1     M         1.398   1.420   1.509   1.591   1.629   1.747   1.503   1.537   1.685
2     A         0.530   0.620   0.375   0.460   0.599   0.274   0.483   0.620   0.176
3     E        -0.996  -1.070  -0.985  -0.835  -0.931  -0.850  -0.945  -1.032  -0.911
4     I        -1.703  -1.605  -1.440  -1.807  -1.730  -1.433  -1.435  -1.338  -1.136
5     K        -1.703  -1.605  -1.440  -1.592  -1.447  -1.232  -1.435  -1.338  -1.136
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     H        -1.063  -1.122  -0.998  -0.913  -1.043  -0.905  -1.045  -1.096  -0.928
8     Y         1.398   1.420   1.509   1.521   1.555   1.681   1.503   1.537   1.685
9     Q        -0.443  -0.524  -0.455  -0.241  -0.361  -0.324  -0.595  -0.686  -0.602
10    F         1.398   1.420   1.509   1.641   1.681   1.793   1.503   1.537   1.685
11    N         0.082   0.125   0.249  -0.025   0.038   0.222  -0.295  -0.229  -0.059
12    V         1.398   1.420   1.509   1.186   1.214   1.368   1.503   1.537   1.685
13    V        -1.207  -1.124  -1.006  -1.276  -1.146  -0.949  -1.195  -1.104  -0.936
14    M         1.398   1.420   1.509   1.599   1.701   1.754   1.503   1.537   1.685
15    T        -0.479  -0.498  -0.432  -0.704  -0.675  -0.571  -0.677  -0.689  -0.580
16    C         1.398   1.420   1.509   1.581   1.603   1.737   1.503   1.537   1.685
17    S        -0.019  -0.231  -0.367   0.035  -0.208  -0.451   0.011  -0.280  -0.478
18    G         1.398   1.420   1.509   1.418   1.423   1.585   1.503   1.537   1.685
19    C         1.398   1.420   1.509   1.581   1.603   1.737   1.503   1.537   1.685
20    S         0.672   0.624   0.420   0.602   0.589   0.213   0.700   0.627   0.258
21    G        -0.687  -0.610  -0.474  -0.774  -0.628  -0.468  -0.907  -0.811  -0.629
22    A         1.398   1.420   1.509   1.563   1.624   1.720   1.503   1.537   1.685
23    V         0.124   0.159   0.257  -0.239  -0.184  -0.026  -0.218  -0.166  -0.044
24    N        -1.147  -1.109  -1.000  -1.109  -1.041  -0.913  -1.136  -1.092  -0.932
25    K         0.672   0.795   0.441   0.972   1.111   0.588   0.700   0.877   0.296
26    V         0.672   0.751   0.433   0.576   0.690   0.305   0.700   0.814   0.282
27    L         1.398   1.420   1.509   1.372   1.358   1.541   1.503   1.537   1.685
28    T        -1.481  -1.401  -1.376  -1.551  -1.436  -1.354  -1.251  -1.166  -1.084
29    K         0.124   0.111   0.241  -0.135  -0.173   0.088  -0.218  -0.255  -0.074
30    L         0.672   0.689   0.417   0.726   0.697   0.320   0.700   0.724   0.253
31    E        -0.443  -0.540  -0.451  -0.480  -0.653  -0.556  -0.595  -0.706  -0.597
32    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    D        -0.939  -0.924  -0.943  -0.779  -0.746  -0.773  -0.907  -0.874  -0.868
37    V        -0.019  -0.156  -0.345  -0.052  -0.228  -0.492   0.011  -0.183  -0.448
38    S        -1.273  -1.404  -1.377  -1.173  -1.353  -1.366  -1.022  -1.153  -1.082
39    K        -1.021  -0.954  -0.951  -1.202  -1.090  -1.014  -1.022  -0.945  -0.883
40    I        -1.815  -1.832  -1.734  -1.545  -1.583  -1.499  -1.366  -1.375  -1.225
41    D        -0.670  -0.807  -0.923  -0.477  -0.698  -0.919  -0.562  -0.732  -0.844
42    I         0.124   0.126   0.246  -0.147  -0.181  -0.007  -0.218  -0.228  -0.064
43    S        -0.019  -0.175  -0.369   0.027  -0.151  -0.473   0.011  -0.207  -0.481
