1     M         1.187   1.215   1.283   1.334   1.368   1.466   1.259   1.300   1.398
2     S         0.535   0.469   0.257   0.713   0.639   0.302   0.534   0.434   0.049
3     N        -0.912  -0.896  -0.957  -0.846  -0.811  -0.891  -0.918  -0.876  -0.913
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     K        -0.809  -0.984  -0.971  -0.675  -0.924  -0.918  -0.772  -0.967  -0.927
8     V        -2.180  -2.113  -1.957  -2.130  -2.070  -1.798  -1.584  -1.517  -1.323
9     K        -1.511  -1.503  -1.374  -1.525  -1.505  -1.298  -1.332  -1.303  -1.125
10    T        -1.511  -1.487  -1.379  -1.493  -1.439  -1.262  -1.332  -1.288  -1.128
11    K        -0.912  -0.937  -0.972  -0.800  -0.841  -0.848  -0.918  -0.955  -0.932
12    A        -1.099  -1.020  -0.996  -1.072  -0.955  -0.879  -1.125  -1.013  -0.954
13    M        -0.671  -0.611  -0.920  -0.411  -0.338  -0.887  -0.607  -0.532  -0.871
14    V        -0.686  -0.610  -0.535  -1.153  -1.027  -0.916  -0.918  -0.816  -0.703
15    P         0.535   0.406   0.271   0.757   0.590   0.337   0.534   0.334   0.074
16    P         1.187   1.215   1.283   1.334   1.382   1.466   1.259   1.300   1.398
17    I         1.187   1.215   1.283   0.946   0.998   1.101   1.259   1.300   1.398
18    N         0.535   0.406   0.271   0.664   0.502   0.268   0.534   0.334   0.074
19    C        -1.099  -1.121  -1.002  -1.007  -1.032  -0.889  -1.125  -1.121  -0.961
20    I         0.214   0.114   0.152  -0.129  -0.314  -0.273   0.015  -0.170  -0.145
21    F         0.535   0.516   0.259   0.736   0.718   0.379   0.534   0.506   0.052
22    N        -0.499  -0.528  -0.500  -0.575  -0.588  -0.529  -0.710  -0.723  -0.663
23    F        -1.099  -1.030  -0.992  -0.993  -0.926  -0.802  -1.125  -1.044  -0.952
24    L         1.187   1.215   1.283   1.032   1.062   1.182   1.259   1.300   1.398
25    Q         0.535   0.516   0.259   0.663   0.648   0.318   0.534   0.506   0.052
26    Q        -0.086  -0.242  -0.421   0.084  -0.138  -0.395  -0.088  -0.297  -0.549
27    Q         0.042   0.027   0.134  -0.006  -0.026   0.144  -0.296  -0.334  -0.180
28    T        -0.499  -0.569  -0.499  -0.485  -0.547  -0.434  -0.710  -0.768  -0.662
29    P        -0.499  -0.442  -0.487  -0.478  -0.417  -0.468  -0.710  -0.649  -0.648
30    V         1.187   1.215   1.283   1.116   1.149   1.261   1.259   1.300   1.398
31    T        -0.371  -0.400  -0.487  -0.310  -0.397  -0.495  -0.503  -0.573  -0.645
32    I        -0.371  -0.462  -0.474  -0.585  -0.703  -0.712  -0.503  -0.605  -0.625
33    W         1.187   1.215   1.283   1.445   1.485   1.571   1.259   1.300   1.398
34    L         1.187   1.215   1.283   1.032   1.062   1.182   1.259   1.300   1.398
35    F         0.042   0.050   0.139   0.112   0.111   0.225  -0.296  -0.289  -0.169
36    E         1.187   1.215   1.283   1.260   1.298   1.397   1.259   1.300   1.398
37    Q         1.187   1.215   1.283   1.192   1.231   1.333   1.259   1.300   1.398
38    I        -1.398  -1.468  -1.369  -1.424  -1.534  -1.429  -1.229  -1.270  -1.120
39    G        -1.212  -1.178  -1.024  -1.189  -1.135  -0.902  -1.229  -1.178  -0.981
40    I        -0.912  -0.825  -0.962  -1.095  -0.977  -1.124  -0.918  -0.844  -0.922
41    R         1.187   1.215   1.283   1.294   1.325   1.429   1.259   1.300   1.398
42    I         0.535   0.619   0.283   0.355   0.478  -0.024   0.534   0.656   0.095
43    K        -0.912  -0.914  -0.974  -0.880  -0.894  -1.009  -0.918  -0.906  -0.933
44    G         1.187   1.215   1.283   1.158   1.197   1.301   1.259   1.300   1.398
45    K        -0.499  -0.451  -0.485  -0.596  -0.528  -0.544  -0.710  -0.659  -0.647
46    I         0.535   0.406   0.271   0.355   0.188  -0.046   0.534   0.334   0.074
47    V         0.214   0.172   0.159   0.240   0.147   0.075   0.015  -0.064  -0.132
48    G         1.187   1.215   1.283   1.158   1.197   1.301   1.259   1.300   1.398
49    F         1.187   1.215   1.283   1.267   1.303   1.403   1.259   1.300   1.398
50    D         1.187   1.215   1.283   1.219   1.259   1.359   1.259   1.300   1.398
