#Given:
my $s5 ='CTGGGTATGGGT';           
my @a5 = qw(GTATG TGGGT);

##</code><code>##

C[TGGGTATGGGT]

##</code><code>##

CTGG[GTATGGGT]

##</code><code>##

$s5 = "CTGGGTATGGGT";
        TGGGT
           GTATG      --
                        |--- Only this two satisfy.
              TGGGT   --     Since it follows order 
                             and delim of the given array.

##</code><code>##

# Given:
my $s6 = 'AGGAACTTGCCTGTACCACAGGAAG'; 
my @a6 = qw( CAGGA AGGAA );

##</code><code>##

[AGGAA]CTTGCCTGTACCA[CAGGAA]G

##</code><code>##

AGGAACTTGCCTGTACCA[CAGGAA]G

##</code><code>##

# Given:
my $s7 = 'CAGGACTTGCCTGTACCACAGGAAG'; 
my @a7 = qw( CAGGA  );

This answer would do:
CAGGACTTGCCTGTACCA[CAGGA]AG

##</code><code>##

# Given:
my $s8 = 'CAGGATTTGAGGAAGTACCACAGGAAG'; 
my @a8 = qw( CAGGA AGGAA );

This answer would do, taking those closest together:
CAGGATTTGAGGAAGTACCA[CAGGAA]G

doesn't have to be this:
[CAGGA]TTTG[AGGAA]GTACCACAGGAAG

##</code><code>##

my $t1 ='CCCATCTGTCCTTATTTGCTG';  
my @ar1 = qw(ATCTG-3 ATTTG-13);

my $t2 ='ACCCATCTGTCCTTGGCCAT';   
my @ar2 = qw(CCATC-2);

my $t3 ='CCACCAGCACCTGTC';        
my @ar3 = qw(CCACC-0 CCAGC-3 GCACC-6);

my $t4 ='CCCAACACCTGCTGCCT';      
my @ar4 = qw(CCAAC-1 ACACC-4);

my $t5 ='CTGGGTATGGGT';           
my @ar5 = qw(GTATG-4 TGGGT-7);

my $t6 = 'AGGAACTTGCCTGTACCACAGGAAG'; 
my @ar6 = qw( CAGGA-18 AGGAA-19 );

my $t7 = 'CAGGACTTGCCTGTACCACAGGAAG'; 
my @ar7 = qw( CAGGA-18  );

my $t8 = 'CAGGATTTGAGGAAGTACCACAGGAAG'; 
my @ar8 = qw( CAGGA-18 AGGAA-19 );

##</code><code>##

sub put_bracket_wth_idx 
{
    my ( $str, $ar ) = @_;
    for my $subs ( @$ar ) 
    {
        my ($sb,$id) = split("-",$subs);
           
        if ( substr( $str, $id ) =~ /$sb/i ) 
        {
         substr( $str, $id, length $sb ) =~ tr/A-Z/a-z/;
        }
    }
    $str =~ s/([a-z]+)/[\U$1\E]/g;
    return $str;
}