Creating the Matching

P

0 (0,0)

1 (1,1)

2 (2,2)

3 (3,2)

4 (4,3)

5 (5,4)

6 (5,5)

7 (6,6)

8 (6,7)

1 2 3 4 5 6

S = A G C A T G
T = A G A T C G T

S’= A G C A T - G -
T’= A G - A T C G T

Score = 5 x 2 + 3 x (-1) = 7

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