1     M         1.513   1.634   1.628   1.761   1.964   1.936   1.650   1.789   1.800
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     G        -0.067   0.114   0.029  -0.448  -0.192  -0.274  -0.271   0.033  -0.117
4     G         1.513   1.634   1.628   1.485   1.626   1.669   1.650   1.789   1.800
5     N        -0.207  -0.078  -0.036  -0.246  -0.055   0.010  -0.511  -0.280  -0.227
6     V         0.117  -0.054  -0.014  -0.006  -0.362  -0.281   0.030  -0.240  -0.189
7     L        -1.067  -1.039  -1.034  -1.043  -0.986  -1.013  -1.051  -0.950  -0.942
8     P         1.513   1.634   1.628   1.812   2.007   1.985   1.650   1.789   1.800
9     I        -1.067  -1.042  -1.032  -1.265  -1.306  -1.223  -1.051  -0.953  -0.938
10    H         1.513   1.634   1.628   1.722   1.884   1.898   1.650   1.789   1.800
11    Y        -0.207  -0.078  -0.036  -0.153   0.064   0.139  -0.511  -0.280  -0.227
12    D         0.117  -0.054  -0.014   0.296   0.001   0.053   0.030  -0.240  -0.189
13    P        -1.067  -1.023  -1.031  -0.868  -0.925  -0.870  -1.051  -0.935  -0.938
14    K        -1.927  -1.746  -1.753  -1.821  -1.534  -1.527  -1.591  -1.299  -1.307
15    T         0.117  -0.054  -0.014   0.199  -0.072  -0.038   0.030  -0.240  -0.189
16    V         1.513   1.634   1.628   1.444   1.645   1.630   1.650   1.789   1.800
17    K         0.117   0.381   0.086   0.126   0.520   0.096   0.030   0.439  -0.024
18    Q         0.117  -0.054  -0.014   0.220  -0.075  -0.012   0.030  -0.240  -0.189
19    L         0.117  -0.054  -0.014  -0.047  -0.403  -0.316   0.030  -0.240  -0.189
20    T         0.117  -0.054  -0.014   0.195  -0.067  -0.045   0.030  -0.240  -0.189
21    K         0.117  -0.054  -0.014   0.152  -0.101  -0.019   0.030  -0.240  -0.189
22    E         1.513   1.634   1.628   1.485   1.698   1.669   1.650   1.789   1.800
23    I         1.513   1.634   1.628   1.431   1.624   1.617   1.650   1.789   1.800
24    T        -1.067  -1.039  -1.034  -1.296  -1.245  -1.183  -1.051  -0.950  -0.942
25    V        -1.067  -1.039  -1.034  -1.107  -0.990  -1.030  -1.051  -0.950  -0.942
26    A         0.117  -0.054  -0.014  -0.138  -0.463  -0.320   0.030  -0.240  -0.189
27    S         0.117   0.381   0.086   0.060   0.510  -0.015   0.030   0.439  -0.024
28    C        -1.067  -1.039  -1.034  -0.957  -0.980  -0.864  -1.051  -0.950  -0.942
29    I         1.513   1.634   1.628   1.431   1.624   1.617   1.650   1.789   1.800
30    G         1.513   1.634   1.628   1.485   1.626   1.669   1.650   1.789   1.800
31    A         0.117  -0.054  -0.014  -0.138  -0.463  -0.320   0.030  -0.240  -0.189
32    A        -1.067  -0.801  -0.959  -1.271  -0.790  -1.091  -1.051  -0.644  -0.851
33    Q         0.117   0.345   0.077   0.212   0.597   0.142   0.030   0.386  -0.038
34    G         1.513   1.634   1.628   1.485   1.626   1.669   1.650   1.789   1.800
35    A         1.513   1.634   1.628   1.224   1.368   1.417   1.650   1.789   1.800
36    L        -1.067  -1.042  -1.032  -1.289  -1.231  -1.244  -1.051  -0.953  -0.938
37    F        -0.207  -0.070  -0.031  -0.351  -0.063  -0.023  -0.511  -0.266  -0.218
38    S        -0.207  -0.068  -0.032  -0.420  -0.199  -0.119  -0.511  -0.263  -0.220
39    I        -1.067  -1.042  -1.032  -1.283  -1.324  -1.247  -1.051  -0.953  -0.938
40    A        -1.067  -0.777  -0.955  -1.289  -0.860  -1.079  -1.051  -0.615  -0.847
41    S        -0.207  -0.070  -0.031  -0.351  -0.070  -0.056  -0.511  -0.266  -0.218
