1     M         0.710   0.728   0.773   0.910   0.929   0.974   0.726   0.751   0.812
2     S         0.710   0.728   0.773   0.832   0.857   0.909   0.726   0.751   0.812
3     S        -0.666  -0.640  -0.608  -0.581  -0.567  -0.587  -0.912  -0.885  -0.853
4     A        -1.530  -1.419  -1.406  -1.463  -1.235  -1.235  -1.657  -1.531  -1.403
5     P         0.710   0.728   0.773   0.825   0.848   0.903   0.726   0.751   0.812
6     L         0.710   0.728   0.773   0.259   0.304   0.430   0.726   0.751   0.812
7     L         0.710   0.728   0.773   0.259   0.304   0.430   0.726   0.751   0.812
8     Q         0.710   0.728   0.773   0.996   1.045   1.046   0.726   0.751   0.812
9     R        -2.347  -2.068  -1.997  -2.088  -1.730  -1.671  -2.173  -1.880  -1.701
10    T        -0.884  -0.811  -0.618  -1.214  -1.112  -0.802  -1.281  -1.174  -0.870
11    P         0.710   0.728   0.773   0.825   0.848   0.903   0.726   0.751   0.812
12    G        -0.583  -0.467  -0.572  -0.618  -0.455  -0.606  -0.779  -0.609  -0.794
13    K         0.710   0.728   0.773   0.910   0.941   0.974   0.726   0.751   0.812
14    K        -0.583  -0.390  -0.581  -0.560  -0.304  -0.573  -0.779  -0.492  -0.809
15    I         0.710   0.728   0.773   0.765   0.778   0.853   0.726   0.751   0.812
16    A         0.710   0.728   0.773   0.553   0.587   0.676   0.726   0.751   0.812
17    L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
18    P         0.710   0.728   0.773   0.844   0.864   0.919   0.726   0.751   0.812
19    T        -1.360  -1.382  -1.396  -1.288  -1.309  -1.420  -1.406  -1.411  -1.389
20    R         0.710   0.728   0.773   0.654   0.674   0.760   0.726   0.751   0.812
21    V         0.710   0.728   0.773   0.641   0.662   0.749   0.726   0.751   0.812
22    E         0.710   0.728   0.773   1.011   1.029   1.058   0.726   0.751   0.812
23    P         0.710   0.728   0.773   0.844   0.864   0.919   0.726   0.751   0.812
24    K         0.710   0.728   0.773   0.910   0.941   0.974   0.726   0.751   0.812
25    V         0.710   0.728   0.773   0.641   0.662   0.749   0.726   0.751   0.812
26    F         0.710   0.728   0.773   0.629   0.645   0.739   0.726   0.751   0.812
27    F         0.710   0.728   0.773   0.629   0.645   0.739   0.726   0.751   0.812
28    A         0.710   0.728   0.773   0.553   0.587   0.676   0.726   0.751   0.812
29    N         0.710   0.728   0.773   0.898   0.934   0.964   0.726   0.751   0.812
30    E         0.710   0.728   0.773   1.011   1.029   1.058   0.726   0.751   0.812
31    R         0.710   0.728   0.773   0.654   0.674   0.760   0.726   0.751   0.812
32    T         0.710   0.728   0.773   0.728   0.753   0.822   0.726   0.751   0.812
33    F         0.710   0.728   0.773   0.629   0.645   0.739   0.726   0.751   0.812
34    L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
35    S         0.710   0.728   0.773   0.832   0.857   0.909   0.726   0.751   0.812
36    W         0.710   0.728   0.773   1.017   1.029   1.063   0.726   0.751   0.812
37    L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
38    N        -0.156  -0.299  -0.564   0.207   0.048  -0.410  -0.152  -0.356  -0.781
39    F         0.710   0.728   0.773   0.629   0.645   0.739   0.726   0.751   0.812
40    T        -0.156  -0.299  -0.564  -0.001  -0.185  -0.659  -0.152  -0.356  -0.781
41    V         0.710   0.728   0.773   0.641   0.662   0.749   0.726   0.751   0.812
42    M        -1.530  -1.502  -1.415  -1.379  -1.338  -1.257  -1.657  -1.574  -1.412
