motifcounter-package	motifcounter-package
.Background	Background-class
.Overlap	Overlap-class
Background-class	Background-class
clumpSizeDist	clumpSizeDist
combinatorialDist	combinatorialDist
compoundPoissonDist	compoundPoissonDist
computeClumpStartProb	computeClumpStartProb
generateDNAString	generateDNAString
generateDNAStringSet	generateDNAStringSet
getAlpha	getAlpha
getBeta	getBeta
getBeta3p	getBeta3p
getBeta5p	getBeta5p
getCounts	getCounts
getGamma	getGamma
getOrder	getOrder
getSinglestranded	getSinglestranded
getStation	getStation
getTrans	getTrans
lenSequences	lenSequences
markovModel	markovModel
motifAndBackgroundValid	motifAndBackgroundValid
motifcounter	motifcounter-package
motifcounterOptions	motifcounterOptions
motifEnrichment	motifEnrichment
motifHitProfile	motifHitProfile
motifHits	motifHits
motifValid	motifValid
normalizeMotif	normalizeMotif
numMotifHits	numMotifHits
Overlap-class	Overlap-class
probOverlapHit	probOverlapHit
readBackground	readBackground
revcompMotif	revcompMotif
scoreDist	scoreDist
scoreDistBf	scoreDistBf
scoreDistEmpirical	scoreDistEmpirical
scoreHistogram	scoreHistogram
scoreHistogramSingleSeq	scoreHistogramSingleSeq
scoreProfile	scoreProfile
scoreSequence	scoreSequence
scoreStrand	scoreStrand
scoreThreshold	scoreThreshold
sigLevel	sigLevel
simulateClumpSizeDist	simulateClumpSizeDist
simulateNumHitsDist	simulateNumHitsDist
