1     M         0.981   1.005   1.071   1.395   1.420   1.476   1.013   1.047   1.143
2     P        -0.561  -0.460  -0.293  -0.925  -0.773  -0.477  -0.928  -0.770  -0.533
3     P         0.981   1.005   1.071   1.354   1.392   1.442   1.013   1.047   1.143
4     K         0.981   1.005   1.071   0.431   0.496   0.664   1.013   1.047   1.143
5     Q        -1.289  -1.228  -1.101  -1.224  -1.188  -0.945  -1.389  -1.320  -1.107
6     Q         0.981   1.005   1.071   1.221   1.249   1.330   1.013   1.047   1.143
7     L        -0.574  -0.493  -0.300  -0.736  -0.587  -0.303  -0.952  -0.827  -0.544
8     S        -0.574  -0.493  -0.300  -0.629  -0.477  -0.210  -0.952  -0.827  -0.544
9     K         0.981   1.005   1.071   0.431   0.496   0.664   1.013   1.047   1.143
10    A         0.981   1.005   1.071   0.685   0.723   0.878   1.013   1.047   1.143
11    A         0.981   1.005   1.071   0.685   0.723   0.878   1.013   1.047   1.143
12    K         0.981   1.005   1.071   0.431   0.496   0.664   1.013   1.047   1.143
13    A         0.981   1.005   1.071   0.685   0.723   0.878   1.013   1.047   1.143
14    A         0.981   1.005   1.071   0.685   0.723   0.878   1.013   1.047   1.143
15    A         0.981   1.005   1.071   0.685   0.723   0.878   1.013   1.047   1.143
16    A         0.981   1.005   1.071   0.711   0.781   0.900   1.013   1.047   1.143
17    L        -1.272  -1.386  -1.094  -1.267  -1.524  -1.091  -1.393  -1.480  -1.099
18    A         0.061  -0.309  -0.256  -0.134  -0.650  -0.564   0.050  -0.518  -0.470
19    G         0.981   1.005   1.071   1.203   1.230   1.315   1.013   1.047   1.143
20    G         0.061  -0.309  -0.256   0.294  -0.362  -0.387   0.050  -0.518  -0.470
21    K         0.981   1.005   1.071   0.413   0.459   0.650   1.013   1.047   1.143
22    K         0.061   0.036  -0.236  -0.396  -0.413  -0.656   0.050   0.012  -0.436
23    S        -1.885  -1.960  -1.677  -1.724  -1.813  -1.422  -1.714  -1.756  -1.396
24    K         0.981   1.005   1.071   0.442   0.498   0.674   1.013   1.047   1.143
25    K         0.981   1.005   1.071   0.442   0.498   0.674   1.013   1.047   1.143
26    K         0.981   1.005   1.071   0.442   0.498   0.674   1.013   1.047   1.143
27    W         0.981   1.005   1.071   1.475   1.497   1.544   1.013   1.047   1.143
28    S        -0.208  -0.029  -0.222  -0.025   0.219  -0.055  -0.346  -0.082  -0.412
29    K         0.198   0.171  -0.200  -0.292  -0.303  -0.875   0.236   0.200  -0.376
30    K        -1.121  -1.000  -1.055  -1.345  -1.018  -1.175  -1.219  -1.026  -1.052
31    S        -0.447  -0.258  -0.245  -1.168  -0.850  -0.757  -0.734  -0.435  -0.451
32    M        -1.252  -1.050  -1.075  -1.146  -0.872  -0.866  -1.316  -1.060  -1.077
33    K         0.981   1.005   1.071   0.442   0.498   0.674   1.013   1.047   1.143
34    D         0.981   1.005   1.071   1.197   1.215   1.309   1.013   1.047   1.143
35    R         0.198   0.369  -0.180  -0.227  -0.004  -0.636   0.236   0.455  -0.344
36    A         0.981   1.005   1.071   0.704   0.762   0.895   1.013   1.047   1.143
37    Q         0.198   0.313  -0.184   0.474   0.627  -0.293   0.236   0.386  -0.350
