<?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 01:01:11"/>
    <gDNA_template_files>
      <temp_name>/tmp/bac-submission-temp-C12HBa0180O10-FFemj/GenomeThreader_SGN_markers/un_xed_seqs</temp_name>
    </gDNA_template_files>
    <reference_files>
      <file ref_name="/tmp/bac-submission-temp-C12HBa0180O10-FFemj/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-C12HBa0180O10-FFemj/gth_cdna_fileCXGN::BACSubmission::Analysis::GenomeThreader_SGN_markers" ref_id="SGN-M2979" ref_strand="+" ref_description="SGN-M2979 cLET-8-K4 [est_clones]">
      <seq>caaaatgtcactttgtggcaatcgacattttcaatgcaaaaaagcttgaagatattgttccttcatcccacaattgtgatgtgccacatgtcaatcgtactgactatcagctgattgacatatctgaagatggttttgtgtctcttcttactgaaaatggaaacaccaaagacgacctcagacttcccaccgatgacaccctgttgaaccaggttaaaggtggatttgaggaaggaaaggatctcgttctgtctgtgatgtctgcaatgggtgaagagcagatctgtgctgtgaaggacattggtaccaagacctagttgtgtgcattctgcagcataaataattgctttttagcgaagacgttttatatcttgttatcgtggtacctttgcaatctgttttatcgtgaaaacaccttatatctattggcatggcttgaatagttgaaactctaatagtttctgtttggcataaggcaatgaactggatttgatagcaaaaataatctacatgtcactttttttttaaaaaaaaaaaa</seq>
    </reference>
    <gDNA_segment>
      <template temp_file="/tmp/bac-submission-temp-C12HBa0180O10-FFemj/GenomeThreader_SGN_markers/un_xed_seqs" temp_id="C12HBa0180O10.1" temp_strand="+" temp_description="C12HBa0180O10.1  AC216346.1 htgs_phase:1 submitted_to_sgn_as:C12HBa0180O10 upload_account_name:italy *** WORKING DRAFT SEQUENCE ***">
        <position start="57764" stop="140936"/>
      </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="58064" g_stop="58143" g_length="80"/>
          <reference_exon_boundary r_type="cDNA" r_start="1" r_stop="80" r_length="80" r_score="1.000"/>
        </exon>
        <intron i_serial="1">
          <gDNA_intron_boundary i_start="58144" i_stop="58227" i_length="84">
            <donor d_prob="0.959" d_score="1.00"/>
            <acceptor a_prob="1.000" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="2">
          <gDNA_exon_boundary g_start="58228" g_stop="58284" g_length="57"/>
          <reference_exon_boundary r_type="cDNA" r_start="81" r_stop="137" r_length="57" r_score="1.000"/>
        </exon>
        <intron i_serial="2">
          <gDNA_intron_boundary i_start="58285" i_stop="58872" i_length="588">
            <donor d_prob="0.983" d_score="1.00"/>
            <acceptor a_prob="0.995" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="3">
          <gDNA_exon_boundary g_start="58873" g_stop="58947" g_length="75"/>
          <reference_exon_boundary r_type="cDNA" r_start="138" r_stop="212" r_length="75" r_score="1.000"/>
        </exon>
        <intron i_serial="3">
          <gDNA_intron_boundary i_start="58948" i_stop="59038" i_length="91">
            <donor d_prob="0.998" d_score="1.00"/>
            <acceptor a_prob="0.997" a_score="1.00"/>
          </gDNA_intron_boundary>
        </intron>
        <exon e_serial="4">
          <gDNA_exon_boundary g_start="59039" g_stop="59364" g_length="326"/>
