1     M         0.851   0.876   0.915   1.062   1.083   1.131   0.909   0.946   1.004
2     S         0.851   0.876   0.915   0.832   0.875   0.931   0.909   0.946   1.004
3     S        -0.003   0.007  -0.216   0.154   0.158  -0.231  -0.083  -0.070  -0.468
4     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     T        -1.448  -1.250  -1.424  -1.226  -0.946  -1.193  -1.435  -1.188  -1.330
6     E         0.851   0.876   0.915   0.783   0.821   0.888   0.909   0.946   1.004
7     R        -0.403  -0.398  -0.279  -0.498  -0.498  -0.314  -0.765  -0.768  -0.583
8     T         0.851   0.876   0.915   0.955   0.989   1.038   0.909   0.946   1.004
9     F         0.851   0.876   0.915   0.933   0.968   1.019   0.909   0.946   1.004
10    I         0.851   0.876   0.915   0.801   0.836   0.904   0.909   0.946   1.004
11    A         0.851   0.876   0.915   0.832   0.859   0.931   0.909   0.946   1.004
12    V        -0.403  -0.399  -0.279  -0.675  -0.679  -0.478  -0.765  -0.770  -0.582
13    K         0.851   0.876   0.915   0.783   0.820   0.888   0.909   0.946   1.004
14    P         0.851   0.876   0.915   0.911   0.945   1.000   0.909   0.946   1.004
15    D         0.851   0.876   0.915   0.924   0.960   1.011   0.909   0.946   1.004
16    G         0.137  -0.079  -0.199   0.044  -0.246  -0.437   0.128  -0.208  -0.437
17    V         0.851   0.876   0.915   0.841   0.882   0.939   0.909   0.946   1.004
18    Q         0.851   0.876   0.915   0.985   1.015   1.064   0.909   0.946   1.004
19    R         0.851   0.876   0.915   0.916   0.949   1.004   0.909   0.946   1.004
20    G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
21    L         0.851   0.876   0.915   0.706   0.763   0.821   0.909   0.946   1.004
22    V        -0.215  -0.218  -0.259  -0.337  -0.348  -0.443  -0.430  -0.443  -0.546
23    S        -0.996  -0.832  -0.940  -1.232  -1.052  -1.086  -1.212  -1.027  -1.068
24    Q        -2.434  -2.364  -2.166  -2.232  -2.073  -1.805  -1.993  -1.881  -1.638
25    I         0.851   0.876   0.915   0.801   0.836   0.904   0.909   0.946   1.004
26    L        -0.215  -0.335  -0.273  -0.443  -0.649  -0.560  -0.430  -0.653  -0.572
27    S        -1.529  -1.298  -1.434  -1.677  -1.302  -1.434  -1.546  -1.271  -1.341
28    R         0.137  -0.079  -0.199   0.279  -0.028  -0.265   0.128  -0.208  -0.437
29    F         0.851   0.876   0.915   0.933   0.968   1.019   0.909   0.946   1.004
30    E         0.851   0.876   0.915   0.783   0.821   0.888   0.909   0.946   1.004
31    K        -2.434  -2.321  -2.162  -2.175  -2.072  -1.838  -1.993  -1.854  -1.636
32    K        -0.215  -0.304  -0.266  -0.244  -0.426  -0.407  -0.430  -0.596  -0.560
33    G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
34    Y        -0.403  -0.319  -0.269  -0.427  -0.293  -0.254  -0.765  -0.623  -0.565
35    K         0.851   0.876   0.915   0.783   0.820   0.888   0.909   0.946   1.004
36    L         0.851   0.876   0.915   0.706   0.763   0.821   0.909   0.946   1.004
37    V         0.137  -0.079  -0.199   0.223  -0.059  -0.268   0.128  -0.208  -0.437
38    A        -0.463  -0.357  -0.265  -0.890  -0.673  -0.524  -0.877  -0.693  -0.557
39    I        -0.543  -0.797  -0.922  -0.433  -0.802  -0.988  -0.542  -0.880  -1.041
