I am not quite in this topic anymore but your problem could maybe be solved using the Vienna package. There are subprograms which calculate alignments between two RNAs (including the minimum free energy). If you are only interested in the alignment maybe you could set the parameter for the minimum free energy constraint to some irrelevant value. This is some workaround but maybe it helps.

Awesome. I will try. Thanks for your help

Thanks. I appreciate it.