1     M         0.737   0.815   0.828   1.045   1.129   1.108   0.753   0.850   0.876
2     S         0.737   0.815   0.828   0.687   0.749   0.838   0.753   0.850   0.876
3     A        -2.080  -2.228  -2.128  -2.053  -2.195  -1.971  -1.839  -1.906  -1.741
4     P        -0.339  -0.756  -0.635  -0.156  -0.750  -0.626  -0.375  -0.991  -0.843
5     N         0.737   0.815   0.828   0.848   0.966   0.959   0.753   0.850   0.876
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     P        -0.251  -0.676  -0.621  -0.072  -0.696  -0.662  -0.255  -0.863  -0.820
8     K        -0.251  -0.676  -0.621  -0.172  -0.864  -0.857  -0.255  -0.863  -0.820
9     A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
10    F        -0.251  -0.676  -0.621   0.267  -0.279  -0.282  -0.255  -0.863  -0.820
11    P         0.737   0.815   0.828   0.758   0.898   0.891   0.753   0.850   0.876
12    L        -0.251  -0.676  -0.621  -0.466  -1.032  -0.907  -0.255  -0.863  -0.820
13    A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    D         0.737   0.815   0.828   0.855   0.956   0.964   0.753   0.850   0.876
16    A        -2.557  -2.288  -2.125  -2.723  -2.288  -1.973  -2.414  -1.988  -1.739
17    A        -2.080  -1.502  -2.089  -2.047  -1.318  -1.949  -1.839  -1.145  -1.706
18    L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
19    T        -1.625  -1.596  -1.498  -1.447  -1.485  -1.380  -1.695  -1.561  -1.431
20    Q         0.737   0.815   0.828   0.813   0.923   0.933   0.753   0.850   0.876
21    Q        -0.251  -0.676  -0.621   0.002  -0.598  -0.567  -0.255  -0.863  -0.820
22    I        -0.251  -0.676  -0.621  -0.310  -0.924  -0.936  -0.255  -0.863  -0.820
23    L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
24    D         0.737   0.815   0.828   0.855   0.956   0.964   0.753   0.850   0.876
25    V        -2.080  -2.228  -2.128  -1.771  -2.008  -1.985  -1.839  -1.906  -1.741
26    V         0.737   0.815   0.828   0.702   0.787   0.848   0.753   0.850   0.876
27    Q         0.737   0.815   0.828   0.813   0.923   0.933   0.753   0.850   0.876
28    Q         0.737   0.815   0.828   0.813   0.923   0.933   0.753   0.850   0.876
29    A        -0.738  -0.275  -0.596  -1.172  -0.483  -0.906  -0.975  -0.269  -0.780
30    A        -2.729  -2.013  -2.100  -2.855  -1.796  -1.946  -2.558  -1.656  -1.717
31    N        -0.998  -0.814  -0.637  -0.913  -0.616  -0.410  -1.407  -1.086  -0.846
32    L        -1.625  -1.406  -1.501  -1.682  -1.349  -1.291  -1.695  -1.438  -1.435
33    R        -0.251  -0.204  -0.595   0.082   0.114  -0.504  -0.255  -0.172  -0.778
34    Q         0.737   0.815   0.828   0.813   0.923   0.933   0.753   0.850   0.876
35    L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
36    K        -0.251  -0.204  -0.595  -0.089  -0.009  -0.554  -0.255  -0.172  -0.778
37    K         0.737   0.815   0.828   0.709   0.833   0.854   0.753   0.850   0.876
38    G         0.737   0.815   0.828   0.923   1.002   1.016   0.753   0.850   0.876
39    A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
40    N         0.737   0.815   0.828   0.848   0.966   0.959   0.753   0.850   0.876
41    E         0.737   0.815   0.828   0.820   0.929   0.938   0.753   0.850   0.876
42    A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
43    T         0.737   0.815   0.828   0.841   0.959   0.954   0.753   0.850   0.876
44    K         0.737   0.815   0.828   0.709   0.833   0.854   0.753   0.850   0.876
45    T        -0.251  -0.676  -0.621   0.011  -0.639  -0.609  -0.255  -0.863  -0.820
