chr            start        end
chr21   9411509 9411529
chr21   9411510 9411529
chr21   9411509 9411529
chr21   9411569 9411589
chr21   9411571 9411591
chr21   9411572 9411592
chr21   9411573 9411593
chr21   9411575 9411595
chr21   9411578 9411598


##</code><code>##

|-----|
    |-----|
          |-----|
   |------|


##</code><code>##

|----|
      |----|
           |-----|
                    |-----|


##</code><code>##

TSSD_ID  Start position End  position  Count overlapped
ID_1        XXXXX               XXXXXX          54


##</code><code>##

#!/usr/bin/perl -w

use strict;
use warnings;
my $data = <>;
my $tol  = 2;
my @chr; 
my @start;
my @end;
my @count;
my @strand;
while ( $data = (<>) ) {
	my (
		$chr,        $start,   $end,      $info,
		$cnt, $strand, $start2, $end2,
		$color,   $cnt2, $length , $zero
	  )
	  = split( "\t", $data );
	push( @chr, $chr);
push (@start, $start);
push (@end, $end);
push (@strand, $strand);
}
my $cl1length = @start;
my $cl2length = @end;
print "TSSD_ID \t Start \t End \t Count\t Strand \n" ;
foreach ( my $i =0 ; $i < $cl1length ; $i = $i++) {
	for ( my $i = 1 ; $i < $cl1length ; $i++ ) {
my $ID = 1;	
my $count = 0;
for (my $j = 0 ; $j < $cl2length ; $j++) {
	if ( $tol < ( $start[$i] - $start[$i+1] ) ) { $ID++; }
if ($start[$i]-$start[$j] == 0) { $count++;}}
	print  "ID_$ID \t $chr[$i] \t $start[$i] \t $end[$i] $count \t $strand[$i]  \n"; }}