Matrices
Overlap Alignment
Matrices will have following scores after Best score calculation.
| M | 0 | 1 | 2 | 3 | 4 | 5 |
| 0 | 0 | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) |
| 1 | - \(\infty\) | 10 | -2 | -2 | -2 | -2 |
| 2 | - \(\infty\) | -2 | 20 | -4 | -4 | -4 |
| 3 | - \(\infty\) | -2 | -4 | 18 | 8 | -6 |
| A | 0 | 1 | 2 | 3 | 4 | 5 |
| 0 | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) |
| 1 | 0 | -22 | -22 | -22 | -22 | -22 |
| 2 | 0 | -12 | -24 | -24 | -24 | -24 |
| 3 | 0 | -19 | -2 | -24 | -26 | -26 |
| B | 0 | 1 | 2 | 3 | 4 | 5 |
| 0 | - \(\infty\) | 0 | 0 | 0 | 0 | 0 |
| 1 | - \(\infty\) | -22 | -12 | -19 | -24 | -24 |
| 2 | - \(\infty\) | -22 | -24 | -2 | -9 | -16 |
| 3 | - \(\infty\) | -2 | -24 | -24 | -4 | -11 |
Non-Overlap Alignment
Matrices will have following scores after Best score calculation.
| M | 0 | 1 | 2 | 3 | 4 | 5 |
| 0 | 0 | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) |
| 1 | - \(\infty\) | 10 | -24 | -31 | -38 | -45 |
| 2 | - \(\infty\) | -24 | 20 | -14 | -21 | -28 |
| 3 | - \(\infty\) | -31 | -14 | 18 | 8 | -11 |
| A | 0 | 1 | 2 | 3 | 4 | 5 |
| 0 | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) | - \(\infty\) |
| 1 | -22 | -44 | -51 | -58 | -65 | -72 |
| 2 | -29 | -12 | -34 | -41 | -48 | -55 |
| 3 | -36 | -19 | -2 | -24 | -31 | -38 |
| B | 0 | 1 | 2 | 3 | 4 | 5 |
| 0 | - \(\infty\) | -22 | -29 | -36 | -43 | -50 |
| 1 | - \(\infty\) | -44 | -12 | -19 | -26 | -33 |
| 2 | - \(\infty\) | -51 | -34 | -2 | -9 | -16 |
| 3 | - \(\infty\) | -58 | -41 | -24 | -4 | -11 |
1.8.11 
