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McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-.
This publication is provided for historical reference only and the information may be out of date.
Table 4Position penalties for SSO nucleotide mismatches
| 5' | 10 | 9 | 8 | 7 | 6 | 5 | 4 | 3 | 2 | 1 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 3' |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0.22 | 0.22 | 0.34 | 0.34 | 0.70 | 0.70 | 0.80 | 0.80 | 0.80 | 0.80 | 0.80 | 0.80 | 0.80 | 0.80 | 0.70 | 0.70 | 0.34 | 0.34 | 0.22 | 0.22 | ||
| Probe | T | T | T | C | T | T | C | A | C | A | T | C | C | G | T | G | T | C | C | C | |
| DNA template | T | T | T | C | T | C | C | A | C | A | T | C | C | G | T | G | T | C | C | C |
Match score calculation for SSO probes.
A 20-mer SSO anneals to a mismatched DNA. Both probe and template are shown in the sense orientation. The substitution of T with C leads to the probe-template mismatch T-G with a penalty of 0.42 (refer to Table 2).
This position has a 70% influence on the overall probe reactivity.
The overall probe score is 1 − (0.7 × 0.42) = 0.71.
- Table 4, Position penalties for SSO nucleotide mismatches - The NCBI HandbookTable 4, Position penalties for SSO nucleotide mismatches - The NCBI Handbook
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