1     M         1.295   1.327   1.427   1.595   1.635   1.779   1.394   1.447   1.616
2     A         0.535   0.390   0.259   0.664   0.464   0.210   0.566   0.344   0.097
3     P         1.295   1.327   1.427   1.513   1.567   1.703   1.394   1.447   1.616
4     N        -0.884  -0.839  -0.658  -1.030  -1.016  -0.756  -1.078  -1.017  -0.776
5     T         0.467   0.369   0.230   0.458   0.352   0.037   0.467   0.311   0.045
6     S        -1.504  -1.364  -1.209  -1.726  -1.562  -1.317  -1.445  -1.287  -1.084
7     R        -0.672  -0.539  -0.562  -0.837  -0.660  -0.629  -0.854  -0.632  -0.647
8     K        -0.190  -0.368  -0.553  -0.280  -0.505  -0.743  -0.144  -0.383  -0.634
9     Q        -1.722  -1.740  -1.631  -1.360  -1.415  -1.299  -1.445  -1.432  -1.262
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    K         0.467   0.544   0.254   0.256   0.363  -0.029   0.467   0.580   0.088
16    I        -1.284  -1.111  -1.149  -1.410  -1.183  -1.196  -1.233  -1.010  -1.020
17    A        -1.434  -1.403  -1.201  -1.623  -1.536  -1.275  -1.388  -1.323  -1.076
18    K         0.160   0.075   0.133  -0.141  -0.267  -0.161  -0.026  -0.189  -0.134
19    T        -0.041   0.188   0.209  -0.515  -0.134  -0.112  -0.380   0.010   0.007
20    F        -0.523  -0.538  -0.602  -0.312  -0.371  -0.464  -0.617  -0.669  -0.706
21    T        -0.672  -0.731  -0.621  -0.914  -0.968  -0.816  -0.854  -0.896  -0.732
22    V         0.160   0.077   0.132  -0.094  -0.229  -0.129  -0.026  -0.186  -0.136
23    D         0.535   0.506   0.269   0.712   0.682   0.353   0.566   0.523   0.114
24    V        -1.154  -1.171  -1.186  -1.171  -1.160  -1.099  -1.090  -1.112  -1.061
25    S        -0.873  -1.064  -1.134  -0.666  -0.958  -1.140  -0.735  -0.952  -1.003
26    S        -0.523  -0.355  -0.525  -0.388  -0.116  -0.369  -0.617  -0.365  -0.596
27    P         0.535   0.390   0.259   0.895   0.727   0.488   0.566   0.344   0.097
28    T        -1.154  -1.234  -1.177  -1.178  -1.330  -1.263  -1.090  -1.168  -1.053
29    E        -0.873  -1.066  -1.165  -0.686  -0.922  -1.091  -0.735  -0.955  -1.037
30    N        -0.041  -0.040   0.102  -0.112  -0.137   0.068  -0.380  -0.401  -0.192
31    G        -0.523  -0.616  -0.617  -0.477  -0.699  -0.714  -0.617  -0.753  -0.725
32    V        -0.041  -0.040   0.102  -0.404  -0.390  -0.147  -0.380  -0.401  -0.192
33    F         1.295   1.327   1.427   1.419   1.465   1.615   1.394   1.447   1.616
34    D         1.295   1.327   1.427   1.339   1.381   1.541   1.394   1.447   1.616
35    P        -0.890  -0.759  -0.645  -0.953  -0.827  -0.636  -1.090  -0.912  -0.759
36    A        -0.804  -0.789  -0.660  -0.893  -0.885  -0.731  -0.972  -0.952  -0.778
37    S         0.160   0.077   0.132   0.139  -0.010   0.052  -0.026  -0.186  -0.136
38    Y        -0.041  -0.040   0.102  -0.081  -0.088   0.114  -0.380  -0.401  -0.192
39    A        -0.890  -0.759  -0.645  -1.198  -0.997  -0.873  -1.090  -0.912  -0.759
40    K         1.295   1.327   1.427   0.979   1.025   1.205   1.394   1.447   1.616
41    Y        -0.041  -0.010   0.107  -0.081  -0.036   0.121  -0.380  -0.345  -0.182
42    L         1.295   1.327   1.427   1.322   1.368   1.525   1.394   1.447   1.616
43    I        -0.523  -0.577  -0.599  -0.460  -0.559  -0.664  -0.617  -0.692  -0.701
44    D        -0.104  -0.031   0.109  -0.386  -0.261  -0.065  -0.499  -0.383  -0.179
45    H        -1.154  -1.169  -1.183  -0.727  -0.809  -0.887  -1.090  -1.110  -1.059
46    I         0.535   0.508   0.264   0.687   0.648   0.241   0.566   0.527   0.106
