Table 1.
Hypothetical alignment of three sub-families to illustrate the SH scores (range from 0 to 1) and mR weights (range from −1 to 1)
| Alignment position |
Distance matrix |
|||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 1 | 2 | 3 | 4 | 1 | 2 | 3 | 1 | 2 | 3 | |
| Group 1 | ||||||||||||||||||
| seq1 | R | E | L | A | A | K | K | A | – | 2 | 4 | 4 | 6 | 7 | 5 | 7 | 7 | 6 |
| seq2 | R | E | L | A | F | K | K | I | 2 | – | 4 | 3 | 6 | 7 | 4 | 7 | 6 | 6 |
| seq3 | R | E | A | A | Y | R | K | L | 4 | 4 | – | 2 | 4 | 5 | 6 | 5 | 6 | 6 |
| seq4 | R | E | A | A | F | R | K | M | 4 | 3 | 2 | – | 5 | 6 | 5 | 6 | 5 | 7 |
| Group 2 | ||||||||||||||||||
| seq1 | H | N | V | A | Y | R | K | K | 6 | 6 | 4 | 5 | – | 1 | 3 | 4 | 5 | 5 |
| seq2 | H | N | V | F | Y | R | K | K | 7 | 7 | 5 | 6 | 1 | – | 4 | 3 | 4 | 4 |
| seq3 | H | N | S | A | F | K | K | K | 5 | 4 | 6 | 5 | 3 | 4 | – | 6 | 5 | 5 |
| Group 3 | ||||||||||||||||||
| seq1 | H | S | F | F | Y | R | K | Q | 7 | 7 | 5 | 6 | 4 | 3 | 6 | – | 3 | 3 |
| seq2 | H | S | M | F | F | R | K | R | 7 | 6 | 6 | 5 | 5 | 4 | 5 | 3 | – | 3 |
| seq3 | H | S | M | F | Y | K | K | S | 6 | 6 | 6 | 7 | 5 | 4 | 5 | 3 | 3 | – |
| SH | 0.42 | 0.00 | 0.00 | 0.57 | 0.87 | 0.99 | 1.00 | 0.00 | ||||||||||
| mR | 1.00 | 1.00 | 0.67 | 1.00 | −0.42 | −0.19 | 0.00 | 0.50 | ||||||||||
The distance matrix is used by mR to find ‘nearest hits’ (within group; in bold italic) and ‘nearest misses’ (between groups; in bold) for each sequence.