1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     M         1.889   1.914   1.969   2.107   2.148   2.223   2.116   2.158   2.253
4     S         0.564   0.605   0.633   0.489   0.557   0.582   0.287   0.358   0.376
5     Q        -1.359  -1.375  -1.286  -1.202  -1.245  -1.080  -1.085  -1.093  -0.981
6     I        -0.879  -0.883  -0.839  -0.844  -0.827  -0.724  -0.856  -0.856  -0.781
7     A         0.847   0.837   0.715   1.097   1.087   0.921   0.799   0.778   0.533
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     Q         1.889   1.914   1.969   1.796   1.839   1.918   2.116   2.158   2.253
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    E         0.951   0.841   0.773   0.905   0.722   0.601   0.973   0.785   0.642
15    M         0.951   0.841   0.773   1.260   1.112   0.995   0.973   0.785   0.642
16    T        -0.879  -0.883  -0.839  -0.723  -0.729  -0.667  -0.856  -0.856  -0.781
17    V        -0.216  -0.172  -0.206  -0.267  -0.197  -0.247  -0.399  -0.354  -0.377
18    S        -0.879  -0.901  -0.844  -0.961  -1.014  -0.905  -0.856  -0.872  -0.786
19    L         1.889   1.914   1.969   1.637   1.659   1.762   2.116   2.158   2.253
20    R        -0.216  -0.274  -0.219  -0.122  -0.195  -0.130  -0.399  -0.462  -0.389
21    N        -1.359  -1.362  -1.305  -1.215  -1.200  -1.140  -1.085  -1.082  -0.999
22    A        -0.697  -0.694  -0.761  -0.565  -0.594  -0.703  -0.627  -0.626  -0.690
23    R        -0.697  -0.733  -0.749  -0.499  -0.564  -0.642  -0.627  -0.670  -0.677
24    T        -0.697  -0.615  -0.754  -0.380  -0.255  -0.475  -0.627  -0.524  -0.683
25    Q         0.446   0.468   0.548   0.061   0.093   0.223   0.058   0.091   0.208
26    L         0.951   0.841   0.773   0.751   0.577   0.478   0.973   0.785   0.642
27    D        -0.879  -0.901  -0.844  -0.850  -0.903  -0.820  -0.856  -0.872  -0.786
28    M         0.083   0.019  -0.098   0.461   0.360   0.185   0.058  -0.037  -0.209
29    V         0.083   0.116  -0.048   0.387   0.429   0.207   0.058   0.107  -0.138
30    N        -0.697  -0.754  -0.773  -0.774  -0.872  -0.983  -0.627  -0.694  -0.704
31    Q        -0.398  -0.373  -0.275  -0.742  -0.678  -0.516  -0.627  -0.592  -0.462
32    Q         1.889   1.914   1.969   1.796   1.839   1.918   2.116   2.158   2.253
33    L         0.951   0.841   0.773   0.816   0.661   0.591   0.973   0.785   0.642
34    A        -0.879  -0.809  -0.816  -0.820  -0.746  -0.725  -0.856  -0.780  -0.757
35    Y        -0.879  -0.883  -0.839  -0.729  -0.753  -0.653  -0.856  -0.856  -0.781
36    L        -0.216  -0.205  -0.216  -0.427  -0.415  -0.373  -0.399  -0.393  -0.390
37    D        -1.359  -1.294  -1.278  -1.212  -1.085  -1.096  -1.085  -1.014  -0.974
38    R         0.564   0.605   0.633   0.603   0.668   0.692   0.287   0.358   0.376
39    Q         0.564   0.605   0.633   0.331   0.418   0.430   0.287   0.358   0.376
40    E        -0.697  -0.615  -0.754  -0.998  -0.877  -1.127  -0.627  -0.524  -0.683
41    K        -0.697  -0.735  -0.785  -0.765  -0.786  -0.866  -0.627  -0.673  -0.718
42    L        -0.216  -0.175  -0.184  -0.311  -0.274  -0.217  -0.399  -0.345  -0.346
43    A         0.446   0.468   0.548   0.432   0.474   0.587   0.058   0.091   0.208
