1     M         1.676   1.689   1.782   1.922   1.946   2.092   1.877   1.896   2.049
2     P         0.290   0.383   0.144   0.452   0.586   0.231   0.230   0.370  -0.008
3     K        -0.547  -0.627  -0.552  -0.674  -0.795  -0.716  -0.667  -0.750  -0.647
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     V        -1.366  -1.385  -1.295  -1.508  -1.533  -1.423  -1.116  -1.129  -1.006
10    Y         0.012   0.005  -0.016   0.055   0.030  -0.011  -0.219  -0.254  -0.268
11    S        -0.332  -0.339  -0.438  -0.171  -0.181  -0.389  -0.368  -0.377  -0.501
12    Y         0.290   0.228   0.106   0.472   0.385   0.176   0.230   0.136  -0.067
13    Q        -0.677  -0.667  -0.580  -0.757  -0.729  -0.621  -0.817  -0.803  -0.680
14    E         0.290   0.264   0.127   0.325   0.284   0.083   0.230   0.189  -0.034
15    V         0.962   0.885   0.825   0.943   0.838   0.737   0.979   0.845   0.696
16    A         0.012  -0.061  -0.016  -0.075  -0.196  -0.162  -0.219  -0.319  -0.268
17    E         0.290   0.334   0.126   0.357   0.427   0.133   0.230   0.298  -0.036
18    H         1.676   1.689   1.782   1.893   1.918   2.063   1.877   1.896   2.049
19    N         0.290   0.376   0.144   0.636   0.758   0.429   0.230   0.360  -0.007
20    G        -0.332  -0.334  -0.451  -0.105  -0.093  -0.316  -0.368  -0.371  -0.518
21    P        -1.366  -1.380  -1.280  -1.279  -1.297  -1.148  -1.116  -1.125  -0.994
22    E        -0.677  -0.648  -0.580  -0.976  -0.898  -0.836  -0.817  -0.784  -0.681
23    N         0.962   1.012   0.845   0.957   1.027   0.815   0.979   1.061   0.734
24    F        -0.332  -0.334  -0.451  -0.184  -0.200  -0.305  -0.368  -0.371  -0.518
25    W         0.635   0.567   0.634   0.841   0.714   0.785   0.380   0.241   0.312
26    I        -0.208  -0.186  -0.094  -0.370  -0.319  -0.197  -0.530  -0.500  -0.376
27    I         0.469   0.482   0.586   0.109   0.108   0.286   0.043   0.065   0.210
28    I         0.395   0.446   0.191   0.503   0.542   0.199   0.387   0.463   0.065
29    D        -0.020  -0.066  -0.010  -0.043  -0.031   0.007  -0.300  -0.339  -0.263
30    D         0.697   0.668   0.669   0.484   0.370   0.385   0.502   0.442   0.384
31    K         0.395   0.440   0.197   0.574   0.680   0.270   0.387   0.455   0.074
32    V         1.676   1.689   1.782   1.608   1.634   1.779   1.877   1.896   2.049
33    Y         1.676   1.689   1.782   1.783   1.840   1.953   1.877   1.896   2.049
34    D         0.962   0.969   0.832   0.930   0.939   0.766   0.979   0.989   0.708
35    V        -0.072  -0.039  -0.039  -0.284  -0.274  -0.187  -0.368  -0.330  -0.306
36    S         0.635   0.661   0.658   0.598   0.678   0.614   0.380   0.428   0.363
37    Q        -0.547  -0.577  -0.531  -0.449  -0.429  -0.403  -0.667  -0.700  -0.625
38    F         0.635   0.637   0.670   0.718   0.730   0.744   0.380   0.380   0.387
39    K        -1.022  -1.024  -0.958  -1.209  -1.252  -1.118  -0.967  -0.965  -0.862
40    D         1.676   1.689   1.782   1.565   1.578   1.736   1.877   1.896   2.049
41    E         0.962   0.892   0.818   0.932   0.897   0.696   0.979   0.857   0.681
42    H         1.676   1.689   1.782   1.885   1.940   2.055   1.877   1.896   2.049
43    P         1.676   1.689   1.782   1.885   1.906   2.055   1.877   1.896   2.049
44    G         1.676   1.689   1.782   1.591   1.551   1.762   1.877   1.896   2.049
45    G         1.676   1.689   1.782   1.591   1.551   1.762   1.877   1.896   2.049
46    D        -0.020  -0.039  -0.013  -0.336  -0.297  -0.320  -0.300  -0.306  -0.268
47    E         1.020   0.963   0.868   1.017   1.006   0.793   1.075   0.980   0.778
