<?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_5 --bgfile memechip_example_output_files/background --motif MA1063.1 JASPAR2018_CORE_non-redundant.meme memechip_example_output_files/Klf1.fna</command-line>
<pattern-file>JASPAR2018_CORE_non-redundant.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="MA1063.1" name="TCP19">
<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>
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</scanned-sequence>
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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="59010859" stop="59010850" score="12.5484" pvalue="1.75e-05">
<sequence>TGGGGTCCAC</sequence>
<mem:qvalue>0.405</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
<matched-element start="60400047" stop="60400038" score="12.3226" pvalue="2.16e-05">
<sequence>CGGGTCCCAC</sequence>
<mem:qvalue>0.405</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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<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="133344041" stop="133344050" score="10.8387" pvalue="8.06e-05">
<sequence>TTGGGCCCAG</sequence>
<mem:qvalue>0.517</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="135694144" stop="135694135" score="14.5968" pvalue="1.65e-06">
<sequence>TGGGCCCCAC</sequence>
<mem:qvalue>0.213</mem:qvalue>
</matched-element>
<matched-element start="135694136" stop="135694145" score="11.7258" pvalue="3.93e-05">
<sequence>TGGGGCCCAT</sequence>
<mem:qvalue>0.405</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="136638716" stop="136638707" score="11.7258" pvalue="3.93e-05">
<sequence>TGGGGCCCAT</sequence>
<mem:qvalue>0.405</mem:qvalue>
</matched-element>
<matched-element start="136638708" stop="136638717" score="11.6613" pvalue="4.18e-05">
<sequence>TGGGCCCCAG</sequence>
<mem:qvalue>0.405</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr1" name="chr1">
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<scanned-sequence accession="chr1" name="chr1">
<matched-element start="169314572" stop="169314581" score="11" pvalue="7.3e-05">
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</scanned-sequence>
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<scanned-sequence accession="chr2" name="chr2">
<matched-element start="28463175" stop="28463184" score="14.1774" pvalue="2.43e-06">
<sequence>CGGGGCCCAC</sequence>
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<matched-element start="28463183" stop="28463174" score="11.9516" pvalue="3.34e-05">
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<sequence>TGTGCCCCAC</sequence>
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<scanned-sequence accession="chr2" name="chr2">
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</matched-element>
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<matched-element start="72859207" stop="72859198" score="11.0484" pvalue="6.87e-05">
<sequence>CAGGACCCAC</sequence>
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<sequence>TGGGGCCCAC</sequence>
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</matched-element>
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<sequence>TGGGCCCCAT</sequence>
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<sequence>GGGGCCCCAC</sequence>
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<sequence>TGGGGCCCAG</sequence>
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</matched-element>
<matched-element start="153395071" stop="153395080" score="11.6613" pvalue="4.18e-05">
<sequence>TGGGCCCCAG</sequence>
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<matched-element start="164599648" stop="164599657" score="10.8226" pvalue="8.32e-05">
<sequence>CGGGCACCAC</sequence>
<mem:qvalue>0.518</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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<sequence>GGGGACCCAC</sequence>
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</matched-element>
</scanned-sequence>
<scanned-sequence accession="chr2" name="chr2">
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