Greetings,
In your example you have two different situations:
The "and" situation "2 CAC and 2 TTT" in which case its really two seperate searches.
And the "single" search situation "1 A|T CAC", "2 C|A TTT T|G".

If your search criteria is submitted as you have specified you could split the query on "and" or "or" to handle your first situation. Once split, capture out the count criteria and test with the scalar return value from your array of matches using the 
(@array) = $string =~ /$pattern/g

[download]
idiom.

Untested Idea! 
my $base_data = 'ATCACTGGTTCCTGGACACTACCCTAAACCTTTGAGGA
AATAACCGCTTTGTTGTTGCGATCGCCTAATAAATATC
AGCGTCTTCGTATGATAAACCAATGCGGAAGTACAAAA
TAAAGAGACTGTATTATGTTACT';

#the user submitted search pattern
my $search_submitted = '2 CAC and 2 TTT';

#split it into chunks if applicable.
my @search_chunks = split /and|or/, $search_submitted;

#for each distinct pattern
foreach my $chunk (@search_chunks){

    #get the count we are looking for and the pattern we want to use
    my ($count, $search_string) = $chunk =~ /\s?(\d+)\s?([ATGCU\s\|]+)
+/;

    #replace the |'s with character classes.
    $search_string =~ s/([ATGCU])\|([ATGCU])/[$1$2]/g;

    #replace all spaces
    $search_string =~ s/\s+//g;

    #run the match and see how many we get.
    my (@search_count) = $base_data =~ /$search_string/g;

    #check our results.
    if(scalar @search_count >= $count){
        print "Found it!\n";
    }else{
        print "Nope...".scalar @search_count."\n";
    }
}

[download]
Is that sort of what you were thinking of?

Update
grep was not what I wanted after all...

-InjunJoel
"I do not feel obliged to believe that the same God who endowed us with sense, reason and intellect has intended us to forego their use." -Galileo

In reply to Re: generate regular expression by injunjoel
in thread generate regular expression by khoueiry

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