1     M         1.637   1.670   1.765   1.862   1.913   2.073   1.784   1.832   1.994
2     -         0.650   0.552   0.544   0.609   0.451   0.418   0.567   0.393   0.345
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     A        -0.357  -0.429  -0.340  -0.438  -0.520  -0.396  -0.539  -0.617  -0.498
8     Y         1.637   1.670   1.765   1.716   1.777   1.926   1.784   1.832   1.994
9     T        -0.357  -0.316  -0.315  -0.445  -0.383  -0.377  -0.539  -0.475  -0.467
10    S        -0.357  -0.322  -0.345  -0.364  -0.334  -0.326  -0.539  -0.501  -0.508
11    H        -1.440  -1.350  -1.354  -1.269  -1.120  -1.143  -1.173  -1.073  -1.044
12    L         0.270   0.296   0.397  -0.186  -0.146   0.006  -0.117  -0.079   0.064
13    S         0.270   0.304   0.401  -0.036   0.033   0.172  -0.117  -0.065   0.072
14    S        -0.357  -0.321  -0.340  -0.429  -0.346  -0.413  -0.539  -0.482  -0.499
15    K         0.748   0.793   0.623   0.785   0.853   0.589   0.728   0.795   0.489
16    T        -0.812  -0.831  -0.872  -0.754  -0.802  -0.905  -0.751  -0.771  -0.794
17    G        -0.984  -0.908  -0.919  -1.173  -1.034  -1.086  -0.962  -0.876  -0.850
18    L        -1.440  -1.408  -1.383  -1.559  -1.526  -1.487  -1.173  -1.134  -1.069
19    H         0.748   0.829   0.631   1.020   1.135   0.856   0.728   0.853   0.504
20    F         1.637   1.670   1.765   1.554   1.609   1.763   1.784   1.832   1.994
21    G        -0.073  -0.143  -0.234  -0.147  -0.266  -0.434  -0.117  -0.219  -0.342
22    R        -0.529  -0.501  -0.400  -0.647  -0.620  -0.470  -0.751  -0.708  -0.575
23    L        -0.357  -0.426  -0.340  -0.603  -0.721  -0.581  -0.539  -0.612  -0.499
24    S        -0.357  -0.305  -0.340  -0.289  -0.204  -0.266  -0.539  -0.469  -0.499
25    L        -0.984  -0.989  -0.924  -1.212  -1.222  -1.127  -0.962  -0.956  -0.855
26    R        -0.812  -0.756  -0.881  -0.736  -0.659  -0.802  -0.751  -0.674  -0.804
27    S        -0.984  -1.022  -0.939  -0.966  -0.993  -0.877  -0.962  -0.984  -0.869
28    L        -0.357  -0.322  -0.345  -0.568  -0.523  -0.545  -0.539  -0.501  -0.508
29    T        -1.440  -1.439  -1.376  -1.283  -1.289  -1.188  -1.173  -1.161  -1.063
30    A        -1.440  -1.451  -1.374  -1.224  -1.249  -1.127  -1.173  -1.171  -1.062
31    Y         0.748   0.614   0.590   0.931   0.764   0.721   0.728   0.501   0.428
32    A        -0.984  -0.933  -0.928  -1.080  -1.024  -0.978  -0.962  -0.899  -0.859
33    P         1.637   1.670   1.765   1.483   1.528   1.691   1.784   1.832   1.994
34    N         0.748   0.614   0.590   0.960   0.758   0.713   0.728   0.501   0.428
35    L         0.748   0.614   0.590   0.663   0.475   0.417   0.728   0.501   0.428
36    M        -1.440  -1.408  -1.383  -1.256  -1.234  -1.221  -1.173  -1.134  -1.069
37    L        -0.812  -0.831  -0.872  -0.874  -0.918  -0.984  -0.751  -0.771  -0.794
38    W         1.637   1.670   1.765   1.795   1.843   2.006   1.784   1.832   1.994
39    G         1.637   1.670   1.765   1.518   1.565   1.727   1.784   1.832   1.994
40    G         0.270   0.298   0.398  -0.141  -0.091   0.054  -0.117  -0.075   0.066
41    A         0.748   0.793   0.623   0.713   0.791   0.544   0.728   0.795   0.489
42    S         0.270   0.296   0.397  -0.036   0.007   0.156  -0.117  -0.079   0.064
43    M        -1.440  -1.374  -1.371  -1.395  -1.283  -1.288  -1.173  -1.096  -1.059
44    L        -1.440  -1.430  -1.370  -1.591  -1.583  -1.507  -1.173  -1.153  -1.058
