Hi sreya,

I would have love to see the result your code was giving. However, If I may advice I will say use warnings and strict in your perl code ALWAYS.
There are also several modern way of doing what you want done. Like your open, using a 3-arguments is preferred.
All that been said, you could get around your code issue like so:

use warnings;
use strict;

use Data::Dumper;

my %data;
my $header;

while (<DATA>) {
    chomp;
    next if /^$/;    # skip on blanck line
    if (/^>\D+?(\d+?)$/) {
        $header = $1;
    }
    else {
        $data{$header}{$_}++ for split //, $_;
    }
}

print Dumper \%data;

__DATA__
>header1

aaaaabbbb

ccccddd

>header2

ggggg

jjj

kkkk
[download]

$VAR1 = {
          '1' => {
                   'a' => 5,
                   'b' => 4,
                   'c' => 4,
                   'd' => 3
                 },
          '2' => {
                   'g' => 5,
                   'j' => 3,
                   'k' => 4
                 }
        };
[download]