1     M         0.761   0.801   0.820   1.088   1.123   1.112   0.795   0.848   0.876
2     S         0.761   0.801   0.820   1.029   1.084   1.065   0.795   0.848   0.876
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     I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
6     E        -0.777  -0.627  -0.560  -1.060  -0.766  -0.712  -1.127  -0.879  -0.799
7     N         0.761   0.801   0.820   0.848   0.917   0.921   0.795   0.848   0.876
8     L        -0.115  -0.161  -0.508  -0.069  -0.089  -0.605  -0.102  -0.161  -0.712
9     K        -0.777  -0.627  -0.560  -1.256  -0.975  -0.830  -1.127  -0.879  -0.799
10    S        -1.655  -1.520  -1.375  -1.590  -1.433  -1.231  -1.767  -1.580  -1.372
11    F        -0.949  -1.297  -1.359  -0.572  -1.018  -1.141  -0.871  -1.294  -1.352
12    D         0.761   0.801   0.820   0.670   0.714   0.779   0.795   0.848   0.876
13    P         0.761   0.801   0.820   1.044   1.086   1.077   0.795   0.848   0.876
14    F         0.761   0.801   0.820   0.909   0.953   0.969   0.795   0.848   0.876
15    A         0.761   0.801   0.820   0.939   0.972   0.994   0.795   0.848   0.876
16    D        -0.115  -0.445  -0.525  -0.101  -0.557  -0.672  -0.102  -0.584  -0.740
17    T        -0.115  -0.445  -0.525   0.044  -0.411  -0.544  -0.102  -0.584  -0.740
18    G        -0.115  -0.445  -0.525  -0.049  -0.532  -0.702  -0.102  -0.584  -0.740
19    D        -0.115  -0.445  -0.525  -0.101  -0.557  -0.672  -0.102  -0.584  -0.740
20    D        -1.331  -1.382  -1.354  -1.361  -1.405  -1.324  -1.383  -1.393  -1.347
21    E        -0.777  -0.733  -0.566  -1.052  -1.029  -0.737  -1.127  -1.057  -0.809
22    T        -1.503  -1.594  -1.375  -1.534  -1.564  -1.240  -1.639  -1.654  -1.372
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    A        -1.331  -0.919  -1.332  -1.422  -0.804  -1.366  -1.383  -0.834  -1.320
28    T        -2.058  -1.800  -1.940  -1.730  -1.447  -1.584  -1.896  -1.626  -1.647
29    S        -2.711  -2.613  -2.408  -2.557  -2.460  -2.131  -2.280  -2.105  -1.834
30    N        -0.115  -0.445  -0.525   0.077  -0.361  -0.550  -0.102  -0.584  -0.740
31    Y        -0.115  -0.161  -0.508   0.337   0.276  -0.340  -0.102  -0.161  -0.712
32    I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
33    H         0.761   0.801   0.820   1.088   1.119   1.112   0.795   0.848   0.876
34    I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
35    R         0.761   0.801   0.820   0.924   0.969   0.982   0.795   0.848   0.876
36    I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
37    Q         0.761   0.801   0.820   0.654   0.725   0.766   0.795   0.848   0.876
38    Q         0.761   0.801   0.820   0.654   0.725   0.766   0.795   0.848   0.876
39    R         0.761   0.801   0.820   0.924   0.969   0.982   0.795   0.848   0.876
40    N         0.761   0.801   0.820   0.848   0.917   0.921   0.795   0.848   0.876
41    G         0.761   0.801   0.820   0.748   0.804   0.841   0.795   0.848   0.876
42    R         0.761   0.801   0.820   0.924   0.969   0.982   0.795   0.848   0.876
43    K         0.761   0.801   0.820   0.519   0.578   0.658   0.795   0.848   0.876
44    T         0.761   0.801   0.820   0.802   0.843   0.884   0.795   0.848   0.876
45    L         0.761   0.801   0.820   0.694   0.767   0.798   0.795   0.848   0.876
46    T         0.761   0.801   0.820   0.802   0.843   0.884   0.795   0.848   0.876
47    T         0.761   0.801   0.820   0.802   0.843   0.884   0.795   0.848   0.876
48    V         0.761   0.801   0.820   0.902   0.955   0.963   0.795   0.848   0.876
49    Q         0.761   0.801   0.820   0.654   0.725   0.766   0.795   0.848   0.876
50    G         0.761   0.801   0.820   0.748   0.804   0.841   0.795   0.848   0.876
51    V        -1.503  -1.600  -1.369  -1.693  -1.824  -1.488  -1.639  -1.661  -1.366
52    P         0.761   0.801   0.820   1.044   1.086   1.077   0.795   0.848   0.876
53    E        -3.114  -2.898  -2.773  -2.880  -2.671  -2.440  -2.408  -2.172  -1.947
54    E        -0.115  -0.445  -0.525   0.038  -0.473  -0.692  -0.102  -0.584  -0.740
55    Y        -0.546  -0.697  -0.573  -0.279  -0.588  -0.455  -0.743  -0.996  -0.820
56    D         0.761   0.801   0.820   0.670   0.714   0.779   0.795   0.848   0.876
57    L        -1.331  -1.506  -1.371  -1.468  -1.654  -1.473  -1.383  -1.543  -1.367
58    K         0.761   0.801   0.820   0.519   0.578   0.658   0.795   0.848   0.876
59    R        -0.777  -0.719  -0.572  -1.068  -1.008  -0.780  -1.127  -1.034  -0.820
60    I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
61    L         0.761   0.801   0.820   0.694   0.767   0.798   0.795   0.848   0.876
