1     M         1.918   1.990   2.176   2.043   2.148   2.457   2.173   2.289   2.642
2     I         1.169   1.129   1.070   1.242   1.191   1.107   1.254   1.181   1.032
3     T         1.169   1.070   1.063   1.222   1.105   1.104   1.254   1.078   1.019
4     K         0.455   0.272   0.206   0.351   0.125   0.049   0.466   0.192   0.066
5     Y         1.169   1.129   1.070   1.463   1.433   1.361   1.254   1.181   1.032
6     F         0.799   0.722   0.818   0.750   0.607   0.715   0.597   0.415   0.510
7     S        -0.495  -0.497  -0.491  -0.557  -0.526  -0.552  -0.585  -0.563  -0.547
8     K         0.127   0.074   0.093  -0.139  -0.212  -0.179  -0.060  -0.131  -0.128
9     V        -0.218  -0.259  -0.420  -0.067  -0.140  -0.400  -0.191  -0.250  -0.446
10    I        -0.495  -0.316  -0.490  -0.624  -0.377  -0.623  -0.585  -0.366  -0.554
11    V         0.455   0.272   0.206   0.594   0.353   0.235   0.466   0.192   0.066
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    R        -0.580  -0.653  -0.557  -0.708  -0.742  -0.611  -0.716  -0.767  -0.637
14    F         1.169   1.070   1.063   1.275   1.164   1.151   1.254   1.078   1.019
15    N         0.455   0.531   0.254   0.634   0.725   0.319   0.466   0.577   0.143
16    P         1.169   1.165   1.071   1.327   1.345   1.213   1.254   1.243   1.036
17    F         0.455   0.557   0.265   0.585   0.734   0.283   0.466   0.612   0.161
18    G        -0.020   0.153   0.092  -0.199   0.035  -0.024  -0.322  -0.069  -0.137
19    K        -0.020   0.033   0.048  -0.429  -0.361  -0.299  -0.322  -0.256  -0.213
20    E        -1.055  -1.074  -1.036  -1.037  -1.088  -1.066  -0.979  -0.986  -0.902
21    A         0.127   0.155   0.089   0.040   0.062  -0.047  -0.060  -0.032  -0.140
22    K        -0.840  -0.844  -0.938  -0.759  -0.747  -0.819  -0.716  -0.716  -0.790
23    V        -0.710  -0.631  -0.597  -0.964  -0.850  -0.800  -0.848  -0.751  -0.683
24    A         1.169   1.301   1.096   1.203   1.378   1.131   1.254   1.465   1.085
25    R         1.169   1.070   1.063   1.321   1.191   1.152   1.254   1.078   1.019
26    L         1.169   1.165   1.071   1.103   1.101   0.985   1.254   1.243   1.036
27    V         0.127   0.183   0.095   0.082   0.143  -0.019  -0.060  -0.002  -0.131
28    L         1.918   1.990   2.176   1.760   1.850   2.160   2.173   2.289   2.642
29    A         0.602   0.618   0.764   0.210   0.215   0.418   0.203   0.200   0.392
30    A        -1.055  -1.093  -1.025  -1.001  -1.032  -0.969  -0.979  -0.994  -0.888
31    I        -0.218  -0.362  -0.443  -0.050  -0.273  -0.427  -0.191  -0.376  -0.476
32    P         1.169   1.070   1.063   1.313   1.194   1.167   1.254   1.078   1.019
33    P         0.334   0.184   0.156   0.439   0.199   0.080   0.286   0.057  -0.014
34    T        -1.017  -1.012  -1.014  -1.010  -0.993  -1.012  -0.915  -0.903  -0.873
35    Q        -0.623  -0.652  -0.581  -0.546  -0.611  -0.502  -0.743  -0.771  -0.663
36    R         0.017  -0.057   0.038  -0.122  -0.253  -0.182  -0.229  -0.326  -0.214
37    N        -0.727  -0.672  -0.595  -0.798  -0.725  -0.604  -0.862  -0.790  -0.678
38    M        -1.530  -1.473  -1.425  -1.307  -1.236  -1.140  -1.242  -1.172  -1.075
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    G         0.455   0.658   0.289   0.722   0.994   0.478   0.466   0.769   0.201
42    T        -0.495  -0.481  -0.508  -0.450  -0.448  -0.441  -0.585  -0.568  -0.577
43    Q        -0.235  -0.220  -0.067  -0.537  -0.520  -0.295  -0.585  -0.561  -0.367
44    I         0.799   0.820   0.847   0.687   0.699   0.678   0.597   0.612   0.572
45    Q        -1.185  -1.211  -1.074  -1.101  -1.126  -0.939  -1.111  -1.103  -0.938
46    S        -1.530  -1.426  -1.426  -1.275  -1.139  -1.104  -1.242  -1.127  -1.076
47    E        -0.710  -0.720  -0.608  -0.962  -0.966  -0.797  -0.848  -0.833  -0.694
48    I        -0.020   0.053   0.049  -0.257  -0.187  -0.163  -0.322  -0.241  -0.214
49    I         0.455   0.421   0.236   0.459   0.402   0.147   0.466   0.407   0.114
50    S        -0.710  -0.646  -0.604  -0.862  -0.781  -0.713  -0.848  -0.785  -0.692
51    D        -1.530  -1.422  -1.413  -1.585  -1.425  -1.419  -1.242  -1.134  -1.066
52    Y        -1.874  -1.814  -1.761  -1.505  -1.428  -1.334  -1.373  -1.304  -1.202
