Table 1. Summary of all the average self/nonself overlaps obtained using peptides predicted to be presented on HLA molecules.

		Recognized peptide positions
	Self	P1–9	P1 and P3–8	P3–8
	percentage	(complete)	(non-anchor)	(middle)
Exact	100	0.15%*	0.41%	2.7%*
	50	0.09%	0.25%	1.6%
Degenerate	100	0.7%	5.2%	29%*

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.