1     M         1.258   1.301   1.372   1.549   1.609   1.707   1.347   1.413   1.519
2     S         1.258   1.301   1.372   1.244   1.320   1.436   1.347   1.413   1.519
3     W         1.258   1.301   1.372   1.538   1.599   1.697   1.347   1.413   1.519
4     Q         1.258   1.301   1.372   1.267   1.365   1.457   1.347   1.413   1.519
5     A         1.258   1.301   1.372   0.952   1.009   1.178   1.347   1.413   1.519
6     Y         1.258   1.301   1.372   1.338   1.409   1.519   1.347   1.413   1.519
7     T        -0.171  -0.148   0.011  -0.352  -0.380  -0.118  -0.514  -0.501  -0.261
8     D         1.258   1.301   1.372   1.279   1.362   1.468   1.347   1.413   1.519
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    N         0.043  -0.092   0.014   0.217  -0.063   0.051  -0.142  -0.398  -0.255
11    L         1.258   1.301   1.372   1.160   1.250   1.362   1.347   1.413   1.519
12    I        -1.081  -0.892  -0.775  -1.410  -1.113  -0.936  -1.258  -1.020  -0.845
13    G        -0.847  -0.594  -0.702  -1.349  -0.937  -1.033  -1.010  -0.670  -0.756
14    T        -0.687  -0.491  -0.708  -0.540  -0.276  -0.571  -0.762  -0.505  -0.763
15    G         1.258   1.301   1.372   1.014   1.085   1.233   1.347   1.413   1.519
16    K         0.444   0.216   0.130   0.689   0.413   0.281   0.478   0.125  -0.050
17    V        -0.240  -0.118   0.021  -0.604  -0.393  -0.169  -0.638  -0.446  -0.242
18    D         1.258   1.301   1.372   1.279   1.362   1.468   1.347   1.413   1.519
19    K         0.444   0.348   0.148   0.680   0.578   0.286   0.478   0.333  -0.018
20    A         0.444   0.637   0.177   0.255   0.483  -0.070   0.478   0.745   0.032
21    V        -0.171   0.071   0.093  -0.693  -0.305  -0.237  -0.514  -0.114  -0.114
22    I         0.043   0.210   0.079  -0.079   0.189  -0.062  -0.142   0.116  -0.138
23    Y        -1.062  -1.295  -1.310  -0.688  -1.070  -1.098  -0.886  -1.149  -1.115
24    S         1.258   1.301   1.372   1.244   1.320   1.436   1.347   1.413   1.519
25    R        -0.332  -0.371  -0.667   0.023  -0.114  -0.562  -0.266  -0.356  -0.704
26    A         1.258   1.301   1.372   0.952   1.009   1.178   1.347   1.413   1.519
27    G         1.258   1.301   1.372   1.014   1.085   1.233   1.347   1.413   1.519
28    D         1.258   1.301   1.372   1.279   1.362   1.468   1.347   1.413   1.519
29    A        -0.240  -0.093   0.037  -0.744  -0.438  -0.229  -0.638  -0.401  -0.214
30    V        -0.687  -0.751  -0.728  -0.746  -0.808  -0.804  -0.762  -0.817  -0.786
31    W         1.258   1.301   1.372   1.538   1.599   1.697   1.347   1.413   1.519
32    A         0.444   0.509   0.168   0.310   0.389   0.051   0.478   0.570   0.016
33    T        -1.596  -1.389  -1.336  -1.720  -1.545  -1.379  -1.506  -1.285  -1.144
34    S         0.043  -0.039   0.022   0.011  -0.135  -0.055  -0.142  -0.305  -0.241
35    G        -1.363  -1.495  -1.331  -1.517  -1.687  -1.430  -1.258  -1.359  -1.138
36    G        -0.332  -0.103  -0.641  -0.327  -0.042  -0.693  -0.266   0.027  -0.671
37    L        -0.171   0.071   0.093  -0.203   0.231   0.207  -0.514  -0.114  -0.114
38    S        -1.971  -1.959  -1.772  -1.713  -1.661  -1.403  -1.630  -1.574  -1.323
39    L         0.444   0.509   0.168   0.455   0.569   0.067   0.478   0.570   0.016
40    Q        -1.363  -1.279  -1.323  -1.325  -1.250  -1.342  -1.258  -1.183  -1.132
41    P        -0.332  -0.036  -0.625   0.038   0.421  -0.487  -0.266   0.109  -0.649
42    N        -2.487  -2.365  -2.142  -2.210  -2.081  -1.752  -1.878  -1.731  -1.452
43    E         1.258   1.301   1.372   1.372   1.441   1.550   1.347   1.413   1.519
