1     M         1.490   1.526   1.610   1.831   1.872   1.985   1.634   1.688   1.831
2     S         1.490   1.526   1.610   1.628   1.656   1.790   1.634   1.688   1.831
3     Q         0.230   0.294   0.403  -0.098  -0.057   0.128  -0.189  -0.081   0.073
4     K         0.267   0.358   0.434  -0.050   0.149   0.212  -0.116   0.044   0.135
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     N        -0.792  -0.836  -0.775  -0.636  -0.736  -0.721  -0.873  -0.893  -0.794
8     G         0.805   0.786   0.617   1.127   1.102   0.799   0.836   0.803   0.486
9     I         1.490   1.526   1.610   1.590   1.631   1.754   1.634   1.688   1.831
10    A         0.287   0.402   0.442   0.122   0.327   0.341  -0.075   0.129   0.150
11    T        -1.541  -1.595  -1.520  -1.179  -1.300  -1.280  -1.215  -1.253  -1.131
12    L         1.490   1.526   1.610   1.569   1.629   1.733   1.634   1.688   1.831
13    L         1.490   1.526   1.610   1.569   1.629   1.733   1.634   1.688   1.831
14    Q        -0.715  -0.855  -0.760  -0.961  -1.142  -0.986  -0.759  -0.900  -0.778
15    A         0.468   0.582   0.519   0.278   0.414   0.354   0.267   0.460   0.300
16    E         1.490   1.526   1.610   1.169   1.213   1.349   1.634   1.688   1.831
17    K         0.805   0.729   0.599   0.554   0.499   0.342   0.836   0.711   0.453
18    E        -0.461  -0.570  -0.676  -0.553  -0.701  -0.865  -0.417  -0.554  -0.672
19    A         1.490   1.526   1.610   1.251   1.276   1.427   1.634   1.688   1.831
20    H        -0.715  -0.818  -0.757  -0.336  -0.440  -0.400  -0.759  -0.852  -0.769
21    E         0.153  -0.059  -0.149  -0.006  -0.284  -0.453   0.153  -0.150  -0.298
22    I         1.490   1.526   1.610   1.590   1.631   1.754   1.634   1.688   1.831
23    V         1.490   1.526   1.610   1.638   1.687   1.800   1.634   1.688   1.831
24    S        -1.660  -1.566  -1.522  -1.308  -1.252  -1.186  -1.329  -1.238  -1.133
25    K         0.287   0.394   0.432  -0.416  -0.190  -0.197  -0.075   0.114   0.130
26    A         1.490   1.526   1.610   1.251   1.276   1.427   1.634   1.688   1.831
27    R         1.490   1.526   1.610   1.733   1.757   1.891   1.634   1.688   1.831
28    K        -0.715  -0.820  -0.764  -0.936  -1.048  -0.939  -0.759  -0.871  -0.783
29    Y         0.468   0.446   0.445   0.841   0.803   0.769   0.267   0.212   0.155
30    R         1.490   1.526   1.610   1.733   1.757   1.891   1.634   1.688   1.831
31    Q         0.287   0.402   0.442   0.358   0.544   0.568  -0.075   0.129   0.150
32    D        -1.660  -1.557  -1.515  -1.537  -1.380  -1.297  -1.329  -1.227  -1.129
33    K        -0.281  -0.167  -0.237  -0.350  -0.158  -0.271  -0.531  -0.382  -0.441
34    L         0.153   0.171  -0.109   0.468   0.502   0.117   0.153   0.169  -0.239
35    K         0.805   0.729   0.599   0.554   0.499   0.342   0.836   0.711   0.453
36    Q        -1.226  -1.198  -1.181  -0.883  -0.898  -0.852  -1.101  -1.070  -0.995
37    A         1.490   1.526   1.610   1.251   1.276   1.427   1.634   1.688   1.831
38    K         0.468   0.364   0.424   0.147   0.032   0.135   0.267   0.057   0.114
39    T        -1.660  -1.577  -1.505  -1.231  -1.118  -1.043  -1.329  -1.247  -1.122
40    D         0.468   0.364   0.424   0.511   0.269   0.290   0.267   0.057   0.114