44    E        -0.879  -0.832  -0.803  -1.024  -0.928  -0.916  -0.856  -0.803  -0.746
45    L         0.083   0.147  -0.046  -0.029   0.047  -0.203   0.058   0.152  -0.133
46    T         0.951   0.841   0.773   1.056   0.900   0.797   0.973   0.785   0.642
47    K        -1.359  -1.375  -1.286  -1.380  -1.357  -1.248  -1.085  -1.093  -0.981
48    K         0.083   0.005  -0.082  -0.080  -0.190  -0.339   0.058  -0.056  -0.186
49    E        -0.697  -0.735  -0.785  -0.759  -0.842  -0.944  -0.627  -0.673  -0.718
50    L         1.889   1.914   1.969   1.637   1.659   1.762   2.116   2.158   2.253
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    E        -0.216  -0.197  -0.192  -0.299  -0.251  -0.227  -0.399  -0.366  -0.351
56    S        -0.216  -0.178  -0.200  -0.260  -0.193  -0.231  -0.399  -0.336  -0.362
57    Y        -0.697  -0.735  -0.785  -0.466  -0.539  -0.709  -0.627  -0.673  -0.718
58    P        -1.359  -1.381  -1.310  -0.946  -1.011  -0.930  -1.085  -1.099  -1.003
59    T        -0.216  -0.258  -0.204  -0.277  -0.302  -0.249  -0.399  -0.438  -0.369
60    D         0.564   0.554   0.577   0.403   0.378   0.411   0.287   0.260   0.266
61    K        -1.359  -1.375  -1.286  -1.433  -1.426  -1.305  -1.085  -1.093  -0.981
62    V         1.889   1.914   1.969   2.000   2.034   2.118   2.116   2.158   2.253
63    W         1.889   1.914   1.969   2.260   2.300   2.373   2.116   2.158   2.253
64    R         0.446   0.468   0.548   0.264   0.285   0.410   0.058   0.091   0.208
65    S         0.446   0.468   0.548   0.420   0.454   0.579   0.058   0.091   0.208
66    C         0.083   0.016  -0.082   0.621   0.521   0.359   0.058  -0.041  -0.186
67    G         1.889   1.914   1.969   2.139   2.183   2.255   2.116   2.158   2.253
68    K         0.951   1.008   0.801   0.823   0.913   0.636   0.973   1.064   0.692
69    S        -0.216  -0.180  -0.205  -0.067  -0.023  -0.048  -0.399  -0.367  -0.377
70    F         1.889   1.914   1.969   2.236   2.275   2.349   2.116   2.158   2.253
71    I         0.446   0.467   0.548   0.414   0.441   0.564   0.058   0.089   0.208
72    L        -0.879  -0.858  -0.821  -1.120  -1.084  -0.973  -0.856  -0.826  -0.763
73    Q        -0.697  -0.735  -0.785  -0.768  -0.836  -0.943  -0.627  -0.673  -0.718
74    D         0.083   0.104  -0.054   0.286   0.329   0.052   0.058   0.091  -0.146
75    K         0.564   0.605   0.633   0.237   0.313   0.345   0.287   0.358   0.376
76    S        -1.359  -1.356  -1.317  -1.236  -1.220  -1.181  -1.085  -1.077  -1.008
77    K        -0.697  -0.627  -0.718  -0.565  -0.444  -0.626  -0.627  -0.538  -0.640
78    Y         1.889   1.914   1.969   2.172   2.213   2.287   2.116   2.158   2.253
79    V        -0.697  -0.615  -0.754  -0.740  -0.644  -0.792  -0.627  -0.524  -0.683
80    N        -0.879  -0.920  -0.811  -1.068  -1.098  -0.955  -0.856  -0.889  -0.754
81    D        -0.216  -0.212  -0.218  -0.286  -0.299  -0.325  -0.399  -0.399  -0.392
82    L         0.951   1.004   0.812   0.817   0.874   0.650   0.973   1.058   0.713
83    S        -1.840  -1.818  -1.711  -1.445  -1.411  -1.260  -1.313  -1.287  -1.162
84    H        -0.879  -0.832  -0.813  -0.838  -0.786  -0.782  -0.856  -0.802  -0.755
