<?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>mcast</program-name>
<parameters>
<pattern-file>/Users/t.bailey/meme_git/meme/tests/meme/meme.lex0.zoops.txt</pattern-file>
<sequence-file>common/lex0.s</sequence-file>
<pattern-pvalue-cutoff>0.0005</pattern-pvalue-cutoff>
<sequence-pvalue-cutoff>1</sequence-pvalue-cutoff>
</parameters>
<multi-pattern-scan score="26.0495" pvalue="0.2407">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="recn" name="recn">
<matched-element start="71" stop="90" pvalue="2.3214e-09">
<sequence>tactgtatataaaaccagtt</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="recn" name="recn">
<matched-element start="111" stop="130" pvalue="7.0292e-07">
<sequence>taatggtttttcatacagga</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-6" seq-name="recn" start="71" stop="130" evalue="3.3698" qvalue="0.56508">tactgtatataaaaccagtttatactgtacacaataacagtaatggtttttcatacagga
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="23.4494" pvalue="0.24112">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="cloacin-df13" name="cloacin-df13">
<matched-element start="97" stop="116" pvalue="4.3652e-11">
<sequence>tactgtgtatatatacagta</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-1" seq-name="cloacin-df13" start="97" stop="116" evalue="3.3756" qvalue="0.56508">tactgtgtatatatacagta
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="19.066" pvalue="0.26499">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="lexA" name="lexA">
<matched-element start="14" stop="33" pvalue="0.00010103">
<sequence>ctctggtttattgtgcagtt</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="lexA" name="lexA">
<matched-element start="55" stop="74" pvalue="1.0177e-05">
<sequence>tgctgtatatactcacagca</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="lexA" name="lexA">
<matched-element start="76" stop="95" pvalue="9.2771e-08">
<sequence>aactgtatatacacccaggg</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-13" seq-name="lexA" start="14" stop="95" evalue="3.7098" qvalue="0.56508">ctctggtttattgtgcagtttatggttccaaaatcgccttttgctgtatatactcacagcataactgtatatacacccaggg
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="20.536" pvalue="0.29486">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="umu-operon" name="umu-operon">
<matched-element start="91" stop="110" pvalue="3.2887e-10">
<sequence>tactgtatataaaaacagta</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-8" seq-name="umu-operon" start="91" stop="110" evalue="4.128" qvalue="0.56508">tactgtatataaaaacagta
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="12.6724" pvalue="0.30546">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="uvrd" name="uvrd">
<matched-element start="102" stop="121" pvalue="7.6593e-08">
<sequence>atctgtatatatacccagct</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-11" seq-name="uvrd" start="102" stop="121" evalue="4.2765" qvalue="0.56508">atctgtatatatacccagct
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="18.8081" pvalue="0.3196">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="muc-operon" name="muc-operon">
<matched-element start="49" stop="68" pvalue="1.0894e-09">
<sequence>tactgtataaataaacagtt</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-14" seq-name="muc-operon" start="49" stop="68" evalue="4.4743" qvalue="0.56508">tactgtataaataaacagtt
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="15.0184" pvalue="0.33492">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="reca" name="reca">
<matched-element start="71" stop="90" pvalue="1.5065e-08">
<sequence>tactgtatgagcatacagta</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-5" seq-name="reca" start="71" stop="90" evalue="4.6888" qvalue="0.56508">tactgtatgagcatacagta
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="12.7583" pvalue="0.40671">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="colicin-a" name="colicin-a">
<matched-element start="34" stop="53" pvalue="7.2166e-08">
<sequence>tactgtatataaacacatgt</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-12" seq-name="colicin-a" start="34" stop="53" evalue="5.694" qvalue="0.56508">tactgtatataaacacatgt
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="11.8537" pvalue="0.42796">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="uvra" name="uvra">
<matched-element start="60" stop="79" pvalue="1.3509e-07">
<sequence>tactgtatattcattcaggt</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-9" seq-name="uvra" start="60" stop="79" evalue="5.9914" qvalue="0.56508">tactgtatattcattcaggt
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="14.989" pvalue="0.44518">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="uvrb" name="uvrb">
<matched-element start="71" stop="90" pvalue="1.5375e-08">
<sequence>aactgtttttttatccagta</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-10" seq-name="uvrb" start="71" stop="90" evalue="6.2325" qvalue="0.56508">aactgtttttttatccagta
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="12.9253" pvalue="0.45163">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="sula" name="sula">
<matched-element start="85" stop="104" pvalue="6.4277e-08">
<sequence>tactgtacatccatacagta</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-7" seq-name="sula" start="85" stop="104" evalue="6.3229" qvalue="0.56508">tactgtacatccatacagta
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="12.6379" pvalue="0.53772">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="colicin-ia" name="colicin-ia">
<matched-element start="99" stop="118" pvalue="7.8448e-08">
<sequence>tactgtatatgtatccatat</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-3" seq-name="colicin-ia" start="99" stop="118" evalue="7.528" qvalue="0.56508">tactgtatatgtatccatat
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="12.6379" pvalue="0.55357">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="colicin-ib" name="colicin-ib">
<matched-element start="99" stop="118" pvalue="7.8448e-08">
<sequence>tactgtatatgtatccatat</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-4" seq-name="colicin-ib" start="99" stop="118" evalue="7.75" qvalue="0.56508">tactgtatatgtatccatat
</mem:match>
</multi-pattern-scan>
<multi-pattern-scan score="12.2975" pvalue="0.56508">
<pattern accession="WACTGTATATATATACAGTW" name="WACTGTATATATATACAGTW">
<scanned-sequence accession="colicin-e1" name="colicin-e1">
<matched-element start="97" stop="116" pvalue="9.9327e-08">
<sequence>tgctgtatataaaaccagtg</sequence>
</matched-element>
</scanned-sequence>
</pattern>
<mem:match cluster-id="cluster-2" seq-name="colicin-e1" start="97" stop="116" evalue="7.9111" qvalue="0.56508">tgctgtatataaaaccagtg
</mem:match>
</multi-pattern-scan>
</cis-element-search>