40    K         0.851   0.876   0.915   0.783   0.820   0.888   0.909   0.946   1.004
41    L         0.137  -0.079  -0.199   0.091  -0.171  -0.367   0.128  -0.208  -0.437
42    V        -1.448  -1.515  -1.451  -1.434  -1.555  -1.471  -1.435  -1.483  -1.357
43    K        -1.777  -1.745  -1.825  -1.418  -1.430  -1.560  -1.546  -1.507  -1.510
44    A        -0.215  -0.147  -0.237  -0.233  -0.130  -0.323  -0.430  -0.321  -0.506
45    D        -1.529  -1.592  -1.448  -1.504  -1.595  -1.419  -1.546  -1.553  -1.354
46    D        -1.448  -1.539  -1.455  -1.396  -1.510  -1.355  -1.435  -1.506  -1.360
47    K        -1.653  -1.610  -1.450  -1.808  -1.709  -1.470  -1.658  -1.567  -1.356
48    L         0.137   0.082  -0.186   0.112   0.076  -0.287   0.128   0.046  -0.415
49    L         0.137  -0.079  -0.199   0.077  -0.194  -0.407   0.128  -0.208  -0.437
50    E        -0.996  -0.758  -0.923  -1.167  -0.803  -1.030  -1.212  -0.879  -1.044
51    Q        -1.448  -1.310  -1.429  -1.419  -1.243  -1.372  -1.435  -1.269  -1.335
52    H         0.851   0.876   0.915   1.075   1.095   1.142   0.909   0.946   1.004
53    Y         0.851   0.876   0.915   1.028   1.051   1.102   0.909   0.946   1.004
54    A        -0.996  -0.793  -0.938  -1.180  -0.904  -1.038  -1.212  -0.961  -1.065
55    E        -0.403  -0.393  -0.280  -0.596  -0.610  -0.437  -0.765  -0.758  -0.584
56    H        -0.403  -0.393  -0.280  -0.630  -0.579  -0.391  -0.765  -0.758  -0.584
57    V        -1.981  -2.003  -1.848  -1.821  -1.880  -1.670  -1.769  -1.741  -1.529
58    G        -1.529  -1.415  -1.442  -1.721  -1.529  -1.533  -1.546  -1.380  -1.348
59    K         0.851   0.876   0.915   0.783   0.820   0.888   0.909   0.946   1.004
60    P         0.851   0.876   0.915   0.911   0.945   1.000   0.909   0.946   1.004
61    F         0.851   0.876   0.915   0.933   0.968   1.019   0.909   0.946   1.004
62    F         0.137  -0.079  -0.199   0.331   0.051  -0.149   0.128  -0.208  -0.437
63    P        -1.184  -1.355  -1.436  -0.993  -1.287  -1.484  -1.100  -1.295  -1.340
64    K        -1.448  -1.469  -1.454  -1.503  -1.578  -1.542  -1.435  -1.445  -1.359
65    M        -0.215  -0.147  -0.237  -0.354  -0.235  -0.364  -0.430  -0.321  -0.506
66    V        -1.448  -1.469  -1.454  -1.554  -1.575  -1.509  -1.435  -1.445  -1.359
67    S        -1.448  -1.515  -1.451  -1.522  -1.669  -1.571  -1.435  -1.483  -1.357
68    F        -0.403  -0.393  -0.280  -0.427  -0.443  -0.278  -0.765  -0.758  -0.584
69    M         0.851   0.876   0.915   1.062   1.083   1.131   0.909   0.946   1.004
70    K        -2.762  -2.641  -2.438  -2.596  -2.402  -2.100  -2.104  -1.962  -1.718
71    S         0.851   0.876   0.915   0.832   0.875   0.931   0.909   0.946   1.004
72    G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
73    P         0.851   0.876   0.915   0.911   0.945   1.000   0.909   0.946   1.004
74    I        -0.403  -0.362  -0.277  -0.661  -0.596  -0.473  -0.765  -0.701  -0.579
75    L        -0.215  -0.335  -0.273  -0.331  -0.480  -0.363  -0.430  -0.653  -0.572
76    A         0.851   0.876   0.915   0.832   0.859   0.931   0.909   0.946   1.004
77    T        -0.215  -0.335  -0.273  -0.117  -0.321  -0.238  -0.430  -0.653  -0.572
