<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<?xml-stylesheet type="text/xsl" href="fimo-to-html.xsl"?>
<!-- Begin document body -->
<fimo version="4.10.0" release="Wed May 21 10:35:36 2014 +1000">
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
>
<command-line>/home/james/reldist/BUILD/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_2 --bgfile memechip_example_output_files/background --motif 2 memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/sample-dna-Klf1.fa</command-line>
<settings>
<setting name="output directory">memechip_example_output_files/fimo_out_2</setting>
<setting name="MEME file name">memechip_example_output_files/meme_out/meme.xml</setting>
<setting name="sequence file name">memechip_example_output_files/sample-dna-Klf1.fa</setting>
<setting name="background file name">memechip_example_output_files/background</setting>
<setting name="allow clobber">true</setting>
<setting name="compute q-values">true</setting>
<setting name="parse genomic coord.">true</setting>
<setting name="text only">false</setting>
<setting name="scan both strands">true</setting>
<setting name="max sequence length">250000000</setting>
<setting name="output threshold">0.0001</setting>
<setting name="threshold type">p-value</setting>
<setting name="max stored scores">100000</setting>
<setting name="pseudocount">0.1</setting>
<setting name="verbosity">1</setting>
<setting name="selected motif">2</setting>
</settings>
<sequence-data num-sequences="904" num-residues="452000" />
<alphabet>nucleotide</alphabet>
<motif name="1" width="12" best-possible-match="CAGCCACACCCA"/>
<motif name="2" width="8" best-possible-match="CAGATAAG"/>
<motif name="3" width="29" best-possible-match="CTGCATCTCTTCAAGACACACCTAACTGC"/>
<background source="memechip_example_output_files/background">
<value letter="A">0.256</value>
<value letter="C">0.244</value>
<value letter="G">0.244</value>
<value letter="T">0.256</value>
</background>
<cisml-file>cisml.xml</cisml-file>
</fimo>
