1     M         1.975   1.981   2.078   2.353   2.354   2.517   2.219   2.228   2.391
2     L         0.480   0.444   0.285   0.608   0.562   0.364   0.445   0.388   0.133
3     N        -0.563  -0.548  -0.497  -0.898  -0.887  -0.798  -0.684  -0.668  -0.590
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     R        -0.934  -0.958  -0.914  -0.750  -0.754  -0.694  -0.845  -0.864  -0.792
9     C        -0.422  -0.390  -0.429  -0.157  -0.105  -0.171  -0.523  -0.494  -0.514
10    I        -0.934  -0.949  -0.896  -0.735  -0.738  -0.648  -0.845  -0.856  -0.776
11    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    R         0.852   0.860   0.862   0.590   0.595   0.537   0.606   0.617   0.567
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    V         0.023   0.068   0.076  -0.033   0.031   0.056  -0.250  -0.186  -0.190
26    N        -0.794  -0.781  -0.840  -0.565  -0.546  -0.615  -0.684  -0.672  -0.716
27    L        -0.934  -0.926  -0.891  -0.971  -0.971  -0.885  -0.845  -0.836  -0.773
28    R        -0.934  -0.966  -0.896  -0.735  -0.744  -0.633  -0.845  -0.870  -0.777
29    I        -0.422  -0.390  -0.429  -0.289  -0.251  -0.315  -0.523  -0.494  -0.514
30    A        -0.563  -0.569  -0.491  -0.509  -0.502  -0.382  -0.684  -0.687  -0.585
31    S        -0.794  -0.752  -0.832  -0.409  -0.357  -0.432  -0.684  -0.641  -0.706
32    R         1.975   1.981   2.078   2.004   2.001   2.165   2.219   2.228   2.391
33    F        -1.306  -1.269  -1.249  -1.207  -1.142  -1.119  -1.006  -0.974  -0.923
34    Y        -0.050  -0.038   0.021   0.079   0.091   0.182  -0.361  -0.347  -0.273
35    S        -0.191  -0.255  -0.342  -0.083  -0.196  -0.373  -0.200  -0.286  -0.393
36    D        -0.794  -0.777  -0.848  -0.435  -0.408  -0.528  -0.684  -0.668  -0.724
37    -        -0.955  -0.944  -0.916  -0.760  -0.730  -0.706  -0.854  -0.846  -0.792
38    -         0.076   0.093   0.091  -0.032  -0.031   0.001  -0.196  -0.187  -0.180
39    G        -1.306  -1.307  -1.264  -1.022  -1.065  -0.981  -1.006  -1.008  -0.935
40    P         0.181   0.218   0.159   0.207   0.262   0.179  -0.039   0.018  -0.075
41    L        -0.191  -0.179  -0.328  -0.126  -0.116  -0.327  -0.200  -0.189  -0.375
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    G        -0.794  -0.854  -0.842  -0.509  -0.623  -0.623  -0.684  -0.750  -0.717
48    G        -1.306  -1.307  -1.260  -0.981  -0.998  -0.923  -1.006  -1.007  -0.932
49    A        -1.306  -1.278  -1.244  -0.859  -0.816  -0.764  -1.006  -0.983  -0.919
50    G        -0.934  -0.930  -0.888  -0.937  -0.948  -0.866  -0.845  -0.837  -0.770
51    P        -0.934  -0.946  -0.891  -0.613  -0.629  -0.531  -0.845  -0.853  -0.772
52    G        -1.306  -1.269  -1.252  -0.911  -0.855  -0.832  -1.006  -0.974  -0.925
53    N        -0.934  -0.927  -0.889  -0.750  -0.732  -0.675  -0.845  -0.837  -0.771
54    P        -1.306  -1.269  -1.252  -1.060  -1.011  -0.999  -1.006  -0.974  -0.925
55    Q        -1.306  -1.317  -1.245  -1.218  -1.238  -1.142  -1.006  -1.015  -0.919
56    D         0.480   0.444   0.285   0.834   0.778   0.544   0.445   0.388   0.133
57    I         0.181   0.236   0.159   0.183   0.254   0.160  -0.039   0.033  -0.077
58    F         1.975   1.981   2.078   2.270   2.270   2.433   2.219   2.228   2.391
59    I        -1.306  -1.306  -1.278  -1.158  -1.168  -1.122  -1.006  -1.006  -0.947
60    K        -0.934  -0.957  -0.910  -1.382  -1.402  -1.329  -0.845  -0.863  -0.789
61    R         1.205   1.188   1.079   1.221   1.185   0.997   1.251   1.220   0.998
62    E         1.975   1.981   2.078   1.875   1.879   2.035   2.219   2.228   2.391
63    R         0.852   0.850   0.853   0.436   0.427   0.405   0.606   0.598   0.550
