Table 3. Comparison of CisModule (CMD), MEME, and BP for CRMs in Drosophila.

TF	L/N	n1/n2	MEME	CMD	BP
Bcd	11,984/10	12/49	—	7/68	1/10
Hb	24,789/19	14/116	3/50	7/138	—
Kr	12,741/10	8/44	—	5/61	1/14
Total reported sites		34	3	19	2

Each data set is denoted by its regulatory TFs. L and N are the total length and number of sequences in each data set, respectively. n₁ and n₂ are the numbers of experimentally reported sites and scanned-based sites, respectively.–indicates that the algorithm fails to find the motif; if the correct motif is found, the number of reported sites/the number of predicted sites are presented in the corresponding entry for each method. The summary of performance on experimentally reported sites is shown in the last row.