1     M         1.207   1.289   1.343   1.410   1.518   1.595   1.279   1.395   1.492
2     V         0.342   0.342   0.166   0.576   0.592   0.312   0.274   0.268  -0.071
3     S         1.207   1.289   1.343   1.248   1.344   1.443   1.279   1.395   1.492
4     Q        -0.663  -0.651  -0.600  -0.687  -0.702  -0.597  -0.869  -0.827  -0.733
5     L        -1.203  -1.305  -1.141  -1.353  -1.458  -1.221  -1.209  -1.254  -1.050
6     F         1.207   1.289   1.343   1.368   1.479   1.556   1.279   1.395   1.492
7     E         0.127   0.227   0.147  -0.011   0.149   0.014  -0.078   0.077  -0.106
8     E        -1.454  -1.592  -1.541  -1.391  -1.677  -1.619  -1.209  -1.319  -1.221
9     K        -0.063  -0.056   0.083  -0.618  -0.649  -0.376  -0.417  -0.427  -0.225
10    A         0.483   0.247   0.224   0.474   0.160   0.163   0.488   0.111   0.034
11    K        -1.329  -1.262  -1.156  -1.635  -1.525  -1.295  -1.322  -1.220  -1.064
12    A        -1.121  -1.102  -1.129  -1.070  -1.089  -1.051  -1.095  -1.073  -1.039
13    V         0.483   0.247   0.224   0.727   0.427   0.368   0.488   0.111   0.034
14    N        -1.329  -1.262  -1.156  -1.294  -1.310  -1.117  -1.322  -1.220  -1.064
15    E        -0.663  -0.592  -0.596  -1.037  -0.980  -0.899  -0.869  -0.773  -0.728
16    L         1.207   1.289   1.343   1.019   1.147   1.230   1.279   1.395   1.492
17    P        -1.121  -1.153  -1.124  -0.806  -0.882  -0.913  -1.095  -1.117  -1.034
18    T        -1.329  -1.276  -1.141  -1.502  -1.416  -1.203  -1.322  -1.227  -1.051
19    K        -1.329  -1.229  -1.140  -1.187  -1.130  -0.976  -1.322  -1.201  -1.050
20    P         1.207   1.289   1.343   1.361   1.480   1.550   1.279   1.395   1.492
21    S         0.127   0.234   0.144   0.220   0.367   0.209  -0.078   0.090  -0.112
22    T        -1.661  -1.528  -1.532  -1.337  -1.151  -1.139  -1.435  -1.291  -1.216
23    D         0.483   0.247   0.224   0.513   0.198   0.120   0.488   0.111   0.034
24    E         0.483   0.247   0.224   0.417   0.130   0.063   0.488   0.111   0.034
25    L         0.483   0.677   0.265   0.467   0.713   0.241   0.488   0.765   0.107
26    L         1.207   1.289   1.343   1.019   1.147   1.230   1.279   1.395   1.492
27    E        -0.663  -0.611  -0.587  -1.126  -1.035  -0.955  -0.869  -0.792  -0.720
28    L         0.483   0.247   0.224   0.469   0.231   0.189   0.488   0.111   0.034
29    Y         1.207   1.289   1.343   1.248   1.359   1.443   1.279   1.395   1.492
30    A        -0.124  -0.046   0.086  -0.337  -0.269  -0.041  -0.530  -0.409  -0.220
31    L         1.207   1.289   1.343   1.019   1.147   1.230   1.279   1.395   1.492
32    Y         0.483   0.503   0.244   0.688   0.737   0.394   0.488   0.517   0.070
33    K         1.207   1.289   1.343   0.803   0.892   1.028   1.279   1.395   1.492
34    Q         0.483   0.247   0.224   0.686   0.418   0.347   0.488   0.111   0.034
35    A         1.207   1.289   1.343   1.042   1.114   1.251   1.279   1.395   1.492
36    T         1.207   1.289   1.343   1.283   1.390   1.477   1.279   1.395   1.492
37    V         0.483   0.247   0.224   0.732   0.438   0.382   0.488   0.111   0.034
38    G         0.483   0.247   0.224   0.678   0.339   0.273   0.488   0.111   0.034
39    D         1.207   1.289   1.343   1.124   1.235   1.328   1.279   1.395   1.492
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    N         0.483   0.247   0.224   0.720   0.434   0.362   0.488   0.111   0.034
42    D        -1.329  -1.331  -1.143  -1.231  -1.288  -1.048  -1.322  -1.269  -1.051
43    K        -0.663  -0.736  -0.589  -0.850  -0.899  -0.720  -0.869  -0.896  -0.714
44    E        -0.663  -0.610  -0.598  -0.885  -0.787  -0.774  -0.869  -0.789  -0.732
45    K        -0.205  -0.091  -0.497  -0.341  -0.202  -0.669  -0.191  -0.025  -0.586
46    P         1.207   1.289   1.343   1.361   1.480   1.550   1.279   1.395   1.492
