1     M         0.820   0.832   0.865   1.123   1.138   1.138   0.845   0.867   0.914
2     G        -1.279  -1.037  -1.154  -1.585  -1.202  -1.348  -1.418  -1.116  -1.198
3     K         0.820   0.832   0.865   0.495   0.512   0.626   0.845   0.867   0.914
4     G         0.820   0.832   0.865   0.681   0.701   0.777   0.845   0.867   0.914
5     T         0.820   0.832   0.865   0.716   0.722   0.806   0.845   0.867   0.914
6     P        -1.794  -1.944  -1.713  -1.326  -1.625  -1.401  -1.656  -1.791  -1.495
7     S         0.820   0.832   0.865   0.716   0.745   0.806   0.845   0.867   0.914
8     F        -0.392  -0.196  -0.376  -0.122   0.137  -0.164  -0.584  -0.292  -0.607
9     G         0.820   0.832   0.865   0.681   0.701   0.777   0.845   0.867   0.914
10    K        -0.392  -0.283  -0.373  -0.647  -0.501  -0.539  -0.584  -0.427  -0.602
11    R         0.008  -0.190  -0.359  -0.175  -0.448  -0.753   0.012  -0.282  -0.578
12    H         0.820   0.832   0.865   0.977   1.003   1.019   0.845   0.867   0.914
13    N        -0.392  -0.549  -0.424  -0.237  -0.581  -0.445  -0.584  -0.867  -0.690
14    K         0.820   0.832   0.865   0.495   0.512   0.626   0.845   0.867   0.914
15    S         0.008  -0.166  -0.367   0.008  -0.221  -0.560   0.012  -0.247  -0.593
16    H         0.820   0.832   0.865   0.977   1.003   1.019   0.845   0.867   0.914
17    T        -0.765  -0.813  -1.133  -0.629  -0.749  -1.119  -0.703  -0.791  -1.172
18    L        -0.392  -0.283  -0.373  -0.031   0.098  -0.070  -0.584  -0.427  -0.602
19    C         0.820   0.832   0.865   0.994   1.002   1.032   0.845   0.867   0.914
20    N        -1.885  -1.837  -1.704  -1.998  -1.989  -1.816  -1.775  -1.710  -1.487
21    R         0.820   0.832   0.865   0.567   0.605   0.684   0.845   0.867   0.914
22    C         0.820   0.832   0.865   0.994   1.002   1.032   0.845   0.867   0.914
23    G         0.820   0.832   0.865   0.681   0.701   0.777   0.845   0.867   0.914
24    R        -0.673  -0.608  -0.428  -1.390  -1.277  -0.911  -1.060  -0.972  -0.696
25    R         0.008   0.115  -0.346  -0.142   0.009  -0.634   0.012   0.150  -0.557
26    S         0.820   0.832   0.865   0.716   0.745   0.806   0.845   0.867   0.914
27    F        -0.765  -0.834  -1.132  -0.235  -0.344  -0.755  -0.703  -0.814  -1.170
28    H         0.820   0.832   0.865   0.977   1.003   1.019   0.845   0.867   0.914
29    V        -1.885  -1.987  -1.710  -1.287  -1.423  -1.116  -1.775  -1.838  -1.492
30    Q         0.820   0.832   0.865   1.123   1.134   1.138   0.845   0.867   0.914
31    K         0.820   0.832   0.865   0.495   0.512   0.626   0.845   0.867   0.914
32    K        -1.120  -0.938  -1.133  -1.414  -1.160  -1.330  -1.180  -0.960  -1.171
33    T         0.008  -0.166  -0.367   0.072  -0.142  -0.367   0.012  -0.247  -0.593
34    C         0.820   0.832   0.865   0.994   1.002   1.032   0.845   0.867   0.914
35    S        -0.605  -0.422  -0.393  -0.886  -0.529  -0.547  -0.941  -0.652  -0.637
36    S        -0.392  -0.283  -0.373  -0.479  -0.316  -0.444  -0.584  -0.427  -0.602
37    C         0.820   0.832   0.865   0.994   1.002   1.032   0.845   0.867   0.914
38    G         0.820   0.832   0.865   0.681   0.701   0.777   0.845   0.867   0.914
39    Y         0.820   0.832   0.865   1.115   1.121   1.132   0.845   0.867   0.914
40    P         0.820   0.832   0.865   1.147   1.158   1.158   0.845   0.867   0.914
41    S        -0.392  -0.408  -0.409  -0.488  -0.503  -0.580  -0.584  -0.629  -0.664
42    A         0.820   0.832   0.865   0.802   0.846   0.876   0.845   0.867   0.914
43    K         0.820   0.832   0.865   0.495   0.512   0.626   0.845   0.867   0.914
44    T        -1.794  -1.710  -1.689  -1.503  -1.395  -1.260  -1.656  -1.563  -1.473
45    R         0.820   0.832   0.865   0.567   0.605   0.684   0.845   0.867   0.914
