We have a set of telomere sequences extending from the TTAGGG array. The closer any sub-sequence is to the array the higher the probability will be the probability that it shares similarities with other members of the set. We want to parse the total set of sequences into subsets corresponding to each of the 4n telomeres in the karyotype. Does anybody know of a good guide to the most appropriate algorithms for doing this and in which packages they are most easily implemented?

Thanks.