1     M         2.224   2.261   2.419   2.334   2.385   2.634   2.585   2.652   2.972
2     A         1.302   1.261   1.241   1.274   1.225   1.173   1.341   1.261   1.184
3     E         0.448   0.355   0.328   0.588   0.446   0.387   0.345   0.198   0.132
4     K         1.302   1.392   1.270   1.226   1.338   1.171   1.341   1.500   1.243
5     Q         0.154   0.111   0.177  -0.146  -0.190  -0.094  -0.152  -0.216  -0.129
6     R         0.921   0.908   0.994   0.634   0.587   0.687   0.594   0.550   0.651
7     Q        -0.971  -0.930  -0.916  -0.947  -0.880  -0.863  -0.899  -0.852  -0.818
8     L        -0.319  -0.408  -0.401  -0.371  -0.524  -0.544  -0.401  -0.515  -0.506
9     K        -0.971  -0.998  -0.933  -1.129  -1.193  -1.101  -0.899  -0.922  -0.835
10    L        -0.971  -0.931  -0.919  -1.194  -1.134  -1.116  -0.899  -0.854  -0.821
11    Q        -0.498  -0.495  -0.445  -0.615  -0.581  -0.491  -0.650  -0.639  -0.569
12    K        -0.319  -0.352  -0.371  -0.328  -0.389  -0.437  -0.401  -0.442  -0.467
13    I        -0.971  -0.967  -0.918  -1.034  -1.013  -0.964  -0.899  -0.892  -0.820
14    Y        -0.319  -0.380  -0.378  -0.454  -0.536  -0.530  -0.401  -0.480  -0.477
15    K         0.154   0.109   0.177  -0.096  -0.182  -0.093  -0.152  -0.218  -0.130
16    Q        -0.498  -0.535  -0.445  -0.711  -0.764  -0.638  -0.650  -0.683  -0.569
17    K         0.921   0.983   1.039   0.607   0.697   0.758   0.594   0.708   0.751
18    Y         1.302   1.261   1.241   1.464   1.410   1.398   1.341   1.261   1.184
19    I        -0.319  -0.297  -0.342  -0.265  -0.227  -0.325  -0.401  -0.370  -0.429
20    G         2.224   2.261   2.419   2.252   2.305   2.549   2.585   2.652   2.972
21    L         0.154   0.215   0.207  -0.029   0.040   0.028  -0.152  -0.082  -0.083
22    G         1.384   1.257   1.312   1.473   1.288   1.373   1.488   1.254   1.329
23    D        -0.795  -0.831  -0.833  -0.584  -0.669  -0.636  -0.706  -0.749  -0.727
24    E        -0.390  -0.443  -0.369  -0.465  -0.519  -0.433  -0.523  -0.570  -0.477
25    S        -0.390  -0.369  -0.381  -0.354  -0.381  -0.327  -0.523  -0.510  -0.494
26    T         1.384   1.403   1.317   1.473   1.501   1.395   1.488   1.519   1.339
27    T         1.384   1.257   1.312   1.453   1.269   1.353   1.488   1.254   1.329
28    R        -0.390  -0.403  -0.376  -0.568  -0.599  -0.550  -0.523  -0.544  -0.488
29    E        -0.138   0.074  -0.219   0.059   0.344  -0.035  -0.157   0.136  -0.260
30    Q         1.384   1.388   1.330   1.433   1.441   1.367   1.488   1.494   1.365
31    W         1.384   1.403   1.317   1.760   1.794   1.715   1.488   1.519   1.339
32    Q        -0.948  -0.952  -0.902  -1.011  -1.048  -0.958  -0.889  -0.889  -0.810
33    R        -0.795  -0.851  -0.838  -0.686  -0.801  -0.765  -0.706  -0.768  -0.732
34    N         0.594   0.461   0.425   0.736   0.530   0.476   0.574   0.361   0.294
35    V         0.268   0.390   0.288   0.317   0.514   0.341   0.025   0.211   0.047
36    R        -0.948  -0.914  -0.918  -0.862  -0.824  -0.826  -0.889  -0.843  -0.823
37    N         0.594   0.575   0.461   0.653   0.631   0.455   0.574   0.547   0.353
38    D         2.224   2.261   2.419   2.285   2.331   2.583   2.585   2.652   2.972
39    T         0.594   0.648   0.464   0.714   0.790   0.524   0.574   0.660   0.359
40    L         0.268   0.190   0.265   0.170   0.062   0.127   0.025  -0.076   0.007
41    N         0.268   0.277   0.274   0.103   0.111   0.104   0.025   0.045   0.024
42    T         1.384   1.388   1.330   1.369   1.355   1.306   1.488   1.494   1.365
43    L        -0.795  -0.725  -0.814  -0.764  -0.663  -0.761  -0.706  -0.630  -0.706
44    Q        -0.543  -0.527  -0.458  -0.599  -0.567  -0.475  -0.706  -0.680  -0.588
45    G         0.268   0.214   0.238   0.215   0.111   0.146   0.025  -0.072  -0.039
