1     M         1.373   1.417   1.484   1.513   1.553   1.680   1.437   1.508   1.612
2     S        -0.404  -0.365  -0.467  -0.569  -0.535  -0.671  -0.505  -0.520  -0.590
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     R         0.563   0.464   0.333   0.422   0.305   0.090   0.542   0.375   0.126
7     E         1.373   1.417   1.484   1.451   1.509   1.622   1.437   1.508   1.612
8     G        -0.199  -0.465  -0.483  -0.032  -0.481  -0.538  -0.205  -0.574  -0.603
9     F         0.563   0.375   0.318   0.835   0.570   0.478   0.542   0.230   0.098
10    Q        -0.514  -0.434  -0.497  -0.535  -0.482  -0.593  -0.652  -0.573  -0.627
11    I        -0.905  -1.060  -1.037  -0.596  -0.874  -0.902  -0.802  -0.990  -0.931
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    P         0.629   0.576   0.375   0.893   0.807   0.467   0.637   0.551   0.199
16    T        -1.577  -1.501  -1.449  -1.539  -1.389  -1.393  -1.305  -1.211  -1.113
17    N         0.004   0.112   0.215  -0.293  -0.170   0.006  -0.391  -0.231  -0.090
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    L        -0.514  -0.566  -0.503  -0.420  -0.463  -0.397  -0.652  -0.709  -0.630
21    D        -0.610  -0.621  -0.501  -0.734  -0.779  -0.597  -0.802  -0.787  -0.628
22    A        -1.148  -1.054  -1.041  -1.204  -1.082  -1.033  -1.100  -1.006  -0.936
23    A        -0.199  -0.465  -0.483  -0.374  -0.765  -0.826  -0.205  -0.574  -0.603
24    A         0.629   0.462   0.378   0.454   0.273   0.135   0.637   0.373   0.203
25    A        -1.577  -1.473  -1.454  -1.700  -1.547  -1.433  -1.305  -1.206  -1.116
26    G         0.629   0.512   0.365   0.781   0.613   0.431   0.637   0.452   0.181
27    T        -1.577  -1.467  -1.449  -1.383  -1.265  -1.256  -1.305  -1.193  -1.112
28    S        -1.235  -1.079  -1.015  -1.513  -1.225  -1.146  -1.191  -1.001  -0.910
29    Q        -1.919  -1.894  -1.799  -1.365  -1.432  -1.247  -1.420  -1.393  -1.241
30    A        -0.551  -0.221  -0.444  -0.702  -0.165  -0.545  -0.734  -0.305  -0.558
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    R        -0.551  -0.573  -0.482  -0.800  -0.833  -0.670  -0.734  -0.740  -0.609
34    T        -0.551  -0.505  -0.443  -0.758  -0.629  -0.533  -0.734  -0.631  -0.550
35    A        -1.022  -1.051  -1.030  -1.164  -1.178  -1.149  -0.962  -0.971  -0.925
36    T        -1.022  -1.051  -1.030  -0.951  -1.037  -1.039  -0.962  -0.971  -0.925
37    L        -0.680  -0.563  -0.499  -0.668  -0.554  -0.423  -0.848  -0.731  -0.627
38    K        -0.079  -0.358  -0.426   0.150  -0.197  -0.271  -0.048  -0.428  -0.527
39    Y         1.373   1.417   1.484   1.532   1.575   1.697   1.437   1.508   1.612
40    I        -1.235  -1.178  -1.050  -1.056  -1.012  -0.839  -1.191  -1.110  -0.946
41    C         1.373   1.417   1.484   1.379   1.442   1.556   1.437   1.508   1.612
42    A         0.629   0.512   0.365   0.457   0.343   0.122   0.637   0.452   0.181
43    E        -1.235  -1.147  -1.054  -0.994  -0.877  -0.737  -1.191  -1.081  -0.950
44    C         1.373   1.417   1.484   1.379   1.442   1.556   1.437   1.508   1.612
45    S        -0.551  -0.605  -0.500  -0.983  -1.015  -0.860  -0.734  -0.777  -0.631