48    I         0.469   0.478   0.585   0.109   0.099   0.285   0.043   0.056   0.207
49    I        -0.509  -0.534  -0.500  -0.658  -0.726  -0.621  -0.644  -0.663  -0.595
50    M        -0.737  -0.630  -0.823  -0.626  -0.515  -0.750  -0.644  -0.516  -0.719
51    D         1.020   1.060   0.879   0.983   1.051   0.784   1.075   1.138   0.799
52    L        -0.925  -0.915  -0.922  -1.008  -0.982  -0.986  -0.873  -0.853  -0.828
53    G        -0.020   0.027  -0.004  -0.230  -0.212  -0.166  -0.300  -0.230  -0.261
54    G         1.676   1.689   1.782   1.591   1.551   1.762   1.877   1.896   2.049
55    Q        -0.435  -0.384  -0.469  -0.154  -0.023  -0.216  -0.530  -0.462  -0.551
56    D         1.020   1.037   0.875   0.983   1.022   0.777   1.075   1.102   0.792
57    A         1.020   0.926   0.863   1.061   0.916   0.849   1.075   0.916   0.768
58    T         1.676   1.689   1.782   1.820   1.866   1.990   1.877   1.896   2.049
59    E        -0.435  -0.442  -0.480  -0.514  -0.450  -0.563  -0.530  -0.523  -0.561
60    S        -0.193  -0.077  -0.376  -0.082   0.052  -0.362  -0.186  -0.031  -0.421
61    F         1.020   0.963   0.868   1.304   1.246   1.101   1.075   0.980   0.778
62    V        -0.623  -0.631  -0.554  -0.870  -0.792  -0.745  -0.759  -0.755  -0.651
63    D         1.676   1.689   1.782   1.586   1.611   1.756   1.877   1.896   2.049
64    I         0.697   0.650   0.671   0.579   0.460   0.483   0.502   0.407   0.389
65    G         1.676   1.689   1.782   1.591   1.551   1.762   1.877   1.896   2.049
66    H         1.676   1.689   1.782   1.888   1.946   2.058   1.877   1.896   2.049
67    S         1.676   1.689   1.782   1.739   1.790   1.910   1.877   1.896   2.049
68    D         0.395   0.348   0.159   0.393   0.336   0.028   0.387   0.317   0.015
69    E        -0.020  -0.065  -0.010  -0.335  -0.362  -0.314  -0.300  -0.353  -0.269
70    A         1.676   1.689   1.782   1.647   1.639   1.817   1.877   1.896   2.049
71    L        -1.340  -1.321  -1.275  -1.159  -1.121  -1.063  -1.102  -1.083  -0.992
72    R        -0.435  -0.360  -0.474  -0.454  -0.278  -0.495  -0.530  -0.427  -0.554
73    L        -0.020  -0.083  -0.011  -0.268  -0.420  -0.256  -0.300  -0.369  -0.271
74    L         1.676   1.689   1.782   1.602   1.579   1.773   1.877   1.896   2.049
75    K        -0.509  -0.478  -0.501  -0.507  -0.388  -0.450  -0.644  -0.607  -0.596
76    G        -1.340  -1.335  -1.262  -1.292  -1.280  -1.192  -1.102  -1.094  -0.982
77    L         0.697   0.698   0.679   0.609   0.583   0.579   0.502   0.499   0.404
78    Y         0.109   0.095   0.046   0.133   0.117   0.009  -0.071  -0.107  -0.172
79    I         0.524   0.520   0.602   0.239   0.196   0.330   0.158   0.144   0.244
80    G         1.676   1.689   1.782   1.591   1.551   1.762   1.877   1.896   2.049
81    D        -0.925  -0.946  -0.904  -0.969  -0.925  -0.911  -0.873  -0.889  -0.812
82    V        -0.020   0.010  -0.007  -0.323  -0.333  -0.296  -0.300  -0.276  -0.266
83    D        -0.020  -0.022  -0.016  -0.251  -0.203  -0.233  -0.300  -0.310  -0.277
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    K        -0.332  -0.234  -0.403  -0.113   0.017  -0.262  -0.368  -0.238  -0.456
90    T        -0.925  -0.936  -0.910  -0.876  -0.901  -0.832  -0.873  -0.875  -0.816
91    S        -1.227  -1.286  -1.255  -0.980  -1.012  -1.035  -0.988  -1.042  -0.973
92    E         0.012  -0.017  -0.007  -0.155  -0.129  -0.209  -0.219  -0.270  -0.251
93    R        -1.022  -1.071  -0.959  -0.853  -0.944  -0.809  -0.967  -1.006  -0.863
