1     M         0.305   0.314   0.327   1.088   1.070   0.982   0.310   0.321   0.338
2     S        -1.187  -1.512  -2.044  -0.361  -0.791  -1.837  -1.141  -1.581  -2.404
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     G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
6     R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
7     G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
8     K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
9     G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
10    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
11    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
12    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
13    L         0.305   0.314   0.327   0.315   0.333   0.354   0.310   0.321   0.338
14    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
15    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
16    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
17    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
18    A         0.305   0.314   0.327   0.529   0.531   0.527   0.310   0.321   0.338
19    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
20    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
21    H         0.305   0.314   0.327   1.001   0.992   0.911   0.310   0.321   0.338
22    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
23    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
24    I         0.305   0.314   0.327   0.498   0.506   0.503   0.310   0.321   0.338
25    L         0.305   0.314   0.327   0.315   0.333   0.354   0.310   0.321   0.338
26    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
27    D         0.305   0.314   0.327   0.903   0.897   0.831   0.310   0.321   0.338
28    N         0.305   0.314   0.327   1.036   1.027   0.940   0.310   0.321   0.338
29    I         0.305   0.314   0.327   0.498   0.506   0.503   0.310   0.321   0.338
30    Q         0.305   0.314   0.327   0.978   0.971   0.893   0.310   0.321   0.338
31    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
32    I         0.305   0.314   0.327   0.498   0.506   0.503   0.310   0.321   0.338
33    T         0.305   0.314   0.327   0.510   0.502   0.513   0.310   0.321   0.338
34    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
35    P         0.305   0.314   0.327   1.099   1.086   0.991   0.310   0.321   0.338
36    A         0.305   0.314   0.327   0.529   0.531   0.527   0.310   0.321   0.338
37    I         0.305   0.314   0.327   0.498   0.506   0.503   0.310   0.321   0.338
38    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
39    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
40    L         0.305   0.314   0.327   0.315   0.333   0.354   0.310   0.321   0.338
41    A         0.305   0.314   0.327   0.529   0.531   0.527   0.310   0.321   0.338
42    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
43    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
44    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
45    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
46    V         0.305   0.314   0.327   0.407   0.423   0.429   0.310   0.321   0.338
47    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
48    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
49    I         0.305   0.314   0.327   0.498   0.506   0.503   0.310   0.321   0.338
50    S         0.305   0.314   0.327   0.809   0.815   0.755   0.310   0.321   0.338
51    G        -2.544  -2.287  -2.048  -3.259  -2.707  -2.562  -3.171  -2.757  -2.410
52    L        -2.615  -2.805  -3.437  -1.841  -2.095  -2.802  -2.397  -2.636  -3.328
53    I        -1.615  -1.874  -2.045  -1.205  -1.624  -2.091  -1.721  -2.108  -2.406
54    Y         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
55    E         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
56    E         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
57    V        -2.486  -2.427  -2.051  -2.597  -2.583  -2.096  -3.074  -2.989  -2.415
58    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
59    A        -5.043  -4.719  -4.429  -4.640  -4.385  -4.119  -4.621  -4.266  -3.792
60    V         0.305   0.314   0.327   0.407   0.423   0.429   0.310   0.321   0.338
61    L         0.305   0.314   0.327   0.315   0.333   0.354   0.310   0.321   0.338
62    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
63    S        -5.022  -4.894  -4.429  -4.204  -4.216  -3.657  -4.621  -4.448  -3.792
64    F         0.305   0.314   0.327   1.001   0.992   0.911   0.310   0.321   0.338
65    L         0.305   0.314   0.327   0.315   0.333   0.354   0.310   0.321   0.338
66    E         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
67    S        -3.699  -3.778  -3.441  -3.000  -3.221  -3.200  -3.848  -3.843  -3.332
68    V         0.305   0.314   0.327   0.407   0.423   0.429   0.310   0.321   0.338
69    I         0.305   0.314   0.327   0.498   0.506   0.503   0.310   0.321   0.338
70    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
71    D         0.305   0.314   0.327   0.903   0.897   0.831   0.310   0.321   0.338
72    S        -0.617  -0.806  -2.042  -0.058  -0.244  -1.847  -0.464  -0.674  -2.401
73    V         0.305   0.314   0.327   0.407   0.423   0.429   0.310   0.321   0.338
74    T         0.305   0.314   0.327   0.510   0.502   0.513   0.310   0.321   0.338
75    Y         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
76    T         0.305   0.314   0.327   0.510   0.502   0.513   0.310   0.321   0.338
77    E         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
78    H         0.305   0.314   0.327   1.001   0.992   0.911   0.310   0.321   0.338
79    A         0.305   0.314   0.327   0.529   0.531   0.527   0.310   0.321   0.338
80    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
81    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
82    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
83    T         0.305   0.314   0.327   0.510   0.502   0.513   0.310   0.321   0.338
84    V         0.305   0.314   0.327   0.407   0.423   0.429   0.310   0.321   0.338
85    T         0.305   0.314   0.327   0.510   0.502   0.513   0.310   0.321   0.338
86    S         0.305   0.314   0.327   0.809   0.815   0.755   0.310   0.321   0.338
87    L         0.305   0.314   0.327   0.315   0.333   0.354   0.310   0.321   0.338
88    D         0.305   0.314   0.327   0.903   0.897   0.831   0.310   0.321   0.338
89    V         0.305   0.314   0.327   0.407   0.423   0.429   0.310   0.321   0.338
90    V         0.305   0.314   0.327   0.407   0.423   0.429   0.310   0.321   0.338
91    Y         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
92    A        -1.615  -1.874  -2.045  -1.090  -1.479  -1.850  -1.721  -2.108  -2.406
93    L         0.305   0.314   0.327   0.315   0.333   0.354   0.310   0.321   0.338
94    K         0.305   0.314   0.327   0.077   0.099   0.161   0.310   0.321   0.338
95    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
96    Q         0.305   0.314   0.327   0.978   0.971   0.893   0.310   0.321   0.338
97    G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
98    R         0.305   0.314   0.327  -0.251  -0.218  -0.106   0.310   0.321   0.338
99    T         0.305   0.314   0.327   0.510   0.502   0.513   0.310   0.321   0.338
100   L        -1.615  -1.874  -2.045  -1.368  -1.765  -2.155  -1.721  -2.108  -2.406
101   Y         0.305   0.314   0.327   0.803   0.800   0.750   0.310   0.321   0.338
102   G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
103   F         0.305   0.314   0.327   1.001   0.992   0.911   0.310   0.321   0.338
104   G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
105   G         0.305   0.314   0.327  -0.457  -0.414  -0.273   0.310   0.321   0.338
* 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/P02309
Output conservation file - output/P02309
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
