1     M         1.690   1.694   1.733   1.901   1.906   1.960   1.808   1.812   1.869
2     L        -1.191  -1.177  -1.108  -1.232  -1.195  -1.103  -1.028  -1.011  -0.921
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     R        -0.470  -0.467  -0.455  -0.528  -0.524  -0.529  -0.555  -0.551  -0.531
7     A        -1.191  -1.177  -1.108  -0.936  -0.908  -0.814  -1.028  -1.011  -0.921
8     F        -0.470  -0.453  -0.451  -0.651  -0.613  -0.618  -0.555  -0.531  -0.526
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    R         1.690   1.694   1.733   1.766   1.774   1.828   1.808   1.812   1.869
11    C        -0.470  -0.467  -0.453  -0.342  -0.330  -0.321  -0.555  -0.551  -0.529
12    S        -1.191  -1.177  -1.108  -1.373  -1.337  -1.240  -1.028  -1.011  -0.921
13    I         0.522   0.514   0.453   0.488   0.486   0.375   0.390   0.375   0.258
14    H        -0.470  -0.467  -0.455  -0.231  -0.218  -0.210  -0.555  -0.551  -0.531
15    T        -0.470  -0.493  -0.472  -0.301  -0.329  -0.307  -0.555  -0.584  -0.553
16    S        -0.470  -0.467  -0.455  -0.337  -0.325  -0.312  -0.555  -0.551  -0.531
17    R        -0.470  -0.453  -0.448  -0.506  -0.472  -0.492  -0.555  -0.531  -0.523
18    V        -1.191  -1.177  -1.108  -1.073  -1.034  -0.948  -1.028  -1.011  -0.921
19    L         0.522   0.556   0.463   0.459   0.515   0.388   0.390   0.445   0.275
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    L        -0.470  -0.453  -0.448  -0.555  -0.515  -0.510  -0.555  -0.531  -0.523
24    H        -1.191  -1.177  -1.108  -0.981  -0.948  -0.858  -1.028  -1.011  -0.921
25    D        -1.191  -1.177  -1.108  -1.442  -1.390  -1.309  -1.028  -1.011  -0.921
26    A        -0.470  -0.425  -0.456  -0.276  -0.200  -0.247  -0.555  -0.494  -0.533
27    G        -0.470  -0.493  -0.472  -0.479  -0.527  -0.547  -0.555  -0.584  -0.553
28    V         0.522   0.490   0.448   0.545   0.504   0.428   0.390   0.336   0.249
29    K        -0.470  -0.493  -0.472  -0.662  -0.678  -0.630  -0.555  -0.584  -0.553
30    L         1.690   1.694   1.733   1.551   1.559   1.618   1.808   1.812   1.869
31    T         1.690   1.694   1.733   1.815   1.819   1.877   1.808   1.812   1.869
32    F         0.250   0.257   0.313  -0.035  -0.014   0.069  -0.083  -0.071   0.009
33    F         1.690   1.694   1.733   1.754   1.758   1.816   1.808   1.812   1.869
34    S         0.522   0.490   0.448   0.617   0.573   0.495   0.390   0.336   0.249
35    K         1.690   1.694   1.733   1.407   1.413   1.477   1.808   1.812   1.869
36    P        -0.470  -0.493  -0.472  -0.266  -0.294  -0.280  -0.555  -0.584  -0.553
37    N        -0.470  -0.467  -0.453  -0.276  -0.264  -0.261  -0.555  -0.551  -0.529
38    C         1.690   1.694   1.733   1.864   1.872   1.924   1.808   1.812   1.869
39    G         0.292   0.352   0.372   0.451   0.606   0.575  -0.007   0.097   0.115
40    L         1.690   1.694   1.733   1.550   1.637   1.617   1.808   1.812   1.869
41    C         1.690   1.694   1.733   1.872   1.914   1.932   1.808   1.812   1.869
42    D        -1.078  -0.990  -1.051  -1.037  -0.964  -0.977  -0.914  -0.819  -0.865
43    Q        -1.078  -1.127  -1.093  -0.799  -0.816  -0.813  -0.914  -0.962  -0.907
44    A         1.690   1.694   1.733   1.872   1.890   1.932   1.808   1.812   1.869
