1     M         0.902   0.926   0.994   1.210   1.231   1.298   0.945   0.982   1.085
2     -        -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     A        -1.225  -1.388  -1.636  -0.852  -1.083  -1.406  -1.013  -1.212  -1.408
5     E        -2.173  -2.292  -2.105  -1.665  -1.896  -1.710  -1.829  -1.930  -1.615
6     S        -1.129  -1.180  -1.102  -1.368  -1.484  -1.228  -1.258  -1.336  -1.142
7     H        -0.544  -0.479  -1.041  -0.101  -0.048  -0.843  -0.442  -0.366  -1.063
8     R         0.166   0.151  -0.248   0.125   0.117  -0.377   0.210   0.189  -0.439
9     L         0.166   0.151  -0.248   0.335   0.320  -0.352   0.210   0.189  -0.439
10    Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.982   1.085
11    V         0.902   0.926   0.994   0.662   0.713   0.857   0.945   0.982   1.085
12    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.982   1.085
13    G        -0.230  -0.275  -0.291  -0.317  -0.413  -0.446  -0.361  -0.446  -0.513
14    K         0.166  -0.079  -0.265   0.102  -0.216  -0.544   0.210  -0.141  -0.469
15    H         0.902   0.926   0.994   1.093   1.107   1.204   0.945   0.982   1.085
16    L        -0.230  -0.161  -0.309  -0.160  -0.066  -0.360  -0.361  -0.265  -0.544
17    S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.982   1.085
18    Y        -0.230  -0.275  -0.291  -0.101  -0.177  -0.239  -0.361  -0.446  -0.513
19    Q         0.902   0.926   0.994   1.192   1.219   1.284   0.945   0.982   1.085
20    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.982   1.085
21    S         0.166  -0.079  -0.265   0.126  -0.187  -0.492   0.210  -0.141  -0.469
22    K         0.166  -0.079  -0.265   0.102  -0.216  -0.544   0.210  -0.141  -0.469
23    R        -1.561  -1.329  -1.114  -1.913  -1.490  -1.227  -1.748  -1.452  -1.153
24    V         0.166  -0.079  -0.265   0.069  -0.218  -0.444   0.210  -0.141  -0.469
25    N        -2.111  -2.071  -1.680  -2.194  -2.151  -1.608  -1.993  -1.931  -1.449
26    N        -0.480  -0.551  -0.345  -0.515  -0.647  -0.347  -0.769  -0.915  -0.606
27    P         0.902   0.926   0.994   1.064   1.089   1.180   0.945   0.982   1.085
28    N        -0.912  -1.164  -1.095  -0.811  -1.203  -1.212  -0.932  -1.242  -1.130
29    V        -0.480  -0.551  -0.345  -0.808  -0.917  -0.535  -0.769  -0.915  -0.606
30    S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.982   1.085
31    L         0.166   0.141  -0.240   0.366   0.341  -0.232   0.210   0.176  -0.426
32    I        -1.232  -1.021  -1.091  -1.579  -1.318  -1.245  -1.421  -1.199  -1.130
33    K        -0.480  -0.281  -0.302  -0.694  -0.393  -0.395  -0.769  -0.456  -0.532
34    I         0.902   0.926   0.994   0.945   0.983   1.084   0.945   0.982   1.085
35    E         0.902   0.926   0.994   1.128   1.159   1.232   0.945   0.982   1.085
36    G         0.166   0.280  -0.239   0.217   0.344  -0.330   0.210   0.358  -0.424
37    V        -0.230  -0.275  -0.291  -0.377  -0.427  -0.385  -0.361  -0.446  -0.513
38    A        -1.993  -1.821  -1.667  -1.965  -1.680  -1.522  -1.911  -1.724  -1.438
39    T        -1.993  -1.959  -1.664  -2.004  -1.910  -1.465  -1.911  -1.832  -1.436
40    P        -0.912  -1.164  -1.095  -0.698  -1.093  -1.054  -0.932  -1.242  -1.130
41    Q        -2.307  -2.260  -2.089  -1.854  -1.810  -1.624  -1.993  -1.900  -1.603
42    D        -1.232  -1.270  -1.092  -1.013  -1.055  -0.845  -1.421  -1.392  -1.128
43    A         0.902   0.926   0.994   0.915   0.950   1.060   0.945   0.982   1.085
44    Q        -1.232  -1.319  -1.099  -1.352  -1.414  -1.072  -1.421  -1.465  -1.138
45    F         0.902   0.926   0.994   1.117   1.146   1.223   0.945   0.982   1.085
46    Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.982   1.085
47    L         0.166   0.151  -0.248   0.335   0.320  -0.352   0.210   0.189  -0.439
48    G         0.902   0.926   0.994   0.824   0.850   0.987   0.945   0.982   1.085
49    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.982   1.085
50    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.982   1.085
51    I        -0.621  -0.500  -0.335  -1.112  -0.912  -0.613  -1.013  -0.826  -0.589
52    A        -0.230  -0.275  -0.291  -0.131  -0.201  -0.214  -0.361  -0.446  -0.513
53    Y         0.166   0.111  -0.242   0.403   0.345  -0.158   0.210   0.134  -0.429
54    V         0.902   0.926   0.994   0.662   0.713   0.857   0.945   0.982   1.085
55    Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.982   1.085
56    R        -0.230  -0.275  -0.291  -0.467  -0.553  -0.602  -0.361  -0.446  -0.513