85    D         1.889   1.914   1.969   2.008   2.051   2.126   2.116   2.158   2.253
86    E         0.083   0.005  -0.082   0.059  -0.084  -0.231   0.058  -0.056  -0.186
87    T         0.083   0.154  -0.058  -0.002   0.113  -0.188   0.058   0.161  -0.152
88    V        -1.359  -1.356  -1.317  -1.314  -1.343  -1.246  -1.085  -1.077  -1.008
89    L        -0.697  -0.735  -0.785  -0.559  -0.611  -0.591  -0.627  -0.673  -0.718
90    L        -1.359  -1.296  -1.279  -1.448  -1.323  -1.337  -1.085  -1.016  -0.974
91    D         0.564   0.626   0.603   0.403   0.496   0.454   0.287   0.396   0.318
92    Q        -0.216  -0.274  -0.219  -0.320  -0.391  -0.299  -0.399  -0.462  -0.389
93    R        -1.359  -1.356  -1.317  -1.372  -1.401  -1.262  -1.085  -1.077  -1.008
94    K         0.083   0.016  -0.082  -0.047  -0.125  -0.288   0.058  -0.041  -0.186
95    T        -0.398  -0.381  -0.279  -0.504  -0.459  -0.324  -0.627  -0.604  -0.468
96    L         1.889   1.914   1.969   1.637   1.659   1.762   2.116   2.158   2.253
97    K        -1.359  -1.316  -1.277  -1.321  -1.272  -1.178  -1.085  -1.035  -0.973
98    I        -0.216  -0.232  -0.202  -0.303  -0.352  -0.328  -0.399  -0.423  -0.372
99    K         1.889   1.914   1.969   1.646   1.699   1.771   2.116   2.158   2.253
100   K        -0.697  -0.765  -0.756  -0.894  -1.015  -0.996  -0.627  -0.706  -0.685
101   N         0.083  -0.022  -0.105   0.302   0.181   0.052   0.058  -0.093  -0.219
102   Y         1.889   1.914   1.969   2.172   2.213   2.287   2.116   2.158   2.253
103   L         0.951   0.841   0.773   0.794   0.631   0.554   0.973   0.785   0.642
104   E        -0.398  -0.377  -0.287  -0.637  -0.591  -0.466  -0.627  -0.598  -0.479
105   T         0.564   0.541   0.573   0.477   0.430   0.470   0.287   0.234   0.258
106   T         0.564   0.541   0.573   0.462   0.406   0.450   0.287   0.234   0.258
107   V        -0.216  -0.162  -0.181  -0.308  -0.226  -0.218  -0.399  -0.323  -0.335
108   E        -0.216  -0.183  -0.199  -0.340  -0.294  -0.313  -0.399  -0.353  -0.368
109   K         0.564   0.525   0.565   0.192   0.153   0.186   0.287   0.204   0.242
110   T         0.951   0.841   0.773   1.068   0.922   0.817   0.973   0.785   0.642
111   I        -0.697  -0.697  -0.738  -0.455  -0.462  -0.536  -0.627  -0.629  -0.664
112   D        -0.697  -0.694  -0.761  -0.670  -0.701  -0.783  -0.627  -0.626  -0.690
113   N        -0.879  -0.920  -0.809  -0.651  -0.679  -0.540  -0.856  -0.889  -0.752
114   L         0.564   0.605   0.633   0.282   0.330   0.393   0.287   0.358   0.376
115   K        -0.879  -0.920  -0.847  -1.043  -1.091  -0.967  -0.856  -0.889  -0.789
116   A        -1.359  -1.294  -1.278  -1.198  -1.098  -1.068  -1.085  -1.014  -0.974
117   L        -0.879  -0.855  -0.822  -0.838  -0.833  -0.755  -0.856  -0.825  -0.763
118   M        -0.879  -0.920  -0.847  -0.715  -0.811  -0.686  -0.856  -0.889  -0.789
119   K         0.446   0.465   0.546   0.195   0.230   0.343   0.058   0.085   0.205
120   N        -0.089  -0.126  -0.148   0.020  -0.022  -0.051  -0.189  -0.247  -0.281
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P46988
Output conservation file - output/P46988
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
