1     M         1.480   1.493   1.572   1.589   1.605   1.719   1.578   1.596   1.715
2     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L        -0.560  -0.546  -0.684  -0.592  -0.577  -0.742  -0.526  -0.514  -0.656
5     P        -0.560  -0.590  -0.727  -0.355  -0.418  -0.619  -0.526  -0.565  -0.706
6     Q        -1.260  -1.256  -1.182  -1.128  -1.118  -1.027  -1.086  -1.078  -0.961
7     T        -1.610  -1.617  -1.527  -1.397  -1.409  -1.283  -1.227  -1.227  -1.098
8     M        -0.428  -0.429  -0.330  -0.725  -0.737  -0.575  -0.666  -0.669  -0.534
9     L        -1.260  -1.217  -1.179  -1.451  -1.393  -1.304  -1.086  -1.046  -0.959
10    R        -0.871  -0.851  -0.793  -0.987  -0.965  -0.868  -0.903  -0.878  -0.783
11    S        -1.279  -1.270  -1.197  -1.196  -1.181  -1.054  -1.094  -1.083  -0.971
12    I        -0.308  -0.261  -0.262  -0.608  -0.534  -0.515  -0.522  -0.453  -0.447
13    S        -1.279  -1.222  -1.185  -1.020  -0.930  -0.897  -1.094  -1.036  -0.961
14    V        -0.200  -0.192  -0.232  -0.342  -0.338  -0.376  -0.346  -0.336  -0.399
15    K        -0.385  -0.334  -0.303  -0.597  -0.532  -0.481  -0.621  -0.561  -0.501
16    H        -0.875  -0.853  -0.797  -0.805  -0.764  -0.704  -0.896  -0.868  -0.784
17    V        -0.200  -0.130  -0.229  -0.109   0.001  -0.195  -0.346  -0.249  -0.394
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    R        -0.875  -0.885  -0.805  -0.831  -0.847  -0.734  -0.896  -0.904  -0.793
28    W        -0.875  -0.871  -0.802  -0.654  -0.651  -0.536  -0.896  -0.889  -0.789
29    P        -0.200  -0.215  -0.249  -0.244  -0.264  -0.311  -0.346  -0.368  -0.422
30    R        -0.717  -0.705  -0.739  -0.700  -0.694  -0.780  -0.712  -0.700  -0.719
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    I        -0.717  -0.679  -0.736  -0.574  -0.514  -0.651  -0.712  -0.667  -0.716
34    L        -0.308  -0.274  -0.272  -0.457  -0.419  -0.371  -0.522  -0.474  -0.463
35    T        -1.610  -1.617  -1.527  -1.561  -1.586  -1.472  -1.227  -1.227  -1.098
36    G        -1.260  -1.249  -1.190  -1.417  -1.393  -1.304  -1.086  -1.072  -0.967
37    S        -0.428  -0.428  -0.331  -0.647  -0.645  -0.492  -0.666  -0.668  -0.535
38    K        -0.778  -0.751  -0.759  -1.045  -1.000  -0.987  -0.806  -0.774  -0.749
39    L         0.072   0.079  -0.157   0.171   0.177  -0.234   0.035   0.043  -0.292
40    W        -1.260  -1.249  -1.179  -1.093  -1.075  -0.933  -1.086  -1.073  -0.959
41    Y         0.072   0.053  -0.169   0.438   0.411   0.073   0.035   0.009  -0.309
42    S         0.755   0.730   0.556   0.722   0.692   0.457   0.736   0.695   0.376
43    T        -0.054  -0.058  -0.174   0.046   0.034  -0.157  -0.140  -0.147  -0.316
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    Q        -0.971  -0.956  -0.836  -1.029  -1.002  -0.828  -0.999  -0.980  -0.825
49    M        -0.971  -0.956  -0.836  -0.959  -0.934  -0.760  -0.999  -0.980  -0.825
50    A        -0.971  -0.956  -0.836  -1.005  -0.982  -0.805  -0.999  -0.980  -0.825
51    M        -0.308  -0.310  -0.278  -0.412  -0.423  -0.378  -0.522  -0.523  -0.468
52    T        -0.308  -0.330  -0.295  -0.303  -0.330  -0.274  -0.522  -0.545  -0.491
53    P        -0.295  -0.249  -0.266  -0.220  -0.164  -0.162  -0.526  -0.475  -0.458
