1     M         0.820   0.827   0.868   1.201   1.193   1.205   0.838   0.850   0.909
2     P        -1.532  -1.616  -1.353  -1.425  -1.642  -1.275  -1.544  -1.658  -1.321
3     K        -0.432  -0.460  -0.499  -0.581  -0.623  -0.602  -0.552  -0.608  -0.707
4     K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
5     R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
6     A        -1.186  -1.346  -1.329  -1.505  -1.780  -1.866  -1.147  -1.338  -1.295
7     S        -0.685  -0.718  -0.534  -0.726  -0.820  -0.557  -0.949  -1.025  -0.764
8     N        -0.005  -0.077  -0.464   0.292   0.210  -0.358   0.044  -0.055  -0.649
9     G         0.820   0.827   0.868   1.125   1.114   1.144   0.838   0.850   0.909
10    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
11    N         0.820   0.827   0.868   0.947   0.963   0.999   0.838   0.850   0.909
12    K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
13    K        -0.432  -0.460  -0.499  -0.599  -0.639  -0.631  -0.552  -0.608  -0.707
14    G         0.820   0.827   0.868   1.125   1.114   1.144   0.838   0.850   0.909
15    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
16    G         0.820   0.827   0.868   1.125   1.114   1.144   0.838   0.850   0.909
17    H         0.820   0.827   0.868   1.172   1.174   1.182   0.838   0.850   0.909
18    V        -0.005  -0.077  -0.464   0.066  -0.021  -0.503   0.044  -0.055  -0.649
19    K        -0.005  -0.128  -0.466  -0.086  -0.226  -0.614   0.044  -0.125  -0.653
20    P        -1.186  -1.308  -1.325  -0.832  -1.008  -1.070  -1.147  -1.295  -1.289
21    V        -0.432  -0.581  -0.527  -0.514  -0.769  -0.672  -0.552  -0.800  -0.752
22    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
23    C         0.820   0.827   0.868   1.084   1.083   1.111   0.838   0.850   0.909
24    V        -2.416  -2.293  -1.935  -2.368  -2.215  -1.703  -2.140  -2.019  -1.602
25    N         0.820   0.827   0.868   0.947   0.963   0.999   0.838   0.850   0.909
26    C         0.820   0.827   0.868   1.084   1.083   1.111   0.838   0.850   0.909
27    S        -0.685  -0.614  -0.524  -0.875  -0.763  -0.712  -0.949  -0.853  -0.749
28    K        -0.685  -0.484  -0.502  -1.431  -1.075  -1.085  -0.949  -0.646  -0.712
29    S        -2.279  -2.245  -1.927  -2.126  -2.079  -1.629  -2.040  -1.981  -1.595
30    I        -0.797  -0.818  -1.294  -0.593  -0.644  -1.216  -0.651  -0.703  -1.253
31    P         0.820   0.827   0.868   0.947   0.962   0.999   0.838   0.850   0.909
32    K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
33    D         0.820   0.827   0.868   1.114   1.119   1.134   0.838   0.850   0.909
34    K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
35    A         0.820   0.827   0.868   0.619   0.667   0.733   0.838   0.850   0.909
36    I         0.820   0.827   0.868   0.959   0.955   1.009   0.838   0.850   0.909
37    K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
38    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
39    M        -2.416  -2.293  -1.935  -1.912  -1.752  -1.365  -2.140  -2.019  -1.602
40    A        -1.395  -1.284  -1.314  -1.288  -1.058  -1.200  -1.445  -1.275  -1.277
41    I         0.820   0.827   0.868   0.959   0.955   1.009   0.838   0.850   0.909
42    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
43    N         0.820   0.827   0.868   0.947   0.963   0.999   0.838   0.850   0.909
44    I        -0.685  -0.482  -0.497  -0.469  -0.163  -0.295  -0.949  -0.642  -0.703
45    V         0.820   0.827   0.868   0.714   0.726   0.810   0.838   0.850   0.909
46    E         0.820   0.827   0.868   1.125   1.124   1.144   0.838   0.850   0.909
47    A        -1.186  -1.346  -1.329  -1.184  -1.381  -1.321  -1.147  -1.338  -1.295
48    A         0.820   0.827   0.868   0.619   0.667   0.733   0.838   0.850   0.909
49    A        -0.005  -0.128  -0.466  -0.057  -0.174  -0.667   0.044  -0.125  -0.653
50    V        -0.804  -0.658  -0.515  -1.065  -0.804  -0.615  -1.147  -0.925  -0.733
51    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
52    D         0.820   0.827   0.868   1.114   1.119   1.134   0.838   0.850   0.909
53    L        -0.005  -0.177  -0.468   0.442   0.244  -0.301   0.044  -0.192  -0.657
54    S         0.820   0.827   0.868   0.923   0.930   0.980   0.838   0.850   0.909
55    E        -0.005  -0.177  -0.468   0.472   0.252  -0.230   0.044  -0.192  -0.657
56    A         0.820   0.827   0.868   0.619   0.667   0.733   0.838   0.850   0.909
57    S         0.820   0.827   0.868   0.923   0.930   0.980   0.838   0.850   0.909
58    V         0.820   0.827   0.868   0.714   0.726   0.810   0.838   0.850   0.909
59    Y        -0.005  -0.177  -0.468   0.461   0.246  -0.192   0.044  -0.192  -0.657
60    P        -2.052  -1.969  -1.907  -1.975  -1.866  -1.699  -1.842  -1.760  -1.579
61    E         0.820   0.827   0.868   1.125   1.124   1.144   0.838   0.850   0.909