43    L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
44    G         0.710   0.728   0.773   0.597   0.625   0.713   0.726   0.751   0.812
45    G        -1.360  -1.437  -1.408  -1.323  -1.437  -1.434  -1.406  -1.477  -1.403
46    L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
47    G        -1.360  -1.500  -1.420  -1.378  -1.586  -1.467  -1.406  -1.572  -1.418
48    V        -0.156  -0.370  -0.575  -0.058  -0.330  -0.643  -0.152  -0.461  -0.799
49    G         0.710   0.728   0.773   0.597   0.625   0.713   0.726   0.751   0.812
50    L        -0.156  -0.370  -0.575  -0.405  -0.637  -0.834  -0.152  -0.461  -0.799
51    L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
52    N         0.710   0.728   0.773   0.898   0.934   0.964   0.726   0.751   0.812
53    F         0.710   0.728   0.773   0.629   0.645   0.739   0.726   0.751   0.812
54    G         0.710   0.728   0.773   0.597   0.625   0.713   0.726   0.751   0.812
55    D         0.710   0.728   0.773   0.964   0.983   1.019   0.726   0.751   0.812
56    K        -2.177  -1.965  -1.988  -1.852  -1.617  -1.587  -2.034  -1.801  -1.693
57    I        -1.360  -1.512  -1.415  -1.252  -1.457  -1.318  -1.406  -1.576  -1.412
58    G        -0.156  -0.370  -0.575  -0.133  -0.414  -0.778  -0.152  -0.461  -0.799
59    R        -1.360  -1.525  -1.417  -1.225  -1.462  -1.326  -1.406  -1.593  -1.415
60    V        -0.156   0.022  -0.552   0.048   0.239  -0.567  -0.152   0.079  -0.760
61    S         0.710   0.728   0.773   0.832   0.857   0.909   0.726   0.751   0.812
62    A         0.710   0.728   0.773   0.553   0.587   0.676   0.726   0.751   0.812
63    G        -0.981  -1.064  -1.396  -0.849  -0.984  -1.513  -0.905  -1.030  -1.389
64    L        -0.156  -0.010  -0.554  -0.405  -0.230  -0.812  -0.152   0.038  -0.764
65    F         0.710   0.728   0.773   0.629   0.645   0.739   0.726   0.751   0.812
66    T         0.710   0.728   0.773   0.728   0.753   0.822   0.726   0.751   0.812
67    F        -2.177  -2.275  -2.000  -2.448  -2.548  -2.111  -2.034  -2.075  -1.704
68    V        -0.811  -0.688  -0.605  -0.987  -0.807  -0.690  -1.155  -0.965  -0.848
69    A         0.710   0.728   0.773   0.553   0.587   0.676   0.726   0.751   0.812
70    M        -0.156  -0.299  -0.564   0.210   0.028  -0.431  -0.152  -0.356  -0.781
71    G        -1.681  -1.612  -1.423  -2.061  -1.964  -1.734  -1.783  -1.699  -1.421
72    T        -0.156  -0.021  -0.556   0.038   0.191  -0.518  -0.152   0.024  -0.767
73    M         0.710   0.728   0.773   0.910   0.929   0.974   0.726   0.751   0.812
74    I        -1.778  -1.674  -1.432  -1.923  -1.802  -1.458  -1.908  -1.773  -1.432
75    Y         0.710   0.728   0.773   0.946   0.964   1.004   0.726   0.751   0.812
76    A         0.710   0.728   0.773   0.553   0.587   0.676   0.726   0.751   0.812
77    L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
78    V        -0.156  -0.299  -0.564  -0.082  -0.268  -0.703  -0.152  -0.356  -0.781
79    T        -0.156  -0.299  -0.564   0.029  -0.146  -0.563  -0.152  -0.356  -0.781
80    Y         0.710   0.728   0.773   0.946   0.964   1.004   0.726   0.751   0.812
81    H         0.710   0.728   0.773   1.063   1.074   1.102   0.726   0.751   0.812
82    W         0.710   0.728   0.773   1.017   1.029   1.063   0.726   0.751   0.812
83    R         0.710   0.728   0.773   0.654   0.674   0.760   0.726   0.751   0.812
84    A         0.710   0.728   0.773   0.553   0.587   0.676   0.726   0.751   0.812
