1     M         1.579   1.589   1.612   1.936   1.954   1.987   1.712   1.725   1.755
2     -        -0.401  -0.392  -0.397  -0.451  -0.419  -0.457  -0.517  -0.503  -0.509
3     -        -0.401  -0.441  -0.426  -0.303  -0.362  -0.336  -0.517  -0.568  -0.546
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     D        -0.401  -0.451  -0.422  -0.480  -0.567  -0.523  -0.517  -0.582  -0.541
6     I        -1.486  -1.475  -1.417  -1.628  -1.593  -1.510  -1.141  -1.125  -1.052
7     L        -0.231  -0.273  -0.334  -0.587  -0.669  -0.730  -0.285  -0.342  -0.424
8     K        -0.958  -0.964  -0.946  -0.819  -0.813  -0.792  -0.856  -0.858  -0.826
9     L        -0.430  -0.418  -0.416  -0.725  -0.727  -0.740  -0.570  -0.552  -0.537
10    S        -0.958  -0.962  -0.967  -0.854  -0.845  -0.850  -0.856  -0.857  -0.848
11    D         0.297   0.321   0.339   0.164   0.208   0.237   0.000   0.040   0.060
12    F         0.626   0.560   0.472   0.885   0.763   0.557   0.571   0.461   0.299
13    I         0.626   0.560   0.472   0.648   0.530   0.331   0.571   0.461   0.299
14    G         0.626   0.560   0.472   0.854   0.753   0.586   0.571   0.461   0.299
15    N        -0.958  -0.970  -0.971  -0.711  -0.732  -0.758  -0.856  -0.865  -0.851
16    T        -0.231  -0.184  -0.330  -0.004   0.074  -0.153  -0.285  -0.220  -0.418
17    L         1.579   1.589   1.612   1.291   1.303   1.354   1.712   1.725   1.755
18    I        -1.486  -1.475  -1.417  -1.034  -1.000  -0.928  -1.141  -1.125  -1.052
19    V        -0.430  -0.415  -0.408  -0.853  -0.811  -0.827  -0.570  -0.548  -0.530
20    S        -0.958  -0.970  -0.971  -0.890  -0.905  -0.909  -0.856  -0.865  -0.851
21    L         0.626   0.641   0.488   0.319   0.342   0.113   0.571   0.594   0.327
22    T        -0.430  -0.401  -0.408  -0.511  -0.463  -0.470  -0.570  -0.534  -0.529
23    E        -0.231  -0.261  -0.338  -0.065  -0.104  -0.217  -0.285  -0.327  -0.429
24    D        -0.958  -0.962  -0.967  -0.990  -1.005  -1.012  -0.856  -0.857  -0.848
25    R         1.579   1.589   1.612   1.838   1.853   1.891   1.712   1.725   1.755
26    I        -0.430  -0.415  -0.408  -0.639  -0.609  -0.607  -0.570  -0.548  -0.530
27    L         1.579   1.589   1.612   1.291   1.303   1.354   1.712   1.725   1.755
28    V        -1.486  -1.475  -1.417  -1.376  -1.348  -1.263  -1.141  -1.125  -1.052
29    G         1.579   1.589   1.612   1.838   1.858   1.891   1.712   1.725   1.755
30    S        -0.958  -0.969  -0.943  -1.061  -1.074  -1.047  -0.856  -0.863  -0.822
31    L         1.579   1.589   1.612   1.291   1.303   1.354   1.712   1.725   1.755
32    V        -0.430  -0.457  -0.429  -0.644  -0.680  -0.628  -0.570  -0.596  -0.553
33    A         0.297   0.321   0.339   0.250   0.303   0.316   0.000   0.040   0.060
34    V         0.297   0.294   0.318  -0.022  -0.028   0.022   0.000  -0.009   0.020
35    D         1.579   1.589   1.612   1.713   1.727   1.768   1.712   1.725   1.755
36    A        -0.430  -0.407  -0.414  -0.047  -0.006  -0.010  -0.570  -0.541  -0.535
37    Q        -0.430  -0.457  -0.429  -0.197  -0.238  -0.203  -0.570  -0.596  -0.553
38    M        -0.430  -0.457  -0.429  -0.229  -0.254  -0.208  -0.570  -0.596  -0.553
39    N         1.579   1.589   1.612   1.801   1.814   1.854   1.712   1.725   1.755
40    L         1.579   1.589   1.612   1.291   1.303   1.354   1.712   1.725   1.755
41    L         1.579   1.589   1.612   1.291   1.303   1.354   1.712   1.725   1.755
42    L         1.579   1.589   1.612   1.291   1.303   1.354   1.712   1.725   1.755
43    D        -0.231  -0.184  -0.330  -0.168  -0.089  -0.338  -0.285  -0.220  -0.418
44    H        -0.430  -0.457  -0.429  -0.283  -0.320  -0.273  -0.570  -0.596  -0.553
45    V         1.579   1.589   1.612   1.506   1.517   1.565   1.712   1.725   1.755
46    E        -1.486  -1.475  -1.417  -1.135  -1.145  -1.026  -1.141  -1.125  -1.052
47    E         1.579   1.589   1.612   1.826   1.845   1.879   1.712   1.725   1.755