62    K        -0.115  -0.161  -0.508  -0.242  -0.274  -0.721  -0.102  -0.161  -0.712
63    V        -0.115  -0.161  -0.508   0.142   0.101  -0.448  -0.102  -0.161  -0.712
64    L        -0.115  -0.445  -0.525  -0.070  -0.490  -0.635  -0.102  -0.584  -0.740
65    K         0.761   0.801   0.820   0.519   0.578   0.658   0.795   0.848   0.876
66    K         0.761   0.801   0.820   0.519   0.578   0.658   0.795   0.848   0.876
67    D        -0.115  -0.445  -0.525  -0.101  -0.557  -0.672  -0.102  -0.584  -0.740
68    F         0.761   0.801   0.820   0.909   0.953   0.969   0.795   0.848   0.876
69    A         0.761   0.801   0.820   0.939   0.972   0.994   0.795   0.848   0.876
70    C         0.761   0.801   0.820   1.139   1.170   1.153   0.795   0.848   0.876
71    N         0.761   0.801   0.820   0.848   0.917   0.921   0.795   0.848   0.876
72    G         0.761   0.801   0.820   0.748   0.804   0.841   0.795   0.848   0.876
73    N        -0.546  -0.697  -0.573  -0.564  -0.841  -0.668  -0.743  -0.996  -0.820
74    I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
75    V        -0.949  -1.198  -1.355  -0.690  -1.099  -1.419  -0.871  -1.185  -1.348
76    K        -0.115  -0.445  -0.525  -0.268  -0.724  -0.827  -0.102  -0.584  -0.740
77    D         0.761   0.801   0.820   0.670   0.714   0.779   0.795   0.848   0.876
78    P        -2.058  -1.652  -1.929  -1.929  -1.376  -1.672  -1.896  -1.444  -1.636
79    E        -0.546  -0.697  -0.573  -0.598  -0.922  -0.739  -0.743  -0.996  -0.820
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    M        -1.503  -1.339  -1.365  -1.437  -1.130  -1.163  -1.639  -1.389  -1.360
83    G         0.761   0.801   0.820   0.748   0.804   0.841   0.795   0.848   0.876
84    E        -0.115  -0.445  -0.525   0.059  -0.431  -0.626  -0.102  -0.584  -0.740
85    I        -0.777  -0.570  -0.554  -1.056  -0.638  -0.701  -1.127  -0.783  -0.788
86    I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
87    Q         0.761   0.801   0.820   0.654   0.725   0.766   0.795   0.848   0.876
88    L         0.761   0.801   0.820   0.694   0.767   0.798   0.795   0.848   0.876
89    Q         0.761   0.801   0.820   0.654   0.725   0.766   0.795   0.848   0.876
90    G         0.761   0.801   0.820   0.748   0.804   0.841   0.795   0.848   0.876
91    D         0.761   0.801   0.820   0.670   0.714   0.779   0.795   0.848   0.876
92    Q         0.761   0.801   0.820   0.654   0.725   0.766   0.795   0.848   0.876
93    R         0.761   0.801   0.820   0.924   0.969   0.982   0.795   0.848   0.876
94    A        -2.058  -1.865  -1.938  -1.934  -1.613  -1.842  -1.896  -1.613  -1.644
95    K         0.761   0.801   0.820   0.519   0.578   0.658   0.795   0.848   0.876
96    V        -0.546  -0.667  -0.571  -0.581  -0.845  -0.751  -0.743  -0.945  -0.817
97    C        -2.711  -2.673  -2.409  -2.262  -2.284  -1.905  -2.280  -2.144  -1.835
98    E        -0.546  -0.667  -0.571  -0.598  -0.855  -0.732  -0.743  -0.945  -0.817
99    F         0.761   0.801   0.820   0.909   0.953   0.969   0.795   0.848   0.876
100   M        -0.777  -0.516  -0.536  -0.971  -0.537  -0.564  -1.127  -0.697  -0.758
101   I        -0.850  -0.666  -0.558  -1.340  -0.944  -0.779  -1.255  -0.943  -0.796
102   S        -2.711  -2.645  -2.406  -2.420  -2.327  -2.048  -2.280  -2.132  -1.833
103   Q        -0.546  -0.667  -0.571  -0.844  -1.093  -0.944  -0.743  -0.945  -0.817
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   L         0.761   0.801   0.820   0.694   0.767   0.798   0.795   0.848   0.876
108   G        -0.777  -0.579  -0.554  -1.157  -0.769  -0.770  -1.127  -0.799  -0.789
109   L        -0.949  -0.720  -1.325  -0.840  -0.516  -1.355  -0.871  -0.576  -1.312
110   Q        -1.655  -1.515  -1.376  -1.918  -1.729  -1.447  -1.767  -1.573  -1.373
111   K        -0.115  -0.445  -0.525  -0.239  -0.666  -0.738  -0.102  -0.584  -0.740
112   K         0.761   0.801   0.820   0.519   0.578   0.658   0.795   0.848   0.876
113   N        -0.546  -0.667  -0.571  -0.564  -0.780  -0.664  -0.743  -0.945  -0.817
114   I         0.761   0.801   0.820   0.583   0.651   0.709   0.795   0.848   0.876
115   K         0.761   0.801   0.820   0.519   0.578   0.658   0.795   0.848   0.876
116   I        -0.949  -1.198  -1.355  -0.995  -1.318  -1.580  -0.871  -1.185  -1.348
117   H         0.761   0.801   0.820   1.088   1.119   1.112   0.795   0.848   0.876
118   G         0.761   0.801   0.820   0.748   0.804   0.841   0.795   0.848   0.876
119   F         0.761   0.801   0.820   0.909   0.953   0.969   0.795   0.848   0.876
* 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/P32911
Output conservation file - output/P32911
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