57    A        -1.561  -1.635  -1.654  -1.407  -1.634  -1.544  -1.421  -1.527  -1.426
58    S        -2.486  -2.558  -2.442  -2.044  -2.138  -1.877  -1.911  -1.968  -1.719
59    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.982   1.085
60    E        -0.544  -0.638  -1.048  -0.076  -0.202  -0.861  -0.442  -0.559  -1.071
61    V        -0.621  -0.515  -0.338  -1.112  -0.937  -0.617  -1.013  -0.852  -0.595
62    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.982   1.085
63    G         0.902   0.926   0.994   0.824   0.850   0.987   0.945   0.982   1.085
64    S        -0.230  -0.328  -0.332  -0.346  -0.492  -0.475  -0.361  -0.533  -0.583
65    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.982   1.085
66    I        -0.230  -0.174  -0.292  -0.258  -0.183  -0.472  -0.361  -0.286  -0.515
67    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.982   1.085
68    V         0.902   0.926   0.994   0.662   0.713   0.857   0.945   0.982   1.085
69    M        -0.480  -0.305  -0.309  -0.495  -0.240  -0.258  -0.769  -0.495  -0.544
70    W         0.902   0.926   0.994   1.267   1.288   1.344   0.945   0.982   1.085
71    G         0.902   0.926   0.994   0.824   0.850   0.987   0.945   0.982   1.085
72    K        -0.230  -0.275  -0.291  -0.358  -0.420  -0.429  -0.361  -0.446  -0.513
73    V        -0.666  -0.576  -0.344  -1.168  -1.032  -0.620  -1.095  -0.961  -0.605
74    T        -2.173  -2.006  -2.082  -1.901  -1.758  -1.953  -1.829  -1.682  -1.598
75    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.982   1.085
76    T        -0.480  -0.551  -0.345  -0.422  -0.602  -0.297  -0.769  -0.915  -0.606
77    H         0.902   0.926   0.994   1.093   1.107   1.204   0.945   0.982   1.085
78    G         0.902   0.926   0.994   0.824   0.850   0.987   0.945   0.982   1.085
79    N         0.166   0.280  -0.239   0.344   0.513  -0.301   0.210   0.358  -0.424
80    S        -0.230  -0.074  -0.276  -0.375  -0.137  -0.446  -0.361  -0.132  -0.487
81    G         0.902   0.926   0.994   0.824   0.850   0.987   0.945   0.982   1.085
82    V        -0.912  -0.768  -1.063  -1.062  -0.878  -1.230  -0.932  -0.766  -1.093
83    V         0.902   0.926   0.994   0.662   0.713   0.857   0.945   0.982   1.085
84    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.982   1.085
85    A         0.902   0.926   0.994   0.915   0.950   1.060   0.945   0.982   1.085
86    T        -2.111  -1.863  -1.668  -2.366  -2.052  -1.707  -1.993  -1.728  -1.438
87    F         0.902   0.926   0.994   1.117   1.146   1.223   0.945   0.982   1.085
88    R        -2.173  -2.299  -2.098  -2.247  -2.439  -2.139  -1.829  -1.911  -1.609
89    N        -2.425  -2.184  -2.091  -2.293  -1.943  -1.919  -2.074  -1.825  -1.604
90    N         0.166  -0.079  -0.265   0.379   0.103  -0.230   0.210  -0.141  -0.469
91    L         0.902   0.926   0.994   0.975   1.013   1.109   0.945   0.982   1.085
92    P         0.902   0.926   0.994   1.064   1.089   1.180   0.945   0.982   1.085
93    A        -0.912  -1.095  -1.085  -0.801  -1.084  -1.110  -0.932  -1.147  -1.121
94    K         0.166  -0.079  -0.265   0.102  -0.216  -0.544   0.210  -0.141  -0.469
95    T         0.166  -0.079  -0.265   0.457   0.111  -0.272   0.210  -0.141  -0.469
96    F         0.902   0.926   0.994   1.117   1.146   1.223   0.945   0.982   1.085
97    G         0.902   0.926   0.994   0.824   0.850   0.987   0.945   0.982   1.085
98    A        -0.480  -0.439  -0.334  -0.709  -0.667  -0.549  -0.769  -0.720  -0.587
99    S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.982   1.085
100   V        -0.480  -0.454  -0.334  -0.857  -0.819  -0.596  -0.769  -0.746  -0.588
101   R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.982   1.085
102   I        -0.230  -0.275  -0.291  -0.258  -0.355  -0.470  -0.361  -0.446  -0.513
103   F        -0.480  -0.191  -0.280  -0.289   0.142  -0.071  -0.769  -0.312  -0.494
104   L         0.902   0.926   0.994   0.975   1.013   1.109   0.945   0.982   1.085
105   Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.982   1.085
106   P         0.902   0.926   0.994   1.064   1.089   1.180   0.945   0.982   1.085
107   S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.982   1.085
108   N         0.166  -0.079  -0.265   0.344   0.044  -0.355   0.210  -0.141  -0.469
109   I         0.166   0.111  -0.242   0.305   0.237  -0.362   0.210   0.134  -0.429
* 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/P05744
Output conservation file - output/P05744
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
