1     M         1.095   1.102   1.172   1.287   1.291   1.394   1.190   1.200   1.302
2     S        -0.869  -0.853  -0.717  -0.905  -0.859  -0.659  -1.071  -1.043  -0.848
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     S        -1.688  -1.712  -1.602  -1.499  -1.510  -1.407  -1.460  -1.475  -1.294
10    Q        -1.487  -1.459  -1.580  -1.213  -1.175  -1.276  -1.239  -1.216  -1.273
11    I        -0.581  -0.604  -0.673  -0.825  -0.856  -0.985  -0.687  -0.700  -0.789
12    I        -1.164  -1.240  -1.211  -1.193  -1.324  -1.294  -1.129  -1.213  -1.122
13    D        -0.904  -0.891  -1.149  -0.514  -0.501  -0.934  -0.798  -0.786  -1.054
14    R        -0.719  -0.787  -0.711  -0.997  -1.126  -1.017  -0.908  -0.979  -0.843
15    P        -0.275  -0.362  -0.628   0.120   0.009  -0.439  -0.245  -0.367  -0.727
16    K        -0.137  -0.088  -0.021  -0.431  -0.342  -0.274  -0.466  -0.382  -0.306
17    H        -0.275  -0.270  -0.620  -0.095  -0.092  -0.573  -0.245  -0.244  -0.716
18    E         0.394   0.409   0.104   0.397   0.420   0.021   0.417   0.439  -0.077
19    L         1.095   1.102   1.172   0.881   0.890   1.022   1.190   1.200   1.302
20    S        -0.196  -0.182  -0.037  -0.356  -0.337  -0.115  -0.577  -0.557  -0.336
21    R        -1.164  -1.122  -1.194  -1.239  -1.194  -1.283  -1.129  -1.093  -1.105
22    A        -2.455  -2.438  -2.220  -2.278  -2.216  -1.903  -1.791  -1.774  -1.505
23    E         1.095   1.102   1.172   0.985   0.999   1.116   1.190   1.200   1.302
24    L         0.394   0.335   0.093   0.261   0.183  -0.173   0.417   0.328  -0.097
25    E        -2.132  -2.150  -1.940  -1.917  -1.923  -1.662  -1.681  -1.686  -1.420
26    E        -2.132  -2.093  -1.934  -2.043  -1.985  -1.807  -1.681  -1.647  -1.416
27    L         1.095   1.102   1.172   0.881   0.890   1.022   1.190   1.200   1.302
28    E         1.095   1.102   1.172   0.985   0.999   1.116   1.190   1.200   1.302
29    E         1.095   1.102   1.172   0.985   0.999   1.116   1.190   1.200   1.302
30    F        -0.719  -0.745  -0.699  -0.468  -0.496  -0.415  -0.908  -0.928  -0.829
31    E         1.095   1.102   1.172   0.985   0.999   1.116   1.190   1.200   1.302
32    F         0.394   0.288   0.089   0.678   0.546   0.242   0.417   0.255  -0.104
33    K        -1.243  -1.177  -1.214  -1.385  -1.305  -1.275  -1.239  -1.177  -1.126
34    H        -0.581  -0.687  -0.687  -0.261  -0.401  -0.422  -0.687  -0.824  -0.809
35    G         1.095   1.102   1.172   1.293   1.300   1.399   1.190   1.200   1.302
36    P         1.095   1.102   1.172   1.315   1.340   1.420   1.190   1.200   1.302
37    M        -0.137  -0.138  -0.028  -0.289  -0.317  -0.179  -0.466  -0.476  -0.319
38    S         1.095   1.102   1.172   1.080   1.097   1.204   1.190   1.200   1.302
39    L        -0.581  -0.582  -0.678  -0.801  -0.812  -0.939  -0.687  -0.695  -0.800
40    I        -0.137  -0.127  -0.020  -0.531  -0.519  -0.335  -0.466  -0.454  -0.304
41    N        -0.719  -0.759  -0.697  -0.624  -0.655  -0.607  -0.908  -0.935  -0.825
42    D        -2.132  -2.157  -1.949  -1.819  -1.877  -1.586  -1.681  -1.690  -1.426
43    A         0.394   0.288   0.089   0.609   0.481   0.130   0.417   0.255  -0.104
44    M        -0.137  -0.127  -0.020  -0.287  -0.281  -0.106  -0.466  -0.454  -0.304
