1     M         1.897   1.907   2.032   2.112   2.126   2.337   2.177   2.190   2.421
2     S         1.897   1.907   2.032   1.618   1.643   1.849   2.177   2.190   2.421
3     N         0.400   0.414   0.556  -0.010   0.005   0.228  -0.008   0.014   0.224
4     S        -0.979  -0.978  -0.895  -0.914  -0.928  -0.734  -0.969  -0.967  -0.848
5     R        -1.449  -1.448  -1.371  -1.550  -1.581  -1.392  -1.212  -1.202  -1.075
6     Y         1.897   1.907   2.032   2.172   2.183   2.398   2.177   2.190   2.421
7     S        -0.166  -0.223  -0.203  -0.384  -0.439  -0.378  -0.320  -0.387  -0.369
8     Q         0.683   0.705   0.672   0.796   0.837   0.790   0.538   0.575   0.459
9     T         0.024   0.096  -0.106   0.211   0.306   0.020  -0.008   0.097  -0.212
10    E         1.897   1.907   2.032   2.129   2.140   2.355   2.177   2.190   2.421
11    S        -2.305  -2.278  -2.114  -1.941  -1.886  -1.681  -1.568  -1.540  -1.349
12    N        -0.860  -0.803  -0.806  -0.693  -0.591  -0.609  -0.855  -0.778  -0.751
13    N         1.897   1.907   2.032   1.797   1.823   2.026   2.177   2.190   2.421
14    D         0.605   0.663   0.667   0.433   0.536   0.524   0.393   0.498   0.450
15    R        -1.288  -1.292  -1.310  -0.891  -0.907  -0.937  -1.033  -1.035  -1.016
16    K         0.423   0.451   0.570   0.307   0.348   0.537   0.037   0.087   0.253
17    L         0.605   0.605   0.657   0.244   0.241   0.328   0.393   0.387   0.430
18    E         0.423   0.425   0.557   0.402   0.397   0.596   0.037   0.036   0.226
19    G        -1.288  -1.233  -1.285  -0.976  -0.888  -1.042  -1.033  -0.971  -0.991
20    L         1.897   1.907   2.032   1.599   1.610   1.830   2.177   2.190   2.421
21    A         1.897   1.907   2.032   2.032   2.037   2.259   2.177   2.190   2.421
22    N        -0.860  -0.804  -0.806  -1.137  -1.034  -1.013  -0.855  -0.779  -0.751
23    K         0.605   0.605   0.657   0.725   0.723   0.784   0.393   0.387   0.430
24    L         0.178   0.082  -0.090   0.053  -0.078  -0.308   0.215   0.076  -0.188
25    A         0.178   0.232  -0.024   0.135   0.213  -0.088   0.215   0.293  -0.089
26    T        -0.860  -0.921  -0.865  -0.761  -0.857  -0.812  -0.855  -0.914  -0.817
27    F         0.605   0.557   0.613   0.491   0.385   0.404   0.393   0.296   0.342
28    R         1.897   1.907   2.032   1.952   1.962   2.179   2.177   2.190   2.421
29    N        -0.594  -0.672  -0.758  -0.542  -0.645  -0.812  -0.498  -0.594  -0.687
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    I         0.423   0.466   0.585   0.292   0.379   0.551   0.037   0.118   0.283
32    N        -0.166  -0.197  -0.197  -0.246  -0.290  -0.269  -0.320  -0.373  -0.358
33    Q        -1.449  -1.451  -1.337  -1.229  -1.240  -1.050  -1.212  -1.204  -1.046
34    E         1.012   1.069   0.838   1.262   1.335   1.053   1.107   1.196   0.781
35    I         1.897   1.907   2.032   1.925   1.941   2.152   2.177   2.190   2.421
36    G        -0.271  -0.315  -0.231  -0.011  -0.055   0.094  -0.498  -0.538  -0.411
37    D        -1.449  -1.433  -1.332  -1.319  -1.282  -1.134  -1.212  -1.188  -1.042
38    R        -0.594  -0.563  -0.744  -0.398  -0.353  -0.716  -0.498  -0.458  -0.670
39    A         0.178   0.168  -0.087   0.483   0.461   0.091   0.215   0.202  -0.183
40    V        -1.288  -1.274  -1.305  -1.021  -1.020  -1.102  -1.033  -1.017  -1.012
41    S        -0.979  -0.946  -0.904  -1.165  -1.096  -1.144  -0.969  -0.925  -0.859
42    D        -0.166  -0.239  -0.204  -0.048  -0.157  -0.128  -0.320  -0.413  -0.363
43    S        -0.860  -0.921  -0.865  -1.023  -1.064  -0.912  -0.855  -0.914  -0.817
44    S         0.178   0.078  -0.073   0.018  -0.110  -0.363   0.215   0.069  -0.162
45    V        -0.271  -0.273  -0.211  -0.508  -0.502  -0.394  -0.498  -0.494  -0.388
46    I         0.605   0.605   0.657   0.394   0.386   0.420   0.393   0.387   0.430
47    N         1.012   1.069   0.838   1.207   1.287   0.949   1.107   1.196   0.781
48    Q        -0.860  -0.831  -0.807  -1.197  -1.144  -1.132  -0.855  -0.825  -0.757
49    M        -1.022  -0.982  -0.896  -1.187  -1.136  -0.950  -1.033  -0.989  -0.852
50    T        -0.860  -0.781  -0.827  -0.893  -0.772  -0.863  -0.855  -0.769  -0.773
51    D         0.178   0.292  -0.042   0.462   0.619   0.136   0.215   0.378  -0.115
