positional conservation scores

Question

[wannabio]

HI all,

I am reframing a question I had asked earlier to make it more general. I need to calculate positional conservation scores of a couple of 6 char patterns in an aligned MSA sequence of a virus. I need a % score of each pattern at each position of the sequence. The output can be the form of a matrix, where the rows are the patterns I want to search for, columns are the coordinates in the sequence and the values are the conservation scores.

I am researching some pattern match algorithms in bioinformatics like the rabin karp technique but I don't know how to perform such a such on multiple sequences at the same time and aggregate the results. Any leads would be appreciated as I am new to the field.