1. Are the motifs in known motifs & de novo motifs results comparable (e.g. their p-value)? Because I want to combine them into one ranked list. Or the “De novo motifs result” is actually the final ranked list of the test set?

2. As the online document mentioned that it is important to check the alignment of called motifs, alignment results can only be found for the de novo motifs results. How can the alignment of known motifs be checked?

3. How to get back the list of peaks hit by the called motifs? Regarding the findMotifsGenome.pl tool e.g. Peak list for motif A: peak1, peak4, peak5, etc. Peak list for motif B: peak2, peak10, peak15, etc. .....

Any replies are appreciated. Thanks in advance!

Kylie