1     M         1.414   1.465   1.566   1.649   1.719   1.866   1.500   1.576   1.736
2     I        -0.558  -0.657  -0.468  -0.716  -0.886  -0.628  -0.777  -0.863  -0.612
3     F         0.584   0.720   0.395   0.677   0.861   0.312   0.561   0.761   0.200
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     K        -0.558  -0.622  -0.461  -0.686  -0.737  -0.538  -0.777  -0.810  -0.600
7     R         0.651   0.442   0.409   0.876   0.598   0.522   0.661   0.329   0.224
8     A        -0.558  -0.652  -0.473  -0.795  -0.914  -0.630  -0.777  -0.856  -0.617
9     V         0.276   0.444   0.353   0.126   0.374   0.231   0.062   0.332   0.123
10    S         0.651   0.442   0.409   0.656   0.354   0.276   0.661   0.329   0.224
11    T         0.651   0.442   0.409   0.974   0.688   0.581   0.661   0.329   0.224
12    L         0.651   0.442   0.409   0.630   0.361   0.308   0.661   0.329   0.224
13    I         1.414   1.465   1.566   1.465   1.549   1.695   1.500   1.576   1.736
14    P         1.414   1.465   1.566   1.303   1.358   1.544   1.500   1.576   1.736
15    P         1.414   1.465   1.566   1.303   1.358   1.544   1.500   1.576   1.736
16    K         0.651   0.442   0.409   0.614   0.384   0.339   0.661   0.329   0.224
17    V         0.075   0.215   0.294  -0.023   0.209   0.294  -0.298  -0.064   0.014
18    V         0.075   0.228   0.302  -0.366  -0.130  -0.007  -0.298  -0.041   0.029
19    S         0.651   0.442   0.409   0.696   0.422   0.379   0.661   0.329   0.224
20    S        -0.558  -0.427  -0.457  -1.009  -0.832  -0.792  -0.777  -0.639  -0.599
21    K        -1.391  -1.402  -1.426  -1.225  -1.220  -1.254  -1.136  -1.149  -1.103
22    N        -1.041  -1.038  -1.021  -0.900  -1.003  -0.902  -1.017  -1.027  -0.934
23    I         0.075   0.172   0.269  -0.209  -0.051   0.085  -0.298  -0.143  -0.032
24    G        -0.075  -0.282  -0.396   0.091  -0.169  -0.357  -0.058  -0.345  -0.505
25    S        -0.558  -0.532  -0.458  -0.929  -0.932  -0.785  -0.777  -0.736  -0.600
26    A        -0.408  -0.486  -0.426  -0.638  -0.720  -0.615  -0.537  -0.616  -0.549
27    P         1.414   1.465   1.566   1.303   1.358   1.544   1.500   1.576   1.736
28    N        -0.075  -0.312  -0.394   0.244  -0.085  -0.219  -0.058  -0.384  -0.503
29    A         0.651   0.442   0.409   0.420   0.145   0.092   0.661   0.329   0.224
30    K        -0.075  -0.312  -0.394  -0.102  -0.452  -0.609  -0.058  -0.384  -0.503
31    R         0.651   0.638   0.437   0.881   0.872   0.583   0.661   0.639   0.275
32    I         0.075   0.228   0.302   0.119   0.385   0.441  -0.298  -0.041   0.029
33    A        -0.759  -0.885  -0.969  -0.834  -1.028  -1.108  -0.657  -0.816  -0.873
34    N        -1.259  -1.176  -1.051  -0.979  -0.877  -0.675  -1.256  -1.162  -0.963
35    V         0.651   0.442   0.409   0.843   0.569   0.498   0.661   0.329   0.224
36    V         1.414   1.465   1.566   1.486   1.552   1.714   1.500   1.576   1.736
37    H        -0.759  -0.755  -0.942  -0.562  -0.560  -0.829  -0.657  -0.674  -0.842
38    F         1.414   1.465   1.566   1.451   1.512   1.682   1.500   1.576   1.736
39    Y         1.414   1.465   1.566   1.437   1.497   1.669   1.500   1.576   1.736
40    K        -0.759  -0.905  -0.969  -0.635  -0.843  -0.897  -0.657  -0.836  -0.873
41    S        -1.127  -1.199  -1.026  -1.353  -1.415  -1.202  -1.136  -1.173  -0.938
42    L         1.414   1.465   1.566   1.274   1.350   1.518   1.500   1.576   1.736
43    P         1.414   1.465   1.566   1.303   1.358   1.544   1.500   1.576   1.736
44    Q        -0.759  -0.885  -0.969  -0.282  -0.485  -0.663  -0.657  -0.816  -0.873
45    G         1.414   1.465   1.566   1.360   1.445   1.597   1.500   1.576   1.736
46    P        -0.075   0.051  -0.333  -0.004   0.132  -0.386  -0.058   0.109  -0.418
47    A         1.414   1.465   1.566   1.083   1.165   1.341   1.500   1.576   1.736
48    P        -0.075   0.143  -0.319  -0.002   0.265  -0.361  -0.058   0.232  -0.398
49    A        -0.075  -0.312  -0.394  -0.201  -0.523  -0.614  -0.058  -0.384  -0.503
50    I        -2.093  -2.022  -1.819  -2.146  -2.066  -1.758  -1.616  -1.532  -1.269
51    K        -0.759  -0.878  -0.975  -0.704  -0.894  -1.035  -0.657  -0.805  -0.879
52    A        -1.610  -1.559  -1.457  -1.774  -1.709  -1.571  -1.376  -1.316  -1.133
53    N        -2.093  -1.981  -1.810  -1.866  -1.653  -1.483  -1.616  -1.495  -1.262
54    T        -1.610  -1.604  -1.453  -1.463  -1.491  -1.286  -1.376  -1.341  -1.128
