open my $file1,"<","1.txt" or die "1.txt: $!\n";
open my $file2,"<","2.txt" or die "2.txt: $!\n";
open my $w1,">","3.txt" or die "3.txt: $!\n";
open my $w2,">","4.txt" or die "4.txt: $!\n";

##</code><code>##

while (
  defined(my $line1=<$file1>) and defined(my $line2=<$file2>)
 ) {
 if (abs(
   (split"\t",$line1)[2]-(split"\t",$line2)[2]
  )>=2) {
  print $w1 "$line1\n";
  print $w2 "$line2\n";
 }
}