          <reference_exon_boundary r_type="cDNA" r_start="213" r_stop="538" r_length="326" r_score="0.972"/>
        </exon>
      </exon-intron_info>
      <MATCH_line gen_id="C12HBa0180O10.1" gen_strand="+" ref_id="SGN-M2979" ref_strand="+">
        <total_alignment_score>0.983</total_alignment_score>
        <cumulative_length_of_scored_exons>538</cumulative_length_of_scored_exons>
        <coverage percentage="1.000" high_type="C"/>
      </MATCH_line>
      <PGS_line>
        <gDNA gen_id="C12HBa0180O10.1" gen_strand="+"/>
        <rDNA rDNA_id="SGN-M2979" rDNA_strand="+"/>
        <gDNA_exon_coordinates>
          <exon e_start="58064" e_stop="58143"/>
          <exon e_start="58228" e_stop="58284"/>
          <exon e_start="58873" e_stop="58947"/>
          <exon e_start="59039" e_stop="59364"/>
        </gDNA_exon_coordinates>
      </PGS_line>
      <alignment>
        <genome_strand>CAAAATGTCACTTTGTGGCAATCGACATTTTCAATGCAAAAAAGCTTGAAGATATTGTTCCTTCATCCCACAATTGTGATGTAAGACAAGATTCTCTCCTTCGTTTGTTCAGTTTTCCGACAATCAAAGTTTGACTTTGTCTGATTTTTAAATGCTTTCTGCAGGTGCCACATGTCAATCGTACTGACTATCAGCTGATTGACATATCTGAAGATGGTTTTGTAAGTTTTCTTTTACCTAGTATATGAAGTGTATAAGTCATCCTCTTACTGGGGAAAAACTTATTGGATACAGTGCTACGTAGTTCTATTGATGACTTATTGCATCGTTTTGATGTCTCTAGTAGTTTCTTCATGAAATTGAGATTTGAATAATGATGAAGTTGTCTTACCTTTCTTTTGTGAGAGAATTCCTACGGGGATTCTTTTCTCAATGAGTCCTGTCGGCTCTTTCCCAAGGTTCCATTGAGGGTCAGTCCCCTCTGGGCTGGTCCTTTTGAAGTTCGATGATGCAACTGAACATATATCTATAAAGTAGAAAATTTCTCCCACTTTAATTGTTTTCTTTTCCCCTTCCAAGAATGTGCGAAGTGGATAATGTGGCCGATGGGGTGTAACTGTGAACACTGATTTTTGTTTTCCACTTAAGGTGTAAAACAGTCCTTCTATTTCCAAAATTTAATACTAAAACCAAAGACTTGAAATTAACAGTTGTTTGTTCTAATTATAATCTTGAAGCTGGACTTGTTTTTGCTAATTCTTTTGTTATACCTGTTTTGAGTGTTGTCATCGGTTCATTCTTTTGGCTAGGTGTCTCTTCTTACTGAAAATGGAAACACCAAAGACGACCTCAGACTTCCCACCGATGACACCCTGTTGAACCAGGTACATTTTTTTGATGGATAAAACACGAAGAACGTTTATTTTCTAGTTTTTTCATGCGTAATATCTGAGCAAAGCTCTCGACTATTTGTAGGTTAAAGGTGGATTTGAGGAAGGAAAGGATCTCGTTCTGTCTGTGATGTCTGCAATGGGTGAAGAGCAGATCTGTGCTGTGAAGGACATTGGTACCAAGACCTAGTTGTGTGCATTCTGCAGCATAAATAATTGCTTTTTAGCGAAGACGTTTTATATCTTGTTATCGTGGTACCTTTGCAATCTGTTTTATCGTGAAAACACCTTATATCTATTGGCATGGCTTGAATAGTTGAAACTCTAATAGTTTCTGTTTGGCATAAGGCAATGAACTGGATTTGATAGCAGAAGTAATCTACATGTCACTTTTTTTTTACTTGAATAGTA</genome_strand>
        <mrna_strand>CAAAATGTCACTTTGTGGCAATCGACATTTTCAATGCAAAAAAGCTTGAAGATATTGTTCCTTCATCCCACAATTGTGAT....................................................................................GTGCCACATGTCAATCGTACTGACTATCAGCTGATTGACATATCTGAAGATGGTTTT............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GTGTCTCTTCTTACTGAAAATGGAAACACCAAAGACGACCTCAGACTTCCCACCGATGACACCCTGTTGAACCAG...........................................................................................GTTAAAGGTGGATTTGAGGAAGGAAAGGATCTCGTTCTGTCTGTGATGTCTGCAATGGGTGAAGAGCAGATCTGTGCTGTGAAGGACATTGGTACCAAGACCTAGTTGTGTGCATTCTGCAGCATAAATAATTGCTTTTTAGCGAAGACGTTTTATATCTTGTTATCGTGGTACCTTTGCAATCTGTTTTATCGTGAAAACACCTTATATCTATTGGCATGGCTTGAATAGTTGAAACTCTAATAGTTTCTGTTTGGCATAAGGCAATGAACTGGATTTGATAGCAAAAATAATCTACATGTCACTTTTTTTTTAAAAAAAAAAAA</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="58064" PGL_stop="59364"/>
