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    M         1.365   1.426   1.523   1.682   1.753   1.898   1.472   1.554   1.692
12    S         0.641   0.684   0.434   0.579   0.612   0.214   0.655   0.714   0.270
13    E        -1.173  -1.067  -0.983  -0.990  -0.838  -0.682  -1.213  -1.081  -0.912
14    Q        -1.632  -1.468  -1.395  -1.454  -1.303  -1.120  -1.446  -1.251  -1.095
15    A        -1.965  -1.841  -1.720  -1.775  -1.590  -1.375  -1.563  -1.424  -1.210
16    Q        -1.632  -1.468  -1.395  -1.541  -1.378  -1.187  -1.446  -1.251  -1.095
17    T        -0.852  -0.772  -0.950  -0.677  -0.629  -0.905  -0.815  -0.742  -0.874
18    Q        -1.634  -1.569  -1.403  -1.260  -1.140  -0.947  -1.433  -1.337  -1.101
19    Q        -2.078  -1.951  -1.756  -2.055  -1.931  -1.574  -1.641  -1.491  -1.234
20    P        -1.728  -1.612  -1.423  -1.643  -1.499  -1.190  -1.517  -1.369  -1.117
21    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    G        -1.195  -1.033  -0.978  -1.465  -1.236  -1.122  -1.218  -1.009  -0.905
34    S        -0.461  -0.323  -0.403  -0.490  -0.282  -0.474  -0.620  -0.423  -0.534
35    S        -0.578  -0.454  -0.429  -0.716  -0.576  -0.495  -0.811  -0.615  -0.572
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    V         0.053   0.151   0.269  -0.475  -0.313  -0.114  -0.358  -0.196  -0.035
42    S        -1.613  -1.410  -1.393  -1.341  -1.035  -1.047  -1.425  -1.187  -1.093
43    T        -1.469  -1.490  -1.389  -1.415  -1.488  -1.236  -1.273  -1.271  -1.089
44    I        -0.565  -0.596  -0.449  -0.698  -0.708  -0.489  -0.815  -0.816  -0.601
45    L         1.365   1.426   1.523   1.261   1.345   1.507   1.472   1.554   1.692
46    D        -0.365  -0.264  -0.389  -0.162   0.004  -0.252  -0.513  -0.353  -0.518
47    T        -1.506  -1.562  -1.400  -1.140  -1.165  -0.951  -1.330  -1.337  -1.099
48    K        -0.365  -0.324  -0.408  -0.210  -0.165  -0.279  -0.513  -0.485  -0.550
49    W         1.365   1.426   1.523   1.650   1.718   1.869   1.472   1.554   1.692
50    D         1.365   1.426   1.523   1.586   1.663   1.809   1.472   1.554   1.692
51    I        -0.048  -0.135  -0.352  -0.069  -0.161  -0.464  -0.046  -0.167  -0.464
52    V         0.285   0.170   0.263   0.138   0.007   0.183   0.071  -0.159  -0.047
53    L         0.641   0.684   0.434   0.635   0.706   0.378   0.655   0.714   0.270
54    S         1.365   1.426   1.523   1.278   1.323   1.523   1.472   1.554   1.692
55    N         1.365   1.426   1.523   1.602   1.676   1.824   1.472   1.554   1.692
56    M        -1.047  -1.022  -0.956  -0.953  -0.891  -0.855  -1.096  -1.030  -0.884
57    L        -0.365  -0.286  -0.408  -0.574  -0.476  -0.642  -0.513  -0.423  -0.549
58    V        -0.507  -0.376  -0.418  -0.742  -0.535  -0.572  -0.746  -0.572  -0.564
59    K         0.641   0.525   0.408   0.876   0.744   0.559   0.655   0.465   0.224
60    T        -0.365  -0.372  -0.438  -0.296  -0.429  -0.437  -0.513  -0.568  -0.589
61    A        -0.365  -0.406  -0.415  -0.710  -0.714  -0.739  -0.513  -0.538  -0.555
62    M        -0.048  -0.121  -0.338   0.043  -0.035  -0.294  -0.046  -0.148  -0.445
63    G         1.365   1.426   1.523   1.086   1.192   1.344   1.472   1.554   1.692
64    F        -0.365  -0.376  -0.443  -0.426  -0.529  -0.637  -0.513  -0.573  -0.594
65    G         1.365   1.426   1.523   1.086   1.192   1.344   1.472   1.554   1.692
66    V        -1.173  -1.155  -0.977  -1.698  -1.568  -1.317  -1.213  -1.151  -0.906
67    G         1.365   1.426   1.523   1.086   1.192   1.344   1.472   1.554   1.692
68    V         0.285   0.282   0.283   0.076   0.096   0.091   0.071   0.047  -0.009
69    F        -0.507  -0.362  -0.389  -0.933  -0.648  -0.676  -0.746  -0.526  -0.520
70    T        -0.966  -1.100  -0.973  -1.019  -1.241  -1.031  -0.979  -1.084  -0.901
