1     M         1.352   1.365   1.444   1.520   1.542   1.646   1.435   1.452   1.570
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     V         1.352   1.365   1.444   1.161   1.189   1.308   1.435   1.452   1.570
4     T        -1.132  -1.106  -0.977  -1.197  -1.114  -0.946  -1.140  -1.101  -0.926
5     Q        -0.768  -0.809  -0.901  -0.555  -0.610  -0.859  -0.711  -0.762  -0.842
6     L        -0.631  -0.572  -0.468  -0.854  -0.755  -0.618  -0.854  -0.773  -0.635
7     K        -0.768  -0.802  -0.890  -0.639  -0.729  -0.903  -0.711  -0.755  -0.830
8     S        -0.768  -0.863  -0.905  -0.542  -0.672  -0.765  -0.711  -0.821  -0.847
9     A        -0.995  -0.911  -0.919  -1.352  -1.171  -1.193  -0.997  -0.890  -0.864
10    S        -0.768  -0.809  -0.901  -0.577  -0.666  -0.814  -0.711  -0.762  -0.842
11    E         0.598   0.600   0.408   0.698   0.704   0.426   0.576   0.577   0.235
12    Y         0.598   0.702   0.422   0.696   0.815   0.481   0.576   0.728   0.259
13    D        -1.496  -1.380  -1.351  -1.359  -1.213  -1.143  -1.283  -1.176  -1.082
14    S        -1.860  -1.837  -1.693  -1.617  -1.576  -1.389  -1.426  -1.397  -1.212
15    A        -0.111  -0.109  -0.321  -0.287  -0.287  -0.557  -0.139  -0.135  -0.434
16    L        -0.404  -0.454  -0.434  -0.452  -0.544  -0.534  -0.568  -0.641  -0.595
17    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    S        -1.496  -1.496  -1.358  -1.476  -1.510  -1.273  -1.283  -1.270  -1.087
19    G        -2.224  -2.174  -1.988  -1.771  -1.724  -1.452  -1.569  -1.520  -1.308
20    D        -0.111  -0.212  -0.345   0.132   0.009  -0.164  -0.139  -0.279  -0.467
21    K        -0.768  -0.809  -0.901  -0.615  -0.670  -0.773  -0.711  -0.762  -0.842
22    L         0.598   0.475   0.387   0.698   0.533   0.391   0.576   0.379   0.197
23    V         0.598   0.600   0.408   0.503   0.517   0.255   0.576   0.577   0.235
24    V         0.598   0.619   0.413   0.498   0.536   0.252   0.576   0.607   0.242
25    V        -0.111  -0.228  -0.352  -0.152  -0.305  -0.486  -0.139  -0.301  -0.476
26    D         1.352   1.365   1.444   1.375   1.394   1.509   1.435   1.452   1.570
27    F         0.598   0.475   0.387   0.606   0.414   0.236   0.576   0.379   0.197
28    F         0.598   0.600   0.408   0.696   0.699   0.461   0.576   0.577   0.235
29    A         1.352   1.365   1.444   1.027   1.040   1.182   1.435   1.452   1.570
30    T         1.352   1.365   1.444   1.403   1.416   1.536   1.435   1.452   1.570
31    W         1.352   1.365   1.444   1.614   1.629   1.734   1.435   1.452   1.570
32    C         1.352   1.365   1.444   1.560   1.578   1.684   1.435   1.452   1.570
33    G         1.352   1.365   1.444   1.451   1.473   1.581   1.435   1.452   1.570
34    P         1.352   1.365   1.444   1.458   1.470   1.588   1.435   1.452   1.570
35    C         1.352   1.365   1.444   1.560   1.578   1.684   1.435   1.452   1.570
36    K         1.352   1.365   1.444   1.255   1.278   1.396   1.435   1.452   1.570
