1     M         1.490   1.584   1.671   1.532   1.677   1.812   1.623   1.755   1.903
2     V         0.004   0.097  -0.258   0.278   0.396  -0.085   0.015   0.125  -0.360
3     A        -0.328  -0.512  -0.391  -0.331  -0.636  -0.466  -0.480  -0.707  -0.554
4     S         1.490   1.584   1.671   1.486   1.631   1.769   1.623   1.755   1.903
5     C         1.490   1.584   1.671   1.479   1.617   1.762   1.623   1.755   1.903
6     K         0.729   0.945   0.556   0.563   0.863   0.363   0.757   1.070   0.426
7     D         0.004  -0.305  -0.310   0.116  -0.308  -0.336   0.015  -0.413  -0.433
8     Q         0.154   0.216   0.348   0.048   0.147   0.354  -0.233  -0.160   0.032
9     K         0.154   0.429   0.411  -0.264   0.236   0.151  -0.233   0.239   0.155
10    K        -1.310  -1.365  -1.374  -1.340  -1.465  -1.416  -1.099  -1.132  -1.077
11    A         0.004  -0.187  -0.289   0.170  -0.112  -0.275   0.015  -0.260  -0.404
12    V         0.090   0.246   0.354  -0.220   0.006   0.168  -0.356  -0.102   0.045
13    A         1.490   1.584   1.671   1.479   1.621   1.762   1.623   1.755   1.903
14    I         0.004  -0.305  -0.310   0.352  -0.099  -0.138   0.015  -0.413  -0.433
15    C         1.490   1.584   1.671   1.479   1.617   1.762   1.623   1.755   1.903
16    L         1.490   1.584   1.671   1.284   1.454   1.579   1.623   1.755   1.903
17    Q         0.729   0.521   0.523   0.822   0.521   0.490   0.757   0.402   0.364
18    R         0.004  -0.305  -0.310   0.138  -0.274  -0.284   0.015  -0.413  -0.433
19    S         1.490   1.584   1.671   1.486   1.631   1.769   1.623   1.755   1.903
20    P         0.004  -0.305  -0.310   0.185  -0.283  -0.334   0.015  -0.413  -0.433
21    C         1.490   1.584   1.671   1.479   1.617   1.762   1.623   1.755   1.903
22    V         0.729   0.521   0.523   0.979   0.695   0.685   0.757   0.402   0.364
23    M        -0.478  -0.491  -0.357  -0.642  -0.546  -0.398  -0.727  -0.675  -0.507
24    I        -0.478  -0.242  -0.358  -0.409  -0.092  -0.253  -0.727  -0.422  -0.512
25    E        -1.310  -1.393  -1.377  -1.177  -1.365  -1.291  -1.099  -1.154  -1.080
26    R         0.729   0.521   0.523   0.719   0.400   0.381   0.757   0.402   0.364
27    H        -0.478  -0.463  -0.345  -0.452  -0.466  -0.285  -0.727  -0.635  -0.490
28    N        -0.960  -0.699  -0.913  -0.847  -0.576  -0.846  -0.975  -0.720  -0.851
29    P         0.354   0.246   0.353   0.329   0.102   0.253   0.138  -0.102   0.043
30    Q        -0.960  -1.014  -0.914  -1.147  -1.209  -1.052  -0.975  -0.974  -0.846
31    E        -0.960  -0.731  -0.903  -1.090  -0.813  -1.034  -0.975  -0.717  -0.840
32    C         1.490   1.584   1.671   1.479   1.617   1.762   1.623   1.755   1.903
33    L         0.729   0.945   0.556   0.653   0.959   0.473   0.757   1.070   0.426
34    D        -2.010  -1.905  -1.765  -2.001  -1.926  -1.680  -1.593  -1.418  -1.240
35    N        -0.538  -0.416  -0.387  -0.789  -0.570  -0.575  -0.801  -0.596  -0.548
36    P         1.490   1.584   1.671   1.508   1.640   1.789   1.623   1.755   1.903
37    E        -0.840  -0.793  -0.909  -0.840  -0.789  -1.011  -0.801  -0.746  -0.839
