<?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 --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_1 --bgfile memechip_example_output_files/background --motif WGGGTGTGGYY memechip_example_output_files/meme_out/meme.xml memechip_example_output_files/Klf1.fna</command-line>
<pattern-file>memechip_example_output_files/meme_out/meme.xml</pattern-file>
<sequence-file>memechip_example_output_files/Klf1.fna</sequence-file>
<site-pvalue-cutoff>0.0001</site-pvalue-cutoff>
<sequence-filtering on-off="off"/>
</parameters>
<pattern accession="WGGGTGTGGYY" name="MEME-1">
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="9738458" stop="9738448" score="10.7887" pvalue="7.66e-05">
<sequence>GGGGTGGGGTG</sequence>
<mem:qvalue>0.0859</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="33631586" stop="33631576" score="15.9577" pvalue="2.61e-06">
<sequence>AGGGCGTGGCC</sequence>
<mem:qvalue>0.0155</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="36976719" stop="36976709" score="12.0563" pvalue="4.02e-05">
<sequence>AGGGTGGGACT</sequence>
<mem:qvalue>0.0594</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="36977418" stop="36977408" score="12.3521" pvalue="3.32e-05">
<sequence>TGGGTGTGGAG</sequence>
<mem:qvalue>0.0542</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="59010734" stop="59010724" score="12.5775" pvalue="2.84e-05">
<sequence>TGGGCGTAGCC</sequence>
<mem:qvalue>0.0491</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="60400035" stop="60400045" score="12.2535" pvalue="3.62e-05">
<sequence>AGGGTGGGACC</sequence>
<mem:qvalue>0.056</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="75175994" stop="75175984" score="11.338" pvalue="5.83e-05">
<sequence>GGGGTGTGTCT</sequence>
<mem:qvalue>0.0739</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="77295348" stop="77295338" score="13.7746" pvalue="1.24e-05">
<sequence>AGGGTGTGACC</sequence>
<mem:qvalue>0.0291</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="82634159" stop="82634149" score="14.1127" pvalue="1.02e-05">
<sequence>AGGGTGTGTCC</sequence>
<mem:qvalue>0.0271</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="88209139" stop="88209129" score="14.8873" pvalue="5.61e-06">
<sequence>AGGGTGTGGTG</sequence>
<mem:qvalue>0.0209</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="92186215" stop="92186205" score="13.4366" pvalue="1.7e-05">
<sequence>AGGGTGTGGGC</sequence>
<mem:qvalue>0.0343</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="133344119" stop="133344129" score="17.2113" pvalue="4.22e-07">
<sequence>AGGGTGTGGCC</sequence>
<mem:qvalue>0.0103</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="134264634" stop="134264624" score="10.7324" pvalue="7.79e-05">
<sequence>TGGGTGGGGGA</sequence>
<mem:qvalue>0.0865</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="134980075" stop="134980065" score="15.5634" pvalue="4.07e-06">
<sequence>TGGGTGGGGCT</sequence>
<mem:qvalue>0.0186</mem:qvalue>
</matched-element>
<matched-element start="134980015" stop="134980025" score="10.7887" pvalue="7.66e-05">
<sequence>AGGGCGGAGCT</sequence>
<mem:qvalue>0.0859</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="135694132" stop="135694142" score="15.6901" pvalue="3.86e-06">
<sequence>AGGGTGGGGCC</sequence>
<mem:qvalue>0.0186</mem:qvalue>
</matched-element>
<matched-element start="135693988" stop="135693978" score="14.4366" pvalue="8.95e-06">
<sequence>AGGGTGGGGCA</sequence>
<mem:qvalue>0.0263</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="135847255" stop="135847245" score="17.2817" pvalue="2.11e-07">
<sequence>TGGGTGTGGCC</sequence>
<mem:qvalue>0.00972</mem:qvalue>
</matched-element>
<matched-element start="135847132" stop="135847142" score="14.1127" pvalue="1.02e-05">
<sequence>AGGGTGTGTCC</sequence>
<mem:qvalue>0.0271</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="136638702" stop="136638692" score="17.2113" pvalue="4.22e-07">
<sequence>AGGGTGTGGCC</sequence>
<mem:qvalue>0.0103</mem:qvalue>
</matched-element>
<matched-element start="136638946" stop="136638956" score="10.7324" pvalue="7.79e-05">
<sequence>TGGGCGGGGGC</sequence>
<mem:qvalue>0.0865</mem:qvalue>
</matched-element>
<matched-element start="136638682" stop="136638672" score="10.662" pvalue="7.96e-05">
<sequence>AGGGTGGGGGA</sequence>
<mem:qvalue>0.0872</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="137838388" stop="137838398" score="17.0845" pvalue="6.43e-07">
<sequence>TGGGTGTGGCT</sequence>
<mem:qvalue>0.0103</mem:qvalue>
</matched-element>
<matched-element start="137838465" stop="137838455" score="12.3239" pvalue="3.38e-05">
<sequence>AGGGCGTGACT</sequence>
<mem:qvalue>0.0545</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="155596817" stop="155596827" score="14.3944" pvalue="9.16e-06">
<sequence>TGGGTGGGGCG</sequence>
<mem:qvalue>0.0266</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="156887430" stop="156887420" score="16.3239" pvalue="1.09e-06">
<sequence>TGGGTGTGGTC</sequence>
<mem:qvalue>0.0109</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="157124024" stop="157124014" score="11.0563" pvalue="6.91e-05">
<sequence>CGGGCGTGGCC</sequence>
<mem:qvalue>0.0826</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="157198864" stop="157198874" score="13.6761" pvalue="1.35e-05">
<sequence>GGGGTGTGGTC</sequence>
<mem:qvalue>0.0306</mem:qvalue>
</matched-element>
<matched-element start="157198853" stop="157198863" score="11.662" pvalue="4.73e-05">
<sequence>GGGGCGGGGCT</sequence>
<mem:qvalue>0.0638</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="169314434" stop="169314424" score="15.9577" pvalue="2.61e-06">
<sequence>AGGGTGTGGCA</sequence>
