Decoding Human Regulatory Circuits

Three of the 24 pairs of sequences contained two distinct modules. The current algorithm can find at most one module per sequence, so in one execution of the algorithm, a maximum of 40 (20 pairs) modules and 96 reported Myf, Mef2, and SRF sites are identifiable. The three sequences with no predicted modules were not found to contain reported modules. A series of predicted motifs was considered as overlapping a reported module if they overlapped the reported module by at least half the length of the reported module as measured from start location of the reported TFBS proximal to the 5′ end of the gene to the end of the most distant TFBS.