So you are doing a letter by letter comparison, <just want to see if i understand you>

assuming

ABAS

ABABAS

seq1
A = 1, 3
B = 2
S = 4

A 1,1 1,3 1,5
3,1 3,3 3,5

B 2,2 2,4
S 4,5

that would be the needed results?