1     M         0.933   0.951   1.003   1.246   1.244   1.297   0.961   0.988   1.067
2     -        -2.023  -1.941  -1.644  -2.226  -2.093  -1.659  -1.845  -1.750  -1.391
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    A        -1.292  -1.496  -1.620  -1.078  -1.345  -1.517  -1.060  -1.288  -1.369
15    P        -0.480  -0.518  -0.324  -0.485  -0.654  -0.410  -0.771  -0.853  -0.575
16    V        -1.292  -0.910  -1.576  -1.268  -0.793  -1.660  -1.060  -0.644  -1.327
17    -        -0.067  -0.025  -0.254  -0.165  -0.100  -0.488  -0.122  -0.066  -0.457
18    -        -0.178  -0.182  -0.266  -0.384  -0.380  -0.466  -0.286  -0.302  -0.477
19    K         0.159  -0.052  -0.247   0.006  -0.274  -0.570   0.191  -0.106  -0.445
20    S        -1.617  -1.538  -1.605  -1.472  -1.353  -1.413  -1.445  -1.346  -1.355
21    Q        -1.763  -1.764  -1.631  -1.619  -1.692  -1.563  -1.638  -1.624  -1.380
22    E        -1.208  -1.267  -1.067  -0.958  -0.989  -0.736  -1.349  -1.364  -1.085
23    S        -1.421  -1.377  -1.093  -1.523  -1.472  -1.089  -1.541  -1.483  -1.115
24    I         0.159   0.082  -0.237   0.363   0.280  -0.224   0.191   0.085  -0.428
25    N         0.159  -0.052  -0.247   0.462   0.189  -0.227   0.191  -0.106  -0.445
26    Q        -1.421  -1.262  -1.078  -1.580  -1.368  -1.127  -1.541  -1.335  -1.097
27    K         0.933   0.951   1.003   0.674   0.697   0.830   0.961   0.988   1.067
28    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
29    A        -0.243  -0.210  -0.292  -0.414  -0.378  -0.546  -0.386  -0.345  -0.521
30    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
31    V        -1.146  -1.161  -1.065  -1.158  -1.159  -1.077  -1.253  -1.248  -1.084
32    I        -1.275  -1.128  -1.060  -1.166  -0.944  -0.896  -1.349  -1.170  -1.075
33    K         0.933   0.951   1.003   0.674   0.697   0.830   0.961   0.988   1.067
34    S         0.933   0.951   1.003   0.829   0.847   0.956   0.961   0.988   1.067
35    G         0.933   0.951   1.003   0.836   0.855   0.962   0.961   0.988   1.067
36    K         0.933   0.951   1.003   0.674   0.697   0.830   0.961   0.988   1.067
37    Y        -0.584  -0.673  -1.029  -0.145  -0.278  -0.780  -0.483  -0.613  -1.036
38    T        -1.146  -1.028  -1.077  -1.160  -1.040  -1.094  -1.253  -1.162  -1.097
39    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
40    G         0.933   0.951   1.003   0.836   0.855   0.962   0.961   0.988   1.067
41    Y         0.933   0.951   1.003   1.095   1.117   1.174   0.961   0.988   1.067
42    K         0.159  -0.052  -0.247   0.056  -0.193  -0.406   0.191  -0.106  -0.445
43    S         0.933   0.951   1.003   0.829   0.847   0.956   0.961   0.988   1.067
44    T        -0.584  -0.342  -1.011  -0.301  -0.017  -0.986  -0.483  -0.195  -1.014
45    V        -1.421  -1.360  -1.102  -1.725  -1.659  -1.262  -1.541  -1.464  -1.125
46    K         0.933   0.951   1.003   0.674   0.697   0.830   0.961   0.988   1.067
47    S        -1.275  -1.357  -1.095  -1.492  -1.673  -1.261  -1.349  -1.456  -1.118
48    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
49    R         0.933   0.951   1.003   1.202   1.205   1.262   0.961   0.988   1.067
50    Q        -1.421  -1.296  -1.094  -1.418  -1.282  -1.017  -1.541  -1.401  -1.116
51    G         0.933   0.951   1.003   0.836   0.855   0.962   0.961   0.988   1.067
52    K         0.933   0.951   1.003   0.674   0.697   0.830   0.961   0.988   1.067
53    S        -0.243  -0.066  -0.252  -0.416  -0.158  -0.472  -0.386  -0.126  -0.453
54    K         0.933   0.951   1.003   0.674   0.697   0.830   0.961   0.988   1.067
55    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
56    I        -0.243  -0.213  -0.296  -0.176  -0.126  -0.330  -0.386  -0.350  -0.527
57    I        -0.480  -0.518  -0.324  -0.746  -0.868  -0.602  -0.771  -0.853  -0.575
58    I         0.933   0.951   1.003   1.006   1.031   1.101   0.961   0.988   1.067
59    A         0.159  -0.052  -0.247   0.149  -0.138  -0.463   0.191  -0.106  -0.445
60    A        -0.480  -0.438  -0.320  -0.833  -0.780  -0.600  -0.771  -0.716  -0.568
61    N         0.933   0.951   1.003   1.127   1.157   1.200   0.961   0.988   1.067
62    T        -0.584  -0.612  -1.023  -0.256  -0.304  -0.890  -0.483  -0.517  -1.030
63    P         0.933   0.951   1.003   1.264   1.269   1.312   0.961   0.988   1.067
64    V        -1.146  -1.207  -1.083  -1.021  -1.078  -0.967  -1.253  -1.316  -1.104
65    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
66    R         0.933   0.951   1.003   1.202   1.205   1.262   0.961   0.988   1.067
67    K         0.933   0.951   1.003   0.674   0.697   0.830   0.961   0.988   1.067
