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def pairwiseScore(seqA, seqB): prev = -1 score = 0 length = len(seqA) similarity = [] relative_similarity = [] for x in xrange(length): if seqA[x] == seqB[x]: if (x >= 1) and (seqA[x - 1] == seqB[x - 1]): score += 3 similarity.append(x) else: score += 1 similarity.append(x) else: score -= 1 for x in similarity: relative_similarity.append(x - prev) prev = x return ''.join((seqA, '\n', ''.join(['|'.rjust(x) for x in relative_similarity]), '\n', seqB, '\n', 'Score: ', str(score))) print pairwiseScore("ATTCGT", "ATCTAT"), '\n', '\n', pairwiseScore("GATAAATCTGGTCT", "CATTCATCATGCAA"), '\n', '\n', pairwiseScore('AGCG', 'ATCG'), '\n', '\n', pairwiseScore('ATCG', 'ATCG')
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