42    A         0.117  -0.054  -0.014  -0.056  -0.309  -0.180   0.030  -0.240  -0.189
43    L         0.117  -0.054  -0.014   0.095  -0.125  -0.071   0.030  -0.240  -0.189
44    L         1.513   1.634   1.628   1.404   1.600   1.590   1.650   1.789   1.800
45    L         0.117  -0.054  -0.014  -0.047  -0.403  -0.316   0.030  -0.240  -0.189
46    R         0.117  -0.054  -0.014   0.042  -0.233  -0.172   0.030  -0.240  -0.189
47    R        -1.067  -1.042  -1.032  -1.032  -0.887  -0.927  -1.051  -0.953  -0.938
48    F        -0.207  -0.078  -0.036  -0.199   0.038   0.085  -0.511  -0.280  -0.227
49    S         0.117  -0.054  -0.014   0.263   0.091   0.125   0.030  -0.240  -0.189
50    S        -1.067  -1.039  -1.034  -0.851  -0.696  -0.767  -1.051  -0.950  -0.942
51    V        -1.927  -1.746  -1.753  -1.747  -1.363  -1.455  -1.591  -1.299  -1.307
52    Y         1.513   1.634   1.628   1.644   1.839   1.823   1.650   1.789   1.800
53    R         0.117  -0.054  -0.014   0.051  -0.237  -0.157   0.030  -0.240  -0.189
54    N         0.117  -0.054  -0.014   0.387   0.083   0.124   0.030  -0.240  -0.189
55    V         0.117  -0.054  -0.014   0.051  -0.233  -0.180   0.030  -0.240  -0.189
56    R         0.117  -0.054  -0.014   0.082  -0.136  -0.105   0.030  -0.240  -0.189
57    T         0.117  -0.054  -0.014   0.199  -0.072  -0.038   0.030  -0.240  -0.189
58    Q         1.513   1.634   1.628   1.591   1.807   1.772   1.650   1.789   1.800
59    V         0.117  -0.054  -0.014   0.134  -0.087  -0.038   0.030  -0.240  -0.189
60    R         0.117  -0.054  -0.014   0.042  -0.233  -0.172   0.030  -0.240  -0.189
61    V         0.117  -0.054  -0.014   0.051  -0.233  -0.180   0.030  -0.240  -0.189
62    F         1.513   1.634   1.628   1.657   1.859   1.836   1.650   1.789   1.800
63    Y         0.117  -0.054  -0.014   0.246  -0.062  -0.012   0.030  -0.240  -0.189
64    H         0.117  -0.054  -0.014   0.379   0.089   0.153   0.030  -0.240  -0.189
65    C        -1.067  -1.023  -1.031  -0.824  -0.806  -0.829  -1.051  -0.935  -0.938
66    S         1.513   1.634   1.628   1.512   1.730   1.695   1.650   1.789   1.800
67    W         0.117  -0.054  -0.014   0.581   0.354   0.392   0.030  -0.240  -0.189
68    I         0.117  -0.054  -0.014   0.051  -0.225  -0.169   0.030  -0.240  -0.189
69    S         0.117  -0.054  -0.014   0.126  -0.144  -0.108   0.030  -0.240  -0.189
70    M         0.117  -0.054  -0.014   0.412   0.156   0.177   0.030  -0.240  -0.189
71    G         1.513   1.634   1.628   1.485   1.626   1.669   1.650   1.789   1.800
72    A        -1.067  -1.042  -1.032  -1.340  -1.319  -1.235  -1.051  -0.953  -0.938
73    V         1.513   1.634   1.628   1.444   1.645   1.630   1.650   1.789   1.800
74    F         0.117  -0.054  -0.014   0.334   0.085   0.128   0.030  -0.240  -0.189
75    R        -1.067  -1.042  -1.032  -1.125  -1.170  -1.043  -1.051  -0.953  -0.938
76    A         1.513   1.634   1.628   1.224   1.368   1.417   1.650   1.789   1.800
77    D         1.513   1.634   1.628   1.670   1.850   1.848   1.650   1.789   1.800
78    K         1.513   1.634   1.628   1.458   1.634   1.643   1.650   1.789   1.800
79    Q         0.117  -0.054  -0.014   0.199  -0.078  -0.049   0.030  -0.240  -0.189
80    L         1.513   1.634   1.628   1.404   1.600   1.590   1.650   1.789   1.800
81    L         0.117   0.351   0.079   0.038   0.417  -0.023   0.030   0.395  -0.036
82    K         0.117  -0.054  -0.014   0.069  -0.229  -0.161   0.030  -0.240  -0.189
