<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
<!-- Document definition -->
<!-- http://zlab.bu.edu/~phaverty/SupplementalData/CisML/cisml.dtd -->
<!DOCTYPE cis-element-search[
<!ELEMENT cis-element-search (program-name, parameters, (pattern | multi-pattern-scan)*)>
<!ELEMENT program-name (#PCDATA)>
<!ELEMENT parameters (
  pattern-file, 
  sequence-file, 
  background-seq-file?,
  pattern-pvalue-cutoff?,
  sequence-pvalue-cutoff?,
  site-pvalue-cutoff?,
  sequence-filtering,
  ANY*
 )>
<!ELEMENT command-line (#PCDATA)>
<!ELEMENT pattern-file (#PCDATA)>
<!ELEMENT sequence-file (#PCDATA)>
<!ELEMENT background-seq-file (#PCDATA)>
<!ELEMENT pattern-pvalue-cutoff (#PCDATA)>
<!ELEMENT sequence-pvalue-cutoff (#PCDATA)>
<!ELEMENT site-pvalue-cutoff (#PCDATA)>
<!ELEMENT sequence-filtering EMPTY>
<!ELEMENT multi-pattern-scan (pattern+, ANY*)>
<!ELEMENT pattern (scanned-sequence+, ANY*)>
<!ELEMENT scanned-sequence (matched-element*, ANY*)>
<!ELEMENT matched-element (sequence)>
<!ELEMENT sequence (#PCDATA)>
<!ATTLIST cis-element-search
xmlns:xsi CDATA #IMPLIED
xmlns:mem CDATA #IMPLIED
xsi:schemaLocation CDATA #IMPLIED
>
<!ATTLIST sequence-filtering
on-off CDATA #REQUIRED
type CDATA #IMPLIED
>
<!ATTLIST multi-pattern-scan
score CDATA #IMPLIED
pvalue CDATA #IMPLIED
>
<!ATTLIST pattern
accession CDATA #REQUIRED
name CDATA #REQUIRED
pvalue CDATA #IMPLIED
score CDATA #IMPLIED
db CDATA #IMPLIED
lsid CDATA #IMPLIED
>
<!ATTLIST scanned-sequence
accession CDATA #REQUIRED
name CDATA #REQUIRED
score CDATA #IMPLIED
pvalue CDATA #IMPLIED
length CDATA #IMPLIED
db CDATA #IMPLIED
lsid CDATA #IMPLIED
>
<!ATTLIST matched-element
start CDATA #REQUIRED
stop CDATA #REQUIRED
score CDATA #IMPLIED
pvalue CDATA #IMPLIED
clusterid CDATA #IMPLIED
>

]>
<cis-element-search
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://zlab.bu.edu/schema/cisml cisml.xsd"
  xmlns="http://zlab.bu.edu/schema/cisml"
  xmlns:mem="http://noble.gs.washington.edu/meme"
>
<program-name>fimo</program-name>
<parameters>
<command-line>fimo --verbosity 1 --oc xstreme_example_output_files/fimo_out_2 --bgfile xstreme_example_output_files/background --motif CCASYAGRKGGCRSY xstreme_example_output_files/meme_out/meme.xml nrmix.nseqs.100.100bp.seed.1.fa</command-line>
<pattern-file>xstreme_example_output_files/meme_out/meme.xml</pattern-file>
<sequence-file>nrmix.nseqs.100.100bp.seed.1.fa</sequence-file>
<site-pvalue-cutoff>0.0001</site-pvalue-cutoff>
<sequence-filtering on-off="off"/>
</parameters>
<pattern accession="CCASYAGRKGGCRSY" name="MEME-4">
<scanned-sequence accession="16" name="16">
<matched-element start="30609465" stop="30609451" score="15.125" pvalue="4.74e-06">
<sequence>CCTGCAGGGGGCAGA</sequence>
<mem:qvalue>0.016</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="12" name="12">
<matched-element start="104026368" stop="104026354" score="19.5139" pvalue="4.82e-08">
<sequence>CCAGTAGAGGGCGCT</sequence>
<mem:qvalue>0.00217</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="5" name="5">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
</scanned-sequence>
<scanned-sequence accession="4" name="4">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="2" name="2">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
<matched-element start="195641881" stop="195641867" score="19.6667" pvalue="3.71e-08">
<sequence>CCACCAGGGGGCACC</sequence>
<mem:qvalue>0.00217</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="15" name="15">
</scanned-sequence>
<scanned-sequence accession="8" name="8">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="4" name="4">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
<matched-element start="106873509" stop="106873495" score="20.4583" pvalue="4.2e-09">
<sequence>CCACCAGGGGGCGCT</sequence>
<mem:qvalue>0.000757</mem:qvalue>
</matched-element>
<matched-element start="106873472" stop="106873458" score="20.3333" pvalue="6.54e-09">
<sequence>CCACTAGGGGGCGCC</sequence>
<mem:qvalue>0.000785</mem:qvalue>
</matched-element>
<matched-element start="106873490" stop="106873476" score="12.5139" pvalue="2.4e-05">
