def pairwiseScore(seqA, seqB):
score = 0
length = len(seqA)
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
return ''.join((seqA, '\n', ''.join(['|'.rjust(x) for x in 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')