45    K         1.690   1.694   1.733   1.381   1.349   1.452   1.808   1.812   1.869
46    E        -1.078  -1.012  -1.067  -0.849  -0.738  -0.830  -0.914  -0.844  -0.882
47    V         0.292   0.270   0.318   0.092   0.020   0.126  -0.007  -0.049   0.019
48    I        -0.502  -0.509  -0.487  -0.658  -0.587  -0.590  -0.612  -0.613  -0.574
49    D        -1.078  -0.990  -1.051  -0.970  -0.988  -0.905  -0.914  -0.819  -0.865
50    D         0.650   0.605   0.490   0.614   0.451   0.401   0.598   0.524   0.321
51    V        -0.285  -0.151  -0.375  -0.126   0.062  -0.252  -0.309  -0.134  -0.427
52    F         0.650   0.585   0.487   0.573   0.581   0.332   0.598   0.492   0.316
53    E        -0.502  -0.509  -0.487  -0.698  -0.719  -0.609  -0.612  -0.613  -0.574
54    R        -1.078  -1.080  -1.047  -1.087  -1.008  -1.063  -0.914  -0.917  -0.862
55    K        -0.502  -0.526  -0.469  -0.706  -0.839  -0.672  -0.612  -0.634  -0.555
56    E        -1.654  -1.630  -1.565  -1.604  -1.618  -1.467  -1.217  -1.193  -1.107
57    F        -0.502  -0.487  -0.475  -0.682  -0.536  -0.612  -0.612  -0.588  -0.560
58    H        -0.470  -0.520  -0.501  -0.627  -0.683  -0.614  -0.555  -0.619  -0.590
59    N        -0.470  -0.426  -0.438  -0.621  -0.604  -0.592  -0.555  -0.498  -0.509
60    K        -0.285  -0.236  -0.358  -0.406  -0.365  -0.476  -0.309  -0.246  -0.405
61    A        -1.654  -1.630  -1.565  -1.382  -1.427  -1.250  -1.217  -1.193  -1.107
62    V        -0.285  -0.370  -0.410  -0.193  -0.325  -0.379  -0.309  -0.423  -0.473
63    S         0.292   0.300   0.335   0.013   0.114   0.061  -0.007   0.006   0.049
64    L        -0.285  -0.326  -0.398  -0.241  -0.206  -0.374  -0.309  -0.364  -0.457
65    E        -1.078  -1.067  -1.045  -1.014  -1.036  -0.976  -0.914  -0.901  -0.860
66    I        -0.502  -0.509  -0.487  -0.532  -0.492  -0.512  -0.612  -0.613  -0.574
67    V         0.292   0.352   0.372   0.101   0.179   0.235  -0.007   0.097   0.115
68    N         0.292   0.277   0.321   0.038  -0.072   0.093  -0.007  -0.036   0.023
69    I         1.690   1.694   1.733   1.670   1.663   1.735   1.808   1.812   1.869
70    T        -0.285  -0.341  -0.425   0.013  -0.006  -0.218  -0.309  -0.384  -0.492
71    D        -0.285  -0.214  -0.354  -0.399  -0.389  -0.513  -0.309  -0.218  -0.399
72    R        -0.285  -0.341  -0.425  -0.080  -0.103  -0.334  -0.309  -0.384  -0.492
73    R        -1.078  -1.076  -1.052  -1.005  -1.000  -0.979  -0.914  -0.911  -0.867
74    N         1.690   1.694   1.733   1.788   1.797   1.850   1.808   1.812   1.869
75    A        -1.078  -1.022  -1.049  -1.092  -0.988  -1.010  -0.914  -0.856  -0.864
76    K        -0.285  -0.268  -0.370  -0.435  -0.445  -0.526  -0.309  -0.289  -0.420
77    W         0.650   0.719   0.524   1.041   1.132   0.848   0.598   0.703   0.380
78    W         0.292   0.277   0.321   0.324   0.353   0.377  -0.007  -0.036   0.023
79    K         0.650   0.585   0.487   0.482   0.245   0.186   0.598   0.492   0.316
80    E        -1.078  -1.062  -1.059  -1.356  -1.356  -1.306  -0.914  -0.897  -0.873
81    Y         1.690   1.694   1.733   1.893   1.900   1.953   1.808   1.812   1.869
82    C         1.690   1.694   1.733   1.872   1.914   1.932   1.808   1.812   1.869
83    F         0.292   0.352   0.372   0.265   0.418   0.389  -0.007   0.097   0.115