44    L         0.672   0.624   0.420   0.727   0.620   0.329   0.700   0.627   0.258
45    E        -0.336  -0.284  -0.408  -0.237  -0.197  -0.325  -0.448  -0.410  -0.543
46    K        -0.019  -0.080  -0.336  -0.036  -0.156  -0.430   0.011  -0.090  -0.435
47    Q         0.672   0.501   0.405   0.900   0.730   0.456   0.700   0.432   0.232
48    L        -0.939  -0.944  -0.963  -1.010  -1.048  -1.056  -0.907  -0.930  -0.894
49    V         0.672   0.501   0.405   0.576   0.394   0.264   0.700   0.432   0.232
50    D        -0.670  -0.854  -0.938  -0.396  -0.652  -0.782  -0.562  -0.782  -0.860
51    V         0.672   0.711   0.433   0.554   0.619   0.252   0.700   0.757   0.282
52    Y        -1.021  -0.910  -0.953  -1.014  -0.871  -0.951  -1.022  -0.895  -0.882
53    T         0.672   0.501   0.405   0.632   0.393   0.216   0.700   0.432   0.232
54    T        -0.479  -0.340  -0.411  -0.660  -0.420  -0.543  -0.677  -0.483  -0.549
55    L        -1.147  -1.093  -1.004  -1.257  -1.264  -1.038  -1.136  -1.086  -0.935
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    P        -0.670  -0.788  -0.926  -0.195  -0.378  -0.679  -0.562  -0.708  -0.847
61    Y         1.398   1.420   1.509   1.536   1.641   1.695   1.503   1.537   1.685
62    D         0.063   0.102   0.241  -0.170  -0.101   0.103  -0.333  -0.274  -0.074
63    F        -1.273  -1.350  -1.372  -1.099  -1.304  -1.262  -1.022  -1.104  -1.077
64    I         0.124   0.146   0.244  -0.147  -0.131  -0.014  -0.218  -0.190  -0.068
65    L        -0.336  -0.317  -0.395  -0.252  -0.236  -0.335  -0.448  -0.407  -0.521
66    E        -1.481  -1.554  -1.417  -1.092  -1.106  -0.950  -1.251  -1.298  -1.118
67    K         0.124   0.233   0.297  -0.281  -0.095  -0.004  -0.218  -0.030   0.033
68    I         1.398   1.420   1.509   1.418   1.437   1.585   1.503   1.537   1.685
69    K         0.124   0.179   0.258  -0.165  -0.106   0.057  -0.218  -0.129  -0.043
70    K         1.398   1.420   1.509   1.153   1.152   1.337   1.503   1.537   1.685
71    T         1.398   1.420   1.509   1.278   1.308   1.453   1.503   1.537   1.685
72    G         1.398   1.420   1.509   1.418   1.423   1.585   1.503   1.537   1.685
73    K         1.398   1.420   1.509   1.153   1.152   1.337   1.503   1.537   1.685
74    E        -0.479  -0.562  -0.452  -0.685  -0.807  -0.627  -0.677  -0.753  -0.603
75    V         0.315   0.399   0.335   0.068   0.202   0.095   0.126   0.263   0.103
76    R        -0.939  -0.784  -0.938  -0.641  -0.412  -0.690  -0.907  -0.737  -0.865
77    S        -0.336  -0.256  -0.409  -0.418  -0.265  -0.519  -0.448  -0.335  -0.544
78    G         0.672   0.501   0.405   0.833   0.597   0.494   0.700   0.432   0.232
79    K        -0.939  -0.985  -0.958  -1.130  -1.225  -1.140  -0.907  -0.939  -0.884
80    Q        -1.147  -1.036  -0.985  -1.349  -1.178  -1.063  -1.136  -1.025  -0.916
81    L         0.124   0.179   0.258  -0.054  -0.019   0.136  -0.218  -0.129  -0.043
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     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.609  -1.465  -1.405  -1.352  -1.126  -1.083  -1.353  -1.208  -1.106
* 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/P38636
Output conservation file - output/P38636
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
