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Substitution score matrices for human-chimp and human-rhesus alignments
| Alignment | A | C | G | T |
| Human-chimp | 90 | -330 | -236 | -356 |
| -330 | 100 | -318 | -236 | |
| -236 | -318 | 100 | -330 | |
| -356 | -236 | -330 | 90 | |
| Human-rhesus | 87 | -226 | -129 | -255 |
| -226 | 100 | -212 | -129 | |
| -129 | -212 | 100 | -226 | |
| -255 | -129 | -226 | 87 |
