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    M         0.796   0.836   0.861   0.961   1.007   1.030   0.821   0.874   0.908
36    I         0.796   0.836   0.861   0.849   0.866   0.936   0.821   0.874   0.908
37    V        -0.621  -0.379  -0.403  -0.766  -0.380  -0.442  -0.958  -0.565  -0.629
38    P         0.796   0.836   0.861   1.031   1.067   1.089   0.821   0.874   0.908
39    V        -0.621  -0.594  -0.443  -0.777  -0.754  -0.519  -0.958  -0.927  -0.697
40    R         0.796   0.836   0.861   0.713   0.771   0.823   0.821   0.874   0.908
41    C         0.796   0.836   0.861   0.849   0.890   0.936   0.821   0.874   0.908
42    F         0.796   0.836   0.861   1.041   1.089   1.097   0.821   0.874   0.908
43    S         0.796   0.836   0.861   1.031   1.079   1.089   0.821   0.874   0.908
44    C         0.796   0.836   0.861   0.849   0.890   0.936   0.821   0.874   0.908
45    G         0.796   0.836   0.861   0.859   0.898   0.945   0.821   0.874   0.908
46    K         0.796   0.836   0.861   0.703   0.772   0.814   0.821   0.874   0.908
47    V         0.796   0.836   0.861   0.818   0.898   0.910   0.821   0.874   0.908
48    V        -0.011  -0.070  -0.387   0.137   0.093  -0.421  -0.010  -0.092  -0.601
49    G         0.796   0.836   0.861   0.859   0.898   0.945   0.821   0.874   0.908
50    D         0.796   0.836   0.861   0.724   0.778   0.832   0.821   0.874   0.908
51    K        -0.011  -0.335  -0.408  -0.049  -0.556  -0.785  -0.010  -0.494  -0.637
52    W         0.796   0.836   0.861   1.100   1.134   1.147   0.821   0.874   0.908
53    E        -0.779  -0.710  -1.157  -0.603  -0.535  -1.123  -0.721  -0.634  -1.175
54    S        -1.801  -1.724  -1.736  -1.435  -1.409  -1.379  -1.670  -1.555  -1.493
55    Y         0.796   0.836   0.861   0.910   0.956   0.988   0.821   0.874   0.908
56    L         0.796   0.836   0.861   0.342   0.424   0.512   0.821   0.874   0.908
57    N        -2.403  -2.290  -2.172  -1.972  -1.819  -1.747  -2.026  -1.885  -1.669
58    L        -1.521  -1.281  -1.191  -1.854  -1.572  -1.360  -1.670  -1.354  -1.217
59    L        -0.011  -0.335  -0.408  -0.340  -0.751  -0.803  -0.010  -0.494  -0.637
60    Q        -0.011  -0.335  -0.408   0.342  -0.165  -0.356  -0.010  -0.494  -0.637
61    E        -1.290  -1.381  -1.201  -1.470  -1.546  -1.277  -1.433  -1.468  -1.229
62    D        -0.621  -0.588  -0.447  -0.922  -0.890  -0.656  -0.958  -0.916  -0.704
63    E        -1.250  -1.168  -1.192  -1.222  -1.068  -1.089  -1.348  -1.204  -1.218
64    L        -1.250  -1.376  -1.204  -1.580  -1.693  -1.363  -1.348  -1.461  -1.232
65    D        -2.032  -1.666  -1.725  -1.895  -1.338  -1.487  -1.907  -1.485  -1.483
66    E        -0.011  -0.335  -0.408   0.036  -0.428  -0.578  -0.010  -0.494  -0.637
67    G         0.796   0.836   0.861   0.859   0.898   0.945   0.821   0.874   0.908
68    T        -1.290  -1.168  -1.178  -1.375  -1.172  -1.201  -1.433  -1.215  -1.201
69    A         0.796   0.836   0.861   1.090   1.126   1.139   0.821   0.874   0.908
70    L         0.796   0.836   0.861   0.342   0.424   0.512   0.821   0.874   0.908
71    S        -1.132  -0.755  -1.156  -1.046  -0.544  -1.049  -1.195  -0.693  -1.174
