<?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>fimo --oc fimo_example_output_files --parse-genomic-coord some_vertebrates.meme mm9_tss_500bp_sampled_1000.fa</command-line>
<settings>
<setting name="output directory">fimo_example_output_files</setting>
<setting name="MEME file name">some_vertebrates.meme</setting>
<setting name="sequence file name">mm9_tss_500bp_sampled_1000.fa</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">2</setting>
</settings>
<sequence-data num-sequences="1000" num-residues="2500000" />
<alphabet>nucleotide</alphabet>
<motif name="MA0108.1" width="15" best-possible-match="GTATAAAAGGCGGGG"/>
<motif name="UP00093_1" width="16" best-possible-match="TCGACCCCGCCCCTAT"/>
<motif name="UP00020_1" width="16" best-possible-match="ACGATGACGTCATCGA"/>
<motif name="UP00002_2" width="15" best-possible-match="CAAAGGCGTGGCCAG"/>
<motif name="MA0060.1" width="16" best-possible-match="CTCAGCCAATCAGCGC"/>
<background source="non-redundant database">
<value letter="A">0.275</value>
<value letter="C">0.225</value>
<value letter="G">0.225</value>
<value letter="T">0.275</value>
</background>
<cisml-file>cisml.xml</cisml-file>
</fimo>
