1     M         1.466   1.500   1.578   1.619   1.672   1.792   1.564   1.610   1.726
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    G        -0.391  -0.142  -0.379  -0.706  -0.394  -0.662  -0.507  -0.180  -0.476
13    P         0.306   0.515   0.377   0.006   0.270   0.127   0.102   0.438   0.161
14    P        -0.544  -0.470  -0.429  -0.820  -0.660  -0.605  -0.751  -0.613  -0.546
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    S        -1.168  -1.096  -1.006  -1.246  -1.214  -0.982  -1.141  -1.044  -0.897
17    G        -0.760  -0.610  -0.487  -1.235  -1.035  -0.803  -0.982  -0.776  -0.619
18    K        -0.051   0.011  -0.327   0.097   0.159  -0.321  -0.019   0.058  -0.402
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    T        -0.766  -0.730  -0.516  -0.986  -0.890  -0.575  -0.994  -0.935  -0.656
22    Y         1.466   1.500   1.578   1.334   1.407   1.533   1.564   1.610   1.726
23    M         0.306   0.199   0.284   0.396   0.184   0.277   0.102  -0.102  -0.009
24    G         1.466   1.500   1.578   1.206   1.216   1.417   1.564   1.610   1.726
25    W         0.689   0.560   0.433   0.843   0.660   0.416   0.712   0.510   0.260
26    W         1.466   1.500   1.578   1.551   1.615   1.730   1.564   1.610   1.726
27    G         1.466   1.500   1.578   1.206   1.216   1.417   1.564   1.610   1.726
28    H        -0.679  -0.602  -0.495  -0.650  -0.540  -0.439  -0.872  -0.769  -0.629
29    M        -1.258  -1.247  -1.028  -1.191  -1.182  -0.857  -1.238  -1.189  -0.922
30    G         1.466   1.500   1.578   1.206   1.216   1.417   1.564   1.610   1.726
31    G         0.101   0.108   0.256  -0.223  -0.295  -0.037  -0.263  -0.270  -0.061
32    P         0.689   0.560   0.433   0.847   0.702   0.511   0.712   0.510   0.260
33    K        -0.051  -0.008  -0.333   0.079   0.153  -0.369  -0.019   0.035  -0.411
34    Q         1.466   1.500   1.578   1.589   1.653   1.765   1.564   1.610   1.726
35    K         0.689   0.560   0.433   0.776   0.623   0.422   0.712   0.510   0.260
36    G         0.306   0.433   0.354  -0.050   0.106   0.015   0.102   0.305   0.120
37    I         0.689   0.774   0.459   0.862   0.974   0.534   0.712   0.831   0.307
38    T        -0.391  -0.514  -0.457  -0.332  -0.561  -0.501  -0.507  -0.682  -0.585
39    S        -1.124  -1.045  -0.987  -1.103  -1.033  -0.911  -1.116  -1.016  -0.883
40    Y         1.466   1.500   1.578   1.334   1.407   1.533   1.564   1.610   1.726
41    A        -1.036  -1.008  -0.995  -1.006  -1.021  -1.039  -0.994  -0.957  -0.888
42    V        -0.544  -0.585  -0.451  -0.624  -0.640  -0.460  -0.751  -0.775  -0.581
43    S         1.466   1.500   1.578   1.498   1.558   1.682   1.564   1.610   1.726
44    P         1.466   1.500   1.578   1.498   1.565   1.682   1.564   1.610   1.726
45    Y        -0.391  -0.552  -0.457  -0.485  -0.718  -0.573  -0.507  -0.715  -0.586
46    A        -0.051  -0.277  -0.379  -0.054  -0.327  -0.477  -0.019  -0.320  -0.473
47    Q        -0.391  -0.298  -0.422  -0.328  -0.191  -0.437  -0.507  -0.385  -0.539
48    K        -0.391  -0.552  -0.457  -0.390  -0.635  -0.511  -0.507  -0.715  -0.586
49    P         1.466   1.500   1.578   1.498   1.565   1.682   1.564   1.610   1.726
50    L        -0.051  -0.198  -0.354   0.166  -0.022  -0.251  -0.019  -0.214  -0.439
51    Q        -1.036  -0.769  -0.949  -1.150  -0.758  -0.987  -0.994  -0.680  -0.836
52    G        -0.051   0.204  -0.310  -0.100   0.166  -0.413  -0.019   0.313  -0.379
53    I        -2.108  -2.077  -1.829  -1.988  -1.930  -1.585  -1.603  -1.539  -1.249
54    F        -1.616  -1.496  -1.433  -1.537  -1.409  -1.295  -1.360  -1.235  -1.090
55    H        -0.391  -0.383  -0.403  -0.258  -0.228  -0.332  -0.507  -0.470  -0.508
56    N        -0.748  -0.990  -0.980  -0.504  -0.799  -0.858  -0.629  -0.900  -0.867
57    A         0.306   0.296   0.296   0.053   0.055   0.033   0.102   0.071   0.013
58    V        -0.051  -0.198  -0.354   0.146   0.006  -0.283  -0.019  -0.214  -0.439
59    F         0.689   0.593   0.443   0.866   0.739   0.536   0.712   0.561   0.278
60    N         1.466   1.500   1.578   1.452   1.551   1.640   1.564   1.610   1.726
