1     M         1.868   1.871   1.963   2.136   2.140   2.302   2.111   2.115   2.271
2     -         0.812   0.794   0.784   0.844   0.817   0.804   0.651   0.618   0.560
3     -        -0.737  -0.733  -0.668  -0.679  -0.682  -0.571  -0.808  -0.803  -0.713
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    N        -1.499  -1.496  -1.438  -1.323  -1.317  -1.228  -1.133  -1.129  -1.045
23    D        -1.065  -1.071  -1.048  -1.174  -1.183  -1.155  -0.917  -0.922  -0.872
24    D        -1.065  -1.074  -1.046  -1.041  -1.051  -1.018  -0.917  -0.925  -0.870
25    E        -0.467  -0.434  -0.516  -0.442  -0.390  -0.513  -0.484  -0.443  -0.533
26    D         0.238   0.235   0.105   0.288   0.282   0.052   0.165   0.160  -0.040
27    -        -0.086  -0.103  -0.064  -0.272  -0.311  -0.283  -0.322  -0.347  -0.296
28    R        -0.631  -0.649  -0.615  -0.789  -0.813  -0.756  -0.700  -0.718  -0.658
29    A        -0.467  -0.493  -0.529  -0.436  -0.482  -0.558  -0.484  -0.517  -0.549
30    Q         0.672   0.654   0.691   0.577   0.539   0.577   0.381   0.343   0.373
31    L         1.868   1.871   1.963   1.633   1.640   1.789   2.111   2.115   2.271
32    K         1.022   1.049   0.919   1.195   1.237   1.038   1.030   1.075   0.823
33    A        -0.032  -0.019  -0.027  -0.081  -0.062  -0.070  -0.268  -0.248  -0.253
34    R        -0.032  -0.019  -0.027  -0.119  -0.097  -0.113  -0.268  -0.248  -0.253
35    L         0.672   0.670   0.698   0.320   0.319   0.365   0.381   0.376   0.387
36    W         1.022   1.046   0.919   1.475   1.508   1.345   1.030   1.071   0.823
37    I        -0.631  -0.620  -0.602  -0.505  -0.482  -0.468  -0.700  -0.689  -0.645
38    R        -1.499  -1.496  -1.438  -1.133  -1.135  -1.035  -1.133  -1.129  -1.045
39    V         1.022   1.004   0.909   1.079   1.053   0.929   1.030   0.999   0.804
40    E        -0.631  -0.638  -0.614  -0.757  -0.764  -0.721  -0.700  -0.706  -0.657
41    E        -0.631  -0.614  -0.604  -0.737  -0.710  -0.703  -0.700  -0.683  -0.647
42    R        -0.631  -0.626  -0.604  -0.616  -0.608  -0.598  -0.700  -0.695  -0.647
43    L        -0.032  -0.012  -0.028  -0.367  -0.336  -0.359  -0.268  -0.241  -0.254
44    Q        -1.499  -1.496  -1.438  -1.454  -1.448  -1.362  -1.133  -1.129  -1.045
45    Q        -0.631  -0.650  -0.612  -0.754  -0.784  -0.733  -0.700  -0.718  -0.655
46    V        -0.467  -0.465  -0.529  -0.536  -0.531  -0.651  -0.484  -0.482  -0.549
47    L         0.812   0.783   0.780   0.486   0.444   0.426   0.651   0.596   0.554
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    S        -1.156  -1.154  -1.092  -1.079  -1.077  -0.979  -1.003  -1.000  -0.912
52    E        -0.114  -0.106  -0.076  -0.358  -0.343  -0.294  -0.380  -0.370  -0.320
53    D        -0.631  -0.649  -0.615  -0.744  -0.766  -0.706  -0.700  -0.718  -0.658
54    I        -0.631  -0.638  -0.605  -0.626  -0.638  -0.583  -0.700  -0.707  -0.648
55    K        -1.065  -1.075  -1.054  -0.857  -0.863  -0.834  -0.917  -0.926  -0.877
56    Y        -0.631  -0.642  -0.613  -0.527  -0.549  -0.498  -0.700  -0.711  -0.656
57    T        -0.467  -0.470  -0.529  -0.326  -0.337  -0.432  -0.484  -0.488  -0.550
58    P        -0.467  -0.470  -0.529  -0.114  -0.116  -0.228  -0.484  -0.488  -0.550
59    R        -1.065  -1.071  -1.048  -0.986  -0.997  -0.973  -0.917  -0.922  -0.872
60    F         1.022   1.049   0.919   1.385   1.421   1.256   1.030   1.075   0.823
61    I         0.672   0.669   0.699   0.541   0.534   0.581   0.381   0.374   0.390
62    N        -1.065  -1.075  -1.054  -0.893  -0.912  -0.893  -0.917  -0.926  -0.877
63    S        -0.032  -0.005  -0.021  -0.133  -0.092  -0.111  -0.268  -0.230  -0.243
64    L         1.868   1.871   1.963   1.633   1.640   1.789   2.111   2.115   2.271
65    L        -0.032  -0.020  -0.022  -0.247  -0.226  -0.262  -0.268  -0.249  -0.246
66    E         1.868   1.871   1.963   1.856   1.861   2.016   2.111   2.115   2.271
67    L         1.868   1.871   1.963   1.633   1.640   1.789   2.111   2.115   2.271
68    A         1.022   1.032   0.917   1.048   1.059   0.892   1.030   1.047   0.820
69    Y         0.238   0.197   0.099   0.664   0.609   0.480   0.165   0.104  -0.050
