1     M         0.884   0.890   0.927   1.149   1.155   1.194   0.916   0.925   0.979
2     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     G        -0.647  -0.609  -0.428  -1.051  -1.025  -0.710  -0.993  -0.936  -0.667
8     F        -0.647  -0.618  -0.432  -0.679  -0.651  -0.380  -0.993  -0.953  -0.673
9     K        -2.053  -2.031  -1.779  -2.313  -2.295  -1.891  -1.842  -1.807  -1.489
10    P        -2.053  -2.031  -1.775  -2.299  -2.203  -1.857  -1.842  -1.807  -1.486
11    G         0.884   0.890   0.927   0.580   0.588   0.704   0.916   0.925   0.979
12    S        -0.437  -0.495  -0.423  -0.307  -0.397  -0.365  -0.642  -0.743  -0.658
13    A        -1.227  -1.295  -1.205  -1.156  -1.268  -1.159  -1.266  -1.343  -1.200
14    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
15    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
16    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
17    A         0.884   0.890   0.927   0.895   0.900   0.975   0.916   0.925   0.979
18    T        -1.227  -1.252  -1.200  -1.204  -1.249  -1.163  -1.266  -1.293  -1.195
19    L         0.884   0.890   0.927   0.944   0.957   1.017   0.916   0.925   0.979
20    F         0.884   0.890   0.927   1.079   1.080   1.133   0.916   0.925   0.979
21    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
22    T         0.884   0.890   0.927   0.855   0.860   0.940   0.916   0.925   0.979
23    R         0.884   0.890   0.927   1.126   1.130   1.174   0.916   0.925   0.979
24    C         0.884   0.890   0.927   1.188   1.192   1.227   0.916   0.925   0.979
25    Q        -1.334  -1.262  -1.197  -1.347  -1.256  -1.107  -1.422  -1.330  -1.191
26    Q         0.884   0.890   0.927   1.180   1.190   1.220   0.916   0.925   0.979
27    C         0.884   0.890   0.927   1.188   1.192   1.227   0.916   0.925   0.979
28    H         0.884   0.890   0.927   1.149   1.155   1.194   0.916   0.925   0.979
29    T         0.884   0.890   0.927   0.855   0.860   0.940   0.916   0.925   0.979
30    I        -1.664  -1.751  -1.764  -1.191  -1.347  -1.477  -1.422  -1.515  -1.475
31    E         0.884   0.890   0.927   0.952   0.957   1.024   0.916   0.925   0.979
32    E        -1.334  -1.343  -1.196  -1.756  -1.740  -1.469  -1.422  -1.418  -1.190
33    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
34    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
35    P        -0.875  -0.996  -1.178  -0.607  -0.811  -1.245  -0.798  -0.951  -1.166
36    N        -0.624  -0.568  -0.426  -0.639  -0.568  -0.365  -0.954  -0.866  -0.664
37    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
38    V        -0.022  -0.110  -0.364   0.344   0.233  -0.192  -0.019  -0.147  -0.561
39    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
40    P         0.884   0.890   0.927   1.039   1.050   1.099   0.916   0.925   0.979
41    N        -0.022  -0.110  -0.364   0.183   0.052  -0.385  -0.019  -0.147  -0.561
42    L         0.884   0.890   0.927   0.944   0.957   1.017   0.916   0.925   0.979
43    H         0.884   0.890   0.927   1.149   1.155   1.194   0.916   0.925   0.979
44    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
45    I        -1.227  -1.254  -1.194  -0.943  -0.988  -0.979  -1.266  -1.287  -1.186
46    F        -0.875  -0.843  -1.165  -0.427  -0.410  -0.890  -0.798  -0.767  -1.151
47    G        -0.022  -0.087  -0.359  -0.199  -0.290  -0.641  -0.019  -0.113  -0.553
48    R         0.884   0.890   0.927   1.126   1.130   1.174   0.916   0.925   0.979
49    H        -1.227  -1.151  -1.196  -1.568  -1.453  -1.421  -1.266  -1.192  -1.190
50    S        -0.437  -0.495  -0.423  -0.378  -0.481  -0.471  -0.642  -0.743  -0.658
51    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
52    Q        -1.664  -1.640  -1.752  -1.117  -1.110  -1.399  -1.422  -1.408  -1.464
53    V        -0.437  -0.459  -0.423  -0.440  -0.486  -0.441  -0.642  -0.685  -0.658
54    K        -2.374  -2.303  -2.203  -2.114  -2.043  -1.996  -1.889  -1.824  -1.646
55    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
56    Y        -0.437  -0.406  -0.416  -0.318  -0.283  -0.351  -0.642  -0.598  -0.647
57    S        -0.022  -0.110  -0.364   0.261   0.163  -0.324  -0.019  -0.147  -0.561
58    Y         0.884   0.890   0.927   1.039   1.048   1.099   0.916   0.925   0.979
59    T        -0.022  -0.087  -0.359   0.082  -0.001  -0.400  -0.019  -0.113  -0.553
60    D        -0.022  -0.069  -0.358   0.255   0.184  -0.300  -0.019  -0.087  -0.551
