1     M         0.823   0.830   0.868   1.208   1.199   1.206   0.842   0.854   0.909
2     P        -1.529  -1.612  -1.352  -1.429  -1.644  -1.276  -1.540  -1.653  -1.321
3     K        -0.429  -0.459  -0.499  -0.581  -0.624  -0.603  -0.548  -0.607  -0.706
4     K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
5     R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
6     A        -1.183  -1.344  -1.329  -1.503  -1.781  -1.863  -1.143  -1.335  -1.294
7     S        -0.682  -0.715  -0.533  -0.727  -0.819  -0.558  -0.945  -1.021  -0.763
8     N        -0.002  -0.076  -0.463   0.295   0.210  -0.359   0.048  -0.054  -0.649
9     G         0.823   0.830   0.868   1.132   1.119   1.144   0.842   0.854   0.909
10    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
11    N         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
12    K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
13    K        -0.429  -0.459  -0.499  -0.599  -0.640  -0.632  -0.548  -0.607  -0.706
14    G         0.823   0.830   0.868   1.132   1.119   1.144   0.842   0.854   0.909
15    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
16    G         0.823   0.830   0.868   1.132   1.119   1.144   0.842   0.854   0.909
17    H         0.823   0.830   0.868   1.179   1.179   1.182   0.842   0.854   0.909
18    V        -0.002  -0.076  -0.463   0.068  -0.021  -0.504   0.048  -0.054  -0.649
19    K        -0.002  -0.127  -0.466  -0.085  -0.226  -0.615   0.048  -0.123  -0.653
20    P        -1.183  -1.307  -1.325  -0.833  -1.012  -1.072  -1.143  -1.294  -1.290
21    V        -0.429  -0.578  -0.526  -0.514  -0.769  -0.673  -0.548  -0.796  -0.751
22    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
23    C         0.823   0.830   0.868   1.091   1.088   1.111   0.842   0.854   0.909
24    V        -2.413  -2.287  -1.934  -2.376  -2.213  -1.704  -2.135  -2.011  -1.601
25    N         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
26    C         0.823   0.830   0.868   1.091   1.088   1.111   0.842   0.854   0.909
27    S        -0.682  -0.610  -0.524  -0.873  -0.759  -0.710  -0.945  -0.848  -0.748
28    K        -0.682  -0.475  -0.500  -1.435  -1.065  -1.084  -0.945  -0.633  -0.709
29    S        -2.276  -2.239  -1.926  -2.130  -2.078  -1.627  -2.036  -1.974  -1.594
30    I        -0.793  -0.829  -1.293  -0.593  -0.659  -1.217  -0.647  -0.714  -1.252
31    P         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
32    K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
33    D         0.823   0.830   0.868   1.120   1.124   1.135   0.842   0.854   0.909
34    K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
35    A         0.823   0.830   0.868   0.630   0.677   0.738   0.842   0.854   0.909
36    I         0.823   0.830   0.868   0.965   0.960   1.009   0.842   0.854   0.909
37    K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
38    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
39    M        -2.413  -2.287  -1.934  -1.918  -1.749  -1.366  -2.135  -2.011  -1.601
40    A        -1.392  -1.277  -1.312  -1.288  -1.050  -1.196  -1.441  -1.266  -1.275
41    I         0.823   0.830   0.868   0.965   0.960   1.009   0.842   0.854   0.909
42    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
43    N         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
44    I        -0.682  -0.473  -0.495  -0.469  -0.152  -0.293  -0.945  -0.629  -0.700
45    V         0.823   0.830   0.868   0.719   0.731   0.810   0.842   0.854   0.909
46    E         0.823   0.830   0.868   1.126   1.125   1.139   0.842   0.854   0.909
47    A        -1.183  -1.344  -1.329  -1.181  -1.378  -1.319  -1.143  -1.335  -1.294
48    A         0.823   0.830   0.868   0.630   0.677   0.738   0.842   0.854   0.909
49    A        -0.002  -0.127  -0.466  -0.048  -0.169  -0.663   0.048  -0.123  -0.653
50    V        -0.801  -0.651  -0.513  -1.067  -0.795  -0.613  -1.143  -0.914  -0.731
51    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
52    D         0.823   0.830   0.868   1.120   1.124   1.135   0.842   0.854   0.909
53    L        -0.002  -0.173  -0.468   0.446   0.248  -0.302   0.048  -0.188  -0.656
54    S         0.823   0.830   0.868   0.929   0.935   0.980   0.842   0.854   0.909
55    E        -0.002  -0.173  -0.468   0.471   0.251  -0.234   0.048  -0.188  -0.656
56    A         0.823   0.830   0.868   0.630   0.677   0.738   0.842   0.854   0.909
57    S         0.823   0.830   0.868   0.929   0.935   0.980   0.842   0.854   0.909
58    V         0.823   0.830   0.868   0.719   0.731   0.810   0.842   0.854   0.909
59    Y        -0.002  -0.173  -0.468   0.465   0.249  -0.193   0.048  -0.188  -0.656
60    P        -2.049  -1.976  -1.906  -1.977  -1.875  -1.698  -1.838  -1.762  -1.578
61    E         0.823   0.830   0.868   1.126   1.125   1.139   0.842   0.854   0.909