44    I        -0.332  -0.507  -0.682  -0.134  -0.345  -0.601  -0.266  -0.511  -0.724
45    G        -2.487  -2.358  -2.148  -2.317  -2.106  -1.894  -1.878  -1.729  -1.456
46    E        -0.687  -0.849  -0.748  -0.580  -0.821  -0.729  -0.762  -0.952  -0.814
47    I         0.043   0.031   0.039  -0.079  -0.107  -0.143  -0.142  -0.182  -0.211
48    V        -0.687  -0.664  -0.686  -0.977  -0.930  -0.932  -0.762  -0.705  -0.730
49    Q        -1.596  -1.350  -1.324  -1.654  -1.427  -1.272  -1.506  -1.249  -1.132
50    G         0.444   0.216   0.130   0.308   0.001  -0.122   0.478   0.125  -0.050
51    F        -0.332  -0.433  -0.676   0.126  -0.068  -0.454  -0.266  -0.426  -0.716
52    D        -0.332  -0.642  -0.713  -0.138  -0.598  -0.780  -0.266  -0.676  -0.764
53    N        -0.847  -0.575  -0.694  -0.786  -0.387  -0.560  -1.010  -0.632  -0.742
54    P        -0.332  -0.450  -0.680   0.073  -0.088  -0.513  -0.266  -0.445  -0.722
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    A        -2.345  -2.192  -2.125  -2.014  -1.819  -1.755  -1.754  -1.612  -1.440
62    G        -1.738  -1.829  -1.774  -1.598  -1.728  -1.576  -1.382  -1.461  -1.324
63    L        -0.332  -0.642  -0.713  -0.181  -0.586  -0.681  -0.266  -0.676  -0.764
64    Q         0.043  -0.092   0.014   0.092  -0.096   0.053  -0.142  -0.398  -0.255
65    S        -1.455  -1.332  -1.297  -1.717  -1.602  -1.473  -1.382  -1.212  -1.104
66    N        -2.345  -2.311  -2.152  -1.784  -1.814  -1.647  -1.754  -1.693  -1.458
67    G         1.258   1.301   1.372   1.014   1.085   1.233   1.347   1.413   1.519
68    L         0.444   0.348   0.148   0.459   0.365   0.044   0.478   0.333  -0.018
69    H         0.444   0.348   0.148   0.797   0.674   0.324   0.478   0.333  -0.018
70    I        -0.847  -0.793  -0.721  -1.059  -0.938  -0.839  -1.010  -0.893  -0.780
71    Q        -0.171  -0.148   0.011  -0.528  -0.576  -0.314  -0.514  -0.501  -0.261
72    G         1.258   1.301   1.372   1.014   1.085   1.233   1.347   1.413   1.519
73    Q         1.258   1.301   1.372   1.267   1.365   1.457   1.347   1.413   1.519
74    K         0.444   0.216   0.130   0.680   0.399   0.256   0.478   0.125  -0.050
75    F        -0.171   0.071   0.093  -0.173   0.197   0.219  -0.514  -0.114  -0.114
76    M        -1.363  -1.500  -1.328  -0.922  -1.192  -0.985  -1.258  -1.364  -1.136
77    L        -0.332  -0.642  -0.713  -0.256  -0.724  -0.869  -0.266  -0.676  -0.764
78    L        -0.687  -0.837  -0.745  -0.710  -0.875  -0.755  -0.762  -0.935  -0.810
79    R        -0.332  -0.397  -0.670   0.107   0.012  -0.377  -0.266  -0.384  -0.708
80    A         0.444   0.216   0.130   0.250  -0.065  -0.162   0.478   0.125  -0.050
81    D         0.043  -0.092   0.014   0.058  -0.164  -0.020  -0.142  -0.398  -0.255
82    D         0.043  -0.092   0.014  -0.056  -0.356  -0.230  -0.142  -0.398  -0.255
83    R         1.258   1.301   1.372   1.436   1.509   1.606   1.347   1.413   1.519
84    S         0.444   0.216   0.130   0.585   0.319   0.196   0.478   0.125  -0.050
85    I         0.444   0.216   0.130   0.503   0.197   0.040   0.478   0.125  -0.050
86    Y         1.258   1.301   1.372   1.338   1.409   1.519   1.347   1.413   1.519
87    G         1.258   1.301   1.372   1.014   1.085   1.233   1.347   1.413   1.519
88    R        -0.171  -0.111   0.010  -0.172  -0.089   0.065  -0.514  -0.434  -0.263
89    H        -0.687  -0.849  -0.748  -0.455  -0.715  -0.661  -0.762  -0.952  -0.814
90    D        -1.455  -1.532  -1.319  -1.394  -1.522  -1.227  -1.382  -1.399  -1.127
91    A        -0.687  -0.744  -0.753  -0.902  -0.986  -0.909  -0.762  -0.871  -0.820
92    E        -0.332  -0.507  -0.682   0.003  -0.250  -0.539  -0.266  -0.511  -0.724
