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Link: http://codepad.org/zwEQKKeV    [ raw code | output | fork ]

Python, pasted on Aug 19:
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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')


Output:
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ATTCGT
||    |
ATCTAT
Score: 2 

GATAAATCTGGTCT
| |    |     |      |         |
CATTCATCATGCAA
Score: 4 

AGCG
| |  |
ATCG
Score: 4 

ATCG
|| |  |
ATCG
Score: 10


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