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

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

my $input_str3 = "TG[CCAAATTT]";

# Desired result is this:

my $rep3 = "TG[CCAAATTT]";

$str =~ s/\][ATCG]+\[/N/;