Histogram of SVM decision values. Distribution of SVM decision values of RNAz-positive alignments. The upper histogram belongs to all alignments of the test set. Whereas the lower one shows the distribution of the decision values for shuffled alignments. Columns of the test alignments were randomly permuted to create shuffled alignments. Red dotted bins denote alignments where the ncRNA has the same reading direction as the alignment. Black bins belong to alignments where the ncRNA is contained in the reverse complement. Note that the shuffling procedure does not completely destroy the direction information.