Here's a more long-winded approach that seems to work for extra letters/rows.

use strict;
use warnings;

my @strings   = qw{
   AABABC
   BAABEC
   AABFBD
   AACBDB
   CBBDEF
   };
my $div       = scalar @strings;

my @stringAoA =
   map { [ split m{} ] }
   @strings;

my %letters;
$letters{ $_ } ++ for map { @{ $_ } } @stringAoA;

my %scores;
for my $posn ( 1 .. length $strings[ 0 ] )
{
    for my $row ( 0 .. $#stringAoA )
    {
        $scores{ $posn }->{ $stringAoA[ $row ]->[ $posn - 1 ] } ++;
    }
}

printf
   qq{%8s@{ [ q{%8s} x scalar keys %letters ] }\n},
   q{},
   sort keys %letters;
for my $posn (sort { $a <=> $b } keys %scores )
{
    printf
       qq{  %8d@{ [ q{%8.2f} x scalar keys %letters ] }\n},
       $posn,
       map {
           defined $scores{ $posn }->{ $_ }
           ? $scores{ $posn }->{ $_ } / $div
           : 0
           } sort keys %letters
}
[download]

The output.

               A       B       C       D       E       F
         1    0.60    0.20    0.20    0.00    0.00    0.00
         2    0.80    0.20    0.00    0.00    0.00    0.00
         3    0.20    0.60    0.20    0.00    0.00    0.00
         4    0.20    0.40    0.00    0.20    0.00    0.20
         5    0.00    0.40    0.00    0.20    0.40    0.00
         6    0.00    0.20    0.40    0.20    0.00    0.20
[download]

I hope this is useful.