<sequence>ACACTAGGGGGCTCA</sequence>
<mem:qvalue>0.046</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="13" name="13">
</scanned-sequence>
<scanned-sequence accession="10" name="10">
</scanned-sequence>
<scanned-sequence accession="15" name="15">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
</scanned-sequence>
<scanned-sequence accession="X" name="X">
</scanned-sequence>
<scanned-sequence accession="19" name="19">
</scanned-sequence>
<scanned-sequence accession="11" name="11">
<matched-element start="111435850" stop="111435864" score="18.5833" pvalue="1.89e-07">
<sequence>CCACCAGGTGGCAGT</sequence>
<mem:qvalue>0.00388</mem:qvalue>
</matched-element>
<matched-element start="111435860" stop="111435846" score="10.8056" pvalue="5.61e-05">
<sequence>CCACCTGGTGGTGAA</sequence>
<mem:qvalue>0.0867</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="20" name="20">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="12" name="12">
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<scanned-sequence accession="17" name="17">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
<matched-element start="6532678" stop="6532692" score="17.9861" pvalue="3.65e-07">
<sequence>CCACAAGAGGGCACC</sequence>
<mem:qvalue>0.00547</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="2" name="2">
<matched-element start="44706513" stop="44706527" score="16.4583" pvalue="1.65e-06">
<sequence>CCAGTAGAGGGTACT</sequence>
<mem:qvalue>0.00861</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="11" name="11">
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</scanned-sequence>
<scanned-sequence accession="5" name="5">
<matched-element start="150494858" stop="150494844" score="11.2222" pvalue="4.63e-05">
<sequence>CTAGCAGGGGGCAGT</sequence>
<mem:qvalue>0.0751</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="9" name="9">
</scanned-sequence>
<scanned-sequence accession="10" name="10">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
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</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="3" name="3">
<matched-element start="60039275" stop="60039261" score="14.1111" pvalue="9.39e-06">
<sequence>CCACAAGGAGGCACA</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="22" name="22">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="16" name="16">
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<scanned-sequence accession="7" name="7">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="228271630" stop="228271616" score="9.80556" pvalue="8.62e-05">
<sequence>ACAGCAGAGGGCCAC</sequence>
<mem:qvalue>0.118</mem:qvalue>
</matched-element>
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="17" name="17">
<matched-element start="65713729" stop="65713743" score="12.0972" pvalue="3e-05">
<sequence>CCGCCAGAGGTCGCA</sequence>
<mem:qvalue>0.0543</mem:qvalue>
</matched-element>
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="11" name="11">
<matched-element start="65188625" stop="65188611" score="9.79167" pvalue="8.67e-05">
<sequence>ACAGAAGGTGGTGAT</sequence>
<mem:qvalue>0.118</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
</scanned-sequence>
<scanned-sequence accession="19" name="19">
<matched-element start="44617247" stop="44617261" score="11.625" pvalue="3.81e-05">
<sequence>CCGGCAGGTGGATCC</sequence>
<mem:qvalue>0.0647</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="14" name="14">
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<matched-element start="30845477" stop="30845463" score="17.7778" pvalue="4.62e-07">
<sequence>CCACTTGGGGGCGCT</sequence>
<mem:qvalue>0.00569</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="7" name="7">
</scanned-sequence>
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<matched-element start="82204412" stop="82204426" score="16.7083" pvalue="1.34e-06">
<sequence>CCTCTAGGTGGCAGT</sequence>
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</matched-element>
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</scanned-sequence>
<scanned-sequence accession="17" name="17">
