1     M         1.063   1.087   1.131   1.225   1.241   1.308   1.117   1.149   1.210
2     Q        -2.180  -2.029  -1.866  -1.990  -1.760  -1.584  -1.751  -1.593  -1.369
3     P         0.357   0.198   0.087   0.393   0.174   0.059   0.345   0.094  -0.122
4     A        -0.622  -0.352  -0.618  -0.677  -0.227  -0.667  -0.758  -0.401  -0.734
5     A        -2.180  -1.982  -1.868  -2.161  -1.825  -1.721  -1.751  -1.563  -1.370
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     R        -0.761  -0.671  -0.667  -1.027  -0.927  -0.855  -0.978  -0.859  -0.801
8     L         0.357   0.198   0.087   0.437   0.200   0.025   0.345   0.094  -0.122
9     L        -1.698  -1.716  -1.573  -1.686  -1.684  -1.572  -1.476  -1.473  -1.273
10    S        -1.734  -1.637  -1.537  -1.652  -1.495  -1.373  -1.530  -1.397  -1.243
11    R         1.063   1.087   1.131   1.025   1.156   1.135   1.117   1.149   1.210
12    S         1.063   1.087   1.131   1.159   1.210   1.251   1.117   1.149   1.210
13    V        -0.622  -0.564  -0.646  -0.760  -0.781  -0.770  -0.758  -0.688  -0.772
14    W         1.063   1.087   1.131   1.304   1.317   1.376   1.117   1.149   1.210
15    K         1.063   1.087   1.131   0.856   0.987   0.989   1.117   1.149   1.210
16    G         0.357   0.238   0.092   0.452   0.276   0.122   0.345   0.158  -0.113
17    P         1.063   1.087   1.131   0.979   0.991   1.096   1.117   1.149   1.210
18    N        -0.235  -0.170  -0.033  -0.334  -0.220  -0.022  -0.648  -0.545  -0.338
19    I         0.010  -0.038  -0.012  -0.142  -0.314  -0.240  -0.206  -0.304  -0.299
20    V         1.063   1.087   1.131   0.933   0.885   1.056   1.117   1.149   1.210
21    P         0.357   0.198   0.087   0.388   0.165   0.046   0.345   0.094  -0.122
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    L        -0.314  -0.575  -0.628  -0.200  -0.639  -0.725  -0.317  -0.666  -0.744
25    P        -0.314  -0.575  -0.628  -0.208  -0.571  -0.615  -0.317  -0.666  -0.744
26    I        -0.622  -0.744  -0.674  -0.729  -1.014  -0.840  -0.758  -0.909  -0.808
27    R        -1.409  -1.249  -1.182  -1.636  -1.322  -1.248  -1.420  -1.251  -1.103
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    E        -1.207  -1.323  -1.173  -1.078  -1.247  -1.055  -1.199  -1.288  -1.093
31    A        -0.946  -1.155  -1.154  -0.714  -1.016  -0.974  -0.868  -1.105  -1.072
32    M        -1.734  -1.579  -1.541  -1.652  -1.512  -1.397  -1.530  -1.351  -1.247
33    T        -1.207  -0.961  -1.137  -1.408  -0.967  -1.259  -1.199  -0.936  -1.058
34    K        -0.946  -0.957  -1.125  -0.984  -0.920  -1.234  -0.868  -0.886  -1.042
35    G        -1.207  -1.287  -1.173  -1.308  -1.426  -1.273  -1.199  -1.265  -1.094
36    T        -1.287  -1.268  -1.158  -1.471  -1.440  -1.216  -1.309  -1.246  -1.080
37    P         1.063   1.087   1.131   0.979   0.991   1.096   1.117   1.149   1.210
38    I         1.063   1.087   1.131   1.025   1.028   1.135   1.117   1.149   1.210
39    R        -0.314  -0.575  -0.628  -0.223  -0.489  -0.718  -0.317  -0.666  -0.744
40    T         1.063   1.087   1.131   0.995   1.105   1.109   1.117   1.149   1.210
41    N        -1.532  -1.631  -1.552  -1.255  -1.399  -1.352  -1.309  -1.395  -1.256
42    A        -0.314  -0.575  -0.628  -0.258  -0.702  -0.813  -0.317  -0.666  -0.744
43    R         1.063   1.087   1.131   1.025   1.156   1.135   1.117   1.149   1.210
44    A        -0.761  -0.632  -0.664  -0.831  -0.644  -0.657  -0.978  -0.813  -0.797
45    A         0.010   0.116   0.029  -0.001   0.114   0.031  -0.206  -0.040  -0.225
46    T         1.063   1.087   1.131   0.995   1.105   1.109   1.117   1.149   1.210
47    I         0.357   0.429   0.114   0.385   0.437   0.010   0.345   0.444  -0.074
48    L         0.010  -0.000  -0.003  -0.076  -0.129  -0.147  -0.206  -0.238  -0.283
49    P         1.063   1.087   1.131   0.979   0.991   1.096   1.117   1.149   1.210
50    Q        -0.314  -0.446  -0.621  -0.042  -0.206  -0.543  -0.317  -0.500  -0.735
