Table 1.

Dynamic Programming (DP) matrix for probabilistic Needleman–Wunsch

j	0	1	2	3	4	5
PWM	A	0.059	0.000	0.172	0.271	0.300
	C	0.108	0.320	0.136	0.209	0.330
	G	0.305	0.317	0.317	0.164	0.045
	T	0.526	0.578	0.375	0.356	0.325
NW		T	T	T	T	C
	0	−2	−4	−6	−8	−10
T	−2	0.052	−1.948	−3.948	−5.948	−1000
T	−4	−1.844	0.208	−1.792	−3.792	−5.792
C	−6	−3.844	−1.792	−0.520	−2.448	−4.448
A	−8	−5.844	−3.792	−2.374	−0.978	−2.978
C	−10	−1000	−5.792	−4.131	−2.774	−1.318

Aligning the genomic sequence TTCAC and read TTTTC, with the optimal alignment shown in bold. Also notice the PWM for the sequence, with several fairly ambiguous positions (especially the final position, probably representing a C, even though the probabilities for the C and T are nearly equal). The underlined position is computed in Equation 3.