38    H         0.981   1.005   1.071   1.375   1.405   1.459   1.013   1.047   1.143
39    A        -1.269  -1.077  -1.599  -1.257  -0.988  -1.621  -1.025  -0.816  -1.323
40    V        -0.208  -0.229  -0.217  -0.166  -0.205  -0.188  -0.346  -0.388  -0.405
41    I        -1.121  -0.992  -1.059  -1.153  -0.989  -1.050  -1.219  -1.079  -1.061
42    L        -0.208  -0.229  -0.217  -0.020  -0.049  -0.050  -0.346  -0.388  -0.405
43    D         0.981   1.005   1.071   1.197   1.215   1.309   1.013   1.047   1.143
44    Q        -0.447  -0.490  -0.303  -0.731  -0.945  -0.675  -0.734  -0.822  -0.549
45    E        -1.960  -1.816  -1.665  -1.732  -1.530  -1.302  -1.801  -1.621  -1.386
46    K        -1.597  -1.789  -1.660  -1.976  -2.156  -1.791  -1.413  -1.593  -1.381
47    Y        -1.876  -1.904  -1.654  -1.448  -1.522  -1.211  -1.704  -1.698  -1.376
48    D         0.981   1.005   1.071   1.197   1.215   1.309   1.013   1.047   1.143
49    R         0.198  -0.017  -0.211   0.418   0.085  -0.408   0.236  -0.065  -0.395
50    I         0.198  -0.017  -0.211   0.470   0.192  -0.162   0.236  -0.065  -0.395
51    L        -2.436  -2.452  -2.112  -1.848  -1.806  -1.380  -1.996  -1.961  -1.561
52    K         0.981   1.005   1.071   0.442   0.498   0.674   1.013   1.047   1.143
53    E        -0.447  -0.422  -0.297  -0.295  -0.278  -0.153  -0.734  -0.707  -0.539
54    V        -0.208  -0.157  -0.271  -0.342  -0.264  -0.578  -0.346  -0.275  -0.494
55    P        -0.553  -0.793  -1.042  -0.023  -0.351  -0.927  -0.443  -0.741  -1.036
56    T        -0.923  -1.126  -1.064  -0.681  -1.029  -1.049  -0.928  -1.161  -1.063
57    Y        -0.447  -0.447  -0.298  -0.156  -0.172  -0.000  -0.734  -0.748  -0.541
58    R        -0.561  -0.497  -0.304  -1.267  -1.149  -0.751  -0.928  -0.834  -0.551
59    Y        -1.252  -1.336  -1.089  -0.899  -1.078  -0.787  -1.316  -1.421  -1.094
60    V        -0.208  -0.229  -0.217  -0.220  -0.261  -0.267  -0.346  -0.388  -0.405
61    S         0.198  -0.017  -0.211   0.461   0.200  -0.104   0.236  -0.065  -0.395
62    V         0.981   1.005   1.071   1.006   1.039   1.149   1.013   1.047   1.143
63    S         0.198  -0.017  -0.211   0.384   0.077  -0.356   0.236  -0.065  -0.395
64    V         0.198  -0.017  -0.211   0.362   0.097  -0.179   0.236  -0.065  -0.395
65    L         0.981   1.005   1.071   1.120   1.158   1.244   1.013   1.047   1.143
66    V         0.981   1.005   1.071   1.006   1.039   1.149   1.013   1.047   1.143
67    D         0.981   1.005   1.071   1.197   1.215   1.309   1.013   1.047   1.143
68    R         0.981   1.005   1.071   1.169   1.204   1.286   1.013   1.047   1.143
69    L        -0.923  -0.856  -1.026  -0.610  -0.542  -0.711  -0.928  -0.866  -1.017
70    K         0.981   1.005   1.071   0.442   0.498   0.674   1.013   1.047   1.143
71    I         0.198   0.313  -0.184   0.470   0.613  -0.113   0.236   0.386  -0.350
72    G        -0.447  -0.490  -0.303  -0.271  -0.342  -0.078  -0.734  -0.822  -0.549
73    G         0.981   1.005   1.071   1.224   1.257   1.333   1.013   1.047   1.143
74    S         0.981   1.005   1.071   1.106   1.144   1.233   1.013   1.047   1.143
