This is an attempt to save a thread in SoPW which I thought can be useful for others.

There are already incredible answers in the thread, so feel free to check in SoPW. Please don't misunderstand me. I honestly think this can be useful. I don't mean to boost my XP here, or in that thread which I posted.

One possible answers is given by good sgifford

#!/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 ) = @_;

    foreach my $subs ( @$ar  )
    {
      # Construct a regexp with [\[\]] between all the letters
      my $newsub = join '[\[\]]?', split //, $subs;
      $str =~ s/($newsub)/[$1]/g;
    }

    # Now de-nest the brackets in the string
    my $depth = 0;
    my $newstr = '';
    foreach my $c ( split //, $str )
    {
      if ( $c eq '[' ) {
        $newstr .= $c
          if $depth++ == 0;
      }
      elsif ( $c eq ']' ) {
        $newstr .= $c
          if --$depth == 0;
      }
      else {
        $newstr .= $c;
      }
    }


    return $newstr;
}
[download]

#!perl
use strict;
use warnings;


my @testdata = (['CCCATCTGTCCTTATTTGCTG', [qw(ATCTG ATTTG)]]
               ,['ACCCATCTGTCCTTGGCCAT',  [qw(CCATC)]]
               ,['CCACCAGCACCTGTC',       [qw(CCACC CCAGC GCACC)]]
               ,['CCCAACACCTGCTGCCT',     [qw(CCAAC ACACC)]]);

for (@testdata) {
  my ($str, $pats) = @$_;
  print put_bracket($str, @$pats), "\n";
}

sub put_bracket
{
    my $str = shift;
    # Combine multiple match strings into alternations
    my $rx = join '|', @_;
    my @brackets;
    # Store bracket points for every match
    while ($str =~ /(?=($rx))/g) {
      push(@brackets, [$-[0], length($1)+$-[0]]);
    }
    # Condense overlapping brackets
    for my $i (0..$#brackets-1) {
      if ($brackets[$i][1] >= $brackets[$i+1][0]) {
        $brackets[$i+1][0] = $brackets[$i][0];
        @{$brackets[$i]} = ();
      }
    }
    # Apply the brackets (from back to front)
    while (@brackets) {
      my $b = pop @brackets;
      next unless @$b;
      substr($str, $b->[1], 0) = ']';
      substr($str, $b->[0], 0) = '[';
    }
    return $str;
}
[download]

sub put_brackets
{
    my( $str, @pats ) = @_;
    my $mask = ' ' x length $str;
    my $ofs = 0;
    for ( @pats )
    {
        $ofs = index $str, $_, $ofs;
        last if $ofs < 0; # this pattern not found; look for no more.
        substr $mask, $ofs, length($_), 'a' x length($_);
    }
    # print "string= '$str'\n";
    # print "mask  = '$mask'\n";

    join '', map sprintf(
        /a/ ? '[%s]' : '%s',
        substr $str, 0, length($_), ''
    ), split /\b/, $mask
}

[download]