Not sure what you mean. Something like this?

use strict;
use warnings;

my @seqs = qw( DFGR----- ----AERGD DOGRGERG- ---QWERTY -----ER-- ---EF
+BEGB -ASDF---- AFBDFBA-- -FGDFBD-- );

my $i=0;
while ($seqs[0]) {
    my $col = join '', map { substr $_, 0, 1, '' } @seqs;
    my $na = $col =~ tr/A/A/;
    my $n  = $col =~ tr/-/-/c;
    printf "%d: na=%d n=%d fau=%.2f\n", $i++, $na, $n, $na/$n;
}
[download]