTTCATCAACAGAAGTTAAGCTCTGTGCTTAGATGTAAACTTGTTTTTCTTCAACTTATGCTATTTGGTATTTTGAACACTAATATTTGTGGTTCCACTAGTTAGTCAACTTGGCATTAAACTAGCTGTGTTACATACA</genome_strand>
        <mrna_strand>ATGTCAAATCCTGCCGTCTTTGTCAATGCTGAGTTCCTCAAGGAGCATGTAGGACGGAAGGTTCGAACAGTGGTTCAGGTTATGCAATCTGATGGTGATAAAGTCATTGGAAAATCCACGGATGAAAAAGAATTAGTTGTGAAAGGAAATCCACCTAATGCTCTTTCAACTTTTGTTGAAGTAATTGGTATAGCTGACACTATCCAGTCTATTGAAGCAGAAATTTGGACCAATTTTGGTGATACATTTG.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ATGTTAATAGCTATGACAAGGTGTGCAGACTAGCAAATGGTGACAGTGAGCACTTGTTTATCTGAGAAATGATTTATAAAAGAGGACATATATCCTCTTATTTCTGCTGCATTGTTCCAGAGTGTCAATGTATTATAAGTAGTTTGAAGTACTCCTGAAAACTTTGGATTTTCAGCTTCTATTTAGGGTTTCATCAACAGAAGGTAAGCTCTGTGCTTAGATGTAAACTTGATTTTCTTCAACTGATGCTATTTGGTATTTTGAACACTAATATTTGTGGTTCCACTAGTTAGTCAACTTGGCATTAAACTAGCTGTGTTACATACA</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="4997" PGL_stop="3326"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="4997" e_stop="4748"/>
            <exon e_start="3652" e_stop="3326"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.976" acc_prob="0.989" e_score="1.000"/>
          <exon-only e_score="0.985"/>
        </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="4997" e_stop="4748" e_length="250"/>
          </exon>
          <intron i_serial="1" don_prob="0.976" acc_prob="0.989">
            <gDNA_intron_boundary i_start="4747" i_stop="3653" i_length="1095"/>
          </intron>
          <exon e_serial="2" e_score="0.985">
            <gDNA_exon_boundary e_start="3652" e_stop="3326" e_length="327"/>
          </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="4997" stop="4748"/>
              <exon start="3652" stop="3326"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M1795" 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>ATGTCAAATCCTGCCGTCTTTGTCAATGCTGAGTTCCTCAAGGAGCATGTAGGACGGAAGGTTCGAACAGTGGTTCAGGTTATGCAATCTGATGGTGATAAAGTCATTGGAAAATCCACGGATGAAAAAGAATTAGTTGTGAAAGGAAATCCACCTAATGCTCTTTCAACTTTTGTTGAAGTAATTGGTATAGCTGACACTATCCAGTCTATTGAAGCAGAAATTTGGACCAATTTTGGTGATACATTTG : ATGTTAATAGCTATGACAAGGTGTGCAGACTAGCAAATGGTGACAGTAAGCACTTGTTTATCTGAGAAATGATTTATAAAAGAGGACATATATCCTCTTATTTCTGCTGCATTGTTCCAGAGTTTCAATGTATTATAAGTAGTTTGAAGTACTCCTGAAAACTTTGGATTTTCAGCTTCTATTTAGGGTTTCATCAACAGAAGTTAAGCTCTGTGCTTAGATGTAAACTTGTTTTTCTTCAACTTATGCTATTTGGTATTTTGAACACTAATATTTGTGGTTCCACTAGTTAGTCAACTTGGCATTAAACTAGCTGTGTTACATACA</gDNA_template>
            <first_frame> M  S  N  P  A  V  F  V  N  A  E  F  L  K  E  H  V  G  R  K  V  R  T  V  V  Q  V  M  Q  S  D  G  D  K  V  I  G  K  S  T  D  E  K  E  L  V  V  K  G  N  P  P  N  A  L  S  T  F  V  E  V  I  G  I  A  D  T  I  Q  S  I  E  A  E  I  W  T  N  F  G  D  T  F   : D  V  N  S  Y  D  K  V  C  R  L  A  N  G  D  S  K  H  L  F  I  *  E  M  I  Y  K  R  G  H  I  S  S  Y  F  C  C  I  V  P  E  F  Q  C  I  I  S  S  L  K  Y  S  *  K  L  W  I  F  S  F  Y  L  G  F  H  Q  Q  K  L  S  S  V  L  R  C  K  L  V  F  L  Q  L  M  L  F  G  I  L  N  T  N  I  C  G  S  T  S  *  S  T  W  H  *  T  S  C  V  T  Y  </first_frame>
            <second_frame>  C  Q  I  L  P  S  L  S  M  L  S  S  S  R  S  M  *  D  G  R  F  E  Q  W  F  R  L  C  N  L  M  V  I  K  S  L  E  N  P  R  M  K  K  N  *  L  *  K  E  I  H  L  M  L  F  Q  L  L  L  K  *  L  V  *  L  T  L  S  S  L  L  K  Q  K  F  G  P  I  L  V  I  H  L  :  M  L  I  A  M  T  R  C  A  D  *  Q  M  V  T  V  S  T  C  L  S  E  K  *  F  I  K  E  D  I  Y  P  L  I  S  A  A  L  F  Q  S  F  N  V  L  *  V  V  *  S  T  P  E  N  F  G  F  S  A  S  I  *  G  F  I  N  R  S  *  A  L  C  L  D  V  N  L  F  F  F  N  L  C  Y  L  V  F  *  T  L  I  F  V  V  P  L  V  S  Q  L  G  I  K  L  A  V  L  H  T </second_frame>
            <third_frame>   V  K  S  C  R  L  C  Q  C  *  V  P  Q  G  A  C  R  T  E  G  S  N  S  G  S  G  Y  A  I  *  W  *  *  S  H  W  K  I  H  G  *  K  R  I  S  C  E  R  K  S  T  *  C  S  F  N  F  C  *  S  N  W  Y  S  *  H  Y  P  V  Y  *  S  R  N  L  D  Q  F  W  *  Y  I  * :   C  *  *  L  *  Q  G  V  Q  T  S  K  W  *  Q  *  A  L  V  Y  L  R  N  D  L  *  K  R  T  Y  I  L  L  F  L  L  H  C  S  R  V  S  M  Y  Y  K  *  F  E  V  L  L  K  T  L  D  F  Q  L  L  F  R  V  S  S  T  E  V  K  L  C  A  *  M  *  T  C  F  S  S  T  Y  A  I  W  Y  F  E  H  *  Y  L  W  F  H  *  L  V  N  L  A  L  N  *  L  C  Y  I   </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="C09SLe0004D19.3" strand="-"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="4997" stop="4748"/>
                    <exon start="3652" stop="3588"/>
                  </exon_boundaries>
                  <frame>0</frame>
                  <number_coding_nucleotides>312</number_coding_nucleotides>
                  <number_encoded_amino_acids>104</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>MSNPAVFVNAEFLKEHVGRKVRTVVQVMQSDGDKVIGKSTDEKELVVKGNPPNALSTFVEVIGIADTIQSIEAEIWTNFGDTFDVNSYDKVCRLANGDSKHLFI*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 16 chains have been computed
$ 
$ memory statistics:
$ 2280 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 2280 bytes was the average size of a spliced alignment
$ 5560 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5560 bytes was the average size of a predicted gene location
$ 0 megabytes was the average size of the backtrace matrix
$ 16 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-19 12:02:20
-->
