problems with really short exons (10-6 bp)

[HegedusB]

Dear all, I am surprised how well the program is working. However, I have a question. Is it possible to fine toon the aligner in order to detect smaller exons (10-6 bp). I believe the word size is the limiting factor here. My fungal strain contains a lot of short exons. So far this is the best aligner which can handle most of them correctly, however the really short exons are not really well aligned here neither. Thanks for any helps!