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')

ATTCGT
||   |
ATCTAT
Score: 2 

GATAAATCTGGTCT
 ||  |||  |
CATTCATCATGCAA
Score: 4 

AGCG
| ||
ATCG
Score: 4 

ATCG
||||
ATCG
Score: 10