1     M         1.032   1.044   1.068   1.204   1.230   1.249   1.076   1.090   1.120
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     S         1.032   1.044   1.068   1.111   1.141   1.162   1.076   1.090   1.120
7     E        -0.401  -0.439  -0.408  -0.966  -1.012  -0.898  -0.584  -0.641  -0.592
8     T        -0.401  -0.386  -0.393  -0.388  -0.363  -0.376  -0.584  -0.555  -0.568
9     G        -0.401  -0.433  -0.403  -0.292  -0.345  -0.327  -0.584  -0.631  -0.585
10    E         1.032   1.044   1.068   0.528   0.545   0.616   1.076   1.090   1.120
11    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -0.234  -0.340  -0.377   0.046  -0.079  -0.143  -0.325  -0.483  -0.543
13    E        -1.309  -1.251  -1.267  -1.604  -1.526  -1.474  -1.259  -1.174  -1.165
14    Y        -0.234  -0.340  -0.377  -0.135  -0.324  -0.479  -0.325  -0.483  -0.543
15    Y        -0.234  -0.340  -0.377  -0.028  -0.181  -0.300  -0.325  -0.483  -0.543
16    K         1.032   1.044   1.068   0.870   0.893   0.936   1.076   1.090   1.120
17    Q        -0.234  -0.106  -0.346  -0.590  -0.432  -0.680  -0.325  -0.131  -0.494
18    A        -0.234  -0.340  -0.377  -0.053  -0.194  -0.268  -0.325  -0.483  -0.543
19    L        -0.234  -0.340  -0.377  -0.048  -0.184  -0.248  -0.325  -0.483  -0.543
20    E        -0.234  -0.210  -0.359  -0.596  -0.564  -0.704  -0.325  -0.285  -0.515
21    E        -0.234  -0.169  -0.352  -0.590  -0.510  -0.687  -0.325  -0.224  -0.504
22    Y        -0.234  -0.340  -0.377  -0.135  -0.324  -0.479  -0.325  -0.483  -0.543
23    K        -1.309  -1.350  -1.282  -1.187  -1.223  -1.117  -1.259  -1.293  -1.182
24    E        -0.234  -0.210  -0.359  -0.667  -0.638  -0.814  -0.325  -0.285  -0.515
25    V        -1.309  -1.289  -1.279  -1.103  -1.134  -1.133  -1.259  -1.227  -1.178
26    Q        -1.442  -1.402  -1.299  -1.530  -1.519  -1.309  -1.415  -1.352  -1.200
27    E        -0.234  -0.210  -0.359  -0.667  -0.638  -0.814  -0.325  -0.285  -0.515
28    D        -1.309  -1.251  -1.267  -1.531  -1.426  -1.504  -1.259  -1.174  -1.165
29    E        -0.234  -0.340  -0.377  -0.667  -0.827  -0.838  -0.325  -0.483  -0.543
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    D        -0.529  -0.499  -0.422  -1.068  -1.046  -0.885  -0.792  -0.738  -0.616
35    P        -0.234  -0.169  -0.352   0.149   0.248  -0.060  -0.325  -0.224  -0.504
36    D         1.032   1.044   1.068   0.870   0.889   0.936   1.076   1.090   1.120
37    V        -2.090  -2.035  -1.918  -1.886  -1.869  -1.642  -1.726  -1.652  -1.490
38    W         1.032   1.044   1.068   1.142   1.160   1.191   1.076   1.090   1.120
39    D         1.032   1.044   1.068   0.870   0.889   0.936   1.076   1.090   1.120
40    T        -1.309  -1.289  -1.279  -1.215  -1.181  -1.148  -1.259  -1.227  -1.178
41    R         1.032   1.044   1.068   1.064   1.096   1.117   1.076   1.090   1.120
42    I         1.032   1.044   1.068   1.250   1.264   1.292   1.076   1.090   1.120
43    S        -1.309  -1.327  -1.278  -0.937  -0.942  -0.898  -1.259  -1.268  -1.177
44    K        -1.309  -1.177  -1.254  -1.194  -0.979  -1.143  -1.259  -1.086  -1.151
45    T         1.032   1.044   1.068   1.000   1.009   1.058   1.076   1.090   1.120
46    G         1.032   1.044   1.068   1.142   1.169   1.191   1.076   1.090   1.120
47    C         1.032   1.044   1.068   1.095   1.117   1.147   1.076   1.090   1.120
48    Y        -0.234  -0.340  -0.377   0.091  -0.030  -0.106  -0.325  -0.483  -0.543
49    V        -0.234  -0.340  -0.377  -0.059  -0.209  -0.325  -0.325  -0.483  -0.543
50    E         1.032   1.044   1.068   0.512   0.523   0.601   1.076   1.090   1.120
51    N         1.032   1.044   1.068   1.064   1.079   1.117   1.076   1.090   1.120
52    L         1.032   1.044   1.068   1.048   1.073   1.103   1.076   1.090   1.120
