1     M         0.902   0.926   0.994   1.210   1.231   1.298   0.945   0.983   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        -1.228  -1.389  -1.636  -0.855  -1.086  -1.408  -1.017  -1.214  -1.408
5     E        -2.176  -2.294  -2.105  -1.674  -1.901  -1.713  -1.835  -1.933  -1.615
6     S        -1.132  -1.182  -1.102  -1.371  -1.487  -1.228  -1.262  -1.339  -1.142
7     H        -0.545  -0.478  -1.041  -0.102  -0.047  -0.843  -0.445  -0.366  -1.063
8     R         0.166   0.151  -0.248   0.124   0.117  -0.377   0.209   0.189  -0.439
9     L         0.166   0.151  -0.248   0.334   0.320  -0.352   0.209   0.189  -0.439
10    Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.983   1.085
11    V         0.902   0.926   0.994   0.661   0.712   0.857   0.945   0.983   1.085
12    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.983   1.085
13    G        -0.231  -0.275  -0.291  -0.319  -0.413  -0.446  -0.363  -0.447  -0.513
14    K         0.166  -0.081  -0.265   0.100  -0.218  -0.544   0.209  -0.142  -0.469
15    H         0.902   0.926   0.994   1.094   1.107   1.204   0.945   0.983   1.085
16    L        -0.231  -0.163  -0.309  -0.162  -0.068  -0.360  -0.363  -0.268  -0.544
17    S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.983   1.085
18    Y        -0.231  -0.275  -0.291  -0.102  -0.178  -0.239  -0.363  -0.447  -0.513
19    Q         0.902   0.926   0.994   1.193   1.219   1.284   0.945   0.983   1.085
20    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.983   1.085
21    S         0.166  -0.081  -0.265   0.125  -0.188  -0.492   0.209  -0.142  -0.469
22    K         0.166  -0.081  -0.265   0.100  -0.218  -0.544   0.209  -0.142  -0.469
23    R        -1.564  -1.332  -1.113  -1.917  -1.494  -1.226  -1.753  -1.456  -1.153
24    V         0.166  -0.081  -0.265   0.067  -0.219  -0.444   0.209  -0.142  -0.469
25    N        -2.115  -2.074  -1.680  -2.199  -2.155  -1.608  -1.998  -1.936  -1.450
26    N        -0.482  -0.552  -0.345  -0.517  -0.649  -0.347  -0.772  -0.917  -0.606
27    P         0.902   0.926   0.994   1.064   1.089   1.180   0.945   0.983   1.085
28    N        -0.914  -1.166  -1.095  -0.814  -1.205  -1.212  -0.935  -1.245  -1.130
29    V        -0.482  -0.552  -0.345  -0.811  -0.920  -0.535  -0.772  -0.917  -0.606
30    S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.983   1.085
31    L         0.166   0.141  -0.240   0.365   0.341  -0.232   0.209   0.176  -0.426
32    I        -1.234  -1.022  -1.091  -1.582  -1.320  -1.244  -1.426  -1.203  -1.129
33    K        -0.482  -0.284  -0.302  -0.696  -0.398  -0.395  -0.772  -0.461  -0.532
34    I         0.902   0.926   0.994   0.945   0.983   1.085   0.945   0.983   1.085
35    E         0.902   0.926   0.994   1.123   1.155   1.228   0.945   0.983   1.085
36    G         0.166   0.277  -0.239   0.216   0.340  -0.330   0.209   0.355  -0.424
37    V        -0.231  -0.275  -0.291  -0.379  -0.428  -0.385  -0.363  -0.447  -0.513
38    A        -1.996  -1.825  -1.667  -1.966  -1.683  -1.518  -1.916  -1.729  -1.438
39    T        -1.996  -1.962  -1.665  -2.008  -1.913  -1.464  -1.916  -1.837  -1.436
40    P        -0.914  -1.166  -1.095  -0.701  -1.095  -1.054  -0.935  -1.245  -1.130
41    Q        -2.310  -2.264  -2.089  -1.861  -1.818  -1.625  -1.998  -1.906  -1.603
42    E        -1.132  -1.174  -1.088  -0.853  -0.906  -0.841  -1.262  -1.256  -1.123
43    A         0.902   0.926   0.994   0.915   0.950   1.060   0.945   0.983   1.085
44    Q        -1.234  -1.322  -1.100  -1.355  -1.418  -1.074  -1.426  -1.469  -1.139
45    F         0.902   0.926   0.994   1.117   1.146   1.223   0.945   0.983   1.085
46    Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.983   1.085
47    L         0.166   0.151  -0.248   0.334   0.320  -0.352   0.209   0.189  -0.439
48    G         0.902   0.926   0.994   0.823   0.849   0.987   0.945   0.983   1.085
49    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.983   1.085
50    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.983   1.085
51    I        -0.622  -0.502  -0.335  -1.115  -0.915  -0.613  -1.017  -0.829  -0.589
52    A        -0.231  -0.275  -0.291  -0.133  -0.202  -0.214  -0.363  -0.447  -0.513
53    Y         0.166   0.111  -0.242   0.402   0.345  -0.158   0.209   0.134  -0.429
54    V         0.902   0.926   0.994   0.661   0.712   0.857   0.945   0.983   1.085
55    Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.983   1.085
56    R        -0.231  -0.275  -0.291  -0.469  -0.553  -0.602  -0.363  -0.447  -0.513
