1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    M         1.602   1.602   1.670   1.965   1.965   2.060   1.761   1.762   1.868
54    T        -0.628  -0.607  -0.581  -0.693  -0.681  -0.600  -0.751  -0.726  -0.665
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -0.721  -0.714  -0.618  -0.937  -0.921  -0.779  -0.856  -0.847  -0.709
57    K         0.544   0.575   0.411   0.357   0.403   0.186   0.505   0.555   0.268
58    N        -0.407  -0.429  -0.500  -0.398  -0.434  -0.512  -0.437  -0.467  -0.553
59    F         0.179   0.166   0.238   0.340   0.321   0.427  -0.123  -0.148  -0.042
60    I         1.602   1.602   1.670   1.497   1.495   1.602   1.761   1.762   1.868
61    V         0.179   0.190   0.253  -0.109  -0.089   0.004  -0.123  -0.103  -0.016
62    T         1.602   1.602   1.670   1.774   1.772   1.872   1.761   1.762   1.868
63    L         0.544   0.586   0.411   0.710   0.766   0.514   0.505   0.571   0.268
64    K         1.602   1.602   1.670   1.321   1.327   1.429   1.761   1.762   1.868
65    K        -0.628  -0.639  -0.582  -0.963  -0.972  -0.877  -0.751  -0.760  -0.666
66    N        -0.407  -0.429  -0.500  -0.393  -0.429  -0.505  -0.437  -0.467  -0.553
67    T        -1.215  -1.239  -1.176  -0.890  -0.914  -0.812  -1.065  -1.090  -0.990
68    P        -0.407  -0.451  -0.522  -0.075  -0.153  -0.316  -0.437  -0.496  -0.583
69    D         0.179   0.204   0.252  -0.018   0.035   0.083  -0.123  -0.078  -0.018
70    V        -1.215  -1.174  -1.183  -1.084  -1.042  -0.998  -1.065  -1.021  -0.997
71    E         0.179   0.184   0.248  -0.068  -0.059   0.038  -0.123  -0.114  -0.025
72    A        -0.407  -0.404  -0.489  -0.300  -0.301  -0.492  -0.437  -0.434  -0.539
73    K         0.179   0.190   0.253  -0.326  -0.303  -0.219  -0.123  -0.103  -0.016
74    K        -1.215  -1.224  -1.172  -1.429  -1.434  -1.342  -1.065  -1.075  -0.986
75    F         0.179   0.190   0.253  -0.009   0.006   0.107  -0.123  -0.103  -0.016
76    L        -0.407  -0.382  -0.505  -0.674  -0.629  -0.828  -0.437  -0.403  -0.560
77    D        -1.215  -1.219  -1.192  -1.174  -1.199  -1.169  -1.065  -1.069  -1.006
78    S         0.179   0.166   0.238  -0.326  -0.361  -0.255  -0.123  -0.148  -0.042
79    V         0.179   0.190   0.253  -0.109  -0.089   0.004  -0.123  -0.103  -0.016
80    H        -1.801  -1.791  -1.682  -1.361  -1.342  -1.195  -1.379  -1.369  -1.225
81    H        -1.215  -1.211  -1.178  -1.214  -1.218  -1.139  -1.065  -1.060  -0.992
82    A        -0.407  -0.382  -0.505  -0.247  -0.208  -0.411  -0.437  -0.403  -0.560
83    G         1.602   1.602   1.670   1.759   1.757   1.858   1.761   1.762   1.868
84    G         1.602   1.602   1.670   1.759   1.757   1.858   1.761   1.762   1.868
85    S        -1.801  -1.791  -1.682  -1.624  -1.630  -1.451  -1.379  -1.369  -1.225
86    I         0.544   0.516   0.396   0.484   0.442   0.252   0.505   0.459   0.241
87    V         0.179   0.166   0.238   0.092   0.073   0.180  -0.123  -0.148  -0.042
88    H        -0.407  -0.451  -0.522  -0.116  -0.191  -0.344  -0.437  -0.496  -0.583
89    E         0.544   0.586   0.411   0.512   0.570   0.310   0.505   0.571   0.268
90    F         0.544   0.586   0.411   0.867   0.923   0.685   0.505   0.571   0.268
91    D         0.544   0.544   0.404   0.465   0.460   0.254   0.505   0.505   0.255
92    I         0.544   0.544   0.404   0.635   0.633   0.384   0.505   0.505   0.255
