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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <?xml-stylesheet type="text/xsl" href="fimo-to-html.xsl"?>
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3 <!-- Begin document body -->
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4 <fimo version="4.7.0" release="0 EST 20">
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5 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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6 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
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7 >
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8 <command-line>fimo --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta</command-line>
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9 <settings>
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10 <setting name="output directory">fimo_out</setting>
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11 <setting name="MEME file name">AATAAA.motif</setting>
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12 <setting name="sequence file name">/Users/xuebing/Downloads/hotair-target.fa.fasta</setting>
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13 <setting name="background file name">(null)</setting>
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14 <setting name="motif name">motif</setting>
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15 <setting name="allow clobber">true</setting>
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16 <setting name="compute q-values">true</setting>
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17 <setting name="output p-threshold set">false</setting>
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18 <setting name="output q-threshold set">false</setting>
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19 <setting name="text only">false</setting>
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20 <setting name="scan both strands">true</setting>
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21 <setting name="max sequence length">250000000</setting>
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22 <setting name="output q-value threshold"> 1</setting>
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23 <setting name="output p-value threshold">0.0001</setting>
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24 <setting name="pseudocount">0.1</setting>
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25 <setting name="verbosity">1</setting>
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26 </settings>
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27 <sequence-data num-sequences="832" num-residues="573269" />
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28 <alphabet>nucleotide</alphabet>
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29 <motif name="AATAAA" width="6" best-possible-match="AATAAA"/>
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30 <motif name="AATAAA" width="6" best-possible-match="TTTATT"/>
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31 <background source="non-redundant database">
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32 <value letter="A">0.275</value>
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33 <value letter="C">0.225</value>
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34 <value letter="G">0.225</value>
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35 <value letter="T">0.275</value>
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36 </background>
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37 <cisml-file>cisml.xml</cisml-file>
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38 </fimo>
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