GU base pair dependency. Scatter plots depicting separability between both strands depending on GU base pair content (histograms). Red data points denote alignments in the reading direction of the ncRNA, while black data points belong to their realigned reverse complements. Alignments of tRNAs and U70 snoRNAs do not have significantly different number of sequences nor differ significantly in mean pairwise identity (see Additional file 1). That alignments in reading direction of U70 snoRNA are well separated from their reverse complements compared to alignments containing tRNAs is due to high content of GU base pairs in the secondary structure of U70 snoRNAs.