Table 1.
Log odds matrices for PBI and NPBI.
| (A) PBI model. | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PBI | A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V |
| A | 3 | −2 | −1 | −1 | −1 | −1 | −1 | −1 | −2 | −2 | −2 | −1 | −1 | −2 | −1 | 0 | 0 | −3 | −2 | 0 |
| R | −2 | 3 | −1 | −2 | −2 | 0 | −1 | −2 | −1 | −2 | −2 | 1 | −2 | −3 | −2 | −1 | −2 | −2 | −2 | −2 |
| N | −1 | −1 | 4 | 0 | −1 | −1 | −1 | −1 | 0 | −2 | −3 | 0 | −2 | −2 | −2 | 0 | −1 | −3 | −2 | −2 |
| D | −1 | −2 | 0 | 3 | −3 | −1 | 1 | −1 | −1 | −3 | −3 | −1 | −3 | −3 | −2 | −1 | −1 | −4 | −3 | −3 |
| C | −1 | −2 | −1 | −3 | 6 | −2 | −3 | −2 | −2 | −2 | −2 | −2 | −1 | −1 | −3 | 0 | −1 | −2 | −1 | −1 |
| Q | −1 | 0 | −1 | −1 | −2 | 4 | 0 | −2 | 0 | −2 | −1 | 0 | −1 | −3 | −2 | −1 | −1 | −2 | −2 | −2 |
| E | −1 | −1 | −1 | 1 | −3 | 0 | 3 | −2 | −2 | −3 | −2 | 0 | −2 | −3 | −2 | −1 | −1 | −3 | −3 | −2 |
| G | −1 | −2 | −1 | −1 | −2 | −2 | −2 | 3 | −2 | −4 | −3 | −2 | −3 | −3 | −2 | −1 | −2 | −3 | −3 | −3 |
| H | −2 | −1 | 0 | −1 | −2 | 0 | −2 | −2 | 4 | −2 | −2 | −1 | −2 | −1 | −2 | −1 | −2 | −2 | 0 | −2 |
| I | −2 | −2 | −2 | −3 | −2 | −2 | −3 | −4 | −2 | 3 | 0 | −2 | 0 | −1 | −2 | −2 | −1 | −3 | −2 | 1 |
| L | −2 | −2 | −3 | −3 | −2 | −1 | −2 | −3 | −2 | 0 | 3 | −2 | 1 | 0 | −2 | −2 | −2 | −2 | −1 | 0 |
| K | −1 | 1 | 0 | −1 | −2 | 0 | 0 | −2 | −1 | −2 | −2 | 3 | −1 | −3 | −2 | −1 | −1 | −3 | −2 | −2 |
| M | −1 | −2 | −2 | −3 | −1 | −1 | −2 | −3 | −2 | 0 | 1 | −1 | 4 | −1 | −3 | −1 | −1 | −2 | −2 | 0 |
| F | −2 | −3 | −2 | −3 | −1 | −3 | −3 | −3 | −1 | −1 | 0 | −3 | −1 | 4 | −3 | −2 | −2 | 0 | 1 | −1 |
| P | −1 | −2 | −2 | −2 | −3 | −2 | −2 | −2 | −2 | −2 | −2 | −2 | −3 | −3 | 4 | −1 | −1 | −3 | −3 | −2 |
| S | 0 | −1 | 0 | −1 | 0 | −1 | −1 | −1 | −1 | −2 | −2 | −1 | −1 | −2 | −1 | 3 | 0 | −2 | −2 | −2 |
| T | 0 | −2 | −1 | −1 | −1 | −1 | −1 | −2 | −2 | −1 | −2 | −1 | −1 | −2 | −1 | 0 | 3 | −3 | −2 | 0 |
| W | −3 | −2 | −3 | −4 | −2 | −2 | −3 | −3 | −2 | −3 | −2 | −3 | −2 | 0 | −3 | −2 | −3 | 6 | 0 | −2 |
| Y | −2 | −2 | −2 | −3 | −1 | −2 | −3 | −3 | 0 | −2 | −1 | −2 | −2 | 1 | −3 | −2 | −2 | 0 | 4 | −2 |
| V | 0 | −2 | −2 | −3 | −1 | −2 | −2 | −3 | −2 | 1 | 0 | −2 | 0 | −1 | −2 | −2 | 0 | −2 | −2 | 3 |
