Dear Oliver, I am exploring cosmo (v 1.22.0 with R 2.15). I am happy to see cosmo finding a motif which is shared across the promoters of some genes with correlated expression. I use all of the default arguments when invoking cosmo, and I am passing in a list of 45 promoter regions, each 1100 bases long. I will use longer sequences after I understand cosmo a little better. I was surprised that just one PWM is found among the 45 sequences: > motifs at pwm 1 2 3 4 5 6 7 A 0.0914 0.4863 0 0.0000 0 0.0000 0.4231 C 0.5009 0.0000 0 0.5808 0 0.3180 0.0000 G 0.4076 0.0586 0 0.0000 1 0.1123 0.0000 T 0.0000 0.4551 1 0.4192 0 0.5697 0.5769 I am stuck at this point: I don't see how to invoke cosmo so that it will find the other shared motifs which I believe can be found among these promoters. I read the man pages and studied the vignette, but came away no wiser. Could you point me in the right direction, please? Thanks! - Paul