<?xml version="1.0"?>
<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"
>
	<program-name>Your Favorite Program</program-name>
	<parameters>
		<pattern-file>patterns.txt</pattern-file>
		<sequence-file>sequence.txt</sequence-file>
		<background-seq-file>bg.sequences.txt</background-seq-file>
		<sequence-pvalue-cutoff>0.01</sequence-pvalue-cutoff>
		<site-pvalue-cutoff>0.001</site-pvalue-cutoff>
		<sequence-filtering type="repeat masker" on-off="on"/>
	</parameters>
	<pattern accession="M00431" name="E2F-1" db="TRANSFAC" pvalue="9.48937e-12">
		<scanned-sequence accession="W10325" name="regulator of G-protein signalling 2" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="816" stop="823" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="148" stop="141" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="596" stop="603" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="328" stop="335" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
		<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="716" stop="723" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="248" stop="241" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="796" stop="803" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="728" stop="735" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
	</pattern>
	<pattern accession="M00440" name="LSF" db="TRANSFAC" pvalue="9.98937e-11">
		<scanned-sequence accession="W10325" name="regulator of G-protein signalling 2" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="216" stop="223" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="48" stop="41" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="596" stop="603" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="928" stop="935" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
		<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="416" stop="423" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="448" stop="441" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="696" stop="703" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="228" stop="235" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
	</pattern>
	<pattern accession="M00437" name="E2F-2" db="TRANSFAC" pvalue="3.342e-5">
		<scanned-sequence accession="W10325" name="regulator of G-protein signalling 2" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="216" stop="223" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="348" stop="341" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="396" stop="403" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="128" stop="135" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
		<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="416" stop="423" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="148" stop="141" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="696" stop="703" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="128" stop="135" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
	</pattern>
	<pattern accession="M00439" name="E2F-3" db="TRANSFAC" pvalue="1.2e-9">
		<scanned-sequence accession="W10325" name="regulator of G-protein signalling 2" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="316" stop="323" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="348" stop="341" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="596" stop="603" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="228" stop="235" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
		<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88937e-09">
			<matched-element start="816" stop="823" pvalue="0.000152806"><sequence>TGTGGCGG</sequence></matched-element>
			<matched-element start="448" stop="441" pvalue="0.000187535"><sequence>CGTGGCGC</sequence></matched-element>
			<matched-element start="496" stop="503" pvalue="0.00023847"><sequence>TTTCCCCC</sequence></matched-element>
			<matched-element start="328" stop="335" pvalue="0.000252362"><sequence>TCTCGCGG</sequence></matched-element>
		</scanned-sequence>
	</pattern>
</cis-element-search>