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    R        -0.958  -0.930  -0.945  -0.760  -0.714  -0.735  -0.856  -0.820  -0.824
55    M        -1.486  -1.475  -1.417  -1.319  -1.295  -1.207  -1.141  -1.125  -1.052
56    G        -0.231  -0.261  -0.338  -0.120  -0.172  -0.300  -0.285  -0.327  -0.429
57    S        -0.958  -0.962  -0.967  -0.809  -0.813  -0.798  -0.856  -0.857  -0.848
58    -         0.367   0.320   0.338  -0.095  -0.173  -0.129   0.127   0.039   0.057
59    S        -0.231  -0.197  -0.336   0.079   0.139  -0.119  -0.285  -0.238  -0.427
60    S        -0.430  -0.417  -0.416  -0.715  -0.700  -0.679  -0.570  -0.552  -0.537
61    R         1.579   1.589   1.612   1.838   1.853   1.891   1.712   1.725   1.755
62    M        -0.958  -0.970  -0.971  -0.760  -0.779  -0.780  -0.856  -0.865  -0.851
63    M        -0.430  -0.402  -0.409  -0.681  -0.619  -0.631  -0.570  -0.536  -0.530
64    G         1.579   1.589   1.612   1.838   1.858   1.891   1.712   1.725   1.755
65    L         1.579   1.589   1.612   1.291   1.303   1.354   1.712   1.725   1.755
66    V         1.579   1.589   1.612   1.506   1.517   1.565   1.712   1.725   1.755
67    S         1.579   1.589   1.612   1.688   1.703   1.743   1.712   1.725   1.755
68    V         1.579   1.589   1.612   1.506   1.517   1.565   1.712   1.725   1.755
69    P         1.579   1.589   1.612   1.984   2.003   2.034   1.712   1.725   1.755
70    R        -0.231  -0.275  -0.343   0.090   0.027  -0.069  -0.285  -0.345  -0.436
71    R        -1.486  -1.475  -1.417  -1.313  -1.318  -1.201  -1.141  -1.125  -1.052
72    S         0.297   0.310   0.326   0.172   0.198   0.220   0.000   0.022   0.035
73    V         0.297   0.291   0.317   0.042   0.021   0.053   0.000  -0.014   0.018
74    K        -0.958  -0.962  -0.967  -0.834  -0.834  -0.839  -0.856  -0.857  -0.848
75    T        -0.430  -0.409  -0.409  -0.484  -0.453  -0.440  -0.570  -0.544  -0.531
76    I         0.297   0.288   0.316   0.042   0.012   0.049   0.000  -0.020   0.016
77    M        -0.231  -0.195  -0.308  -0.216  -0.154  -0.368  -0.285  -0.234  -0.389
78    I        -0.430  -0.401  -0.412  -0.667  -0.630  -0.626  -0.570  -0.535  -0.532
79    D        -0.231  -0.275  -0.343  -0.152  -0.222  -0.339  -0.285  -0.345  -0.436
80    K        -0.430  -0.416  -0.407  -0.358  -0.330  -0.301  -0.570  -0.550  -0.528
81    P        -0.958  -0.970  -0.971  -0.706  -0.721  -0.697  -0.856  -0.865  -0.851
82    V        -0.958  -0.970  -0.971  -1.174  -1.225  -1.260  -0.856  -0.865  -0.851
83    L        -0.958  -0.970  -0.971  -0.921  -0.959  -1.007  -0.856  -0.865  -0.851
84    Q        -1.486  -1.475  -1.417  -1.276  -1.264  -1.165  -1.141  -1.125  -1.052
85    E        -0.958  -0.914  -0.938  -0.784  -0.704  -0.749  -0.856  -0.803  -0.817
86    L         0.297   0.294   0.318  -0.211  -0.211  -0.151   0.000  -0.009   0.020
87    T        -1.486  -1.475  -1.417  -1.613  -1.591  -1.496  -1.141  -1.125  -1.052
88    A        -0.430  -0.418  -0.416  -0.295  -0.266  -0.269  -0.570  -0.552  -0.537
89    N        -1.061  -1.049  -0.997  -1.296  -1.314  -1.185  -0.963  -0.945  -0.877
90    K         0.508   0.475   0.427   0.623   0.567   0.483   0.374   0.316   0.219
91    V        -1.061  -1.049  -0.997  -1.393  -1.369  -1.279  -0.963  -0.945  -0.877
92    E         0.259   0.273   0.311   0.203   0.222   0.292  -0.071  -0.048   0.006
93    L         0.367   0.327   0.342  -0.112  -0.177  -0.137   0.127   0.051   0.064
94    M        -0.513  -0.499  -0.456  -0.482  -0.467  -0.386  -0.666  -0.644  -0.585
95    A        -0.513  -0.499  -0.456  -0.530  -0.518  -0.433  -0.666  -0.644  -0.585
96    N         0.367   0.327   0.342   0.481   0.409   0.435   0.127   0.051   0.064
97    I         0.367   0.327   0.342   0.436   0.383   0.409   0.127   0.051   0.064
98    V        -0.231  -0.184  -0.330  -0.362  -0.293  -0.513  -0.285  -0.220  -0.418
* 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/P23059
Output conservation file - output/P23059
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
