MHC-II Allele RANK POS. N SEQUENCE C MW (Da) SCORE % OPT. MHC-II I_Ab 1 42 GQL YNAVITSHA IMM 957.05 10.099 28.34% MHC-II I_Ab 2 80 APD MSFPRLNNV SYW 1059.25 10.012 28.10% MHC-II I_Ab 3 187 LTL PVLAGAITM LLM 854.07 9.53 26.75% MHC-II I_Ab 4 90 NVS YWLMPVSLM LIL 1098.42 8.674 24.34% MHC-II I_Ab 5 16 WSG MVGAGLSIL IRA 842.06 8.556 24.01% MHC-II I_Ad 1 43 QLY NAVITSHAI MMI 907.03 18.11 34.08% MHC-II I_Ad 2 166 ISL EHLSLFVWT VFV 1090.28 8.935 16.81% MHC-II I_Ad 3 157 TVK NMRSASISL EHL 960.12 7.307 13.75% MHC-II I_Ad 4 140 LHC SGVSSILGG INF 757.84 5.106 9.61% MHC-II I_Ad 5 135 LAI FSLHCSGVS SIL 918.04 4.79 9.01% MHC-II I_Ag7 1 80 APD MSFPRLNNV SYW 1059.25 8.379 20.50% MHC-II I_Ag7 2 57 IFF MVMPSLIGG FGN 886.13 7.943 19.43% MHC-II I_Ag7 3 16 WSG MVGAGLSIL IRA 842.06 7.45 18.23% MHC-II I_Ag7 4 46 NAV ITSHAIMMI FFM 998.26 7.024 17.18% MHC-II I_Ag7 5 25 SIL IRAELCKPG FFF 968.19 6.141 15.02% MHC-II I_Ak 1 107 CLV DSSCGTSWT IYP 901.93 17.05 42.73% MHC-II I_Ak 2 65 LIG GFGNWMVPL MLG 979.19 16.596 41.59% MHC-II I_Ak 3 11 LIF GFWSGMVGA GLS 870.02 11.251 28.20% MHC-II I_Ak 4 37 FFF GSGQLYNAV ITS 889.96 9.513 23.84% MHC-II I_Ak 5 79 GAP DMSFPRLNN VSY 1075.21 8.672 21.73%

Table 3: Prediction of MHC II ligands all rows highlighted in red represent predicted binders to the MHC-II Allele i.e. MHC-II I_Ab, MHC-II I_Ad, MHC-II I_Ag7. (All rows highlighted in red represent predicted binders).