my $input_str1 = "TG[CCC]CC[TTT]";

# Desired result is this:

my $rep1 = "TG[CCCNNTTT]";  
# Two Ns replace two Cs in between ][.

# Similarly 
my $input_str2 = "TG[CCC][TTT]";
my $rep2 = "TG[CCCTTT]";