<?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
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  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 xstreme_example_output_files/fimo_out_5 --bgfile xstreme_example_output_files/background --motif 3-GCGCATGCGCAC xstreme_example_output_files/streme_out/streme.xml nrmix.nseqs.100.100bp.seed.1.fa</command-line>
<pattern-file>xstreme_example_output_files/streme_out/streme.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="3-GCGCATGCGCAC" name="STREME-3">
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</scanned-sequence>
<scanned-sequence accession="1" name="1">
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</scanned-sequence>
<scanned-sequence accession="1" name="1">
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<scanned-sequence accession="1" name="1">
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<scanned-sequence accession="3" name="3">
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</scanned-sequence>
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<scanned-sequence accession="8" name="8">
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<scanned-sequence accession="12" name="12">
</scanned-sequence>
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<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="4" name="4">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
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<scanned-sequence accession="7" name="7">
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<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">
<matched-element start="124457562" stop="124457551" score="17.1196" pvalue="1.02e-06">
<sequence>GCGCGTGCGCAC</sequence>
<mem:qvalue>0.0135</mem:qvalue>
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<matched-element start="124457592" stop="124457603" score="9.13043" pvalue="8.96e-05">
<sequence>GAGCGCGCGCGC</sequence>
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<matched-element start="124457564" stop="124457553" score="9.05435" pvalue="9.42e-05">
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</scanned-sequence>
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<matched-element start="1510391" stop="1510402" score="10.4239" pvalue="5.3e-05">
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