<?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>fimo</program-name>
<parameters>
<command-line>fimo --oc OUTPUT_fimo MA0007.3.meme LTR3B_sequences.fa</command-line>
<pattern-file>MA0007.3.meme</pattern-file>
<sequence-file>LTR3B_sequences.fa</sequence-file>
<site-pvalue-cutoff>0.0001</site-pvalue-cutoff>
<sequence-filtering on-off="off"/>
</parameters>
<pattern accession="MA0007.3" name="Ar">
<scanned-sequence accession="LTR3B_1" name="LTR3B_1">
</scanned-sequence>
<scanned-sequence accession="LTR3B_2" name="LTR3B_2">
</scanned-sequence>
<scanned-sequence accession="LTR3B_3" name="LTR3B_3">
</scanned-sequence>
<scanned-sequence accession="LTR3B_4" name="LTR3B_4">
</scanned-sequence>
<scanned-sequence accession="LTR3B_5" name="LTR3B_5">
</scanned-sequence>
<scanned-sequence accession="LTR3B_6" name="LTR3B_6">
</scanned-sequence>
<scanned-sequence accession="LTR3B_7" name="LTR3B_7">
</scanned-sequence>
<scanned-sequence accession="LTR3B_8" name="LTR3B_8">
</scanned-sequence>
<scanned-sequence accession="LTR3B_9" name="LTR3B_9">
</scanned-sequence>
<scanned-sequence accession="LTR3B_10" name="LTR3B_10">
</scanned-sequence>
<scanned-sequence accession="LTR3B_11" name="LTR3B_11">
</scanned-sequence>
<scanned-sequence accession="LTR3B_12" name="LTR3B_12">
</scanned-sequence>
<scanned-sequence accession="LTR3B_13" name="LTR3B_13">
</scanned-sequence>
<scanned-sequence accession="LTR3B_14" name="LTR3B_14">
</scanned-sequence>
<scanned-sequence accession="LTR3B_15" name="LTR3B_15">
</scanned-sequence>
<scanned-sequence accession="LTR3B_16" name="LTR3B_16">
</scanned-sequence>
<scanned-sequence accession="LTR3B_17" name="LTR3B_17">
</scanned-sequence>
<scanned-sequence accession="LTR3B_18" name="LTR3B_18">
<matched-element start="81" stop="65" score="5.60345" pvalue="9.34e-05">
<sequence>AAGAACAGTTTGCTCTT</sequence>
<mem:qvalue>0.609</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="LTR3B_19" name="LTR3B_19">
</scanned-sequence>
<scanned-sequence accession="LTR3B_20" name="LTR3B_20">
</scanned-sequence>
<scanned-sequence accession="LTR3B_21" name="LTR3B_21">
</scanned-sequence>
<scanned-sequence accession="LTR3B_22" name="LTR3B_22">
</scanned-sequence>
<scanned-sequence accession="LTR3B_23" name="LTR3B_23">
</scanned-sequence>
<scanned-sequence accession="LTR3B_24" name="LTR3B_24">
</scanned-sequence>
<scanned-sequence accession="LTR3B_25" name="LTR3B_25">
</scanned-sequence>
<scanned-sequence accession="LTR3B_26" name="LTR3B_26">
</scanned-sequence>
<scanned-sequence accession="LTR3B_27" name="LTR3B_27">
</scanned-sequence>
<scanned-sequence accession="LTR3B_28" name="LTR3B_28">
</scanned-sequence>
<scanned-sequence accession="LTR3B_29" name="LTR3B_29">
</scanned-sequence>
<scanned-sequence accession="LTR3B_30" name="LTR3B_30">
</scanned-sequence>
<scanned-sequence accession="LTR3B_31" name="LTR3B_31">
</scanned-sequence>
<scanned-sequence accession="LTR3B_32" name="LTR3B_32">
</scanned-sequence>
<scanned-sequence accession="LTR3B_33" name="LTR3B_33">
</scanned-sequence>
<scanned-sequence accession="LTR3B_34" name="LTR3B_34">
</scanned-sequence>
<scanned-sequence accession="LTR3B_35" name="LTR3B_35">
</scanned-sequence>
<scanned-sequence accession="LTR3B_36" name="LTR3B_36">
</scanned-sequence>
<scanned-sequence accession="LTR3B_37" name="LTR3B_37">
</scanned-sequence>
<scanned-sequence accession="LTR3B_38" name="LTR3B_38">
</scanned-sequence>
<scanned-sequence accession="LTR3B_39" name="LTR3B_39">
<matched-element start="130" stop="146" score="5.62069" pvalue="9.29e-05">
<sequence>gggaacgctgagtgcag</sequence>
<mem:qvalue>0.609</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="LTR3B_40" name="LTR3B_40">
</scanned-sequence>
<scanned-sequence accession="LTR3B_41" name="LTR3B_41">
</scanned-sequence>
<scanned-sequence accession="LTR3B_42" name="LTR3B_42">
</scanned-sequence>
<scanned-sequence accession="LTR3B_43" name="LTR3B_43">
</scanned-sequence>
<scanned-sequence accession="LTR3B_44" name="LTR3B_44">
</scanned-sequence>
<scanned-sequence accession="LTR3B_45" name="LTR3B_45">
</scanned-sequence>
<scanned-sequence accession="LTR3B_46" name="LTR3B_46">
</scanned-sequence>
<scanned-sequence accession="LTR3B_47" name="LTR3B_47">
