<?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 xstreme_example_output_files/fimo_out_1 --bgfile xstreme_example_output_files/background --motif 2-GCTGAGTCATN 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="2-GCTGAGTCATN" name="STREME-2">
<scanned-sequence accession="16" name="16">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="161346779" stop="161346789" score="12.7439" pvalue="1.67e-05">
<sequence>GGTGACTCATA</sequence>
<mem:qvalue>0.0346</mem:qvalue>
</matched-element>
<matched-element start="161346789" stop="161346779" score="10" pvalue="5.38e-05">
<sequence>TATGAGTCACC</sequence>
<mem:qvalue>0.0688</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="5" name="5">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
<matched-element start="37011460" stop="37011470" score="8.36585" pvalue="9.78e-05">
<sequence>TCTTAGTCATC</sequence>
<mem:qvalue>0.104</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="7" name="7">
<matched-element start="107724368" stop="107724358" score="12.561" pvalue="1.81e-05">
<sequence>GATGACTCACA</sequence>
<mem:qvalue>0.0363</mem:qvalue>
</matched-element>
<matched-element start="107724358" stop="107724368" score="10.1829" pvalue="4.97e-05">
<sequence>TGTGAGTCATC</sequence>
<mem:qvalue>0.0646</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="4" name="4">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
<matched-element start="27281814" stop="27281804" score="16.2317" pvalue="3.38e-06">
<sequence>GATGAGTCATT</sequence>
<mem:qvalue>0.0152</mem:qvalue>
</matched-element>
<matched-element start="27281804" stop="27281814" score="9.39024" pvalue="6.52e-05">
<sequence>AATGACTCATC</sequence>
<mem:qvalue>0.078</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="2" name="2">
<matched-element start="202223393" stop="202223383" score="11.7927" pvalue="2.57e-05">
<sequence>TATGAGTCATT</sequence>
<mem:qvalue>0.0423</mem:qvalue>
</matched-element>
<matched-element start="202223383" stop="202223393" score="9.30488" pvalue="6.77e-05">
<sequence>AATGACTCATA</sequence>
<mem:qvalue>0.0786</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="15" name="15">
</scanned-sequence>
<scanned-sequence accession="8" name="8">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
<matched-element start="71039616" stop="71039626" score="12.2195" pvalue="2.16e-05">
<sequence>GATGACTCACT</sequence>
<mem:qvalue>0.0397</mem:qvalue>
</matched-element>
<matched-element start="71039626" stop="71039616" score="9.14634" pvalue="7.31e-05">
<sequence>AGTGAGTCATC</sequence>
<mem:qvalue>0.0833</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="14" name="14">
<matched-element start="103603312" stop="103603302" score="18.7561" pvalue="2.49e-07">
<sequence>GCTGAGTCATG</sequence>
<mem:qvalue>0.00705</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="110444343" stop="110444333" score="10.7561" pvalue="4.15e-05">
<sequence>GCTGTGTCACA</sequence>
<mem:qvalue>0.057</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="4" name="4">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="44992396" stop="44992386" score="13.5122" pvalue="1.26e-05">
<sequence>GATGAGTCAGA</sequence>
<mem:qvalue>0.0284</mem:qvalue>
</matched-element>
<matched-element start="44992386" stop="44992396" score="12.3902" pvalue="2e-05">
<sequence>TCTGACTCATC</sequence>
<mem:qvalue>0.0378</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="7" name="7">
<matched-element start="101546128" stop="101546138" score="12.3171" pvalue="2.09e-05">
<sequence>GGTGAGTCACA</sequence>
<mem:qvalue>0.0392</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="13" name="13">
<matched-element start="52123199" stop="52123209" score="14.439" pvalue="7.53e-06">
<sequence>GATGACTCATT</sequence>
<mem:qvalue>0.0224</mem:qvalue>
</matched-element>
<matched-element start="52123209" stop="52123199" score="11.1829" pvalue="3.37e-05">
<sequence>AATGAGTCATC</sequence>
<mem:qvalue>0.0498</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="10" name="10">
<matched-element start="134498465" stop="134498475" score="11.5366" pvalue="2.82e-05">
<sequence>TCTGAGTCACT</sequence>
<mem:qvalue>0.0446</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="15" name="15">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
</scanned-sequence>
<scanned-sequence accession="X" name="X">
</scanned-sequence>
<scanned-sequence accession="19" name="19">
</scanned-sequence>
<scanned-sequence accession="11" name="11">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
<matched-element start="116798674" stop="116798684" score="14.2805" pvalue="8.32e-06">
<sequence>GTTGAGTCATG</sequence>
<mem:qvalue>0.0235</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="20" name="20">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="2" name="2">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
<matched-element start="83409943" stop="83409933" score="14.5244" pvalue="7.12e-06">
<sequence>GCTGACTCACA</sequence>
<mem:qvalue>0.0221</mem:qvalue>
</matched-element>
<matched-element start="83409975" stop="83409985" score="8.69512" pvalue="8.77e-05">
