1     M         1.120   1.200   1.262   1.219   1.329   1.430   1.204   1.316   1.414
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     L         0.307   0.178   0.165   0.284   0.109   0.068   0.218  -0.015  -0.075
4     S        -1.185  -1.255  -1.084  -1.211  -1.300  -1.054  -1.258  -1.277  -1.051
5     F         1.120   1.200   1.262   1.079   1.178   1.300   1.204   1.316   1.414
6     C         1.120   1.200   1.262   1.011   1.124   1.237   1.204   1.316   1.414
7     P         1.120   1.200   1.262   1.153   1.252   1.369   1.204   1.316   1.414
8     S        -2.034  -1.779  -1.785  -1.967  -1.599  -1.610  -1.692  -1.421  -1.340
9     C         1.120   1.200   1.262   1.011   1.124   1.237   1.204   1.316   1.414
10    N        -1.677  -1.609  -1.473  -1.707  -1.611  -1.405  -1.547  -1.426  -1.226
11    N         1.120   1.200   1.262   1.113   1.214   1.331   1.204   1.316   1.414
12    M        -0.208  -0.451  -0.517   0.057  -0.237  -0.404  -0.237  -0.563  -0.660
13    L         1.120   1.200   1.262   1.067   1.199   1.288   1.204   1.316   1.414
14    L        -0.638  -0.664  -0.568  -0.773  -0.745  -0.620  -0.902  -0.886  -0.737
15    I        -1.264  -1.081  -1.077  -1.299  -1.056  -1.009  -1.346  -1.126  -1.044
16    T        -0.638  -0.441  -0.549  -0.763  -0.483  -0.603  -0.902  -0.643  -0.715
17    S        -2.320  -2.143  -2.054  -2.140  -1.920  -1.761  -1.789  -1.599  -1.424
18    G        -1.694  -1.588  -1.469  -1.797  -1.632  -1.453  -1.567  -1.413  -1.225
19    D        -0.208  -0.415  -0.512  -0.209  -0.522  -0.686  -0.237  -0.512  -0.652
20    S        -1.694  -1.685  -1.477  -1.795  -1.733  -1.454  -1.567  -1.481  -1.231
21    G         1.120   1.200   1.262   1.030   1.121   1.255   1.204   1.316   1.414
22    V        -2.007  -1.993  -1.801  -1.958  -1.888  -1.657  -1.678  -1.593  -1.351
23    Y        -0.113   0.063   0.115  -0.348  -0.015   0.019  -0.534  -0.225  -0.169
24    T        -1.382  -1.120  -1.409  -1.220  -0.898  -1.293  -1.235  -0.931  -1.169
25    L        -0.131  -0.047   0.076  -0.466  -0.301  -0.131  -0.570  -0.435  -0.244
26    A        -2.007  -1.753  -1.779  -1.970  -1.651  -1.639  -1.678  -1.408  -1.336
27    C         1.120   1.200   1.262   1.018   1.191   1.243   1.204   1.316   1.414
28    R        -0.817  -0.417  -0.975  -0.679  -0.171  -0.948  -0.792  -0.276  -0.928
29    S        -0.074   0.145   0.143  -0.300   0.073   0.047  -0.459  -0.075  -0.115
30    C         1.120   1.200   1.262   1.018   1.191   1.243   1.204   1.316   1.414
31    P         1.120   1.200   1.262   1.150   1.277   1.366   1.204   1.316   1.414
32    Y         1.120   1.200   1.262   1.150   1.252   1.366   1.204   1.316   1.414
33    E        -0.208  -0.171  -0.478  -0.087  -0.071  -0.442  -0.237  -0.190  -0.606
34    F        -0.208  -0.455  -0.510  -0.062  -0.364  -0.468  -0.237  -0.568  -0.650
35    P        -1.069  -0.916  -1.029  -1.052  -0.770  -0.993  -1.124  -0.898  -0.990
36    I         0.440   0.356   0.228   0.595   0.486   0.263   0.428   0.289   0.042
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    E        -1.069  -0.888  -1.019  -1.179  -0.890  -1.076  -1.124  -0.866  -0.978
39    G        -0.817  -0.909  -1.028  -0.747  -0.925  -1.071  -0.792  -0.897  -0.987
