1     M         1.570   1.628   1.731   1.723   1.810   1.954   1.716   1.796   1.970
2     S         0.085  -0.123  -0.161  -0.065  -0.332  -0.408   0.032  -0.272  -0.344
3     S        -0.692  -0.613  -0.710  -0.889  -0.766  -0.915  -0.745  -0.676  -0.725
4     L        -0.247  -0.207  -0.171  -0.419  -0.328  -0.271  -0.510  -0.421  -0.373
5     S        -0.692  -0.789  -0.735  -0.792  -0.846  -0.783  -0.745  -0.843  -0.752
6     T        -0.893  -0.829  -0.744  -0.882  -0.797  -0.653  -0.979  -0.876  -0.762
7     S        -1.662  -1.593  -1.508  -1.573  -1.456  -1.360  -1.330  -1.232  -1.103
8     D        -0.771  -0.753  -0.720  -0.654  -0.636  -0.543  -0.862  -0.808  -0.736
9     L         0.521   0.578   0.535   0.343   0.419   0.321   0.310   0.386   0.250
10    A        -1.540  -1.467  -1.465  -1.266  -1.202  -1.219  -1.213  -1.127  -1.068
11    S        -0.692  -0.682  -0.712  -0.895  -0.876  -0.925  -0.745  -0.739  -0.728
12    L         1.570   1.628   1.731   1.433   1.519   1.672   1.716   1.796   1.970
13    D        -0.432  -0.603  -0.677  -0.279  -0.567  -0.723  -0.393  -0.601  -0.677
14    D        -0.247  -0.188  -0.173  -0.408  -0.319  -0.288  -0.510  -0.394  -0.371
15    T        -1.662  -1.546  -1.496  -1.591  -1.486  -1.354  -1.330  -1.202  -1.095
16    S         0.198  -0.005  -0.101   0.116  -0.118  -0.311   0.193  -0.103  -0.255
17    K        -0.247  -0.229  -0.186  -0.352  -0.340  -0.257  -0.510  -0.457  -0.393
18    K        -0.432  -0.662  -0.695  -0.377  -0.759  -0.839  -0.393  -0.669  -0.699
19    E         0.867   1.058   0.731   0.902   1.128   0.725   0.896   1.172   0.625
20    I         0.521   0.436   0.499   0.408   0.217   0.282   0.310   0.118   0.178
21    A        -1.216  -1.294  -1.169  -0.922  -1.054  -0.890  -1.096  -1.124  -0.971
22    T        -1.216  -1.226  -1.159  -1.129  -1.139  -1.014  -1.096  -1.060  -0.961
23    F         0.867   0.921   0.709   1.108   1.191   0.934   0.896   0.967   0.583
24    L        -0.771  -0.659  -0.701  -0.817  -0.648  -0.646  -0.862  -0.712  -0.713
25    E         0.198   0.079  -0.075   0.272   0.083  -0.167   0.193   0.012  -0.217
26    G        -0.692  -0.681  -0.712  -0.775  -0.757  -0.750  -0.745  -0.736  -0.727
27    E         1.570   1.628   1.731   1.502   1.580   1.739   1.716   1.796   1.970
28    N        -0.692  -0.804  -0.723  -0.720  -0.870  -0.752  -0.745  -0.846  -0.739
29    S         0.521   0.436   0.499   0.204   0.079   0.113   0.310   0.118   0.178
30    K         0.867   0.733   0.680   0.878   0.708   0.652   0.896   0.661   0.531
31    Q        -0.692  -0.665  -0.686  -0.784  -0.689  -0.743  -0.745  -0.673  -0.690
32    K         0.867   0.733   0.680   0.878   0.708   0.652   0.896   0.661   0.531
33    V         0.198   0.085  -0.064   0.406   0.238  -0.007   0.193   0.030  -0.201
34    Q         0.867   0.921   0.709   0.878   0.950   0.694   0.896   0.967   0.583
35    M        -1.540  -1.583  -1.500  -1.191  -1.296  -1.226  -1.213  -1.220  -1.096
36    S        -0.432  -0.662  -0.695  -0.452  -0.749  -0.822  -0.393  -0.669  -0.699
37    I         0.198   0.008  -0.092   0.353   0.087  -0.058   0.193  -0.085  -0.242
38    H         0.867   0.921   0.709   1.188   1.259   0.942   0.896   0.967   0.583
39    Q        -0.692  -0.723  -0.702  -0.734  -0.753  -0.727  -0.745  -0.744  -0.709
40    F         0.867   0.733   0.680   1.049   0.871   0.757   0.896   0.661   0.531
41    T         1.570   1.628   1.731   1.562   1.640   1.797   1.716   1.796   1.970
42    N        -0.247  -0.221  -0.174  -0.454  -0.392  -0.355  -0.510  -0.444  -0.377
43    I        -1.338  -1.323  -1.180  -1.338  -1.362  -1.150  -1.213  -1.149  -0.980
44    C         1.570   1.628   1.731   1.629   1.710   1.862   1.716   1.796   1.970
45    F         0.336   0.349   0.468   0.392   0.412   0.593  -0.042  -0.054   0.116
