1     M         1.073   1.079   1.137   1.443   1.458   1.509   1.120   1.127   1.214
2     T         0.306   0.351  -0.094   0.285   0.337  -0.217   0.358   0.415  -0.258
3     V        -1.015  -1.193  -1.007  -1.010  -1.357  -1.136  -1.039  -1.265  -1.025
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         0.172   0.195  -0.137  -0.117  -0.087  -0.629   0.176   0.206  -0.329
7     T        -1.258  -1.243  -0.985  -1.132  -1.120  -0.778  -1.355  -1.334  -1.001
8     G         1.073   1.079   1.137   1.154   1.167   1.259   1.120   1.127   1.214
9     I        -0.326  -0.344  -0.204  -0.333  -0.371  -0.217  -0.593  -0.627  -0.443
10    A        -0.091  -0.088  -0.134  -0.266  -0.265  -0.346  -0.213  -0.212  -0.325
11    I        -0.792  -0.802  -0.951  -0.655  -0.683  -0.971  -0.784  -0.810  -0.960
12    G         1.073   1.079   1.137   1.154   1.167   1.259   1.120   1.127   1.214
13    L        -0.429  -0.505  -0.910  -0.109  -0.201  -0.774  -0.308  -0.404  -0.907
14    N         0.306   0.236  -0.107   0.709   0.622  -0.044   0.358   0.263  -0.281
15    K         1.073   1.079   1.137   0.757   0.771   0.914   1.120   1.127   1.214
16    G         1.073   1.079   1.137   1.154   1.167   1.259   1.120   1.127   1.214
17    K        -1.597  -1.529  -1.530  -1.629  -1.530  -1.517  -1.450  -1.397  -1.274
18    K        -0.429  -0.431  -0.918  -0.487  -0.489  -1.101  -0.308  -0.309  -0.916
19    V        -1.113  -1.127  -0.980  -1.071  -1.104  -0.925  -1.164  -1.181  -0.995
20    T        -0.429  -0.318  -0.897   0.042   0.163  -0.647  -0.308  -0.176  -0.891
21    S        -1.724  -1.632  -1.539  -1.834  -1.736  -1.535  -1.545  -1.446  -1.279
22    M        -1.724  -1.591  -1.543  -1.994  -1.830  -1.713  -1.545  -1.407  -1.283
23    T        -1.724  -1.743  -1.554  -1.347  -1.375  -1.196  -1.545  -1.550  -1.293
24    P        -1.724  -1.743  -1.554  -1.409  -1.439  -1.277  -1.545  -1.550  -1.293
25    A        -0.792  -0.853  -0.946  -0.832  -0.923  -1.122  -0.784  -0.851  -0.951
26    P        -0.792  -0.890  -0.941  -0.336  -0.466  -0.638  -0.784  -0.894  -0.945
27    K        -0.437  -0.437  -0.221  -1.206  -1.224  -0.818  -0.784  -0.788  -0.473
28    I        -1.258  -1.262  -0.988  -1.174  -1.196  -0.834  -1.355  -1.359  -1.005
29    S         1.073   1.079   1.137   1.181   1.194   1.282   1.120   1.127   1.214
30    Y        -0.437  -0.437  -0.221  -0.585  -0.651  -0.333  -0.784  -0.788  -0.473
31    K        -0.792  -0.788  -0.930  -1.112  -1.083  -1.280  -0.784  -0.762  -0.931
32    K         1.073   1.079   1.137   0.757   0.771   0.914   1.120   1.127   1.214
33    G         1.073   1.079   1.137   1.154   1.167   1.259   1.120   1.127   1.214
34    A        -0.792  -0.833  -0.966  -0.691  -0.745  -0.806  -0.784  -0.839  -0.977
35    A        -0.986  -0.895  -0.955  -1.107  -0.953  -1.038  -1.069  -0.947  -0.963
36    S         1.073   1.079   1.137   1.181   1.194   1.282   1.120   1.127   1.214
37    N        -1.113  -0.998  -0.965  -1.210  -1.075  -0.932  -1.164  -1.016  -0.974
38    R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
39    T         0.306   0.192  -0.109   0.641   0.502   0.017   0.358   0.202  -0.283
40    K        -2.612  -2.497  -2.342  -2.650  -2.477  -2.205  -1.926  -1.826  -1.577
41    F         1.073   1.079   1.137   1.462   1.474   1.526   1.120   1.127   1.214
42    V         1.073   1.079   1.137   1.113   1.126   1.224   1.120   1.127   1.214
43    R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
44    S        -0.429  -0.506  -0.909   0.013  -0.074  -0.582  -0.308  -0.405  -0.905
45    L        -0.326  -0.322  -0.205  -0.333  -0.330  -0.220  -0.593  -0.592  -0.445
46    V         1.073   1.079   1.137   1.113   1.126   1.224   1.120   1.127   1.214
47    R        -1.047  -1.083  -0.978  -1.604  -1.633  -1.299  -1.164  -1.187  -0.994
48    E         1.073   1.079   1.137   1.208   1.227   1.305   1.120   1.127   1.214
49    I        -0.091  -0.013  -0.128  -0.019   0.093  -0.112  -0.213  -0.096  -0.315
50    A        -0.429  -0.506  -0.909  -0.333  -0.427  -0.955  -0.308  -0.405  -0.905
51    G         0.306   0.392  -0.099   0.528   0.627  -0.055   0.358   0.467  -0.267
52    L        -0.792  -0.890  -0.941  -0.490  -0.606  -0.651  -0.784  -0.894  -0.945
