Is f'(f'(A,B),C)) the same as F(A,B,C)? If so, then just run a loop on your array of strings, replacing the first two with the results if f'(A,B). By the time you are down to a single string left, you will have the same results as F(A,B,C,....).

List::Util's reduce function can be helpful in implementing this.

would this still work for more than 2 strings

As long as the ambiguous bases are in distinct positions, yes.

In the general case, you can then write:

my @s = (
    "AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA",
    "ACGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA",
    "ACGTACTAGWCTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA",
    "ACGTACTAGACTACAGACTACAGMCATCTACAGACTCATCAGCAGCATATTTA",
    "ACGTACTAGACTACAGACTACAGACATCTACAGACTCATRAGCAGCATATTTA",
    # ...
);

my $m = shift @s;
for my $s (@s) {
    my $m_ = $m;  $m_ =~ tr/ACGT/\0/c;
    my $s_ = $s;  $s_ =~ tr/ACGT/\0/c;
    $m = $m ^ $m_ ^ $s ^ $s_ | $m_ & $s_;  
}
say $m;   # AYGTACTAGWCTACAGACTACAGMCATCTACAGACTCATRAGCAGCATATTKA
             ^       ^             ^               ^           ^
[download]

(P.S., sorry — meant to reply to garyboyd... )

Thanks Eliya that is now working perfectly!