85    A        -1.530  -1.572  -1.420  -1.510  -1.491  -1.292  -1.657  -1.673  -1.418
86    A        -0.156  -0.370  -0.575  -0.136  -0.385  -0.674  -0.152  -0.461  -0.799
87    I         0.710   0.728   0.773   0.765   0.778   0.853   0.726   0.751   0.812
88    R         0.710   0.728   0.773   0.654   0.674   0.760   0.726   0.751   0.812
89    R        -2.079  -1.938  -1.994  -2.017  -1.935  -1.877  -1.908  -1.782  -1.698
90    R         0.710   0.728   0.773   0.654   0.674   0.760   0.726   0.751   0.812
91    G         0.710   0.728   0.773   0.597   0.625   0.713   0.726   0.751   0.812
92    S        -0.156  -0.370  -0.575   0.168  -0.073  -0.390  -0.152  -0.461  -0.799
93    G        -0.156  -0.370  -0.575  -0.133  -0.414  -0.778  -0.152  -0.461  -0.799
94    P        -0.156  -0.370  -0.575   0.121  -0.167  -0.575  -0.152  -0.461  -0.799
95    Y        -0.156  -0.370  -0.575   0.227  -0.064  -0.487  -0.152  -0.461  -0.799
96    D         0.710   0.728   0.773   0.964   0.983   1.019   0.726   0.751   0.812
97    D         0.710   0.728   0.773   0.964   0.983   1.019   0.726   0.751   0.812
98    R         0.710   0.728   0.773   0.654   0.674   0.760   0.726   0.751   0.812
99    L        -0.884  -0.813  -0.619  -1.479  -1.364  -1.017  -1.281  -1.177  -0.871
100   G         0.710   0.728   0.773   0.597   0.625   0.713   0.726   0.751   0.812
101   P         0.710   0.728   0.773   0.844   0.864   0.919   0.726   0.751   0.812
102   T         0.710   0.728   0.773   0.728   0.753   0.822   0.726   0.751   0.812
103   L        -2.177  -2.274  -2.002  -2.210  -2.303  -1.933  -2.034  -2.074  -1.705
104   L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
105   C        -0.156  -0.370  -0.575   0.340   0.041  -0.431  -0.152  -0.461  -0.799
106   F        -1.530  -1.582  -1.419  -1.655  -1.771  -1.579  -1.657  -1.672  -1.417
107   F        -0.981  -1.303  -1.404  -0.779  -1.226  -1.403  -0.905  -1.307  -1.399
108   L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
109   L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
110   V        -2.079  -2.108  -1.999  -2.121  -2.276  -2.156  -1.908  -1.933  -1.703
111   A         0.710   0.728   0.773   0.553   0.587   0.676   0.726   0.751   0.812
112   V        -0.156  -0.299  -0.564  -0.058  -0.236  -0.626  -0.152  -0.356  -0.781
113   I        -0.811  -0.735  -0.611  -0.987  -0.884  -0.699  -1.155  -1.043  -0.858
114   I        -1.681  -1.557  -1.424  -1.722  -1.564  -1.382  -1.783  -1.631  -1.422
115   N         0.710   0.728   0.773   0.898   0.934   0.964   0.726   0.751   0.812
116   F         0.710   0.728   0.773   0.629   0.645   0.739   0.726   0.751   0.812
117   I        -1.530  -1.372  -1.412  -1.547  -1.396  -1.404  -1.657  -1.496  -1.409
118   L         0.710   0.728   0.773   0.272   0.313   0.441   0.726   0.751   0.812
119   R        -0.156   0.016  -0.553  -0.024   0.159  -0.532  -0.152   0.071  -0.761
120   L        -2.327  -2.106  -2.002  -2.297  -1.945  -1.865  -2.159  -1.931  -1.706
121   K        -2.725  -2.731  -2.454  -2.452  -2.551  -2.282  -2.285  -2.255  -1.878
122   Y        -0.441  -0.505  -0.580  -0.149  -0.269  -0.500  -0.558  -0.667  -0.807
123   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   L        -2.853  -2.748  -2.457  -2.780  -2.617  -2.096  -2.387  -2.268  -1.880
* 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/P40046
Output conservation file - output/P40046
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
