Enhancers-class         Class '"Enhancers"'
alignment               Output
alignmentOne            Get alignment scores
conservedMotifs         check the conserved motifs in the orthologs
getENCODEdata           Download enhancer sequences from ENCODE
motifs                  Pre-clustered motifs from human and mouse
queryEncode             query data from ENCODE by predefined criteria
saveAlignments          output alignments
searchTFBPS             Transcription Factor Binding Pattern Similarity
                        (TFBPS) search
shuffle                 shuffle reads