46    S        -1.022  -1.028  -1.029  -1.245  -1.283  -1.261  -0.962  -0.978  -0.927
47    K        -0.764  -0.597  -0.506  -1.213  -0.967  -0.834  -0.962  -0.761  -0.637
48    L        -1.235  -1.199  -1.048  -1.089  -1.074  -0.832  -1.191  -1.131  -0.944
49    S        -0.747  -1.038  -1.021  -0.661  -1.050  -0.999  -0.620  -0.956  -0.915
50    L         0.629   0.462   0.378   0.789   0.612   0.456   0.637   0.373   0.203
51    S        -1.364  -1.519  -1.454  -1.196  -1.387  -1.266  -1.077  -1.229  -1.115
52    R        -0.551  -0.605  -0.500  -0.910  -0.993  -0.835  -0.734  -0.777  -0.631
53    T        -1.235  -1.199  -1.048  -1.338  -1.293  -1.079  -1.191  -1.131  -0.944
54    D        -0.079  -0.358  -0.426   0.274  -0.147  -0.326  -0.048  -0.428  -0.527
55    A        -1.022  -0.915  -0.987  -0.856  -0.715  -0.884  -0.962  -0.839  -0.884
56    V         0.004   0.112   0.215  -0.131   0.030   0.189  -0.391  -0.231  -0.090
57    R         1.373   1.417   1.484   1.121   1.198   1.318   1.437   1.508   1.612
58    C         1.373   1.417   1.484   1.379   1.442   1.556   1.437   1.508   1.612
59    K        -0.079  -0.358  -0.426   0.055  -0.361  -0.491  -0.048  -0.428  -0.527
60    D        -1.022  -0.780  -0.973  -0.732  -0.465  -0.690  -0.962  -0.688  -0.865
61    C         1.373   1.417   1.484   1.379   1.442   1.556   1.437   1.508   1.612
62    G         1.373   1.417   1.484   1.389   1.438   1.565   1.437   1.508   1.612
63    H         0.629   0.512   0.365   0.904   0.737   0.443   0.637   0.452   0.181
64    R         1.373   1.417   1.484   1.121   1.198   1.318   1.437   1.508   1.612
65    I         0.067   0.321   0.314  -0.032   0.332   0.338  -0.277   0.139   0.092
66    L        -0.404  -0.416  -0.439  -0.249  -0.232  -0.292  -0.505  -0.506  -0.544
67    L         0.067   0.321   0.314   0.055   0.458   0.431  -0.277   0.139   0.092
68    K         1.373   1.417   1.484   1.321   1.396   1.502   1.437   1.508   1.612
69    A        -0.404  -0.588  -0.500  -0.561  -0.780  -0.607  -0.505  -0.751  -0.632
70    R         1.373   1.417   1.484   1.121   1.198   1.318   1.437   1.508   1.612
71    T         0.629   0.576   0.375   0.704   0.632   0.285   0.637   0.551   0.199
72    K        -0.404  -0.291  -0.435  -0.461  -0.264  -0.530  -0.505  -0.339  -0.544
73    R         0.629   0.576   0.375   0.520   0.468   0.229   0.637   0.551   0.199
74    L        -0.079   0.027  -0.365   0.274   0.361  -0.167  -0.048   0.068  -0.445
75    V         1.373   1.417   1.484   1.379   1.420   1.556   1.437   1.508   1.612
76    Q         1.373   1.417   1.484   1.466   1.530   1.636   1.437   1.508   1.612
77    F         1.373   1.417   1.484   1.513   1.577   1.680   1.437   1.508   1.612
78    E         0.629   0.576   0.375   0.789   0.710   0.375   0.637   0.551   0.199
79    A         1.373   1.417   1.484   1.081   1.186   1.280   1.437   1.508   1.612
80    R         1.373   1.417   1.484   1.121   1.198   1.318   1.437   1.508   1.612
* 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/P40422
Output conservation file - output/P40422
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