46    L        -0.251  -0.676  -0.621  -0.468  -1.053  -0.910  -0.255  -0.863  -0.820
47    N        -0.251  -0.676  -0.621   0.018  -0.632  -0.604  -0.255  -0.863  -0.820
48    R         0.737   0.815   0.828   0.910   0.984   1.006   0.753   0.850   0.876
49    G         0.737   0.815   0.828   0.923   1.002   1.016   0.753   0.850   0.876
50    I        -0.251  -0.676  -0.621  -0.241  -0.729  -0.714  -0.255  -0.863  -0.820
51    S         0.737   0.815   0.828   0.687   0.749   0.838   0.753   0.850   0.876
52    E         0.737   0.815   0.828   0.820   0.929   0.938   0.753   0.850   0.876
53    F        -0.251  -0.676  -0.621   0.158  -0.567  -0.625  -0.255  -0.863  -0.820
54    I        -0.251  -0.676  -0.621  -0.262  -0.803  -0.778  -0.255  -0.863  -0.820
55    I        -0.251  -0.204  -0.595  -0.262  -0.110  -0.735  -0.255  -0.172  -0.778
56    M        -0.251  -0.676  -0.621   0.171  -0.577  -0.617  -0.255  -0.863  -0.820
57    A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
58    A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
59    D         0.737   0.815   0.828   0.855   0.956   0.964   0.753   0.850   0.876
60    C        -1.819  -1.318  -1.482  -1.679  -0.974  -1.343  -1.983  -1.236  -1.412
61    E        -0.251  -0.676  -0.621   0.008  -0.595  -0.566  -0.255  -0.863  -0.820
62    P         0.737   0.815   0.828   0.758   0.898   0.891   0.753   0.850   0.876
63    I        -0.251  -0.676  -0.621  -0.310  -0.924  -0.936  -0.255  -0.863  -0.820
64    E        -0.251  -0.676  -0.621  -0.010  -0.667  -0.622  -0.255  -0.863  -0.820
65    I         0.737   0.815   0.828   0.566   0.767   0.746   0.753   0.850   0.876
66    L        -0.251  -0.676  -0.621  -0.468  -1.053  -0.910  -0.255  -0.863  -0.820
67    L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
68    H         0.737   0.815   0.828   1.098   1.162   1.149   0.753   0.850   0.876
69    L        -0.251  -0.676  -0.621  -0.488  -1.062  -0.976  -0.255  -0.863  -0.820
70    P         0.737   0.815   0.828   0.758   0.898   0.891   0.753   0.850   0.876
71    L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
72    L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
73    C         0.737   0.815   0.828   1.038   1.116   1.103   0.753   0.850   0.876
74    E         0.737   0.815   0.828   0.820   0.929   0.938   0.753   0.850   0.876
75    D         0.737   0.815   0.828   0.855   0.956   0.964   0.753   0.850   0.876
76    K         0.737   0.815   0.828   0.709   0.833   0.854   0.753   0.850   0.876
77    N         0.737   0.815   0.828   0.848   0.966   0.959   0.753   0.850   0.876
78    V         0.737   0.815   0.828   0.702   0.787   0.848   0.753   0.850   0.876
79    P         0.737   0.815   0.828   0.758   0.898   0.891   0.753   0.850   0.876
80    Y         0.737   0.815   0.828   1.065   1.134   1.123   0.753   0.850   0.876
81    V        -0.251  -0.064  -0.593  -0.145   0.075  -0.697  -0.255   0.010  -0.775
82    F        -0.251  -0.676  -0.621   0.253  -0.315  -0.325  -0.255  -0.863  -0.820
83    V         0.737   0.815   0.828   0.702   0.787   0.848   0.753   0.850   0.876
84    P         0.737   0.815   0.828   0.758   0.898   0.891   0.753   0.850   0.876
85    S         0.737   0.815   0.828   0.687   0.749   0.838   0.753   0.850   0.876
86    R        -0.998  -0.526  -0.609  -1.132  -0.432  -0.575  -1.407  -0.632  -0.801
87    V        -2.102  -1.702  -1.509  -2.385  -1.742  -1.555  -2.270  -1.668  -1.443
88    A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