<sequence>CCTGACTCACT</sequence>
<mem:qvalue>0.0953</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="17" name="17">
<matched-element start="75830557" stop="75830547" score="14.0122" pvalue="1e-05">
<sequence>GATGAGTCACT</sequence>
<mem:qvalue>0.0267</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="2" name="2">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
<matched-element start="34191696" stop="34191706" score="10.8293" pvalue="4.03e-05">
<sequence>CCTGAGTCACA</sequence>
<mem:qvalue>0.0555</mem:qvalue>
</matched-element>
<matched-element start="34191729" stop="34191719" score="9.2561" pvalue="7.02e-05">
<sequence>CCTGACTCACG</sequence>
<mem:qvalue>0.0807</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="11" name="11">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="202777029" stop="202777019" score="12.5366" pvalue="1.84e-05">
<sequence>GGTGAGTCACG</sequence>
<mem:qvalue>0.0368</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="16" name="16">
</scanned-sequence>
<scanned-sequence accession="11" name="11">
</scanned-sequence>
<scanned-sequence accession="5" name="5">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
<matched-element start="110871002" stop="110871012" score="18.622" pvalue="4.98e-07">
<sequence>GCTGAGTCATC</sequence>
<mem:qvalue>0.00705</mem:qvalue>
</matched-element>
<matched-element start="110871012" stop="110871002" score="11.8049" pvalue="2.56e-05">
<sequence>GATGACTCAGC</sequence>
<mem:qvalue>0.0423</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="10" name="10">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
<matched-element start="28076917" stop="28076927" score="14.7561" pvalue="5.55e-06">
<sequence>GGTGAGTCATG</sequence>
<mem:qvalue>0.0189</mem:qvalue>
</matched-element>
<matched-element start="28076880" stop="28076870" score="12.7073" pvalue="1.72e-05">
<sequence>CCTGAGTCATT</sequence>
<mem:qvalue>0.0353</mem:qvalue>
</matched-element>
<matched-element start="28076855" stop="28076845" score="11.0854" pvalue="3.61e-05">
<sequence>CATGAGTCATA</sequence>
<mem:qvalue>0.0519</mem:qvalue>
</matched-element>
<matched-element start="28076845" stop="28076855" score="10.561" pvalue="4.49e-05">
<sequence>TATGACTCATG</sequence>
<mem:qvalue>0.0603</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="9" name="9">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="13" name="13">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
<matched-element start="60039234" stop="60039244" score="14.0976" pvalue="9.52e-06">
<sequence>TCTGAGTCATA</sequence>
<mem:qvalue>0.0261</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="22" name="22">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
<matched-element start="75091880" stop="75091890" score="12.2195" pvalue="2.16e-05">
<sequence>GATGACTCACT</sequence>
<mem:qvalue>0.0397</mem:qvalue>
</matched-element>
<matched-element start="75091890" stop="75091880" score="9.14634" pvalue="7.31e-05">
<sequence>AGTGAGTCATC</sequence>
<mem:qvalue>0.0833</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="31229439" stop="31229449" score="10.9146" pvalue="3.92e-05">
<sequence>CCTGAGTCACC</sequence>
<mem:qvalue>0.0548</mem:qvalue>
</matched-element>
<matched-element start="31229449" stop="31229439" score="9.90244" pvalue="5.53e-05">
<sequence>GGTGACTCAGG</sequence>
<mem:qvalue>0.07</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="16" name="16">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
<matched-element start="73498819" stop="73498809" score="16.7927" pvalue="1.59e-06">
<sequence>GATGAGTCATG</sequence>
<mem:qvalue>0.0103</mem:qvalue>
</matched-element>
<matched-element start="73498809" stop="73498819" score="9.37805" pvalue="6.55e-05">
<sequence>CATGACTCATC</sequence>
<mem:qvalue>0.078</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="17" name="17">
<matched-element start="66086042" stop="66086052" score="14.7805" pvalue="5.3e-06">
<sequence>GATGACTCATA</sequence>
<mem:qvalue>0.0189</mem:qvalue>
</matched-element>
<matched-element start="66086052" stop="66086042" score="12.2195" pvalue="2.16e-05">
<sequence>TATGAGTCATC</sequence>
<mem:qvalue>0.0397</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
<matched-element start="38369000" stop="38369010" score="18.1951" pvalue="8.95e-07">
<sequence>GCTGAGTCATT</sequence>
<mem:qvalue>0.0078</mem:qvalue>
</matched-element>
<matched-element start="38369046" stop="38369036" score="11.7683" pvalue="2.61e-05">
<sequence>GCTGACTCAAC</sequence>
<mem:qvalue>0.0427</mem:qvalue>
</matched-element>
<matched-element start="38369036" stop="38369046" score="11.0854" pvalue="3.61e-05">
<sequence>GTTGAGTCAGC</sequence>
<mem:qvalue>0.0519</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="17" name="17">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
</scanned-sequence>
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</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="13" name="13">
</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="19" name="19">