41    A         1.490   1.526   1.610   1.251   1.276   1.427   1.634   1.688   1.831
42    A        -0.911  -0.828  -0.792  -1.217  -1.198  -1.053  -0.987  -0.901  -0.813
43    K        -0.792  -0.820  -0.751  -1.145  -1.147  -0.985  -0.873  -0.885  -0.771
44    E         0.805   0.786   0.617   0.619   0.601   0.410   0.836   0.803   0.486
45    I         1.490   1.526   1.610   1.590   1.631   1.754   1.634   1.688   1.831
46    D        -0.281  -0.200  -0.239  -0.352  -0.280  -0.290  -0.531  -0.441  -0.446
47    S        -0.911  -0.814  -0.783  -1.134  -1.083  -0.929  -0.987  -0.880  -0.803
48    Y         1.490   1.526   1.610   1.800   1.842   1.955   1.634   1.688   1.831
49    K         0.805   0.676   0.602   0.477   0.320   0.169   0.836   0.621   0.457
50    I        -0.911  -0.858  -0.799  -1.265  -1.185  -1.042  -0.987  -0.931  -0.821
51    Q         0.230   0.267   0.387  -0.171  -0.124   0.058  -0.189  -0.135   0.039
52    K         1.490   1.526   1.610   1.092   1.166   1.275   1.634   1.688   1.831
53    D         0.805   0.915   0.622   0.619   0.745   0.417   0.836   1.002   0.495
54    K        -1.226  -1.139  -1.147  -1.431  -1.341  -1.362  -1.101  -0.994  -0.962
55    E         0.805   0.786   0.617   0.619   0.601   0.410   0.836   0.803   0.486
56    L         0.287   0.267   0.387   0.381   0.372   0.533  -0.075  -0.135   0.040
57    K         0.805   0.786   0.617   0.537   0.546   0.327   0.836   0.803   0.486
58    E        -0.715  -0.497  -0.697  -0.906  -0.600  -0.882  -0.759  -0.488  -0.700
59    F        -0.461  -0.570  -0.676   0.227   0.067  -0.075  -0.417  -0.554  -0.672
60    E         0.805   0.786   0.617   0.533   0.508   0.219   0.836   0.803   0.486
61    Q        -1.345  -1.293  -1.188  -1.466  -1.356  -1.153  -1.215  -1.152  -1.001
62    K        -1.541  -1.480  -1.495  -1.639  -1.564  -1.577  -1.215  -1.153  -1.112
63    N        -0.792  -0.864  -0.773  -0.396  -0.505  -0.404  -0.873  -0.922  -0.792
64    A        -0.911  -0.922  -0.800  -1.173  -1.108  -0.930  -0.987  -0.981  -0.821
65    G         0.805   0.729   0.599   1.186   1.096   0.899   0.836   0.711   0.453
66    G        -0.715  -0.781  -0.742  -0.292  -0.362  -0.345  -0.759  -0.812  -0.752
67    V        -0.281  -0.314  -0.239  -0.005   0.008   0.094  -0.531  -0.537  -0.439
68    G        -1.226  -1.264  -1.174  -1.108  -1.130  -0.929  -1.101  -1.124  -0.989
69    E        -1.660  -1.656  -1.522  -1.931  -1.916  -1.643  -1.329  -1.306  -1.134
70    L        -0.477  -0.376  -0.289  -0.667  -0.572  -0.423  -0.759  -0.617  -0.504
71    E        -0.146  -0.138  -0.195  -0.307  -0.286  -0.331  -0.303  -0.269  -0.368
72    K        -0.146  -0.286  -0.248  -0.658  -0.912  -0.899  -0.303  -0.505  -0.452
73    K        -0.146   0.008  -0.162  -0.534  -0.270  -0.535  -0.303  -0.071  -0.320
74    A         0.805   0.676   0.602   0.697   0.520   0.455   0.836   0.621   0.457
75    E        -0.792  -0.894  -0.771  -0.901  -1.064  -0.887  -0.873  -0.951  -0.791
76    A        -0.461  -0.538  -0.678  -0.557  -0.749  -0.961  -0.417  -0.518  -0.674
77    G        -0.911  -0.853  -0.791  -0.948  -0.888  -0.722  -0.987  -0.925  -0.812
78    V         0.468   0.415   0.440   0.520   0.394   0.359   0.267   0.153   0.146
79    Q        -0.281  -0.283  -0.250  -0.512  -0.530  -0.534  -0.531  -0.522  -0.458
