Your inner loop might be clearer as 
   for my $window_offset (0 .. $window_size-1)
   {
        my $j = $i + $window_offset;
        print OUTFILE "$i\t$j\n";
   }

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In reply to Re: Incrementing one "for" loop within another "for" loop by ikegami
in thread Incrementing one "for" loop within another "for" loop by krish28

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