1     M         0.805   0.805   0.814   1.045   1.030   1.051   0.827   0.827   0.836
2     S         0.805   0.805   0.814   0.976   0.971   0.983   0.827   0.827   0.836
3     K        -0.798  -0.798  -0.766  -0.730  -0.742  -0.675  -0.989  -0.988  -0.931
4     S        -0.798  -0.798  -0.766  -0.637  -0.644  -0.584  -0.989  -0.988  -0.931
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     N         0.805   0.805   0.814   0.976   0.955   0.983   0.827   0.827   0.836
7     T        -1.736  -1.735  -1.690  -1.577  -1.631  -1.498  -1.594  -1.593  -1.521
8     Y         0.805   0.805   0.814   1.165   1.156   1.167   0.827   0.827   0.836
9     R         0.805   0.805   0.814   1.215   1.210   1.216   0.827   0.827   0.836
10    M         0.805   0.805   0.814   1.045   1.030   1.051   0.827   0.827   0.836
11    L        -0.667  -0.654  -0.739  -0.660  -0.693  -0.739  -0.787  -0.767  -0.889
12    V        -0.667  -0.682  -0.744  -0.651  -0.715  -0.794  -0.787  -0.810  -0.898
13    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
14    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
15    E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
16    D        -0.667  -0.664  -0.739  -1.195  -1.082  -1.275  -0.787  -0.782  -0.890
17    D        -0.667  -0.664  -0.739  -0.481  -0.464  -0.643  -0.787  -0.782  -0.890
18    T        -1.736  -1.735  -1.690  -1.439  -1.499  -1.363  -1.594  -1.593  -1.521
19    K        -1.736  -1.735  -1.690  -1.962  -1.920  -1.872  -1.594  -1.593  -1.521
20    I        -0.667  -0.664  -0.739  -1.166  -1.093  -1.238  -0.787  -0.782  -0.890
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    N        -1.736  -1.735  -1.690  -1.367  -1.408  -1.293  -1.594  -1.593  -1.521
24    K        -1.736  -1.735  -1.690  -1.545  -1.578  -1.466  -1.594  -1.593  -1.521
25    E        -1.736  -1.735  -1.690  -1.734  -1.699  -1.650  -1.594  -1.593  -1.521
26    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
27    E        -1.736  -1.735  -1.690  -1.746  -1.712  -1.662  -1.594  -1.593  -1.521
28    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    K         0.805   0.805   0.814   0.762   0.746   0.775   0.827   0.827   0.836
32    G        -1.736  -1.735  -1.690  -1.876  -1.847  -1.788  -1.594  -1.593  -1.521
33    K        -0.667  -0.654  -0.739  -0.962  -0.914  -1.148  -0.787  -0.767  -0.889
34    P        -1.736  -1.735  -1.690  -1.387  -1.399  -1.313  -1.594  -1.593  -1.521
35    G        -1.736  -1.735  -1.690  -1.481  -1.524  -1.404  -1.594  -1.593  -1.521
36    K        -1.736  -1.735  -1.690  -1.491  -1.511  -1.414  -1.594  -1.593  -1.521
37    M        -0.667  -0.682  -0.744  -0.356  -0.409  -0.476  -0.787  -0.810  -0.898
38    H         0.805   0.805   0.814   1.148   1.138   1.151   0.827   0.827   0.836
39    E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
40    F         0.805   0.805   0.814   1.010   0.993   1.017   0.827   0.827   0.836
41    V        -0.667  -0.654  -0.739  -0.529  -0.536  -0.625  -0.787  -0.767  -0.889
42    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
43    E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
44    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
45    I        -1.736  -1.735  -1.690  -1.418  -1.460  -1.343  -1.594  -1.593  -1.521
46    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
47    P         0.805   0.805   0.814   1.080   1.083   1.084   0.827   0.827   0.836
48    F        -0.667  -0.682  -0.744  -0.521  -0.592  -0.680  -0.787  -0.810  -0.898
49    N        -0.667  -0.664  -0.739  -0.310  -0.316  -0.447  -0.787  -0.782  -0.890
50    V        -0.667  -0.654  -0.739  -0.651  -0.664  -0.783  -0.787  -0.767  -0.889
51    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
52    E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
53    L        -1.736  -1.735  -1.690  -1.655  -1.722  -1.573  -1.594  -1.593  -1.521
54    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
55    E        -0.667  -0.664  -0.739  -0.998  -0.993  -1.182  -0.787  -0.782  -0.890
56    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
57    N         0.805   0.805   0.814   0.976   0.955   0.983   0.827   0.827   0.836
58    T        -1.736  -1.735  -1.690  -1.491  -1.525  -1.414  -1.594  -1.593  -1.521
59    W         0.805   0.805   0.814   1.215   1.210   1.216   0.827   0.827   0.836
60    F         0.805   0.805   0.814   1.010   0.993   1.017   0.827   0.827   0.836
61    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
62    K         0.805   0.805   0.814   0.762   0.746   0.775   0.827   0.827   0.836
