I'd suggest s/\]([ATCG]+)\[/"N" x length($1)/e, which replaces the ]...[ part with one "N" for each letter in between the closing and opening bracket.
Jeff japhy Pinyan, P.L., P.M., P.O.D, X.S.: Perl, regex, and perl hacker
How can we ever be the sold short or the cheated, we who for every service have long ago been overpaid? ~~ Meister Eckhart

In reply to Re: Quantified Regex Replacement by japhy
in thread Quantified Regex Replacement by monkfan

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