What is the best program for partially factoring large numbers?

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(I'm not sure what forum to put this on: number theory because of factoring, programming because I want to automate it, computers because I don't intend to actually program anything myself, or general because it combines these.)

I'm looking for a program that I can use to partially factor numbers that are too large to fully factor (thousands of digits -- 500 to 35,000 bits). I'd like a 'high' chance of finding all factors below 15 digits or so.

A program that has trouble with repeated factors (squareful numbers) is inappropriate, as these numbers may well be divisible by the square of a large (> 1e9) prime. I don't know of any that have trouble with these other than prime powers, but I thought I'd mention it just in case.

So what's out there?
 
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Yes, I'm probably looking for some kind of ECM. But I want to check a large number of, uh, large numbers -- too many to enter by hand, too many even to check by hand (~9,000). Also, something downloadable and fast (not Java) would be nice. I suppose that applet does have source code I could modify, if it came to that... but I was hoping there was something else out there.