38    L         1.490   1.584   1.671   1.276   1.448   1.572   1.623   1.755   1.903
39    N        -1.178  -0.901  -0.947  -1.348  -0.960  -0.963  -1.222  -0.895  -0.886
40    K         0.354   0.246   0.353   0.011  -0.182  -0.021   0.138  -0.102   0.043
41    D         0.004  -0.305  -0.310   0.109  -0.340  -0.352   0.015  -0.413  -0.433
42    L         0.729   0.801   0.545   0.635   0.779   0.415   0.757   0.858   0.405
43    P         1.490   1.584   1.671   1.519   1.663   1.800   1.623   1.755   1.903
44    E         0.729   0.656   0.518   0.726   0.638   0.466   0.757   0.629   0.356
45    L        -0.328  -0.462  -0.389  -0.547  -0.759  -0.638  -0.480  -0.655  -0.552
46    C         1.490   1.584   1.671   1.479   1.617   1.762   1.623   1.755   1.903
47    I        -1.528  -1.436  -1.374  -1.362  -1.316  -1.184  -1.346  -1.196  -1.080
48    A        -0.678  -0.935  -0.929  -0.483  -0.872  -0.917  -0.604  -0.891  -0.861
49    Q        -0.960  -0.932  -0.937  -0.922  -0.942  -0.914  -0.975  -0.928  -0.875
50    M        -0.960  -1.043  -0.936  -0.805  -0.920  -0.799  -0.975  -1.007  -0.871
51    K        -1.046  -1.049  -0.930  -1.328  -1.300  -1.091  -1.099  -1.027  -0.866
52    A         0.729   0.801   0.545   0.824   0.939   0.574   0.757   0.858   0.405
53    F         0.729   0.521   0.523   1.006   0.762   0.750   0.757   0.402   0.364
54    L        -0.610  -0.493  -0.418  -0.858  -0.637  -0.544  -0.851  -0.695  -0.587
55    D        -0.478  -0.387  -0.367  -0.724  -0.599  -0.529  -0.727  -0.584  -0.526
56    C         1.490   1.584   1.671   1.479   1.617   1.762   1.623   1.755   1.903
57    K         0.154   0.242   0.341  -0.336  -0.198  -0.037  -0.233  -0.109   0.019
58    R         0.354   0.620   0.470   0.237   0.626   0.398   0.138   0.569   0.266
59    G         0.729   0.521   0.523   0.898   0.631   0.608   0.757   0.402   0.364
60    I         0.354   0.626   0.457   0.395   0.795   0.535   0.138   0.579   0.242
61    V        -0.960  -1.043  -0.936  -0.705  -0.861  -0.708  -0.975  -1.007  -0.871
62    D         1.490   1.584   1.671   1.413   1.561   1.700   1.623   1.755   1.903
63    M         1.490   1.584   1.671   1.532   1.677   1.812   1.623   1.755   1.903
64    T         0.154   0.280   0.349  -0.001   0.182   0.258  -0.233  -0.037   0.034
65    K         1.490   1.584   1.671   1.215   1.373   1.514   1.623   1.755   1.903
66    R         1.490   1.584   1.671   1.413   1.544   1.700   1.623   1.755   1.903
67    F        -0.328  -0.333  -0.320  -0.117  -0.068  -0.092  -0.480  -0.452  -0.449
68    T         0.004   0.374  -0.205   0.085   0.556  -0.230   0.015   0.519  -0.283
69    G         0.729   0.521   0.523   0.919   0.671   0.658   0.757   0.402   0.364
70    N         0.729   0.521   0.523   0.856   0.577   0.564   0.757   0.402   0.364
71    A        -0.678  -0.835  -0.893  -0.430  -0.680  -0.750  -0.604  -0.791  -0.821
72    P         0.004  -0.064  -0.260   0.196   0.056  -0.220   0.015  -0.111  -0.362
73    L         0.004  -0.305  -0.310  -0.035  -0.466  -0.494   0.015  -0.413  -0.433
74    S         0.004  -0.305  -0.310   0.206  -0.217  -0.236   0.015  -0.413  -0.433
