I get the correct output too (on AS v 5.61 for WinXP). Try updating your perl as Joost suggests.

If you still get strange results, maybe your input file is corrupt in some way? I doubt if this would work, but try putting:

s/[^acgt]//ig;

at the top of your while loop.

dave

In reply to Re: Continueing probles w/ "index" -- more info by Not_a_Number
in thread Continueing probles w/ "index" -- more info by jkmiller

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