71    S         1.365   1.426   1.523   1.278   1.323   1.523   1.472   1.554   1.692
72    V         0.285   0.527   0.394   0.076   0.454   0.256   0.071   0.469   0.198
73    L         1.365   1.426   1.523   1.261   1.345   1.507   1.472   1.554   1.692
74    F        -0.048  -0.037  -0.338   0.148   0.179  -0.304  -0.046  -0.048  -0.444
75    F         1.365   1.426   1.523   1.438   1.524   1.672   1.472   1.554   1.692
76    K         0.641   0.525   0.408   0.848   0.705   0.487   0.655   0.465   0.224
77    R         1.365   1.426   1.523   1.438   1.514   1.672   1.472   1.554   1.692
78    R         0.641   0.525   0.408   0.775   0.607   0.396   0.655   0.465   0.224
79    A        -0.365  -0.203  -0.360  -0.492  -0.240  -0.477  -0.513  -0.260  -0.479
80    F         0.285   0.170   0.263   0.335   0.153   0.288   0.071  -0.159  -0.047
81    P         1.365   1.426   1.523   1.650   1.720   1.869   1.472   1.554   1.692
82    V         0.641   0.510   0.397   0.527   0.364   0.155   0.655   0.441   0.202
83    W         0.641   0.510   0.397   1.002   0.817   0.598   0.655   0.441   0.202
84    L        -0.365  -0.495  -0.442  -0.675  -0.903  -0.914  -0.513  -0.674  -0.593
85    G         1.365   1.426   1.523   1.086   1.192   1.344   1.472   1.554   1.692
86    I        -0.365  -0.438  -0.405  -0.549  -0.625  -0.595  -0.513  -0.587  -0.541
87    G         1.365   1.426   1.523   1.086   1.192   1.344   1.472   1.554   1.692
88    F         1.365   1.426   1.523   1.438   1.524   1.672   1.472   1.554   1.692
89    G         1.365   1.426   1.523   1.086   1.192   1.344   1.472   1.554   1.692
90    V        -0.507  -0.437  -0.421  -0.882  -0.781  -0.735  -0.746  -0.651  -0.570
91    G         1.365   1.426   1.523   1.086   1.192   1.344   1.472   1.554   1.692
92    R         0.641   0.525   0.408   0.799   0.651   0.458   0.655   0.465   0.224
93    G        -0.048  -0.312  -0.399  -0.251  -0.634  -0.807  -0.046  -0.403  -0.528
94    Y         0.641   0.684   0.434   1.032   1.088   0.644   0.655   0.714   0.270
95    A        -0.365  -0.349  -0.396  -0.465  -0.410  -0.486  -0.513  -0.455  -0.527
96    E         0.641   0.525   0.408   1.006   0.852   0.659   0.655   0.465   0.224
97    G        -0.048  -0.312  -0.399  -0.171  -0.496  -0.602  -0.046  -0.403  -0.528
98    D         0.285   0.170   0.263   0.459   0.252   0.365   0.071  -0.159  -0.047
99    A        -0.048  -0.176  -0.351   0.012  -0.182  -0.479  -0.046  -0.221  -0.463
100   I        -0.048  -0.312  -0.399   0.273  -0.129  -0.349  -0.046  -0.403  -0.528
101   F         0.285   0.170   0.263   0.209  -0.037   0.051   0.071  -0.159  -0.047
102   R         0.641   0.510   0.397   0.799   0.630   0.437   0.655   0.441   0.202
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   S        -0.365  -0.500  -0.443  -0.429  -0.625  -0.479  -0.513  -0.678  -0.594
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   S        -1.839  -1.888  -1.739  -1.438  -1.543  -1.347  -1.446  -1.448  -1.222
114   A         0.285   0.527   0.394   0.271   0.581   0.448   0.071   0.469   0.198
115   G        -0.048  -0.312  -0.399  -0.231  -0.592  -0.755  -0.046  -0.403  -0.528
116   L        -0.698  -0.930  -0.950  -0.690  -1.027  -1.103  -0.629  -0.892  -0.875
117   R        -0.048  -0.312  -0.399   0.186  -0.164  -0.315  -0.046  -0.403  -0.528
118   S        -1.506  -1.508  -1.390  -1.455  -1.440  -1.216  -1.330  -1.283  -1.090
119   S        -0.698  -0.896  -0.947  -0.762  -1.044  -1.155  -0.629  -0.855  -0.871
120   K        -0.698  -0.740  -0.909  -0.345  -0.387  -0.640  -0.629  -0.673  -0.829
121   V        -0.365  -0.392  -0.400  -0.507  -0.512  -0.558  -0.513  -0.518  -0.534
* 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/Q96VH5
Output conservation file - output/Q96VH5
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
