1     M         1.723   1.724   1.760   1.957   1.954   2.020   1.904   1.905   1.958
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S        -0.519  -0.504  -0.409  -0.594  -0.571  -0.441  -0.682  -0.663  -0.539
4     F         1.723   1.724   1.760   1.670   1.676   1.742   1.904   1.905   1.958
5     I        -0.341  -0.322  -0.340  -0.510  -0.477  -0.492  -0.466  -0.440  -0.448
6     P         0.424   0.447   0.474   0.176   0.216   0.254   0.180   0.220   0.243
7     I        -0.341  -0.298  -0.362  -0.572  -0.497  -0.599  -0.466  -0.409  -0.481
8     V        -0.990  -1.020  -0.979  -0.994  -1.018  -0.969  -0.897  -0.922  -0.857
9     C        -0.519  -0.502  -0.411  -0.852  -0.828  -0.683  -0.682  -0.660  -0.542
10    G         1.723   1.724   1.760   1.800   1.799   1.868   1.904   1.905   1.958
11    M        -1.462  -1.453  -1.435  -1.411  -1.403  -1.358  -1.113  -1.104  -1.059
12    K        -0.047  -0.114  -0.251  -0.018  -0.119  -0.352  -0.035  -0.132  -0.324
13    S        -0.990  -1.020  -0.979  -0.876  -0.934  -0.868  -0.897  -0.922  -0.857
14    F         0.424   0.439   0.435   0.291   0.316   0.314   0.180   0.205   0.172
15    D        -0.341  -0.394  -0.370  -0.332  -0.407  -0.381  -0.466  -0.525  -0.488
16    S        -0.341  -0.388  -0.359  -0.418  -0.474  -0.422  -0.466  -0.516  -0.477
17    S        -0.047   0.017  -0.232   0.040   0.123  -0.233  -0.035   0.050  -0.298
18    Y        -0.990  -1.020  -0.979  -0.807  -0.838  -0.761  -0.897  -0.922  -0.857
19    D        -0.990  -0.937  -0.925  -1.028  -0.966  -0.917  -0.897  -0.845  -0.807
20    T        -1.462  -1.453  -1.435  -1.236  -1.232  -1.243  -1.113  -1.104  -1.059
21    V        -0.812  -0.874  -0.885  -0.638  -0.730  -0.766  -0.682  -0.754  -0.757
22    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    G        -0.341  -0.398  -0.360  -0.382  -0.463  -0.403  -0.466  -0.531  -0.479
24    H        -1.462  -1.453  -1.435  -1.219  -1.217  -1.153  -1.113  -1.104  -1.059
25    Q        -1.462  -1.453  -1.435  -1.318  -1.307  -1.260  -1.113  -1.104  -1.059
26    N        -1.462  -1.445  -1.383  -1.390  -1.368  -1.281  -1.113  -1.098  -1.014
27    L        -0.990  -1.020  -0.979  -1.028  -1.053  -0.996  -0.897  -0.922  -0.857
28    Y         1.723   1.724   1.760   1.946   1.951   2.010   1.904   1.905   1.958
29    C         1.723   1.724   1.760   1.746   1.748   1.816   1.904   1.905   1.958
30    P         0.424   0.447   0.474   0.237   0.271   0.315   0.180   0.220   0.243
31    N         0.424   0.440   0.417   0.316   0.339   0.302   0.180   0.205   0.138
32    C         1.723   1.724   1.760   1.746   1.748   1.816   1.904   1.905   1.958
33    H         1.723   1.724   1.760   1.926   1.925   1.990   1.904   1.905   1.958
34    N         1.723   1.724   1.760   1.725   1.728   1.795   1.904   1.905   1.958
35    Y        -0.990  -1.020  -0.979  -0.890  -0.925  -0.875  -0.897  -0.922  -0.857
36    S         0.803   0.807   0.597   0.972   0.975   0.651   0.827   0.829   0.464
37    V        -0.341  -0.394  -0.370  -0.341  -0.416  -0.395  -0.466  -0.525  -0.488
38    G        -1.933  -1.906  -1.804  -1.867  -1.819  -1.690  -1.328  -1.304  -1.190
39    P         0.308   0.318   0.382   0.123   0.144   0.249  -0.035  -0.020   0.072
40    I        -0.341  -0.376  -0.334  -0.424  -0.451  -0.412  -0.466  -0.499  -0.450
41    K         0.424   0.447   0.474   0.281   0.319   0.361   0.180   0.220   0.243
42    R         0.424   0.447   0.474   0.473   0.506   0.546   0.180   0.220   0.243
43    K        -0.341  -0.274  -0.328  -0.397  -0.293  -0.371  -0.466  -0.384  -0.431
44    E        -0.341  -0.306  -0.337  -0.365  -0.313  -0.349  -0.466  -0.420  -0.443
45    F         0.424   0.447   0.474   0.181   0.225   0.261   0.180   0.220   0.243
46    F        -0.519  -0.502  -0.411  -0.818  -0.784  -0.654  -0.682  -0.660  -0.542
47    T         0.424   0.439   0.435   0.469   0.492   0.464   0.180   0.205   0.172
48    I        -0.047   0.038  -0.232   0.045   0.179  -0.262  -0.035   0.079  -0.298
