1     M         1.612   1.692   1.775   1.757   1.865   1.997   1.767   1.880   2.021
2     S        -0.530  -0.587  -0.575  -0.583  -0.659  -0.655  -0.622  -0.672  -0.643
3     G        -1.754  -1.724  -1.638  -1.521  -1.525  -1.378  -1.304  -1.243  -1.124
4     K         0.947   0.834   0.799   0.796   0.685   0.605   0.971   0.763   0.666
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     P         0.206   0.346   0.055   0.243   0.434   0.031   0.133   0.332  -0.114
9     P         0.206   0.123   0.013   0.252   0.141  -0.014   0.133   0.002  -0.177
10    V        -1.230  -1.159  -1.051  -1.390  -1.285  -1.128  -1.145  -1.047  -0.917
11    Y        -0.251  -0.140  -0.142  -0.438  -0.310  -0.260  -0.563  -0.411  -0.410
12    R        -0.109   0.003  -0.053  -0.385  -0.214  -0.316  -0.394  -0.261  -0.299
13    L         1.612   1.692   1.775   1.375   1.461   1.617   1.767   1.880   2.021
14    P         0.947   0.894   0.806   0.963   0.914   0.776   0.971   0.868   0.679
15    P         0.313   0.103   0.053   0.352   0.071  -0.060   0.288  -0.023  -0.117
16    L         1.612   1.692   1.775   1.375   1.461   1.617   1.767   1.880   2.021
17    P         0.022  -0.112  -0.073  -0.168  -0.416  -0.404  -0.167  -0.371  -0.320
18    R         0.313   0.133   0.051   0.511   0.295   0.154   0.288   0.021  -0.119
19    L         1.612   1.692   1.775   1.375   1.461   1.617   1.767   1.880   2.021
20    K         0.444   0.456   0.558   0.035   0.095   0.224   0.061   0.041   0.186
21    V         0.947   1.037   0.830   1.148   1.283   1.006   0.971   1.102   0.725
22    K         0.388   0.462   0.563  -0.035   0.120   0.246  -0.053   0.052   0.197
23    K        -0.425  -0.603  -0.580  -0.559  -0.839  -0.785  -0.462  -0.678  -0.642
24    P         0.313   0.133   0.051   0.330   0.041  -0.111   0.288   0.021  -0.119
25    I        -1.333  -1.410  -1.353  -1.061  -1.226  -1.161  -1.077  -1.118  -1.025
26    I        -0.836  -1.018  -0.980  -0.535  -0.822  -0.811  -0.735  -0.912  -0.850
27    R        -1.754  -1.530  -1.604  -1.510  -1.238  -1.287  -1.304  -1.092  -1.101
28    Q        -0.299  -0.249  -0.143  -0.601  -0.520  -0.369  -0.622  -0.549  -0.411
29    E        -0.530  -0.641  -0.577  -0.483  -0.677  -0.591  -0.622  -0.721  -0.641
30    A         0.388   0.490   0.575   0.194   0.334   0.485  -0.053   0.111   0.221
31    N         0.313   0.103   0.053   0.394   0.129   0.019   0.288  -0.023  -0.117
32    K        -1.142  -0.997  -1.006  -1.294  -1.033  -1.039  -1.077  -0.917  -0.879
33    C         0.947   0.834   0.799   1.117   0.949   0.899   0.971   0.763   0.666
34    L        -1.027  -1.137  -1.028  -0.959  -1.026  -0.861  -0.963  -1.028  -0.897
35    V         0.022  -0.095  -0.073   0.112  -0.112  -0.080  -0.167  -0.354  -0.321
36    L        -0.284  -0.328  -0.484  -0.268  -0.355  -0.492  -0.280  -0.336  -0.524
37    M         0.947   0.834   0.799   1.137   0.959   0.885   0.971   0.763   0.666
38    S         0.947   0.894   0.806   0.971   0.910   0.769   0.971   0.868   0.679
39    N        -0.605  -0.685  -0.591  -0.753  -0.827  -0.702  -0.735  -0.778  -0.659
40    L         0.947   0.930   0.812   0.803   0.771   0.641   0.971   0.928   0.691
41    L         1.612   1.692   1.775   1.375   1.461   1.617   1.767   1.880   2.021
42    Q        -0.721  -0.720  -0.629  -0.808  -0.814  -0.675  -0.849  -0.818  -0.702
43    C         1.612   1.692   1.775   1.709   1.817   1.949   1.767   1.880   2.021
44    W         1.612   1.692   1.775   1.865   1.981   2.103   1.767   1.880   2.021
45    S        -0.109  -0.130  -0.079  -0.300  -0.342  -0.235  -0.394  -0.402  -0.331
46    S         0.313   0.281   0.090   0.380   0.344   0.035   0.288   0.236  -0.061
47    Y        -0.284  -0.286  -0.476  -0.121  -0.115  -0.371  -0.280  -0.288  -0.514
48    G         1.612   1.692   1.775   1.709   1.878   1.949   1.767   1.880   2.021
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    H        -1.027  -1.137  -1.028  -0.704  -0.828  -0.689  -0.963  -1.028  -0.897
52    M        -0.721  -0.720  -0.629  -0.643  -0.607  -0.514  -0.849  -0.818  -0.702
