1     M         0.936   0.956   1.009   1.040   1.070   1.145   0.980   1.011   1.087
2     S         0.936   0.956   1.009   0.907   0.953   1.031   0.980   1.011   1.087
3     S        -0.686  -0.948  -1.105  -0.471  -0.816  -1.069  -0.596  -0.928  -1.103
4     S         0.031  -0.226  -0.307   0.095  -0.269  -0.462   0.030  -0.360  -0.517
5     V        -0.058   0.034  -0.309  -0.192  -0.068  -0.588  -0.097   0.031  -0.522
6     P         0.936   0.956   1.009   1.060   1.090   1.162   0.980   1.011   1.087
7     Y         0.936   0.956   1.009   1.189   1.216   1.272   0.980   1.011   1.087
8     D         0.936   0.956   1.009   0.887   0.920   1.014   0.980   1.011   1.087
9     P         0.936   0.956   1.009   1.060   1.090   1.162   0.980   1.011   1.087
10    Y         0.936   0.956   1.009   1.189   1.216   1.272   0.980   1.011   1.087
11    V        -0.523  -0.458  -0.336  -1.065  -0.954  -0.730  -0.838  -0.742  -0.567
12    P         0.105   0.101  -0.275   0.378   0.376  -0.168   0.131   0.125  -0.465
13    P        -1.996  -1.957  -1.702  -2.006  -1.983  -1.586  -1.821  -1.773  -1.426
14    E        -1.977  -1.863  -1.689  -1.780  -1.639  -1.381  -1.808  -1.690  -1.415
15    E        -1.213  -1.194  -1.113  -1.095  -1.057  -0.925  -1.323  -1.273  -1.116
16    S        -2.359  -2.353  -2.131  -2.012  -1.970  -1.675  -1.929  -1.900  -1.589
17    N        -2.359  -2.432  -2.140  -2.010  -2.146  -1.761  -1.929  -1.965  -1.597
18    S        -1.160  -0.964  -1.101  -1.229  -0.964  -1.134  -1.192  -0.949  -1.099
19    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -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    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    N        -1.880  -1.809  -1.696  -1.801  -1.715  -1.578  -1.711  -1.636  -1.421
28    P        -2.482  -2.443  -2.140  -2.243  -2.240  -1.828  -2.028  -1.980  -1.597
29    N        -1.880  -1.851  -1.695  -1.674  -1.669  -1.420  -1.711  -1.679  -1.420
30    S        -1.608  -1.687  -1.690  -1.350  -1.472  -1.480  -1.394  -1.488  -1.415
31    Q        -1.739  -1.531  -1.671  -1.538  -1.259  -1.503  -1.565  -1.351  -1.398
32    N        -2.121  -2.154  -2.132  -1.726  -1.833  -1.744  -1.686  -1.727  -1.590
33    K        -1.049  -1.069  -1.105  -0.995  -1.002  -1.090  -1.080  -1.079  -1.104
34    T         0.105   0.101  -0.275   0.353   0.343  -0.273   0.131   0.125  -0.465
35    A         0.936   0.956   1.009   0.798   0.819   0.938   0.980   1.011   1.087
36    A         0.105  -0.103  -0.288   0.089  -0.197  -0.474   0.131  -0.170  -0.487
37    L        -0.593  -0.536  -0.350  -1.021  -0.909  -0.594  -0.959  -0.877  -0.591
38    R        -1.049  -0.926  -1.104  -0.897  -0.759  -1.038  -1.080  -0.944  -1.104
39    Q        -1.213  -1.162  -1.111  -1.337  -1.273  -1.126  -1.323  -1.271  -1.115
40    E        -0.523  -0.458  -0.336  -0.553  -0.466  -0.290  -0.838  -0.742  -0.567
41    I         0.936   0.956   1.009   0.645   0.682   0.808   0.980   1.011   1.087
42    D         0.936   0.956   1.009   0.887   0.920   1.014   0.980   1.011   1.087
43    D         0.936   0.956   1.009   0.887   0.920   1.014   0.980   1.011   1.087
44    T         0.936   0.956   1.009   1.073   1.098   1.173   0.980   1.011   1.087
45    V         0.936   0.956   1.009   0.770   0.812   0.915   0.980   1.011   1.087
