$ perl -le'
my @x = (
    [ q/CCCATCTGTCCTTATTTGCTG/, [ qw(ATCTG ATTTG) ] ],
    [ q/ACCCATCTGTCCTTGGCCAT/,  [ qw(CCATC) ] ],
    [ q/CCACCAGCACCTGTC/,       [ qw(CCACC CCAGC GCACC) ] ],
    [ q/CCCAACACCTGCTGCCT/,     [ qw(CCAAC ACACC) ] ],
    );
for ( @x ) {
    my $str = $_->[0];
    for my $subs ( @{ $_->[1] } ) {
        ( $regex = $subs ) =~ s/(.)(?=.)/$1\[][]?/g;
        $str =~ s{($regex)}{ ( $1 =~ /]/ ? "" : "[" ) . "$subs]" }eg;
        }
    print $str;
    }
'
CCC[ATCTG]TCCTT[ATTTG]CTG
AC[CCATC]TGTCCTTGGCCAT
[CCACCAGCACC]TGTC
C[CCAACACC]TGCTGCCT