1     M         2.250   2.345   2.450   2.455   2.582   2.762   2.546   2.698   2.913
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     T         0.423   0.264   0.270   0.575   0.323   0.334   0.322   0.067   0.059
8     M        -1.038  -1.044  -1.007  -0.900  -0.911  -0.825  -0.913  -0.909  -0.853
9     -         0.060   0.010   0.099  -0.341  -0.475  -0.368  -0.233  -0.319  -0.210
10    -         0.060   0.010   0.099  -0.239  -0.331  -0.230  -0.233  -0.319  -0.210
11    -         0.060   0.010   0.099  -0.008  -0.045   0.064  -0.233  -0.319  -0.210
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    D        -1.038  -1.044  -1.007  -1.058  -1.058  -0.988  -0.913  -0.909  -0.853
14    T        -0.440  -0.364  -0.384  -0.535  -0.376  -0.408  -0.540  -0.423  -0.443
15    A        -0.440  -0.515  -0.450  -0.373  -0.487  -0.363  -0.540  -0.606  -0.529
16    Q        -0.180  -0.313  -0.344  -0.139  -0.311  -0.419  -0.177  -0.350  -0.387
17    L        -1.015  -1.073  -0.988  -1.059  -1.099  -0.973  -0.903  -0.935  -0.836
18    K        -0.440  -0.542  -0.453  -0.400  -0.533  -0.396  -0.540  -0.642  -0.536
19    S        -0.180  -0.313  -0.344  -0.098  -0.330  -0.365  -0.177  -0.350  -0.387
20    Q        -0.440  -0.471  -0.421  -0.535  -0.567  -0.504  -0.540  -0.569  -0.501
21    I         0.573   0.557   0.404   0.751   0.750   0.535   0.549   0.524   0.272
22    Q         0.573   0.402   0.360   0.674   0.467   0.395   0.549   0.281   0.202
23    Q        -0.440  -0.325  -0.378  -0.758  -0.573  -0.690  -0.540  -0.386  -0.441
24    Y        -1.849  -1.794  -1.745  -1.384  -1.382  -1.220  -1.266  -1.204  -1.135
25    L         2.250   2.345   2.450   1.922   2.036   2.209   2.546   2.698   2.913
26    V        -0.440  -0.501  -0.438  -0.322  -0.366  -0.276  -0.540  -0.588  -0.511
27    E        -0.440  -0.398  -0.404  -0.638  -0.545  -0.572  -0.540  -0.463  -0.468
28    S         0.573   0.402   0.360   0.701   0.462   0.429   0.549   0.281   0.202
29    G         1.386   1.411   1.300   1.665   1.699   1.520   1.457   1.486   1.263
30    N         0.573   0.418   0.367   0.758   0.524   0.414   0.549   0.303   0.213
31    Y         1.386   1.411   1.300   1.712   1.750   1.628   1.457   1.486   1.263
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    E         0.237   0.336   0.290  -0.021   0.144   0.054   0.005   0.171   0.085
34    L        -1.015  -0.908  -0.944  -0.914  -0.696  -0.800  -0.903  -0.780  -0.793
35    I         0.990   0.942   1.007   0.746   0.591   0.647   0.731   0.590   0.662
36    S         0.237   0.211   0.255   0.188   0.175   0.235   0.005  -0.012   0.030
37    N         0.237   0.351   0.295   0.204   0.418   0.293   0.005   0.192   0.093
38    E         0.135   0.170   0.195  -0.115  -0.041   0.015  -0.177  -0.124  -0.085
39    L         1.386   1.430   1.310   1.153   1.204   1.050   1.457   1.518   1.284
40    K        -0.857  -0.972  -0.935  -0.802  -1.009  -0.945  -0.721  -0.834  -0.782
41    A        -1.015  -1.056  -0.971  -1.094  -1.092  -0.988  -0.903  -0.921  -0.820
42    R        -0.440  -0.501  -0.438  -0.285  -0.354  -0.260  -0.540  -0.588  -0.511
43    L         2.250   2.345   2.450   1.922   2.036   2.209   2.546   2.698   2.913
44    L        -0.440  -0.491  -0.441  -0.565  -0.680  -0.559  -0.540  -0.576  -0.515
45    Q        -1.432  -1.442  -1.401  -1.511  -1.511  -1.468  -1.084  -1.076  -1.013
46    E        -0.440  -0.446  -0.446  -0.487  -0.461  -0.479  -0.540  -0.550  -0.527
47    G         2.250   2.345   2.450   2.480   2.610   2.788   2.546   2.698   2.913
48    W         2.250   2.345   2.450   2.554   2.691   2.864   2.546   2.698   2.913
49    V        -1.432  -1.398  -1.362  -1.087  -1.064  -0.996  -1.084  -1.041  -0.980
50    D         1.386   1.250   1.273   1.423   1.236   1.282   1.457   1.196   1.212
51    K         0.573   0.462   0.381   0.568   0.396   0.246   0.549   0.367   0.236
52    V         1.386   1.250   1.273   1.470   1.256   1.274   1.457   1.196   1.212
53    K        -0.440  -0.447  -0.436  -0.480  -0.477  -0.448  -0.540  -0.541  -0.516
54    D        -0.440  -0.431  -0.429  -0.545  -0.521  -0.531  -0.540  -0.525  -0.510
55    L         0.573   0.535   0.407   0.449   0.392   0.235   0.549   0.469   0.278
56    T         0.812   0.857   0.957   0.709   0.743   0.906   0.368   0.410   0.554
57    K        -0.857  -0.627  -0.840  -0.550  -0.178  -0.550  -0.721  -0.449  -0.679
