[Computational-biology] Nucleotide Pairing

[Richard Horler]

Hi

I was wondering if anyone knows of a software which would allow me to 
compare sequences to look for the maximum RNA:RNA base pairing. i.e. if 
I input two RNA sequences the program could run through all possible 
alignments and determine which is most stable i.e. most cognate base 
pairs preferably including the none standard Watson Crick base pairs.

Richard