note Enlil I am still reading through your code, but the first thing i notice is:<code> my @Motif = split(//,'$origin[$y]'); # This is a loop to get the motif template from origin8 </code> is probably not doing what you intended. You probably mean the following: <code> # This is a loop to get the motif template from origin8 my @Motif = split(//,$origin[$y]); </code> (note the missing single-quotes) <p> Also it might help if you give us a short bit of the long_sequences.txt so we can run your code. <p>-enlil 479570 479570