Calculating values of a 2d array by comparison of 2 strings

Hi. I am having a hard time dealing with a problem And I was wondering if anyone has a suggestion to how I should do this.

I have 2 strings that I want to compare. These strings are composed of amino acid residues (long sequences of any of 20 characters) these string are aligned to each other and I want to compare each position of the two strings and fill up a matrix of 21*21 so that for eg:

AAAAAA....
ATLL_Y....

1 pos: A-A -> counts 1 and adds to position [0][0] on the matrix
2 pos: A-T -> counts 1 and adds to position [0][1] on the matrix
3 pos: A-L -> counts 1 and adds to position [0][2] on the matrix
4 pos: A-L -> counts 1 and adds to position [0][2] on the matrix
5 pos: A-_ -> counts 1 and adds to position [0][21] on the matrix
6 pos: A-Y -> counts 1 and adds to position [0][10] on the matrix
....


I've been suggested by a friend to use a switch but this ends up needing 441 cases of assignments in other to fill up every position of the matrix.

Does anyone know of a better way of dealing with this? I appreciate any suggestions. Thanks

Duarte
.

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