<?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>
<pattern-file>JASPAR_CORE_2014.meme</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="MA0545.1" name="MA0545.1">
<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">
</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">
</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">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="59010747" stop="59010737" score="13.4085" pvalue="1.63e-05">
<sequence>GAACAGCTGTG</sequence>
<mem:qvalue>0.306</mem:qvalue>
</matched-element>
<matched-element start="59010966" stop="59010956" score="11.8028" pvalue="5.07e-05">
<sequence>CAACAGATGTT</sequence>
<mem:qvalue>0.334</mem:qvalue>
</matched-element>
<matched-element start="59010736" stop="59010746" score="11.7606" pvalue="5.23e-05">
<sequence>GCACAGCTGTT</sequence>
<mem:qvalue>0.334</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="75176015" stop="75176025" score="11.9859" pvalue="4.6e-05">
<sequence>CACCAGCTGGC</sequence>
<mem:qvalue>0.334</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="82634219" stop="82634209" score="16.8873" pvalue="4.64e-07">
<sequence>CAACAGCTGTC</sequence>
<mem:qvalue>0.06</mem:qvalue>
</matched-element>
<matched-element start="82634208" stop="82634218" score="11.8873" pvalue="4.85e-05">
<sequence>AGACAGCTGTT</sequence>
<mem:qvalue>0.334</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">
</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="134264672" stop="134264662" score="10.5915" pvalue="9.74e-05">
<sequence>CATCAGCTGAC</sequence>
<mem:qvalue>0.411</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">
</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">
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<scanned-sequence accession="chr1" name="chr1">
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<scanned-sequence accession="chr1" name="chr1">
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<scanned-sequence accession="chr1" name="chr1">
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</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="169314684" stop="169314694" score="12.0845" pvalue="4.3e-05">
<sequence>GACCAGCTGGC</sequence>
<mem:qvalue>0.334</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">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
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<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">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="183187604" stop="183187594" score="12.4085" pvalue="3.64e-05">
<sequence>CCACAGCTGCC</sequence>
<mem:qvalue>0.329</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="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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<scanned-sequence accession="chr2" name="chr2">
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<scanned-sequence accession="chr2" name="chr2">
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<scanned-sequence accession="chr2" name="chr2">
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<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="32629471" stop="32629461" score="12.1549" pvalue="4.18e-05">
<sequence>GAGCAACTGGC</sequence>
<mem:qvalue>0.334</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">
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<scanned-sequence accession="chr2" name="chr2">
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<scanned-sequence accession="chr2" name="chr2">
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<scanned-sequence accession="chr2" name="chr2">
<matched-element start="84852757" stop="84852747" score="10.8169" pvalue="8.55e-05">
<sequence>CAGCAACTGAT</sequence>
<mem:qvalue>0.395</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
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<scanned-sequence accession="chr2" name="chr2">
<matched-element start="103324374" stop="103324364" score="11.0141" pvalue="7.64e-05">
<sequence>GAGCAGATGAC</sequence>
<mem:qvalue>0.374</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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<scanned-sequence accession="chr2" name="chr2">
<matched-element start="131039747" stop="131039737" score="12.5915" pvalue="3.11e-05">
<sequence>CAACAGATGGC</sequence>
<mem:qvalue>0.329</mem:qvalue>
</matched-element>
<matched-element start="131039939" stop="131039929" score="11.7042" pvalue="5.44e-05">
<sequence>AAGCAGTTGAC</sequence>
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</matched-element>
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</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
<matched-element start="166529341" stop="166529351" score="13.2113" pvalue="1.89e-05">
<sequence>AAGCAGCTGGC</sequence>
<mem:qvalue>0.306</mem:qvalue>
</matched-element>
</scanned-sequence>
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<scanned-sequence accession="chr2" name="chr2">
<matched-element start="172174167" stop="172174177" score="13.1549" pvalue="2.04e-05">
<sequence>CCACAGCTGTC</sequence>
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<scanned-sequence accession="chr3" name="chr3">
<matched-element start="19087407" stop="19087417" score="14.6479" pvalue="6.57e-06">
<sequence>CAACAGCTGCT</sequence>
<mem:qvalue>0.294</mem:qvalue>
</matched-element>
<matched-element start="19087418" stop="19087408" score="13.4648" pvalue="1.61e-05">
<sequence>CAGCAGCTGTT</sequence>
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</matched-element>
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<scanned-sequence accession="chr3" name="chr3">
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<sequence>AGACAGTTGAC</sequence>
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<scanned-sequence accession="chr3" name="chr3">
<matched-element start="84162733" stop="84162723" score="11.8873" pvalue="4.85e-05">
<sequence>AAACAGTTGGT</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr3" name="chr3">
</scanned-sequence>
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<matched-element start="100351363" stop="100351353" score="10.7042" pvalue="9.06e-05">
<sequence>AGGCAGCTGCC</sequence>
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</scanned-sequence>
<scanned-sequence accession="chr3" name="chr3">
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<sequence>CAACAGCTGTC</sequence>
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</matched-element>
<matched-element start="101356005" stop="101355995" score="13.0282" pvalue="2.13e-05">
<sequence>GGACAGCTGTT</sequence>
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</matched-element>
<matched-element start="101355967" stop="101355957" score="12.4507" pvalue="3.55e-05">
<sequence>CCACAGCTGGC</sequence>
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<sequence>GAACAGATGAC</sequence>
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<matched-element start="138480483" stop="138480473" score="10.5915" pvalue="9.74e-05">
<sequence>CATCAGCTGAC</sequence>
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<sequence>GAACAACTGTC</sequence>
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<sequence>GAGCAGATGTC</sequence>
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<sequence>GGGCAGCTGGC</sequence>
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</matched-element>
</scanned-sequence>
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