53    S        -0.091  -0.013  -0.128  -0.246  -0.135  -0.307  -0.213  -0.096  -0.315
54    P         1.073   1.079   1.137   1.398   1.411   1.470   1.120   1.127   1.214
55    Y         1.073   1.079   1.137   1.474   1.490   1.537   1.120   1.127   1.214
56    E         1.073   1.079   1.137   1.208   1.227   1.305   1.120   1.127   1.214
57    R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
58    R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
59    L        -0.986  -1.083  -0.985  -0.983  -1.118  -0.964  -1.069  -1.170  -1.001
60    I        -0.091  -0.088  -0.134   0.161   0.172   0.062  -0.213  -0.212  -0.325
61    D        -0.091  -0.013  -0.128   0.148   0.254   0.072  -0.213  -0.096  -0.315
62    L         1.073   1.079   1.137   1.113   1.123   1.224   1.120   1.127   1.214
63    I        -0.091  -0.196  -0.190   0.070  -0.100  -0.188  -0.213  -0.383  -0.420
64    R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
65    N         1.073   1.079   1.137   1.385   1.401   1.459   1.120   1.127   1.214
66    S        -0.437  -0.393  -0.212  -0.745  -0.650  -0.398  -0.784  -0.713  -0.457
67    G        -1.452  -1.592  -1.541  -1.131  -1.336  -1.389  -1.259  -1.394  -1.281
68    E        -0.437  -0.437  -0.221  -0.335  -0.323  -0.032  -0.784  -0.788  -0.473
69    K         1.073   1.079   1.137   0.757   0.771   0.914   1.120   1.127   1.214
70    R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
71    A         1.073   1.079   1.137   0.899   0.913   1.038   1.120   1.127   1.214
72    R        -0.091  -0.044  -0.159  -0.515  -0.445  -0.679  -0.213  -0.143  -0.367
73    K         1.073   1.079   1.137   0.757   0.771   0.914   1.120   1.127   1.214
74    V        -0.326  -0.247  -0.176  -0.450  -0.319  -0.254  -0.593  -0.465  -0.395
75    A         1.073   1.079   1.137   0.899   0.913   1.038   1.120   1.127   1.214
76    K         1.073   1.079   1.137   0.757   0.771   0.914   1.120   1.127   1.214
77    K         1.073   1.079   1.137   0.757   0.771   0.914   1.120   1.127   1.214
78    R         0.306   0.192  -0.109   0.074  -0.083  -0.575   0.358   0.202  -0.283
79    L         1.073   1.079   1.137   1.113   1.123   1.224   1.120   1.127   1.214
80    G         1.073   1.079   1.137   1.154   1.167   1.259   1.120   1.127   1.214
81    S        -0.091  -0.013  -0.128   0.114   0.223  -0.017  -0.213  -0.096  -0.315
82    F        -1.113  -1.078  -0.972  -0.692  -0.652  -0.600  -1.164  -1.119  -0.982
83    T        -1.258  -1.220  -0.990  -1.582  -1.537  -1.145  -1.355  -1.314  -1.007
84    R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
85    A         1.073   1.079   1.137   0.899   0.913   1.038   1.120   1.127   1.214
86    K        -0.091  -0.044  -0.159  -0.408  -0.340  -0.501  -0.213  -0.143  -0.367
87    A        -1.113  -1.078  -0.972  -1.450  -1.396  -1.300  -1.164  -1.119  -0.982
88    K         1.073   1.079   1.137   0.757   0.771   0.914   1.120   1.127   1.214
89    V        -0.326  -0.309  -0.206  -0.391  -0.365  -0.243  -0.593  -0.568  -0.447
90    E         1.073   1.079   1.137   1.208   1.227   1.305   1.120   1.127   1.214
91    E        -0.091  -0.196  -0.190   0.148   0.004  -0.013  -0.213  -0.383  -0.420
92    M        -0.326  -0.344  -0.204  -0.148  -0.195  -0.073  -0.593  -0.627  -0.443
93    N        -0.986  -1.028  -0.975  -0.630  -0.674  -0.619  -1.069  -1.104  -0.990
94    N        -2.612  -2.575  -2.346  -2.192  -2.172  -1.961  -1.926  -1.896  -1.581
95    I        -0.326  -0.247  -0.176  -0.391  -0.262  -0.192  -0.593  -0.465  -0.395
96    I         1.073   1.079   1.137   1.241   1.262   1.334   1.120   1.127   1.214
97    A        -1.113  -1.129  -0.975  -1.129  -1.157  -0.912  -1.164  -1.184  -0.988
98    A        -1.258  -1.250  -0.991  -1.471  -1.460  -1.070  -1.355  -1.342  -1.008
99    S         0.306   0.236  -0.107   0.521   0.434  -0.158   0.358   0.263  -0.281
100   R         1.073   1.079   1.137   0.757   0.765   0.914   1.120   1.127   1.214
101   R        -0.792  -0.890  -0.941  -0.952  -1.071  -1.044  -0.784  -0.894  -0.945
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         0.306   0.192  -0.109   0.802   0.653   0.067   0.358   0.202  -0.283
* 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/P05745
Output conservation file - output/P05745
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