53    S        -0.284  -0.160  -0.430  -0.127   0.049  -0.326  -0.280  -0.126  -0.457
54    P        -1.754  -1.554  -1.612  -1.617  -1.374  -1.411  -1.304  -1.117  -1.107
55    K        -1.448  -1.281  -1.319  -1.328  -1.098  -1.134  -1.191  -1.027  -1.001
56    C         1.612   1.692   1.775   1.709   1.817   1.949   1.767   1.880   2.021
57    A        -1.027  -0.945  -0.959  -1.070  -1.014  -1.004  -0.963  -0.846  -0.831
58    G        -1.027  -1.103  -0.994  -0.869  -0.948  -0.838  -0.963  -1.002  -0.868
59    L        -0.530  -0.619  -0.575  -0.568  -0.673  -0.564  -0.622  -0.696  -0.639
60    V        -0.224  -0.062  -0.087  -0.275  -0.036  -0.082  -0.508  -0.276  -0.331
61    T        -1.448  -1.391  -1.326  -1.321  -1.239  -1.159  -1.191  -1.106  -1.006
62    E        -0.299  -0.263  -0.151  -0.329  -0.323  -0.134  -0.622  -0.567  -0.423
63    L         0.947   0.834   0.799   0.823   0.673   0.664   0.971   0.763   0.666
64    K         0.313   0.186   0.061   0.229   0.098  -0.111   0.288   0.101  -0.104
65    S        -1.448  -1.308  -1.319  -1.475  -1.266  -1.284  -1.191  -1.051  -1.001
66    C         0.947   0.834   0.799   1.117   0.949   0.899   0.971   0.763   0.666
67    T        -0.109  -0.092  -0.043  -0.075  -0.036   0.041  -0.394  -0.324  -0.268
68    S        -1.448  -1.445  -1.357  -1.328  -1.317  -1.193  -1.191  -1.149  -1.029
69    E        -0.605  -0.666  -0.593  -0.592  -0.717  -0.604  -0.735  -0.758  -0.662
70    S        -1.448  -1.363  -1.332  -1.255  -1.135  -1.114  -1.191  -1.089  -1.010
71    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    K         0.313   0.103   0.053   0.258   0.035  -0.063   0.288  -0.023  -0.117
75    R        -1.027  -0.927  -0.976  -1.094  -0.960  -1.031  -0.963  -0.854  -0.852
76    N        -1.448  -1.358  -1.328  -1.526  -1.444  -1.350  -1.191  -1.085  -1.007
77    N        -1.448  -1.447  -1.335  -1.475  -1.407  -1.295  -1.191  -1.151  -1.012
78    V        -0.721  -0.462  -0.568  -0.877  -0.528  -0.646  -0.849  -0.529  -0.630
79    Q        -0.530  -0.539  -0.576  -0.485  -0.507  -0.580  -0.622  -0.619  -0.645
80    K        -1.333  -1.410  -1.353  -1.404  -1.455  -1.398  -1.077  -1.118  -1.025
81    S         0.022  -0.136  -0.073  -0.028  -0.231  -0.172  -0.167  -0.395  -0.317
82    N        -0.299  -0.236  -0.133  -0.515  -0.392  -0.259  -0.622  -0.530  -0.397
83    I         1.612   1.692   1.775   1.750   1.870   1.990   1.767   1.880   2.021
84    N         1.612   1.692   1.775   1.549   1.684   1.790   1.767   1.880   2.021
85    Y         0.947   0.834   0.799   1.229   1.107   1.051   0.971   0.763   0.666
86    H         1.612   1.692   1.775   1.791   1.935   2.030   1.767   1.880   2.021
87    A         0.022   0.011  -0.044  -0.133  -0.275  -0.304  -0.167  -0.211  -0.274
88    A        -0.284  -0.374  -0.493  -0.202  -0.420  -0.568  -0.280  -0.399  -0.536
89    R         1.612   1.692   1.775   1.640   1.765   1.880   1.767   1.880   2.021
90    L         0.947   0.930   0.812   0.823   0.795   0.683   0.971   0.928   0.691
91    Y         0.313   0.186   0.061   0.640   0.496   0.273   0.288   0.101  -0.104
92    D        -0.530  -0.522  -0.530  -0.515  -0.487  -0.527  -0.622  -0.572  -0.583
93    R        -0.109  -0.109  -0.055  -0.479  -0.456  -0.406  -0.394  -0.366  -0.298
94    I        -0.530  -0.406  -0.526  -0.612  -0.458  -0.558  -0.622  -0.448  -0.578
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    N        -0.775  -0.610  -0.627  -0.855  -0.599  -0.609  -0.907  -0.709  -0.699
98    G         1.612   1.692   1.775   1.721   1.851   1.960   1.767   1.880   2.021
99    K         0.888   1.079   0.790   0.692   0.944   0.542   0.876   1.167   0.650
100   P        -0.775  -0.762  -0.631  -0.972  -0.933  -0.760  -0.907  -0.860  -0.703
101   H        -0.425  -0.603  -0.580  -0.209  -0.527  -0.559  -0.462  -0.678  -0.642
102   D         0.206  -0.017  -0.024   0.475   0.113   0.033   0.133  -0.203  -0.234
* 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/O75012
Output conservation file - output/O75012
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
