In the example for STEMLOOP there are obviously several competing structures. The program MFOLD calculates energy matrices that determine all optimal and suboptimal secondary structures for an RNA molecule. The program PLOTFOLD offers different ways of displaying this information.
For anything other than a very short sequence MFOLD should be run in batch mode. The AGRENET version of MFOLD does not run interactively, but submits a batch job.
$ Mfold
(Linear) MFOLD what sequence ? Rna1.seq
Begin (* 1 *) ?
End (* 121 *) ?
What should I call the energy matrix output file (* Rna1.mfold *) ?
Submit MFold job to which batch queue (* LONG *) ? short