#!usr/bin/perl
use strict;
use warnings;

my $sequence='ABCD';
my @headings= qw/ Tags Frequency /;
my @input_files=<*.seq>;

foreach my $input_file ('o66.txt')
{
	open INPUT, "<", $input_file or die "Cannot open file \"$input_file\". $!";
	(my $outfile = $input_file) =~ s/.seq/.tag.txt/i;
	my %freq;
	
	while (my $line=<INPUT>)
	{
	    
		if ($line=~m/$sequence(.{11})(.{11})$sequence/i){
	     	$freq{$_}++ for $1, $2;
	   	}
		
	}
	close INPUT or die "Cannot close file \"$input_file\". $!";
	#open OUTPUT, ">", $outfile or die "Cannot open file \"$outfile\". $!";
	#printf OUTPUT "%-12s%s\n", @headings;
	printf "%-12s%s\n", @headings;
	for my $tag (sort {$freq{$b} <=> $freq{$a}} keys %freq) {
		#printf OUTPUT "%-12s%5s\n", $tag, $freq{ $tag };
		printf "%-12s%5s\n", $tag, $freq{ $tag};
	}

	#close OUTPUT or die "Unable to close \"$outfile\". $!";
}

__END__
o66.txt is below:
@HWDFFFDDABCDEFFFFDDDDDRFFFFEFFEEDDABCDEDDDDDD
@HWDFFFDDABCDEFFDFEDEDDRFFFFEFFEEDDABCDEDDDDDD
@HWDFFFDDABCDEFFFFDDDDDRFFFFEFFEEDDABCDEDDDDDD
@HWDFFFDDABCDEFFFFDDDDDRFFFFEFFEEDDABCDEDDDDDD
@HWDFFFDDABCDEFFDFEDEDDRFFFFEFFEEDDABCDEDDDDDD

output is:

C:\Old_Data\perlp>perl t.pl
Tags        Frequency
FFFFEFFEEDD     5
EFFFFDDDDDR     3
EFFDFEDEDDR     2