1     M         1.127   1.262   1.296   1.193   1.387   1.433   1.184   1.351   1.418
2     D         1.127   1.262   1.296   1.176   1.339   1.418   1.184   1.351   1.418
3     A        -1.162  -1.313  -1.328  -1.148  -1.259  -1.261  -1.057  -1.171  -1.136
4     L         1.127   1.262   1.296   0.979   1.151   1.248   1.184   1.351   1.418
5     N         0.323   0.030   0.057   0.477   0.078   0.095   0.313  -0.151  -0.147
6     S        -2.059  -1.621  -1.742  -1.783  -1.259  -1.357  -1.804  -1.285  -1.306
7     K        -0.442  -0.561  -0.729  -0.398  -0.536  -0.761  -0.434  -0.600  -0.779
8     E         1.127   1.262   1.296   0.952   1.134   1.225   1.184   1.351   1.418
9     Q         0.323   0.030   0.057   0.115  -0.231  -0.250   0.313  -0.151  -0.147
10    Q        -0.442  -0.815  -0.762  -0.577  -1.014  -1.028  -0.434  -0.878  -0.821
11    E        -0.442  -0.331  -0.694  -0.353  -0.184  -0.626  -0.434  -0.267  -0.733
12    F        -0.072  -0.165  -0.032  -0.199  -0.454  -0.245  -0.310  -0.490  -0.306
13    Q        -0.442  -0.815  -0.762  -0.520  -0.934  -0.881  -0.434  -0.878  -0.821
14    K        -0.284   0.083   0.037  -0.865  -0.142  -0.323  -0.683  -0.065  -0.183
15    V        -1.689  -1.568  -1.344  -1.560  -1.380  -1.117  -1.679  -1.393  -1.153
16    V        -0.072  -0.165  -0.032  -0.116  -0.403  -0.190  -0.310  -0.490  -0.306
17    E         0.323   0.030   0.057   0.221  -0.221  -0.231   0.313  -0.151  -0.147
18    Q        -0.442  -0.815  -0.762  -0.555  -1.012  -0.972  -0.434  -0.878  -0.821
19    K         0.323   0.030   0.057   0.256  -0.085  -0.106   0.313  -0.151  -0.147
20    Q         1.127   1.262   1.296   0.818   1.089   1.110   1.184   1.351   1.418
21    M        -0.442  -0.815  -0.762  -0.187  -0.734  -0.732  -0.434  -0.878  -0.821
22    K         1.127   1.262   1.296   0.943   1.180   1.218   1.184   1.351   1.418
23    D        -0.072  -0.165  -0.032  -0.124  -0.414  -0.207  -0.310  -0.490  -0.306
24    F         0.323   0.271   0.088   0.445   0.419   0.169   0.313   0.234  -0.094
25    M         0.323   0.271   0.088   0.486   0.437   0.089   0.313   0.234  -0.094
26    R        -0.793  -0.944  -0.781  -0.768  -1.009  -0.800  -0.932  -1.035  -0.848
27    L        -0.442  -0.815  -0.762  -0.365  -0.869  -0.785  -0.434  -0.878  -0.821
28    Y         0.323   0.030   0.057   0.707   0.257   0.235   0.313  -0.151  -0.147
29    S         0.323   0.030   0.057   0.356  -0.049   0.017   0.313  -0.151  -0.147
30    N        -1.162  -0.860  -1.257  -0.848  -0.468  -1.012  -1.057  -0.657  -1.064
31    L         1.127   1.262   1.296   0.979   1.151   1.248   1.184   1.351   1.418
32    V         0.323   0.271   0.088   0.502   0.435   0.165   0.313   0.234  -0.094
33    E        -1.689  -1.564  -1.343  -2.059  -1.756  -1.507  -1.679  -1.390  -1.152
34    R        -0.793  -0.678  -0.772  -0.782  -0.650  -0.812  -0.932  -0.793  -0.838
35    C         1.127   1.262   1.296   1.210   1.375   1.447   1.184   1.351   1.418
36    F         1.127   1.262   1.296   1.091   1.275   1.345   1.184   1.351   1.418
37    T        -1.090  -0.778  -0.776  -1.144  -0.720  -0.736  -1.306  -0.832  -0.840
38    D         0.323   0.030   0.057   0.507   0.079   0.128   0.313  -0.151  -0.147
39    C         1.127   1.262   1.296   1.210   1.375   1.447   1.184   1.351   1.418
40    V         1.127   1.262   1.296   1.176   1.340   1.418   1.184   1.351   1.418
41    N        -0.442  -0.815  -0.762  -0.254  -0.793  -0.828  -0.434  -0.878  -0.821
42    D         1.127   1.262   1.296   1.176   1.339   1.418   1.184   1.351   1.418
43    F         1.127   1.262   1.296   1.091   1.275   1.345   1.184   1.351   1.418
44    T         1.127   1.262   1.296   1.219   1.355   1.455   1.184   1.351   1.418
45    T         0.323   0.638   0.115   0.349   0.708   0.087   0.313   0.747  -0.047