54    E        -0.295  -0.344  -0.275  -0.207  -0.264  -0.160  -0.526  -0.572  -0.468
55    E         1.480   1.493   1.572   1.529   1.549   1.662   1.578   1.596   1.715
56    K         0.072   0.038  -0.170  -0.012  -0.052  -0.375   0.035  -0.018  -0.311
57    M        -1.260  -1.225  -1.181  -1.324  -1.252  -1.188  -1.086  -1.051  -0.960
58    I         1.480   1.493   1.572   1.368   1.388   1.505   1.578   1.596   1.715
59    T        -1.260  -1.294  -1.192  -1.089  -1.162  -1.008  -1.086  -1.108  -0.969
60    D        -1.128  -1.092  -1.156  -0.806  -0.755  -0.860  -0.946  -0.907  -0.934
61    K        -0.295  -0.303  -0.269  -0.599  -0.590  -0.506  -0.526  -0.528  -0.460
62    L         1.480   1.493   1.572   1.236   1.251   1.376   1.578   1.596   1.715
63    Q        -0.910  -0.886  -0.810  -1.047  -1.001  -0.901  -0.946  -0.917  -0.801
64    Q        -0.910  -0.931  -0.813  -0.966  -0.972  -0.804  -0.946  -0.957  -0.804
65    E        -0.560  -0.612  -0.727  -0.342  -0.435  -0.613  -0.526  -0.589  -0.706
66    L         0.273   0.282   0.369  -0.039  -0.028   0.130  -0.105  -0.093   0.025
67    E        -1.128  -1.178  -1.165  -0.942  -1.045  -1.055  -0.946  -0.994  -0.943
68    P         0.755   0.785   0.569   0.976   1.011   0.702   0.736   0.782   0.399
69    E        -1.260  -1.226  -1.179  -1.273  -1.231  -1.151  -1.086  -1.053  -0.958
70    V        -1.128  -1.048  -1.138  -0.995  -0.887  -0.985  -0.946  -0.861  -0.918
71    C         0.072   0.160  -0.127  -0.003   0.109  -0.258   0.035   0.156  -0.249
72    K        -1.260  -1.235  -1.179  -1.290  -1.226  -1.149  -1.086  -1.059  -0.959
73    V         0.755   0.822   0.570   0.883   0.968   0.594   0.736   0.838   0.401
74    Q        -1.260  -1.276  -1.189  -1.273  -1.301  -1.151  -1.086  -1.095  -0.967
75    D         1.480   1.493   1.572   1.575   1.595   1.706   1.578   1.596   1.715
76    V         0.422   0.441   0.435   0.363   0.389   0.336   0.176   0.204   0.152
77    S         1.480   1.493   1.572   1.348   1.365   1.485   1.578   1.596   1.715
78    G         1.480   1.493   1.572   1.503   1.518   1.636   1.578   1.596   1.715
79    G         1.480   1.493   1.572   1.503   1.518   1.636   1.578   1.596   1.715
80    C         1.480   1.493   1.572   1.724   1.740   1.850   1.578   1.596   1.715
81    G         1.480   1.493   1.572   1.503   1.518   1.636   1.578   1.596   1.715
82    S         1.480   1.493   1.572   1.348   1.365   1.485   1.578   1.596   1.715
83    M         1.480   1.493   1.572   1.589   1.605   1.719   1.578   1.596   1.715
84    F         0.422   0.389   0.395   0.555   0.497   0.490   0.176   0.109   0.076
85    A        -0.210  -0.235  -0.226  -0.159  -0.180  -0.193  -0.385  -0.403  -0.396
86    I         0.755   0.662   0.542   0.738   0.619   0.444   0.736   0.586   0.350
87    N        -1.610  -1.617  -1.527  -1.295  -1.312  -1.185  -1.227  -1.227  -1.098
88    I         0.422   0.445   0.418   0.263   0.299   0.243   0.176   0.212   0.120
89    T        -0.778  -0.836  -0.786  -0.746  -0.836  -0.773  -0.806  -0.858  -0.776
90    S         1.480   1.493   1.572   1.348   1.365   1.485   1.578   1.596   1.715