47    K         1.295   1.327   1.427   0.979   1.025   1.205   1.394   1.447   1.616
48    V         1.295   1.327   1.427   1.034   1.078   1.256   1.394   1.447   1.616
49    E         0.160   0.078   0.119   0.038  -0.078  -0.050  -0.026  -0.184  -0.160
50    G         0.535   0.747   0.289   0.763   1.006   0.430   0.566   0.864   0.150
51    A        -2.204  -1.955  -1.977  -1.868  -1.613  -1.608  -1.682  -1.478  -1.384
52    V        -0.523  -0.538  -0.602  -0.679  -0.712  -0.727  -0.617  -0.669  -0.706
53    G         0.535   0.502   0.275   0.763   0.731   0.408   0.566   0.518   0.125
54    N         0.535   0.502   0.275   0.766   0.744   0.434   0.566   0.518   0.125
55    L         1.295   1.327   1.427   1.322   1.368   1.525   1.394   1.447   1.616
56    G         1.295   1.327   1.427   1.390   1.435   1.588   1.394   1.447   1.616
57    N        -1.504  -1.537  -1.602  -1.084  -1.179  -1.286  -1.209  -1.242  -1.238
58    A        -0.804  -0.819  -0.672  -0.824  -0.875  -0.672  -0.972  -0.991  -0.794
59    V         0.160   0.174   0.135   0.120   0.119  -0.041  -0.026  -0.014  -0.130
60    T        -1.372  -1.384  -1.207  -1.637  -1.707  -1.470  -1.327  -1.307  -1.082
61    V        -0.041  -0.009   0.104  -0.404  -0.359  -0.156  -0.380  -0.343  -0.188
62    T        -0.890  -0.700  -0.637  -1.120  -0.790  -0.744  -1.090  -0.855  -0.751
63    E        -1.504  -1.677  -1.623  -1.205  -1.400  -1.320  -1.209  -1.363  -1.255
64    D        -1.240  -1.191  -1.151  -1.283  -1.192  -1.171  -1.209  -1.113  -1.022
65    G         0.535   0.508   0.264   0.749   0.722   0.355   0.566   0.527   0.106
66    T        -1.722  -1.583  -1.604  -1.505  -1.331  -1.341  -1.445  -1.311  -1.241
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    V        -0.672  -0.539  -0.562  -1.156  -0.887  -0.883  -0.854  -0.632  -0.647
69    V         0.160   0.077   0.132  -0.094  -0.229  -0.129  -0.026  -0.186  -0.136
70    T        -1.154  -1.256  -1.189  -1.203  -1.331  -1.302  -1.090  -1.179  -1.063
71    V        -0.041   0.087   0.136  -0.404  -0.214  -0.124  -0.380  -0.168  -0.129
72    V        -0.190  -0.366  -0.540  -0.217  -0.442  -0.663  -0.144  -0.379  -0.617
73    S        -0.523  -0.616  -0.617  -0.504  -0.676  -0.712  -0.617  -0.753  -0.725
74    T        -1.154  -1.167  -1.184  -0.908  -0.876  -0.912  -1.090  -1.108  -1.060
75    A        -1.504  -1.531  -1.586  -1.243  -1.285  -1.412  -1.209  -1.236  -1.223
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    K        -1.504  -1.677  -1.623  -1.474  -1.698  -1.573  -1.209  -1.363  -1.255
79    F         0.535   0.506   0.269   0.783   0.755   0.402   0.566   0.523   0.114
80    S         1.295   1.327   1.427   1.282   1.323   1.487   1.394   1.447   1.616
81    G         1.295   1.327   1.427   1.390   1.435   1.588   1.394   1.447   1.616
82    K         0.160   0.077   0.132  -0.110  -0.227  -0.109  -0.026  -0.186  -0.136
83    Y         1.295   1.327   1.427   1.368   1.420   1.567   1.394   1.447   1.616
84    L         1.295   1.327   1.427   1.322   1.368   1.525   1.394   1.447   1.616
85    K         1.295   1.327   1.427   0.979   1.025   1.205   1.394   1.447   1.616
86    Y         1.295   1.327   1.427   1.368   1.420   1.567   1.394   1.447   1.616
87    L         1.295   1.327   1.427   1.322   1.368   1.525   1.394   1.447   1.616
88    T         1.295   1.327   1.427   1.253   1.339   1.460   1.394   1.447   1.616
89    K         0.535   0.508   0.264   0.366   0.345   0.066   0.566   0.527   0.106
