Table 3Position penalties for SSP nucleotide mismatches

5'1817161514131211109876543213'
0.030.030.030.030.030.040.040.050.050.060.070.120.170.210.250.300.500.90
PrimerTTTCTTCACCTCCGTGTC
DNA templateTTTCTTCACATCCGTGTC

Match score calculation for SSPs.
An 18-mer primer anneals to a mismatched DNA. Primer and template are shown in the sense orientation. The substitution of C with A leads to the mismatch C-T with a penalty of 0.94 (refer to Table 2).
This position has a 6% influence on the overall probe reactivity.
The overall probe score is 1 − (0.06 × 0.94) = 0.94.

From: Chapter 11, The Major Histocompatibility Complex Database, dbMHC

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