RNAz

This link will bring you to the download page for RNAz which "is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs." The web-server version of this program can be found here: http://rna.tbi.univie.ac.at/