      <AGS_information>
        <AGS_line AGS_serial="1">
          <exon_coordinates>
            <exon e_start="58064" e_stop="58143"/>
            <exon e_start="58228" e_stop="58284"/>
            <exon e_start="58873" e_stop="58947"/>
            <exon e_start="59039" e_stop="59364"/>
          </exon_coordinates>
        </AGS_line>
        <SCR_line>
          <exon-intron don_prob="0.959" acc_prob="1.000" e_score="1.000"/>
          <exon-intron don_prob="0.983" acc_prob="0.995" e_score="1.000"/>
          <exon-intron don_prob="0.998" acc_prob="0.997" e_score="1.000"/>
          <exon-only e_score="0.972"/>
        </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="58064" e_stop="58143" e_length="80"/>
          </exon>
          <intron i_serial="1" don_prob="0.959" acc_prob="1.000">
            <gDNA_intron_boundary i_start="58144" i_stop="58227" i_length="84"/>
          </intron>
          <exon e_serial="2" e_score="1.000">
            <gDNA_exon_boundary e_start="58228" e_stop="58284" e_length="57"/>
          </exon>
          <intron i_serial="2" don_prob="0.983" acc_prob="0.995">
            <gDNA_intron_boundary i_start="58285" i_stop="58872" i_length="588"/>
          </intron>
          <exon e_serial="3" e_score="1.000">
            <gDNA_exon_boundary e_start="58873" e_stop="58947" e_length="75"/>
          </exon>
          <intron i_serial="3" don_prob="0.998" acc_prob="0.997">
            <gDNA_intron_boundary i_start="58948" i_stop="59038" i_length="91"/>
          </intron>
          <exon e_serial="4" e_score="0.972">
            <gDNA_exon_boundary e_start="59039" e_stop="59364" e_length="326"/>
          </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="58064" stop="58143"/>
              <exon start="58228" stop="58284"/>
              <exon start="58873" stop="58947"/>
              <exon start="59039" stop="59364"/>
            </gDNA_exon_coordinates>
            <referenceDNA id="SGN-M2979" 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>CAAAATGTCACTTTGTGGCAATCGACATTTTCAATGCAAAAAAGCTTGAAGATATTGTTCCTTCATCCCACAATTGTGAT : GTGCCACATGTCAATCGTACTGACTATCAGCTGATTGACATATCTGAAGATGGTTTT : GTGTCTCTTCTTACTGAAAATGGAAACACCAAAGACGACCTCAGACTTCCCACCGATGACACCCTGTTGAACCAG : GTTAAAGGTGGATTTGAGGAAGGAAAGGATCTCGTTCTGTCTGTGATGTCTGCAATGGGTGAAGAGCAGATCTGTGCTGTGAAGGACATTGGTACCAAGACCTAGTTGTGTGCATTCTGCAGCATAAATAATTGCTTTTTAGCGAAGACGTTTTATATCTTGTTATCGTGGTACCTTTGCAATCTGTTTTATCGTGAAAACACCTTATATCTATTGGCATGGCTTGAATAGTTGAAACTCTAATAGTTTCTGTTTGGCATAAGGCAATGAACTGGATTTGATAGCAGAAGTAATCTACATGTCACTTTTTTTTTACTTGAATAGTA</gDNA_template>
            <first_frame> Q  N  V  T  L  W  Q  S  T  F  S  M  Q  K  S  L  K  I  L  F  L  H  P  T  I  V  M :   C  H  M  S  I  V  L  T  I  S  *  L  T  Y  L  K  M  V  L :   C  L  F  L  L  K  M  E  T  P  K  T  T  S  D  F  P  P  M  T  P  C  *  T  R :   L  K  V  D  L  R  K  E  R  I  S  F  C  L  *  C  L  Q  W  V  K  S  R  S  V  L  *  R  T  L  V  P  R  P  S  C  V  H  S  A  A  *  I  I  A  F  *  R  R  R  F  I  S  C  Y  R  G  T  F  A  I  C  F  I  V  K  T  P  Y  I  Y  W  H  G  L  N  S  *  N  S  N  S  F  C  L  A  *  G  N  E  L  D  L  I  A  E  V  I  Y  M  S  L  F  F  Y  L  N  S  </first_frame>
