#!/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);

put_bracket($s1,\@a1);
put_bracket($s2,\@a2);

put_bracket($s3,\@a3);
put_bracket($s4,\@a4);

sub put_bracket
{
    my  ($str,$ar) = @_;
    my  $slen = length $ar->[0];
    my  @brackets;
    foreach my $subs ( @$ar  )
    {
        my $idx  = index($str,$subs);
        my $bgn = $idx;
        my $end = $idx + $slen + 1;
        push @brackets, ($bgn, $end);
    }
    
    my @filtered = $brackets[0];
    for (1..$#brackets-1)
    {
        push @filtered, $brackets[$_] if 
        ($brackets[$_] < $brackets[$_+1] and
        $brackets[$_-1] < $brackets[$_]);
    }
    push @filtered, $brackets[-1];
    while (@filtered)
    {
        substr($str, pop @filtered, 0, ']');
        substr($str, pop @filtered, 0, '[');
    }
    print $str,"\n";
    return;
}