75    T         0.729   0.656   0.518   0.955   0.877   0.678   0.757   0.629   0.356
76    G         0.004  -0.305  -0.310   0.241  -0.205  -0.253   0.015  -0.413  -0.433
77    K         0.354   0.287   0.361   0.043  -0.066   0.048   0.138  -0.024   0.058
78    Y        -0.678  -0.935  -0.929  -0.244  -0.685  -0.732  -0.604  -0.891  -0.861
79    D         0.004  -0.305  -0.310   0.133  -0.279  -0.297   0.015  -0.413  -0.433
80    Q        -0.328   0.080  -0.257  -0.432   0.143  -0.319  -0.480   0.110  -0.359
81    Q        -0.696  -0.576  -0.429  -0.923  -0.801  -0.569  -0.975  -0.791  -0.600
82    Y        -0.678  -0.815  -0.888  -0.210  -0.481  -0.585  -0.604  -0.772  -0.816
83    E        -0.960  -1.020  -0.917  -1.027  -1.097  -0.950  -0.975  -0.981  -0.851
84    N        -0.478  -0.429  -0.363  -0.731  -0.587  -0.528  -0.727  -0.604  -0.519
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   L        -0.118  -0.351  -0.369  -0.147  -0.430  -0.463  -0.154  -0.482  -0.517
104   C        -0.440  -0.420  -0.361  -0.470  -0.415  -0.341  -0.639  -0.575  -0.507
105   K        -1.090  -0.969  -0.935  -1.093  -0.925  -0.919  -1.124  -0.948  -0.871
106   G         1.490   1.584   1.671   1.537   1.674   1.816   1.623   1.755   1.903
107   K        -1.090  -0.864  -0.931  -1.091  -0.691  -0.855  -1.124  -0.819  -0.865
108   F         0.662   0.463   0.463   0.880   0.589   0.562   0.653   0.300   0.253
109   D        -1.641  -1.547  -1.404  -1.630  -1.492  -1.298  -1.447  -1.285  -1.104
110   P         0.111   0.210   0.339  -0.131  -0.005   0.208  -0.316  -0.171   0.015
111   R        -1.490  -1.449  -1.395  -1.426  -1.434  -1.327  -1.285  -1.202  -1.096
112   E         0.662   0.463   0.463   0.653   0.375   0.364   0.653   0.300   0.253
113   E         0.662   0.463   0.463   0.638   0.354   0.326   0.653   0.300   0.253
114   M        -0.840  -0.937  -0.946  -0.550  -0.679  -0.701  -0.801  -0.903  -0.880
115   E        -1.641  -1.390  -1.384  -1.707  -1.324  -1.324  -1.447  -1.149  -1.087
116   K        -0.118  -0.351  -0.369  -0.231  -0.547  -0.584  -0.154  -0.482  -0.517
117   L         0.662   0.654   0.481   0.535   0.570   0.282   0.653   0.626   0.286
118   K        -1.663  -1.503  -1.411  -1.853  -1.581  -1.453  -1.456  -1.246  -1.110
119   L        -1.196  -1.072  -0.980  -1.249  -1.079  -0.916  -1.236  -1.056  -0.917
120   L         0.580   0.444   0.409   0.398   0.223   0.143   0.523   0.266   0.151
121   N        -0.262  -0.312  -0.388  -0.170  -0.259  -0.426  -0.356  -0.436  -0.543
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   S        -1.490  -1.439  -1.403  -1.358  -1.365  -1.286  -1.285  -1.194  -1.102
143   Q        -2.010  -1.759  -1.728  -1.886  -1.503  -1.499  -1.593  -1.323  -1.214
144   Q        -2.361  -2.156  -2.056  -2.262  -1.956  -1.838  -1.717  -1.482  -1.327
145   K         0.004  -0.187  -0.289  -0.096  -0.367  -0.501   0.015  -0.260  -0.404
146   D        -2.010  -1.883  -1.751  -2.013  -1.862  -1.678  -1.593  -1.406  -1.230
* 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/Q02772
Output conservation file - output/Q02772
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