93    I         1.602   1.602   1.670   1.497   1.495   1.602   1.761   1.762   1.868
94    K         0.544   0.516   0.396   0.357   0.325   0.165   0.505   0.459   0.241
95    G         1.602   1.602   1.670   1.759   1.757   1.858   1.761   1.762   1.868
96    Y         0.179   0.190   0.253   0.340   0.357   0.447  -0.123  -0.103  -0.016
97    T        -1.215  -1.219  -1.192  -1.065  -1.087  -1.067  -1.065  -1.069  -1.006
98    I        -0.628  -0.602  -0.589  -0.721  -0.678  -0.653  -0.751  -0.721  -0.674
99    K         0.544   0.515   0.392   0.393   0.361   0.217   0.505   0.458   0.234
100   V        -0.407  -0.382  -0.505  -0.185  -0.151  -0.327  -0.437  -0.403  -0.560
101   P         1.602   1.602   1.670   1.922   1.921   2.017   1.761   1.762   1.868
102   D        -1.215  -1.239  -1.176  -1.267  -1.309  -1.208  -1.065  -1.090  -0.990
103   V        -1.215  -1.211  -1.178  -1.526  -1.517  -1.494  -1.065  -1.060  -0.992
104   L        -1.215  -1.224  -1.172  -0.907  -0.913  -0.836  -1.065  -1.075  -0.986
105   H        -1.215  -1.205  -1.163  -1.288  -1.265  -1.203  -1.065  -1.055  -0.977
106   L        -1.215  -1.219  -1.192  -1.181  -1.190  -1.177  -1.065  -1.069  -1.006
107   N        -1.215  -1.205  -1.163  -1.154  -1.145  -1.058  -1.065  -1.055  -0.977
108   K        -1.215  -1.224  -1.172  -1.572  -1.582  -1.502  -1.065  -1.075  -0.986
109   L        -0.596  -0.618  -0.568  -0.427  -0.456  -0.380  -0.692  -0.724  -0.644
110   K         0.544   0.516   0.396   0.357   0.325   0.165   0.505   0.459   0.241
111   E         0.544   0.544   0.404   0.639   0.638   0.390   0.505   0.505   0.255
112   K        -1.215  -1.219  -1.192  -1.194  -1.182  -1.090  -1.065  -1.069  -1.006
113   H        -0.407  -0.451  -0.522  -0.066  -0.136  -0.273  -0.437  -0.496  -0.583
114   N        -0.628  -0.639  -0.582  -0.431  -0.445  -0.352  -0.751  -0.760  -0.666
115   D         0.256   0.294   0.278   0.261   0.318   0.283   0.017   0.083   0.030
116   V         0.256   0.215   0.257   0.121   0.069   0.133   0.017  -0.058  -0.008
117   I        -0.407  -0.396  -0.489  -0.413  -0.401  -0.529  -0.437  -0.423  -0.539
118   E         0.544   0.515   0.392   0.535   0.494   0.316   0.505   0.458   0.234
119   N        -1.215  -1.189  -1.160  -0.937  -0.895  -0.873  -1.065  -1.037  -0.974
120   V         0.179   0.190   0.253  -0.109  -0.089   0.004  -0.123  -0.103  -0.016
121   E         1.602   1.602   1.670   1.513   1.513   1.617   1.761   1.762   1.868
122   E         1.602   1.602   1.670   1.513   1.513   1.617   1.761   1.762   1.868
123   D         1.602   1.602   1.670   1.683   1.684   1.784   1.761   1.762   1.868
124   K         0.544   0.515   0.392   0.340   0.306   0.132   0.505   0.458   0.234
125   E         1.602   1.602   1.670   1.513   1.513   1.617   1.761   1.762   1.868
126   V         1.602   1.602   1.670   1.637   1.644   1.739   1.761   1.762   1.868
127   H        -0.407  -0.429  -0.500  -0.428  -0.447  -0.490  -0.437  -0.467  -0.553
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   T        -0.628  -0.637  -0.572  -0.575  -0.595  -0.505  -0.751  -0.758  -0.655
130   N        -1.215  -1.174  -1.183  -0.937  -0.862  -0.944  -1.065  -1.021  -0.997
* 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/P01095
Output conservation file - output/P01095
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
