Research Article
An Improved Scoring Matrix for Multiple Sequence Alignment
Table 3
Weight matrix of 16 OxyR-binding sequences from base positions −8 to +6.
| | −8 | −7 | −6 | −5 | −4 | −3 | −2 | −1 | 0 | +1 | +2 | +3 | +4 | +5 | +6 |
| | 1 | T | C | A | C | A | C | C | G | A | C | T | T | G | T | G | | 2 | A | C | T | T | A | T | C | G | A | T | C | C | G | C | A | | 3 | C | A | T | T | A | A | C | A | A | T | A | G | G | G | C | | 4 | T | A | C | G | A | T | A | A | T | A | G | G | C | A | A | | 5 | C | G | T | A | C | A | T | T | A | T | C | C | A | T | A | | 6 | C | T | A | T | T | A | T | T | G | T | A | A | C | A | G | | 7 | A | C | T | T | T | C | C | C | A | G | A | G | T | T | C | | 8 | C | A | G | A | G | A | T | C | G | C | T | C | T | A | A | | 9 | A | C | T | A | A | A | C | T | T | C | T | G | A | T | A | | 10 | A | G | T | T | A | T | C | G | G | T | A | T | A | A | T | | 11 | A | C | G | A | T | G | G | A | A | T | C | C | A | T | A | | 12 | C | A | G | A | G | A | T | C | G | C | T | C | T | A | A | | 13 | A | T | C | A | C | T | G | A | C | T | A | C | A | A | T | | 14 | A | T | T | A | G | C | G | A | T | T | A | C | C | G | T | | 15 | A | T | T | A | C | C | T | A | T | C | G | C | T | G | C | | 16 | C | T | A | T | T | A | T | T | G | T | A | A | C | A | G |
| | A | 8 | 4 | 3 | 8 | 6 | 7 | 1 | 6 | 6 | 1 | 7 | 2 | 5 | 7 | 7 | | C | 6 | 5 | 2 | 1 | 3 | 4 | 6 | 3 | 1 | 5 | 3 | 8 | 4 | 1 | 3 | | T | 2 | 5 | 8 | 6 | 4 | 4 | 6 | 4 | 4 | 9 | 4 | 2 | 4 | 5 | 3 | | G | 0 | 2 | 3 | 1 | 3 | 1 | 3 | 3 | 5 | 1 | 2 | 4 | 3 | 3 | 3 |
| | %A | 0.50 | 0.25 | 0.19 | 0.50 | 0.38 | 0.44 | 0.06 | 0.38 | 0.38 | 0.06 | 0.44 | 0.13 | 0.31 | 0.44 | 0.44 | | %C | 0.38 | 0.31 | 0.13 | 0.06 | 0.19 | 0.25 | 0.38 | 0.19 | 0.06 | 0.31 | 0.19 | 0.50 | 0.25 | 0.06 | 0.19 | | %T | 0.13 | 0.31 | 0.50 | 0.38 | 0.25 | 0.25 | 0.38 | 0.25 | 0.25 | 0.56 | 0.25 | 0.13 | 0.25 | 0.31 | 0.19 | | %G | 0.00 | 0.13 | 0.19 | 0.06 | 0.19 | 0.06 | 0.19 | 0.19 | 0.31 | 0.06 | 0.13 | 0.25 | 0.19 | 0.19 | 0.19 |
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