<?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>cbust</program-name>
	<parameters>
		<sequence-file>Your_seqs.fa</sequence-file>
		<pattern-file>Your_mats.fa</pattern-file>
		<expected-gap>1</expected-gap>
		<bg-range>100</bg-range>
		<pseudocounts>0.375</pseudocounts>
		<cluster-score-cutoff>5</cluster-score-cutoff>
		<matrix-score-cutoff>4</matrix-score-cutoff>
	</parameters>
	<pattern accession="M00196" name="SRF" >
		<scanned-sequence accession="X12345" name="Your favorite gene" length="1101">
			<matched-element start="526" stop="538" score="5.02" cluster_id="1"><sequence>ggagggagggagc</sequence></matched-element>
		</scanned-sequence>
		<scanned-sequence accession="X54321" name="Your other favorite gene" length="1101">
			<matched-element start="545" stop="557" score="6.88" cluster_id="1"><sequence>aaggggaggggac</sequence></matched-element>
			<matched-element start="140" stop="152" score="7.61" cluster_id="2"><sequence>agggggcgggaga</sequence></matched-element>
		</scanned-sequence>
	</pattern>
	<pattern accession="M00807" name="CREB" >
		<scanned-sequence accession="X12345" name="Your favorite gene" length="1101">
			<matched-element start="527" stop="537" score="4.39" cluster_id="1"><sequence>gagggagggag</sequence></matched-element>
			<matched-element start="531" stop="541" score="5.31" cluster_id="1"><sequence>gagggagcgag</sequence></matched-element>
			<matched-element start="539" stop="549" score="5.55" cluster_id="1"><sequence>gagggagcaac</sequence></matched-element>
		</scanned-sequence>
		<scanned-sequence accession="X54321" name="Your other favorite gene" length="1101">
			<matched-element start="528" stop="538" score="5.6" cluster_id="1"><sequence>gcggggggaag</sequence></matched-element>
			<matched-element start="550" stop="560" score="4.92" cluster_id="1"><sequence>gaggggacaag</sequence></matched-element>
			<matched-element start="141" stop="151" score="4.37" cluster_id="2"><sequence>gggggcgggag</sequence></matched-element>
		</scanned-sequence>
	</pattern>
</cis-element-search>
