String               Substrings          Desired Result
1.CCCATCTGTCCTTATTTGCTG  ATCTG ATTTG        CCC[ATCTG]TCCTT[ATTTG]CTG
2.ACCCATCTGTCCTTGGCCAT   CCATC              AC[CCATC]TGTCCTTGGCCAT
3.CCACCAGCACCTGTC        CCACC CCAGC GCACC  [CCACCAGCACC]TGTC   *
4.CCCAACACCTGCTGCCT      CCAAC ACACC        C[CCAACACC]TGCTGCCT *

##</code><code>##

#!/usr/bin/perl -w
use strict;

my $s1 ='CCCATCTGTCCTTATTTGCTG';  my @a1 = qw(ATCTG ATTTG);
my $s2 ='ACCCATCTGTCCTTGGCCAT';   my @a2 = qw(CCATC);
my $s3 ='CCACCAGCACCTGTC';        my @a3 = qw(CCACC CCAGC GCACC);
my $s4 ='CCCAACACCTGCTGCCT';      my @a4 = qw(CCAAC ACACC);

#These two work fine.
put_bracket($s1,\@a1);
put_bracket($s2,\@a2);

#But these two don't work
put_bracket($s3,\@a3);
put_bracket($s4,\@a4);

sub put_bracket
{
	my	($str,$ar)	= @_;
    my  $bstr;
    my  $slen = length $ar->[0];

    foreach my $subs ( @$ar  )
    {
      my $idx  = index($str,$subs);
      my $bgn = $idx;
      my $end = $idx+$slen+1;
      substr($str,$bgn,0,"[");
      substr($str,$end,0,"]");
    }
      print "$str\n";
	return ;
}