45    V        -2.455  -2.422  -2.208  -2.435  -2.429  -2.083  -1.791  -1.764  -1.498
46    T        -1.164  -1.229  -1.201  -0.987  -1.061  -1.028  -1.129  -1.185  -1.110
47    R        -1.243  -1.177  -1.214  -1.036  -0.966  -0.957  -1.239  -1.177  -1.126
48    T        -1.243  -1.186  -1.192  -1.140  -1.069  -1.041  -1.239  -1.185  -1.105
49    P        -0.137  -0.138  -0.028  -0.024  -0.017   0.113  -0.466  -0.476  -0.319
50    V         0.394   0.431   0.109   0.440   0.484   0.027   0.417   0.471  -0.070
51    I        -0.719  -0.674  -0.702  -0.982  -0.936  -0.947  -0.908  -0.864  -0.832
52    I         1.095   1.102   1.172   1.115   1.128   1.236   1.190   1.200   1.302
53    S         0.394   0.409   0.102   0.470   0.497   0.043   0.417   0.438  -0.082
54    L        -0.719  -0.752  -0.705  -0.727  -0.786  -0.736  -0.908  -0.939  -0.835
55    R         1.095   1.102   1.172   1.103   1.106   1.225   1.190   1.200   1.302
56    N         1.095   1.102   1.172   1.121   1.131   1.241   1.190   1.200   1.302
57    N         0.394   0.335   0.093   0.536   0.466   0.130   0.417   0.328  -0.097
58    H        -0.581  -0.617  -0.687  -0.425  -0.479  -0.681  -0.687  -0.728  -0.808
59    K         1.095   1.102   1.172   0.930   0.940   1.066   1.190   1.200   1.302
60    I         0.048   0.052  -0.006  -0.219  -0.217  -0.314  -0.135  -0.133  -0.278
61    I        -0.137  -0.138  -0.028  -0.446  -0.463  -0.312  -0.466  -0.476  -0.319
62    A         0.394   0.431   0.109   0.640   0.694   0.242   0.417   0.471  -0.070
63    R         0.048   0.106   0.044  -0.062   0.027  -0.125  -0.135  -0.040  -0.185
64    V         1.095   1.102   1.172   1.050   1.057   1.176   1.190   1.200   1.302
65    K         0.394   0.431   0.109   0.318   0.364  -0.083   0.417   0.471  -0.070
66    A         0.394   0.288   0.089   0.609   0.481   0.130   0.417   0.255  -0.104
67    F         1.095   1.102   1.172   1.265   1.274   1.373   1.190   1.200   1.302
68    D         1.095   1.102   1.172   1.270   1.278   1.378   1.190   1.200   1.302
69    R         0.394   0.288   0.089   0.467   0.313  -0.033   0.417   0.255  -0.104
70    H         1.095   1.102   1.172   1.332   1.343   1.435   1.190   1.200   1.302
71    C        -0.581  -0.617  -0.687  -0.267  -0.312  -0.484  -0.687  -0.728  -0.808
72    N         1.095   1.102   1.172   1.121   1.131   1.241   1.190   1.200   1.302
73    M        -0.137  -0.083  -0.009  -0.289  -0.181  -0.122  -0.466  -0.373  -0.284
74    V         0.394   0.455   0.110   0.440   0.512   0.029   0.417   0.505  -0.067
75    L         1.095   1.102   1.172   0.881   0.890   1.022   1.190   1.200   1.302
76    E         1.095   1.102   1.172   0.985   0.999   1.116   1.190   1.200   1.302
77    N         1.095   1.102   1.172   1.121   1.131   1.241   1.190   1.200   1.302
78    V         1.095   1.102   1.172   1.050   1.057   1.176   1.190   1.200   1.302
79    K         1.095   1.102   1.172   0.930   0.940   1.066   1.190   1.200   1.302
80    E         1.095   1.102   1.172   0.985   0.999   1.116   1.190   1.200   1.302
81    L        -0.719  -0.787  -0.711  -0.904  -0.980  -0.837  -0.908  -0.979  -0.843
82    W         1.095   1.102   1.172   1.415   1.424   1.511   1.190   1.200   1.302