<mem:qvalue>0.0155</mem:qvalue>
</matched-element>
<matched-element start="169314414" stop="169314404" score="13.5211" pvalue="1.55e-05">
<sequence>TGGGTGTGGAT</sequence>
<mem:qvalue>0.0329</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="169323165" stop="169323155" score="14.4366" pvalue="8.95e-06">
<sequence>AGGGTGGGGCA</sequence>
<mem:qvalue>0.0263</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="170140905" stop="170140915" score="11.7887" pvalue="4.45e-05">
<sequence>TGGGTGGGGGT</sequence>
<mem:qvalue>0.0628</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="173211174" stop="173211164" score="16.0282" pvalue="2.19e-06">
<sequence>TGGGCGTGGCC</sequence>
<mem:qvalue>0.0139</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="173447997" stop="173447987" score="11.2958" pvalue="5.98e-05">
<sequence>TGGGAGTGGCT</sequence>
<mem:qvalue>0.0753</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="183078970" stop="183078960" score="13.8451" pvalue="1.15e-05">
<sequence>TGGGTGTGCCT</sequence>
<mem:qvalue>0.0281</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
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<sequence>TGGGTGTGGCT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="196502201" stop="196502191" score="14.9577" pvalue="5.39e-06">
<sequence>TGGGTGTGGTG</sequence>
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</matched-element>
<matched-element start="196502020" stop="196502030" score="14.0423" pvalue="1.04e-05">
<sequence>TGGGTGTGCCC</sequence>
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</matched-element>
<matched-element start="196502251" stop="196502261" score="10.8732" pvalue="7.43e-05">
<sequence>GGGGTGTGGAT</sequence>
<mem:qvalue>0.0859</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="5220509" stop="5220519" score="13.5211" pvalue="1.55e-05">
<sequence>TGGGTGTGGAT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="24832582" stop="24832592" score="14.8028" pvalue="6.26e-06">
<sequence>AGGGCGTGGTT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="25743057" stop="25743067" score="17.2817" pvalue="2.11e-07">
<sequence>TGGGTGTGGCC</sequence>
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</matched-element>
<matched-element start="25742975" stop="25742985" score="16.0282" pvalue="2.19e-06">
<sequence>TGGGTGTGGCA</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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<sequence>TGGGTGTGGGT</sequence>
<mem:qvalue>0.0357</mem:qvalue>
</matched-element>
<matched-element start="25869333" stop="25869343" score="11.6901" pvalue="4.69e-05">
<sequence>AGGGTGAGGCC</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="28463192" stop="28463182" score="14.9577" pvalue="5.39e-06">
<sequence>TGGGTGTGGTG</sequence>
<mem:qvalue>0.0209</mem:qvalue>
</matched-element>
<matched-element start="28463171" stop="28463181" score="14.507" pvalue="8.34e-06">
<sequence>TGGGCGGGGCC</sequence>
<mem:qvalue>0.0263</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="31940985" stop="31940995" score="13.9718" pvalue="1.09e-05">
<sequence>AGGGTGTGCCC</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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<sequence>TGGGTGTGCCT</sequence>
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</matched-element>
<matched-element start="72859376" stop="72859366" score="12.9155" pvalue="2.19e-05">
<sequence>GGGGTGGGGCT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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<sequence>AGGGTGTGGTC</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="78556484" stop="78556474" score="10.662" pvalue="7.96e-05">
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</matched-element>
<matched-element start="78556478" stop="78556468" score="10.6056" pvalue="8.11e-05">
<sequence>GGGGCGGGGCA</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="84682302" stop="84682292" score="11.8592" pvalue="4.34e-05">
<sequence>GGGGTGGGGCA</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="84852513" stop="84852523" score="10.9296" pvalue="7.22e-05">
<sequence>AGGGCGTGGGA</sequence>
<mem:qvalue>0.0852</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="93306685" stop="93306695" score="14.4366" pvalue="8.95e-06">
<sequence>AGGGCGGGGCC</sequence>
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</matched-element>
<matched-element start="93306914" stop="93306924" score="12.0704" pvalue="3.97e-05">
<sequence>AGGGTGTGGGG</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="103324496" stop="103324506" score="16.2535" pvalue="1.31e-06">
<sequence>AGGGTGTGGTC</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="103797993" stop="103797983" score="14.507" pvalue="8.34e-06">
<sequence>TGGGTGGGGCA</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="103962283" stop="103962293" score="14.9577" pvalue="5.39e-06">
<sequence>TGGGTGTGGTG</sequence>
<mem:qvalue>0.0209</mem:qvalue>
</matched-element>
<matched-element start="103962073" stop="103962063" score="11.8592" pvalue="4.34e-05">
<sequence>GGGGTGGGGCA</sequence>
<mem:qvalue>0.0616</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="112350433" stop="112350443" score="11.9859" pvalue="4.12e-05">
<sequence>AGGGCGTGGGT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="121964041" stop="121964051" score="15.7606" pvalue="3.66e-06">
<sequence>TGGGTGGGGCC</sequence>
<mem:qvalue>0.0186</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="122090875" stop="122090865" score="12.6197" pvalue="2.66e-05">
<sequence>AGGGTGTGATT</sequence>
<mem:qvalue>0.0463</mem:qvalue>
</matched-element>
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