<?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="MA0531.1" name="MA0531.1">
<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 accession="chr1" name="chr1">
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<scanned-sequence accession="chr1" name="chr1">
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<scanned-sequence accession="chr1" name="chr1">
<matched-element start="60399998" stop="60400012" score="10.3276" pvalue="8.18e-05">
<sequence>CGGACTGGTGTCGCA</sequence>
<mem:qvalue>0.795</mem:qvalue>
</matched-element>
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<scanned-sequence accession="chr1" name="chr1">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
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<scanned-sequence accession="chr1" name="chr1">
<matched-element start="77295214" stop="77295200" score="10.4655" pvalue="7.65e-05">
<sequence>CAGCTAGATGGCTTA</sequence>
<mem:qvalue>0.795</mem:qvalue>
</matched-element>
</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">
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="134264331" stop="134264345" score="11.1034" pvalue="5.52e-05">
<sequence>TCAGCAGAGGGAGCC</sequence>
<mem:qvalue>0.789</mem:qvalue>
</matched-element>
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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">
<matched-element start="170140667" stop="170140653" score="10.3621" pvalue="8.04e-05">
<sequence>TAGATGGATGGAGCT</sequence>
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<matched-element start="25148582" stop="25148568" score="15.931" pvalue="2.17e-06">
<sequence>CCACTAGGGGGCGCA</sequence>
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</matched-element>
<matched-element start="25148382" stop="25148396" score="14" pvalue="9.56e-06">
<sequence>GCTCCAGATGGAGCC</sequence>
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