The Vienna RNA Package is available from ftp.itc.univie.ac.at
We have used it sofar for sequences up to approx. 4200 bp
(Qbeta virus). Prediction of the minimum free energy structure is
limited only by the memory of your maschine.
calculates also the partition function (McCaskill 1991) and
the base pairing probabilities. This function is limited by
numerical accuracy, we don't recommand to use it beyond about
2500-4000 bp (You need more than 256 Megabyte of memory then