1     M         1.285   1.291   1.366   1.510   1.518   1.630   1.389   1.398   1.506
2     -        -0.305  -0.387  -0.475  -0.245  -0.372  -0.558  -0.364  -0.478  -0.599
3     -        -1.157  -1.186  -1.060  -1.262  -1.360  -1.196  -1.136  -1.164  -0.988
4     -        -0.621  -0.589  -0.523  -0.802  -0.757  -0.641  -0.803  -0.760  -0.664
5     -        -0.621  -0.608  -0.529  -0.672  -0.646  -0.567  -0.803  -0.787  -0.672
6     -         0.014   0.029   0.148  -0.042  -0.021   0.163  -0.364  -0.342  -0.162
7     -        -0.621  -0.650  -0.553  -0.951  -1.015  -0.862  -0.803  -0.842  -0.705
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    E        -1.556  -1.529  -1.435  -1.432  -1.381  -1.298  -1.330  -1.301  -1.142
13    T        -0.556  -0.510  -0.506  -0.704  -0.638  -0.588  -0.758  -0.698  -0.647
14    P         1.285   1.291   1.366   1.527   1.542   1.646   1.389   1.398   1.506
15    L         1.285   1.291   1.366   0.981   0.986   1.131   1.389   1.398   1.506
16    D         1.285   1.291   1.366   1.284   1.309   1.417   1.389   1.398   1.506
17    L         1.285   1.291   1.366   0.981   0.986   1.131   1.389   1.398   1.506
18    L        -0.693  -0.700  -0.564  -1.204  -1.219  -0.945  -0.901  -0.910  -0.719
19    K        -0.556  -0.591  -0.523  -0.559  -0.609  -0.492  -0.758  -0.785  -0.669
20    L        -0.175  -0.145  -0.425  -0.296  -0.268  -0.571  -0.185  -0.146  -0.531
21    N        -0.693  -0.695  -0.559  -0.627  -0.652  -0.459  -0.901  -0.905  -0.713
22    L         1.285   1.291   1.366   0.981   0.986   1.131   1.389   1.398   1.506
23    D         0.533   0.446   0.302   0.627   0.530   0.313   0.530   0.392   0.120
24    E         1.285   1.291   1.366   1.158   1.196   1.298   1.389   1.398   1.506
25    R        -1.419  -1.475  -1.437  -1.233  -1.328  -1.297  -1.187  -1.240  -1.143
26    V         1.285   1.291   1.366   1.167   1.170   1.306   1.389   1.398   1.506
27    Y        -0.467  -0.517  -0.498  -0.440  -0.517  -0.505  -0.615  -0.672  -0.633
28    I         0.533   0.563   0.316   0.491   0.521   0.189   0.530   0.574   0.145
29    K         1.285   1.291   1.366   1.450   1.454   1.574   1.389   1.398   1.506
30    L         1.285   1.291   1.366   0.981   0.986   1.131   1.389   1.398   1.506
31    R         1.285   1.291   1.366   1.363   1.380   1.492   1.389   1.398   1.506
32    G         0.533   0.584   0.316   0.718   0.779   0.369   0.530   0.606   0.147
33    A        -0.175  -0.298  -0.448   0.090  -0.092  -0.368  -0.185  -0.356  -0.563
34    R         1.285   1.291   1.366   1.363   1.380   1.492   1.389   1.398   1.506
35    T        -0.175  -0.049  -0.403  -0.167   0.020  -0.478  -0.185  -0.019  -0.501
36    L         0.188   0.247   0.197  -0.150  -0.073  -0.104  -0.042   0.058  -0.071
37    V        -1.556  -1.544  -1.447  -1.499  -1.460  -1.324  -1.330  -1.314  -1.153
38    G         1.285   1.291   1.366   1.415   1.418   1.541   1.389   1.398   1.506
39    T        -1.556  -1.544  -1.447  -1.569  -1.593  -1.485  -1.330  -1.314  -1.153
40    L         1.285   1.291   1.366   0.981   0.986   1.131   1.389   1.398   1.506
41    Q         0.188   0.127   0.174   0.408   0.304   0.353  -0.042  -0.158  -0.115
42    A         0.188   0.209   0.217   0.255   0.284   0.267  -0.042  -0.009  -0.033
43    F         0.033   0.080   0.173   0.100   0.173   0.310  -0.329  -0.245  -0.116
44    D         1.285   1.291   1.366   1.284   1.309   1.417   1.389   1.398   1.506
45    S        -0.175  -0.298  -0.448  -0.056  -0.236  -0.521  -0.185  -0.356  -0.563
46    H         1.285   1.291   1.366   1.594   1.600   1.710   1.389   1.398   1.506
47    C         0.533   0.484   0.304   0.875   0.798   0.425   0.530   0.452   0.123
48    N         0.533   0.446   0.302   0.827   0.711   0.450   0.530   0.392   0.120
49    I         0.033   0.080   0.173   0.007   0.092   0.224  -0.329  -0.245  -0.116
50    V         0.533   0.532   0.312   0.491   0.482   0.183   0.530   0.528   0.139
