How do I put bracket on substring(s) of a string?

monkfan has asked for the wisdom of the Perl Monks concerning the following question:

I am trying to put the bracket in a string given the set of its substrings. Like this:

    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
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