Tags        Frequency     
EFFFFDDDDDR   3
FFFFEFFEEDD   3 
EFFDFEDEDDR   2 
FFFFEFFEEDD   2
............
[download]

I got different results from your dataset using the code below. I am assuming you want a new output file for every *.seq input file. You would just need to uncomment the 4 commented statements and change the foreach my $input_file ('o66.txt') line to foreach my $input_file (@input_files).

#!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_fil
+e\". $!";
    (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
[download]

---

---

• Are you posting in the right place? Check out Where do I post X? to know for sure.
• Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:

  <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>

• Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
• Want more info? How to link or How to display code and escape characters are good places to start.