I improved my script for comparing three files, now it is comparing file 1 to 2, file 1 to 3 but it is not able to compare file 2 to 3.

file 1

AT4G01510.1 1 6993 7241
AT1G01020.2 1 7320 8668
AT1G01050.1 1 31388 32672

file 2

AT1G43722.1 1 13306624 13307584
AT3G30520.1 1 13307748 13309520
AT5G59280.1 1 13330509 13331505

file 3

AT1G01010.1 1 3760 5627
AT1G01020.1 1 6918 7232
AT1G01020.1 1 8236 8666

#!/usr/bin/perl -w
use strict;
use Getopt::Std;
use vars qw ($opt_s $opt_p $opt_t);
getopts ('s:p:t:');

if(! $opt_s || !$opt_p || !$opt_t){
   print "Usage: $0\n";
   print "-s file1 output file \n";
   print "-p file2 output file \n";
    print "-t file3 output file \n";
   exit;
}

my $tablefile1 = $opt_s;
my $tablefile3 = $opt_p;
my $tablefile2 = $opt_t;



if(!$tablefile1){
   die "Invalid data file name $tablefile1.\n";
}
if(!$tablefile2){
   die "Invalid data file name $tablefile2.\n";
}
if(!$tablefile3){
   die "Invalid data file name $tablefile3.\n";
}

open(IN,$tablefile1) || die "Can't open $tablefile1..exiting.\n";

my %hash = ();
my @coord_arr = ();
my @chrs = ();
while(<IN>){
 chomp;
 next if (/^\s*$/);
 my @cols = split(/\t/, $_);

      my $id = $cols[0];

      my $chr = $cols[1];
      my $s = $cols[2];
      my $e = $cols[3];

     if (exists($hash{$chr})) {
      my $str = $hash{$chr};
      $hash{$chr} = "$str/$id:$s:$e";
    } else {
      $hash{$chr} = "$id:$s:$e";
    }

}
close IN;

open(IN,$tablefile2) || die "Can't open $tablefile1..exiting.\n";

while(<IN>){
 chomp;
 next if (/^\s*$/);
 my @cols = split(/\t/, $_);

      my $id = $cols[0];

      my $chr = $cols[1];
      my $s = $cols[2];
      my $e = $cols[3];

     if (exists($hash{$chr})) {
      my $str = $hash{$chr};
      $hash{$chr} = "$str/$id:$s:$e";
    } else {
      $hash{$chr} = "$id:$s:$e";
    }

}
close IN;

open(IN,$tablefile3) || die "Can't open $tablefile3..exiting.\n";
my $found = 0;
print "Chr\tfile1-ID\tStart\tEnd\tfile2-ID\tStart\tEnd\tStart-diff\tend-diff\tfile3-ID\tStart\tEnd\tstart-diff\tend-diff\n";
while(<IN>){
 chomp;
 next if (/^\s*$/);
 my @cols = split(/\t/, $_);

      my $id = $cols[0];

      my $chr = $cols[1];
      my $s = $cols[2];
      my $e = $cols[3];

      my $info_str = $hash{$chr};
      next if (!$info_str);

      my @pseudos = split(/\//, $info_str);
      #my @pseudos2 = split(/\//, $info_str);

      for (my $i = 0; $i < @pseudos; $i++) {
         my ($id1, $s1, $e1) = split(/:/, $pseudos[$i]);

         if (&is_overlap($s, $e, $s1, $e1)) {
            print "$chr\t$id\t$s\t$e\t$id1\t$s1\t$e1\t";
           my $d1 = $s1-$s;
           my $d2 = $e1-$e;
           print "$d1\t$d2\t";
         }
      }

      for (my $j = 0; $j < @pseudos; $j++) {
         my ($id2, $s2, $e2) = split(/:/, $pseudos[$j]);

         if (&is_overlap2($s, $e, $s2, $e2)) {
           print "$id\t$s2\t$e2\t";
           my $d3 = $s2-$s;
           my $d4 = $e2-$e;
           print "$d3\t$d4\n";
         }     
      }
}

close IN;

sub is_overlap {
   my ($s, $e, $s1, $e1) = @_;

   my $found = 0;

   if ($s >= $s1 && $s < $e1 ||
       $s1 >= $s && $s1 < $e ||
       $s1 >= $s && $e1 <= $e ||
       $s1 <= $s && $e1 >= $e) {
      $found = 1;
   }

   return $found;
}

sub is_overlap2 {
   my ($s, $e, $s2, $e2) = @_;

   my $found = 0;

   if ($s >= $s2 && $s < $e2 ||
       $s2 >= $s && $s2 < $e ||
       $s2 >= $s && $e2 <= $e ||
       $s2 <= $s && $e2 >= $e) {
      $found = 1;
   }

   return $found;
}