52    S        -0.433  -0.446  -0.297  -0.879  -0.871  -0.644  -0.677  -0.694  -0.495
53    L         0.178   0.214  -0.045   0.413   0.474   0.046   0.215   0.266  -0.120
54    G        -0.271  -0.255  -0.202  -0.547  -0.535  -0.460  -0.498  -0.473  -0.374
55    S        -0.166  -0.152  -0.168  -0.466  -0.431  -0.458  -0.320  -0.292  -0.318
56    M         0.423   0.423   0.558   0.027   0.034   0.265   0.037   0.032   0.228
57    F        -0.860  -0.853  -0.834  -0.693  -0.659  -0.686  -0.855  -0.834  -0.783
58    T        -1.877  -1.862  -1.751  -1.744  -1.725  -1.605  -1.390  -1.370  -1.218
59    D        -1.449  -1.450  -1.344  -1.672  -1.670  -1.562  -1.212  -1.204  -1.052
60    I        -0.166  -0.143  -0.190  -0.215  -0.207  -0.317  -0.320  -0.299  -0.351
61    K         1.012   1.003   0.824   1.311   1.304   1.049   1.107   1.091   0.753
62    N        -0.860  -0.882  -0.858  -0.842  -0.861  -0.800  -0.855  -0.880  -0.812
63    S         0.605   0.605   0.657   0.266   0.272   0.350   0.393   0.387   0.430
64    S         0.605   0.557   0.613   0.266   0.194   0.283   0.393   0.296   0.342
65    S        -0.433  -0.433  -0.288  -0.723  -0.713  -0.483  -0.677  -0.676  -0.483
66    R        -0.594  -0.614  -0.769  -0.264  -0.296  -0.497  -0.498  -0.521  -0.700
67    L         1.897   1.907   2.032   1.599   1.610   1.830   2.177   2.190   2.421
68    T        -1.022  -0.973  -0.896  -0.910  -0.854  -0.709  -1.033  -0.982  -0.852
69    R         0.178   0.168  -0.087   0.372   0.355  -0.040   0.215   0.202  -0.183
70    S        -0.166  -0.239  -0.204  -0.371  -0.449  -0.368  -0.320  -0.413  -0.363
71    L        -0.166  -0.221  -0.202  -0.149  -0.225  -0.257  -0.320  -0.384  -0.366
72    K        -0.860  -0.876  -0.838  -0.919  -0.920  -0.891  -0.855  -0.865  -0.791
73    A        -0.860  -0.886  -0.844  -0.784  -0.858  -0.784  -0.855  -0.880  -0.794
74    G         0.605   0.605   0.657   0.614   0.606   0.652   0.393   0.387   0.430
75    N        -0.860  -0.838  -0.833  -0.896  -0.851  -0.846  -0.855  -0.828  -0.781
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    S        -1.288  -1.277  -1.296  -1.228  -1.197  -1.185  -1.033  -1.020  -1.002
79    I        -0.166  -0.131  -0.179  -0.317  -0.277  -0.328  -0.320  -0.277  -0.326
80    W        -0.166  -0.239  -0.204   0.094  -0.037  -0.040  -0.320  -0.413  -0.363
81    R         0.605   0.555   0.599   0.610   0.523   0.585   0.393   0.292   0.312
82    M        -0.860  -0.921  -0.865  -0.759  -0.880  -0.821  -0.855  -0.914  -0.817
83    V         1.012   0.921   0.805   1.223   1.091   0.876   1.107   0.954   0.718
84    G         1.012   1.064   0.828   1.297   1.360   1.053   1.107   1.189   0.761
85    L        -0.860  -0.796  -0.814  -0.945  -0.853  -0.875  -0.855  -0.780  -0.766
86    A        -0.860  -0.868  -0.845  -0.943  -0.981  -1.013  -0.855  -0.862  -0.794
87    L         1.012   0.921   0.805   0.803   0.679   0.525   1.107   0.954   0.718
88    L        -0.594  -0.641  -0.764  -0.742  -0.805  -1.000  -0.498  -0.557  -0.694
89    I        -1.877  -1.862  -1.751  -1.522  -1.550  -1.337  -1.390  -1.370  -1.218
90    F         1.012   1.003   0.824   1.228   1.225   0.965   1.107   1.091   0.753
91    F         0.605   0.557   0.613   0.491   0.385   0.404   0.393   0.296   0.342
92    I        -0.166  -0.213  -0.202  -0.209  -0.291  -0.300  -0.320  -0.394  -0.370
93    L         0.423   0.452   0.575  -0.028   0.036   0.210   0.037   0.090   0.263
94    Y         0.423   0.428   0.559   0.587   0.592   0.799   0.037   0.042   0.230
95    T        -0.860  -0.921  -0.865  -0.574  -0.649  -0.552  -0.855  -0.914  -0.817
96    L         1.012   1.093   0.833   0.803   0.903   0.569   1.107   1.234   0.770
97    F         0.605   0.630   0.635   0.787   0.825   0.798   0.393   0.436   0.385
98    K         1.012   0.921   0.805   1.311   1.192   1.018   1.107   0.954   0.718
99    L        -0.166  -0.090  -0.169  -0.421  -0.325  -0.384  -0.320  -0.218  -0.320
100   F         0.178   0.168  -0.087   0.452   0.444   0.041   0.215   0.202  -0.183
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -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/P43682
Output conservation file - output/P43682
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
