observed and predicted values. By this token, a terminal position is included in the motif if it contributes with information at a level above what could be considered to be noise. In contrast, if the inclusion of a putative terminal position does not lead to a reduction in the RSME then it can be concluded that it does not add useful parameters to the model; rather, it lowers the predictive performance and should be omitted. This approach was used to suggest the motif length of the 14 MHC class II HLA-DR alleles, which were searched for optimal predictive performance by scanning through possible lengths from 6 to 11 amino acids. NNalign will report the length associated with the lowest RMSE value as the optimal motif length (see Figure 2 , left hand panel). Nonetheless, the user is advised to inspect the sequence logo as well as the performance plot of the RMSE as a function of the motif length to evaluate whether the dependence upon length appears significant. As defined here and illustrated in Figure 2 right panel, the 9-mer preference of HLA-DRB1*01:01 is significant, whereas the apparent 8-mer preference of HLA-DRB1*15:01 is not significant. In fact, for the 14 HLA-DR molecules included in the benchmark, only one was found to have a single consistent optimal motif length (DRB1*0101 with a motif length of 9 amino acids). For all other molecules the method did identify more than one possible optimal motif length. However, all motif lengths fell in the range of 7 to 10 amino acids, and in all cases a 9-mer motif was compatible with being the optimal motif length.