90    K         0.535   0.614   0.276   0.366   0.465   0.083   0.566   0.682   0.127
91    Y         0.160   0.077   0.132   0.247   0.113   0.162  -0.026  -0.186  -0.136
92    L         1.295   1.327   1.427   1.322   1.368   1.525   1.394   1.447   1.616
93    K         0.535   0.508   0.264   0.349   0.325   0.023   0.566   0.527   0.106
94    K         1.295   1.327   1.427   0.979   1.025   1.205   1.394   1.447   1.616
95    N        -1.504  -1.677  -1.623  -0.933  -1.119  -1.061  -1.209  -1.363  -1.255
96    Q         0.535   0.390   0.259   0.838   0.656   0.424   0.566   0.344   0.097
97    L        -0.190  -0.166  -0.537   0.061   0.090  -0.443  -0.144  -0.112  -0.612
98    R         1.295   1.327   1.427   1.469   1.507   1.662   1.394   1.447   1.616
99    D         0.535   0.508   0.264   0.706   0.678   0.332   0.566   0.527   0.106
100   W         1.295   1.327   1.427   1.601   1.641   1.784   1.394   1.447   1.616
101   I         0.160   0.077   0.132   0.210   0.053   0.105  -0.026  -0.186  -0.136
102   R         1.295   1.327   1.427   1.469   1.507   1.662   1.394   1.447   1.616
103   F        -0.041  -0.040   0.102  -0.234  -0.314  -0.111  -0.380  -0.401  -0.192
104   V         0.535   0.502   0.275   0.404   0.371   0.088   0.566   0.518   0.125
105   S         1.295   1.327   1.427   1.282   1.323   1.487   1.394   1.447   1.616
106   T         0.160   0.190   0.159   0.013   0.088  -0.075  -0.026   0.014  -0.084
107   K         0.160   0.132   0.149  -0.176  -0.229  -0.195  -0.026  -0.088  -0.105
108   T        -1.372  -1.338  -1.203  -1.407  -1.369  -1.152  -1.327  -1.268  -1.077
109   N        -0.041  -0.040   0.102  -0.086  -0.100   0.102  -0.380  -0.401  -0.192
110   E        -1.854  -1.669  -1.629  -1.834  -1.585  -1.500  -1.564  -1.382  -1.261
111   Y         1.295   1.327   1.427   1.368   1.420   1.567   1.394   1.447   1.616
112   R        -1.854  -1.721  -1.623  -1.851  -1.670  -1.527  -1.564  -1.414  -1.257
113   L         1.295   1.327   1.427   1.322   1.368   1.525   1.394   1.447   1.616
114   A        -1.372  -1.384  -1.207  -1.340  -1.366  -1.108  -1.327  -1.307  -1.082
115   F         0.535   0.390   0.259   0.789   0.615   0.402   0.566   0.344   0.097
116   Y         0.535   0.506   0.269   0.746   0.727   0.392   0.566   0.523   0.114
117   Q        -1.240  -1.115  -1.170  -0.990  -0.806  -0.908  -1.209  -1.038  -1.042
118   V         0.535   0.735   0.289   0.404   0.633   0.109   0.566   0.848   0.150
119   T        -0.890  -0.759  -0.645  -1.216  -1.020  -0.850  -1.090  -0.912  -0.759
120   P        -2.072  -2.141  -1.995  -1.589  -1.791  -1.652  -1.564  -1.591  -1.396
121   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   E        -0.733  -0.741  -0.612  -0.839  -0.764  -0.589  -0.924  -0.892  -0.714
124   D        -0.313  -0.307  -0.545  -0.224  -0.214  -0.543  -0.306  -0.331  -0.624
125   E         0.386   0.161   0.166   0.310  -0.004  -0.016   0.343  -0.037  -0.071
126   E         0.535   0.390   0.259   0.545   0.394   0.181   0.566   0.344   0.097
127   E         1.295   1.327   1.427   1.177   1.250   1.390   1.394   1.447   1.616
128   D         0.535   0.390   0.259   0.684   0.495   0.262   0.566   0.344   0.097
129   E         1.295   1.327   1.427   1.177   1.250   1.390   1.394   1.447   1.616
130   E         0.535   0.390   0.259   0.566   0.427   0.236   0.566   0.344   0.097
* 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/P05749
Output conservation file - output/P05749
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
