Another solution might just to generate the regular expression based on the user input. Assuming simple command-line script (or something similar, I didn't see the source of 'users query'. Easily ported to a web-app or something along those lines). You could do something along the lines of:

#!/usr/bin/perl

use strict;
use warnings;

my $regex_cache = {};

die "Usage $0 [CAC <NUM> TTT <NUM>]\n" if ( @ARGV % 2 );
my %input = @ARGV; # Where the input would be : CAC 2 TTT 2

my $data_set = <DATA>;

for my $in ( keys %input ) {
    my $reg_key = "($in)\{$input{$in}\}";
    my $reg = $regex_cache->{$in} ||= qr/($reg_key)/s;
    print "$1\n" if ( $data_set =~ $reg );
}

__DATA__
ATCACCACTTCCTGGACACTACCCTAAACCTTTGAGGA
AATAACCGCTTTGTTGTTGCGATCGCCTAATAAATATC
AGCGTCTTCGTATGATAAACCAATGCGGAAGTACAAAA
[download]

Now, much like the other comments in this thread, I'm not really sure what type of order you are looking for in the set. If 2 CAC means 'CACCAC' or 'CAC\w*CAC', etc. Given the fact that I may have missed this, the compilation of the $reg_key can be changed to be something else. Nevertheless, it will still be able to parse the file based of some sort of input, which is what I believe you were generally looking for.

Sorry if I'm way off base here and my input doesn't help, although I certainly hope it does. Good luck!