1     M         1.217   1.248   1.309   1.353   1.390   1.480   1.312   1.351   1.445
2     S         0.537   0.414   0.269   0.623   0.460   0.242   0.547   0.347   0.071
3     D         0.023   0.061   0.139  -0.414  -0.336  -0.235  -0.326  -0.272  -0.172
4     S        -1.285  -1.195  -1.036  -1.463  -1.308  -1.075  -1.309  -1.188  -0.988
5     E        -1.793  -1.719  -1.695  -1.671  -1.581  -1.481  -1.419  -1.336  -1.239
6     V        -1.480  -1.402  -1.371  -1.463  -1.362  -1.258  -1.309  -1.214  -1.116
7     N        -1.088  -1.073  -0.992  -0.995  -0.991  -0.862  -1.113  -1.063  -0.944
8     -        -0.687  -0.575  -0.518  -0.847  -0.690  -0.577  -0.925  -0.777  -0.680
9     Q        -2.017  -1.879  -1.723  -1.958  -1.749  -1.532  -1.601  -1.454  -1.259
10    E        -0.608  -0.565  -0.497  -0.820  -0.718  -0.645  -0.824  -0.738  -0.650
11    A        -1.188  -1.140  -1.024  -1.443  -1.362  -1.173  -1.205  -1.139  -0.976
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    K        -0.498  -0.445  -0.492  -0.590  -0.530  -0.594  -0.645  -0.588  -0.640
15    P        -0.498  -0.603  -0.529  -0.441  -0.639  -0.551  -0.645  -0.790  -0.690
16    E        -1.188  -1.140  -1.024  -1.453  -1.344  -1.195  -1.205  -1.139  -0.976
17    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    K        -0.498  -0.637  -0.540  -0.642  -0.883  -0.739  -0.645  -0.836  -0.706
19    P        -0.220  -0.195  -0.431   0.027   0.032  -0.307  -0.257  -0.243  -0.557
20    E        -1.938  -1.881  -1.719  -2.006  -1.874  -1.666  -1.541  -1.457  -1.256
21    V        -1.088  -1.010  -0.996  -1.040  -0.976  -0.926  -1.113  -1.024  -0.950
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    K        -1.088  -1.071  -1.005  -1.226  -1.147  -1.097  -1.113  -1.070  -0.957
32    P        -1.088  -1.060  -0.981  -1.089  -1.040  -0.936  -1.113  -1.044  -0.931
33    E        -1.793  -1.858  -1.717  -1.714  -1.797  -1.546  -1.419  -1.437  -1.255
34    T         0.023   0.022   0.138  -0.285  -0.337  -0.146  -0.326  -0.347  -0.174
35    H         1.217   1.248   1.309   1.423   1.456   1.544   1.312   1.351   1.445
36    I        -0.111  -0.247  -0.448   0.079  -0.092  -0.426  -0.108  -0.297  -0.580
37    N         1.217   1.248   1.309   1.327   1.351   1.457   1.312   1.351   1.445
38    L        -0.408  -0.465  -0.502  -0.420  -0.494  -0.546  -0.545  -0.633  -0.659
39    K         1.217   1.248   1.309   1.122   1.172   1.271   1.312   1.351   1.445
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    V         1.217   1.248   1.309   1.307   1.327   1.439   1.312   1.351   1.445
42    S        -0.408  -0.526  -0.512  -0.428  -0.637  -0.609  -0.545  -0.703  -0.671
43    D         0.537   0.458   0.268   0.475   0.392   0.113   0.547   0.419   0.068
44    G        -0.721  -0.913  -0.986  -0.565  -0.862  -0.991  -0.654  -0.873  -0.935
45    S        -0.408  -0.486  -0.504  -0.379  -0.520  -0.520  -0.545  -0.667  -0.662
46    S        -0.972  -0.977  -0.992  -0.874  -0.900  -0.878  -0.982  -0.988  -0.946
47    E         1.217   1.248   1.309   1.041   1.099   1.196   1.312   1.351   1.445
48    I         0.023   0.022   0.139  -0.103  -0.115   0.071  -0.326  -0.347  -0.173
49    F         1.217   1.248   1.309   1.307   1.339   1.439   1.312   1.351   1.445
50    F         1.217   1.248   1.309   1.307   1.339   1.439   1.312   1.351   1.445
51    K         1.217   1.248   1.309   1.122   1.172   1.271   1.312   1.351   1.445
52    I         0.537   0.541   0.279   0.669   0.692   0.309   0.547   0.548   0.089
53    K         1.217   1.248   1.309   1.122   1.172   1.271   1.312   1.351   1.445
54    K         0.023   0.036   0.138  -0.241  -0.212  -0.054  -0.326  -0.320  -0.174
55    T        -0.541  -0.518  -0.502  -0.656  -0.630  -0.546  -0.763  -0.719  -0.661
56    T         1.217   1.248   1.309   1.203   1.224   1.344   1.312   1.351   1.445
57    P        -0.972  -1.058  -1.001  -0.914  -1.089  -1.034  -0.982  -1.059  -0.955
58    L        -0.408  -0.394  -0.486  -0.389  -0.368  -0.476  -0.545  -0.544  -0.639
59    R        -0.972  -1.065  -0.999  -0.987  -1.121  -1.082  -0.982  -1.051  -0.952
60    R         0.023   0.022   0.138  -0.194  -0.226  -0.054  -0.326  -0.347  -0.174
61    L         1.217   1.248   1.309   1.176   1.239   1.319   1.312   1.351   1.445
62    M         0.537   0.534   0.277   0.764   0.765   0.373   0.547   0.537   0.085
63    E        -0.721  -0.913  -0.986  -0.765  -1.042  -1.201  -0.654  -0.873  -0.935