53    N        -0.218  -0.301  -0.434  -0.133  -0.249  -0.423  -0.191  -0.299  -0.465
54    K        -1.055  -0.920  -0.984  -0.995  -0.797  -0.904  -0.979  -0.831  -0.849
55    V        -1.874  -1.867  -1.772  -1.792  -1.754  -1.661  -1.373  -1.344  -1.210
56    K        -1.055  -0.998  -1.014  -1.245  -1.151  -1.162  -0.979  -0.908  -0.880
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    P         1.102   1.086   1.038   1.257   1.256   1.188   1.144   1.107   0.969
60    L        -0.377  -0.412  -0.483  -0.522  -0.621  -0.775  -0.400  -0.450  -0.529
61    V         0.127   0.074   0.093   0.081   0.002  -0.007  -0.060  -0.131  -0.128
62    K        -0.020  -0.054   0.044  -0.320  -0.312  -0.149  -0.322  -0.357  -0.220
63    V         1.169   1.301   1.096   1.242   1.420   1.175   1.254   1.465   1.085
64    T         0.127  -0.018   0.055  -0.033  -0.293  -0.246  -0.060  -0.274  -0.194
65    Y         0.602   0.645   0.784   0.502   0.576   0.773   0.203   0.256   0.436
66    K         1.918   1.990   2.176   1.601   1.693   1.994   2.173   2.289   2.642
67    D         1.918   1.990   2.176   1.943   2.041   2.352   2.173   2.289   2.642
68    K         0.602   0.598   0.760   0.185   0.190   0.453   0.203   0.157   0.384
69    K        -0.020   0.122   0.061  -0.266  -0.091  -0.136  -0.322  -0.142  -0.187
70    E        -0.495  -0.513  -0.533  -0.440  -0.498  -0.533  -0.585  -0.605  -0.603
71    M        -0.020  -0.019   0.057  -0.131  -0.121  -0.015  -0.322  -0.308  -0.200
72    E        -1.055  -1.074  -1.036  -0.970  -1.023  -0.970  -0.979  -0.986  -0.902
73    V        -0.235  -0.184  -0.044  -0.569  -0.487  -0.302  -0.585  -0.511  -0.332
74    D         1.169   1.255   1.092   1.301   1.418   1.237   1.254   1.391   1.076
75    P         1.169   1.129   1.070   1.332   1.304   1.221   1.254   1.181   1.032
76    S        -1.530  -1.528  -1.438  -1.559  -1.544  -1.434  -1.242  -1.214  -1.085
77    N        -1.530  -1.495  -1.438  -1.538  -1.535  -1.437  -1.242  -1.192  -1.085
78    M         0.455   0.512   0.258   0.807   0.896   0.593   0.466   0.550   0.150
79    N        -0.840  -0.852  -0.942  -0.604  -0.628  -0.802  -0.716  -0.718  -0.794
80    F         0.127   0.088   0.069   0.115   0.025  -0.023  -0.060  -0.154  -0.173
81    Q        -1.874  -1.814  -1.761  -1.721  -1.629  -1.522  -1.373  -1.304  -1.202
82    E        -0.580  -0.670  -0.572  -0.558  -0.654  -0.534  -0.716  -0.784  -0.653
83    L         1.169   1.129   1.070   1.110   1.060   0.997   1.254   1.181   1.032
84    A        -1.055  -1.060  -1.041  -1.110  -1.118  -1.065  -0.979  -0.963  -0.904
85    N        -0.580  -0.501  -0.523  -0.506  -0.369  -0.386  -0.716  -0.608  -0.596
86    H        -0.840  -0.973  -0.988  -0.361  -0.565  -0.583  -0.716  -0.856  -0.844
87    F         0.455   0.272   0.206   0.633   0.400   0.278   0.466   0.192   0.066
88    D         1.918   1.990   2.176   1.943   2.041   2.352   2.173   2.289   2.642
89    R        -0.495  -0.540  -0.533  -0.418  -0.468  -0.500  -0.585  -0.625  -0.603
90    H         1.169   1.070   1.063   1.510   1.412   1.426   1.254   1.078   1.019
91    S         1.918   1.990   2.176   1.753   1.851   2.153   2.173   2.289   2.642
92    K         0.127   0.075   0.078   0.136   0.047  -0.003  -0.060  -0.141  -0.155
93    Q        -0.580  -0.671  -0.549  -0.744  -0.864  -0.691  -0.716  -0.786  -0.629
94    L         1.918   1.990   2.176   1.760   1.850   2.160   2.173   2.289   2.642
95    D        -0.710  -0.669  -0.606  -0.907  -0.890  -0.781  -0.848  -0.802  -0.694
96    L        -0.495  -0.565  -0.520  -0.581  -0.668  -0.671  -0.585  -0.637  -0.583
97    K         0.455   0.356   0.222   0.322   0.202   0.012   0.466   0.321   0.092
98    H        -0.218  -0.181  -0.384   0.090   0.149  -0.127  -0.191  -0.138  -0.398
99    M        -1.530  -1.487  -1.431  -1.533  -1.438  -1.404  -1.242  -1.182  -1.080
100   L         0.127   0.029   0.072   0.097  -0.041  -0.017  -0.060  -0.195  -0.164
101   E        -1.055  -1.074  -1.036  -0.865  -0.864  -0.837  -0.979  -0.986  -0.902
102   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   H        -1.530  -1.568  -1.456  -1.279  -1.368  -1.173  -1.242  -1.245  -1.100
* 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/P19956
Output conservation file - output/P19956
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