83    F         0.117  -0.054  -0.014   0.334   0.085   0.128   0.030  -0.240  -0.189
84    Q         0.117  -0.054  -0.014   0.220  -0.037  -0.012   0.030  -0.240  -0.189
85    T        -1.927  -1.746  -1.753  -1.585  -1.239  -1.299  -1.591  -1.299  -1.307
86    N        -1.067  -0.801  -0.959  -1.009  -0.585  -0.815  -1.051  -0.644  -0.851
87    Y         0.117  -0.054  -0.014   0.246  -0.062  -0.012   0.030  -0.240  -0.189
88    Y         0.117  -0.054  -0.014   0.250  -0.050  -0.005   0.030  -0.240  -0.189
89    R        -1.927  -1.746  -1.753  -2.104  -1.749  -1.800  -1.591  -1.299  -1.307
90    E        -1.067  -1.023  -1.031  -0.879  -0.769  -0.764  -1.051  -0.935  -0.938
91    E         0.117  -0.054  -0.014   0.152  -0.070  -0.042   0.030  -0.240  -0.189
92    Q        -1.927  -1.746  -1.753  -1.725  -1.427  -1.435  -1.591  -1.299  -1.307
93    K         0.117  -0.054  -0.014   0.186  -0.025   0.039   0.030  -0.240  -0.189
94    R         0.117  -0.054  -0.014   0.025  -0.252  -0.203   0.030  -0.240  -0.189
95    R         0.117  -0.054  -0.014   0.034  -0.239  -0.188   0.030  -0.240  -0.189
96    E         0.117  -0.054  -0.014   0.034  -0.313  -0.246   0.030  -0.240  -0.189
97    K        -1.067  -1.023  -1.031  -1.137  -1.045  -1.073  -1.051  -0.935  -0.938
98    I         0.117  -0.054  -0.014   0.042  -0.238  -0.184   0.030  -0.240  -0.189
99    M        -1.067  -1.039  -1.034  -1.143  -1.192  -1.064  -1.051  -0.950  -0.942
100   D         0.117  -0.054  -0.014   0.216  -0.176  -0.086   0.030  -0.240  -0.189
101   E         0.117  -0.054  -0.014   0.034  -0.313  -0.246   0.030  -0.240  -0.189
102   A         1.513   1.634   1.628   1.224   1.368   1.417   1.650   1.789   1.800
103   A         0.117  -0.054  -0.014  -0.138  -0.420  -0.320   0.030  -0.240  -0.189
104   E         0.117  -0.054  -0.014   0.034  -0.313  -0.246   0.030  -0.240  -0.189
105   R         1.513   1.634   1.628   1.417   1.622   1.604   1.650   1.789   1.800
106   G         1.513   1.634   1.628   1.485   1.626   1.669   1.650   1.789   1.800
107   L        -1.067  -1.039  -1.034  -1.167  -1.083  -1.105  -1.051  -0.950  -0.942
108   F         0.117  -0.054  -0.014   0.334   0.085   0.128   0.030  -0.240  -0.189
109   L         0.117  -0.054  -0.014   0.020  -0.258  -0.199   0.030  -0.240  -0.189
110   E         0.117  -0.054  -0.014   0.177  -0.046   0.002   0.030  -0.240  -0.189
111   D        -1.067  -1.039  -1.034  -0.901  -0.810  -0.794  -1.051  -0.950  -0.942
112   E         0.117  -0.054  -0.014   0.177  -0.046   0.002   0.030  -0.240  -0.189
113   S        -1.067  -1.042  -1.032  -1.173  -1.146  -1.140  -1.051  -0.953  -0.938
114   L        -1.927  -1.746  -1.753  -1.958  -1.557  -1.660  -1.591  -1.299  -1.307
115   N        -1.927  -1.746  -1.753  -1.866  -1.544  -1.570  -1.591  -1.299  -1.307
116   S        -1.927  -1.746  -1.753  -1.690  -1.394  -1.400  -1.591  -1.299  -1.307
117   S         0.117  -0.054  -0.014   0.203  -0.019   0.024   0.030  -0.240  -0.189
118   R        -1.927  -1.746  -1.753  -1.873  -1.493  -1.578  -1.591  -1.299  -1.307
119   S        -1.067  -0.777  -0.955  -1.113  -0.581  -0.926  -1.051  -0.615  -0.847
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   T        -1.067  -1.042  -1.032  -1.043  -0.995  -1.002  -1.051  -0.953  -0.938
125   T         0.117   0.351   0.079   0.121   0.480   0.080   0.030   0.395  -0.036
* 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/Q3E776
Output conservation file - output/Q3E776
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