64    A         0.537   0.458   0.268   0.674   0.566   0.279   0.547   0.419   0.068
65    F         0.537   0.458   0.268   0.752   0.659   0.403   0.547   0.419   0.068
66    A        -0.034   0.057   0.154  -0.079   0.083   0.229  -0.436  -0.281  -0.144
67    K        -0.721  -0.913  -0.986  -0.645  -0.930  -1.059  -0.654  -0.873  -0.935
68    R         1.217   1.248   1.309   1.255   1.301   1.392   1.312   1.351   1.445
69    Q         1.217   1.248   1.309   1.262   1.290   1.398   1.312   1.351   1.445
70    G         1.217   1.248   1.309   1.196   1.221   1.338   1.312   1.351   1.445
71    K         0.537   0.541   0.279   0.527   0.545   0.162   0.547   0.548   0.089
72    E        -1.167  -1.138  -1.012  -1.383  -1.302  -1.081  -1.200  -1.141  -0.966
73    M        -1.285  -1.287  -1.358  -0.956  -0.979  -1.136  -1.091  -1.083  -1.103
74    D        -1.285  -1.338  -1.377  -1.246  -1.305  -1.374  -1.091  -1.137  -1.119
75    S         0.202   0.245   0.195   0.131   0.185   0.084   0.001   0.062  -0.066
76    L        -0.111  -0.241  -0.435   0.036  -0.112  -0.395  -0.108  -0.289  -0.561
77    R         1.217   1.248   1.309   1.255   1.301   1.392   1.312   1.351   1.445
78    F         1.217   1.248   1.309   1.307   1.339   1.439   1.312   1.351   1.445
79    L         1.217   1.248   1.309   1.176   1.239   1.319   1.312   1.351   1.445
80    Y        -0.972  -1.032  -0.993  -0.639  -0.753  -0.723  -0.982  -1.036  -0.947
81    D         0.537   0.414   0.269   0.442   0.289   0.030   0.547   0.347   0.071
82    G         1.217   1.248   1.309   1.196   1.221   1.338   1.312   1.351   1.445
83    I        -2.224  -1.982  -1.967  -2.028  -1.706  -1.682  -1.637  -1.423  -1.326
84    R         1.217   1.248   1.309   1.255   1.301   1.392   1.312   1.351   1.445
85    I         0.023   0.118   0.155  -0.082   0.071   0.107  -0.326  -0.166  -0.141
86    Q        -1.793  -1.726  -1.680  -1.509  -1.425  -1.373  -1.419  -1.333  -1.228
87    A        -0.541  -0.461  -0.480  -0.581  -0.429  -0.488  -0.763  -0.623  -0.629
88    D         0.202   0.140   0.159  -0.013  -0.121  -0.099   0.001  -0.126  -0.134
89    Q        -0.408  -0.414  -0.492  -0.405  -0.475  -0.562  -0.545  -0.576  -0.646
90    T         1.217   1.248   1.309   1.203   1.224   1.344   1.312   1.351   1.445
91    P         1.217   1.248   1.309   1.320   1.360   1.451   1.312   1.351   1.445
92    E        -0.408  -0.505  -0.494  -0.633  -0.767  -0.756  -0.545  -0.670  -0.649
93    D        -0.408  -0.526  -0.512  -0.600  -0.787  -0.774  -0.545  -0.703  -0.671
94    L         1.217   1.248   1.309   1.176   1.239   1.319   1.312   1.351   1.445
95    D        -0.111  -0.247  -0.448  -0.139  -0.321  -0.648  -0.108  -0.297  -0.580
96    M        -0.111  -0.073  -0.401   0.172   0.230  -0.284  -0.108  -0.056  -0.514
97    E        -0.111  -0.241  -0.435  -0.157  -0.314  -0.635  -0.108  -0.289  -0.561
98    D         1.217   1.248   1.309   1.061   1.116   1.215   1.312   1.351   1.445
99    N         0.023   0.228   0.215  -0.138   0.177   0.166  -0.326   0.033  -0.029
100   D         1.217   1.248   1.309   1.061   1.116   1.215   1.312   1.351   1.445
101   I        -1.911  -1.814  -1.698  -1.678  -1.521  -1.356  -1.528  -1.411  -1.242
102   I         0.537   0.414   0.269   0.650   0.506   0.244   0.547   0.347   0.071
103   E         1.217   1.248   1.309   1.041   1.099   1.196   1.312   1.351   1.445
104   A         0.537   0.414   0.269   0.682   0.510   0.304   0.547   0.347   0.071
105   H         0.537   0.458   0.268   0.842   0.736   0.436   0.547   0.419   0.068
106   R        -0.408  -0.526  -0.512  -0.365  -0.550  -0.551  -0.545  -0.703  -0.671
107   E         0.537   0.541   0.279   0.454   0.482   0.114   0.547   0.548   0.089
108   Q         1.217   1.248   1.309   1.262   1.290   1.398   1.312   1.351   1.445
109   I        -0.660  -0.680  -0.549  -0.747  -0.780  -0.600  -0.873  -0.893  -0.717
110   G         1.217   1.248   1.309   1.196   1.221   1.338   1.312   1.351   1.445
111   G         1.217   1.248   1.309   1.196   1.221   1.338   1.312   1.351   1.445
112   A        -0.972  -0.797  -0.948  -0.632  -0.358  -0.596  -0.982  -0.755  -0.895
113   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   Y         0.002   0.158   0.180  -0.098   0.141   0.173  -0.366  -0.093  -0.094
* 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/Q12306
Output conservation file - output/Q12306
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