</scanned-sequence>
<scanned-sequence accession="LTR3B_48" name="LTR3B_48">
</scanned-sequence>
<scanned-sequence accession="LTR3B_49" name="LTR3B_49">
</scanned-sequence>
<scanned-sequence accession="LTR3B_51" name="LTR3B_51">
</scanned-sequence>
<scanned-sequence accession="LTR3B_52" name="LTR3B_52">
</scanned-sequence>
<scanned-sequence accession="LTR3B_53" name="LTR3B_53">
</scanned-sequence>
<scanned-sequence accession="LTR3B_54" name="LTR3B_54">
</scanned-sequence>
<scanned-sequence accession="LTR3B_55" name="LTR3B_55">
</scanned-sequence>
<scanned-sequence accession="LTR3B_56" name="LTR3B_56">
</scanned-sequence>
<scanned-sequence accession="LTR3B_57" name="LTR3B_57">
</scanned-sequence>
<scanned-sequence accession="LTR3B_58" name="LTR3B_58">
</scanned-sequence>
<scanned-sequence accession="LTR3B_61" name="LTR3B_61">
</scanned-sequence>
<scanned-sequence accession="LTR3B_62" name="LTR3B_62">
</scanned-sequence>
<scanned-sequence accession="LTR3B_63" name="LTR3B_63">
</scanned-sequence>
<scanned-sequence accession="LTR3B_64" name="LTR3B_64">
</scanned-sequence>
<scanned-sequence accession="LTR3B_65" name="LTR3B_65">
</scanned-sequence>
<scanned-sequence accession="LTR3B_66" name="LTR3B_66">
</scanned-sequence>
<scanned-sequence accession="LTR3B_67" name="LTR3B_67">
</scanned-sequence>
<scanned-sequence accession="LTR3B_68" name="LTR3B_68">
</scanned-sequence>
<scanned-sequence accession="LTR3B_69" name="LTR3B_69">
</scanned-sequence>
<scanned-sequence accession="LTR3B_70" name="LTR3B_70">
</scanned-sequence>
<scanned-sequence accession="LTR3B_71" name="LTR3B_71">
</scanned-sequence>
<scanned-sequence accession="LTR3B_72" name="LTR3B_72">
</scanned-sequence>
<scanned-sequence accession="LTR3B_73" name="LTR3B_73">
</scanned-sequence>
<scanned-sequence accession="LTR3B_74" name="LTR3B_74">
</scanned-sequence>
<scanned-sequence accession="LTR3B_75" name="LTR3B_75">
</scanned-sequence>
<scanned-sequence accession="LTR3B_76" name="LTR3B_76">
</scanned-sequence>
<scanned-sequence accession="LTR3B_77" name="LTR3B_77">
</scanned-sequence>
<scanned-sequence accession="LTR3B_78" name="LTR3B_78">
<matched-element start="80" stop="64" score="6.94828" pvalue="6.11e-05">
<sequence>GAGAACAGTTTGCTCTC</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
<matched-element start="64" stop="80" score="6.58621" pvalue="6.87e-05">
<sequence>gagagcaaactgttctc</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="LTR3B_79" name="LTR3B_79">
</scanned-sequence>
<scanned-sequence accession="LTR3B_80" name="LTR3B_80">
</scanned-sequence>
<scanned-sequence accession="LTR3B_81" name="LTR3B_81">
<matched-element start="80" stop="64" score="6.94828" pvalue="6.11e-05">
<sequence>GAGAACAGTTTGCTCTC</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
<matched-element start="64" stop="80" score="6.58621" pvalue="6.87e-05">
<sequence>gagagcaaactgttctc</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="LTR3B_82" name="LTR3B_82">
</scanned-sequence>
<scanned-sequence accession="LTR3B_83" name="LTR3B_83">
</scanned-sequence>
<scanned-sequence accession="LTR3B_84" name="LTR3B_84">
<matched-element start="80" stop="64" score="6.94828" pvalue="6.11e-05">
<sequence>GAGAACAGTTTGCTCTC</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
<matched-element start="64" stop="80" score="6.58621" pvalue="6.87e-05">
<sequence>gagagcaaactgttctc</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="LTR3B_85" name="LTR3B_85">
</scanned-sequence>
<scanned-sequence accession="LTR3B_86" name="LTR3B_86">
</scanned-sequence>
<scanned-sequence accession="LTR3B_87" name="LTR3B_87">
</scanned-sequence>
<scanned-sequence accession="LTR3B_88" name="LTR3B_88">
</scanned-sequence>
<scanned-sequence accession="LTR3B_89" name="LTR3B_89">
<matched-element start="80" stop="64" score="6.94828" pvalue="6.11e-05">
<sequence>GAGAACAGTTTGCTCTC</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
<matched-element start="64" stop="80" score="6.58621" pvalue="6.87e-05">
<sequence>gagagcaaactgttctc</sequence>
<mem:qvalue>0.56</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="LTR3B_90" name="LTR3B_90">
</scanned-sequence>
<mem:has-qvalues>yes</mem:has-qvalues>
</pattern>
</cis-element-search>