94    V        -0.435  -0.542  -0.496  -0.441  -0.580  -0.489  -0.530  -0.646  -0.582
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    S        -1.642  -1.566  -1.545  -1.517  -1.391  -1.375  -1.217  -1.151  -1.084
99    V        -1.642  -1.610  -1.550  -1.462  -1.366  -1.345  -1.217  -1.189  -1.087
100   E        -1.340  -1.352  -1.269  -1.330  -1.266  -1.200  -1.102  -1.107  -0.987
101   K        -1.642  -1.646  -1.550  -1.304  -1.281  -1.193  -1.217  -1.217  -1.087
102   V        -1.642  -1.655  -1.550  -1.456  -1.469  -1.335  -1.217  -1.224  -1.087
103   S        -1.642  -1.666  -1.558  -1.464  -1.450  -1.356  -1.217  -1.231  -1.093
104   T        -1.039  -1.008  -0.953  -0.975  -0.902  -0.841  -0.988  -0.956  -0.860
105   S        -1.340  -1.322  -1.267  -1.189  -1.135  -1.080  -1.102  -1.084  -0.986
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   E        -0.925  -0.855  -0.899  -0.720  -0.577  -0.707  -0.873  -0.807  -0.807
109   N        -1.227  -1.211  -1.232  -0.816  -0.744  -0.824  -0.988  -0.969  -0.953
110   Q        -0.925  -0.929  -0.921  -1.016  -1.017  -1.004  -0.873  -0.878  -0.828
111   S        -1.039  -1.035  -0.950  -1.069  -1.012  -0.931  -0.988  -0.981  -0.858
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   K        -1.642  -1.661  -1.559  -1.443  -1.412  -1.312  -1.217  -1.228  -1.094
120   G         1.020   0.963   0.868   1.026   0.896   0.843   1.075   0.980   0.778
121   S        -0.925  -0.924  -0.906  -0.917  -0.959  -0.903  -0.873  -0.875  -0.813
122   G        -0.435  -0.447  -0.491  -0.449  -0.500  -0.494  -0.530  -0.538  -0.576
123   T        -1.227  -1.151  -1.216  -1.022  -0.922  -0.987  -0.988  -0.909  -0.938
124   L        -0.623  -0.653  -0.559  -0.611  -0.654  -0.497  -0.759  -0.778  -0.658
125   V        -0.925  -0.937  -0.910  -0.986  -1.038  -0.961  -0.873  -0.878  -0.815
126   V        -0.925  -0.960  -0.913  -0.999  -1.115  -0.994  -0.873  -0.907  -0.821
127   I        -0.509  -0.456  -0.499  -0.747  -0.738  -0.731  -0.644  -0.584  -0.594
128   L        -0.208  -0.214  -0.104  -0.582  -0.644  -0.430  -0.530  -0.535  -0.389
129   A        -1.340  -1.330  -1.265  -1.478  -1.555  -1.368  -1.102  -1.091  -0.984
130   I        -1.039  -1.053  -0.956  -1.330  -1.450  -1.214  -0.988  -0.995  -0.863
131   L        -1.227  -1.261  -1.235  -1.185  -1.326  -1.214  -0.988  -1.019  -0.955
132   M        -0.509  -0.447  -0.504  -0.614  -0.594  -0.551  -0.644  -0.581  -0.599
133   L        -0.435  -0.516  -0.495  -0.591  -0.793  -0.711  -0.530  -0.626  -0.584
134   G         0.697   0.668   0.669   0.541   0.435   0.440   0.502   0.442   0.384
135   V        -0.623  -0.598  -0.560  -0.773  -0.752  -0.677  -0.759  -0.735  -0.659
136   -        -0.160  -0.176  -0.079  -0.541  -0.652  -0.417  -0.470  -0.486  -0.355
137   A         0.697   0.674   0.672   0.546   0.475   0.454   0.502   0.453   0.390
138   Y         0.697   0.672   0.673   0.772   0.774   0.716   0.502   0.449   0.393
139   Y        -0.435  -0.542  -0.496  -0.259  -0.357  -0.345  -0.530  -0.646  -0.582
140   L        -0.193  -0.182  -0.387   0.054   0.120  -0.255  -0.186  -0.172  -0.435
141   L        -0.193  -0.100  -0.352  -0.101  -0.018  -0.327  -0.186  -0.061  -0.391
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   N        -0.332  -0.397  -0.453   0.038  -0.021  -0.148  -0.368  -0.451  -0.520
152   E        -0.547  -0.525  -0.526  -0.574  -0.535  -0.543  -0.667  -0.643  -0.618
* 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/P40312
Output conservation file - output/P40312
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