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    R        -1.127  -0.908  -0.992  -1.162  -0.885  -0.939  -1.136  -0.909  -0.905
59    L        -1.127  -1.011  -0.996  -1.088  -0.896  -0.825  -1.136  -0.994  -0.909
60    A        -1.041  -1.105  -1.002  -1.205  -1.271  -1.221  -1.017  -1.059  -0.912
61    R        -1.127  -1.199  -1.014  -1.113  -1.148  -0.917  -1.136  -1.173  -0.926
62    Y         1.414   1.465   1.566   1.437   1.497   1.669   1.500   1.576   1.736
63    K        -1.041  -1.056  -1.018  -1.020  -1.037  -0.911  -1.017  -1.042  -0.931
64    A        -0.759  -0.878  -0.975  -0.866  -1.057  -1.179  -0.657  -0.805  -0.879
65    K         0.276   0.423   0.357  -0.049   0.211   0.026   0.062   0.298   0.131
66    Y        -0.075   0.018  -0.333   0.159   0.262  -0.214  -0.058   0.063  -0.418
67    F        -0.075  -0.197  -0.373   0.142  -0.070  -0.333  -0.058  -0.242  -0.473
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    D        -0.342  -0.374  -0.461  -0.001  -0.078  -0.279  -0.417  -0.466  -0.594
71    G         0.651   0.673   0.436   0.699   0.747   0.386   0.661   0.692   0.272
72    D        -1.259  -1.203  -1.048  -1.080  -1.069  -0.855  -1.256  -1.178  -0.960
73    N         0.651   0.673   0.436   0.832   0.876   0.483   0.661   0.692   0.272
74    A         0.651   0.638   0.437   0.416   0.413   0.129   0.661   0.639   0.275
75    S         1.414   1.465   1.566   1.331   1.392   1.571   1.500   1.576   1.736
76    G         0.651   0.638   0.437   0.664   0.664   0.304   0.661   0.639   0.275
77    K         0.276   0.176   0.264  -0.049  -0.256  -0.184   0.062  -0.135  -0.042
78    P         1.414   1.465   1.566   1.303   1.358   1.544   1.500   1.576   1.736
79    L         0.276   0.328   0.302   0.120   0.201   0.138   0.062   0.135   0.030
80    W        -0.690  -0.556  -0.478  -0.741  -0.568  -0.433  -0.897  -0.714  -0.618
81    H         1.414   1.465   1.566   1.444   1.510   1.676   1.500   1.576   1.736
82    F        -0.075   0.034  -0.331  -0.064   0.068  -0.473  -0.058   0.082  -0.415
83    A        -1.041  -1.127  -1.025  -1.223  -1.307  -1.127  -1.017  -1.105  -0.937
84    L        -1.041  -1.134  -1.006  -1.039  -1.155  -0.974  -1.017  -1.089  -0.916
85    G        -0.558  -0.452  -0.446  -0.881  -0.761  -0.700  -0.777  -0.662  -0.589
86    I        -0.558  -0.510  -0.446  -0.579  -0.488  -0.422  -0.777  -0.687  -0.583
87    I        -1.610  -1.412  -1.424  -1.530  -1.249  -1.261  -1.376  -1.158  -1.102
88    A        -1.610  -1.581  -1.456  -1.399  -1.343  -1.257  -1.376  -1.326  -1.131
89    F        -0.408  -0.306  -0.404  -0.370  -0.197  -0.391  -0.537  -0.375  -0.522
90    G         0.651   0.442   0.409   0.699   0.424   0.338   0.661   0.329   0.224
91    Y         1.414   1.465   1.566   1.437   1.497   1.669   1.500   1.576   1.736
92    S        -1.041  -1.022  -1.017  -1.101  -1.185  -1.074  -1.017  -1.013  -0.930
93    M        -1.742  -1.616  -1.470  -1.493  -1.362  -1.100  -1.496  -1.354  -1.144
94    E        -0.075  -0.109  -0.361   0.391   0.359  -0.010  -0.058  -0.099  -0.456
95    Y         1.414   1.465   1.566   1.437   1.497   1.669   1.500   1.576   1.736
96    Y        -0.558  -0.427  -0.444  -0.483  -0.320  -0.306  -0.777  -0.606  -0.581
97    F        -0.198  -0.298  -0.391  -0.017  -0.190  -0.349  -0.222  -0.374  -0.498
98    H         1.414   1.465   1.566   1.444   1.510   1.676   1.500   1.576   1.736
99    L         0.651   0.442   0.409   0.632   0.371   0.313   0.661   0.329   0.224
100   R         0.075   0.167   0.273  -0.114   0.052   0.156  -0.298  -0.152  -0.025
101   H         1.414   1.465   1.566   1.444   1.510   1.676   1.500   1.576   1.736
102   H         0.651   0.770   0.456   0.749   0.903   0.417   0.661   0.833   0.308
103   K        -0.075  -0.198  -0.368   0.017  -0.119  -0.303  -0.058  -0.243  -0.466
104   G        -0.721  -0.640  -0.502  -0.815  -0.666  -0.490  -0.954  -0.841  -0.651
105   A        -1.282  -1.217  -1.049  -1.383  -1.263  -1.069  -1.261  -1.178  -0.959
106   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   E        -1.259  -1.137  -1.033  -1.232  -1.063  -0.917  -1.256  -1.116  -0.945
108   H         1.414   1.465   1.566   1.444   1.510   1.676   1.500   1.576   1.736
* 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/Q06405
Output conservation file - output/Q06405
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
