use strict;
use warnings;

my @sequences = qw(ACGCATTCA ACTGGATAC TCAGCCATC);
my %matches;

for my $outer (0 .. $#sequences - 1) {
    for my $inner ($outer + 1 .. $#sequences) {
        my $mask = $sequences[$outer] ^ $sequences[$inner];
        
        next if index ($mask, "\0") == -1; # No matching characters
        
        $mask =~ tr/\0/\xff/c;
        $mask |= $sequences[$outer];
        $mask =~ tr/\xff/./;
        
        push @{$matches{$mask}}, [$outer + 1, $inner + 1];
    }
}

for my $match (sort keys %matches) {
    print "$match pattern between ",
        join (', ', map {"$_->[0] and $_->[1]"} @{$matches{$match}}),
        "\n";
}