There are lots of tools or methods can be used to predict secondary structure of RNAs, such as Mfold, RNAStructure, Sfold, MC-Fold.......[the following review would be helpful].
Best whishes!
What are the online tools by which I can predict the secondary structure of RNA??? - ResearchGate. Available from: https://www.researchgate.net/post/What_are_the_online_tools_by_which_I_can_predict_the_secondary_structure_of_RNA [accessed Apr 15, 2016].
Article RNA structure prediction: Progress and perspective