<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
<!DOCTYPE spamo[
<!ELEMENT spamo (model, files, primary_motif, run_time)>
<!ATTLIST spamo version CDATA #REQUIRED release CDATA #REQUIRED>
<!ELEMENT model (command_line, seed, margin, bin_size,
  bin_pvalue_calc_range, bin_pvalue_cutoff, seq_max_shared_fract,
  seq_min_hit_score, redundant_overlap, redundant_joint,
  motif_pseudocount, motif_trim, bin_max, host, when)>
<!ELEMENT command_line (#PCDATA)>
<!ELEMENT seed (#PCDATA)>
<!ELEMENT margin (#PCDATA)>
<!ELEMENT bin_size (#PCDATA)>
<!ELEMENT bin_pvalue_calc_range (#PCDATA)>
<!ELEMENT bin_pvalue_cutoff (#PCDATA)>
<!ELEMENT seq_max_shared_fract (#PCDATA)>
<!ELEMENT seq_min_hit_score (#PCDATA)>
<!ELEMENT redundant_overlap (#PCDATA)>
<!ELEMENT redundant_joint (#PCDATA)>
<!ELEMENT motif_pseudocount (#PCDATA)>
<!ELEMENT motif_trim (#PCDATA)>
<!ELEMENT bin_max (#PCDATA)>
<!ELEMENT host (#PCDATA)>
<!ELEMENT when (#PCDATA)>
<!ELEMENT files (sequence_db, motif_db*)>
<!ELEMENT sequence_db EMPTY>
<!ATTLIST sequence_db name CDATA #REQUIRED loaded CDATA #REQUIRED
  excluded_too_short CDATA #REQUIRED excluded_no_match CDATA #REQUIRED
  excluded_similar CDATA #REQUIRED last_modified CDATA #REQUIRED
  source CDATA #REQUIRED>
<!ELEMENT motif_db EMPTY>
<!ATTLIST motif_db id ID #REQUIRED name CDATA #REQUIRED
  loaded CDATA #REQUIRED excluded CDATA #REQUIRED
  last_modified CDATA #REQUIRED source CDATA #REQUIRED
  cisml CDATA #IMPLIED>
<!ELEMENT primary_motif (motif, secondary_motif*)>
<!ELEMENT secondary_motif (spacing*, motif, histogram, redundant?)>
<!ATTLIST secondary_motif evalue CDATA #REQUIRED>
<!ELEMENT spacing EMPTY>
<!ATTLIST spacing strand (same|opposite) #REQUIRED
  side (left|right) #REQUIRED bin CDATA #REQUIRED num CDATA #REQUIRED
  pvalue CDATA #REQUIRED>
<!ELEMENT histogram (same_strand, opposite_strand)>
<!ATTLIST histogram total CDATA #REQUIRED max CDATA #REQUIRED>
<!ELEMENT same_strand (left_side, right_side)>
<!ELEMENT opposite_strand (left_side, right_side)>
<!ELEMENT left_side (bin*)>
<!ELEMENT right_side (bin*)>
<!ELEMENT bin EMPTY>
<!-- i: index, n: number in bin, p: pvalue (only supplied when bin
  is tested) -->
<!ATTLIST bin i CDATA #REQUIRED n CDATA #REQUIRED p CDATA #IMPLIED>
<!ELEMENT redundant (secondary_motif*)>
<!-- motif contains the probability of each of the nucleotide bases at each
  position; i starts at 1; A, C, G and T are probabilities that sum to 1 -->
<!ELEMENT motif (pos*)>
<!ATTLIST motif db IDREF #REQUIRED name CDATA #REQUIRED alt CDATA #IMPLIED 
  length CDATA #REQUIRED nsites CDATA #IMPLIED evalue CDATA #IMPLIED
  ltrim CDATA #IMPLIED rtrim CDATA #IMPLIED url CDATA #IMPLIED>
<!ELEMENT pos EMPTY>
<!ATTLIST pos i CDATA #REQUIRED A CDATA #REQUIRED C CDATA #REQUIRED
  G CDATA #REQUIRED T CDATA #REQUIRED>
<!-- run time is measured in real time and cpu time -->
<!ELEMENT run_time EMPTY>
<!ATTLIST run_time cpu CDATA #REQUIRED real CDATA #REQUIRED>
]>
<spamo version="4.10.0" release="Wed May 21 10:35:36 2014 +1000">
  <model>
    <command_line>spamo  -verbosity 1 -oc memechip_example_output_files/spamo_out_4 -bgfile memechip_example_output_files/background -primary MA0036.1 memechip_example_output_files/sample-dna-Klf1.fa JASPAR_CORE_2009.meme memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/dreme_out/dreme.xml JASPAR_CORE_2009.meme</command_line>
    <seed>1</seed>
    <margin>150</margin>
    <bin_size>1</bin_size>
    <bin_pvalue_calc_range>150</bin_pvalue_calc_range>
    <bin_pvalue_cutoff>0.05</bin_pvalue_cutoff>
    <motif_evalue_cutoff>10</motif_evalue_cutoff>
    <seq_max_shared_fract>0.5</seq_max_shared_fract>
    <seq_min_hit_score>7</seq_min_hit_score>
    <redundant_overlap>2</redundant_overlap>
    <redundant_joint>0.5</redundant_joint>
    <motif_pseudocount>0.1</motif_pseudocount>
    <motif_trim>0.25</motif_trim>
    <bin_max>0</bin_max>
    <host>IMB12-010665</host>
    <when>Tue Oct  7 17:18:56 2014</when>
  </model>
  <files>
    <sequence_db name="sample-dna-Klf1" loaded="904" excluded_too_short="0"
        excluded_no_match="904" excluded_similar="0" last_modified="Tue Oct  7 14:14:10 2014"
        source="memechip_example_output_files/sample-dna-Klf1.fa"/>
    <motif_db id="primary_file" name="JASPAR CORE 2009" loaded="475" excluded="474" last_modified="Wed Dec  5 17:04:00 2012"
        source="JASPAR_CORE_2009.meme"/>
    <motif_db id="db1" name="meme.xml" loaded="3" excluded="0" last_modified="Tue Oct  7 17:17:30 2014"
        source="memechip_example_output_files/meme_out/meme.xml"/>
    <motif_db id="db2" name="dreme.xml" loaded="3" excluded="0" last_modified="Tue Oct  7 17:17:48 2014"
        source="memechip_example_output_files/dreme_out/dreme.xml"/>
    <motif_db id="db3" name="JASPAR CORE 2009" loaded="476" excluded="1" last_modified="Wed Dec  5 17:04:00 2012"
        source="JASPAR_CORE_2009.meme"/>
  </files>
  <primary_motif>
    <motif db="primary_file" name="MA0036.1" alt="GATA2" length="5" nsites="53" evalue="0" ltrim="1" rtrim="1" url="http://jaspar.genereg.net/cgi-bin/jaspar_db.pl?ID=MA0036.1&amp;rm=present&amp;collection=CORE">
      <pos i="1" A="0.245303" C="0.245281" G="0.339443" T="0.169973"/>
      <pos i="2" A="0.000482109" C="0.0946218" G="0.904414" T="0.000482109"/>
      <pos i="3" A="0.979766" C="0.00045951" G="0.019292" T="0.000482109"/>
      <pos i="4" A="0.000482109" C="0.00045951" G="0.00045951" T="0.998599"/>
      <pos i="5" A="0.471292" C="0.132286" G="0.282946" T="0.113477"/>
    </motif>
  </primary_motif>
  <run_time cpu="0.6" real="0.0"/>
</spamo>