46    S         0.008  -0.166  -0.367  -0.023  -0.268  -0.656   0.012  -0.247  -0.593
47    H        -0.673  -0.564  -0.419  -0.621  -0.425  -0.259  -1.060  -0.894  -0.681
48    N         0.820   0.832   0.865   1.059   1.073   1.085   0.845   0.867   0.914
49    W         0.820   0.832   0.865   1.211   1.213   1.210   0.845   0.867   0.914
50    A        -1.279  -1.341  -1.172  -1.510  -1.592  -1.335  -1.418  -1.468  -1.220
51    A        -2.167  -2.182  -2.119  -1.680  -1.671  -1.574  -1.775  -1.815  -1.650
52    K         0.820   0.832   0.865   0.495   0.512   0.626   0.845   0.867   0.914
53    A         0.820   0.832   0.865   0.802   0.846   0.876   0.845   0.867   0.914
54    K         0.820   0.832   0.865   0.495   0.512   0.626   0.845   0.867   0.914
55    R         0.820   0.832   0.865   0.567   0.605   0.684   0.845   0.867   0.914
56    R         0.820   0.832   0.865   0.567   0.605   0.684   0.845   0.867   0.914
57    H        -1.120  -1.261  -1.162  -1.333  -1.546  -1.386  -1.180  -1.355  -1.208
58    T         0.820   0.832   0.865   0.716   0.722   0.806   0.845   0.867   0.914
59    T         0.820   0.832   0.865   0.716   0.722   0.806   0.845   0.867   0.914
60    G         0.820   0.832   0.865   0.681   0.701   0.777   0.845   0.867   0.914
61    T         0.820   0.832   0.865   0.716   0.722   0.806   0.845   0.867   0.914
62    G         0.820   0.832   0.865   0.681   0.701   0.777   0.845   0.867   0.914
63    R         0.820   0.832   0.865   0.567   0.605   0.684   0.845   0.867   0.914
64    M         0.008  -0.166  -0.367   0.470   0.252  -0.101   0.012  -0.247  -0.593
65    R        -1.420  -1.193  -1.148  -1.828  -1.445  -1.380  -1.537  -1.259  -1.190
66    Y         0.008  -0.190  -0.359   0.409   0.123  -0.247   0.012  -0.282  -0.578
67    L         0.820   0.832   0.865   1.107   1.108   1.125   0.845   0.867   0.914
68    K         0.008  -0.166  -0.367  -0.215  -0.451  -0.725   0.012  -0.247  -0.593
69    H        -1.794  -1.944  -1.713  -1.666  -1.890  -1.598  -1.656  -1.791  -1.495
70    V         0.820   0.832   0.865   1.147   1.155   1.158   0.845   0.867   0.914
71    S        -1.794  -1.714  -1.692  -1.650  -1.498  -1.447  -1.656  -1.582  -1.475
72    R         0.820   0.832   0.865   0.567   0.605   0.684   0.845   0.867   0.914
73    R        -1.420  -1.398  -1.176  -1.976  -2.006  -1.592  -1.537  -1.527  -1.224
74    F         0.820   0.832   0.865   1.051   1.059   1.079   0.845   0.867   0.914
75    K         0.008  -0.190  -0.359  -0.237  -0.520  -0.777   0.012  -0.282  -0.578
76    N         0.820   0.832   0.865   1.059   1.073   1.085   0.845   0.867   0.914
77    G         0.820   0.832   0.865   0.681   0.701   0.777   0.845   0.867   0.914
78    F         0.820   0.832   0.865   1.051   1.059   1.079   0.845   0.867   0.914
79    Q        -0.469  -0.413  -0.395  -0.374  -0.295  -0.397  -0.710  -0.637  -0.640
80    T        -1.239  -1.148  -1.165  -1.418  -1.275  -1.316  -1.333  -1.218  -1.211
81    G         0.820   0.832   0.865   0.685   0.704   0.780   0.845   0.867   0.914
82    S        -1.932  -1.728  -1.704  -1.723  -1.452  -1.415  -1.799  -1.601  -1.486
83    A        -1.279  -1.353  -1.168  -1.221  -1.283  -1.067  -1.418  -1.481  -1.215
84    K        -1.493  -1.514  -1.687  -1.537  -1.565  -1.736  -1.299  -1.347  -1.470
85    A        -2.167  -2.262  -2.118  -1.963  -2.236  -2.015  -1.775  -1.879  -1.649
86    T        -1.885  -1.781  -1.709  -1.727  -1.621  -1.561  -1.775  -1.670  -1.491
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    S        -0.765  -0.875  -1.130  -0.684  -0.833  -1.249  -0.703  -0.861  -1.167
92    A         0.008  -0.190  -0.359   0.173  -0.028  -0.251   0.012  -0.282  -0.578
* 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/P51402
Output conservation file - output/P51402
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
