Pairwise alignment of 200,000 and 20,000 bp sequences

[Max V Myakishev]

I am looking for the tool to perform 
pairwise alignment of 200,000 and 20,000 bp sequences.

Preferable computer platforms: WWW > PC > Mac > UNIX.

I already tried many programs and most of them 
are limited by the input sequence size 32000.

Thanks

Max V Myakishev, Ph.D.
Email: max at scientist.com