57    A        -1.564  -1.639  -1.655  -1.410  -1.638  -1.544  -1.426  -1.532  -1.426
58    S        -2.490  -2.562  -2.442  -2.049  -2.142  -1.877  -1.916  -1.973  -1.719
59    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.983   1.085
60    E        -0.545  -0.638  -1.048  -0.083  -0.205  -0.864  -0.445  -0.560  -1.071
61    V        -0.622  -0.517  -0.338  -1.115  -0.941  -0.617  -1.017  -0.856  -0.595
62    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.983   1.085
63    G         0.902   0.926   0.994   0.823   0.849   0.987   0.945   0.983   1.085
64    S        -0.231  -0.329  -0.332  -0.348  -0.493  -0.475  -0.363  -0.535  -0.583
65    K         0.902   0.926   0.994   0.737   0.790   0.917   0.945   0.983   1.085
66    I        -0.231  -0.175  -0.292  -0.260  -0.183  -0.472  -0.363  -0.286  -0.515
67    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.983   1.085
68    V         0.902   0.926   0.994   0.661   0.712   0.857   0.945   0.983   1.085
69    M        -0.482  -0.304  -0.308  -0.497  -0.239  -0.256  -0.772  -0.494  -0.542
70    W         0.902   0.926   0.994   1.267   1.288   1.344   0.945   0.983   1.085
71    G         0.902   0.926   0.994   0.823   0.849   0.987   0.945   0.983   1.085
72    K        -0.231  -0.275  -0.291  -0.360  -0.421  -0.429  -0.363  -0.447  -0.513
73    V        -0.668  -0.578  -0.344  -1.171  -1.035  -0.620  -1.099  -0.964  -0.605
74    T        -2.176  -2.009  -2.082  -1.905  -1.761  -1.953  -1.835  -1.686  -1.598
75    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.983   1.085
76    T        -0.482  -0.552  -0.345  -0.424  -0.604  -0.297  -0.772  -0.917  -0.606
77    H         0.902   0.926   0.994   1.094   1.107   1.204   0.945   0.983   1.085
78    G         0.902   0.926   0.994   0.823   0.849   0.987   0.945   0.983   1.085
79    N         0.166   0.277  -0.239   0.343   0.509  -0.301   0.209   0.355  -0.424
80    S        -0.231  -0.078  -0.276  -0.377  -0.143  -0.446  -0.363  -0.138  -0.487
81    G         0.902   0.926   0.994   0.823   0.849   0.987   0.945   0.983   1.085
82    V        -0.914  -0.771  -1.063  -1.064  -0.881  -1.230  -0.935  -0.770  -1.093
83    V         0.902   0.926   0.994   0.661   0.712   0.857   0.945   0.983   1.085
84    R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.983   1.085
85    A         0.902   0.926   0.994   0.915   0.950   1.060   0.945   0.983   1.085
86    T        -2.115  -1.867  -1.668  -2.371  -2.059  -1.707  -1.998  -1.734  -1.439
87    F         0.902   0.926   0.994   1.117   1.146   1.223   0.945   0.983   1.085
88    R        -2.176  -2.303  -2.098  -2.252  -2.445  -2.139  -1.835  -1.917  -1.610
89    N        -2.429  -2.189  -2.091  -2.298  -1.950  -1.919  -2.080  -1.831  -1.604
90    N         0.166  -0.081  -0.265   0.378   0.102  -0.230   0.209  -0.142  -0.469
91    L         0.902   0.926   0.994   0.975   1.013   1.109   0.945   0.983   1.085
92    P         0.902   0.926   0.994   1.064   1.089   1.180   0.945   0.983   1.085
93    A        -0.914  -1.098  -1.085  -0.803  -1.088  -1.110  -0.935  -1.151  -1.121
94    K         0.166  -0.081  -0.265   0.100  -0.218  -0.544   0.209  -0.142  -0.469
95    T         0.166  -0.081  -0.265   0.456   0.109  -0.272   0.209  -0.142  -0.469
96    F         0.902   0.926   0.994   1.117   1.146   1.223   0.945   0.983   1.085
97    G         0.902   0.926   0.994   0.823   0.849   0.987   0.945   0.983   1.085
98    A        -0.482  -0.440  -0.334  -0.712  -0.667  -0.549  -0.772  -0.722  -0.587
99    S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.983   1.085
100   V        -0.482  -0.455  -0.335  -0.859  -0.820  -0.596  -0.772  -0.747  -0.588
101   R         0.902   0.926   0.994   0.718   0.759   0.902   0.945   0.983   1.085
102   I        -0.231  -0.275  -0.291  -0.260  -0.355  -0.470  -0.363  -0.447  -0.513
103   F        -0.482  -0.191  -0.280  -0.291   0.142  -0.071  -0.772  -0.313  -0.494
104   L         0.902   0.926   0.994   0.975   1.013   1.109   0.945   0.983   1.085
105   Y         0.902   0.926   0.994   0.993   1.030   1.123   0.945   0.983   1.085
106   P         0.902   0.926   0.994   1.064   1.089   1.180   0.945   0.983   1.085
107   S         0.902   0.926   0.994   0.749   0.800   0.927   0.945   0.983   1.085
108   N         0.166  -0.081  -0.265   0.343   0.043  -0.355   0.209  -0.142  -0.469
109   I         0.166   0.111  -0.242   0.304   0.237  -0.362   0.209   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/P41056
Output conservation file - output/P41056
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
