1     M         1.183   1.228   1.282   1.473   1.531   1.619   1.262   1.325   1.398
2     A         0.005   0.052   0.127  -0.088  -0.023   0.085  -0.323  -0.259  -0.174
3     R        -0.388  -0.439  -0.519  -0.328  -0.436  -0.646  -0.499  -0.620  -0.674
4     E        -0.388  -0.499  -0.485  -0.082  -0.243  -0.291  -0.499  -0.626  -0.621
5     I        -0.388  -0.462  -0.490  -0.284  -0.424  -0.527  -0.499  -0.574  -0.633
6     T        -1.458  -1.304  -1.361  -1.407  -1.139  -1.273  -1.292  -1.099  -1.103
7     D         0.537   0.329   0.256   0.767   0.472   0.372   0.558   0.228   0.063
8     I         1.183   1.228   1.282   1.237   1.281   1.405   1.262   1.325   1.398
9     K         1.183   1.228   1.282   0.711   0.812   0.926   1.262   1.325   1.398
10    Q        -1.528  -1.584  -1.409  -1.302  -1.437  -1.300  -1.380  -1.375  -1.147
11    F         1.183   1.228   1.282   1.378   1.450   1.533   1.262   1.325   1.398
12    L        -0.388  -0.320  -0.449  -0.447  -0.320  -0.541  -0.499  -0.379  -0.571
13    E        -0.083  -0.243  -0.435   0.323   0.090  -0.232  -0.059  -0.291  -0.552
14    L        -0.388  -0.566  -0.515  -0.434  -0.689  -0.630  -0.499  -0.722  -0.665
15    T        -1.173  -1.071  -1.026  -1.042  -0.889  -0.818  -1.203  -1.090  -0.976
16    R        -0.083  -0.243  -0.435   0.198  -0.016  -0.247  -0.059  -0.291  -0.552
17    R         1.183   1.228   1.282   1.199   1.278   1.370   1.262   1.325   1.398
18    A        -2.313  -2.155  -2.001  -2.134  -1.987  -1.714  -1.732  -1.570  -1.351
19    D         1.183   1.228   1.282   1.290   1.329   1.452   1.262   1.325   1.398
20    V        -0.780  -0.640  -0.544  -0.932  -0.745  -0.618  -1.027  -0.842  -0.703
21    K        -1.921  -1.874  -1.737  -1.952  -1.820  -1.572  -1.556  -1.478  -1.271
22    T        -0.083  -0.070  -0.413   0.206   0.188  -0.313  -0.059  -0.047  -0.521
23    A         0.537   0.329   0.256   0.596   0.337   0.203   0.558   0.228   0.063
24    T        -1.066  -0.864  -1.006  -0.997  -0.776  -0.929  -1.115  -0.898  -0.957
25    V         0.202   0.220   0.173   0.215   0.229   0.124   0.029   0.042  -0.088
26    K         1.183   1.228   1.282   0.711   0.812   0.926   1.262   1.325   1.398
27    I        -1.243  -1.220  -1.041  -1.513  -1.460  -1.184  -1.292  -1.216  -0.990
28    N         0.537   0.329   0.256   0.781   0.542   0.385   0.558   0.228   0.063
29    K        -0.944  -0.890  -0.985  -1.270  -1.205  -1.257  -0.939  -0.890  -0.936
30    K         0.005  -0.022   0.109  -0.658  -0.692  -0.425  -0.323  -0.399  -0.208
31    L         0.257   0.326   0.151   0.127   0.228  -0.066   0.121   0.222  -0.129
32    N         1.183   1.228   1.282   1.213   1.285   1.383   1.262   1.325   1.398
33    K        -0.063   0.006   0.115  -0.735  -0.629  -0.413  -0.450  -0.346  -0.197
34    A         0.257   0.309   0.146   0.304   0.376   0.059   0.121   0.194  -0.138
35    G         1.183   1.228   1.282   1.392   1.461   1.546   1.262   1.325   1.398
36    K         1.183   1.228   1.282   0.661   0.744   0.880   1.262   1.325   1.398
37    P        -1.283  -1.182  -1.064  -1.593  -1.466  -1.162  -1.306  -1.171  -1.011
38    F        -1.062  -1.074  -1.035  -0.736  -0.780  -0.785  -1.078  -1.076  -0.983
39    R        -1.066  -1.171  -1.026  -1.372  -1.415  -1.201  -1.115  -1.169  -0.975
40    Q        -0.388  -0.417  -0.506  -0.163  -0.254  -0.417  -0.499  -0.565  -0.657
41    T        -0.388  -0.381  -0.487  -0.281  -0.281  -0.468  -0.499  -0.468  -0.624
