RNA molecules and their reverse complements in general form fairly similar secondary structures [25]. For individual sequences, small differences between plus and minus strand arise from small asymmetries in the energy model [9]. In a multiple sequence alignment, GU pairs in an evolutionary conserved stem provide information on the correct reading direction since their reverse complement, AC, is not a canonical base pair. Nevertheless, it is a surprisingly hard problem to recognize the correct reading direction of a structured RNA from a multiple sequence alignment in practise. This is an important task in genome annotation, however, since without reliable strand information it is not even possible to determine whether an evolutionarily conserved secondary structure is located in an UTR or intron, or in an antisense transcript. The reading direction is also of obvious importance in context of recognizing class membership by means of short sequence motifs such as SMN-binding sites [26] or a Cajal body localization signal [27].