46    K         0.198   0.085  -0.064   0.297   0.151  -0.042   0.193   0.030  -0.201
47    K         0.867   1.071   0.726   0.842   1.088   0.644   0.896   1.191   0.616
48    C         1.570   1.628   1.731   1.629   1.710   1.862   1.716   1.796   1.970
49    V        -0.369  -0.235  -0.207  -0.512  -0.307  -0.283  -0.627  -0.443  -0.415
50    E        -1.662  -1.554  -1.506  -1.642  -1.475  -1.374  -1.330  -1.208  -1.102
51    S        -1.216  -1.144  -1.130  -1.306  -1.205  -1.182  -1.096  -1.002  -0.938
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    V         0.277   0.354   0.470   0.061   0.160   0.341  -0.159  -0.044   0.120
55    N        -1.662  -1.596  -1.510  -1.557  -1.483  -1.343  -1.330  -1.234  -1.105
56    D        -0.771  -0.711  -0.718  -1.019  -0.894  -0.895  -0.862  -0.780  -0.734
57    S        -0.812  -0.757  -0.732  -0.725  -0.681  -0.658  -0.886  -0.812  -0.747
58    N        -1.338  -1.184  -1.167  -1.436  -1.249  -1.193  -1.213  -1.036  -0.969
59    L         1.570   1.628   1.731   1.433   1.519   1.672   1.716   1.796   1.970
60    S         0.336   0.487   0.530   0.019   0.303   0.309  -0.042   0.216   0.240
61    S        -0.369  -0.366  -0.265  -0.646  -0.628  -0.474  -0.627  -0.628  -0.495
62    Q        -0.247  -0.304  -0.197  -0.575  -0.630  -0.494  -0.510  -0.556  -0.411
63    E         1.570   1.628   1.731   1.502   1.580   1.739   1.716   1.796   1.970
64    E         0.198   0.008  -0.092   0.310   0.037  -0.114   0.193  -0.085  -0.242
65    Q        -0.432  -0.439  -0.628  -0.291  -0.334  -0.566  -0.393  -0.411  -0.619
66    C         1.570   1.628   1.731   1.629   1.710   1.862   1.716   1.796   1.970
67    L         0.198   0.008  -0.092   0.291   0.056  -0.068   0.193  -0.085  -0.242
68    S        -1.662  -1.440  -1.484  -1.607  -1.283  -1.385  -1.330  -1.119  -1.086
69    N        -0.109  -0.157  -0.187  -0.230  -0.321  -0.399  -0.276  -0.373  -0.394
70    C         1.570   1.628   1.731   1.629   1.710   1.862   1.716   1.796   1.970
71    V         0.521   0.729   0.631   0.495   0.806   0.628   0.310   0.653   0.438
72    N        -0.109  -0.220  -0.202  -0.168  -0.346  -0.298  -0.276  -0.448  -0.414
73    R         1.570   1.628   1.731   1.702   1.781   1.933   1.716   1.796   1.970
74    F         0.867   0.838   0.701   1.108   1.095   0.924   0.896   0.836   0.569
75    L         1.570   1.628   1.731   1.433   1.519   1.672   1.716   1.796   1.970
76    D         1.570   1.628   1.731   1.554   1.629   1.790   1.716   1.796   1.970
77    T         0.198  -0.005  -0.101   0.394   0.111  -0.021   0.193  -0.103  -0.255
78    N         1.570   1.628   1.731   1.456   1.565   1.694   1.716   1.796   1.970
79    I         0.198  -0.005  -0.101   0.340   0.050  -0.102   0.193  -0.103  -0.255
80    R        -1.216  -1.275  -1.173  -0.964  -1.053  -0.891  -1.096  -1.105  -0.973
81    I         0.336   0.472   0.515   0.159   0.366   0.417  -0.042   0.187   0.210
82    V         0.198  -0.005  -0.101   0.454   0.177   0.033   0.193  -0.103  -0.255
83    N        -1.540  -1.345  -1.452  -1.381  -1.129  -1.271  -1.213  -1.018  -1.057
84    G        -0.812  -0.871  -0.764  -0.600  -0.690  -0.566  -0.886  -0.915  -0.780
85    L         0.805   0.651   0.633   0.755   0.543   0.519   0.797   0.518   0.442
86    Q         0.805   0.740   0.656   0.787   0.695   0.561   0.797   0.673   0.486
87    N        -0.951  -0.920  -0.774  -1.157  -1.119  -0.936  -1.039  -0.968  -0.791
88    T        -0.910  -0.804  -0.743  -0.991  -0.852  -0.762  -0.992  -0.855  -0.760
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    R        -0.893  -0.763  -0.730  -0.935  -0.758  -0.675  -0.979  -0.793  -0.744
* 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/P57744
Output conservation file - output/P57744
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