78    V         0.137  -0.079  -0.199   0.207  -0.090  -0.317   0.128  -0.208  -0.437
79    W         0.851   0.876   0.915   1.058   1.084   1.128   0.909   0.946   1.004
80    E         0.851   0.876   0.915   0.783   0.821   0.888   0.909   0.946   1.004
81    G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
82    K         0.851   0.876   0.915   0.783   0.820   0.888   0.909   0.946   1.004
83    D         0.137  -0.079  -0.199   0.316   0.034  -0.174   0.128  -0.208  -0.437
84    V        -0.403  -0.398  -0.279  -0.644  -0.659  -0.460  -0.765  -0.769  -0.583
85    V         0.851   0.876   0.915   0.841   0.882   0.939   0.909   0.946   1.004
86    R         0.137   0.177  -0.176   0.165   0.224  -0.276   0.128   0.187  -0.397
87    Q        -0.215  -0.335  -0.273  -0.123  -0.346  -0.278  -0.430  -0.653  -0.572
88    G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
89    R         0.851   0.876   0.915   0.916   0.949   1.004   0.909   0.946   1.004
90    T        -1.448  -1.510  -1.451  -1.397  -1.527  -1.396  -1.435  -1.483  -1.357
91    I        -0.215  -0.293  -0.266  -0.264  -0.387  -0.333  -0.430  -0.576  -0.559
92    L         0.851   0.876   0.915   0.706   0.763   0.821   0.909   0.946   1.004
93    G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
94    A         0.851   0.876   0.915   0.832   0.859   0.931   0.909   0.946   1.004
95    T         0.137  -0.079  -0.199   0.325   0.026  -0.214   0.128  -0.208  -0.437
96    N         0.851   0.876   0.915   0.994   1.023   1.072   0.909   0.946   1.004
97    P         0.851   0.876   0.915   0.911   0.945   1.000   0.909   0.946   1.004
98    L         0.137   0.209  -0.174   0.094   0.211  -0.318   0.128   0.233  -0.394
99    G        -1.184  -1.379  -1.440  -0.892  -1.204  -1.384  -1.100  -1.319  -1.344
100   S         0.851   0.876   0.915   0.832   0.875   0.931   0.909   0.946   1.004
101   A         0.851   0.876   0.915   0.832   0.859   0.931   0.909   0.946   1.004
102   P         0.851   0.876   0.915   0.911   0.945   1.000   0.909   0.946   1.004
103   G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
104   T         0.851   0.876   0.915   0.955   0.989   1.038   0.909   0.946   1.004
105   I         0.851   0.876   0.915   0.801   0.836   0.904   0.909   0.946   1.004
106   R         0.851   0.876   0.915   0.916   0.949   1.004   0.909   0.946   1.004
107   G         0.137   0.235  -0.176   0.059   0.193  -0.356   0.128   0.270  -0.397
108   D         0.851   0.876   0.915   0.924   0.960   1.011   0.909   0.946   1.004
109   F        -0.215  -0.284  -0.269  -0.149  -0.268  -0.265  -0.430  -0.559  -0.564
110   G        -0.403  -0.393  -0.280  -0.736  -0.760  -0.566  -0.765  -0.758  -0.584
111   I        -0.543  -0.439  -0.886  -0.471  -0.345  -1.020  -0.542  -0.413  -0.993
112   D         0.137   0.277  -0.174   0.288   0.466  -0.210   0.128   0.327  -0.394
113   L        -1.529  -1.327  -1.440  -1.548  -1.291  -1.420  -1.546  -1.314  -1.346
114   G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
115   R         0.851   0.876   0.915   0.916   0.949   1.004   0.909   0.946   1.004
116   N         0.851   0.876   0.915   0.994   1.023   1.072   0.909   0.946   1.004
117   V         0.851   0.876   0.915   0.841   0.882   0.939   0.909   0.946   1.004
