#This part was revised by you but this is the old version of  mine
my %file1=();
while(<INPUT1>){
         chomp;
         (my $id, my $number) = split("\t", $_);

          if ($id=~ m/^(CLS_S3_Contig[0-9]+)([-]?)([0-9]+)([_]?)([0-9]+)$/i) {

              my $matched_id=$id; # breaks the CLS_Contig1000_200-202 to its componenents
                  for (my $i=$3-8;$i<$5+8;$i++){
              print join ("\t", $1, $i), "\n";
              push (@{$file1{$1}}, $i);

       }
   }
}
        
close(INPUT1);

#################################
THIS IS YOUR MODIFIED YOUR VERSION 

my %file2 =(); my @true_positives = ();
while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
          if (exists $file1{$current_line[1]} ) {
               my $key = $current_line[1];
                  foreach my $position1 (@{$file1{$key}}){
          if (   $current_line[0] eq $key 
                 && $current_line[1] == $position1
                 && $current_line[2] == 1
                 && $current_line[3] >= 3)
              {
    print join ("\t", @current_line[0..3], "***", $key, $position1), "\n";

          push (@true_positives, $current_line[1]); # I made this up to count the number of true positives but it does not consider duplicates
          push (@{$file2{$current_line[0]}}, $current_line[2]);

                }#end inner if
           }#end foreach
     } #end if
} #end while
        

#############################################
IDENTIFY COMMON ELEMENTS
#############################################
my @common =(); my $common_element ="";
  foreach (keys %file1) {
         push(@common, $_) if exists $file2{$_};
  }

#############################################
IDENTIFY NOT COMMON ELEMENTS
#############################################
my @not_common =();
foreach (keys %file1){
        push(@not_common, $_) unless exists $file2{$_};
}
############ making calculations##########################

my $found_true_markers =""; my $found_false_positives = "";

$found_true_markers = scalar @true_positives;
$found_false_positives = $comnon_element_numbers - $found_true_markers ;
my $truepositive = sprintf ("%.2f", $found_true_markers/$comnon_element_numbers*100);
my $false_positive_rate = sprintf ("%.2f",  $found_false_positives/$comnon_element_numbers*100);
print "$truepositive \% is the rate of true positives\n";
print "$false_positive_rate \% is the rate of fales positives\n";

####################################################
I AM STUCK AT THIS POINT - SOMETIMES IT CALCULATES 
NEGATIVE RATES OR MORE THAN 100%