47    G         0.483   0.571   0.253   0.706   0.817   0.396   0.488   0.616   0.085
48    I        -2.119  -2.025  -1.880  -1.527  -1.370  -1.282  -1.661  -1.527  -1.347
49    F         0.483   0.503   0.244   0.759   0.803   0.377   0.488   0.517   0.070
50    N        -0.063  -0.056   0.083  -0.126  -0.152   0.026  -0.417  -0.427  -0.224
51    M        -0.789  -0.588  -0.584  -0.764  -0.483  -0.476  -0.982  -0.694  -0.706
52    K         1.207   1.289   1.343   0.803   0.892   1.028   1.279   1.395   1.492
53    D        -0.663  -0.478  -0.557  -0.655  -0.342  -0.495  -0.869  -0.586  -0.672
54    R        -0.063   0.136   0.154  -0.365  -0.132  -0.050  -0.417  -0.080  -0.092
55    Y        -0.205  -0.462  -0.548   0.091  -0.272  -0.406  -0.191  -0.534  -0.656
56    K         1.207   1.289   1.343   0.803   0.892   1.028   1.279   1.395   1.492
57    W         0.483   0.247   0.224   0.832   0.545   0.459   0.488   0.111   0.034
58    E        -1.661  -1.534  -1.541  -1.533  -1.292  -1.421  -1.435  -1.290  -1.223
59    A         1.207   1.289   1.343   1.042   1.114   1.251   1.279   1.395   1.492
60    W         1.207   1.289   1.343   1.410   1.527   1.595   1.279   1.395   1.492
61    E        -1.121  -1.217  -1.132  -1.205  -1.277  -1.263  -1.095  -1.166  -1.040
62    N        -1.994  -1.783  -1.848  -2.043  -1.739  -1.832  -1.548  -1.317  -1.322
63    L         0.483   0.247   0.224   0.451   0.191   0.143   0.488   0.111   0.034
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    K        -0.205  -0.383  -0.530  -0.408  -0.664  -0.870  -0.191  -0.440  -0.631
67    G         1.207   1.289   1.343   1.283   1.384   1.477   1.279   1.395   1.492
68    K        -1.121  -1.135  -1.105  -1.231  -1.296  -1.133  -1.095  -1.084  -1.013
69    S         1.207   1.289   1.343   1.248   1.344   1.443   1.279   1.395   1.492
70    Q        -0.205  -0.462  -0.548   0.007  -0.372  -0.628  -0.191  -0.534  -0.656
71    E         1.207   1.289   1.343   1.012   1.138   1.223   1.279   1.395   1.492
72    D        -0.063  -0.042   0.085  -0.340  -0.327  -0.163  -0.417  -0.402  -0.221
73    A         1.207   1.289   1.343   1.042   1.114   1.251   1.279   1.395   1.492
74    E        -0.205  -0.462  -0.548  -0.164  -0.471  -0.646  -0.191  -0.534  -0.656
75    K        -1.203  -1.312  -1.130  -1.270  -1.354  -1.107  -1.209  -1.262  -1.040
76    E        -0.789  -0.754  -0.637  -1.093  -1.084  -0.925  -0.982  -0.926  -0.776
77    Y         1.207   1.289   1.343   1.248   1.359   1.443   1.279   1.395   1.492
78    I         0.483   0.247   0.224   0.847   0.569   0.486   0.488   0.111   0.034
79    A        -1.661  -1.539  -1.514  -1.752  -1.542  -1.570  -1.435  -1.260  -1.198
80    L        -0.521  -0.712  -0.601  -0.580  -0.878  -0.724  -0.643  -0.863  -0.733
81    V         0.127   0.227   0.146   0.195   0.332   0.139  -0.078   0.078  -0.107
82    D        -0.854  -0.975  -1.085  -0.605  -0.797  -0.949  -0.756  -0.895  -0.988
83    Q        -0.521  -0.286  -0.514  -0.541  -0.187  -0.500  -0.643  -0.295  -0.611
84    L         0.483   0.247   0.224   0.467   0.225   0.186   0.488   0.111   0.034
85    I        -1.121  -1.118  -1.129  -0.915  -1.063  -1.086  -1.095  -1.087  -1.039
86    A        -1.661  -1.526  -1.541  -1.582  -1.354  -1.439  -1.435  -1.284  -1.223
87    K         0.483   0.247   0.224   0.226  -0.067  -0.068   0.488   0.111   0.034
88    Y         1.207   1.289   1.343   1.248   1.359   1.443   1.279   1.395   1.492
89    S        -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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   S        -1.454  -1.235  -1.479  -0.994  -0.700  -1.104  -1.209  -0.949  -1.165
* 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/P31787
Output conservation file - output/P31787
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