61    A         0.884   0.890   0.927   0.895   0.900   0.975   0.916   0.925   0.979
62    N         0.884   0.890   0.927   0.984   0.987   1.051   0.916   0.925   0.979
63    I        -1.227  -1.223  -1.190  -1.515  -1.490  -1.330  -1.266  -1.252  -1.181
64    N        -2.374  -2.453  -2.219  -2.354  -2.400  -1.970  -1.889  -1.952  -1.658
65    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
66    N        -0.437  -0.389  -0.397  -0.782  -0.723  -0.695  -0.642  -0.570  -0.616
67    V        -0.624  -0.618  -0.430  -0.557  -0.567  -0.307  -0.954  -0.953  -0.670
68    K        -1.334  -1.278  -1.200  -1.552  -1.485  -1.441  -1.422  -1.354  -1.195
69    W         0.884   0.890   0.927   1.241   1.246   1.273   0.916   0.925   0.979
70    D        -1.227  -1.097  -1.191  -1.088  -0.918  -1.095  -1.266  -1.114  -1.184
71    E        -0.022  -0.087  -0.359   0.144   0.047  -0.418  -0.019  -0.113  -0.553
72    D        -2.102  -2.069  -1.780  -1.843  -1.841  -1.464  -1.889  -1.843  -1.490
73    S        -1.937  -1.901  -1.763  -1.772  -1.728  -1.517  -1.733  -1.685  -1.475
74    M        -0.624  -0.554  -0.416  -0.671  -0.571  -0.378  -0.954  -0.843  -0.647
75    S        -0.624  -0.618  -0.430  -0.618  -0.612  -0.359  -0.954  -0.953  -0.670
76    E        -1.334  -1.318  -1.197  -1.301  -1.295  -1.135  -1.422  -1.386  -1.191
77    Y         0.884   0.890   0.927   1.039   1.048   1.099   0.916   0.925   0.979
78    L         0.884   0.890   0.927   0.944   0.957   1.017   0.916   0.925   0.979
79    T        -0.437  -0.389  -0.397  -0.484  -0.420  -0.493  -0.642  -0.570  -0.616
80    N         0.884   0.890   0.927   0.984   0.987   1.051   0.916   0.925   0.979
81    P         0.884   0.890   0.927   1.039   1.050   1.099   0.916   0.925   0.979
82    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
83    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
84    Y         0.884   0.890   0.927   1.039   1.048   1.099   0.916   0.925   0.979
85    I         0.884   0.890   0.927   1.118   1.115   1.167   0.916   0.925   0.979
86    P         0.884   0.890   0.927   1.039   1.050   1.099   0.916   0.925   0.979
87    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
88    T         0.884   0.890   0.927   0.855   0.860   0.940   0.916   0.925   0.979
89    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
90    M         0.884   0.890   0.927   1.149   1.155   1.194   0.916   0.925   0.979
91    A         0.884   0.890   0.927   0.895   0.900   0.975   0.916   0.925   0.979
92    F         0.884   0.890   0.927   1.079   1.080   1.133   0.916   0.925   0.979
93    A        -0.437  -0.438  -0.422  -0.819  -0.838  -0.776  -0.642  -0.650  -0.657
94    G         0.884   0.890   0.927   0.587   0.593   0.710   0.916   0.925   0.979
95    L        -0.022  -0.069  -0.358   0.173   0.114  -0.324  -0.019  -0.087  -0.551
96    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
97    K         0.884   0.890   0.927   0.422   0.463   0.568   0.916   0.925   0.979
98    E        -1.937  -1.890  -1.766  -1.714  -1.665  -1.535  -1.733  -1.682  -1.477
99    K        -0.022  -0.069  -0.358  -0.382  -0.416  -0.812  -0.019  -0.087  -0.551
100   D         0.884   0.890   0.927   1.047   1.051   1.106   0.916   0.925   0.979
101   R         0.884   0.890   0.927   1.126   1.130   1.174   0.916   0.925   0.979
102   N        -0.022   0.026  -0.341   0.108   0.167  -0.534  -0.019   0.044  -0.523
103   D        -0.022  -0.069  -0.358   0.260   0.189  -0.287  -0.019  -0.087  -0.551
104   L        -0.875  -0.996  -1.178  -0.557  -0.720  -0.995  -0.798  -0.951  -1.166
105   I        -0.022   0.160  -0.346   0.351   0.547  -0.159  -0.019   0.220  -0.531
106   T        -0.875  -0.740  -1.146  -0.698  -0.538  -1.121  -0.798  -0.637  -1.128
107   Y        -0.875  -1.011  -1.178  -0.446  -0.635  -0.897  -0.798  -0.970  -1.167
108   M        -0.624  -0.616  -0.431  -0.671  -0.660  -0.385  -0.954  -0.948  -0.672
109   T        -1.227  -1.180  -1.196  -1.589  -1.505  -1.447  -1.266  -1.212  -1.190
110   K        -0.437  -0.502  -0.425  -0.956  -1.037  -0.857  -0.642  -0.755  -0.661
111   A        -0.022  -0.087  -0.359   0.109   0.016  -0.404  -0.019  -0.113  -0.553
112   A        -0.875  -0.903  -1.170  -0.672  -0.722  -1.103  -0.798  -0.838  -1.156
113   K        -1.350  -1.393  -1.211  -1.581  -1.659  -1.460  -1.417  -1.457  -1.207
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P00045
Output conservation file - output/P00045
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