68    S         0.933   0.951   1.003   0.829   0.847   0.956   0.961   0.988   1.067
69    E         0.933   0.951   1.003   1.202   1.218   1.262   0.961   0.988   1.067
70    L         0.159   0.082  -0.237  -0.012  -0.071  -0.507   0.191   0.085  -0.428
71    E         0.933   0.951   1.003   1.202   1.218   1.262   0.961   0.988   1.067
72    Y         0.933   0.951   1.003   1.095   1.117   1.174   0.961   0.988   1.067
73    Y         0.933   0.951   1.003   1.095   1.117   1.174   0.961   0.988   1.067
74    A         0.159  -0.052  -0.247   0.149  -0.138  -0.463   0.191  -0.106  -0.445
75    M         0.933   0.951   1.003   1.246   1.244   1.297   0.961   0.988   1.067
76    L         0.159  -0.052  -0.247   0.021  -0.196  -0.417   0.191  -0.106  -0.445
77    S         0.159   0.082  -0.237   0.161   0.059  -0.438   0.191   0.085  -0.428
78    K         0.159   0.120  -0.232   0.056   0.016  -0.386   0.191   0.137  -0.420
79    T        -0.950  -0.989  -1.062  -0.717  -0.790  -0.919  -0.964  -1.029  -1.080
80    K        -3.130  -3.103  -2.726  -2.858  -2.888  -2.227  -2.215  -2.171  -1.752
81    V         0.933   0.951   1.003   1.019   1.057   1.111   0.961   0.988   1.067
82    Y        -0.591  -0.532  -0.316  -0.510  -0.397  -0.114  -0.964  -0.878  -0.562
83    Y        -0.591  -0.532  -0.316  -0.510  -0.397  -0.114  -0.964  -0.878  -0.562
84    F        -0.480  -0.518  -0.324  -0.282  -0.388  -0.166  -0.771  -0.853  -0.575
85    Q        -1.292  -1.496  -1.620  -0.713  -1.011  -1.431  -1.060  -1.288  -1.369
86    G         0.933   0.951   1.003   0.836   0.855   0.962   0.961   0.988   1.067
87    G        -0.950  -1.076  -1.077  -0.936  -1.131  -1.084  -0.964  -1.136  -1.097
88    N         0.933   0.951   1.003   1.127   1.157   1.200   0.961   0.988   1.067
89    N        -0.480  -0.518  -0.324  -0.468  -0.556  -0.315  -0.771  -0.853  -0.575
90    E        -0.243  -0.248  -0.280   0.056   0.033  -0.096  -0.386  -0.405  -0.499
91    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
92    G         0.933   0.951   1.003   0.836   0.855   0.962   0.961   0.988   1.067
93    T         0.933   0.951   1.003   1.006   1.018   1.101   0.961   0.988   1.067
94    A        -0.950  -0.875  -1.042  -1.001  -0.880  -1.163  -0.964  -0.846  -1.053
95    V        -0.480  -0.290  -0.272  -0.282   0.028  -0.061  -0.771  -0.472  -0.487
96    G         0.933   0.951   1.003   0.836   0.855   0.962   0.961   0.988   1.067
97    K         0.159   0.082  -0.237   0.056  -0.028  -0.392   0.191   0.085  -0.428
98    L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
99    F         0.933   0.951   1.003   1.289   1.301   1.333   0.961   0.988   1.067
100   R         0.933   0.951   1.003   1.202   1.205   1.262   0.961   0.988   1.067
101   V         0.159  -0.052  -0.247   0.415   0.188  -0.108   0.191  -0.106  -0.445
102   G         0.159  -0.052  -0.247   0.169  -0.114  -0.448   0.191  -0.106  -0.445
103   V        -1.146  -1.180  -1.071  -1.158  -1.197  -1.087  -1.253  -1.276  -1.091
104   V        -1.208  -1.285  -1.077  -1.473  -1.482  -1.142  -1.349  -1.390  -1.098
105   S        -1.421  -1.275  -1.088  -1.775  -1.535  -1.245  -1.541  -1.353  -1.109
106   I        -0.243  -0.189  -0.301  -0.176  -0.090  -0.339  -0.386  -0.313  -0.536
107   L        -1.292  -1.389  -1.600  -1.235  -1.321  -1.546  -1.060  -1.164  -1.350
108   E         0.159   0.308  -0.226   0.551   0.692  -0.015   0.191   0.381  -0.410
109   A         0.933   0.951   1.003   0.816   0.831   0.945   0.961   0.988   1.067
110   G         0.933   0.951   1.003   0.836   0.855   0.962   0.961   0.988   1.067
111   D         0.933   0.951   1.003   1.171   1.169   1.236   0.961   0.988   1.067
112   S         0.933   0.951   1.003   0.829   0.847   0.956   0.961   0.988   1.067
113   D         0.933   0.951   1.003   1.171   1.169   1.236   0.961   0.988   1.067
114   I         0.933   0.951   1.003   1.006   1.031   1.101   0.961   0.988   1.067
115   L         0.933   0.951   1.003   0.633   0.684   0.796   0.961   0.988   1.067
116   T        -1.892  -1.826  -1.640  -1.917  -1.872  -1.575  -1.734  -1.664  -1.388
117   T        -1.617  -1.543  -1.608  -1.602  -1.479  -1.548  -1.445  -1.356  -1.357
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   L        -1.188  -1.288  -1.087  -1.446  -1.504  -1.175  -1.266  -1.368  -1.107
120   A        -1.824  -1.933  -1.652  -1.779  -1.922  -1.510  -1.638  -1.751  -1.398
* 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/P14120
Output conservation file - output/P14120
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