93    G         1.258   1.301   1.372   1.014   1.085   1.233   1.347   1.413   1.519
94    V        -0.171  -0.100   0.012  -0.473  -0.367  -0.192  -0.514  -0.413  -0.259
95    V        -0.240  -0.088   0.038  -0.604  -0.333  -0.135  -0.638  -0.393  -0.212
96    C        -0.989  -0.915  -0.782  -0.953  -0.890  -0.778  -1.134  -1.039  -0.853
97    V         1.258   1.301   1.372   1.178   1.247   1.378   1.347   1.413   1.519
98    R        -0.332  -0.642  -0.713   0.023  -0.440  -0.652  -0.266  -0.676  -0.764
99    T         1.258   1.301   1.372   1.332   1.391   1.514   1.347   1.413   1.519
100   K        -0.332  -0.507  -0.682  -0.057  -0.313  -0.642  -0.266  -0.511  -0.724
101   Q         0.444   0.348   0.148   0.560   0.473   0.116   0.478   0.333  -0.018
102   T        -0.847  -0.851  -0.739  -0.993  -1.030  -0.782  -1.010  -0.980  -0.803
103   V         0.043   0.320   0.149  -0.073   0.352   0.074  -0.142   0.291  -0.017
104   I         0.043   0.216   0.068  -0.110   0.175  -0.100  -0.142   0.126  -0.159
105   I        -0.171  -0.148   0.011  -0.462  -0.459  -0.194  -0.514  -0.501  -0.261
106   A        -0.687  -0.661  -0.712  -1.044  -0.993  -1.065  -0.762  -0.702  -0.768
107   H         1.258   1.301   1.372   1.498   1.561   1.662   1.347   1.413   1.519
108   Y         1.258   1.301   1.372   1.338   1.409   1.519   1.347   1.413   1.519
109   P         0.444   0.216   0.130   0.737   0.401   0.190   0.478   0.125  -0.050
110   P        -1.455  -1.165  -1.288  -1.281  -0.874  -1.113  -1.382  -1.045  -1.095
111   T        -0.847  -0.913  -0.747  -1.045  -1.071  -0.786  -1.010  -1.043  -0.813
112   V        -0.332  -0.642  -0.713  -0.238  -0.728  -0.855  -0.266  -0.676  -0.764
113   Q        -0.687  -0.809  -0.747  -0.687  -0.884  -0.843  -0.762  -0.917  -0.814
114   A        -0.171  -0.111   0.010  -0.530  -0.439  -0.187  -0.514  -0.434  -0.263
115   G         1.258   1.301   1.372   1.014   1.085   1.233   1.347   1.413   1.519
116   E         0.444   0.216   0.130   0.711   0.433   0.295   0.478   0.125  -0.050
117   A         0.444   0.216   0.130   0.255  -0.055  -0.146   0.478   0.125  -0.050
118   T         0.444   0.348   0.148   0.596   0.452   0.094   0.478   0.333  -0.018
119   K        -0.687  -0.751  -0.728  -0.532  -0.611  -0.625  -0.762  -0.817  -0.786
120   I        -1.363  -1.359  -1.314  -1.351  -1.343  -1.296  -1.258  -1.233  -1.122
121   V         0.444   0.348   0.148   0.495   0.384   0.107   0.478   0.333  -0.018
122   E         1.258   1.301   1.372   1.372   1.441   1.550   1.347   1.413   1.519
123   Q        -1.081  -0.852  -0.753  -1.422  -1.127  -0.932  -1.258  -0.956  -0.817
124   L         1.258   1.301   1.372   1.160   1.250   1.362   1.347   1.413   1.519
125   A         0.043   0.193   0.064  -0.381  -0.159  -0.370  -0.142   0.088  -0.165
126   D         1.258   1.301   1.372   1.279   1.362   1.468   1.347   1.413   1.519
127   Y         1.258   1.301   1.372   1.338   1.409   1.519   1.347   1.413   1.519
128   L         1.258   1.301   1.372   1.160   1.250   1.362   1.347   1.413   1.519
129   I         0.043  -0.092   0.014  -0.073  -0.339  -0.184  -0.142  -0.398  -0.255
130   G        -1.596  -1.584  -1.338  -1.613  -1.583  -1.237  -1.506  -1.447  -1.145
131   V         0.043  -0.039   0.022  -0.175  -0.383  -0.319  -0.142  -0.305  -0.241
132   Q        -1.081  -0.879  -0.754  -1.314  -1.037  -0.817  -1.258  -0.989  -0.817
133   Y         1.258   1.301   1.372   1.338   1.409   1.519   1.347   1.413   1.519
* 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/P07274
Output conservation file - output/P07274
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