53    A        -0.234  -0.340  -0.377  -0.120  -0.278  -0.377  -0.325  -0.483  -0.543
54    L         1.032   1.044   1.068   1.048   1.073   1.103   1.076   1.090   1.120
55    Q         1.032   1.044   1.068   1.080   1.097   1.132   1.076   1.090   1.120
56    L         1.032   1.044   1.068   1.048   1.073   1.103   1.076   1.090   1.120
57    C         1.032   1.044   1.068   1.095   1.117   1.147   1.076   1.090   1.120
58    H         1.032   1.044   1.068   1.250   1.267   1.292   1.076   1.090   1.120
59    A         1.032   1.044   1.068   1.064   1.090   1.117   1.076   1.090   1.120
60    E        -0.234  -0.340  -0.377  -0.667  -0.827  -0.838  -0.325  -0.483  -0.543
61    T         1.032   1.044   1.068   1.000   1.009   1.058   1.076   1.090   1.120
62    G        -0.529  -0.505  -0.424  -0.454  -0.409  -0.298  -0.792  -0.748  -0.618
63    D         1.032   1.044   1.068   0.870   0.889   0.936   1.076   1.090   1.120
64    W         1.032   1.044   1.068   1.142   1.160   1.191   1.076   1.090   1.120
65    R         1.032   1.044   1.068   1.064   1.096   1.117   1.076   1.090   1.120
66    Q         1.032   1.044   1.068   1.080   1.097   1.132   1.076   1.090   1.120
67    C         1.032   1.044   1.068   1.095   1.117   1.147   1.076   1.090   1.120
68    F        -1.309  -1.350  -1.282  -0.905  -0.981  -0.915  -1.259  -1.293  -1.182
69    N        -2.090  -2.035  -1.918  -1.598  -1.546  -1.373  -1.726  -1.652  -1.490
70    E         1.032   1.044   1.068   0.512   0.523   0.601   1.076   1.090   1.120
71    M        -0.234  -0.340  -0.377   0.071  -0.075  -0.173  -0.325  -0.483  -0.543
72    A        -1.309  -1.350  -1.282  -1.103  -1.154  -1.088  -1.259  -1.293  -1.182
73    L        -1.309  -1.327  -1.278  -1.124  -1.135  -1.100  -1.259  -1.268  -1.177
74    F         1.032   1.044   1.068   1.250   1.274   1.292   1.076   1.090   1.120
75    R        -0.234  -0.106  -0.346  -0.245  -0.066  -0.388  -0.325  -0.131  -0.494
76    K        -1.309  -1.207  -1.259  -1.705  -1.564  -1.582  -1.259  -1.122  -1.156
77    C         1.032   1.044   1.068   1.095   1.117   1.147   1.076   1.090   1.120
78    W         1.032   1.044   1.068   1.142   1.160   1.191   1.076   1.090   1.120
79    E        -1.309  -1.350  -1.282  -1.596  -1.645  -1.471  -1.259  -1.293  -1.182
80    K        -0.529  -0.505  -0.424  -0.615  -0.571  -0.456  -0.792  -0.748  -0.618
81    N        -0.234  -0.210  -0.359  -0.120  -0.085  -0.343  -0.325  -0.285  -0.515
82    G        -0.234  -0.340  -0.377  -0.043  -0.204  -0.312  -0.325  -0.483  -0.543
83    N         1.032   1.044   1.068   1.064   1.079   1.117   1.076   1.090   1.120
84    R        -1.309  -1.350  -1.282  -1.110  -1.162  -1.097  -1.259  -1.293  -1.182
85    E        -1.309  -1.251  -1.267  -1.596  -1.520  -1.465  -1.259  -1.174  -1.165
86    R         1.032   1.044   1.068   1.064   1.096   1.117   1.076   1.090   1.120
87    V        -0.234  -0.340  -0.377  -0.018  -0.162  -0.259  -0.325  -0.483  -0.543
88    S        -1.309  -1.251  -1.267  -1.036  -0.926  -0.998  -1.259  -1.174  -1.165
89    T         1.032   1.044   1.068   1.000   1.009   1.058   1.076   1.090   1.120
90    V         1.032   1.044   1.068   1.127   1.164   1.176   1.076   1.090   1.120
91    D         1.032   1.044   1.068   0.870   0.889   0.936   1.076   1.090   1.120
92    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   K        -0.401  -0.380  -0.403  -0.500  -0.461  -0.492  -0.584  -0.547  -0.585
103   K        -1.442  -1.413  -1.299  -1.771  -1.722  -1.534  -1.415  -1.364  -1.200
104   K        -2.090  -2.035  -1.918  -1.631  -1.535  -1.404  -1.726  -1.652  -1.490
* 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/Q05809
Output conservation file - output/Q05809
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