62    Y         0.823   0.830   0.868   1.102   1.100   1.120   0.842   0.854   0.909
63    A        -1.529  -1.550  -1.352  -1.724  -1.747  -1.438  -1.540  -1.578  -1.320
64    L        -1.183  -1.344  -1.329  -0.801  -1.057  -1.191  -1.143  -1.335  -1.294
65    P         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
66    K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
67    T        -2.049  -2.075  -1.909  -1.531  -1.535  -1.375  -1.838  -1.817  -1.579
68    Y         0.823   0.830   0.868   1.102   1.100   1.120   0.842   0.854   0.909
69    N        -1.894  -2.011  -1.926  -1.523  -1.716  -1.658  -1.639  -1.777  -1.594
70    K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
71    L        -0.002  -0.127  -0.466   0.446   0.309  -0.297   0.048  -0.123  -0.653
72    H        -0.801  -0.731  -0.527  -0.574  -0.492  -0.238  -1.143  -1.048  -0.753
73    Y         0.823   0.830   0.868   1.102   1.100   1.120   0.842   0.854   0.909
74    C         0.823   0.830   0.868   1.091   1.088   1.111   0.842   0.854   0.909
75    V        -0.002   0.176  -0.455   0.045   0.236  -0.566   0.048   0.263  -0.635
76    S         0.823   0.830   0.868   0.929   0.935   0.980   0.842   0.854   0.909
77    C         0.823   0.830   0.868   1.091   1.088   1.111   0.842   0.854   0.909
78    A         0.823   0.830   0.868   0.630   0.677   0.738   0.842   0.854   0.909
79    I         0.823   0.830   0.868   0.965   0.960   1.009   0.842   0.854   0.909
80    H         0.823   0.830   0.868   1.179   1.179   1.182   0.842   0.854   0.909
81    A        -1.183  -1.367  -1.331  -1.218  -1.444  -1.333  -1.143  -1.366  -1.298
82    R        -0.429  -0.578  -0.526  -0.975  -1.255  -1.129  -0.548  -0.796  -0.751
83    I        -0.682  -0.704  -0.533  -0.800  -0.914  -0.664  -0.945  -1.004  -0.762
84    V         0.823   0.830   0.868   0.719   0.731   0.810   0.842   0.854   0.909
85    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
86    V         0.823   0.830   0.868   0.719   0.731   0.810   0.842   0.854   0.909
87    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
88    S         0.823   0.830   0.868   0.929   0.935   0.980   0.842   0.854   0.909
89    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
90    E        -0.682  -0.480  -0.504  -0.466  -0.181  -0.288  -0.945  -0.641  -0.715
91    D        -1.458  -1.221  -1.329  -1.223  -0.921  -1.141  -1.540  -1.280  -1.295
92    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
93    K        -0.682  -0.620  -0.530  -1.435  -1.336  -1.135  -0.945  -0.865  -0.757
94    N        -1.183  -1.304  -1.328  -0.953  -1.170  -1.286  -1.143  -1.290  -1.295
95    R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
96    A        -0.801  -0.719  -0.531  -0.980  -0.842  -0.595  -1.143  -1.028  -0.760
97    P         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
98    P         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
99    Q        -0.682  -0.715  -0.533  -0.448  -0.580  -0.370  -0.945  -1.021  -0.763
100   R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
101   P        -1.685  -1.405  -1.332  -2.019  -1.585  -1.518  -1.738  -1.406  -1.297
102   R         0.823   0.830   0.868   0.376   0.401   0.532   0.842   0.854   0.909
103   F        -0.682  -0.715  -0.533  -0.363  -0.486  -0.277  -0.945  -1.021  -0.763
104   N        -0.429  -0.239  -0.481  -0.237   0.011  -0.366  -0.548  -0.280  -0.677
105   R        -1.894  -1.760  -1.914  -2.345  -2.263  -2.318  -1.639  -1.566  -1.584
106   E        -0.429  -0.228  -0.474  -0.080   0.179  -0.245  -0.548  -0.265  -0.666
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   N        -1.392  -1.116  -1.309  -1.734  -1.329  -1.655  -1.441  -1.101  -1.271
109   K        -0.002  -0.076  -0.463  -0.184  -0.283  -0.951   0.048  -0.054  -0.649
110   V        -0.002  -0.127  -0.466   0.045  -0.111  -0.583   0.048  -0.123  -0.653
111   S        -1.458  -1.475  -1.327  -1.397  -1.376  -1.142  -1.540  -1.515  -1.293
112   P         0.823   0.830   0.868   0.953   0.968   0.999   0.842   0.854   0.909
113   A        -1.183  -1.153  -1.317  -1.128  -1.113  -1.181  -1.143  -1.154  -1.282
114   D        -1.392  -1.497  -1.341  -1.253  -1.444  -1.193  -1.441  -1.547  -1.309
115   A        -1.548  -1.742  -1.908  -1.372  -1.611  -1.827  -1.242  -1.458  -1.578
116   A         0.823   0.830   0.868   0.630   0.677   0.738   0.842   0.854   0.909
117   K         0.823   0.830   0.868   0.566   0.586   0.686   0.842   0.854   0.909
118   K        -1.894  -2.032  -1.925  -1.882  -2.080  -1.835  -1.639  -1.792  -1.593
119   A        -0.068  -0.195  -0.472  -0.188  -0.323  -0.787  -0.037  -0.218  -0.663
120   L        -1.305  -1.321  -1.330  -1.001  -1.054  -1.207  -1.293  -1.295  -1.295
* 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/P39938
Output conservation file - output/P39938
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