63    F         0.805   0.805   0.814   1.010   0.993   1.017   0.827   0.827   0.836
64    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
65    A        -1.736  -1.735  -1.690  -1.840  -1.772  -1.753  -1.594  -1.593  -1.521
66    E        -0.667  -0.682  -0.744  -1.176  -1.121  -1.256  -0.787  -0.810  -0.898
67    I         0.805   0.805   0.814   0.780   0.743   0.793   0.827   0.827   0.836
68    C         0.805   0.805   0.814   1.215   1.210   1.216   0.827   0.827   0.836
69    I         0.805   0.805   0.814   0.780   0.743   0.793   0.827   0.827   0.836
70    P         0.805   0.805   0.814   1.080   1.083   1.084   0.827   0.827   0.836
71    N         0.805   0.805   0.814   0.976   0.955   0.983   0.827   0.827   0.836
72    E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
73    G         0.805   0.805   0.814   1.097   1.084   1.101   0.827   0.827   0.836
74    H         0.805   0.805   0.814   1.148   1.138   1.151   0.827   0.827   0.836
75    I         0.805   0.805   0.814   0.780   0.743   0.793   0.827   0.827   0.836
76    K         0.805   0.805   0.814   0.762   0.746   0.775   0.827   0.827   0.836
77    Y         0.805   0.805   0.814   1.165   1.156   1.167   0.827   0.827   0.836
78    E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
79    I         0.805   0.805   0.814   0.780   0.743   0.793   0.827   0.827   0.836
80    S        -0.667  -0.654  -0.739  -0.418  -0.419  -0.522  -0.787  -0.767  -0.889
81    S         0.805   0.805   0.814   0.976   0.971   0.983   0.827   0.827   0.836
82    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
83    G         0.805   0.805   0.814   1.097   1.084   1.101   0.827   0.827   0.836
84    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
85    I         0.805   0.805   0.814   0.780   0.743   0.793   0.827   0.827   0.836
86    V         0.805   0.805   0.814   0.870   0.859   0.880   0.827   0.827   0.836
87    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
88    M        -0.667  -0.664  -0.739  -0.610  -0.655  -0.697  -0.787  -0.782  -0.890
89    L         0.805   0.805   0.814   0.725   0.686   0.740   0.827   0.827   0.836
90    D         0.805   0.805   0.814   0.725   0.765   0.740   0.827   0.827   0.836
91    K         0.805   0.805   0.814   0.762   0.746   0.775   0.827   0.827   0.836
92    E        -0.667  -0.682  -0.744  -1.063  -1.001  -1.108  -0.787  -0.810  -0.898
93    I        -0.667  -0.654  -0.739  -0.761  -0.800  -0.890  -0.787  -0.767  -0.889
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
96    E        -0.667  -0.682  -0.744  -0.971  -0.912  -0.989  -0.787  -0.810  -0.898
97    V        -1.736  -1.735  -1.690  -1.588  -1.649  -1.509  -1.594  -1.593  -1.521
98    V         0.805   0.805   0.814   0.870   0.859   0.880   0.827   0.827   0.836
99    E        -1.736  -1.735  -1.690  -1.621  -1.581  -1.541  -1.594  -1.593  -1.521
100   K        -0.667  -0.682  -0.744  -0.962  -0.974  -1.164  -0.787  -0.810  -0.898
101   V         0.805   0.805   0.814   0.870   0.859   0.880   0.827   0.827   0.836
102   K        -0.667  -0.682  -0.744  -0.610  -0.662  -0.695  -0.787  -0.810  -0.898
103   K        -1.736  -1.735  -1.690  -1.491  -1.529  -1.414  -1.594  -1.593  -1.521
104   F         0.805   0.805   0.814   1.010   0.993   1.017   0.827   0.827   0.836
105   V         0.805   0.805   0.814   0.870   0.859   0.880   0.827   0.827   0.836
106   E         0.805   0.805   0.814   0.325   0.426   0.351   0.827   0.827   0.836
107   E        -0.667  -0.664  -0.739  -0.585  -0.539  -0.808  -0.787  -0.782  -0.890
108   N         0.805   0.805   0.814   0.976   0.955   0.983   0.827   0.827   0.836
109   N        -0.667  -0.682  -0.744  -0.513  -0.573  -0.655  -0.787  -0.810  -0.898
110   -        -0.798  -0.798  -0.766  -0.672  -0.676  -0.619  -0.989  -0.988  -0.931
111   -         0.805   0.805   0.814   0.300   0.302   0.327   0.827   0.827   0.836
112   -        -0.798  -0.798  -0.766  -0.894  -0.899  -0.834  -0.989  -0.988  -0.931
113   -         0.805   0.805   0.814   0.300   0.302   0.327   0.827   0.827   0.836
114   -        -0.798  -0.798  -0.766  -0.972  -0.977  -0.909  -0.989  -0.988  -0.931
115   -         0.805   0.805   0.814   0.300   0.302   0.327   0.827   0.827   0.836
116   -        -0.798  -0.798  -0.766  -1.070  -1.076  -1.005  -0.989  -0.988  -0.931
117   -         0.805   0.805   0.814   0.713   0.717   0.728   0.827   0.827   0.836
118   -        -0.798  -0.798  -0.766  -1.011  -1.016  -0.947  -0.989  -0.988  -0.931
* 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/Q03759
Output conservation file - output/Q03759
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