49    W        -0.341  -0.394  -0.370  -0.332  -0.416  -0.392  -0.466  -0.525  -0.488
50    F         1.723   1.724   1.760   1.670   1.676   1.742   1.904   1.905   1.958
51    I         0.424   0.385   0.405   0.237   0.167   0.188   0.180   0.105   0.114
52    P         1.723   1.724   1.760   1.703   1.702   1.774   1.904   1.905   1.958
53    L        -0.341  -0.381  -0.350  -0.442  -0.489  -0.463  -0.466  -0.506  -0.464
54    V        -0.990  -1.020  -0.979  -1.061  -1.103  -1.058  -0.897  -0.922  -0.857
55    P         1.723   1.724   1.760   1.703   1.702   1.774   1.904   1.905   1.958
56    V        -0.990  -0.934  -0.956  -1.157  -1.072  -1.086  -0.897  -0.842  -0.834
57    F        -0.519  -0.504  -0.409  -0.587  -0.557  -0.422  -0.682  -0.663  -0.539
58    W        -0.341  -0.306  -0.337  -0.170  -0.115  -0.170  -0.466  -0.420  -0.443
59    G        -0.341  -0.349  -0.370  -0.379  -0.402  -0.428  -0.466  -0.482  -0.494
60    K         0.424   0.385   0.405   0.202   0.125   0.143   0.180   0.105   0.114
61    Q        -0.341  -0.394  -0.370  -0.335  -0.408  -0.364  -0.466  -0.525  -0.488
62    L         0.803   0.699   0.577   0.884   0.734   0.522   0.827   0.655   0.429
63    H         0.308   0.318   0.382   0.123   0.131   0.238  -0.035  -0.020   0.072
64    C         1.723   1.724   1.760   1.746   1.748   1.816   1.904   1.905   1.958
65    P        -0.519  -0.505  -0.419  -0.697  -0.669  -0.537  -0.682  -0.664  -0.552
66    I         1.723   1.724   1.760   1.703   1.706   1.774   1.904   1.905   1.958
67    C         1.723   1.724   1.760   1.746   1.748   1.816   1.904   1.905   1.958
68    N        -0.047  -0.006  -0.262   0.038   0.094  -0.298  -0.035   0.020  -0.339
69    W        -0.047  -0.006  -0.262   0.333   0.386  -0.002  -0.035   0.020  -0.339
70    R        -0.341  -0.349  -0.370  -0.257  -0.286  -0.303  -0.466  -0.482  -0.494
71    Q        -0.341  -0.394  -0.370  -0.442  -0.522  -0.498  -0.466  -0.525  -0.488
72    D         0.424   0.385   0.406   0.440   0.363   0.372   0.180   0.105   0.117
73    F        -0.341  -0.394  -0.370  -0.525  -0.589  -0.556  -0.466  -0.525  -0.488
74    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    N        -0.990  -0.968  -0.955  -0.890  -0.863  -0.842  -0.897  -0.873  -0.832
76    D        -0.990  -0.944  -0.933  -0.901  -0.837  -0.811  -0.897  -0.850  -0.814
77    E        -0.047  -0.006  -0.262   0.254   0.300  -0.071  -0.035   0.020  -0.339
78    Q        -0.812  -0.847  -0.929  -0.603  -0.661  -0.774  -0.682  -0.725  -0.804
79    L         0.424   0.447   0.474   0.369   0.410   0.447   0.180   0.220   0.243
80    N        -1.933  -1.906  -1.804  -1.680  -1.655  -1.508  -1.328  -1.304  -1.190
81    K        -0.047  -0.133  -0.241   0.061  -0.061  -0.216  -0.035  -0.157  -0.311
82    V         0.308   0.318   0.382   0.215   0.239   0.336  -0.035  -0.020   0.072
83    I        -0.990  -1.020  -0.979  -1.072  -1.110  -1.022  -0.897  -0.922  -0.857
84    Q        -1.462  -1.421  -1.396  -1.280  -1.228  -1.194  -1.113  -1.073  -1.026
85    E        -0.341  -0.394  -0.370  -0.283  -0.360  -0.313  -0.466  -0.525  -0.488
86    Q         1.723   1.724   1.760   1.778   1.786   1.847   1.904   1.905   1.958
87    Q        -0.399  -0.307  -0.363  -0.495  -0.331  -0.469  -0.520  -0.396  -0.477
88    N        -0.399  -0.435  -0.401  -0.488  -0.536  -0.493  -0.520  -0.574  -0.528
89    L        -0.399  -0.438  -0.395  -0.536  -0.617  -0.565  -0.520  -0.578  -0.520
90    R         0.575   0.612   0.493   0.638   0.692   0.469   0.450   0.509   0.277
91    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    P         1.723   1.724   1.760   1.723   1.712   1.793   1.904   1.905   1.958
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   N        -0.341  -0.279  -0.363  -0.347  -0.262  -0.387  -0.466  -0.393  -0.483
* 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/Q3E756
Output conservation file - output/Q3E756
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
