Just for interest, here's a Perl 6 solution that works for arbitrary sets of input characters and arbitrary input lengths:

    #! /usr/bin/env perl6
    use v6;

    my @data = < AABBC BAABC AABBD AACBB >;

    # Use mixhashes (self-totalling, and they default to zero)
    my @freq = MixHash.new xx max @data».chars;

    # Count everything
    for @data».comb -> @chars {
        for @chars.kv -> $pos, $char {
            @freq[$pos]{$char}++;
        }
    }

    # Column labels
    my @labels = @data.join.comb.unique.sort;
    say join "\t", '', @labels;

    # Table rows
    for @freq.kv -> $pos, %score {
        say join "\t",
            ($pos+1).fmt("%2d"),
            %score{@labels}.map( * / %score.total )».fmt("%.2f")
    }
[download]

...and the output:

           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]

Or with:

    my @data = < AABBC BAABC AABBD AECBBF >;
[download]

...you get:

           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    1.00
[download]