Summary of all the average self/nonself overlaps obtained using peptides predicted to be presented on HLA molecules.

Overlaps were determined using all positions of the peptide (P1–9), the non-anchor positions (P1 and P3–8) or the middle positions between the anchors (P3–8). Further, overlaps were determined as exact, i.e. every position should be identical, or as degenerate, i.e. with 1 or 2 substitutions being allowed to mimic T-cell recognition (see Methods). Finally, overlaps with 100% or (a randomly chosen) 50% of the human proteome are shown. Self/nonself overlaps indicated with a star (*) are shown per HLA molecule in Figure 2.