<?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>
	<multi-pattern-scan pvalue="11.88e-09">
		<pattern accession="M00431" name="E2F-1" db="TRANSFAC" pvalue="9.48e-12">
			<scanned-sequence accession="W10325" name="regulator of G-protein signalling" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="946" stop="953" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="278" stop="285" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="856" stop="863" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="698" stop="705" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
			<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="166" stop="173" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="498" stop="491" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="446" stop="453" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="278" stop="285" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
		</pattern>
		<pattern accession="M00440" name="LSF" db="TRANSFAC" pvalue="9.98e-11">
			<scanned-sequence accession="W10325" name="regulator of G-protein signalling" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="916" stop="923" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="248" stop="241" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="796" stop="803" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="728" stop="735" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
			<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="116" stop="123" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="448" stop="441" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="396" stop="403" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="228" stop="235" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
		</pattern>
	</multi-pattern-scan>
	<multi-pattern-scan pvalue="12.37e-19">
		<pattern accession="M00431" name="E2F-1" db="TRANSFAC" pvalue="9.37e-12">
			<scanned-sequence accession="W10325" name="regulator of G-protein signalling 2" length="1050" db="genbank" pvalue="9.97e-09">
				<matched-element start="916" stop="923" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="248" stop="241" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="796" stop="803" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="728" stop="735" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
			<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="916" stop="923" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="248" stop="241" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="796" stop="803" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="728" stop="735" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
		</pattern>
		<pattern accession="M00437" name="E2F-3" db="TRANSFAC" pvalue="3.34e-5">
			<scanned-sequence accession="W10325" name="regulator of G-protein signalling" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="116" stop="123" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="448" stop="441" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="396" stop="403" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="228" stop="235" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
			<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="1916" stop="1923" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="4248" stop="4241" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="3796" stop="3803" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="2728" stop="2735" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
		</pattern>
	</multi-pattern-scan>
	<multi-pattern-scan pvalue="5.87e-7">
		<pattern accession="M00439" name="E2F-3" db="TRANSFAC" pvalue="1.25e-9">
			<scanned-sequence accession="W10325" name="regulator of G-protein signalling" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="916" stop="923" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="248" stop="241" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="796" stop="803" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="728" stop="735" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
			<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="116" stop="123" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="448" stop="441" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="396" stop="403" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="228" stop="235" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
			</pattern>
		<pattern accession="M00437" name="E2F-2" db="TRANSFAC" pvalue="3.31e-5">
			<scanned-sequence accession="W10325" name="regulator of G-protein signalling" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="116" stop="123" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="448" stop="441" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="396" stop="403" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="228" stop="235" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
			<scanned-sequence accession="W10326" name="small inducible cytokine" length="1050" db="genbank" pvalue="9.88e-09">
				<matched-element start="916" stop="923" pvalue="0.000152806" clusterid="1"><sequence>TGTGGCGG</sequence></matched-element>
				<matched-element start="248" stop="241" pvalue="0.000187535" clusterid="1"><sequence>CGTGGCGC</sequence></matched-element>
				<matched-element start="796" stop="803" pvalue="0.00023847" clusterid="1"><sequence>TTTCCCCC</sequence></matched-element>
				<matched-element start="728" stop="735" pvalue="0.000252362" clusterid="1"><sequence>TCTCGCGG</sequence></matched-element>
			</scanned-sequence>
		</pattern>
	</multi-pattern-scan>
</cis-element-search>