72    R        -1.290  -1.349  -1.193  -1.464  -1.428  -1.202  -1.433  -1.427  -1.219
73    L         0.796   0.836   0.861   0.342   0.424   0.512   0.821   0.874   0.908
74    G        -1.132  -0.866  -1.173  -1.081  -0.681  -1.209  -1.195  -0.833  -1.196
75    L         0.796   0.836   0.861   0.342   0.424   0.512   0.821   0.874   0.908
76    K        -0.408  -0.334  -0.430  -0.460  -0.346  -0.474  -0.602  -0.493  -0.674
77    R         0.796   0.836   0.861   0.713   0.771   0.823   0.821   0.874   0.908
78    Y         0.796   0.836   0.861   0.910   0.956   0.988   0.821   0.874   0.908
79    C         0.796   0.836   0.861   0.849   0.890   0.936   0.821   0.874   0.908
80    C         0.796   0.836   0.861   0.849   0.890   0.936   0.821   0.874   0.908
81    R         0.796   0.836   0.861   0.713   0.771   0.823   0.821   0.874   0.908
82    R         0.796   0.836   0.861   0.713   0.771   0.823   0.821   0.874   0.908
83    M         0.796   0.836   0.861   0.961   1.007   1.030   0.821   0.874   0.908
84    I        -0.621  -0.585  -0.448  -0.766  -0.738  -0.530  -0.958  -0.911  -0.706
85    L        -0.011  -0.335  -0.408  -0.322  -0.699  -0.743  -0.010  -0.494  -0.637
86    T         0.796   0.836   0.861   0.930   0.965   1.005   0.821   0.874   0.908
87    H         0.796   0.836   0.861   1.100   1.134   1.147   0.821   0.874   0.908
88    V         0.796   0.836   0.861   0.818   0.898   0.910   0.821   0.874   0.908
89    D         0.796   0.836   0.861   0.724   0.778   0.832   0.821   0.874   0.908
90    L         0.796   0.836   0.861   0.342   0.424   0.512   0.821   0.874   0.908
91    I         0.796   0.836   0.861   0.849   0.866   0.936   0.821   0.874   0.908
92    E         0.796   0.836   0.861   0.734   0.785   0.841   0.821   0.874   0.908
93    K         0.796   0.836   0.861   0.703   0.772   0.814   0.821   0.874   0.908
94    F        -0.408  -0.564  -0.448  -0.350  -0.779  -0.684  -0.602  -0.875  -0.705
95    L         0.796   0.836   0.861   0.342   0.424   0.512   0.821   0.874   0.908
96    R        -0.779  -1.134  -1.188  -0.661  -1.179  -1.278  -0.721  -1.167  -1.213
97    Y         0.796   0.836   0.861   0.910   0.956   0.988   0.821   0.874   0.908
98    N        -0.011  -0.335  -0.408   0.361  -0.063  -0.269  -0.010  -0.494  -0.637
99    P        -0.011   0.102  -0.378   0.361   0.483  -0.215  -0.010   0.143  -0.587
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   L        -0.011  -0.335  -0.408  -0.362  -0.786  -0.874  -0.010  -0.494  -0.637
113   E        -0.779  -1.134  -1.188  -0.553  -0.982  -1.036  -0.721  -1.167  -1.213
114   K        -0.011  -0.335  -0.408   0.006  -0.438  -0.596  -0.010  -0.494  -0.637
115   R        -1.892  -1.971  -1.751  -1.964  -2.021  -1.666  -1.788  -1.785  -1.507
116   D        -1.503  -1.731  -1.740  -1.265  -1.578  -1.591  -1.314  -1.557  -1.497
117   -        -2.650  -2.401  -2.179  -2.506  -2.131  -1.871  -2.215  -1.946  -1.674
118   -        -2.056  -1.972  -1.755  -1.954  -1.874  -1.632  -1.912  -1.784  -1.511
* 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/P22139
Output conservation file - output/P22139
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
