1     M         1.348   1.374   1.464   1.571   1.609   1.747   1.471   1.506   1.639
2     P         0.680   0.669   0.495   0.838   0.813   0.586   0.692   0.672   0.339
3     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     R         0.287   0.294   0.327  -0.150  -0.149  -0.132   0.018   0.021   0.021
5     L         1.348   1.374   1.464   1.172   1.217   1.370   1.471   1.506   1.639
6     S         1.348   1.374   1.464   1.490   1.525   1.671   1.471   1.506   1.639
7     G         1.348   1.374   1.464   1.514   1.551   1.694   1.471   1.506   1.639
8     L         1.348   1.374   1.464   1.172   1.217   1.370   1.471   1.506   1.639
9     Q         1.348   1.374   1.464   1.474   1.502   1.656   1.471   1.506   1.639
10    K         0.118   0.147   0.288  -0.497  -0.450  -0.206  -0.310  -0.266  -0.057
11    E         0.043   0.014  -0.206   0.152   0.108  -0.180   0.024  -0.021  -0.345
12    V         1.348   1.374   1.464   1.482   1.522   1.664   1.471   1.506   1.639
13    L         0.174   0.225   0.313  -0.216  -0.123   0.010  -0.198  -0.112  -0.008
14    H        -1.112  -1.105  -1.177  -1.027  -1.022  -1.221  -0.977  -0.963  -0.993
15    L         0.680   0.602   0.483   0.577   0.486   0.319   0.692   0.563   0.318
16    Y         1.348   1.374   1.464   1.474   1.507   1.656   1.471   1.506   1.639
17    R         1.348   1.374   1.464   1.128   1.171   1.329   1.471   1.506   1.639
18    A        -1.303  -1.203  -1.196  -1.458  -1.374  -1.289  -1.200  -1.097  -1.015
19    S         0.043   0.120  -0.192   0.450   0.547   0.078   0.024   0.129  -0.324
20    I        -0.497  -0.436  -0.363  -0.698  -0.620  -0.537  -0.755  -0.674  -0.573
21    R         0.680   0.602   0.483   0.524   0.431   0.259   0.692   0.563   0.318
22    T        -1.727  -1.624  -1.539  -1.505  -1.394  -1.244  -1.423  -1.323  -1.162
23    A        -0.249  -0.206  -0.281  -0.156  -0.092  -0.182  -0.421  -0.343  -0.457
24    H        -0.381  -0.384  -0.335  -0.695  -0.697  -0.656  -0.643  -0.637  -0.542
25    T        -0.249  -0.276  -0.303  -0.250  -0.274  -0.386  -0.421  -0.440  -0.491
26    K         1.348   1.374   1.464   1.189   1.223   1.387   1.471   1.506   1.639
27    P         0.043  -0.109  -0.232   0.315   0.104  -0.131   0.024  -0.190  -0.383
28    K        -2.034  -1.983  -1.817  -1.894  -1.828  -1.585  -1.534  -1.480  -1.256
29    E        -1.112  -1.112  -1.188  -0.931  -0.942  -1.020  -0.977  -0.971  -1.003
30    N        -0.249  -0.306  -0.308  -0.096  -0.174  -0.211  -0.421  -0.489  -0.500
31    Q        -1.303  -1.343  -1.215  -1.407  -1.447  -1.231  -1.200  -1.220  -1.031
32    V        -0.880  -0.893  -0.822  -0.894  -0.911  -0.785  -0.977  -0.973  -0.840
33    N        -0.557  -0.715  -0.762  -0.402  -0.644  -0.765  -0.532  -0.723  -0.764
34    F         0.174   0.198   0.301   0.175   0.205   0.368  -0.198  -0.165  -0.031
35    V        -2.034  -2.010  -1.828  -2.215  -2.135  -1.888  -1.534  -1.499  -1.263
36    N        -1.419  -1.315  -1.236  -1.363  -1.241  -1.113  -1.311  -1.214  -1.051
37    Y        -0.381  -0.397  -0.315  -0.383  -0.385  -0.248  -0.643  -0.639  -0.514
38    I        -0.249  -0.361  -0.329  -0.222  -0.398  -0.359  -0.421  -0.577  -0.530
39    H         0.118   0.145   0.288  -0.333  -0.277  -0.055  -0.310  -0.269  -0.057
40    E        -1.303  -1.313  -1.220  -1.331  -1.367  -1.217  -1.200  -1.194  -1.036
41    E         0.680   0.612   0.484   0.718   0.632   0.456   0.692   0.580   0.320
