G'day reebee3,

Welcome to the Monastery.

I'd use substr to get the individual bases. Then a simple comparison will identify your SNPs.

#!/usr/bin/env perl -l

use strict;
use warnings;

my ($seq1, $seq2) = qw{ATGGAT ACGGAG};
my $snp = 0;

for my $pos (1 .. length $seq1) {
    my $base1 = substr $seq1, $pos - 1, 1;
    my $base2 = substr $seq2, $pos - 1, 1;
    next if $base1 eq $base2;
    ++$snp;
    print "SNP $snp is the $base1 --> $base2 at position $pos";
}
[download]

Output:

SNP 1 is the T --> C at position 2
SNP 2 is the T --> G at position 6
[download]