83    T         1.095   1.102   1.172   1.265   1.269   1.373   1.190   1.200   1.302
84    E         1.095   1.102   1.172   0.985   0.999   1.116   1.190   1.200   1.302
85    K        -1.487  -1.537  -1.581  -1.373  -1.453  -1.481  -1.239  -1.295  -1.274
86    -        -1.902  -1.875  -1.636  -1.847  -1.798  -1.482  -1.637  -1.609  -1.320
87    -        -0.158  -0.152  -0.032  -0.544  -0.535  -0.330  -0.506  -0.502  -0.326
88    -        -0.869  -0.875  -0.737  -1.018  -1.042  -0.875  -1.071  -1.075  -0.874
89    -        -0.158  -0.140  -0.025  -0.273  -0.242  -0.087  -0.506  -0.478  -0.314
90    -        -0.869  -0.875  -0.737  -1.211  -1.218  -0.986  -1.071  -1.075  -0.874
91    -         1.095   1.102   1.172   1.265   1.274   1.374   1.190   1.200   1.302
92    K         0.394   0.288   0.089   0.310   0.169  -0.137   0.417   0.255  -0.104
93    G        -1.164  -1.122  -1.194  -1.184  -1.145  -1.149  -1.129  -1.093  -1.105
94    K        -0.841  -0.746  -0.694  -0.884  -0.709  -0.708  -1.018  -0.890  -0.816
95    N        -0.275  -0.152  -0.610  -0.240  -0.092  -0.670  -0.245  -0.085  -0.703
96    V        -2.132  -2.139  -1.935  -1.909  -1.930  -1.651  -1.681  -1.679  -1.417
97    I        -0.719  -0.684  -0.690  -0.831  -0.814  -0.749  -0.908  -0.881  -0.819
98    N        -0.581  -0.522  -0.653  -0.542  -0.448  -0.643  -0.687  -0.603  -0.762
99    R        -0.137  -0.127  -0.020  -0.494  -0.486  -0.305  -0.466  -0.454  -0.304
100   E        -0.137  -0.138  -0.028  -0.353  -0.355  -0.173  -0.466  -0.476  -0.319
101   R         1.095   1.102   1.172   1.103   1.106   1.225   1.190   1.200   1.302
102   F         1.095   1.102   1.172   1.265   1.274   1.373   1.190   1.200   1.302
103   I         0.048   0.019  -0.004  -0.012  -0.065  -0.159  -0.135  -0.189  -0.274
104   S         0.394   0.288   0.089   0.486   0.362   0.062   0.417   0.255  -0.104
105   K         1.095   1.102   1.172   0.930   0.940   1.066   1.190   1.200   1.302
106   L        -0.137  -0.127  -0.020  -0.289  -0.286  -0.154  -0.466  -0.454  -0.304
107   F         1.095   1.102   1.172   1.265   1.274   1.373   1.190   1.200   1.302
108   L         1.095   1.102   1.172   0.881   0.890   1.022   1.190   1.200   1.302
109   R         1.095   1.102   1.172   1.103   1.106   1.225   1.190   1.200   1.302
110   G         1.095   1.102   1.172   1.293   1.300   1.399   1.190   1.200   1.302
111   D         1.095   1.102   1.172   1.270   1.278   1.378   1.190   1.200   1.302
112   S        -0.275  -0.251  -0.616  -0.078  -0.044  -0.530  -0.245  -0.216  -0.712
113   V         1.095   1.102   1.172   1.050   1.057   1.176   1.190   1.200   1.302
114   I         0.048   0.092   0.005  -0.012   0.059  -0.139  -0.135  -0.064  -0.256
115   V        -0.920  -0.873  -0.730  -1.301  -1.235  -0.998  -1.129  -1.073  -0.865
116   V         0.048   0.110   0.021  -0.054   0.039  -0.129  -0.135  -0.034  -0.227
117   L        -0.137  -0.150  -0.034  -0.568  -0.601  -0.394  -0.466  -0.497  -0.329
118   K        -0.904  -0.934  -1.173  -0.934  -0.992  -1.400  -0.798  -0.835  -1.080
119   T        -1.164  -1.210  -1.196  -0.948  -1.020  -1.042  -1.129  -1.182  -1.107
120   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q06217
Output conservation file - output/Q06217
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
