MOSAL (MultiObjective Sequence Alignment) is a software tool that computes Pareto optimal alignments for bicriteria pairwise sequence alignment. Thus, it provides solutions for detailed analysis on the relations between two biological sequence, e.g. DNA and RNA.
For more information please take a look at http://mosal.dei.uc.pt.
There is an online tool at http://mosal.dei.uc.pt/align that lets you align two sequences and visualize the results of the alignment (see screenshots below).
 M. Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P. Matias, Improvements on bicriteria pairwise sequence alignment: algorithms and applications, Bioinformatics, 29(8):996-1003, 2013.
 L. Paquete, P. Matias, M. Abbasi, M. Pinheiro, MOSAL: Software tools for multiobjective sequence alignment, Source Code for Biology and Medicine, 9(2), 2014.