46    G         0.105   0.161  -0.258   0.273   0.334  -0.275   0.131   0.207  -0.435
47    I        -0.304  -0.340  -0.342  -0.673  -0.739  -0.740  -0.474  -0.543  -0.577
48    M         0.936   0.956   1.009   1.040   1.070   1.145   0.980   1.011   1.087
49    R         0.936   0.956   1.009   0.880   0.911   1.008   0.980   1.011   1.087
50    D        -0.523  -0.535  -0.353  -0.686  -0.709  -0.412  -0.838  -0.875  -0.597
51    N         0.936   0.956   1.009   1.007   1.047   1.117   0.980   1.011   1.087
52    I         0.936   0.956   1.009   0.645   0.682   0.808   0.980   1.011   1.087
53    N         0.105   0.034  -0.279   0.302   0.227  -0.286   0.131   0.032  -0.471
54    K         0.936   0.956   1.009   0.940   0.968   1.060   0.980   1.011   1.087
55    V         0.936   0.956   1.009   0.770   0.812   0.915   0.980   1.011   1.087
56    A        -0.304  -0.438  -0.347  -0.476  -0.718  -0.562  -0.474  -0.707  -0.587
57    E         0.105  -0.103  -0.288   0.380   0.116  -0.200   0.131  -0.170  -0.487
58    R         0.936   0.956   1.009   0.880   0.911   1.008   0.980   1.011   1.087
59    G         0.936   0.956   1.009   0.980   1.001   1.094   0.980   1.011   1.087
60    E         0.936   0.956   1.009   1.066   1.101   1.167   0.980   1.011   1.087
61    R         0.936   0.956   1.009   0.880   0.911   1.008   0.980   1.011   1.087
62    L         0.105  -0.103  -0.288   0.246  -0.055  -0.433   0.131  -0.170  -0.487
63    T        -0.523  -0.458  -0.336  -0.682  -0.588  -0.391  -0.838  -0.742  -0.567
64    S         0.105  -0.103  -0.288   0.187  -0.084  -0.428   0.131  -0.170  -0.487
65    I        -0.523  -0.535  -0.353  -0.942  -0.957  -0.611  -0.838  -0.875  -0.597
66    E        -0.593  -0.527  -0.348  -0.678  -0.587  -0.311  -0.959  -0.861  -0.587
67    D        -1.049  -1.069  -1.105  -0.980  -0.977  -1.030  -1.080  -1.079  -1.104
68    K         0.936   0.956   1.009   0.940   0.968   1.060   0.980   1.011   1.087
69    A        -0.523  -0.458  -0.336  -0.663  -0.567  -0.407  -0.838  -0.742  -0.567
70    D         0.936   0.956   1.009   0.887   0.920   1.014   0.980   1.011   1.087
71    N         0.105  -0.103  -0.288   0.300   0.032  -0.312   0.131  -0.170  -0.487
72    L         0.936   0.956   1.009   0.987   1.014   1.100   0.980   1.011   1.087
73    A         0.936   0.956   1.009   0.798   0.819   0.938   0.980   1.011   1.087
74    I        -0.523  -0.480  -0.346  -1.065  -0.994  -0.747  -0.838  -0.779  -0.585
75    S         0.936   0.956   1.009   0.907   0.953   1.031   0.980   1.011   1.087
76    A         0.936   0.956   1.009   0.798   0.819   0.938   0.980   1.011   1.087
77    Q         0.936   0.956   1.009   1.040   1.058   1.145   0.980   1.011   1.087
78    G         0.936   0.956   1.009   0.980   1.001   1.094   0.980   1.011   1.087
79    F         0.936   0.956   1.009   1.164   1.198   1.250   0.980   1.011   1.087
80    K        -0.523  -0.458  -0.336  -0.760  -0.664  -0.467  -0.838  -0.742  -0.567
81    R         0.936   0.956   1.009   0.880   0.911   1.008   0.980   1.011   1.087
82    G         0.936   0.956   1.009   0.980   1.001   1.094   0.980   1.011   1.087
83    A         0.936   0.956   1.009   0.798   0.819   0.938   0.980   1.011   1.087
84    N         0.936   0.956   1.009   1.007   1.047   1.117   0.980   1.011   1.087