75    L        -0.553  -0.279  -0.986  -0.191   0.136  -0.816  -0.443  -0.117  -0.967
76    A         0.981   1.005   1.071   0.704   0.762   0.895   1.013   1.047   1.143
77    R         0.981   1.005   1.071   1.169   1.204   1.286   1.013   1.047   1.143
78    I        -1.121  -1.235  -1.079  -1.191  -1.324  -1.074  -1.219  -1.314  -1.083
79    A         0.198  -0.017  -0.211   0.089  -0.130  -0.315   0.236  -0.065  -0.395
80    L        -0.208  -0.229  -0.217  -0.109  -0.147  -0.181  -0.346  -0.388  -0.405
81    R         0.198  -0.017  -0.211   0.418   0.085  -0.408   0.236  -0.065  -0.395
82    H        -1.399  -1.156  -1.066  -1.261  -0.915  -0.811  -1.510  -1.201  -1.066
83    L         0.981   1.005   1.071   1.120   1.158   1.244   1.013   1.047   1.143
84    E        -0.208  -0.229  -0.217  -0.008  -0.065  -0.184  -0.346  -0.388  -0.405
85    K        -2.221  -1.935  -2.081  -1.881  -1.433  -1.876  -1.801  -1.509  -1.538
86    E        -2.091  -1.993  -1.664  -2.204  -2.219  -1.722  -1.898  -1.785  -1.385
87    G         0.981   1.005   1.071   1.224   1.257   1.333   1.013   1.047   1.143
88    I        -0.923  -1.126  -1.064  -0.752  -1.049  -1.000  -0.928  -1.161  -1.063
89    I         0.981   1.005   1.071   1.141   1.177   1.262   1.013   1.047   1.143
90    K        -1.252  -1.134  -1.049  -1.738  -1.569  -1.301  -1.316  -1.172  -1.045
91    P        -0.923  -1.126  -1.064  -0.711  -1.052  -1.084  -0.928  -1.161  -1.063
92    I        -0.208   0.014  -0.207  -0.220   0.103  -0.248  -0.346  -0.019  -0.387
93    S        -1.960  -1.795  -1.641  -2.005  -1.791  -1.519  -1.801  -1.632  -1.364
94    K        -0.923  -1.126  -1.064  -1.363  -1.590  -1.362  -0.928  -1.161  -1.063
95    H         0.981   1.005   1.071   1.375   1.405   1.459   1.013   1.047   1.143
96    S         0.981   1.005   1.071   1.106   1.144   1.233   1.013   1.047   1.143
97    K         0.981   1.005   1.071   0.442   0.498   0.674   1.013   1.047   1.143
98    Q         0.198  -0.017  -0.211   0.588   0.325   0.011   0.236  -0.065  -0.395
99    A        -0.553  -0.793  -1.042  -0.694  -1.053  -1.437  -0.443  -0.741  -1.036
100   I         0.198   0.171  -0.200   0.496   0.472  -0.060   0.236   0.200  -0.376
101   Y         0.198   0.171  -0.200   0.737   0.711   0.159   0.236   0.200  -0.376
102   T         0.981   1.005   1.071   1.327   1.347   1.419   1.013   1.047   1.143
103   R         0.981   1.005   1.071   1.169   1.204   1.286   1.013   1.047   1.143
104   A        -0.553  -0.627  -1.003  -0.618  -0.685  -1.167  -0.443  -0.529  -0.989
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   T        -2.003  -1.937  -1.678  -2.086  -1.976  -1.574  -1.826  -1.740  -1.397
107   A         0.981   1.005   1.071   0.692   0.750   0.884   1.013   1.047   1.143
108   S        -1.807  -1.812  -1.645  -1.747  -1.784  -1.574  -1.607  -1.603  -1.368
109   E        -0.923  -0.822  -1.022  -0.649  -0.560  -0.896  -0.928  -0.832  -1.012
* 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/Q3E792
Output conservation file - output/Q3E792
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
