Hi kulakrnineha220,
And your question is?
Please read How do I post a question effectively?
You are welcome to the monastery.

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;
}
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This is my query

Which course are you taking? You'll have better luck on http://www.biostars.org