1     M         1.233   1.237   1.298   1.400   1.406   1.499   1.313   1.317   1.405
2     S         0.508   0.378   0.307   0.726   0.554   0.458   0.489   0.283   0.137
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    L        -0.631  -0.618  -0.526  -1.181  -1.163  -0.967  -0.841  -0.823  -0.686
19    P        -0.806  -0.702  -0.945  -0.638  -0.490  -0.897  -0.747  -0.623  -0.886
20    E        -1.156  -1.141  -1.027  -1.118  -1.075  -0.914  -1.160  -1.141  -0.975
21    I        -0.174  -0.279  -0.392  -0.203  -0.385  -0.619  -0.198  -0.344  -0.500
22    L         1.233   1.237   1.298   0.972   0.977   1.098   1.313   1.317   1.405
23    P         1.233   1.237   1.298   1.474   1.483   1.568   1.313   1.317   1.405
24    L         1.233   1.237   1.298   0.972   0.977   1.098   1.313   1.317   1.405
25    E         1.233   1.237   1.298   1.232   1.243   1.342   1.313   1.317   1.405
26    V        -0.554  -0.611  -0.525  -1.048  -1.138  -0.993  -0.744  -0.807  -0.684
27    I         0.437   0.443   0.278   0.407   0.418   0.128   0.378   0.388   0.085
28    D         1.233   1.237   1.298   1.360   1.367   1.461   1.313   1.317   1.405
29    K         1.233   1.237   1.298   1.286   1.287   1.392   1.313   1.317   1.405
30    T        -0.554  -0.611  -0.525  -0.420  -0.505  -0.371  -0.744  -0.807  -0.684
31    I         1.233   1.237   1.298   1.221   1.229   1.332   1.313   1.317   1.405
32    N        -0.300  -0.227  -0.429  -0.267  -0.161  -0.464  -0.370  -0.269  -0.551
33    Q        -0.554  -0.611  -0.525  -0.406  -0.481  -0.354  -0.744  -0.807  -0.684
34    K        -0.963  -0.930  -0.963  -0.884  -0.840  -0.885  -0.931  -0.889  -0.906
35    V        -0.554  -0.563  -0.524  -0.977  -0.994  -0.944  -0.744  -0.759  -0.683
36    L        -1.525  -1.541  -1.397  -1.421  -1.420  -1.159  -1.305  -1.315  -1.130
37    I         0.008   0.016   0.128  -0.423  -0.410  -0.207  -0.370  -0.356  -0.189
38    V        -0.554  -0.496  -0.499  -1.059  -0.965  -0.948  -0.744  -0.671  -0.652
39    L        -0.554  -0.568  -0.524  -0.943  -0.954  -0.857  -0.744  -0.764  -0.683
40    Q        -0.554  -0.596  -0.507  -0.549  -0.613  -0.460  -0.744  -0.784  -0.659
41    S        -0.300  -0.366  -0.455  -0.154  -0.261  -0.411  -0.370  -0.462  -0.586
42    N        -1.525  -1.544  -1.410  -1.392  -1.433  -1.226  -1.305  -1.318  -1.141
43    R        -0.300  -0.378  -0.459  -0.009  -0.139  -0.360  -0.370  -0.478  -0.591
44    E         1.233   1.237   1.298   1.239   1.252   1.348   1.313   1.317   1.405
45    F         1.233   1.237   1.298   1.455   1.462   1.551   1.313   1.317   1.405
46    E        -1.856  -1.803  -1.716  -1.520  -1.438  -1.356  -1.434  -1.388  -1.248
47    G         1.233   1.237   1.298   1.210   1.214   1.321   1.313   1.317   1.405
48    T         0.508   0.524   0.285   0.710   0.736   0.356   0.489   0.512   0.098
49    L         1.233   1.237   1.298   0.972   0.977   1.098   1.313   1.317   1.405
50    V         0.508   0.455   0.274   0.452   0.392   0.091   0.489   0.406   0.077
51    G         1.233   1.237   1.298   1.210   1.214   1.321   1.313   1.317   1.405
52    F         1.233   1.237   1.298   1.455   1.462   1.551   1.313   1.317   1.405
53    D         1.233   1.237   1.298   1.353   1.359   1.455   1.313   1.317   1.405
54    D         0.508   0.524   0.285   0.664   0.685   0.302   0.489   0.512   0.098
55    F         0.026   0.054   0.131   0.107   0.161   0.260  -0.335  -0.283  -0.184
56    V         1.233   1.237   1.298   1.142   1.163   1.257   1.313   1.317   1.405
57    N         1.233   1.237   1.298   1.353   1.356   1.455   1.313   1.317   1.405
