I have no understanding of the problem domain so the following code is not a solution to your actual problem, but is an alternative way of finding changes between adjacent strings in a list and counting those changes by column.

use strict;
use warnings;

my $sites = [
    'CGGCGGAAAACTGTCCTCCGTGC',    # mouse
    'CGACGGAACATTCTCCTCCGCGC',    # rat
    'CGACGGAATATTCCCCTCCGTGC',    # human
    'CGACGGAAGACTCTCCTCCGTGC',    # chimp
    ];

my @val = my_parsimony ($sites);
print @val;


sub my_parsimony {
    my ($sites) = @_;
    my $lastSite = $sites->[0];
    my @mincol = (0) x length $lastSite;

    for my $nextSite (@$sites) {
        my $changes = $lastSite ^ $nextSite;
        
        $lastSite = $nextSite;
        next unless $changes =~ s/[^\0]/+/g;

        my $pos = 0;

        ++$mincol[$pos++] while -1 != ($pos = index $changes, '+', $po
+s);
    }

    return @mincol;
}
[download]

Prints:

00100000302012000000200
[download]