64    A         1.975   1.981   2.078   2.043   2.042   2.204   2.219   2.228   2.391
65    K        -0.422  -0.397  -0.425  -0.728  -0.677  -0.713  -0.523  -0.492  -0.503
66    E         1.975   1.981   2.078   1.875   1.879   2.035   2.219   2.228   2.391
67    D         0.852   0.885   0.903   0.983   1.041   1.050   0.606   0.666   0.652
68    Y        -0.050  -0.050   0.030   0.165   0.161   0.281  -0.361  -0.364  -0.260
69    Y         0.090   0.071   0.104   0.269   0.238   0.291  -0.200  -0.220  -0.168
70    A         0.181   0.200   0.156   0.321   0.351   0.280  -0.039  -0.012  -0.083
71    R         0.090   0.068   0.105  -0.299  -0.310  -0.231  -0.200  -0.223  -0.165
72    Q         0.852   0.885   0.903   0.667   0.741   0.711   0.606   0.666   0.652
73    Q         0.480   0.451   0.304   0.848   0.799   0.555   0.445   0.398   0.163
74    E         1.975   1.981   2.078   1.875   1.879   2.035   2.219   2.228   2.391
75    R        -0.563  -0.572  -0.499  -0.954  -0.965  -0.852  -0.684  -0.689  -0.592
76    E         1.205   1.188   1.079   1.141   1.114   0.953   1.251   1.220   0.998
77    Q         1.205   1.164   1.072   1.299   1.243   1.063   1.251   1.179   0.985
78    L         1.975   1.981   2.078   1.945   1.949   2.106   2.219   2.228   2.391
79    A        -0.794  -0.837  -0.852  -1.114  -1.190  -1.227  -0.684  -0.732  -0.728
80    H        -0.794  -0.728  -0.805  -0.981  -0.891  -0.990  -0.684  -0.614  -0.678
81    V         1.205   1.218   1.088   1.258   1.274   1.117   1.251   1.271   1.015
82    K         0.852   0.929   0.888   0.436   0.566   0.469   0.606   0.751   0.621
83    E         1.205   1.164   1.072   1.090   1.024   0.853   1.251   1.179   0.985
84    Q         0.090   0.066   0.100  -0.292  -0.315  -0.261  -0.200  -0.225  -0.173
85    L         1.975   1.981   2.078   1.945   1.949   2.106   2.219   2.228   2.391
86    K        -0.422  -0.426  -0.421  -0.834  -0.831  -0.848  -0.523  -0.523  -0.499
87    E        -0.563  -0.570  -0.499  -0.719  -0.738  -0.638  -0.684  -0.688  -0.592
88    H         0.693   0.701   0.783   0.667   0.683   0.795   0.284   0.294   0.402
89    K        -0.191  -0.278  -0.340  -0.465  -0.606  -0.737  -0.200  -0.315  -0.390
90    K         0.181   0.179   0.147  -0.211  -0.229  -0.297  -0.039  -0.050  -0.095
91    K        -1.306  -1.290  -1.258  -1.433  -1.400  -1.333  -1.006  -0.993  -0.931
92    L         0.181   0.214   0.176   0.112   0.166   0.134  -0.039   0.012  -0.043
93    E        -0.934  -0.919  -0.901  -1.118  -1.088  -1.092  -0.845  -0.830  -0.781
94    N        -0.934  -0.958  -0.914  -1.046  -1.075  -0.982  -0.845  -0.864  -0.792
95    L         1.205   1.219   1.084   1.234   1.250   1.070   1.251   1.272   1.008
96    E         0.480   0.451   0.304   0.440   0.399   0.171   0.445   0.398   0.163
97    N        -0.934  -0.949  -0.896  -1.050  -1.067  -0.991  -0.845  -0.856  -0.776
98    K        -0.422  -0.463  -0.441  -0.837  -0.882  -0.830  -0.523  -0.564  -0.523
99    I         0.480   0.417   0.282   0.755   0.666   0.449   0.445   0.348   0.129
100   N         0.181   0.265   0.184   0.286   0.429   0.272  -0.039   0.084  -0.039
101   N        -0.422  -0.436  -0.428  -0.692  -0.711  -0.683  -0.523  -0.532  -0.512
102   L        -0.422  -0.457  -0.427  -0.484  -0.546  -0.511  -0.523  -0.560  -0.510
103   S        -0.563  -0.572  -0.499  -0.692  -0.681  -0.544  -0.684  -0.689  -0.592
104   -         0.191   0.150   0.148  -0.103  -0.158  -0.168   0.006  -0.060  -0.079
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   K         0.181   0.147   0.140  -0.167  -0.213  -0.237  -0.039  -0.084  -0.106
* 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/P01098
Output conservation file - output/P01098
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