91    K        -0.428  -0.419  -0.327  -0.570  -0.566  -0.446  -0.666  -0.655  -0.531
92    K         0.755   0.662   0.542   0.660   0.547   0.386   0.736   0.586   0.350
93    F         1.480   1.493   1.572   1.621   1.636   1.751   1.578   1.596   1.715
94    N        -0.210  -0.259  -0.261  -0.359  -0.411  -0.399  -0.385  -0.439  -0.445
95    G         0.755   0.785   0.569   0.865   0.903   0.599   0.736   0.782   0.399
96    L        -0.210  -0.289  -0.269  -0.562  -0.691  -0.676  -0.385  -0.485  -0.457
97    S        -0.910  -0.931  -0.813  -0.914  -0.921  -0.746  -0.946  -0.957  -0.803
98    L        -0.778  -0.733  -0.763  -0.748  -0.687  -0.768  -0.806  -0.765  -0.753
99    I        -0.210  -0.272  -0.252  -0.360  -0.462  -0.446  -0.385  -0.460  -0.433
100   K         0.755   0.662   0.542   0.660   0.547   0.386   0.736   0.586   0.350
101   Q         1.480   1.493   1.572   1.543   1.559   1.674   1.578   1.596   1.715
102   H         1.480   1.493   1.572   1.679   1.696   1.807   1.578   1.596   1.715
103   Q        -0.210  -0.136  -0.232  -0.221  -0.110  -0.280  -0.385  -0.287  -0.406
104   L         0.755   0.785   0.569   0.614   0.650   0.379   0.736   0.782   0.399
105   V         1.480   1.493   1.572   1.543   1.556   1.674   1.578   1.596   1.715
106   N         1.480   1.493   1.572   1.569   1.586   1.700   1.578   1.596   1.715
107   R        -0.560  -0.631  -0.734  -0.340  -0.458  -0.622  -0.526  -0.613  -0.714
108   I         0.072   0.053  -0.169   0.064   0.035  -0.320   0.035   0.009  -0.309
109   L         1.480   1.493   1.572   1.236   1.251   1.376   1.578   1.596   1.715
110   R         0.072   0.079  -0.157   0.043   0.057  -0.256   0.035   0.043  -0.292
111   D         0.422   0.389   0.395   0.454   0.395   0.366   0.176   0.109   0.076
112   D         0.273   0.304   0.389   0.169   0.224   0.344  -0.105  -0.051   0.064
113   I         1.480   1.493   1.572   1.368   1.388   1.505   1.578   1.596   1.715
114   S        -0.778  -0.809  -0.769  -0.955  -0.990  -0.901  -0.806  -0.833  -0.760
115   R        -0.778  -0.830  -0.771  -0.864  -0.916  -0.810  -0.806  -0.851  -0.758
116   W         0.755   0.662   0.542   1.097   0.978   0.786   0.736   0.586   0.350
117   H         1.480   1.493   1.572   1.679   1.696   1.807   1.578   1.596   1.715
118   G         1.480   1.493   1.572   1.503   1.518   1.636   1.578   1.596   1.715
119   L         0.755   0.770   0.566   0.575   0.593   0.295   0.736   0.758   0.393
120   Q         0.755   0.662   0.542   0.916   0.795   0.615   0.736   0.586   0.350
121   L         1.480   1.493   1.572   1.236   1.251   1.376   1.578   1.596   1.715
122   T        -1.128  -1.178  -1.165  -1.005  -1.102  -1.112  -0.946  -0.994  -0.943
123   T         1.480   1.493   1.572   1.503   1.523   1.636   1.578   1.596   1.715
124   K         0.755   0.662   0.542   0.646   0.532   0.356   0.736   0.586   0.350
125   K        -0.560  -0.652  -0.739  -0.577  -0.701  -0.821  -0.526  -0.636  -0.720
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   S        -1.260  -1.195  -1.181  -1.212  -1.135  -1.099  -1.086  -1.028  -0.960
* 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/P39724
Output conservation file - output/P39724
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