42    F         1.348   1.374   1.464   1.458   1.491   1.640   1.471   1.506   1.639
43    G        -1.303  -1.248  -1.212  -1.310  -1.307  -1.221  -1.200  -1.146  -1.030
44    K         1.348   1.374   1.464   1.189   1.223   1.387   1.471   1.506   1.639
45    Y        -0.804  -0.698  -0.803  -0.654  -0.534  -0.666  -0.866  -0.765  -0.817
46    R        -0.880  -0.798  -0.808  -1.127  -0.978  -0.992  -0.977  -0.886  -0.825
47    N        -1.727  -1.719  -1.552  -1.526  -1.516  -1.279  -1.423  -1.396  -1.171
48    L         0.043  -0.062  -0.232  -0.010  -0.142  -0.392   0.024  -0.124  -0.383
49    P        -0.804  -0.870  -0.821  -0.582  -0.663  -0.604  -0.866  -0.927  -0.837
50    R        -0.381  -0.390  -0.321  -0.841  -0.815  -0.683  -0.643  -0.628  -0.520
51    K         0.350   0.299   0.334   0.012  -0.105  -0.093   0.136   0.029   0.034
52    D        -0.557  -0.521  -0.740  -0.258  -0.212  -0.627  -0.532  -0.488  -0.738
53    F         1.348   1.374   1.464   1.458   1.491   1.640   1.471   1.506   1.639
54    T        -0.880  -0.879  -0.819  -0.774  -0.772  -0.663  -0.977  -0.962  -0.837
55    T        -0.557  -0.599  -0.756  -0.264  -0.332  -0.584  -0.532  -0.584  -0.756
56    I         1.348   1.374   1.464   1.408   1.455   1.594   1.471   1.506   1.639
57    E         1.348   1.374   1.464   1.308   1.343   1.499   1.471   1.506   1.639
58    H         0.043   0.072  -0.201   0.224   0.274  -0.131   0.024   0.064  -0.337
59    L         1.348   1.374   1.464   1.172   1.217   1.370   1.471   1.506   1.639
60    L         0.350   0.437   0.390   0.089   0.235   0.143   0.136   0.283   0.143
61    R         1.348   1.374   1.464   1.128   1.171   1.329   1.471   1.506   1.639
62    V        -0.249  -0.246  -0.308  -0.231  -0.272  -0.373  -0.421  -0.437  -0.500
63    G         1.348   1.374   1.464   1.514   1.551   1.694   1.471   1.506   1.639
64    N        -1.303  -1.376  -1.234  -1.105  -1.198  -1.010  -1.200  -1.245  -1.048
65    K         0.680   0.669   0.495   0.493   0.485   0.207   0.692   0.672   0.339
66    K        -0.996  -1.030  -0.861  -1.356  -1.364  -1.099  -1.089  -1.107  -0.880
67    I        -0.249  -0.276  -0.297  -0.440  -0.473  -0.491  -0.421  -0.458  -0.486
68    A         0.043   0.120  -0.192   0.080   0.184  -0.300   0.024   0.129  -0.324
69    T        -0.557  -0.715  -0.762  -0.192  -0.430  -0.548  -0.532  -0.723  -0.764
70    F         0.680   0.669   0.495   0.878   0.865   0.612   0.692   0.672   0.339
71    S        -0.804  -0.775  -0.798  -0.718  -0.666  -0.749  -0.866  -0.819  -0.811
72    H        -2.034  -2.010  -1.828  -1.738  -1.738  -1.482  -1.534  -1.499  -1.263
73    P         0.680   0.612   0.484   0.882   0.791   0.547   0.692   0.580   0.320
74    E        -0.804  -0.782  -0.807  -0.781  -0.764  -0.750  -0.866  -0.840  -0.822
75    L        -0.381  -0.330  -0.329  -0.642  -0.547  -0.502  -0.643  -0.592  -0.536
76    T         0.680   0.669   0.495   0.598   0.586   0.362   0.692   0.672   0.339
77    N         0.043  -0.049  -0.214   0.357   0.224  -0.077   0.024  -0.105  -0.356
78    I         0.680   0.612   0.484   0.839   0.769   0.594   0.692   0.580   0.320
79    H         0.043  -0.053  -0.225   0.172   0.049  -0.279   0.024  -0.111  -0.373
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -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/Q3E785
Output conservation file - output/Q3E785
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