46    H         2.224   2.261   2.419   2.401   2.455   2.705   2.585   2.652   2.972
47    S        -0.390  -0.421  -0.411  -0.428  -0.494  -0.467  -0.523  -0.564  -0.531
48    A        -0.543  -0.527  -0.458  -0.608  -0.559  -0.476  -0.706  -0.680  -0.588
49    S        -0.138  -0.114  -0.248  -0.209  -0.177  -0.367  -0.157  -0.122  -0.301
50    L         1.384   1.257   1.312   1.231   1.064   1.139   1.488   1.254   1.329
51    E        -0.390  -0.283  -0.367  -0.479  -0.299  -0.434  -0.523  -0.376  -0.474
52    Y         1.384   1.461   1.335   1.567   1.664   1.536   1.488   1.620   1.376
53    V        -0.948  -0.957  -0.905  -0.746  -0.754  -0.659  -0.889  -0.887  -0.812
54    S        -0.390  -0.430  -0.370  -0.484  -0.517  -0.429  -0.523  -0.552  -0.473
55    L         0.594   0.681   0.467   0.512   0.638   0.346   0.574   0.709   0.365
56    S         0.594   0.583   0.445   0.665   0.665   0.442   0.574   0.560   0.327
57    R        -1.354  -1.372  -1.322  -1.517  -1.562  -1.465  -1.071  -1.083  -1.006
58    G         0.999   1.078   1.080   0.918   1.045   1.016   0.757   0.904   0.841
59    D        -0.390  -0.390  -0.397  -0.336  -0.334  -0.315  -0.523  -0.531  -0.514
60    L        -0.138  -0.222  -0.268   0.004  -0.103  -0.215  -0.157  -0.275  -0.328
61    S        -1.354  -1.306  -1.305  -1.170  -1.067  -1.074  -1.071  -1.026  -0.991
62    I        -1.354  -1.384  -1.322  -1.263  -1.308  -1.209  -1.071  -1.093  -1.007
63    R        -0.795  -0.632  -0.817  -0.831  -0.560  -0.896  -0.706  -0.511  -0.708
64    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    T        -0.390  -0.340  -0.368  -0.417  -0.316  -0.396  -0.523  -0.440  -0.470
66    R         0.999   0.939   1.038   0.816   0.701   0.826   0.757   0.617   0.749
67    I        -0.795  -0.677  -0.819  -0.760  -0.572  -0.832  -0.706  -0.566  -0.711
68    H        -1.759  -1.733  -1.688  -1.520  -1.458  -1.397  -1.254  -1.228  -1.156
69    L         0.594   0.648   0.464   0.564   0.641   0.420   0.574   0.660   0.359
70    L         0.826   0.840   0.964   0.376   0.390   0.568   0.391   0.402   0.582
71    K        -0.543  -0.508  -0.458  -0.751  -0.706  -0.618  -0.706  -0.666  -0.589
72    S         1.384   1.388   1.330   1.332   1.325   1.257   1.488   1.494   1.365
73    M         0.268   0.180   0.254   0.217   0.098   0.160   0.025  -0.094  -0.009
74    -        -0.319  -0.264  -0.328  -0.304  -0.177  -0.318  -0.401  -0.340  -0.410
75    S        -0.948  -0.830  -0.900  -0.966  -0.813  -0.885  -0.889  -0.773  -0.808
76    P         0.594   0.518   0.455   0.763   0.662   0.568   0.574   0.447   0.343
77    G        -1.354  -1.332  -1.310  -0.924  -0.879  -0.819  -1.071  -1.050  -0.996
78    Y        -1.354  -1.395  -1.339  -1.204  -1.252  -1.180  -1.071  -1.102  -1.021
79    K        -0.795  -0.866  -0.855  -0.668  -0.763  -0.781  -0.706  -0.784  -0.752
80    A        -0.795  -0.903  -0.882  -0.608  -0.750  -0.746  -0.706  -0.822  -0.782
81    Y        -0.948  -0.997  -0.917  -0.895  -0.921  -0.826  -0.889  -0.926  -0.823
82    L        -1.354  -1.395  -1.339  -1.307  -1.398  -1.307  -1.071  -1.102  -1.021
83    R        -1.354  -1.360  -1.308  -1.291  -1.292  -1.218  -1.071  -1.073  -0.995
84    E        -0.948  -0.999  -0.908  -0.878  -0.936  -0.803  -0.889  -0.928  -0.816
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -         0.096   0.097   0.177  -0.083  -0.078   0.018  -0.215  -0.219  -0.116
96    E        -0.948  -0.960  -0.910  -0.925  -0.961  -0.866  -0.889  -0.894  -0.817
97    R        -1.354  -1.332  -1.310  -1.174  -1.163  -1.089  -1.071  -1.050  -0.996
* 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/P0C074
Output conservation file - output/P0C074
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
