def pairwiseScore(seqA, seqB):

	score = 0
	bars = [str(' ') for x in seqA] #create a list filled with number of spaces equal to length of seqA string. It could be also seqB, because both are meant to have same length
	length = len(seqA)
	similarity = []
	
	for x in xrange(length):
		
		if seqA[x] == seqB[x]: #check if for every index 'x', corresponding character is same in both seqA and seqB strings
			if (x >= 1) and (seqA[x - 1] == seqB[x - 1]): #if 'x' is greater than or equal to 1 and characters under the previous index, were same in both seqA and seqB strings, do..
				score += 3
				similarity.append(x)
			else:
				score += 1
				similarity.append(x)				
		else:
			score -= 1
		
	for x in similarity:
		bars[x] = '|' #for every index 'x' in 'bars' list, replace space with '|' (pipe/vertical bar) character 
	
	return ''.join((seqA, '\n', ''.join(bars), '\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