118   C         0.851   0.876   0.915   1.130   1.149   1.190   0.909   0.946   1.004
119   H         0.851   0.876   0.915   1.075   1.095   1.142   0.909   0.946   1.004
120   G         0.851   0.876   0.915   0.674   0.718   0.793   0.909   0.946   1.004
121   S         0.851   0.876   0.915   0.832   0.875   0.931   0.909   0.946   1.004
122   D         0.851   0.876   0.915   0.924   0.960   1.011   0.909   0.946   1.004
123   S         0.851   0.876   0.915   0.832   0.875   0.931   0.909   0.946   1.004
124   V         0.137  -0.079  -0.199   0.207  -0.090  -0.317   0.128  -0.208  -0.437
125   D         0.137   0.177  -0.176   0.167   0.226  -0.272   0.128   0.187  -0.397
126   S         0.137   0.082  -0.186   0.226   0.173  -0.222   0.128   0.046  -0.415
127   A         0.851   0.876   0.915   0.832   0.859   0.931   0.909   0.946   1.004
128   E        -1.200  -1.112  -0.972  -1.406  -1.246  -1.051  -1.435  -1.301  -1.105
129   R        -0.403  -0.393  -0.280  -0.651  -0.635  -0.445  -0.765  -0.758  -0.584
130   E         0.851   0.876   0.915   0.783   0.821   0.888   0.909   0.946   1.004
131   I         0.851   0.876   0.915   0.801   0.836   0.904   0.909   0.946   1.004
132   N        -1.777  -1.806  -1.831  -1.726  -1.816  -1.770  -1.546  -1.569  -1.515
133   L        -0.215  -0.113  -0.245  -0.443  -0.260  -0.509  -0.430  -0.264  -0.521
134   W         0.851   0.876   0.915   1.058   1.084   1.128   0.909   0.946   1.004
135   F         0.851   0.876   0.915   0.933   0.968   1.019   0.909   0.946   1.004
136   K         0.137  -0.079  -0.199   0.175  -0.102  -0.284   0.128  -0.208  -0.437
137   K        -0.403  -0.398  -0.279  -0.653  -0.644  -0.442  -0.765  -0.768  -0.583
138   E         0.137  -0.079  -0.199   0.153  -0.139  -0.350   0.128  -0.208  -0.437
139   E         0.851   0.876   0.915   0.783   0.821   0.888   0.909   0.946   1.004
140   L         0.137  -0.079  -0.199   0.071  -0.207  -0.425   0.128  -0.208  -0.437
141   V        -1.777  -1.805  -1.834  -1.545  -1.587  -1.643  -1.546  -1.565  -1.518
142   D        -1.981  -1.978  -1.841  -1.881  -1.865  -1.684  -1.769  -1.720  -1.524
143   W        -0.403  -0.362  -0.277  -0.363  -0.313  -0.198  -0.765  -0.701  -0.579
144   E        -1.777  -1.867  -1.840  -1.590  -1.724  -1.665  -1.546  -1.618  -1.522
145   S        -1.777  -1.841  -1.837  -1.497  -1.600  -1.638  -1.546  -1.597  -1.520
146   N        -1.981  -2.003  -1.848  -1.786  -1.789  -1.559  -1.769  -1.741  -1.529
147   Q        -2.105  -2.064  -1.847  -2.068  -1.985  -1.687  -1.881  -1.785  -1.528
148   A        -2.105  -2.008  -1.844  -2.217  -2.080  -1.834  -1.881  -1.746  -1.526
149   K        -1.981  -1.946  -1.843  -2.105  -2.029  -1.847  -1.769  -1.703  -1.526
150   W         0.851   0.876   0.915   1.058   1.084   1.128   0.909   0.946   1.004
151   I         0.851   0.876   0.915   0.801   0.836   0.904   0.909   0.946   1.004
152   Y         0.137   0.082  -0.186   0.412   0.337  -0.093   0.128   0.046  -0.415
153   E         0.851   0.876   0.915   0.783   0.821   0.888   0.909   0.946   1.004
* 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/P36010
Output conservation file - output/P36010
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