46    S        -1.689  -1.331  -1.327  -1.843  -1.364  -1.292  -1.679  -1.199  -1.137
47    K        -1.459  -1.118  -1.310  -1.487  -1.029  -1.227  -1.430  -1.020  -1.122
48    L         1.127   1.262   1.296   0.979   1.151   1.248   1.184   1.351   1.418
49    T        -0.284  -0.150  -0.016  -0.461  -0.369  -0.120  -0.683  -0.463  -0.277
50    N        -1.459  -1.427  -1.331  -1.391  -1.325  -1.148  -1.430  -1.289  -1.141
51    K        -0.072  -0.111  -0.028  -0.295  -0.321  -0.243  -0.310  -0.394  -0.297
52    E         1.127   1.262   1.296   0.952   1.134   1.225   1.184   1.351   1.418
53    Q        -1.829  -1.369  -1.338  -2.187  -1.416  -1.438  -1.804  -1.183  -1.146
54    T        -2.059  -1.757  -1.750  -1.929  -1.506  -1.468  -1.804  -1.385  -1.311
55    C         1.127   1.262   1.296   1.210   1.375   1.447   1.184   1.351   1.418
56    I         0.323   0.598   0.119   0.684   1.024   0.307   0.313   0.695  -0.041
57    M        -2.568  -2.183  -2.122  -2.330  -1.889  -1.769  -2.053  -1.576  -1.445
58    K        -0.072  -0.102  -0.029  -0.295  -0.305  -0.244  -0.310  -0.378  -0.299
59    C         1.127   1.262   1.296   1.210   1.375   1.447   1.184   1.351   1.418
60    S        -0.442  -0.815  -0.762  -0.311  -0.856  -0.730  -0.434  -0.878  -0.821
61    E        -0.442  -0.815  -0.762  -0.428  -0.992  -0.898  -0.434  -0.878  -0.821
62    K         1.127   1.262   1.296   0.943   1.180   1.218   1.184   1.351   1.418
63    F         0.323   0.030   0.057   0.390  -0.051  -0.033   0.313  -0.151  -0.147
64    L         0.323   0.030   0.057   0.302  -0.089  -0.049   0.313  -0.151  -0.147
65    K         0.323   0.030   0.057   0.241  -0.142  -0.151   0.313  -0.151  -0.147
66    H         0.323   0.030   0.057   0.732   0.296   0.292   0.313  -0.151  -0.147
67    S         0.323   0.030   0.057   0.292  -0.179  -0.174   0.313  -0.151  -0.147
68    E         0.323   0.030   0.057   0.279  -0.117  -0.059   0.313  -0.151  -0.147
69    R         1.127   1.262   1.296   1.126   1.324   1.374   1.184   1.351   1.418
70    V         0.323   0.030   0.057   0.469   0.002   0.016   0.313  -0.151  -0.147
71    G         1.127   1.262   1.296   1.269   1.427   1.498   1.184   1.351   1.418
72    Q         0.323   0.030   0.057   0.105  -0.247  -0.281   0.313  -0.151  -0.147
73    R         1.127   1.262   1.296   1.126   1.324   1.374   1.184   1.351   1.418
74    F         1.127   1.262   1.296   1.091   1.275   1.345   1.184   1.351   1.418
75    Q        -0.442  -0.815  -0.762  -0.498  -0.889  -0.824  -0.434  -0.878  -0.821
76    E         1.127   1.262   1.296   0.952   1.134   1.225   1.184   1.351   1.418
77    Q        -0.442  -0.815  -0.762  -0.578  -1.055  -1.033  -0.434  -0.878  -0.821
78    N         1.127   1.262   1.296   1.151   1.340   1.396   1.184   1.351   1.418
79    A         1.127   1.262   1.296   1.252   1.360   1.483   1.184   1.351   1.418
80    A        -0.793  -0.601  -0.733  -0.726  -0.457  -0.729  -0.932  -0.590  -0.784
81    L        -0.793  -0.888  -0.774  -0.817  -0.887  -0.697  -0.932  -0.983  -0.840
82    G        -1.459  -1.280  -1.316  -1.213  -0.977  -1.025  -1.430  -1.136  -1.125
83    Q        -0.442  -0.815  -0.762  -0.498  -0.901  -0.824  -0.434  -0.878  -0.821
84    G        -2.177  -1.858  -1.771  -2.214  -1.798  -1.645  -1.906  -1.465  -1.327
85    L        -1.030  -0.608  -0.744  -1.131  -0.472  -0.686  -1.251  -0.621  -0.799
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    G        -1.596  -1.455  -1.352  -1.459  -1.324  -1.103  -1.580  -1.304  -1.159
88    R         0.252   0.532   0.079   0.304   0.631  -0.006   0.208   0.608  -0.110
* 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/O74700
Output conservation file - output/O74700
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
