Example showing mismatched stems in an alignment produced by CARNA. (a) The alignment of two pseudoknot structures with PDB IDs 1L2X and 1RNK respectively produced by CARNA. (b) Illustration of mismatched stems in the alignment produced by CARNA. There is a stem mismatch between the blue stem of 1L2X and the red stem of 1RNK, a situation that is not favored when performing pseudoknot alignment. (c) The alignment of 1L2X and 1RNK produced by RKalign where there is no stem mismatch.