By base i assume you mean each occurence of the four letters representing A is for adenine, G is for guanine, C is for cytosine, T is for thymine, and so you would want to count each of those occurences? so you could

while(<input>)
{
 $sequence = $_;
 chomp($sequence);
 $count=length($sequence);
 if ($count >= $ideal)
 {
   print "$sequence\n"; # or whatever you want here
 }
}
[download]

Hope this is what you had in mind and that it helps
"when a new client is created, we have to kill all the children..." --Sams Teach yourself Perl 5