<?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:mem="http://noble.gs.washington.edu/meme"
>
<program-name>ama</program-name>
<parameters>
<command-line>ama --verbosity 1 --scoring max-odds /Users/t.bailey/meme_git/meme/tests/gomo/motif.meme.txt /Users/t.bailey/meme_git/meme/tests/gomo/seqs.fasta /Users/t.bailey/meme_git/meme/tests/gomo/seqs.bg</command-line>
<pattern-file>/Users/t.bailey/meme_git/meme/tests/gomo/motif.meme.txt</pattern-file>
<sequence-file>/Users/t.bailey/meme_git/meme/tests/gomo/seqs.fasta</sequence-file>
<background-seq-file>/Users/t.bailey/meme_git/meme/tests/gomo/seqs.bg</background-seq-file>
<sequence-filtering on-off="off"/>
</parameters>
<pattern accession="HSF1" name="">
<scanned-sequence accession="S000000001" name="S000000001" score="19.9139" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000002" name="S000000002" score="24.1213" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000003" name="S000000003" score="2.32365e+06" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000004" name="S000000004" score="2.32365e+06" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000005" name="S000000005" score="45.5042" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000006" name="S000000006" score="213786" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000007" name="S000000007" score="21.6929" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000008" name="S000000008" score="213786" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000009" name="S000000009" score="61.073" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000010" name="S000000010" score="2724.29" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000011" name="S000000011" score="92.173" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000012" name="S000000012" score="2724.29" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000013" name="S000000013" score="0.16762" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000014" name="S000000014" score="112.113" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000015" name="S000000015" score="0.245037" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000016" name="S000000016" score="95.8504" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000017" name="S000000017" score="6225.56" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000018" name="S000000018" score="1239.87" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000019" name="S000000019" score="6225.56" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000020" name="S000000020" score="0.143856" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000021" name="S000000021" score="171.805" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000022" name="S000000022" score="980.499" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000023" name="S000000023" score="50.9388" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000024" name="S000000024" score="2691.51" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000025" name="S000000025" score="187.045" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000026" name="S000000026" score="1038.17" length="1000">
</scanned-sequence>
</pattern>
<pattern accession="RPN4" name="">
<scanned-sequence accession="S000000001" name="S000000001" score="2.18048" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000002" name="S000000002" score="0.605917" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000003" name="S000000003" score="43686.2" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000004" name="S000000004" score="43686.2" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000005" name="S000000005" score="1.85784" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000006" name="S000000006" score="406.133" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000007" name="S000000007" score="4377.05" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000008" name="S000000008" score="406.133" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000009" name="S000000009" score="16.3223" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000010" name="S000000010" score="51.6488" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000011" name="S000000011" score="22037.1" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000012" name="S000000012" score="51.6488" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000013" name="S000000013" score="22037.1" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000014" name="S000000014" score="0.161001" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000015" name="S000000015" score="7.03206" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000016" name="S000000016" score="0.326014" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000017" name="S000000017" score="10.3812" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000018" name="S000000018" score="6.57003" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000019" name="S000000019" score="11.0269" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000020" name="S000000020" score="0.876446" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000021" name="S000000021" score="16.3223" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000022" name="S000000022" score="15.5004" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000023" name="S000000023" score="1.28071" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000024" name="S000000024" score="1.28071" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000025" name="S000000025" score="12.1504" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000026" name="S000000026" score="883.586" length="1000">
</scanned-sequence>
</pattern>
</cis-element-search>