37    M         0.253   0.192   0.251   0.215   0.069   0.094   0.004  -0.112  -0.052
38    I         1.352   1.365   1.444   1.375   1.389   1.509   1.435   1.452   1.570
39    A         1.352   1.365   1.444   1.027   1.040   1.182   1.435   1.452   1.570
40    P         1.352   1.365   1.444   1.458   1.470   1.588   1.435   1.452   1.570
41    M        -1.132  -1.102  -0.980  -1.075  -1.036  -0.865  -1.140  -1.097  -0.929
42    I        -0.995  -1.005  -0.951  -1.026  -1.072  -0.979  -0.997  -1.006  -0.900
43    E        -0.404  -0.475  -0.423  -0.481  -0.607  -0.561  -0.568  -0.646  -0.579
44    K         0.598   0.591   0.410   0.612   0.612   0.374   0.576   0.563   0.237
45    F         0.598   0.475   0.387   0.704   0.551   0.447   0.576   0.379   0.197
46    A        -0.404  -0.316  -0.385  -0.506  -0.318  -0.462  -0.568  -0.434  -0.525
47    E        -0.995  -0.905  -0.930  -1.020  -0.880  -0.957  -0.997  -0.900  -0.879
48    Q        -0.404  -0.330  -0.402  -0.364  -0.277  -0.346  -0.568  -0.483  -0.552
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    Y         0.253   0.195   0.252   0.366   0.251   0.290   0.004  -0.105  -0.051
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    S        -1.359  -1.354  -1.329  -1.067  -1.065  -1.031  -1.140  -1.133  -1.060
54    D        -1.359  -1.343  -1.336  -1.102  -1.086  -1.079  -1.140  -1.122  -1.066
55    A        -0.111  -0.212  -0.345  -0.330  -0.490  -0.673  -0.139  -0.279  -0.467
56    A        -1.496  -1.486  -1.364  -1.432  -1.373  -1.225  -1.283  -1.264  -1.092
57    F         1.352   1.365   1.444   1.326   1.341   1.463   1.435   1.452   1.570
58    Y        -1.132  -1.152  -0.980  -1.127  -1.191  -0.930  -1.140  -1.143  -0.929
59    K         0.598   0.600   0.408   0.637   0.648   0.422   0.576   0.577   0.235
60    L        -1.359  -1.366  -1.329  -1.292  -1.303  -1.216  -1.140  -1.145  -1.060
61    D         1.352   1.365   1.444   1.375   1.394   1.509   1.435   1.452   1.570
62    V         1.352   1.365   1.444   1.161   1.189   1.308   1.435   1.452   1.570
63    D         1.352   1.365   1.444   1.375   1.394   1.509   1.435   1.452   1.570
64    E        -0.404  -0.493  -0.428  -0.426  -0.579  -0.500  -0.568  -0.673  -0.587
65    V        -0.768  -0.649  -0.862  -0.719  -0.539  -0.945  -0.711  -0.567  -0.799
66    S        -0.631  -0.615  -0.484  -0.646  -0.613  -0.429  -0.854  -0.831  -0.657
67    D        -0.995  -0.972  -0.936  -1.026  -0.988  -0.967  -0.997  -0.963  -0.886
68    V        -0.631  -0.628  -0.491  -0.911  -0.893  -0.674  -0.854  -0.848  -0.665
69    A         1.352   1.365   1.444   1.027   1.040   1.182   1.435   1.452   1.570
70    Q        -0.111  -0.057  -0.313   0.091   0.167  -0.291  -0.139  -0.067  -0.422
71    K        -0.111   0.044  -0.304   0.043   0.251  -0.247  -0.139   0.070  -0.410
72    A        -1.496  -1.496  -1.365  -1.509  -1.510  -1.320  -1.283  -1.271  -1.093
73    E        -0.995  -0.888  -0.934  -0.850  -0.675  -0.755  -0.997  -0.867  -0.882
74    V         0.598   0.475   0.387   0.498   0.344   0.212   0.576   0.379   0.197