45    G         0.748   0.860   0.631   0.680   0.835   0.499   0.728   0.900   0.504
46    L        -0.984  -1.016  -0.945  -1.151  -1.208  -1.105  -0.962  -0.978  -0.876
47    F        -0.529  -0.495  -0.393  -0.920  -0.852  -0.719  -0.751  -0.701  -0.566
48    V        -0.357  -0.405  -0.345  -0.435  -0.488  -0.427  -0.539  -0.581  -0.503
49    F         0.748   0.614   0.590   0.711   0.517   0.452   0.728   0.501   0.428
50    T        -0.073  -0.173  -0.246   0.069  -0.091  -0.216  -0.117  -0.258  -0.360
51    E         0.748   0.813   0.621   0.987   1.077   0.824   0.728   0.828   0.485
52    G         1.637   1.670   1.765   1.518   1.565   1.727   1.784   1.832   1.994
53    W        -0.357  -0.322  -0.345  -0.314  -0.283  -0.319  -0.539  -0.501  -0.508
54    P         1.637   1.670   1.765   1.483   1.528   1.691   1.784   1.832   1.994
55    K        -0.812  -0.871  -0.883  -0.754  -0.813  -0.835  -0.751  -0.814  -0.806
56    F         0.748   0.614   0.590   0.748   0.572   0.524   0.728   0.501   0.428
57    Q        -0.073  -0.143  -0.234   0.277   0.187   0.038  -0.117  -0.219  -0.342
58    D        -0.357  -0.311  -0.333  -0.197  -0.137  -0.161  -0.539  -0.494  -0.493
59    T        -0.073  -0.156  -0.241   0.088  -0.014  -0.175  -0.117  -0.236  -0.353
60    L        -0.357  -0.433  -0.347  -0.599  -0.721  -0.593  -0.539  -0.623  -0.508
61    Y        -0.073  -0.173  -0.246   0.057  -0.097  -0.259  -0.117  -0.258  -0.360
62    K        -1.440  -1.358  -1.363  -1.104  -0.996  -0.978  -1.173  -1.081  -1.052
63    K         1.637   1.670   1.765   1.624   1.673   1.833   1.784   1.832   1.994
64    I         1.637   1.670   1.765   1.601   1.609   1.810   1.784   1.832   1.994
65    P         1.637   1.670   1.765   1.483   1.528   1.691   1.784   1.832   1.994
66    L        -1.440  -1.439  -1.376  -1.371  -1.384  -1.308  -1.173  -1.161  -1.063
67    L        -0.073  -0.185  -0.247  -0.091  -0.273  -0.390  -0.117  -0.274  -0.361
68    G         1.637   1.670   1.765   1.518   1.565   1.727   1.784   1.832   1.994
69    P        -1.440  -1.457  -1.397  -1.108  -1.136  -1.072  -1.173  -1.176  -1.082
70    T         0.748   0.777   0.616   1.020   1.066   0.830   0.728   0.771   0.476
71    L         0.748   0.777   0.616   0.951   0.995   0.734   0.728   0.771   0.476
72    E        -0.073  -0.018  -0.219   0.032   0.078  -0.177  -0.117  -0.035  -0.322
73    D        -0.984  -1.022  -0.939  -0.824  -0.846  -0.721  -0.962  -0.984  -0.869
74    H        -0.984  -0.937  -0.920  -0.743  -0.663  -0.638  -0.962  -0.899  -0.850
75    T        -0.984  -0.937  -0.920  -1.113  -1.055  -0.992  -0.962  -0.899  -0.850
76    P        -0.357  -0.267  -0.302  -0.508  -0.379  -0.433  -0.539  -0.408  -0.444
77    P         0.748   0.614   0.590   0.644   0.445   0.391   0.728   0.501   0.428
78    E         0.748   0.614   0.590   0.960   0.769   0.724   0.728   0.501   0.428
79    D         0.748   0.829   0.631   1.004   1.114   0.854   0.728   0.853   0.504
80    K        -0.984  -1.007  -0.940  -0.947  -0.950  -0.859  -0.962  -0.970  -0.870
81    P         0.748   0.793   0.623   0.673   0.733   0.501   0.728   0.795   0.489
82    N        -0.984  -1.007  -0.940  -0.854  -0.882  -0.774  -0.962  -0.970  -0.870
* 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/P37299
Output conservation file - output/P37299
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
