Statistical the DNA mutation types

Question

[xzpgocxx]

Hi,

I want to statistical the mutation types based on sequence alignment. Besides, I'm only interested in the mutation present in the red frame[1] (The first sequence is the reference sequence). I have a huge amount of fasta sequences and cannot be count by the manual.

So, is there any software or scripts can do this job?

Thanks!

[GenoMax]

I think you are looking for something along the lines of: Conservation score calculation for gene sequences and
Conservation Score Calculator