1     M         0.972   1.017   1.044   1.188   1.226   1.271   1.016   1.079   1.118
2     A        -0.791  -0.626  -0.738  -0.917  -0.612  -0.737  -0.990  -0.785  -0.867
3     A        -1.433  -1.243  -1.245  -1.749  -1.539  -1.539  -1.424  -1.190  -1.160
4     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    E        -1.831  -1.688  -1.620  -1.761  -1.506  -1.467  -1.604  -1.430  -1.319
13    P        -1.338  -1.367  -1.255  -1.145  -1.160  -1.025  -1.328  -1.308  -1.169
14    K        -0.225  -0.114  -0.096  -0.624  -0.439  -0.459  -0.568  -0.387  -0.388
15    K        -0.970  -1.089  -1.206  -1.092  -1.271  -1.385  -0.884  -1.029  -1.120
16    R        -1.731  -1.756  -1.615  -1.998  -2.037  -1.794  -1.518  -1.481  -1.315
17    T        -0.657  -0.623  -0.745  -0.551  -0.700  -0.798  -0.779  -0.787  -0.876
18    T        -1.731  -1.622  -1.604  -1.246  -1.168  -1.110  -1.518  -1.383  -1.307
19    R        -0.359  -0.589  -0.718  -0.258  -0.583  -0.834  -0.357  -0.670  -0.837
20    R        -0.791  -0.764  -0.749  -1.241  -1.157  -1.147  -0.990  -0.928  -0.881
21    K         0.972   1.017   1.044   0.572   0.652   0.718   1.016   1.079   1.118
22    K         0.972   1.017   1.044   0.572   0.652   0.718   1.016   1.079   1.118
23    D         0.972   1.017   1.044   1.043   1.090   1.142   1.016   1.079   1.118
24    P         0.972   1.017   1.044   1.043   1.094   1.142   1.016   1.079   1.118
25    N        -0.046   0.159  -0.029   0.070   0.360   0.053  -0.251   0.073  -0.268
26    A         0.290   0.048  -0.019   0.177  -0.043  -0.186   0.277  -0.107  -0.249
27    P         0.972   1.017   1.044   1.043   1.094   1.142   1.016   1.079   1.118
28    K         0.972   1.017   1.044   0.572   0.652   0.718   1.016   1.079   1.118
29    R         0.972   1.017   1.044   0.881   0.930   0.996   1.016   1.079   1.118
30    G        -1.417  -1.393  -1.243  -1.365  -1.260  -1.088  -1.412  -1.335  -1.159
31    L         0.290   0.048  -0.019   0.573   0.277   0.165   0.277  -0.107  -0.249
32    S         0.972   1.017   1.044   1.107   1.151   1.199   1.016   1.079   1.118
33    A         0.972   1.017   1.044   0.712   0.851   0.844   1.016   1.079   1.118
34    Y         0.290   0.048  -0.019   0.579   0.272   0.157   0.277  -0.107  -0.249
35    M         0.972   1.017   1.044   1.188   1.226   1.271   1.016   1.079   1.118
36    F         0.972   1.017   1.044   1.144   1.188   1.232   1.016   1.079   1.118
37    F         0.972   1.017   1.044   1.144   1.188   1.232   1.016   1.079   1.118
38    A         0.290   0.048  -0.019   0.180  -0.040  -0.177   0.277  -0.107  -0.249
39    N         0.290   0.048  -0.019   0.529   0.256   0.133   0.277  -0.107  -0.249
40    E         0.290   0.307  -0.001   0.279   0.290  -0.090   0.277   0.299  -0.218
41    N         0.290   0.274   0.002   0.530   0.534   0.165   0.277   0.251  -0.213
42    R         0.972   1.017   1.044   0.881   0.930   0.996   1.016   1.079   1.118
43    D        -0.046  -0.160  -0.103  -0.006  -0.282  -0.210  -0.251  -0.469  -0.401
44    I        -0.970  -1.193  -1.229  -0.545  -0.978  -1.162  -0.884  -1.130  -1.144
45    V        -0.359  -0.589  -0.718   0.164  -0.131  -0.321  -0.357  -0.670  -0.837
46    R         0.290   0.048  -0.019   0.273  -0.117  -0.267   0.277  -0.107  -0.249
47    S        -1.222  -1.288  -1.230  -1.216  -1.237  -1.191  -1.201  -1.230  -1.145
48    E        -0.046  -0.151  -0.104  -0.151  -0.341  -0.236  -0.251  -0.453  -0.402
49    N         0.972   1.017   1.044   1.050   1.123   1.147   1.016   1.079   1.118
50    P         0.972   1.017   1.044   1.043   1.094   1.142   1.016   1.079   1.118
51    D        -0.225  -0.188  -0.105  -0.188  -0.171  -0.051  -0.568  -0.521  -0.403
52    V        -0.791  -0.875  -0.753  -0.514  -0.656  -0.544  -0.990  -1.041  -0.885
53    T        -0.791  -0.711  -0.744  -0.651  -0.539  -0.645  -0.990  -0.855  -0.875
54    F         0.972   1.017   1.044   1.144   1.188   1.232   1.016   1.079   1.118
