1     M         1.063   1.068   1.120   1.436   1.450   1.494   1.107   1.114   1.192
2     A         1.063   1.068   1.120   0.885   0.899   1.016   1.107   1.114   1.192
3     V        -1.029  -1.214  -1.026  -1.021  -1.388  -1.155  -1.045  -1.281  -1.039
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     K         0.160   0.177  -0.157  -0.127  -0.103  -0.651   0.166   0.188  -0.350
7     T        -1.273  -1.252  -1.003  -1.135  -1.115  -0.787  -1.360  -1.334  -1.014
8     G         1.063   1.068   1.120   1.147   1.159   1.243   1.107   1.114   1.192
9     I        -0.339  -0.359  -0.223  -0.343  -0.388  -0.236  -0.601  -0.642  -0.460
10    A        -0.103  -0.107  -0.154  -0.283  -0.290  -0.373  -0.221  -0.231  -0.345
11    I        -0.806  -0.800  -0.968  -0.667  -0.671  -0.989  -0.791  -0.795  -0.972
12    G         1.063   1.068   1.120   1.147   1.159   1.243   1.107   1.114   1.192
13    L        -0.443  -0.526  -0.932  -0.118  -0.222  -0.795  -0.316  -0.423  -0.924
14    N         0.295   0.220  -0.128   0.701   0.608  -0.067   0.348   0.246  -0.302
15    K         1.063   1.068   1.120   0.749   0.764   0.898   1.107   1.114   1.192
16    G         1.063   1.068   1.120   1.147   1.159   1.243   1.107   1.114   1.192
17    K        -1.612  -1.544  -1.549  -1.641  -1.536  -1.530  -1.455  -1.403  -1.287
18    K        -0.443  -0.453  -0.939  -0.497  -0.510  -1.119  -0.316  -0.331  -0.933
19    V        -1.128  -1.147  -1.000  -1.080  -1.126  -0.940  -1.170  -1.196  -1.009
20    T        -0.443  -0.335  -0.919   0.039   0.155  -0.664  -0.316  -0.190  -0.908
21    Q        -1.273  -1.219  -0.996  -1.497  -1.459  -1.136  -1.360  -1.290  -1.004
22    M        -1.740  -1.588  -1.560  -2.007  -1.825  -1.731  -1.550  -1.394  -1.293
23    T        -1.740  -1.763  -1.573  -1.356  -1.396  -1.214  -1.550  -1.562  -1.306
24    P        -1.740  -1.763  -1.573  -1.420  -1.464  -1.295  -1.550  -1.562  -1.306
25    A        -0.806  -0.875  -0.967  -0.851  -0.952  -1.148  -0.791  -0.870  -0.967
26    P        -0.806  -0.912  -0.962  -0.346  -0.489  -0.657  -0.791  -0.912  -0.961
27    K        -0.450  -0.447  -0.238  -1.218  -1.231  -0.833  -0.791  -0.792  -0.487
28    I        -1.273  -1.275  -1.007  -1.186  -1.208  -0.851  -1.360  -1.364  -1.018
29    S         1.063   1.068   1.120   1.180   1.193   1.272   1.107   1.114   1.192
30    Y        -0.450  -0.447  -0.238  -0.596  -0.664  -0.352  -0.791  -0.792  -0.487
31    K        -0.806  -0.780  -0.945  -1.123  -1.055  -1.286  -0.791  -0.741  -0.941
32    K         1.063   1.068   1.120   0.749   0.764   0.898   1.107   1.114   1.192
33    G         1.063   1.068   1.120   1.147   1.159   1.243   1.107   1.114   1.192
34    A        -0.806  -0.855  -0.986  -0.710  -0.773  -0.830  -0.791  -0.858  -0.993
35    A        -1.000  -0.896  -0.971  -1.122  -0.939  -1.050  -1.076  -0.935  -0.974
36    S         1.063   1.068   1.120   1.180   1.193   1.272   1.107   1.114   1.192
37    N        -1.128  -0.990  -0.979  -1.225  -1.061  -0.948  -1.170  -0.997  -0.984
38    R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
39    T         0.295   0.175  -0.130   0.641   0.493   0.003   0.348   0.184  -0.304
40    K        -2.629  -2.504  -2.360  -2.667  -2.470  -2.216  -1.930  -1.822  -1.587
41    F         1.063   1.068   1.120   1.455   1.466   1.510   1.107   1.114   1.192
42    V         1.063   1.068   1.120   1.106   1.117   1.208   1.107   1.114   1.192
43    R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
44    S        -0.443  -0.526  -0.930   0.010  -0.086  -0.598  -0.316  -0.423  -0.922
45    L        -0.339  -0.323  -0.221  -0.343  -0.316  -0.232  -0.601  -0.580  -0.457
46    V         1.063   1.068   1.120   1.106   1.117   1.208   1.107   1.114   1.192
47    R        -1.062  -1.096  -0.997  -1.619  -1.643  -1.317  -1.170  -1.191  -1.008
48    E         1.063   1.068   1.120   1.200   1.218   1.289   1.107   1.114   1.192
49    I        -0.103   0.002  -0.140  -0.028   0.122  -0.119  -0.221  -0.064  -0.321
50    A        -0.443  -0.526  -0.930  -0.348  -0.450  -0.975  -0.316  -0.423  -0.922
51    G         0.295   0.380  -0.120   0.521   0.618  -0.074   0.348   0.455  -0.288
52    L        -0.806  -0.912  -0.962  -0.502  -0.631  -0.673  -0.791  -0.912  -0.961
