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  1. or download this
    while(<DATA>){
s/\]([ATCG]*)\[/'N' x length($1)/e;
...
TG[CCCNNTTT]
TG[CCCTTT]
TG[CCAAATTT]
  2. or download this
    while(<DATA>){
s/\]([ATCG]*)\[/my $a = $1; $a =~ s![^C]+!'N' x length($1)!e; $a/e;
...

Respective Output is:
TG[CCCCCTTT]