70    L        -1.499  -1.496  -1.438  -1.612  -1.612  -1.524  -1.133  -1.129  -1.045
71    Q         1.868   1.871   1.963   2.012   2.017   2.176   2.111   2.115   2.271
72    L        -0.032  -0.050  -0.033  -0.337  -0.358  -0.320  -0.268  -0.289  -0.262
73    G        -1.065  -1.048  -1.037  -1.125  -1.101  -1.085  -0.917  -0.899  -0.861
74    E        -0.032  -0.050  -0.040  -0.130  -0.153  -0.127  -0.268  -0.290  -0.272
75    M        -0.032  -0.028  -0.029  -0.361  -0.357  -0.356  -0.268  -0.262  -0.256
76    G         1.022   1.004   0.909   1.250   1.221   1.080   1.030   0.999   0.804
77    S        -0.631  -0.634  -0.605  -0.659  -0.660  -0.608  -0.700  -0.703  -0.648
78    D         1.022   1.022   0.917   1.135   1.135   0.986   1.030   1.030   0.820
79    L         1.868   1.871   1.963   1.633   1.640   1.789   2.111   2.115   2.271
80    Q         1.022   1.032   0.917   1.038   1.054   0.888   1.030   1.047   0.820
81    A        -0.631  -0.627  -0.609  -0.817  -0.807  -0.801  -0.700  -0.696  -0.651
82    F         1.022   1.022   0.917   1.385   1.385   1.253   1.030   1.030   0.820
83    A         1.022   1.004   0.909   1.135   1.108   0.966   1.030   0.999   0.804
84    R        -0.467  -0.465  -0.529  -0.314  -0.310  -0.417  -0.484  -0.482  -0.549
85    H         1.022   0.994   0.905   1.383   1.338   1.169   1.030   0.981   0.797
86    A         0.238   0.212   0.102   0.360   0.317   0.145   0.165   0.126  -0.045
87    G         0.672   0.671   0.692   0.729   0.726   0.751   0.381   0.378   0.375
88    R         1.868   1.871   1.963   1.925   1.929   2.087   2.111   2.115   2.271
89    G        -1.499  -1.496  -1.438  -1.364  -1.368  -1.270  -1.133  -1.129  -1.045
90    V         0.672   0.675   0.699   0.492   0.492   0.520   0.381   0.385   0.389
91    V         0.672   0.670   0.698   0.541   0.536   0.579   0.381   0.376   0.387
92    N        -0.467  -0.446  -0.517  -0.302  -0.272  -0.384  -0.484  -0.457  -0.535
93    K        -1.065  -1.048  -1.037  -0.782  -0.755  -0.739  -0.917  -0.899  -0.861
94    S        -1.065  -1.070  -1.046  -1.129  -1.139  -1.118  -0.917  -0.921  -0.870
95    D         1.868   1.871   1.963   1.954   1.958   2.117   2.111   2.115   2.271
96    L         0.238   0.244   0.112   0.028   0.037  -0.162   0.165   0.173  -0.029
97    M        -1.065  -1.064  -1.042  -1.187  -1.186  -1.127  -0.917  -0.915  -0.866
98    L         0.672   0.670   0.698   0.329   0.330   0.376   0.381   0.376   0.387
99    Y        -0.631  -0.614  -0.606  -0.952  -0.931  -0.900  -0.700  -0.683  -0.648
100   L        -0.032  -0.032  -0.023  -0.402  -0.401  -0.379  -0.268  -0.261  -0.248
101   R         1.868   1.871   1.963   1.925   1.929   2.087   2.111   2.115   2.271
102   K         0.566   0.569   0.648   0.355   0.360   0.483   0.165   0.170   0.283
103   Q         0.238   0.245   0.120   0.503   0.516   0.310   0.165   0.175  -0.017
104   P        -1.065  -1.064  -1.046  -0.871  -0.873  -0.868  -0.917  -0.915  -0.869
105   D        -0.467  -0.472  -0.539  -0.376  -0.385  -0.495  -0.484  -0.491  -0.562
106   L         1.868   1.871   1.963   1.633   1.640   1.789   2.111   2.115   2.271
107   Q        -0.467  -0.472  -0.539  -0.436  -0.444  -0.593  -0.484  -0.491  -0.562
108   E        -1.065  -1.052  -1.035  -1.088  -1.070  -1.041  -0.917  -0.903  -0.860
109   -        -0.635  -0.643  -0.614  -0.653  -0.664  -0.607  -0.692  -0.701  -0.652
110   -        -0.635  -0.642  -0.607  -0.789  -0.798  -0.729  -0.692  -0.700  -0.644
111   -        -0.086  -0.063  -0.060  -0.218  -0.180  -0.194  -0.322  -0.288  -0.290
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   R        -1.065  -1.075  -1.054  -0.839  -0.849  -0.795  -0.917  -0.926  -0.877
129   V        -1.065  -1.070  -1.046  -1.121  -1.128  -1.092  -0.917  -0.921  -0.870
130   T        -1.499  -1.496  -1.438  -1.187  -1.181  -1.090  -1.133  -1.129  -1.045
131   Q        -0.467  -0.434  -0.516  -0.385  -0.328  -0.484  -0.484  -0.443  -0.533
132   E        -1.065  -1.063  -1.044  -1.002  -0.992  -0.982  -0.917  -0.914  -0.868
* 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/Q3E835
Output conservation file - output/Q3E835
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
