| BLOSUM50 |
∞a |
0−∞ |
0.110 |
0.232 |
0.34 |
| BLOSUM50 |
15 |
8−15 |
0.090 |
0.222 |
0.31 |
| BLOSUM50 |
11 |
8−11 |
0.050 |
0.197 |
0.21 |
| BLOSUM50 |
11 |
1 |
-- |
-- |
-- |
|
| BLOSUM62 |
∞c |
0−∞ |
0.13 |
0.318 |
0.40 |
| BLOSUM62 |
12 |
3−12 |
0.100 |
0.305 |
0.38 |
| BLOSUM62 |
8 |
7−88 |
0.060 |
0.270 |
0.25 |
| BLOSUM62 |
7 |
1 |
-- |
-- |
-- |
|
| PAM250 |
∞a |
0−∞ |
0.09 |
0.229 |
0.23 |
| PAM250 |
15 |
5−15 |
0.060 |
0.215 |
0.20 |
| PAM250 |
10 |
8−10 |
0.031 |
0.175 |
0.11 |
| PAM250 |
11 |
1 |
-- |
-- |
-- |
| Dashes indicate that no value can be calculated because the relationship between alignment score and sequence length is linear
and not logarithmic, indicating that the alignment is global, not local, in character. Statistical significance may not be
calculated for these gap penalty-scoring matrix combinations. The corresponding values for gap penalties define approximate
lower limits that should be used.
|
| aThe penalty for a gap opening of length l is the value of the gap opening penalty shown. The gap extension penalty is not
added until the gap length is 2. Make sure that the alignment program uses this same scheme for scoring gaps. The extension
penalty is shown over a range of values; values within this range did not change K and λ.
|
| bThe entropy in units of the natural logarithm.
|
| cA value of ∞ for gap penalty will produce alignments with no gaps.
|