40    I        -1.576  -1.599  -1.474  -1.487  -1.503  -1.359  -1.457  -1.423  -1.228
41    E        -0.705  -0.757  -0.610  -0.823  -0.894  -0.656  -0.964  -0.994  -0.789
42    I        -1.264  -1.217  -1.087  -1.245  -1.149  -0.993  -1.346  -1.237  -1.053
43    Y         1.120   1.200   1.262   1.150   1.252   1.366   1.204   1.316   1.414
44    D         0.105   0.011   0.088  -0.073  -0.251  -0.131  -0.126  -0.324  -0.221
45    R         1.120   1.200   1.262   1.114   1.180   1.333   1.204   1.316   1.414
46    K         0.440   0.361   0.221   0.501   0.392   0.229   0.428   0.296   0.028
47    K        -1.069  -1.218  -1.078  -1.104  -1.328  -1.113  -1.124  -1.240  -1.045
48    L         0.105   0.011   0.088  -0.028  -0.188  -0.110  -0.126  -0.324  -0.221
49    P        -1.382  -1.339  -1.443  -1.181  -1.135  -1.313  -1.235  -1.167  -1.199
50    R        -0.208  -0.415  -0.512  -0.081  -0.414  -0.550  -0.237  -0.512  -0.652
51    K         1.120   1.200   1.262   1.073   1.155   1.294   1.204   1.316   1.414
52    E         0.440   0.356   0.228   0.459   0.305   0.145   0.428   0.289   0.042
53    V         0.440   0.313   0.219   0.537   0.352   0.197   0.428   0.218   0.025
54    D         0.440   0.313   0.219   0.398   0.214   0.074   0.428   0.218   0.025
55    D         0.440   0.356   0.228   0.408   0.303   0.114   0.428   0.289   0.042
56    V         1.120   1.200   1.262   1.144   1.242   1.360   1.204   1.316   1.414
57    L         0.440   0.313   0.219   0.462   0.323   0.136   0.428   0.218   0.025
58    G         1.120   1.200   1.262   1.030   1.121   1.255   1.204   1.316   1.414
59    -         1.120   1.200   1.262   1.036   1.144   1.260   1.204   1.316   1.414
60    -         0.307   0.246   0.192   0.307   0.204   0.123   0.218   0.103  -0.025
61    G        -0.208  -0.415  -0.512  -0.171  -0.475  -0.632  -0.237  -0.512  -0.652
62    G        -0.505  -0.159  -0.480  -0.550  -0.040  -0.512  -0.681  -0.177  -0.608
63    W         0.440   0.361   0.221   0.696   0.596   0.343   0.428   0.296   0.028
64    D         0.105   0.027   0.095  -0.094  -0.280  -0.157  -0.126  -0.292  -0.208
65    N         0.440   0.361   0.221   0.516   0.450   0.196   0.428   0.296   0.028
66    V        -0.208  -0.451  -0.517  -0.047  -0.388  -0.523  -0.237  -0.563  -0.660
67    D         0.105   0.011   0.088  -0.069  -0.254  -0.124  -0.126  -0.324  -0.221
68    Q         0.105   0.009   0.089   0.041  -0.185  -0.059  -0.126  -0.327  -0.219
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    T        -0.208  -0.455  -0.510  -0.099  -0.453  -0.570  -0.237  -0.568  -0.650
71    K        -1.576  -1.531  -1.463  -1.614  -1.583  -1.455  -1.457  -1.353  -1.219
72    T        -1.146  -1.032  -1.047  -1.176  -0.994  -0.999  -1.235  -1.062  -1.012
73    Q         0.440   0.361   0.221   0.541   0.431   0.211   0.428   0.296   0.028
74    C         1.120   1.200   1.262   1.018   1.191   1.243   1.204   1.316   1.414
75    P        -0.208  -0.451  -0.517  -0.069  -0.420  -0.587  -0.237  -0.563  -0.660
76    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    Y        -1.677  -1.660  -1.492  -1.536  -1.490  -1.252  -1.547  -1.467  -1.242
78    D        -0.317  -0.617  -0.568  -0.370  -0.851  -0.776  -0.389  -0.797  -0.731