75    S        -0.768  -0.877  -0.916  -0.415  -0.536  -0.579  -0.711  -0.836  -0.859
76    S         0.097   0.144   0.237  -0.360  -0.290  -0.126  -0.282  -0.201  -0.078
77    M         1.352   1.365   1.444   1.520   1.542   1.646   1.435   1.452   1.570
78    P         1.352   1.365   1.444   1.458   1.470   1.588   1.435   1.452   1.570
79    T         0.598   0.591   0.410   0.742   0.732   0.471   0.576   0.563   0.237
80    L        -0.494  -0.430  -0.434  -0.656  -0.562  -0.568  -0.711  -0.631  -0.597
81    I        -0.995  -1.010  -0.947  -1.161  -1.211  -1.142  -0.997  -1.008  -0.897
82    F        -0.404  -0.493  -0.428  -0.442  -0.572  -0.478  -0.568  -0.673  -0.587
83    Y         0.097   0.123   0.231  -0.001   0.036   0.205  -0.282  -0.239  -0.090
84    K         1.352   1.365   1.444   1.255   1.278   1.396   1.435   1.452   1.570
85    G        -0.404  -0.274  -0.389  -0.279  -0.080  -0.260  -0.568  -0.386  -0.532
86    G         1.352   1.365   1.444   1.451   1.473   1.581   1.435   1.452   1.570
87    K        -0.404  -0.430  -0.405  -0.458  -0.464  -0.461  -0.568  -0.579  -0.553
88    E        -0.494  -0.430  -0.434  -0.709  -0.613  -0.620  -0.711  -0.631  -0.597
89    V        -0.494  -0.551  -0.437  -0.800  -0.889  -0.719  -0.711  -0.760  -0.601
90    T        -1.496  -1.499  -1.368  -1.290  -1.297  -1.111  -1.283  -1.273  -1.095
91    R        -0.995  -0.976  -0.951  -0.748  -0.754  -0.737  -0.997  -0.980  -0.901
92    V        -0.111  -0.236  -0.352  -0.159  -0.328  -0.500  -0.139  -0.311  -0.476
93    V        -0.995  -0.927  -0.926  -1.069  -0.966  -0.924  -0.997  -0.916  -0.873
94    G         1.352   1.365   1.444   1.451   1.473   1.581   1.435   1.452   1.570
95    A         1.352   1.365   1.444   1.027   1.040   1.182   1.435   1.452   1.570
96    N         1.352   1.365   1.444   1.458   1.477   1.588   1.435   1.452   1.570
97    P         0.598   0.677   0.415   0.792   0.886   0.520   0.576   0.692   0.247
98    A        -0.768  -0.823  -0.899  -0.854  -0.929  -0.974  -0.711  -0.778  -0.840
99    A         0.598   0.591   0.410   0.342   0.330   0.081   0.576   0.563   0.237
100   I         0.097   0.147   0.242  -0.092  -0.006   0.133  -0.282  -0.195  -0.069
101   K        -0.768  -0.877  -0.916  -0.661  -0.814  -0.867  -0.711  -0.836  -0.859
102   Q         0.097   0.097   0.221  -0.192  -0.242  -0.046  -0.282  -0.288  -0.109
103   A        -0.995  -0.973  -0.939  -1.267  -1.223  -1.140  -0.997  -0.973  -0.889
104   I         0.598   0.619   0.413   0.710   0.735   0.441   0.576   0.607   0.242
105   A        -0.995  -1.027  -0.955  -1.285  -1.317  -1.153  -0.997  -1.025  -0.904
106   S        -0.995  -1.039  -0.940  -1.214  -1.269  -1.079  -0.997  -1.028  -0.889
107   N        -0.111  -0.212  -0.345   0.166   0.032  -0.182  -0.139  -0.279  -0.467
108   V        -0.631  -0.625  -0.487  -1.102  -1.069  -0.863  -0.854  -0.844  -0.660
* 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/P22803
Output conservation file - output/P22803
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