42    K         1.183   1.228   1.282   0.711   0.812   0.926   1.262   1.325   1.398
43    F         1.183   1.228   1.282   1.378   1.450   1.533   1.262   1.325   1.398
44    K         1.183   1.228   1.282   0.711   0.812   0.926   1.262   1.325   1.398
45    V        -0.551  -0.637  -0.519  -0.669  -0.762  -0.635  -0.763  -0.826  -0.674
46    R         1.183   1.228   1.282   1.199   1.278   1.370   1.262   1.325   1.398
47    G        -0.089  -0.021   0.119   0.086   0.178   0.366  -0.499  -0.397  -0.189
48    S        -0.083  -0.361  -0.466   0.256  -0.115  -0.273  -0.059  -0.439  -0.594
49    S        -0.388  -0.302  -0.474  -0.430  -0.342  -0.661  -0.499  -0.398  -0.610
50    S        -0.673  -0.657  -0.943  -0.049  -0.075  -0.436  -0.587  -0.593  -0.883
51    L         0.202   0.377   0.246   0.092   0.353   0.154   0.029   0.306   0.045
52    Y         1.183   1.228   1.282   1.429   1.491   1.580   1.262   1.325   1.398
53    T         1.183   1.228   1.282   1.207   1.261   1.377   1.262   1.325   1.398
54    L         1.183   1.228   1.282   1.037   1.127   1.223   1.262   1.325   1.398
55    V        -0.388  -0.361  -0.496  -0.296  -0.306  -0.499  -0.499  -0.490  -0.642
56    I        -0.083  -0.070  -0.413   0.106   0.117  -0.410  -0.059  -0.047  -0.521
57    N        -0.944  -1.102  -1.027  -0.780  -1.034  -1.088  -0.939  -1.085  -0.975
58    D         1.183   1.228   1.282   1.290   1.329   1.452   1.262   1.325   1.398
59    A        -0.083  -0.361  -0.466   0.081  -0.290  -0.470  -0.059  -0.439  -0.594
60    G        -1.921  -1.877  -1.741  -1.707  -1.709  -1.560  -1.556  -1.479  -1.274
61    K         1.183   1.228   1.282   0.711   0.812   0.926   1.262   1.325   1.398
62    A         1.183   1.228   1.282   1.131   1.207   1.308   1.262   1.325   1.398
63    K        -0.551  -0.669  -0.541  -0.890  -0.967  -0.739  -0.763  -0.876  -0.701
64    K         1.183   1.228   1.282   0.711   0.812   0.926   1.262   1.325   1.398
65    L         0.537   0.329   0.256   0.509   0.262   0.142   0.558   0.228   0.063
66    I        -2.028  -1.976  -1.748  -1.953  -1.963  -1.736  -1.644  -1.544  -1.278
67    Q         0.537   0.474   0.273   0.771   0.706   0.372   0.558   0.458   0.093
68    S         1.183   1.228   1.282   1.275   1.321   1.439   1.262   1.325   1.398
69    L         1.183   1.228   1.282   1.037   1.127   1.223   1.262   1.325   1.398
70    P         1.183   1.228   1.282   1.386   1.450   1.540   1.262   1.325   1.398
71    P         0.537   0.329   0.256   0.862   0.590   0.454   0.558   0.228   0.063
72    T        -0.944  -0.936  -1.015  -0.744  -0.830  -0.899  -0.939  -0.959  -0.966
73    L        -0.083  -0.210  -0.440   0.009  -0.162  -0.452  -0.059  -0.251  -0.558
74    K        -1.066  -0.895  -1.002  -1.350  -1.142  -1.150  -1.115  -0.925  -0.953
75    V        -0.089  -0.028   0.112  -0.278  -0.208   0.018  -0.499  -0.410  -0.203
76    N        -1.528  -1.553  -1.412  -1.424  -1.474  -1.405  -1.380  -1.355  -1.149
77    R        -1.636  -1.504  -1.406  -1.726  -1.571  -1.401  -1.468  -1.300  -1.143
78    L        -0.551  -0.669  -0.541  -0.723  -0.863  -0.680  -0.763  -0.876  -0.701
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     *
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     *
* 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/P49167
Output conservation file - output/P49167
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
