If it helps the program reads in strings of DNA and prints to an output file the bits that don't overlap. $counter reads along one string, and $orf_counter counts the position in the second file. $pos_start and $pos_end just refer to the start and stop positions of matches. Hope someone can spot the mistake!

#! /usr/local/bin/perl -w

use strict;

my($num_of_params,$line,$key,$name);
my @keys;
my %orf_hash_pos;                              
$num_of_params = @ARGV;

if($num_of_params < 3)
{
  die ("\n Not enough params have been entered!!!!\n");

}

open (ORF_POS, $ARGV[0]) or die "unable to open file";
open (FASTA, $ARGV[1]) or die "unable to open file";


 open (OUTFILE, ">$ARGV[2]");

foreach $line (<ORF_POS>)
{
  if(! ($line =~ /(\d+)\s+(\d+)\s+(\d+)/))
  {
    print "CHECK YOR FILE .... continue \n";
    next;
  }

 if($2 <= $3)                               
 {
    $orf_hash_pos{$2} = $3;
  }
  else
  {
    $orf_hash_pos{$3} = $2;
  }

}

@keys = sort { $a <=> $b } ( keys %orf_hash_pos );

#--------------- step 2 ---------------------------

my $counter=0;
my $orf_counter=0;
my $new_pos;
my $pos_start=0;
my $pos_end=0;
my $found_new=0;
my @lines;
my @dna;
my @orf_array_pos;
my $base;
my $dna;
my $orf_names;


@lines = <FASTA>;

chomp @lines;       
$dna = join( '', @lines);

@dna = split( '', $dna);

foreach $key (@keys)
{
  push @orf_array_pos , $key;
  push @orf_array_pos , $orf_hash_pos{$key};
}                                                 
$pos_start = $orf_array_pos[$orf_counter];
$pos_end = $orf_array_pos[$orf_counter+1];
$found_new=0;

foreach $base (@dna)
{

  if( ($counter > $pos_end) && ($orf_counter < @orf_array_pos) )
    {
    $orf_counter += 2;
    $new_pos = $orf_array_pos[$orf_counter];            
 
if($new_pos < $pos_end)
      {
      $pos_start = $pos_end;
      }
    else
      {
      $pos_start = $new_pos;
      }
    $pos_end = $orf_array_pos[$orf_counter+1];
   }                                  

 if( ($counter >= $pos_start) && ($counter <= $pos_end) )
  {
    $found_new=0;
  }
  else
  {
    if($found_new==0)
      {
      $orf_names = $orf_counter + 1;
      $found_new=1;
      print "\n\n> dORF$orf_names \n";
      print OUTFILE "\n\n> dORF$orf_names \n";

      }
    print $base;
    print OUTFILE $base;

  }
$counter++;
}


print "\n";
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Edit by tye