80    G        -1.660  -1.638  -1.513  -1.290  -1.281  -1.145  -1.329  -1.295  -1.128
81    E         0.153  -0.059  -0.149   0.101  -0.147  -0.222   0.153  -0.150  -0.298
82    L         0.153  -0.059  -0.149   0.499   0.260   0.122   0.153  -0.150  -0.298
83    A        -1.030  -0.877  -1.082  -0.936  -0.745  -0.998  -0.873  -0.705  -0.894
84    E        -0.146  -0.121  -0.223  -0.310  -0.293  -0.355  -0.303  -0.284  -0.417
85    I         1.490   1.526   1.610   1.590   1.631   1.754   1.634   1.688   1.831
86    K         0.805   0.676   0.602   0.465   0.306   0.140   0.836   0.621   0.457
87    K        -0.911  -0.939  -0.794  -1.288  -1.290  -1.090  -0.987  -0.994  -0.815
88    I        -1.660  -1.583  -1.515  -1.531  -1.466  -1.355  -1.329  -1.248  -1.129
89    A        -1.345  -1.303  -1.202  -0.964  -0.888  -0.760  -1.215  -1.159  -1.013
90    E        -1.030  -1.097  -1.132  -0.901  -0.980  -0.947  -0.873  -0.945  -0.945
91    K         0.153   0.312  -0.078  -0.090   0.136  -0.422   0.153   0.375  -0.193
92    K        -0.146  -0.260  -0.248  -0.433  -0.537  -0.535  -0.303  -0.482  -0.453
93    K        -0.715  -0.854  -0.766  -1.054  -1.181  -1.048  -0.759  -0.898  -0.784
94    D        -0.715  -0.678  -0.725  -0.668  -0.633  -0.779  -0.759  -0.710  -0.738
95    D        -1.226  -1.206  -1.167  -1.003  -1.035  -1.006  -1.101  -1.075  -0.983
96    V         1.490   1.526   1.610   1.638   1.687   1.800   1.634   1.688   1.831
97    V         0.153   0.037  -0.131   0.525   0.386   0.122   0.153  -0.010  -0.271
98    K         0.468   0.452   0.441   0.117   0.121   0.105   0.267   0.223   0.148
99    I        -1.030  -1.160  -1.147  -0.760  -1.005  -1.053  -0.873  -1.008  -0.959
100   L         0.468   0.428   0.442   0.558   0.499   0.473   0.267   0.179   0.150
101   I        -0.477  -0.401  -0.289  -0.418  -0.302  -0.161  -0.759  -0.655  -0.506
102   E        -1.226  -1.251  -1.178  -1.093  -1.039  -1.041  -1.101  -1.105  -0.990
103   T        -0.461  -0.542  -0.673  -0.459  -0.607  -0.769  -0.417  -0.523  -0.668
104   V        -0.146  -0.121  -0.223   0.075   0.102  -0.093  -0.303  -0.284  -0.417
105   I        -1.327  -1.340  -1.201  -0.853  -0.833  -0.677  -1.194  -1.187  -1.012
106   K         0.249   0.265   0.387  -0.165  -0.073   0.102  -0.152  -0.139   0.040
107   P         1.490   1.526   1.610   1.823   1.865   1.977   1.634   1.688   1.831
108   S        -0.247  -0.317  -0.264  -0.085  -0.206  -0.202  -0.450  -0.545  -0.475
109   A        -0.607  -0.409  -0.704  -0.049   0.219  -0.254  -0.599  -0.345  -0.705
110   E         0.042   0.067  -0.152  -0.066  -0.045  -0.289  -0.003   0.025  -0.302
111   V        -1.191  -1.162  -1.173  -0.764  -0.781  -0.783  -1.045  -1.011  -0.984
112   H         1.490   1.526   1.610   1.802   1.847   1.957   1.634   1.688   1.831
113   I        -0.461  -0.582  -0.698   0.059  -0.070  -0.196  -0.417  -0.573  -0.698
114   N         0.805   0.729   0.599   1.106   1.005   0.760   0.836   0.711   0.453
115   A         0.805   0.676   0.602   0.699   0.527   0.459   0.836   0.621   0.457
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   L        -1.687  -1.558  -1.518  -1.594  -1.401  -1.322  -1.343  -1.220  -1.129
* 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/P48836
Output conservation file - output/P48836
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
