1     M         0.987   1.011   1.074   1.410   1.435   1.482   1.017   1.052   1.144
2     P        -0.580  -0.477  -0.303  -0.955  -0.799  -0.490  -0.947  -0.786  -0.540
3     P         0.987   1.011   1.074   1.368   1.406   1.448   1.017   1.052   1.144
4     K         0.987   1.011   1.074   0.426   0.492   0.662   1.017   1.052   1.144
5     Q        -1.319  -1.261  -1.115  -1.254  -1.222  -0.957  -1.414  -1.347  -1.114
6     Q         0.987   1.011   1.074   1.232   1.261   1.334   1.017   1.052   1.144
7     L        -0.594  -0.510  -0.309  -0.758  -0.606  -0.311  -0.972  -0.843  -0.550
8     S        -0.594  -0.510  -0.309  -0.627  -0.476  -0.201  -0.972  -0.843  -0.550
9     K         0.987   1.011   1.074   0.426   0.492   0.662   1.017   1.052   1.144
10    A         0.987   1.011   1.074   0.674   0.716   0.869   1.017   1.052   1.144
11    A         0.987   1.011   1.074   0.674   0.716   0.869   1.017   1.052   1.144
12    K         0.987   1.011   1.074   0.426   0.492   0.662   1.017   1.052   1.144
13    A         0.987   1.011   1.074   0.674   0.716   0.869   1.017   1.052   1.144
14    A         0.987   1.011   1.074   0.674   0.716   0.869   1.017   1.052   1.144
15    A         0.987   1.011   1.074   0.674   0.716   0.869   1.017   1.052   1.144
16    A         0.987   1.011   1.074   0.702   0.775   0.892   1.017   1.052   1.144
17    L        -1.303  -1.419  -1.107  -1.301  -1.565  -1.104  -1.418  -1.506  -1.106
18    A         0.052  -0.324  -0.264  -0.155  -0.675  -0.573   0.043  -0.532  -0.475
19    G         0.987   1.011   1.074   1.214   1.241   1.320   1.017   1.052   1.144
20    G         0.052  -0.324  -0.264   0.287  -0.381  -0.400   0.043  -0.532  -0.475
21    K         0.987   1.011   1.074   0.407   0.452   0.646   1.017   1.052   1.144
22    K         0.052   0.031  -0.244  -0.414  -0.429  -0.663   0.043   0.010  -0.441
23    S        -1.925  -2.002  -1.696  -1.749  -1.846  -1.428  -1.743  -1.785  -1.405
24    K         0.987   1.011   1.074   0.440   0.497   0.674   1.017   1.052   1.144
25    K         0.987   1.011   1.074   0.440   0.497   0.674   1.017   1.052   1.144
26    K         0.987   1.011   1.074   0.440   0.497   0.674   1.017   1.052   1.144
27    W         0.987   1.011   1.074   1.491   1.513   1.551   1.017   1.052   1.144
28    S        -0.221  -0.042  -0.226  -0.034   0.210  -0.055  -0.358  -0.095  -0.411
29    K         0.191   0.172  -0.207  -0.306  -0.307  -0.889   0.231   0.206  -0.380
30    K        -1.149  -1.021  -1.070  -1.376  -1.040  -1.191  -1.242  -1.042  -1.061
31    S        -0.465  -0.275  -0.255  -1.196  -0.878  -0.769  -0.751  -0.452  -0.460
32    M        -1.282  -1.076  -1.089  -1.173  -0.893  -0.876  -1.340  -1.078  -1.084
33    K         0.987   1.011   1.074   0.440   0.497   0.674   1.017   1.052   1.144
34    D         0.987   1.011   1.074   1.208   1.227   1.314   1.017   1.052   1.144
35    R         0.191   0.368  -0.187  -0.239  -0.011  -0.645   0.231   0.455  -0.348
36    A         0.987   1.011   1.074   0.700   0.760   0.891   1.017   1.052   1.144
37    Q         0.191   0.301  -0.191   0.474   0.618  -0.299   0.231   0.373  -0.355
