And, in the spirit of TIMTOWTDI, here's one without RegExes:

#!perl

use strict;
use warnings;

my $seq   
 = 'GUAUGUUUAACAGUGAUACUAAAUUUUGAACCUUUCACAAGAUUUAUCUUUAAAUAUGUUAUGA';
my $search = 'UUUAA';


my $max = length($seq) - length($search);
my $i = 0;

my @results;

while ($i < $max) {
   $i = index($seq, $search, $i);
   if ($i == -1) {
      last;
   } else {
      push @results, $i;
   }
   ++$i;
}

print @results . " match(es)\n\n";
print "    $seq\n";
for (@results) {
   printf "%02.2d: %s%s\n", $_, ' ' x $_, $search;
}
[download]

It might be faster or not ;-).

Hope this helped.
CombatSquirrel.

---

Entropy is the tendency of everything going to hell.