<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
<!DOCTYPE tomtom[
<!ELEMENT tomtom (model, targets, queries, runtime)>
<!ATTLIST tomtom version CDATA #REQUIRED release CDATA #REQUIRED>
<!ELEMENT model (command_line, distance_measure, threshold, background, host, when)>
<!ELEMENT command_line (#PCDATA)>
<!ELEMENT distance_measure EMPTY>
<!ATTLIST distance_measure value (allr|blic1|blic5|ed|kullback|llr1|llr5|pearson|sandelin) #REQUIRED>
<!ELEMENT threshold (#PCDATA)>
<!ATTLIST threshold type (evalue|qvalue) #REQUIRED>
<!ELEMENT background EMPTY>
<!ATTLIST background from (first_target|file) #REQUIRED A CDATA #REQUIRED C CDATA #REQUIRED G CDATA #REQUIRED T CDATA #REQUIRED file CDATA #IMPLIED>
<!ELEMENT host (#PCDATA)>
<!ELEMENT when (#PCDATA)>
<!-- each target is listed in order that the target was specified to the command line
     the motifs are not listed in any particular order -->
<!ELEMENT targets (target_file*)>
<!ELEMENT target_file (motif*)>
<!ATTLIST target_file index CDATA #REQUIRED source CDATA #REQUIRED name CDATA #REQUIRED 
  loaded CDATA #REQUIRED excluded CDATA #REQUIRED last_mod_date CDATA #REQUIRED>
<!-- currently there can only be one query file (but users should not assume this will always be true)
     the query motifs are specified in the order that they appear in the file
     the matches are ordered from best to worst -->
<!ELEMENT queries (query_file*)>
<!ELEMENT query_file (query*)>
<!ATTLIST query_file source CDATA #REQUIRED name CDATA #REQUIRED last_mod_date CDATA #REQUIRED>
<!ELEMENT query (motif,match*)>
<!ELEMENT match EMPTY>
<!ATTLIST match target IDREF #REQUIRED orientation (forward|reverse) "forward" 
  offset CDATA #REQUIRED pvalue CDATA #REQUIRED evalue CDATA #REQUIRED qvalue CDATA #REQUIRED>
<!-- motif contains the probability of each of the nucleotide bases at each position;
     i starts at 1; A, C, G and T are probabilities that sum to 1 -->
<!ELEMENT motif (pos*)>
<!ATTLIST motif id ID #REQUIRED name CDATA #REQUIRED alt CDATA #IMPLIED length CDATA #REQUIRED 
  nsites CDATA #IMPLIED evalue CDATA #IMPLIED url CDATA #IMPLIED>
<!ELEMENT pos EMPTY>
<!ATTLIST pos i CDATA #REQUIRED A CDATA #REQUIRED C CDATA #REQUIRED G CDATA #REQUIRED T CDATA #REQUIRED>
<!ELEMENT runtime EMPTY>
<!ATTLIST runtime cycles CDATA #REQUIRED seconds CDATA #REQUIRED>
]>
<tomtom version="4.10.0" release="Wed May 21 10:35:36 2014 +1000">
	<model>
		<command_line>tomtom -verbosity 1 -oc Dynamic_Sex-independent_Output/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile Dynamic_Sex-independent_Output/background Dynamic_Sex-independent_Output/dreme_out/dreme.xml ./JASPAR_CORE_2014_vertebrates.meme ./uniprobe_mouse.meme</command_line>
		<distance_measure value="pearson"/>
		<threshold type="evalue">1</threshold>
		<background from="file" A="0.269" C="0.231" G="0.231" T="0.269" file="Dynamic_Sex-independent_Output/background"/>
		<host>scc-ph1</host>
		<when>Wed Jun  7 10:43:19 2017</when>
	</model>
	<targets>
		<target_file index="1" source="./JASPAR_CORE_2014_vertebrates.meme" name="JASPAR_CORE_2014_vertebrates.meme" loaded="205" excluded="0" last_mod_date="Wed Jun  7 10:39:12 2017">
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				<pos i="1" A="0.272067" C="0.319733" G="0.166928" T="0.241271"/>
				<pos i="2" A="0.419969" C="0.207925" G="0.155355" T="0.216752"/>
				<pos i="3" A="0.142605" C="0.29541" G="0.173401" T="0.388584"/>
				<pos i="4" A="0.297568" C="0.101805" G="0.193213" T="0.407415"/>
				<pos i="5" A="0.010985" C="0.23519" G="0.728129" T="0.025696"/>
				<pos i="6" A="0" C="1" G="0" T="0"/>
				<pos i="7" A="0" C="0.934092" G="0" T="0.065908"/>
				<pos i="8" A="0.012162" C="0.340526" G="0.016673" T="0.630639"/>
				<pos i="9" A="0.06787" C="0.535308" G="0.336406" T="0.060416"/>
				<pos i="10" A="0.733229" C="0.046293" G="0.180463" T="0.040016"/>
				<pos i="11" A="0.090231" C="0" G="0.909769" T="0"/>
				<pos i="12" A="0" C="0" G="1" T="0"/>
				<pos i="13" A="0.022754" C="0.283052" G="0.677717" T="0.016477"/>
				<pos i="14" A="0.088466" C="0.720282" G="0.091212" T="0.100039"/>
				<pos i="15" A="0.617105" C="0.135347" G="0.032954" T="0.214594"/>
			</motif>
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				<pos i="2" A="0.205855" C="0" G="0.593012" T="0.201133"/>
				<pos i="3" A="0.135977" C="0.258735" G="0.605288" T="0"/>
				<pos i="4" A="0" C="0" G="1" T="0"/>
				<pos i="5" A="0" C="1" G="0" T="0"/>
				<pos i="6" A="0" C="0" G="1" T="0"/>
				<pos i="7" A="0" C="0.318225" G="0.681775" T="0"/>
				<pos i="8" A="0" C="0.270066" G="0.729934" T="0"/>
				<pos i="9" A="1" C="0" G="0" T="0"/>
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				<pos i="11" A="0.288008" C="0.254013" G="0.457979" T="0"/>
			</motif>
			<motif id="t_1_MA0039.2" name="MA0039.2" alt="Klf4" length="10" evalue="0.0e+000" nsites="4340" url="http://jaspar.genereg.net?ID=MA0039.2&amp;rm=present&amp;collection=CORE">
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				<pos i="2" A="0.020276" C="0.002074" G="0.976267" T="0.001382"/>
				<pos i="3" A="0.003223" C="0.002993" G="0.990792" T="0.002993"/>
				<pos i="4" A="0.003221" C="0.008282" G="0.984817" T="0.003681"/>
				<pos i="5" A="0.063693" C="0.441941" G="0.002529" T="0.491837"/>
				<pos i="6" A="0.005064" C="0.003453" G="0.983656" T="0.007827"/>
				<pos i="7" A="0.009671" C="0.01842" G="0.501727" T="0.470182"/>
				<pos i="8" A="0.060872" C="0.010606" G="0.8997" T="0.028822"/>
				<pos i="9" A="0.0284" C="0.030016" G="0.874856" T="0.066728"/>
				<pos i="10" A="0.058742" C="0.660962" G="0.064755" T="0.215541"/>
			</motif>
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			</motif>
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			</motif>
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