85    R         0.105  -0.103  -0.288   0.195  -0.071  -0.339   0.131  -0.170  -0.487
86    V         0.936   0.956   1.009   0.770   0.812   0.915   0.980   1.011   1.087
87    R         0.936   0.956   1.009   0.880   0.911   1.008   0.980   1.011   1.087
88    K         0.936   0.956   1.009   0.940   0.968   1.060   0.980   1.011   1.087
89    Q        -1.357  -1.303  -1.136  -1.371  -1.335  -1.095  -1.444  -1.393  -1.141
90    M         0.936   0.956   1.009   1.040   1.070   1.145   0.980   1.011   1.087
91    W         0.936   0.956   1.009   1.202   1.229   1.283   0.980   1.011   1.087
92    W         0.105   0.101  -0.275   0.536   0.532  -0.014   0.131   0.125  -0.465
93    K         0.936   0.956   1.009   0.940   0.968   1.060   0.980   1.011   1.087
94    D         0.936   0.956   1.009   0.887   0.920   1.014   0.980   1.011   1.087
95    L        -1.451  -1.331  -1.140  -1.402  -1.250  -0.953  -1.565  -1.427  -1.146
96    K         0.105   0.034  -0.279   0.232   0.141  -0.348   0.131   0.032  -0.471
97    M         0.936   0.956   1.009   1.040   1.070   1.145   0.980   1.011   1.087
98    R        -0.304  -0.237  -0.334  -0.386  -0.292  -0.465  -0.474  -0.378  -0.565
99    M        -1.739  -1.820  -1.692  -1.577  -1.755  -1.540  -1.565  -1.645  -1.418
100   C         0.936   0.956   1.009   1.240   1.266   1.316   0.980   1.011   1.087
101   L         0.105   0.034  -0.279   0.246   0.147  -0.413   0.131   0.032  -0.471
102   F        -1.049  -0.953  -1.103  -1.205  -1.071  -1.233  -1.080  -0.960  -1.102
103   L        -1.977  -1.883  -1.698  -2.105  -2.053  -1.678  -1.808  -1.725  -1.423
104   V        -0.523  -0.458  -0.336  -0.760  -0.659  -0.487  -0.838  -0.742  -0.567
105   V        -0.593  -0.521  -0.343  -1.189  -1.071  -0.742  -0.959  -0.850  -0.579
106   I         0.936   0.956   1.009   0.645   0.682   0.808   0.980   1.011   1.087
107   I         0.105   0.101  -0.275  -0.009  -0.001  -0.404   0.131   0.125  -0.465
108   L        -0.304  -0.111  -0.292  -0.336  -0.038  -0.385  -0.474  -0.182  -0.493
109   L        -0.304  -0.146  -0.316  -0.375  -0.123  -0.499  -0.474  -0.235  -0.534
110   V        -0.523  -0.393  -0.325  -1.018  -0.765  -0.684  -0.838  -0.632  -0.549
111   V        -0.686  -0.891  -1.099  -0.694  -1.006  -1.383  -0.596  -0.860  -1.096
112   I         0.936   0.956   1.009   0.645   0.682   0.808   0.980   1.011   1.087
113   I        -0.523  -0.434  -0.347  -1.065  -0.908  -0.748  -0.838  -0.700  -0.585
114   V         0.936   0.956   1.009   0.770   0.812   0.915   0.980   1.011   1.087
115   P         0.936   0.956   1.009   1.060   1.090   1.162   0.980   1.011   1.087
116   I         0.105  -0.103  -0.288  -0.077  -0.356  -0.631   0.131  -0.170  -0.487
117   V        -0.304  -0.360  -0.348  -0.521  -0.642  -0.643  -0.474  -0.577  -0.587
118   V        -0.686  -0.655  -1.080  -0.646  -0.594  -1.225  -0.596  -0.565  -1.074
119   H        -0.686  -0.948  -1.105  -0.169  -0.563  -0.932  -0.596  -0.928  -1.103
120   F         0.105  -0.103  -0.288   0.481   0.220  -0.114   0.131  -0.170  -0.487
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   S        -0.686  -0.948  -1.105  -0.493  -0.849  -1.127  -0.596  -0.928  -1.103
* 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/P33328
Output conservation file - output/P33328
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
