use strict;
use warnings;

my $count_A = 0;
while ( my $line = <DATA> ) {
    next if $line =~ m/^>/; # This line probably unnecessary if your data set is as well-behaved as it looks.
    $count_A++ if $line =~ m/A$/;
}
print "$count_A\n";

__DATA__
>2
AAAAAAAAACAAAAGAACGAAGAAGT
>3
AAAAAAAAACAACCGAAAAATAGAAAC
>4
AAAAAAAAACAAGAAGGACTAGACC
>7
AAAAAAAAACAAGGACTGGTTTATCAG
>8
AAAAAAAAACAAGTTTCTCTGTGACT
>12
AAAAAAAAACACAGACGTAGAATTGT
>14
AAAAAAAAACACGACCGTTCGCTTTGA
>15
AAAAAAAAACACGACTGTTCGCTTT
>16
AAAAAAAAACACTATGAGCCAGAAC