89    L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
90    G         0.737   0.815   0.828   0.923   1.002   1.016   0.753   0.850   0.876
91    R         0.737   0.815   0.828   0.910   0.984   1.006   0.753   0.850   0.876
92    A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
93    C         0.737   0.815   0.828   1.038   1.116   1.103   0.753   0.850   0.876
94    G         0.737   0.815   0.828   0.923   1.002   1.016   0.753   0.850   0.876
95    V         0.737   0.815   0.828   0.702   0.787   0.848   0.753   0.850   0.876
96    S         0.737   0.815   0.828   0.687   0.749   0.838   0.753   0.850   0.876
97    R         0.737   0.815   0.828   0.910   0.984   1.006   0.753   0.850   0.876
98    P        -0.251  -0.676  -0.621  -0.072  -0.696  -0.662  -0.255  -0.863  -0.820
99    V         0.737   0.815   0.828   0.702   0.787   0.848   0.753   0.850   0.876
100   I         0.737   0.815   0.828   0.566   0.767   0.746   0.753   0.850   0.876
101   A        -0.738  -0.587  -0.639  -1.172  -0.933  -0.964  -0.975  -0.723  -0.849
102   A        -0.251  -0.676  -0.621  -0.505  -1.061  -0.935  -0.255  -0.863  -0.820
103   S         0.737   0.815   0.828   0.687   0.749   0.838   0.753   0.850   0.876
104   I        -1.819  -1.798  -1.509  -2.111  -2.118  -1.684  -1.983  -1.780  -1.444
105   T         0.737   0.815   0.828   0.841   0.959   0.954   0.753   0.850   0.876
106   T        -0.998  -0.847  -0.649  -1.133  -1.001  -0.677  -1.407  -1.139  -0.865
107   N         0.737   0.815   0.828   0.848   0.966   0.959   0.753   0.850   0.876
108   D        -0.998  -0.837  -0.647  -1.052  -0.853  -0.590  -1.407  -1.123  -0.862
109   A         0.737   0.815   0.828   0.324   0.495   0.563   0.753   0.850   0.876
110   S         0.737   0.815   0.828   0.687   0.749   0.838   0.753   0.850   0.876
111   A        -2.445  -2.029  -2.115  -2.565  -1.897  -1.959  -2.270  -1.752  -1.730
112   I        -1.819  -1.319  -1.488  -2.179  -1.522  -1.553  -1.983  -1.309  -1.420
113   K        -1.193  -1.545  -1.503  -0.968  -1.489  -1.534  -1.119  -1.509  -1.436
114   T        -3.183  -2.672  -2.593  -2.778  -2.235  -2.075  -2.702  -2.075  -1.909
115   Q        -0.251  -0.676  -0.621  -0.014  -0.638  -0.617  -0.255  -0.863  -0.820
116   I         0.737   0.815   0.828   0.566   0.767   0.746   0.753   0.850   0.876
117   Y        -2.080  -2.228  -2.128  -1.357  -1.701  -1.692  -1.839  -1.906  -1.741
118   A        -1.625  -1.098  -1.472  -1.823  -1.092  -1.498  -1.695  -0.948  -1.401
119   V        -2.557  -2.372  -2.127  -2.617  -2.454  -1.991  -2.414  -2.035  -1.740
120   K        -0.251  -0.676  -0.621  -0.089  -0.657  -0.593  -0.255  -0.863  -0.820
121   D        -0.251  -0.204  -0.595  -0.020   0.030  -0.679  -0.255  -0.172  -0.778
122   K        -0.251  -0.204  -0.595  -0.172  -0.094  -0.795  -0.255  -0.172  -0.778
123   I        -0.251  -0.676  -0.621  -0.262  -0.803  -0.778  -0.255  -0.863  -0.820
124   E         0.737   0.815   0.828   0.820   0.929   0.938   0.753   0.850   0.876
125   T        -1.625  -1.616  -1.502  -1.364  -1.410  -1.281  -1.695  -1.607  -1.436
126   L         0.737   0.815   0.828   0.362   0.504   0.591   0.753   0.850   0.876
127   L        -0.251  -0.676  -0.621  -0.523  -1.185  -1.093  -0.255  -0.863  -0.820
128   I        -0.251  -0.676  -0.621  -0.210  -0.654  -0.619  -0.255  -0.863  -0.820
* 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/P39990
Output conservation file - output/P39990
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
