Like this?:

Perhaps this is closer to what you are after (Updated: corrected output ordering):

#! perl -slw
use strict;
use Data::Dump qw[ pp ];


my @freq;
my @data = qw[ AABBC BAABC AABBD AACBB ];

for my $s ( @data ) {
    ++$freq[ $_ ]{ substr $s, $_, 1 } for 0 .. length( $s ) -1;
}
##pp \@freq;

for my $pos ( @freq ) {
    ( $pos->{ $_ } //= 0 ) /= 4 for 'A' .. 'D';
}
##pp \@freq;

print join "\t", '', 'A'..'D';
for my $pos ( 0 .. $#freq ) {
    printf "%2d\t%s\n", $pos+1,  join "\t", map sprintf("%.2f", $_ ), 
+ @{ $freq[ $pos ] }{ 'A' .. 'D' };
}

__DATA__
C:\test>1162755
        A       B       C       D
 1      0.75    0.25    0.00    0.00
 2      1.00    0.00    0.00    0.00
 3      0.25    0.50    0.25    0.00
 4      0.00    1.00    0.00    0.00
 5      0.00    0.25    0.50    0.25
[download]

Another variations that doesn't hard code the keys:

#! perl -slw
use strict;
use Data::Dump qw[ pp ];


my( @freq, %c, $c );
#my @data = qw[ AABBC BAABC AABBD AACBB ];
my @data = qw[ AABBC BAABC AABBD AECBBF ];

for my $s ( @data ) {
    ++$freq[ $_ ]{ $c = substr $s, $_, 1 }, undef $c{ $c } for 0 .. le
+ngth( $s ) -1;
}
##pp \@freq;
my @oK = sort keys %c;

for my $pos ( @freq ) {
    ( $pos->{ $_ } //= 0 ) /= 4 for @oK;
}
##pp \@freq;

print join "\t", '', @oK;
for my $pos ( 0 .. $#freq ) {
    printf "%2d\t%s\n", $pos+1,  join "\t", map sprintf("%.2f", $_ ), 
+ @{ $freq[ $pos ] }{ @oK };
}

__DATA__
C:\test>1162755
        A       B       C       D       E       F
 1      0.75    0.25    0.00    0.00    0.00    0.00
 2      0.75    0.00    0.00    0.00    0.25    0.00
 3      0.25    0.50    0.25    0.00    0.00    0.00
 4      0.00    1.00    0.00    0.00    0.00    0.00
 5      0.00    0.25    0.50    0.25    0.00    0.00
 6      0.00    0.00    0.00    0.00    0.00    0.25
[download]