<matched-element start="38511254" stop="38511240" score="12.1806" pvalue="2.87e-05">
<sequence>CCACCGGGGGGCGTG</sequence>
<mem:qvalue>0.0526</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="6" name="6">
<matched-element start="148466038" stop="148466052" score="15.5556" pvalue="3.45e-06">
<sequence>ACACCAGGGGGCGCA</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
<matched-element start="126964759" stop="126964745" score="13.0417" pvalue="1.8e-05">
<sequence>TCAGAAGGTGGCAGT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="15" name="15">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
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<matched-element start="27906375" stop="27906361" score="18.6667" pvalue="1.74e-07">
<sequence>CCACCAGAGGGCAGT</sequence>
<mem:qvalue>0.00388</mem:qvalue>
</matched-element>
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</scanned-sequence>
<scanned-sequence accession="16" name="16">
<matched-element start="2265134" stop="2265120" score="11.375" pvalue="4.3e-05">
<sequence>CCACGTGGTGGCCCC</sequence>
<mem:qvalue>0.0705</mem:qvalue>
</matched-element>
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="4" name="4">
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</scanned-sequence>
<scanned-sequence accession="4" name="4">
<matched-element start="18023276" stop="18023262" score="12.6667" pvalue="2.21e-05">
<sequence>CCTCCGGGGGGCGCG</sequence>
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</matched-element>
</scanned-sequence>
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</scanned-sequence>
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<matched-element start="113357578" stop="113357592" score="17.4861" pvalue="6.19e-07">
<sequence>CCAGGAGGTGGCGCT</sequence>
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</matched-element>
</scanned-sequence>
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<matched-element start="125792905" stop="125792919" score="14.1806" pvalue="8.94e-06">
<sequence>TCACAAGAGGGCGGT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="2" name="2">
</scanned-sequence>
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<matched-element start="203185318" stop="203185304" score="17.9028" pvalue="4.06e-07">
<sequence>CCACTAGATGGCAGC</sequence>
<mem:qvalue>0.00563</mem:qvalue>
</matched-element>
</scanned-sequence>
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</scanned-sequence>
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<scanned-sequence accession="19" name="19">
<matched-element start="50486880" stop="50486866" score="17.2222" pvalue="8.28e-07">
<sequence>CCACAAGGGGGCGAT</sequence>
<mem:qvalue>0.00662</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="2" name="2">
<matched-element start="97616896" stop="97616882" score="17.25" pvalue="7.95e-07">
<sequence>CCACTAGGTGGCGGG</sequence>
<mem:qvalue>0.00662</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="16" name="16">
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</scanned-sequence>
<scanned-sequence accession="9" name="9">
<matched-element start="131486959" stop="131486945" score="13.5278" pvalue="1.35e-05">
<sequence>CCTGTAGGTGGTGGC</sequence>
<mem:qvalue>0.0315</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="19" name="19">
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="224701388" stop="224701402" score="19.0417" pvalue="1.05e-07">
<sequence>CCAGCAGGGGGCACC</sequence>
<mem:qvalue>0.00377</mem:qvalue>
</matched-element>
<matched-element start="224701420" stop="224701434" score="12.3056" pvalue="2.69e-05">
<sequence>CCGGGAGAGGGCGTC</sequence>
<mem:qvalue>0.0501</mem:qvalue>
</matched-element>
</scanned-sequence>
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<scanned-sequence accession="6" name="6">
<matched-element start="34165424" stop="34165438" score="13.4722" pvalue="1.4e-05">
<sequence>CCAGGAGAGGGAGAC</sequence>
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</matched-element>
</scanned-sequence>
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