1     M         1.476   1.489   1.562   1.748   1.758   1.857   1.583   1.601   1.710
2     G         1.476   1.489   1.562   1.511   1.502   1.629   1.583   1.601   1.710
3     A         0.207   0.256   0.156  -0.031   0.054  -0.091   0.091   0.168  -0.011
4     A         1.476   1.489   1.562   1.171   1.213   1.303   1.583   1.601   1.710
5     Y         1.476   1.489   1.562   1.731   1.737   1.841   1.583   1.601   1.710
6     H        -0.905  -0.856  -0.821  -0.695  -0.615  -0.569  -0.963  -0.902  -0.821
7     F         0.347   0.327   0.179   0.549   0.485   0.321   0.310   0.277   0.027
8     M        -0.669  -0.589  -0.742  -0.462  -0.388  -0.516  -0.645  -0.544  -0.719
9     G         1.476   1.489   1.562   1.511   1.502   1.629   1.583   1.601   1.710
10    K         0.347   0.371   0.186   0.268   0.344   0.116   0.310   0.345   0.040
11    A        -0.905  -0.903  -0.822  -0.868  -0.885  -0.760  -0.963  -0.953  -0.823
12    I        -0.905  -0.898  -0.823  -0.712  -0.750  -0.587  -0.963  -0.946  -0.824
13    P        -0.905  -0.931  -0.820  -0.759  -0.795  -0.609  -0.963  -0.982  -0.820
14    P         0.347   0.401   0.193   0.383   0.441   0.157   0.310   0.390   0.051
15    H         1.476   1.489   1.562   1.630   1.670   1.744   1.583   1.601   1.710
16    Q         0.347   0.401   0.193   0.520   0.614   0.232   0.310   0.390   0.051
17    L         1.476   1.489   1.562   1.370   1.370   1.495   1.583   1.601   1.710
18    A         1.476   1.489   1.562   1.171   1.213   1.303   1.583   1.601   1.710
19    I        -0.043   0.025   0.079  -0.178  -0.098   0.011  -0.327  -0.214  -0.142
20    G        -0.043   0.025   0.079  -0.305  -0.182  -0.110  -0.327  -0.214  -0.142
21    T         1.476   1.489   1.562   1.664   1.677   1.777   1.583   1.601   1.710
22    L         0.347   0.260   0.161   0.361   0.210   0.096   0.310   0.174  -0.003
23    G        -0.669  -0.723  -0.774  -0.462  -0.590  -0.627  -0.645  -0.714  -0.759
24    L        -0.043  -0.034   0.042  -0.223  -0.248  -0.109  -0.327  -0.315  -0.207
25    L         0.347   0.327   0.179   0.477   0.417   0.199   0.310   0.277   0.027
26    G        -0.669  -0.672  -0.774  -0.544  -0.581  -0.754  -0.645  -0.647  -0.759
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    L         0.347   0.260   0.161   0.361   0.210   0.096   0.310   0.174  -0.003
30    L        -0.043  -0.004   0.047  -0.178  -0.144  -0.055  -0.327  -0.264  -0.197
31    V        -0.669  -0.723  -0.774  -0.539  -0.658  -0.746  -0.645  -0.714  -0.759
32    V        -1.531  -1.463  -1.451  -1.500  -1.417  -1.334  -1.281  -1.207  -1.146
33    P         0.347   0.260   0.161   0.383   0.243   0.104   0.310   0.174  -0.003
34    N        -0.905  -0.928  -0.835  -0.899  -0.895  -0.750  -0.963  -0.978  -0.836
35    P         0.347   0.260   0.161   0.391   0.253   0.120   0.310   0.174  -0.003
36    F        -0.905  -0.928  -0.835  -0.637  -0.694  -0.585  -0.963  -0.978  -0.836
37    K        -0.905  -0.869  -0.823  -1.191  -1.138  -1.094  -0.963  -0.914  -0.821
38    S        -0.905  -0.894  -0.827  -1.171  -1.167  -1.030  -0.963  -0.941  -0.826
39    A        -1.531  -1.566  -1.485  -1.710  -1.729  -1.697  -1.281  -1.310  -1.179
40    K        -0.669  -0.527  -0.748  -0.889  -0.637  -1.017  -0.645  -0.463  -0.726
41    P         0.347   0.371   0.186   0.308   0.338   0.019   0.310   0.345   0.040
42    K        -1.531  -1.481  -1.462  -1.508  -1.451  -1.355  -1.281  -1.227  -1.157
43    T        -1.531  -1.534  -1.453  -1.286  -1.291  -1.203  -1.281  -1.279  -1.148
44    V        -0.043  -0.034   0.042  -0.193  -0.206  -0.062  -0.327  -0.315  -0.207
45    D        -2.156  -2.119  -1.990  -1.891  -1.808  -1.638  -1.600  -1.559  -1.383
46    I         1.476   1.489   1.562   1.528   1.510   1.646   1.583   1.601   1.710
47    K        -0.905  -0.862  -0.820  -0.899  -0.800  -0.730  -0.963  -0.910  -0.821
48    T         0.347   0.327   0.179   0.200   0.195   0.008   0.310   0.277   0.027
49    D        -0.669  -0.756  -0.789  -0.403  -0.556  -0.544  -0.645  -0.755  -0.777
50    N         0.347   0.327   0.179   0.520   0.471   0.311   0.310   0.277   0.027
51    K        -0.669  -0.643  -0.755  -0.810  -0.745  -0.918  -0.645  -0.617  -0.735
52    D        -0.043  -0.059   0.033  -0.074  -0.019   0.079  -0.327  -0.359  -0.222
53    E         1.476   1.489   1.562   1.370   1.469   1.495   1.583   1.601   1.710
54    E         1.476   1.489   1.562   1.370   1.469   1.495   1.583   1.601   1.710
55    K         1.476   1.489   1.562   1.190   1.257   1.321   1.583   1.601   1.710
56    F         1.476   1.489   1.562   1.664   1.671   1.777   1.583   1.601   1.710
57    I         0.347   0.401   0.193   0.516   0.546   0.287   0.310   0.390   0.051
58    E        -1.531  -1.566  -1.485  -1.516  -1.554  -1.542  -1.281  -1.310  -1.179
59    N        -0.043  -0.059   0.033  -0.094  -0.052   0.056  -0.327  -0.359  -0.222
60    Y        -0.905  -0.928  -0.835  -0.443  -0.490  -0.342  -0.963  -0.978  -0.836
61    L         1.476   1.489   1.562   1.370   1.370   1.495   1.583   1.601   1.710
62    K        -0.905  -0.869  -0.823  -1.383  -1.239  -1.214  -0.963  -0.914  -0.821
63    K         0.347   0.260   0.161   0.140   0.085  -0.138   0.310   0.174  -0.003
64    H         0.347   0.260   0.161   0.637   0.539   0.361   0.310   0.174  -0.003
65    S        -1.531  -1.496  -1.444  -1.424  -1.370  -1.301  -1.281  -1.243  -1.140
66    E         0.040   0.044   0.086  -0.369  -0.357  -0.288  -0.185  -0.181  -0.131
67    K        -0.870  -0.934  -0.848  -1.142  -1.298  -1.174  -0.903  -0.980  -0.851
68    Q         0.207   0.142   0.120   0.232   0.151   0.113   0.091  -0.017  -0.072
69    D         0.207   0.142   0.120   0.084  -0.014   0.008   0.091  -0.017  -0.072
70    A        -0.870  -0.934  -0.848  -0.942  -1.114  -1.009  -0.903  -0.980  -0.851
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/P81451
Output conservation file - output/P81451
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
