Let me point out that the result of a single comparison is going to be a list of mismatches. If your array of DNA samples is of size N, then the matrix of comparisons ends up being N x N in size (with N*(N-1) unique sets of data, as you can ignore the self comparisons).

How you handle storing that is really up to you.

A function for handling a single comparison and returning the results as a reference to an array is:

sub dna_mismatches {
    my $dna_standard   = shift;
    my $dna_to_compare = shift;
    my @mismatches = ( 0 );
#
# assume same length strands
#
    my $last_std = length($dna_standard);
    for ( 0 .. $last_std - 1 ) {
    if ( substr( $dna_standard, $_, 1 ) ne 
         substr ( $dna_to_compare, $_, 1 )) {
        $mismatches[0]++;
        push @mismatches, $_ + 1;
    }
    }
    return \@mismatches;
}
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