38    H         0.987   1.011   1.074   1.389   1.419   1.465   1.017   1.052   1.144
39    A        -1.299  -1.101  -1.617  -1.294  -1.014  -1.641  -1.046  -0.829  -1.331
40    V        -0.221  -0.242  -0.225  -0.175  -0.214  -0.190  -0.358  -0.399  -0.409
41    I        -1.149  -1.021  -1.073  -1.181  -1.019  -1.061  -1.242  -1.103  -1.068
42    L        -0.221  -0.242  -0.225  -0.029  -0.058  -0.054  -0.358  -0.399  -0.409
43    D         0.987   1.011   1.074   1.208   1.227   1.314   1.017   1.052   1.144
44    Q        -0.465  -0.508  -0.311  -0.752  -0.971  -0.684  -0.751  -0.840  -0.554
45    E        -2.002  -1.854  -1.684  -1.770  -1.564  -1.315  -1.831  -1.647  -1.395
46    K        -1.633  -1.824  -1.679  -2.016  -2.194  -1.804  -1.439  -1.616  -1.390
47    Y        -1.916  -1.948  -1.673  -1.481  -1.562  -1.224  -1.733  -1.729  -1.384
48    D         0.987   1.011   1.074   1.208   1.227   1.314   1.017   1.052   1.144
49    R         0.191  -0.030  -0.219   0.416   0.073  -0.415   0.231  -0.077  -0.400
50    I         0.191  -0.030  -0.219   0.469   0.183  -0.168   0.231  -0.077  -0.400
51    L        -2.486  -2.501  -2.135  -1.888  -1.845  -1.394  -2.028  -1.992  -1.571
52    K         0.987   1.011   1.074   0.440   0.497   0.674   1.017   1.052   1.144
53    E        -0.465  -0.442  -0.304  -0.309  -0.296  -0.157  -0.751  -0.726  -0.543
54    V        -0.221  -0.168  -0.279  -0.358  -0.277  -0.590  -0.358  -0.285  -0.499
55    P        -0.572  -0.810  -1.056  -0.033  -0.359  -0.940  -0.456  -0.751  -1.044
56    T        -0.948  -1.155  -1.079  -0.697  -1.054  -1.059  -0.947  -1.184  -1.071
57    Y        -0.465  -0.462  -0.305  -0.168  -0.180  -0.002  -0.751  -0.760  -0.544
58    R        -0.580  -0.516  -0.312  -1.296  -1.179  -0.759  -0.947  -0.854  -0.556
59    Y        -1.282  -1.367  -1.103  -0.923  -1.103  -0.796  -1.340  -1.444  -1.102
60    V        -0.221  -0.242  -0.225  -0.232  -0.274  -0.273  -0.358  -0.399  -0.409
61    S         0.191  -0.030  -0.219   0.461   0.192  -0.107   0.231  -0.077  -0.400
62    V         0.987   1.011   1.074   1.014   1.047   1.153   1.017   1.052   1.144
63    S         0.191  -0.030  -0.219   0.381   0.064  -0.366   0.231  -0.077  -0.400
64    V         0.191  -0.030  -0.219   0.360   0.087  -0.181   0.231  -0.077  -0.400
65    L         0.987   1.011   1.074   1.130   1.168   1.249   1.017   1.052   1.144
66    V         0.987   1.011   1.074   1.014   1.047   1.153   1.017   1.052   1.144
67    D         0.987   1.011   1.074   1.208   1.227   1.314   1.017   1.052   1.144
68    R         0.987   1.011   1.074   1.180   1.215   1.291   1.017   1.052   1.144
69    L        -0.948  -0.886  -1.040  -0.629  -0.566  -0.720  -0.947  -0.890  -1.024
70    K         0.987   1.011   1.074   0.440   0.497   0.674   1.017   1.052   1.144
71    I         0.191   0.301  -0.191   0.469   0.606  -0.118   0.231   0.373  -0.355
72    G        -0.465  -0.508  -0.311  -0.284  -0.358  -0.083  -0.751  -0.840  -0.554
73    G         0.987   1.011   1.074   1.236   1.268   1.338   1.017   1.052   1.144
74    S         0.987   1.011   1.074   1.115   1.154   1.237   1.017   1.052   1.144