51    F         0.357   0.198   0.087   0.531   0.365   0.148   0.345   0.094  -0.122
52    V         1.063   1.087   1.131   0.933   0.885   1.056   1.117   1.149   1.210
53    G         1.063   1.087   1.131   1.033   1.033   1.142   1.117   1.149   1.210
54    L        -0.314  -0.575  -0.628  -0.199  -0.634  -0.722  -0.317  -0.666  -0.744
55    K        -0.314  -0.575  -0.628  -0.369  -0.613  -0.792  -0.317  -0.666  -0.744
56    F         1.063   1.087   1.131   1.130   1.205   1.225   1.117   1.149   1.210
57    Q        -1.207  -1.298  -1.162  -0.971  -1.074  -0.906  -1.199  -1.259  -1.083
58    I        -0.175  -0.029   0.003  -0.535  -0.373  -0.233  -0.537  -0.288  -0.272
59    H         1.063   1.087   1.131   1.247   1.263   1.326   1.117   1.149   1.210
60    N         1.063   1.087   1.131   1.137   1.195   1.232   1.117   1.149   1.210
61    G         1.063   1.087   1.131   1.033   1.033   1.142   1.117   1.149   1.210
62    K         1.063   1.087   1.131   0.856   0.987   0.989   1.117   1.149   1.210
63    E        -0.622  -0.671  -0.662  -0.472  -0.536  -0.537  -0.758  -0.797  -0.792
64    Y         1.063   1.087   1.131   1.247   1.318   1.326   1.117   1.149   1.210
65    V        -0.622  -0.642  -0.669  -0.786  -0.942  -0.854  -0.758  -0.796  -0.803
66    P        -1.734  -1.646  -1.555  -1.647  -1.547  -1.358  -1.530  -1.422  -1.260
67    I        -1.409  -1.137  -1.155  -1.619  -1.312  -1.204  -1.420  -1.111  -1.075
68    E        -0.946  -1.155  -1.154  -0.730  -1.034  -1.145  -0.868  -1.105  -1.072
69    I        -0.235  -0.174  -0.037  -0.643  -0.630  -0.303  -0.648  -0.551  -0.345
70    S         0.010   0.214   0.070  -0.098   0.283  -0.010  -0.206   0.121  -0.151
71    E        -0.622  -0.641  -0.654  -0.467  -0.489  -0.515  -0.758  -0.759  -0.780
72    D         0.357   0.389   0.096   0.657   0.676   0.246   0.345   0.387  -0.105
73    M         1.063   1.087   1.131   1.225   1.241   1.308   1.117   1.149   1.210
74    V         0.010  -0.005  -0.006  -0.202  -0.331  -0.249  -0.206  -0.246  -0.288
75    G         1.063   1.087   1.131   1.033   1.033   1.142   1.117   1.149   1.210
76    H        -1.287  -1.207  -1.154  -1.176  -1.025  -1.004  -1.309  -1.201  -1.076
77    K         1.063   1.087   1.131   0.856   0.987   0.989   1.117   1.149   1.210
78    L         1.063   1.087   1.131   1.063   1.086   1.168   1.117   1.149   1.210
79    G         1.063   1.087   1.131   1.033   1.033   1.142   1.117   1.149   1.210
80    E         1.063   1.087   1.131   1.144   1.172   1.238   1.117   1.149   1.210
81    F         0.357   0.238   0.092   0.534   0.436   0.164   0.345   0.158  -0.113
82    A        -0.314  -0.142  -0.587  -0.208  -0.023  -0.625  -0.317  -0.097  -0.688
83    P        -1.207  -1.181  -1.164  -1.212  -1.185  -1.096  -1.199  -1.153  -1.085
84    T         1.063   1.087   1.131   0.989   1.021   1.104   1.117   1.149   1.210
85    R         1.063   1.087   1.131   1.014   1.063   1.126   1.117   1.149   1.210
86    K         1.063   1.087   1.131   0.850   0.914   0.984   1.117   1.149   1.210
87    R        -0.428  -0.660  -0.663  -0.397  -0.748  -0.803  -0.467  -0.781  -0.790
88    F         1.063   1.087   1.131   1.132   1.172   1.227   1.117   1.149   1.210
89    S        -1.698  -1.745  -1.573  -1.452  -1.542  -1.325  -1.476  -1.497  -1.273
90    Y         1.063   1.087   1.131   1.239   1.262   1.320   1.117   1.149   1.210
91    T        -0.957  -0.885  -0.717  -1.376  -1.235  -0.990  -1.188  -1.085  -0.859
92    Q        -0.428  -0.323  -0.623  -0.147  -0.021  -0.465  -0.467  -0.328  -0.737
93    T        -0.057   0.021   0.002  -0.213  -0.091  -0.128  -0.323  -0.201  -0.273
94    K         1.063   1.087   1.131   0.850   0.914   0.984   1.117   1.149   1.210
95    N         1.063   1.087   1.131   1.124   1.154   1.220   1.117   1.149   1.210
96    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P53733
Output conservation file - output/P53733
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
