I have the MSA consensus sequence at 60 % threshold, but I need to know the positions in the alignments at which the target sequence is not identical to the consensus. Is there an easier way to do that?
I have tried using this for two of my sequences (s1 and s2):
[i for i,(a1,a2) in enumerate(izip(s1,s2)) if a1!=a2]
And it gives me a lot of numbers. Maybe there is a better way to find the positions?