Hi,
In the MEME html output, Sites says that "The number of sites contributing to the construction of the motif." I used nmotifs = 50 and for few motifs, sites showed a value of 2 and the maximum for few motifs were 14. My search set had a total of 63 sequences. Since, MEME searches for short subpatterns in whole dataset the site should be of greater value right, if not it is present in all 63 ? Does it mean that, I need to run a randomly generated control sequence set of same size & length to validate my results ?
Thanks in Advance,
AP