view tools/mytools/fimo_out/fimo.xml @ 0:9071e359b9a3

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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<?xml-stylesheet type="text/xsl" href="fimo-to-html.xsl"?>
<!-- Begin document body -->
<fimo version="4.7.0" release="0 EST 20">
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
>
<command-line>fimo --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta</command-line>
<settings>
<setting name="output directory">fimo_out</setting>
<setting name="MEME file name">AATAAA.motif</setting>
<setting name="sequence file name">/Users/xuebing/Downloads/hotair-target.fa.fasta</setting>
<setting name="background file name">(null)</setting>
<setting name="motif name">motif</setting>
<setting name="allow clobber">true</setting>
<setting name="compute q-values">true</setting>
<setting name="output p-threshold set">false</setting>
<setting name="output q-threshold set">false</setting>
<setting name="text only">false</setting>
<setting name="scan both strands">true</setting>
<setting name="max sequence length">250000000</setting>
<setting name="output q-value threshold">  1</setting>
<setting name="output p-value threshold">0.0001</setting>
<setting name="pseudocount">0.1</setting>
<setting name="verbosity">1</setting>
</settings>
<sequence-data num-sequences="832" num-residues="573269" />
<alphabet>nucleotide</alphabet>
<motif name="AATAAA" width="6" best-possible-match="AATAAA"/>
<motif name="AATAAA" width="6" best-possible-match="TTTATT"/>
<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>