<?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>motiph</program-name>
<parameters>
<command-line>motiph -oc motiph_example_output_files --seed 0 --bg 2 --pseudocount 0.01 spiked.aln yeast.tree MCM1.meme.html</command-line>
<pattern-file>MCM1.meme.html</pattern-file>
<sequence-file>clustal-w alignment</sequence-file>
<site-pvalue-cutoff>0.0001</site-pvalue-cutoff>
<sequence-filtering on-off="off"/>
</parameters>
<pattern accession="+1" name="+1">
<scanned-sequence accession="spiked.aln" name="spiked.aln" length="3144">
<matched-element start="121" stop="133" score="12214" pvalue="8.14e-18">
<sequence>TTTCCTAAATGGG</sequence>
<mem:qvalue>6.15e-15</mem:qvalue>
</matched-element>
<matched-element start="2124" stop="2136" score="11530" pvalue="2.48e-08">
<sequence>TAACCTCTTTGGG</sequence>
<mem:qvalue>9.37e-06</mem:qvalue>
</matched-element>
<matched-element start="1915" stop="1927" score="10939" pvalue="6.84e-06">
<sequence>GAGCCCGTTTAGG</sequence>
<mem:qvalue>0.00172</mem:qvalue>
</matched-element>
<matched-element start="1977" stop="1989" score="10836" pvalue="1.47e-05">
<sequence>CGACCGAATCAGG</sequence>
<mem:qvalue>0.00278</mem:qvalue>
</matched-element>
<matched-element start="2222" stop="2234" score="10715" pvalue="3.37e-05">
<sequence>TTTGCCAATTTAG</sequence>
<mem:qvalue>0.00435</mem:qvalue>
</matched-element>
<matched-element start="122" stop="134" score="10711" pvalue="3.46e-05">
<sequence>TTCCTAAATGGGT</sequence>
<mem:qvalue>0.00435</mem:qvalue>
</matched-element>
<matched-element start="2223" stop="2235" score="10594" pvalue="7.32e-05">
<sequence>TTGCCAATTTAGC</sequence>
<mem:qvalue>0.00729</mem:qvalue>
</matched-element>
<matched-element start="1948" stop="1960" score="10571" pvalue="8.42e-05">
<sequence>TAATCAAAAAAGG</sequence>
<mem:qvalue>0.00729</mem:qvalue>
</matched-element>
<matched-element start="2104" stop="2116" score="10566" pvalue="8.68e-05">
<sequence>TTTGCTCTTAATG</sequence>
<mem:qvalue>0.00729</mem:qvalue>
</matched-element>
</scanned-sequence>
<mem:has-qvalues>yes</mem:has-qvalues>
</pattern>
<pattern accession="-1" name="-1">
<scanned-sequence accession="spiked.aln" name="spiked.aln" length="3144">
<matched-element start="1930" stop="1918" score="12150" pvalue="8.37e-15">
<sequence>CCCGTTTAGGAAA</sequence>
<mem:qvalue>5.98e-12</mem:qvalue>
</matched-element>
<matched-element start="136" stop="124" score="11961" pvalue="3.04e-11">
<sequence>CCTAAATGGGTAA</sequence>
<mem:qvalue>1.09e-08</mem:qvalue>
</matched-element>
<matched-element start="2139" stop="2127" score="11792" pvalue="6.5e-10">
<sequence>CCTCTTTGGGGAA</sequence>
<mem:qvalue>1.55e-07</mem:qvalue>
</matched-element>
<matched-element start="2140" stop="2128" score="11745" pvalue="1.4e-09">
<sequence>CTCTTTGGGGAAA</sequence>
<mem:qvalue>2.5e-07</mem:qvalue>
</matched-element>
<matched-element start="1992" stop="1980" score="11635" pvalue="6.63e-09">
<sequence>CCGAATCAGGAAA</sequence>
<mem:qvalue>9.47e-07</mem:qvalue>
</matched-element>
<matched-element start="2120" stop="2108" score="11028" pvalue="3.42e-06">
<sequence>CTCTTAATGGAAA</sequence>
<mem:qvalue>0.000407</mem:qvalue>
</matched-element>
<matched-element start="2051" stop="2039" score="10769" pvalue="2.34e-05">
<sequence>CCTCGAGGAAATA</sequence>
<mem:qvalue>0.00209</mem:qvalue>
</matched-element>
<matched-element start="2314" stop="2302" score="10769" pvalue="2.34e-05">
<sequence>CCTCAAGAAGTAA</sequence>
<mem:qvalue>0.00209</mem:qvalue>
</matched-element>
<matched-element start="1887" stop="1875" score="10670" pvalue="4.52e-05">
<sequence>CCAAATGCGGGTA</sequence>
<mem:qvalue>0.00359</mem:qvalue>
</matched-element>
<matched-element start="137" stop="125" score="10637" pvalue="5.59e-05">
<sequence>CTAAATGGGTAAA</sequence>
<mem:qvalue>0.00399</mem:qvalue>
</matched-element>
<matched-element start="135" stop="123" score="10609" pvalue="6.67e-05">
<sequence>TCCTAAATGGGTA</sequence>
<mem:qvalue>0.00433</mem:qvalue>
</matched-element>
</scanned-sequence>
<mem:has-qvalues>yes</mem:has-qvalues>
</pattern>
</cis-element-search>
