Your code is very confusing to me as I haven't seen the previous post. Is something like this what you meant? 
#!usr/bin/perl -w
use strict;

my @input_files=<*.seq>;

my $sequence='ABCD';
my @headings=('Tags', 'Frequency');
my $headings=join("\t",@headings);  #"Tags\nFrequency"

foreach my $input_file(@input_files)
{
   open(INPUT, '<', $input_file) or die "Cannot open file: $!\n";

   my $outfile=$input_file;
   $outfile =~ s/.seq/.tag.txt/i;  #/g makes no sense
   open (OUTPUT, '>', $outfile") or die "Cannot open file $!\n";
   
   print OUTPUT "\n$headings\n";
   while (my $line=<INPUT>)
   {
      if ($line=~m/$sequence(.{11})(.{11})$sequence/o)
      {
          print OUTPUT  "$1\n$2\n";
      }
   }
}

[download]
I'm sure that there is still stuff wrong with this code. Can you show one input file (a few lines) and the expected output of your program?

In reply to Re: Creating a column of frequency for the unique entries of another column by Marshall
in thread Creating a column of frequency for the unique entries of another column by bluray

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