What to use to edit RNA alignments?
I would suggest use RALEE—RNALignment Editor in Emacs. It can get for you the consensus secondary structure, you can move left/right sequences and their secondary structures (you can't do it in JalView!), and more.

It's an Emacs mode, so could be a bit hard to start off, but just try, you don't have to use all Emacs features to edit your alignments! 


  The RALEE (RNA ALignment Editor in Emacs) tool provides a simple
  environment for RNA multiple sequence alignment editing, including
  structure-specific colour schemes, utilizing helper applications for
  structure prediction and many more conventional editing functions.


Sam Griffiths-Jones Bioinformatics (2005) 21 (2): 257-259.




Fig. You can move left/right sequences and their secondary structures (you can't do it in JalView!)