51    E         1.187   1.215   1.283   1.260   1.298   1.397   1.259   1.300   1.398
52    F         1.187   1.215   1.283   1.267   1.303   1.403   1.259   1.300   1.398
53    M         1.187   1.215   1.283   1.334   1.368   1.466   1.259   1.300   1.398
54    N         1.187   1.215   1.283   1.233   1.278   1.371   1.259   1.300   1.398
55    V        -0.371  -0.361  -0.469  -0.563  -0.528  -0.774  -0.503  -0.465  -0.618
56    V         1.187   1.215   1.283   1.116   1.149   1.261   1.259   1.300   1.398
57    I         0.214   0.178   0.177  -0.129  -0.192  -0.224   0.015  -0.054  -0.098
58    D         0.535   0.406   0.271   0.663   0.499   0.289   0.534   0.334   0.074
59    E        -0.086  -0.105  -0.424   0.112   0.087  -0.375  -0.088  -0.113  -0.553
60    A         1.187   1.215   1.283   1.367   1.406   1.497   1.259   1.300   1.398
61    V        -0.912  -0.909  -0.966  -0.999  -1.075  -1.060  -0.918  -0.931  -0.926
62    E         0.214   0.178   0.177   0.232   0.163   0.124   0.015  -0.054  -0.098
63    I        -0.499  -0.443  -0.486  -0.859  -0.808  -0.841  -0.710  -0.651  -0.648
64    P        -1.118  -1.145  -1.014  -1.009  -1.052  -0.873  -1.129  -1.145  -0.972
65    V        -1.118  -1.083  -1.004  -1.393  -1.336  -1.234  -1.129  -1.082  -0.961
66    N        -1.495  -1.461  -1.373  -1.396  -1.360  -1.209  -1.313  -1.266  -1.123
67    S        -1.495  -1.422  -1.368  -1.237  -1.130  -1.058  -1.313  -1.233  -1.119
68    A        -0.467  -0.358  -0.479  -0.516  -0.324  -0.503  -0.636  -0.471  -0.629
69    D        -1.365  -1.374  -1.358  -1.141  -1.150  -1.164  -1.178  -1.174  -1.109
70    G        -0.680  -0.639  -0.536  -0.886  -0.819  -0.659  -0.907  -0.848  -0.705
71    K        -0.457  -0.420  -0.491  -0.428  -0.376  -0.494  -0.598  -0.549  -0.644
72    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    V        -1.118  -1.155  -1.014  -1.277  -1.325  -1.105  -1.129  -1.155  -0.972
75    E         0.022   0.053   0.135  -0.144  -0.094   0.021  -0.333  -0.284  -0.177
76    K        -0.457  -0.397  -0.468  -0.455  -0.364  -0.489  -0.598  -0.516  -0.613
77    G        -1.118  -1.155  -1.014  -1.116  -1.158  -0.938  -1.129  -1.155  -0.972
78    T        -1.398  -1.262  -1.358  -1.200  -1.007  -1.142  -1.229  -1.080  -1.110
79    P        -0.912  -0.922  -0.971  -0.766  -0.794  -0.844  -0.918  -0.925  -0.931
80    L         0.535   0.406   0.271   0.430   0.239   0.000   0.534   0.334   0.074
81    G         1.187   1.215   1.283   1.158   1.197   1.301   1.259   1.300   1.398
82    K        -0.371  -0.472  -0.486  -0.275  -0.444  -0.490  -0.503  -0.633  -0.644
83    I         1.187   1.215   1.283   0.946   0.998   1.101   1.259   1.300   1.398
84    L         0.214   0.134   0.154   0.058  -0.075  -0.021   0.015  -0.133  -0.140
85    L         1.187   1.215   1.283   1.032   1.062   1.182   1.259   1.300   1.398
86    K         1.187   1.215   1.283   1.172   1.220   1.314   1.259   1.300   1.398
87    G         1.187   1.215   1.283   1.158   1.197   1.301   1.259   1.300   1.398
88    D         1.187   1.215   1.283   1.219   1.259   1.359   1.259   1.300   1.398
89    N         1.187   1.215   1.283   1.233   1.278   1.371   1.259   1.300   1.398
90    I         0.535   0.469   0.257   0.368   0.296  -0.036   0.534   0.434   0.049
91    T         0.535   0.469   0.257   0.678   0.607   0.283   0.534   0.434   0.049
92    L         1.187   1.215   1.283   1.032   1.062   1.182   1.259   1.300   1.398
93    I         0.535   0.516   0.259   0.368   0.360  -0.033   0.534   0.506   0.052
94    T        -1.099  -1.081  -1.000  -1.098  -1.064  -0.958  -1.125  -1.086  -0.959
95    S        -0.912  -0.942  -0.960  -0.676  -0.718  -0.726  -0.918  -0.941  -0.919
96    A        -1.513  -1.523  -1.393  -1.472  -1.428  -1.230  -1.321  -1.313  -1.138
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    D        -2.111  -2.106  -1.954  -2.009  -1.974  -1.768  -1.540  -1.513  -1.321
* 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/Q12330
Output conservation file - output/Q12330
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