62    Y         0.820   0.827   0.868   1.096   1.095   1.120   0.838   0.850   0.909
63    A        -1.532  -1.562  -1.353  -1.725  -1.763  -1.441  -1.544  -1.592  -1.321
64    L        -1.186  -1.346  -1.329  -0.800  -1.054  -1.190  -1.147  -1.338  -1.295
65    P         0.820   0.827   0.868   0.947   0.962   0.999   0.838   0.850   0.909
66    K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
67    T        -2.052  -2.081  -1.910  -1.527  -1.537  -1.374  -1.842  -1.825  -1.580
68    Y         0.820   0.827   0.868   1.096   1.095   1.120   0.838   0.850   0.909
69    N        -1.897  -2.012  -1.926  -1.519  -1.711  -1.656  -1.643  -1.780  -1.594
70    K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
71    L        -0.005  -0.128  -0.466   0.442   0.308  -0.297   0.044  -0.125  -0.653
72    H        -0.804  -0.737  -0.528  -0.574  -0.497  -0.239  -1.147  -1.057  -0.755
73    Y         0.820   0.827   0.868   1.096   1.095   1.120   0.838   0.850   0.909
74    C         0.820   0.827   0.868   1.084   1.083   1.111   0.838   0.850   0.909
75    V        -0.005   0.172  -0.455   0.043   0.231  -0.565   0.044   0.258  -0.636
76    S         0.820   0.827   0.868   0.923   0.930   0.980   0.838   0.850   0.909
77    C         0.820   0.827   0.868   1.084   1.083   1.111   0.838   0.850   0.909
78    A         0.820   0.827   0.868   0.619   0.667   0.733   0.838   0.850   0.909
79    I         0.820   0.827   0.868   0.959   0.955   1.009   0.838   0.850   0.909
80    H         0.820   0.827   0.868   1.172   1.174   1.182   0.838   0.850   0.909
81    A        -1.186  -1.369  -1.332  -1.221  -1.446  -1.336  -1.147  -1.369  -1.299
82    R        -0.432  -0.581  -0.527  -0.973  -1.254  -1.128  -0.552  -0.800  -0.752
83    I        -0.685  -0.707  -0.533  -0.798  -0.912  -0.662  -0.949  -1.007  -0.763
84    V         0.820   0.827   0.868   0.714   0.726   0.810   0.838   0.850   0.909
85    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
86    V         0.820   0.827   0.868   0.714   0.726   0.810   0.838   0.850   0.909
87    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
88    S         0.820   0.827   0.868   0.923   0.930   0.980   0.838   0.850   0.909
89    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
90    E        -0.685  -0.486  -0.505  -0.462  -0.182  -0.283  -0.949  -0.648  -0.716
91    D        -1.461  -1.244  -1.330  -1.221  -0.943  -1.143  -1.544  -1.300  -1.296
92    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
93    K        -0.685  -0.619  -0.530  -1.431  -1.327  -1.133  -0.949  -0.861  -0.757
94    N        -1.186  -1.300  -1.329  -0.952  -1.158  -1.285  -1.147  -1.285  -1.296
95    R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
96    A        -0.804  -0.721  -0.532  -0.982  -0.842  -0.598  -1.147  -1.031  -0.761
97    P         0.820   0.827   0.868   0.947   0.962   0.999   0.838   0.850   0.909
98    P         0.820   0.827   0.868   0.947   0.962   0.999   0.838   0.850   0.909
99    Q        -0.685  -0.718  -0.534  -0.449  -0.580  -0.369  -0.949  -1.025  -0.764
100   R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
101   P        -1.688  -1.415  -1.333  -2.013  -1.593  -1.517  -1.743  -1.418  -1.299
102   R         0.820   0.827   0.868   0.372   0.396   0.532   0.838   0.850   0.909
103   F        -0.685  -0.718  -0.534  -0.364  -0.486  -0.276  -0.949  -1.025  -0.764
104   N        -0.432  -0.244  -0.481  -0.238   0.006  -0.365  -0.552  -0.287  -0.677
105   R        -1.897  -1.766  -1.914  -2.339  -2.264  -2.320  -1.643  -1.572  -1.585
106   D        -0.005   0.140  -0.457   0.462   0.608  -0.214   0.044   0.219  -0.638
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   N        -1.395  -1.126  -1.310  -1.729  -1.338  -1.654  -1.445  -1.113  -1.273
109   K        -0.005  -0.077  -0.464  -0.185  -0.283  -0.950   0.044  -0.055  -0.649
110   V        -0.005  -0.128  -0.466   0.043  -0.111  -0.582   0.044  -0.125  -0.653
111   S        -1.461  -1.481  -1.328  -1.394  -1.380  -1.142  -1.544  -1.524  -1.294
112   P         0.820   0.827   0.868   0.947   0.962   0.999   0.838   0.850   0.909
113   A        -1.186  -1.157  -1.318  -1.131  -1.118  -1.184  -1.147  -1.159  -1.282
114   A        -1.461  -1.479  -1.325  -1.467  -1.469  -1.196  -1.544  -1.521  -1.291
115   A        -1.551  -1.743  -1.909  -1.375  -1.610  -1.830  -1.246  -1.460  -1.579
116   A         0.820   0.827   0.868   0.619   0.667   0.733   0.838   0.850   0.909
117   K         0.820   0.827   0.868   0.562   0.581   0.686   0.838   0.850   0.909
118   K        -1.897  -2.034  -1.925  -1.876  -2.076  -1.834  -1.643  -1.795  -1.594
119   A        -0.071  -0.195  -0.472  -0.196  -0.325  -0.791  -0.042  -0.217  -0.663
120   L        -1.308  -1.325  -1.330  -0.999  -1.054  -1.206  -1.298  -1.299  -1.296
* 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/P39939
Output conservation file - output/P39939
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