58    V        -0.542  -0.499  -0.516  -0.744  -0.656  -0.678  -0.747  -0.696  -0.674
59    I         0.176   0.219   0.185  -0.078   0.013  -0.075  -0.061   0.015  -0.083
60    L         0.508   0.554   0.283   0.280   0.342  -0.047   0.489   0.558   0.093
61    E         0.508   0.562   0.293   0.559   0.638   0.234   0.489   0.569   0.111
62    D         0.176   0.170   0.154   0.168   0.153   0.097  -0.061  -0.071  -0.142
63    A        -0.456  -0.398  -0.502  -0.497  -0.409  -0.498  -0.610  -0.522  -0.654
64    V        -1.024  -1.020  -1.008  -1.119  -1.081  -1.126  -1.022  -1.006  -0.957
65    E         1.233   1.237   1.298   1.239   1.252   1.348   1.313   1.317   1.405
66    W        -1.024  -0.983  -0.987  -0.735  -0.707  -0.692  -1.022  -0.992  -0.935
67    L        -1.024  -0.951  -1.002  -1.169  -1.026  -1.121  -1.022  -0.935  -0.950
68    I        -1.374  -1.415  -1.361  -1.151  -1.200  -1.157  -1.160  -1.201  -1.100
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    N        -1.933  -1.919  -1.729  -1.974  -1.969  -1.659  -1.492  -1.476  -1.257
79    E        -1.506  -1.546  -1.401  -1.441  -1.510  -1.259  -1.297  -1.325  -1.135
80    K        -1.374  -1.330  -1.387  -1.389  -1.316  -1.420  -1.160  -1.114  -1.122
81    V        -1.024  -1.072  -0.996  -1.213  -1.274  -1.137  -1.022  -1.071  -0.945
82    M        -1.856  -1.860  -1.719  -1.648  -1.645  -1.462  -1.434  -1.435  -1.250
83    Q        -1.506  -1.475  -1.394  -1.339  -1.305  -1.138  -1.297  -1.268  -1.129
84    H        -1.506  -1.482  -1.403  -1.336  -1.331  -1.201  -1.297  -1.272  -1.136
85    H        -0.806  -0.911  -0.949  -0.468  -0.687  -0.786  -0.747  -0.873  -0.891
86    G        -0.674  -0.678  -0.553  -0.914  -0.929  -0.707  -0.885  -0.890  -0.718
87    R        -0.456  -0.381  -0.482  -0.401  -0.290  -0.440  -0.610  -0.507  -0.627
88    M        -0.174  -0.248  -0.394  -0.020  -0.141  -0.443  -0.198  -0.305  -0.503
89    L         1.233   1.237   1.298   0.972   0.977   1.098   1.313   1.317   1.405
90    L         1.233   1.237   1.298   0.972   0.977   1.098   1.313   1.317   1.405
91    S        -0.542  -0.503  -0.512  -0.584  -0.536  -0.505  -0.747  -0.701  -0.669
92    G         1.233   1.237   1.298   1.210   1.214   1.321   1.313   1.317   1.405
93    N        -0.174  -0.179  -0.426   0.019   0.005  -0.386  -0.198  -0.206  -0.547
94    N        -0.806  -0.770  -0.950  -0.588  -0.537  -0.821  -0.747  -0.705  -0.892
95    I        -0.174  -0.177  -0.425  -0.117  -0.123  -0.523  -0.198  -0.203  -0.546
96    A        -1.024  -1.002  -0.986  -0.616  -0.599  -0.562  -1.022  -1.005  -0.934
97    I         0.508   0.576   0.295   0.710   0.802   0.362   0.489   0.589   0.115
98    L         1.233   1.237   1.298   0.972   0.977   1.098   1.313   1.317   1.405
99    V         0.026   0.054   0.131  -0.345  -0.271  -0.167  -0.335  -0.283  -0.184
100   P         1.233   1.237   1.298   1.474   1.483   1.568   1.313   1.317   1.405
101   G         1.233   1.237   1.298   1.203   1.203   1.314   1.313   1.317   1.405
102   G         1.233   1.237   1.298   1.203   1.203   1.314   1.313   1.317   1.405
103   K         0.349   0.216   0.223   0.423   0.198   0.170   0.236   0.011  -0.015
104   K        -0.631  -0.684  -0.537  -0.691  -0.796  -0.554  -0.841  -0.897  -0.698
105   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   A         0.239   0.245   0.189   0.360   0.369   0.255   0.051   0.061  -0.077
110   L        -0.806  -0.832  -0.925  -0.947  -0.978  -1.065  -0.747  -0.784  -0.864
* 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/P40089
Output conservation file - output/P40089
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