58    S        -0.440  -0.390  -0.410  -0.419  -0.334  -0.360  -0.540  -0.469  -0.475
59    E         1.386   1.250   1.273   1.290   1.103   1.132   1.457   1.196   1.212
60    M        -1.015  -1.050  -0.979  -0.949  -0.963  -0.840  -0.903  -0.915  -0.828
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    N        -0.440  -0.375  -0.392  -0.421  -0.338  -0.353  -0.540  -0.459  -0.462
79    I        -1.432  -1.398  -1.362  -1.185  -1.154  -1.064  -1.084  -1.041  -0.980
80    N        -1.432  -1.335  -1.343  -1.460  -1.299  -1.343  -1.084  -0.979  -0.964
81    E        -0.857  -0.742  -0.879  -0.763  -0.625  -0.815  -0.721  -0.597  -0.721
82    S        -0.440  -0.318  -0.429  -0.573  -0.442  -0.573  -0.540  -0.417  -0.510
83    T        -1.015  -1.003  -0.953  -0.864  -0.847  -0.775  -0.903  -0.878  -0.805
84    N        -0.857  -0.843  -0.913  -0.671  -0.683  -0.808  -0.721  -0.704  -0.758
85    F         1.386   1.430   1.310   1.615   1.678   1.488   1.457   1.518   1.284
86    T        -1.015  -1.011  -0.973  -1.034  -1.042  -0.960  -0.903  -0.884  -0.821
87    Q        -0.440  -0.474  -0.440  -0.617  -0.671  -0.643  -0.540  -0.573  -0.523
88    I         0.237   0.333   0.249  -0.076   0.051  -0.050   0.005   0.146   0.011
89    L         0.237   0.211   0.255   0.050   0.025   0.111   0.005  -0.012   0.030
90    S        -0.440  -0.402  -0.421  -0.542  -0.534  -0.514  -0.540  -0.504  -0.501
91    T        -1.015  -0.983  -0.960  -0.911  -0.912  -0.864  -0.903  -0.858  -0.809
92    V         0.573   0.462   0.381   0.792   0.646   0.522   0.549   0.367   0.236
93    E        -0.440  -0.491  -0.441  -0.769  -0.878  -0.822  -0.540  -0.576  -0.515
94    P         1.386   1.250   1.273   1.747   1.563   1.585   1.457   1.196   1.212
95    K         0.135   0.080   0.187  -0.168  -0.221  -0.090  -0.177  -0.227  -0.093
96    A         2.250   2.345   2.450   2.363   2.493   2.666   2.546   2.698   2.913
97    L        -0.440  -0.491  -0.441  -0.677  -0.719  -0.602  -0.540  -0.576  -0.515
98    E         0.237   0.245   0.231   0.019   0.030   0.004   0.005   0.016  -0.019
99    M         0.135   0.067   0.201  -0.083  -0.203   0.005  -0.177  -0.248  -0.078
100   V         1.386   1.250   1.273   1.518   1.335   1.363   1.457   1.196   1.212
101   S        -0.857  -0.785  -0.902  -0.457  -0.322  -0.577  -0.721  -0.629  -0.746
102   D        -0.180   0.042  -0.254  -0.087   0.234  -0.212  -0.177   0.124  -0.270
103   S        -0.857  -0.750  -0.872  -0.833  -0.674  -0.888  -0.721  -0.591  -0.714
104   T        -0.023   0.012   0.087  -0.130  -0.093   0.009  -0.358  -0.317  -0.228
105   R         0.990   1.094   1.079   0.868   1.011   0.989   0.731   0.897   0.815
106   E        -1.432  -1.450  -1.371  -1.315  -1.267  -1.208  -1.084  -1.082  -0.989
107   T        -0.440  -0.325  -0.426  -0.527  -0.399  -0.503  -0.540  -0.411  -0.505
108   V        -0.440  -0.484  -0.400  -0.485  -0.584  -0.441  -0.540  -0.567  -0.472
109   L         1.386   1.482   1.315   1.196   1.312   1.131   1.457   1.608   1.293
110   K        -0.857  -0.716  -0.850  -0.763  -0.547  -0.761  -0.721  -0.550  -0.691
111   Q        -1.432  -1.442  -1.401  -1.078  -1.116  -1.066  -1.084  -1.076  -1.013
112   I         1.386   1.560   1.335   1.401   1.646   1.311   1.457   1.737   1.332
113   R        -0.440  -0.303  -0.365  -0.376  -0.206  -0.245  -0.540  -0.364  -0.432
114   E        -1.432  -1.402  -1.375  -1.410  -1.352  -1.320  -1.084  -1.043  -0.991
115   F         0.237   0.211   0.255   0.535   0.538   0.611   0.005  -0.012   0.030
116   L         1.386   1.250   1.273   1.165   0.972   1.016   1.457   1.196   1.212
117   E        -0.440  -0.501  -0.438  -0.691  -0.814  -0.709  -0.540  -0.588  -0.511
118   E        -0.440  -0.505  -0.439  -0.545  -0.636  -0.528  -0.540  -0.596  -0.516
119   I        -0.180  -0.244  -0.309  -0.052  -0.197  -0.272  -0.177  -0.268  -0.342
120   V        -0.440  -0.491  -0.441  -0.453  -0.502  -0.473  -0.540  -0.576  -0.515
121   D         0.060   0.101   0.143  -0.241  -0.180  -0.131  -0.233  -0.192  -0.141
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   Q        -0.857  -0.972  -0.935  -0.769  -0.893  -0.898  -0.721  -0.834  -0.782
* 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/Q6WNK7
Output conservation file - output/Q6WNK7
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