79    T        -1.264  -1.093  -1.085  -1.384  -1.166  -1.102  -1.346  -1.136  -1.052
80    C         1.120   1.200   1.262   1.018   1.191   1.243   1.204   1.316   1.414
81    G        -1.382  -1.548  -1.468  -1.310  -1.576  -1.457  -1.235  -1.369  -1.222
82    G         0.105   0.027   0.095  -0.055  -0.209  -0.111  -0.126  -0.292  -0.208
83    E        -1.264  -1.219  -1.091  -1.433  -1.286  -1.130  -1.346  -1.238  -1.057
84    S        -1.694  -1.681  -1.475  -1.777  -1.797  -1.450  -1.567  -1.478  -1.229
85    A         1.120   1.200   1.262   1.132   1.226   1.349   1.204   1.316   1.414
86    Y         0.440   0.313   0.219   0.551   0.378   0.224   0.428   0.218   0.025
87    F         1.120   1.200   1.262   1.090   1.214   1.310   1.204   1.316   1.414
88    F         0.440   0.356   0.228   0.494   0.408   0.194   0.428   0.289   0.042
89    Q         0.440   0.356   0.228   0.559   0.459   0.269   0.428   0.289   0.042
90    L         0.440   0.313   0.219   0.470   0.329   0.156   0.428   0.218   0.025
91    Q         1.120   1.200   1.262   1.144   1.241   1.360   1.204   1.316   1.414
92    I         1.120   1.200   1.262   1.203   1.305   1.415   1.204   1.316   1.414
93    R         1.120   1.200   1.262   1.114   1.180   1.333   1.204   1.316   1.414
94    S         1.120   1.200   1.262   1.132   1.247   1.349   1.204   1.316   1.414
95    A         1.120   1.200   1.262   1.132   1.226   1.349   1.204   1.316   1.414
96    D         1.120   1.200   1.262   1.006   1.109   1.232   1.204   1.316   1.414
97    E         1.120   1.200   1.262   1.067   1.131   1.288   1.204   1.316   1.414
98    P         1.120   1.200   1.262   1.150   1.277   1.366   1.204   1.316   1.414
99    M         1.120   1.200   1.262   1.226   1.366   1.436   1.204   1.316   1.414
100   T         0.440   0.361   0.221   0.504   0.405   0.186   0.428   0.296   0.028
101   T         0.440   0.356   0.228   0.495   0.379   0.177   0.428   0.289   0.042
102   F         1.120   1.200   1.262   1.090   1.214   1.310   1.204   1.316   1.414
103   Y         0.440   0.356   0.228   0.535   0.433   0.200   0.428   0.289   0.042
104   K         0.105   0.027   0.095  -0.014  -0.213  -0.078  -0.126  -0.292  -0.208
105   C         0.440   0.313   0.219   0.422   0.322   0.114   0.428   0.218   0.025
106   V        -0.505  -0.686  -0.584  -0.510  -0.830  -0.664  -0.681  -0.910  -0.757
107   N        -1.146  -1.232  -1.077  -1.237  -1.338  -1.098  -1.235  -1.252  -1.043
108   C         0.440   0.313   0.219   0.405   0.293   0.071   0.428   0.218   0.025
109   G        -1.889  -1.901  -1.791  -1.823  -1.869  -1.686  -1.567  -1.531  -1.344
110   H        -0.208  -0.451  -0.517   0.123  -0.231  -0.390  -0.237  -0.563  -0.660
111   R        -1.146  -1.066  -1.062  -1.203  -1.087  -1.054  -1.235  -1.094  -1.027
112   W         0.440   0.313   0.219   0.684   0.502   0.311   0.428   0.218   0.025
113   K        -0.638  -0.613  -0.549  -0.829  -0.784  -0.667  -0.902  -0.798  -0.709
114   E         0.440   0.313   0.219   0.478   0.278   0.178   0.428   0.218   0.025
115   N         0.440   0.313   0.219   0.507   0.360   0.171   0.428   0.218   0.025
* 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/Q04307
Output conservation file - output/Q04307
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