61    S        -0.748  -0.668  -0.911  -0.422  -0.317  -0.682  -0.629  -0.537  -0.791
62    F         1.466   1.500   1.578   1.521   1.562   1.703   1.564   1.610   1.726
63    R         1.466   1.500   1.578   1.498   1.550   1.682   1.564   1.610   1.726
64    R         1.466   1.500   1.578   1.498   1.550   1.682   1.564   1.610   1.726
65    F        -0.391  -0.232  -0.403  -0.351  -0.097  -0.374  -0.507  -0.311  -0.513
66    K        -0.051  -0.277  -0.379   0.139  -0.154  -0.316  -0.019  -0.320  -0.473
67    S        -0.544  -0.572  -0.454  -0.632  -0.633  -0.472  -0.751  -0.754  -0.584
68    Q         0.689   0.593   0.443   0.928   0.824   0.581   0.712   0.561   0.278
69    F        -1.616  -1.541  -1.430  -1.613  -1.571  -1.378  -1.360  -1.263  -1.087
70    L         1.466   1.500   1.578   1.467   1.531   1.654   1.564   1.610   1.726
71    Y         0.306   0.330   0.310   0.138   0.178   0.131   0.102   0.130   0.039
72    V        -0.051  -0.090  -0.349   0.163   0.161  -0.239  -0.019  -0.082  -0.432
73    L        -1.036  -0.889  -0.952  -1.150  -0.893  -0.996  -0.994  -0.793  -0.838
74    I        -0.391  -0.478  -0.437  -0.306  -0.441  -0.412  -0.507  -0.604  -0.558
75    P         0.689   0.560   0.433   0.830   0.678   0.469   0.712   0.510   0.260
76    A        -1.036  -1.152  -1.007  -1.141  -1.275  -1.058  -0.994  -1.095  -0.901
77    G        -1.124  -1.056  -0.997  -1.379  -1.255  -1.161  -1.116  -1.023  -0.892
78    I        -1.393  -1.380  -1.409  -1.111  -1.144  -1.229  -1.116  -1.094  -1.065
79    Y        -1.616  -1.704  -1.471  -1.743  -1.909  -1.575  -1.360  -1.395  -1.120
80    W         0.036   0.115   0.267  -0.277  -0.157   0.080  -0.385  -0.257  -0.041
81    Y        -0.748  -0.511  -0.907  -0.687  -0.345  -0.956  -0.629  -0.342  -0.787
82    W        -0.766  -0.681  -0.502  -0.871  -0.729  -0.493  -0.994  -0.871  -0.638
83    W        -0.051  -0.277  -0.379   0.219  -0.086  -0.290  -0.019  -0.320  -0.473
84    K        -2.466  -2.327  -2.118  -2.102  -1.874  -1.668  -1.725  -1.594  -1.332
85    N        -1.258  -1.169  -1.046  -1.216  -1.074  -0.898  -1.238  -1.138  -0.939
86    G        -1.036  -0.824  -0.971  -1.205  -0.955  -1.057  -0.994  -0.765  -0.863
87    N        -1.393  -1.497  -1.437  -1.094  -1.282  -1.219  -1.116  -1.210  -1.090
88    E         0.036   0.118   0.268   0.017   0.144   0.350  -0.385  -0.251  -0.038
89    Y        -0.391  -0.514  -0.457  -0.496  -0.692  -0.590  -0.507  -0.682  -0.585
90    N         1.466   1.500   1.578   1.452   1.551   1.640   1.564   1.610   1.726
91    E        -0.051  -0.090  -0.349   0.211   0.185  -0.255  -0.019  -0.082  -0.432
92    F        -0.391  -0.418  -0.425  -0.466  -0.496  -0.493  -0.507  -0.532  -0.542
93    L         1.466   1.500   1.578   1.467   1.531   1.654   1.564   1.610   1.726
94    Y         0.306   0.199   0.284   0.115  -0.048   0.050   0.102  -0.102  -0.009
95    S         0.101   0.108   0.256  -0.044  -0.059   0.167  -0.263  -0.270  -0.061
96    K         1.466   1.500   1.578   1.444   1.510   1.633   1.564   1.610   1.726
97    A        -0.051  -0.042  -0.328  -0.034   0.004  -0.363  -0.019  -0.017  -0.403
98    G         1.466   1.500   1.578   1.206   1.216   1.417   1.564   1.610   1.726
99    R         1.466   1.500   1.578   1.498   1.550   1.682   1.564   1.610   1.726
100   E        -0.391  -0.552  -0.457  -0.268  -0.517  -0.421  -0.507  -0.715  -0.586
101   E        -0.051  -0.088  -0.334   0.261   0.224  -0.129  -0.019  -0.073  -0.412
102   L        -0.051  -0.277  -0.379   0.139  -0.156  -0.348  -0.019  -0.320  -0.473
103   E         0.306   0.223   0.284   0.264   0.109   0.114   0.102  -0.058  -0.008
104   R        -1.036  -1.181  -1.015  -0.992  -1.258  -1.019  -0.994  -1.122  -0.908
105   V        -0.505  -0.642  -0.475  -0.666  -0.874  -0.647  -0.663  -0.824  -0.607
106   N        -0.177  -0.423  -0.422  -0.050  -0.400  -0.423  -0.186  -0.523  -0.531
107   V        -1.168  -1.158  -1.027  -1.320  -1.325  -1.118  -1.141  -1.122  -0.919
108   -        -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/P08525
Output conservation file - output/P08525
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