53    S        -0.103   0.002  -0.140  -0.261  -0.109  -0.316  -0.221  -0.064  -0.321
54    P         1.063   1.068   1.120   1.391   1.403   1.454   1.107   1.114   1.192
55    Y         1.063   1.068   1.120   1.468   1.482   1.521   1.107   1.114   1.192
56    E         1.063   1.068   1.120   1.200   1.218   1.289   1.107   1.114   1.192
57    R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
58    R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
59    L        -1.000  -1.100  -1.005  -0.994  -1.138  -0.982  -1.076  -1.182  -1.015
60    I        -0.103  -0.107  -0.154   0.152   0.155   0.041  -0.221  -0.231  -0.345
61    D        -0.103   0.002  -0.140   0.139   0.280   0.064  -0.221  -0.064  -0.321
62    L         1.063   1.068   1.120   1.106   1.114   1.208   1.107   1.114   1.192
63    I        -0.103  -0.213  -0.210   0.060  -0.117  -0.208  -0.221  -0.399  -0.438
64    R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
65    N         1.063   1.068   1.120   1.378   1.394   1.443   1.107   1.114   1.192
66    S        -0.450  -0.406  -0.230  -0.755  -0.660  -0.414  -0.791  -0.721  -0.473
67    G        -1.467  -1.616  -1.562  -1.144  -1.363  -1.409  -1.265  -1.410  -1.295
68    E        -0.450  -0.447  -0.238  -0.346  -0.328  -0.046  -0.791  -0.792  -0.487
69    K         1.063   1.068   1.120   0.749   0.764   0.898   1.107   1.114   1.192
70    R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
71    A         1.063   1.068   1.120   0.885   0.899   1.016   1.107   1.114   1.192
72    R        -0.103  -0.061  -0.179  -0.525  -0.462  -0.701  -0.221  -0.159  -0.386
73    K         1.063   1.068   1.120   0.749   0.764   0.898   1.107   1.114   1.192
74    V        -0.339  -0.241  -0.190  -0.460  -0.300  -0.263  -0.601  -0.445  -0.404
75    A         1.063   1.068   1.120   0.885   0.899   1.016   1.107   1.114   1.192
76    K         1.063   1.068   1.120   0.749   0.764   0.898   1.107   1.114   1.192
77    K         1.063   1.068   1.120   0.749   0.764   0.898   1.107   1.114   1.192
78    R         0.295   0.175  -0.130   0.064  -0.100  -0.597   0.348   0.184  -0.304
79    L         1.063   1.068   1.120   1.106   1.114   1.208   1.107   1.114   1.192
80    G         1.063   1.068   1.120   1.147   1.159   1.243   1.107   1.114   1.192
81    S        -0.103   0.002  -0.140   0.113   0.261  -0.015  -0.221  -0.064  -0.321
82    F        -1.128  -1.098  -0.992  -0.703  -0.676  -0.621  -1.170  -1.135  -0.998
83    T        -1.273  -1.216  -1.005  -1.592  -1.525  -1.156  -1.360  -1.302  -1.016
84    R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
85    A         1.063   1.068   1.120   0.885   0.899   1.016   1.107   1.114   1.192
86    K        -0.103  -0.061  -0.179  -0.418  -0.356  -0.521  -0.221  -0.159  -0.386
87    A        -1.128  -1.098  -0.992  -1.469  -1.426  -1.326  -1.170  -1.135  -0.998
88    K         1.063   1.068   1.120   0.749   0.764   0.898   1.107   1.114   1.192
89    V        -0.339  -0.325  -0.225  -0.401  -0.382  -0.261  -0.601  -0.584  -0.465
90    E         1.063   1.068   1.120   1.200   1.218   1.289   1.107   1.114   1.192
91    E        -0.103  -0.213  -0.210   0.139  -0.013  -0.031  -0.221  -0.399  -0.438
92    M        -0.339  -0.359  -0.223  -0.158  -0.215  -0.093  -0.601  -0.642  -0.460
93    N        -1.000  -1.046  -0.995  -0.638  -0.691  -0.637  -1.076  -1.117  -1.005
94    N        -2.629  -2.588  -2.364  -2.203  -2.182  -1.977  -1.930  -1.896  -1.591
95    I        -0.339  -0.241  -0.190  -0.401  -0.243  -0.202  -0.601  -0.445  -0.404
96    I         1.063   1.068   1.120   1.234   1.256   1.318   1.107   1.114   1.192
97    A        -1.128  -1.148  -0.994  -1.147  -1.180  -0.932  -1.170  -1.198  -1.003
98    A        -1.273  -1.265  -1.009  -1.487  -1.475  -1.087  -1.360  -1.351  -1.021
99    S         0.295   0.220  -0.128   0.518   0.425  -0.178   0.348   0.246  -0.302
100   R         1.063   1.068   1.120   0.749   0.756   0.898   1.107   1.114   1.192
101   R        -0.806  -0.912  -0.962  -0.963  -1.096  -1.063  -0.791  -0.912  -0.961
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   H         0.295   0.175  -0.130   0.794   0.635   0.042   0.348   0.184  -0.304
* 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/O14455
Output conservation file - output/O14455
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