55    G         0.972   1.017   1.044   1.088   1.140   1.182   1.016   1.079   1.118
56    Q         0.972   1.017   1.044   1.200   1.247   1.283   1.016   1.079   1.118
57    V        -0.359  -0.466  -0.696   0.149  -0.022  -0.324  -0.357  -0.529  -0.807
58    G         0.972   1.017   1.044   1.088   1.140   1.182   1.016   1.079   1.118
59    R        -0.791  -0.836  -0.745  -1.146  -1.143  -0.975  -0.990  -0.987  -0.873
60    I        -0.791  -0.706  -0.737  -0.593  -0.462  -0.577  -0.990  -0.848  -0.865
61    L         0.972   1.017   1.044   1.094   1.155   1.187   1.016   1.079   1.118
62    G         0.972   1.017   1.044   1.088   1.140   1.182   1.016   1.079   1.118
63    E         0.290   0.048  -0.019   0.211  -0.181  -0.320   0.277  -0.107  -0.249
64    R        -0.282  -0.180  -0.105  -0.802  -0.603  -0.490  -0.673  -0.507  -0.404
65    W         0.972   1.017   1.044   1.249   1.299   1.327   1.016   1.079   1.118
66    K         0.972   1.017   1.044   0.572   0.652   0.718   1.016   1.079   1.118
67    A        -0.359  -0.589  -0.718  -0.392  -0.664  -0.867  -0.357  -0.670  -0.837
68    L         0.972   1.017   1.044   1.094   1.155   1.187   1.016   1.079   1.118
69    T        -0.657  -0.506  -0.710  -0.381  -0.166  -0.477  -0.779  -0.545  -0.828
70    A        -1.849  -1.595  -1.609  -1.703  -1.313  -1.367  -1.623  -1.369  -1.311
71    E        -1.536  -1.595  -1.609  -1.440  -1.579  -1.651  -1.307  -1.352  -1.310
72    E        -0.791  -0.685  -0.727  -0.808  -0.669  -0.657  -0.990  -0.806  -0.852
73    K        -0.046  -0.160  -0.103  -0.453  -0.642  -0.519  -0.251  -0.469  -0.401
74    Q        -2.163  -2.020  -1.926  -1.714  -1.612  -1.420  -1.729  -1.565  -1.424
75    P         0.972   1.017   1.044   1.043   1.094   1.142   1.016   1.079   1.118
76    Y         0.972   1.017   1.044   1.107   1.162   1.199   1.016   1.079   1.118
77    E         0.972   1.017   1.044   0.821   0.867   0.942   1.016   1.079   1.118
78    S        -1.417  -1.229  -1.237  -1.528  -1.284  -1.237  -1.412  -1.199  -1.153
79    K         0.972   1.017   1.044   0.572   0.652   0.718   1.016   1.079   1.118
80    A         0.972   1.017   1.044   0.712   0.851   0.844   1.016   1.079   1.118
81    Q        -2.044  -1.990  -1.922  -1.768  -1.792  -1.608  -1.623  -1.542  -1.421
82    A        -0.359  -0.461  -0.698  -0.324  -0.379  -0.677  -0.357  -0.524  -0.810
83    D         0.972   1.017   1.044   1.043   1.090   1.142   1.016   1.079   1.118
84    K         0.972   1.017   1.044   0.572   0.652   0.718   1.016   1.079   1.118
85    K         0.290   0.048  -0.019  -0.007  -0.331  -0.428   0.277  -0.107  -0.249
86    R         0.972   1.017   1.044   0.881   0.930   0.996   1.016   1.079   1.118
87    Y         0.972   1.017   1.044   1.107   1.162   1.199   1.016   1.079   1.118
88    E         0.972   1.017   1.044   0.821   0.867   0.942   1.016   1.079   1.118
89    S        -1.417  -1.403  -1.249  -1.400  -1.403  -1.207  -1.412  -1.345  -1.164
90    E         0.972   1.017   1.044   0.821   0.867   0.942   1.016   1.079   1.118
91    K         0.290   0.048  -0.019   0.003  -0.310  -0.400   0.277  -0.107  -0.249
92    E        -1.299  -1.359  -1.244  -1.527  -1.625  -1.416  -1.307  -1.308  -1.159
93    L        -0.986  -0.883  -0.775  -1.170  -1.054  -0.927  -1.201  -1.048  -0.911
94    Y         0.972   1.017   1.044   1.107   1.162   1.199   1.016   1.079   1.118
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    N        -1.299  -1.255  -1.234  -1.326  -1.250  -1.132  -1.307  -1.231  -1.151
97    A        -1.222  -1.284  -1.233  -1.410  -1.342  -1.333  -1.201  -1.225  -1.147
98    T        -0.845  -0.903  -0.768  -0.805  -0.997  -0.798  -1.052  -1.075  -0.902
99    R        -1.831  -1.683  -1.624  -1.917  -1.632  -1.621  -1.604  -1.434  -1.322
100   A         0.972   1.017   1.044   0.713   0.818   0.845   1.016   1.079   1.118
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P11633
Output conservation file - output/P11633
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
