Sorry I couldn't access the net yesterday.

Aaand... YES! That works. Fanfare and fireworks! :)

So as you also found out, the problem was caused by some hits that have multiple <Hsp>-s within one <Hit>. Funny how it was right in front of my eyes yet I couldn't realize it for the first time. Actually the first two hits I sent as a a sample file were just incidental exceptions.

I've edited the original script to include your code, and now it processes every file without any problem.

Excellent work, thank you very much for doing my job and saving me a lot of headache! It was also nice to learn about Perl. Thanks a lot again!