            <second_frame>  K  M  S  L  C  G  N  R  H  F  Q  C  K  K  A  *  R  Y  C  S  F  I  P  Q  L  *   : C  A  T  C  Q  S  Y  *  L  S  A  D  *  H  I  *  R  W  F   : C  V  S  S  Y  *  K  W  K  H  Q  R  R  P  Q  T  S  H  R  *  H  P  V  E  P   : G  *  R  W  I  *  G  R  K  G  S  R  S  V  C  D  V  C  N  G  *  R  A  D  L  C  C  E  G  H  W  Y  Q  D  L  V  V  C  I  L  Q  H  K  *  L  L  F  S  E  D  V  L  Y  L  V  I  V  V  P  L  Q  S  V  L  S  *  K  H  L  I  S  I  G  M  A  *  I  V  E  T  L  I  V  S  V  W  H  K  A  M  N  W  I  *  *  Q  K  *  S  T  C  H  F  F  F  T  *  I  V </second_frame>
            <third_frame>   K  C  H  F  V  A  I  D  I  F  N  A  K  K  L  E  D  I  V  P  S  S  H  N  C  D  :  V  P  H  V  N  R  T  D  Y  Q  L  I  D  I  S  E  D  G  F  :  V  S  L  L  T  E  N  G  N  T  K  D  D  L  R  L  P  T  D  D  T  L  L  N  Q  :  V  K  G  G  F  E  E  G  K  D  L  V  L  S  V  M  S  A  M  G  E  E  Q  I  C  A  V  K  D  I  G  T  K  T  *  L  C  A  F  C  S  I  N  N  C  F  L  A  K  T  F  Y  I  L  L  S  W  Y  L  C  N  L  F  Y  R  E  N  T  L  Y  L  L  A  W  L  E  *  L  K  L  *  *  F  L  F  G  I  R  Q  *  T  G  F  D  S  R  S  N  L  H  V  T  F  F  L  L  E  *   </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="C12HBa0180O10.1" strand="+"/>
                <serials PGL_serial="1" AGS_serial="1" PPS_serial="1"/>
                <orf_info>
                  <exon_boundaries>
                    <exon start="58066" stop="58143"/>
                    <exon start="58228" stop="58284"/>
                    <exon start="58873" stop="58947"/>
                    <exon start="59039" stop="59143"/>
                  </exon_boundaries>
                  <frame>2</frame>
                  <number_coding_nucleotides>312</number_coding_nucleotides>
                  <number_encoded_amino_acids>104</number_encoded_amino_acids>
                </orf_info>
              </id_line>
              <predicted_protein_sequence>KCHFVAIDIFNAKKLEDIVPSSHNCDVPHVNRTDYQLIDISEDGFVSLLTENGNTKDDLRLPTDDTLLNQVKGGFEEGKDLVLSVMSAMGEEQICAVKDIGTKT*</predicted_protein_sequence>
            </orf_entry>
          </probable_ORFs>
        </three_phase_translation>
      </AGS_information>
    </predicted_gene_location>
  </PGL_module>
</GTH_output>
<!--
$ general statistics:
$ 17 chains have been computed
$ 
$ memory statistics:
$ 164840 bytes spliced alignments in total
$ 1 spliced alignments have been stored
$ 164840 bytes was the average size of a spliced alignment
$ 5624 bytes predicted gene locations in total
$ 1 predicted gene locations have been stored
$ 5624 bytes was the average size of a predicted gene location
$ 1 megabytes was the average size of the backtrace matrix
$ 17 backtrace matrices have been allocated
$ 
$ date finished: 2009-01-16 01:01:19
-->
