while ($l=<DATA>) {
        %count = ();
        $count{$1}++ while ($l =~ /(.)/g);

        $max = 0;
        $max_key;
        foreach (keys %count) {
                $max = $count{$_}, $max_key = $_ if ($count{$_} > $max);
        }
        push @consensus, $max_key;
}

print "@consensus\n";
__END__
---ADGRCMNAAAPPRS
ASAMNP-PRCM--MWQZ
TYYCYLCKLKDUEAOLE

$ perl cons.pl
A - Y