<matched-element start="35880296" stop="35880306" score="14.2805" pvalue="8.32e-06">
<sequence>GTTGAGTCATG</sequence>
<mem:qvalue>0.0235</mem:qvalue>
</matched-element>
<matched-element start="35880303" stop="35880313" score="11.3049" pvalue="3.14e-05">
<sequence>CATGAGTCATG</sequence>
<mem:qvalue>0.0481</mem:qvalue>
</matched-element>
<matched-element start="35880313" stop="35880303" score="9.5122" pvalue="6.28e-05">
<sequence>CATGACTCATG</sequence>
<mem:qvalue>0.0762</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="11" name="11">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="228122418" stop="228122428" score="10.8293" pvalue="4.03e-05">
<sequence>CCTGAGTCACA</sequence>
<mem:qvalue>0.0555</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="9" name="9">
</scanned-sequence>
<scanned-sequence accession="19" name="19">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
<matched-element start="74926285" stop="74926295" score="18.7561" pvalue="2.49e-07">
<sequence>GCTGAGTCATG</sequence>
<mem:qvalue>0.00705</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="9" name="9">
<matched-element start="36148672" stop="36148682" score="13.5122" pvalue="1.26e-05">
<sequence>GATGAGTCAGA</sequence>
<mem:qvalue>0.0284</mem:qvalue>
</matched-element>
<matched-element start="36148682" stop="36148672" score="12.3902" pvalue="2e-05">
<sequence>TCTGACTCATC</sequence>
<mem:qvalue>0.0378</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="22" name="22">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
</scanned-sequence>
<scanned-sequence accession="5" name="5">
<matched-element start="67715431" stop="67715421" score="15.561" pvalue="4.25e-06">
<sequence>GCTGAGTCAGC</sequence>
<mem:qvalue>0.0166</mem:qvalue>
</matched-element>
<matched-element start="67715421" stop="67715431" score="13.7683" pvalue="1.07e-05">
<sequence>GCTGACTCAGC</sequence>
<mem:qvalue>0.0274</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="2" name="2">
</scanned-sequence>
<scanned-sequence accession="5" name="5">
<matched-element start="39158243" stop="39158233" score="11.4878" pvalue="2.9e-05">
<sequence>ACTGACTCATG</sequence>
<mem:qvalue>0.0454</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="19" name="19">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
</scanned-sequence>
<scanned-sequence accession="12" name="12">
</scanned-sequence>
<scanned-sequence accession="20" name="20">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
</scanned-sequence>
<scanned-sequence accession="5" name="5">
<matched-element start="56467688" stop="56467678" score="10.7439" pvalue="4.2e-05">
<sequence>GGTGACTCACG</sequence>
<mem:qvalue>0.0574</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="1" name="1">
<matched-element start="111019766" stop="111019756" score="12.7195" pvalue="1.7e-05">
<sequence>ACTGAGTCATT</sequence>
<mem:qvalue>0.0351</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="10" name="10">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="17" name="17">
<matched-element start="78806868" stop="78806858" score="14.0122" pvalue="1e-05">
<sequence>GATGAGTCACT</sequence>
<mem:qvalue>0.0267</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="16" name="16">
</scanned-sequence>
<scanned-sequence accession="17" name="17">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="1" name="1">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
<matched-element start="126964804" stop="126964794" score="15.9756" pvalue="3.63e-06">
<sequence>GCTGAGTCACT</sequence>
<mem:qvalue>0.0154</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="15" name="15">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="2" name="2">
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</scanned-sequence>
<scanned-sequence accession="11" name="11">
</scanned-sequence>
<scanned-sequence accession="2" name="2">
</scanned-sequence>
<scanned-sequence accession="9" name="9">
</scanned-sequence>
<scanned-sequence accession="19" name="19">
</scanned-sequence>
<scanned-sequence accession="10" name="10">
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="16" name="16">
</scanned-sequence>
<scanned-sequence accession="7" name="7">
<matched-element start="100828441" stop="100828451" score="14.7561" pvalue="5.55e-06">
<sequence>GGTGAGTCATG</sequence>
<mem:qvalue>0.0189</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="4" name="4">
</scanned-sequence>
<scanned-sequence accession="3" name="3">
</scanned-sequence>
<scanned-sequence accession="22" name="22">
</scanned-sequence>
<scanned-sequence accession="16" name="16">
<matched-element start="76980763" stop="76980773" score="18.5366" pvalue="6.96e-07">
<sequence>GCTGAGTCATA</sequence>
<mem:qvalue>0.00705</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="6" name="6">
</scanned-sequence>
<scanned-sequence accession="14" name="14">
</scanned-sequence>
<scanned-sequence accession="11" name="11">
</scanned-sequence>
<scanned-sequence accession="4" name="4">
</scanned-sequence>
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