I'd like to propose a different approach, but it relies on one feature of the problem that you haven't made explicit: that all the strings you're dealing with, and all the substrings, are uppercase letters only. If so, then what we can do is make each match case-insensitive and lowercase any region that's found to match. Then, simply place brackets at uppercase/lowercase boundaries, and we're set:

sub put_bracket
{
    my    ($str,$ar)    = @_;

    foreach my $subs ( @$ar  )
    {
      my $lsub = lc($subs);
      s/$lsub/$lsub/ig;
    }
    # add brackets
    $str =~ s/(?:(?<=[A-Z])|^)(?=[a-z])/[/g;
    $str =~ s/(?<=[a-z])(?:(?=[A-Z])|$)/]/g;
    # re-uppercase
    $str = uc($str);
    print "$str\n";
    return ;
}
[download]

But wait! Here's a test case that this code - and all the other code posted to this thread that I've tried - fails on:

my $s5 ='CCACCACCACCTGTC';        my @a5 = qw(CCACC);
put_bracket($s5,\@a5);            # should be [CCACCACCACC]TGTC
[download]

sub put_bracket
{
    my    ($str,$ar)    = @_;

    foreach my $subs ( @$ar  )
    {
      my $lsub = lc($subs);
      do {} while ($str =~ s/(?!$lsub)(?i:$lsub)/$lsub/g);
    }
    # add brackets
    $str =~ s/(?:(?<=[A-Z])|^)(?=[a-z])/[/g;
    $str =~ s/(?<=[a-z])(?:(?=[A-Z])|$)/]/g;
    # re-uppercase
    $str = uc($str);
    print "$str\n";
    return ;
}
[download]

• Repeat as many times as successful:
  • Look for a spot not followed exactly by $lsub, followed by $lsub in some case. (in other words, it finds $lsub not all in lowercase)
  • Replace this by (all lowercase) $lsub.

--
@/=map{[/./g]}qw/.h_nJ Xapou cets krht ele_ r_ra/;
map{y/X_/\n /;print}map{pop@$_}@/for@/
[download]