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";
    }
}