51    L         1.285   1.291   1.366   0.981   0.986   1.131   1.389   1.398   1.506
52    S         0.188   0.127   0.174   0.140   0.025   0.087  -0.042  -0.158  -0.115
53    D         0.533   0.446   0.302   0.627   0.530   0.313   0.530   0.392   0.120
54    A        -0.175  -0.211  -0.425   0.051  -0.019  -0.400  -0.185  -0.240  -0.530
55    V        -0.556  -0.507  -0.505  -0.909  -0.833  -0.776  -0.758  -0.699  -0.649
56    E         1.285   1.291   1.366   1.158   1.196   1.298   1.389   1.398   1.506
57    T        -0.175  -0.223  -0.427   0.092   0.023  -0.282  -0.185  -0.253  -0.534
58    I         0.188   0.127   0.174   0.122  -0.020   0.011  -0.042  -0.158  -0.115
59    Y        -0.175  -0.298  -0.448   0.206   0.028  -0.214  -0.185  -0.356  -0.563
60    Q        -1.419  -1.409  -1.412  -1.358  -1.326  -1.317  -1.187  -1.175  -1.122
61    L        -1.419  -1.475  -1.437  -1.547  -1.620  -1.484  -1.187  -1.240  -1.143
62    N        -1.056  -1.066  -1.020  -1.064  -1.085  -0.971  -1.044  -1.046  -0.950
63    N        -0.467  -0.421  -0.489  -0.648  -0.552  -0.649  -0.615  -0.553  -0.625
64    E        -0.569  -0.595  -0.522  -0.716  -0.758  -0.682  -0.754  -0.782  -0.668
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    E        -1.919  -1.922  -1.773  -1.848  -1.819  -1.605  -1.474  -1.468  -1.270
72    L        -0.175  -0.145  -0.425  -0.376  -0.335  -0.723  -0.185  -0.146  -0.531
73    S        -0.556  -0.523  -0.513  -0.725  -0.679  -0.641  -0.758  -0.717  -0.658
74    E        -1.556  -1.515  -1.433  -1.377  -1.312  -1.239  -1.330  -1.292  -1.142
75    S        -1.919  -1.864  -1.758  -1.700  -1.651  -1.491  -1.474  -1.425  -1.258
76    E        -1.419  -1.475  -1.437  -1.440  -1.504  -1.455  -1.187  -1.240  -1.143
77    R         0.033   0.080   0.173  -0.068   0.018   0.153  -0.329  -0.245  -0.116
78    R        -1.919  -1.850  -1.755  -1.432  -1.351  -1.211  -1.474  -1.412  -1.256
79    C        -1.056  -1.055  -1.023  -0.907  -0.906  -0.807  -1.044  -1.037  -0.951
80    E        -0.175  -0.145  -0.425  -0.192  -0.125  -0.559  -0.185  -0.146  -0.531
81    M         1.285   1.291   1.366   1.510   1.518   1.630   1.389   1.398   1.506
82    V        -0.693  -0.668  -0.551  -1.152  -1.173  -0.949  -0.901  -0.870  -0.703
83    F         1.285   1.291   1.366   1.552   1.561   1.670   1.389   1.398   1.506
84    I         0.533   0.563   0.316   0.491   0.521   0.189   0.530   0.574   0.145
85    R         1.285   1.291   1.366   1.363   1.380   1.492   1.389   1.398   1.506
86    G         1.285   1.291   1.366   1.415   1.418   1.541   1.389   1.398   1.506
87    D         0.533   0.584   0.316   0.609   0.687   0.298   0.530   0.606   0.147
88    T        -0.175  -0.106  -0.408  -0.090   0.011  -0.511  -0.185  -0.092  -0.508
89    V         1.285   1.291   1.366   1.167   1.170   1.306   1.389   1.398   1.506
90    T        -0.467  -0.367  -0.480  -0.382  -0.229  -0.401  -0.615  -0.473  -0.609
91    L         1.285   1.291   1.366   0.981   0.986   1.131   1.389   1.398   1.506
92    I         0.188   0.169   0.182   0.122   0.070   0.033  -0.042  -0.081  -0.099
93    S        -0.556  -0.574  -0.516  -0.606  -0.623  -0.516  -0.758  -0.769  -0.662
94    T        -1.056  -1.014  -1.023  -0.845  -0.793  -0.818  -1.044  -0.997  -0.952
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    P        -0.467  -0.392  -0.486  -0.388  -0.258  -0.461  -0.615  -0.509  -0.620
98    S        -1.919  -1.922  -1.773  -1.674  -1.668  -1.464  -1.474  -1.468  -1.270
99    E        -1.157  -1.172  -1.058  -1.313  -1.310  -1.133  -1.136  -1.152  -0.986
100   D        -0.621  -0.667  -0.553  -0.831  -0.843  -0.690  -0.803  -0.870  -0.705
101   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   I        -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/P57743
Output conservation file - output/P57743
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