75    L        -0.572  -0.295  -1.000  -0.203   0.127  -0.826  -0.456  -0.128  -0.974
76    A         0.987   1.011   1.074   0.700   0.760   0.891   1.017   1.052   1.144
77    R         0.987   1.011   1.074   1.180   1.215   1.291   1.017   1.052   1.144
78    I        -1.149  -1.267  -1.093  -1.220  -1.357  -1.086  -1.242  -1.338  -1.091
79    A         0.191  -0.030  -0.219   0.074  -0.149  -0.327   0.231  -0.077  -0.400
80    L        -0.221  -0.242  -0.225  -0.119  -0.157  -0.186  -0.358  -0.399  -0.409
81    R         0.191  -0.030  -0.219   0.416   0.073  -0.415   0.231  -0.077  -0.400
82    H        -1.432  -1.189  -1.084  -1.291  -0.946  -0.826  -1.537  -1.228  -1.078
83    L         0.987   1.011   1.074   1.130   1.168   1.249   1.017   1.052   1.144
84    E        -0.221  -0.242  -0.225  -0.019  -0.076  -0.193  -0.358  -0.399  -0.409
85    K        -2.267  -1.976  -2.103  -1.923  -1.463  -1.896  -1.831  -1.534  -1.547
86    E        -2.134  -2.038  -1.683  -2.249  -2.266  -1.737  -1.930  -1.815  -1.393
87    G         0.987   1.011   1.074   1.236   1.268   1.338   1.017   1.052   1.144
88    I        -0.948  -1.155  -1.079  -0.773  -1.077  -1.011  -0.947  -1.184  -1.071
89    I         0.987   1.011   1.074   1.151   1.188   1.267   1.017   1.052   1.144
90    K        -1.282  -1.165  -1.059  -1.773  -1.605  -1.309  -1.340  -1.195  -1.047
91    P        -0.948  -1.155  -1.079  -0.732  -1.080  -1.096  -0.947  -1.184  -1.071
92    I        -0.221   0.006  -0.214  -0.232   0.098  -0.254  -0.358  -0.025  -0.392
93    S        -2.002  -1.837  -1.660  -2.048  -1.833  -1.534  -1.831  -1.661  -1.373
94    K        -0.948  -1.155  -1.079  -1.395  -1.628  -1.375  -0.947  -1.184  -1.071
95    H         0.987   1.011   1.074   1.389   1.419   1.465   1.017   1.052   1.144
96    S         0.987   1.011   1.074   1.115   1.154   1.237   1.017   1.052   1.144
97    K         0.987   1.011   1.074   0.440   0.497   0.674   1.017   1.052   1.144
98    Q         0.191  -0.030  -0.219   0.589   0.318   0.007   0.231  -0.077  -0.400
99    A        -0.572  -0.810  -1.056  -0.722  -1.081  -1.457  -0.456  -0.751  -1.044
100   I         0.191   0.172  -0.207   0.497   0.482  -0.062   0.231   0.206  -0.380
101   Y         0.191   0.172  -0.207   0.741   0.724   0.155   0.231   0.206  -0.380
102   T         0.987   1.011   1.074   1.348   1.366   1.431   1.017   1.052   1.144
103   R         0.987   1.011   1.074   1.180   1.215   1.291   1.017   1.052   1.144
104   A        -0.572  -0.639  -1.017  -0.643  -0.701  -1.182  -0.456  -0.534  -0.996
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   A        -1.644  -1.557  -1.653  -1.733  -1.601  -1.633  -1.418  -1.332  -1.365
107   A         0.987   1.011   1.074   0.685   0.746   0.878   1.017   1.052   1.144
108   S        -1.180  -1.180  -1.084  -1.118  -1.144  -0.988  -1.211  -1.219  -1.077
109   E        -0.948  -0.847  -1.036  -0.671  -0.581  -0.909  -0.947  -0.850  -1.019
* 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/P0C0T4
Output conservation file - output/P0C0T4
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