| (B)NPBI model. | ||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NPBI | A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V |
| A | 3 | −1 | −1 | −1 | −1 | −1 | −1 | −1 | −1 | −1 | −1 | −1 | −1 | −2 | −1 | 0 | 0 | −2 | −2 | 0 |
| R | −1 | 3 | −1 | −2 | −2 | 0 | −1 | −2 | 0 | −2 | −1 | 1 | −1 | −2 | −2 | −1 | −1 | −2 | −2 | −2 |
| N | −1 | −1 | 3 | 0 | −2 | −1 | −1 | −1 | 0 | −2 | −2 | 0 | −2 | −2 | −2 | 0 | 0 | −3 | −1 | −2 |
| D | −1 | −2 | 0 | 3 | −3 | −1 | 0 | −1 | −1 | −3 | −3 | −1 | −2 | −3 | −1 | −1 | −1 | −3 | −2 | −2 |
| C | −1 | −2 | −2 | −3 | 6 | −2 | −3 | −2 | −1 | −1 | −1 | −2 | −1 | −1 | −2 | −1 | −1 | −1 | −1 | −1 |
| Q | −1 | 0 | −1 | −1 | −2 | 3 | 0 | −2 | 0 | −2 | −1 | 0 | −1 | −2 | −1 | −1 | −1 | −2 | −2 | −1 |
| E | −1 | −1 | −1 | 0 | −3 | 0 | 2 | −2 | −1 | −2 | −2 | 0 | −2 | −3 | −1 | −1 | −1 | −3 | −2 | −2 |
| G | −1 | −2 | −1 | −1 | −2 | −2 | −2 | 3 | −2 | −3 | −3 | −2 | −2 | −3 | −2 | −1 | −2 | −3 | −3 | −3 |
| H | −1 | 0 | 0 | −1 | −1 | 0 | −1 | −2 | 4 | −2 | −1 | −1 | −2 | −1 | −2 | −1 | −1 | −1 | 1 | −2 |
| I | −1 | −2 | −2 | −3 | −1 | −2 | −2 | −3 | −2 | 4 | 1 | −2 | 1 | 0 | −2 | −2 | −1 | −2 | −1 | 2 |
| L | −1 | −1 | −2 | −3 | −1 | −1 | −2 | −3 | −1 | 1 | 3 | −2 | 1 | 0 | −2 | −2 | −1 | −1 | −1 | 0 |
| K | −1 | 1 | 0 | −1 | −2 | 0 | 0 | −2 | −1 | −2 | −2 | 3 | −1 | −2 | −1 | −1 | −1 | −3 | −2 | −2 |
| M | −1 | −1 | −2 | −2 | −1 | −1 | −2 | −2 | −2 | 1 | 1 | −1 | 5 | 0 | −2 | −1 | 0 | −1 | −1 | 0 |
| F | −2 | −2 | −2 | −3 | −1 | −2 | −3 | −3 | −1 | 0 | 0 | −2 | 0 | 4 | −3 | −2 | −2 | 1 | 2 | −1 |
| P | −1 | −2 | −2 | −1 | −2 | −1 | −1 | −2 | −2 | −2 | −2 | −1 | −2 | −3 | 4 | −1 | −1 | −3 | −2 | −2 |
| S | 0 | −1 | 0 | −1 | −1 | −1 | −1 | −1 | −1 | −2 | −2 | −1 | −1 | −2 | −1 | 3 | 0 | −2 | −2 | −1 |
| T | 0 | −1 | 0 | −1 | −1 | −1 | −1 | −2 | −1 | −1 | −1 | −1 | 0 | −2 | −1 | 0 | 3 | −2 | −2 | 0 |
| W | −2 | −2 | −3 | −3 | −1 | −2 | −3 | −3 | −1 | −2 | −1 | −3 | −1 | 1 | −3 | −2 | −2 | 6 | 1 | −2 |
| Y | −2 | −2 | −1 | −2 | −1 | −2 | −2 | −3 | 1 | −1 | −1 | −2 | −1 | 2 | −2 | −2 | −2 | 1 | 4 | −1 |
| V | 0 | −2 | −2 | −2 | −1 | −1 | −2 | −3 | −2 | 2 | 0 | −2 | 0 | −1 | −2 | −1 | 0 | −2 | −1 | 3 |