Thanks Farhat, if I understand it right this means that if in size 16 I replace A/T it results in 15 (or also in 17) so all three motifs are quite similar.
But this only works if I'm dealing with DNA sequences but in my problem A, C and T have a different meaning, they are not nucleotides so A and T have different meanings and I cannot replace one for another..
Does a situation like mine happen when working with motifs? I mean if in real DNA sequences does it happen that when the lenght of the motif changes it also changes the identified motifs? I can't find any example of a similar situation, intuitively I should think that the identified motifs should not change that much but I don't know..
Could you provide us with more information on what your research question is and what you are trying to accomplish? I'm unclear as to why you should be getting such differences, but I don't have any context with which to understand. Thanks.
Yes, I'm studing 50 sequences of letters (A, C and T) where I'm trying to find patters of different sizes. Each sequence length ranges from 100 letters to 500 and all the sequences lengths are different. I'm trying to find if there are subsequences of different lengths (5,10,15,20) that are repeated or slightly different and represent them using sequence logos.