| 5' | 18 | 17 | 16 | 15 | 14 | 13 | 12 | 11 | 10 | 9 | 8 | 7 | 6 | 5 | 4 | 3 | 2 | 1 | 3' |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0.03 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.05 | 0.05 | 0.06 | 0.07 | 0.12 | 0.17 | 0.21 | 0.25 | 0.30 | 0.50 | 0.90 | ||
| Primer | T | T | T | C | T | T | C | A | C | C | T | C | C | G | T | G | T | C | |
| DNA template | T | T | T | C | T | T | C | A | C | A | T | C | C | G | T | G | T | C |
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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