84    D         1.690   1.694   1.733   1.550   1.435   1.617   1.808   1.812   1.869
85    I         0.292   0.277   0.321   0.101   0.037   0.134  -0.007  -0.036   0.023
86    P         1.690   1.694   1.733   1.851   1.857   1.912   1.808   1.812   1.869
87    V         1.690   1.694   1.733   1.703   1.671   1.766   1.808   1.812   1.869
88    L         1.690   1.694   1.733   1.550   1.637   1.617   1.808   1.812   1.869
89    H         1.690   1.694   1.733   1.872   1.877   1.932   1.808   1.812   1.869
90    I        -0.502  -0.509  -0.487  -0.554  -0.574  -0.503  -0.612  -0.613  -0.574
91    E        -1.078  -1.012  -1.067  -0.926  -0.906  -0.916  -0.914  -0.844  -0.882
92    K        -0.502  -0.509  -0.487  -0.686  -0.677  -0.661  -0.612  -0.613  -0.574
93    V        -1.078  -1.127  -1.093  -0.974  -1.137  -1.047  -0.914  -0.962  -0.907
94    G        -0.502  -0.526  -0.467  -0.539  -0.612  -0.460  -0.612  -0.635  -0.553
95    D        -0.502  -0.509  -0.487  -0.524  -0.609  -0.504  -0.612  -0.613  -0.574
96    P        -0.285  -0.341  -0.425  -0.107  -0.190  -0.382  -0.309  -0.384  -0.492
97    K        -0.593  -0.579  -0.518  -0.838  -0.791  -0.717  -0.713  -0.695  -0.611
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   S         0.292   0.277   0.321  -0.107  -0.071  -0.037  -0.007  -0.036   0.023
101   C        -1.078  -1.127  -1.093  -0.892  -0.930  -0.946  -0.914  -0.962  -0.907
102   T        -1.078  -1.127  -1.093  -0.931  -0.967  -0.942  -0.914  -0.962  -0.907
103   K         1.690   1.694   1.733   1.381   1.349   1.452   1.808   1.812   1.869
104   I        -1.078  -1.127  -1.093  -0.988  -0.984  -1.026  -0.914  -0.962  -0.907
105   L        -0.285  -0.370  -0.410  -0.080  -0.153  -0.321  -0.309  -0.423  -0.473
106   H         1.690   1.694   1.733   1.872   1.877   1.932   1.808   1.812   1.869
107   F        -0.502  -0.519  -0.474  -0.349  -0.280  -0.311  -0.612  -0.625  -0.558
108   L        -0.285  -0.341  -0.425  -0.234  -0.247  -0.499  -0.309  -0.384  -0.492
109   E        -0.502  -0.519  -0.474  -0.539  -0.687  -0.509  -0.612  -0.625  -0.558
110   E         0.650   0.746   0.520   0.798   0.864   0.603   0.598   0.744   0.373
111   D         0.650   0.605   0.490   0.482   0.278   0.192   0.598   0.524   0.321
112   D        -0.285  -0.341  -0.425  -0.581  -0.767  -0.799  -0.309  -0.384  -0.492
113   I        -0.285  -0.370  -0.410  -0.374  -0.443  -0.570  -0.309  -0.423  -0.473
114   S        -1.078  -1.127  -1.093  -1.028  -0.958  -1.007  -0.914  -0.962  -0.907
115   D         0.650   0.719   0.524   0.579   0.540   0.399   0.598   0.703   0.380
116   K        -0.502  -0.509  -0.487  -0.833  -0.904  -0.829  -0.612  -0.613  -0.574
117   I        -0.502  -0.509  -0.487  -0.585  -0.573  -0.557  -0.612  -0.613  -0.574
118   R        -1.654  -1.630  -1.565  -1.275  -1.098  -1.145  -1.217  -1.193  -1.107
119   R        -0.593  -0.579  -0.518  -0.731  -0.719  -0.613  -0.713  -0.695  -0.611
120   M        -0.593  -0.579  -0.518  -0.482  -0.463  -0.369  -0.713  -0.695  -0.611
121   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   R         0.650   0.585   0.487   0.431   0.339   0.215   0.598   0.492   0.316
* 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/Q05530
Output conservation file - output/Q05530
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
