1     M         1.218   1.219   1.300   1.266   1.269   1.392   1.295   1.297   1.420
2     T        -0.494  -0.518  -0.568  -0.481  -0.513  -0.628  -0.606  -0.633  -0.694
3     M        -0.590  -0.643  -0.587  -0.512  -0.603  -0.555  -0.709  -0.784  -0.714
4     N        -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     G        -0.297  -0.274  -0.518  -0.280  -0.260  -0.587  -0.312  -0.284  -0.621
7     I         0.502   0.468   0.233   0.554   0.510   0.144   0.512   0.463   0.053
8     P         0.502   0.468   0.233   0.608   0.576   0.288   0.512   0.463   0.053
9     V        -0.635  -0.665  -0.592  -0.890  -0.931  -0.799  -0.830  -0.864  -0.727
10    K         0.502   0.530   0.240   0.587   0.628   0.176   0.512   0.553   0.067
11    L         1.218   1.219   1.300   1.101   1.103   1.243   1.295   1.297   1.420
12    L         1.218   1.219   1.300   1.101   1.103   1.243   1.295   1.297   1.420
13    N        -0.494  -0.509  -0.562  -0.414  -0.424  -0.512  -0.606  -0.620  -0.685
14    E         1.218   1.219   1.300   1.286   1.286   1.410   1.295   1.297   1.420
15    A        -0.181  -0.240  -0.499   0.097   0.017  -0.388  -0.159  -0.237  -0.594
16    Q         1.218   1.219   1.300   1.363   1.365   1.479   1.295   1.297   1.420
17    G         1.218   1.219   1.300   1.088   1.086   1.230   1.295   1.297   1.420
18    H         1.218   1.219   1.300   1.401   1.401   1.514   1.295   1.297   1.420
19    I        -0.494  -0.506  -0.565  -0.546  -0.556  -0.668  -0.606  -0.617  -0.688
20    V        -0.040  -0.031   0.091  -0.360  -0.343  -0.150  -0.382  -0.368  -0.203
21    S        -0.040  -0.018   0.097  -0.188  -0.146   0.011  -0.382  -0.344  -0.192
22    L        -1.089  -1.103  -1.072  -1.181  -1.189  -1.151  -1.053  -1.057  -0.985
23    E         1.218   1.219   1.300   1.286   1.286   1.410   1.295   1.297   1.420
24    L         0.502   0.500   0.236   0.474   0.472   0.102   0.512   0.509   0.059
25    T        -1.089  -1.079  -1.070  -0.964  -0.945  -0.951  -1.053  -1.039  -0.981
26    T        -0.760  -0.755  -0.610  -0.831  -0.824  -0.626  -0.941  -0.937  -0.745
27    G         1.218   1.219   1.300   1.088   1.086   1.230   1.295   1.297   1.420
28    A        -1.419  -1.458  -1.486  -1.005  -1.060  -1.123  -1.165  -1.206  -1.177
29    T         0.502   0.472   0.230   0.662   0.625   0.269   0.512   0.468   0.048
30    Y         1.218   1.219   1.300   1.451   1.453   1.559   1.295   1.297   1.420
31    R         1.218   1.219   1.300   1.054   1.053   1.200   1.295   1.297   1.420
32    G         1.218   1.219   1.300   1.088   1.086   1.230   1.295   1.297   1.420
33    K         1.218   1.219   1.300   1.234   1.240   1.363   1.295   1.297   1.420
34    L         1.218   1.219   1.300   1.101   1.103   1.243   1.295   1.297   1.420
35    V        -0.841  -0.820  -0.630  -1.195  -1.157  -0.865  -1.053  -1.029  -0.771
36    E         1.218   1.219   1.300   1.286   1.286   1.410   1.295   1.297   1.420
37    S        -0.841  -0.814  -0.637  -0.941  -0.897  -0.646  -1.053  -1.022  -0.780
38    E         1.218   1.219   1.300   1.286   1.286   1.410   1.295   1.297   1.420
39    D         1.218   1.219   1.300   1.318   1.321   1.439   1.295   1.297   1.420
40    S         0.502   0.518   0.233   0.638   0.662   0.247   0.512   0.535   0.053
41    M         1.218   1.219   1.300   1.266   1.269   1.392   1.295   1.297   1.420
42    N         1.218   1.219   1.300   1.260   1.265   1.386   1.295   1.297   1.420
43    V        -0.760  -0.759  -0.612  -0.909  -0.895  -0.656  -0.941  -0.942  -0.748
44    Q         0.148   0.181   0.160   0.233   0.286   0.202  -0.047   0.006  -0.076
45    L        -0.181  -0.247  -0.501  -0.134  -0.220  -0.589  -0.159  -0.246  -0.597
46    R        -0.494  -0.469  -0.540  -0.555  -0.521  -0.588  -0.606  -0.568  -0.651
47    D         0.502   0.530   0.240   0.704   0.739   0.327   0.512   0.553   0.067
48    V        -0.494  -0.486  -0.547  -0.588  -0.585  -0.642  -0.606  -0.604  -0.662
49    I        -1.089  -1.068  -1.087  -0.989  -0.968  -1.003  -1.053  -1.036  -0.999
50    A        -1.089  -1.077  -1.088  -1.097  -1.071  -1.041  -1.053  -1.035  -0.998
51    T         1.218   1.219   1.300   1.279   1.280   1.404   1.295   1.297   1.420
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    E        -1.624  -1.576  -1.517  -1.469  -1.395  -1.309  -1.388  -1.343  -1.205
54    P        -1.419  -1.359  -1.470  -1.338  -1.257  -1.405  -1.165  -1.106  -1.163
55    Q        -2.079  -2.075  -1.847  -1.828  -1.828  -1.529  -1.612  -1.607  -1.324
56    G         0.502   0.569   0.239   0.485   0.560   0.156   0.512   0.607   0.064
57    A        -1.170  -1.139  -1.102  -1.275  -1.242  -1.111  -1.165  -1.135  -1.016
58    V        -0.824  -0.772  -1.027  -0.734  -0.661  -1.041  -0.718  -0.660  -0.931
59    T         0.148   0.141   0.128   0.123   0.113   0.058  -0.047  -0.061  -0.135
60    H        -0.494  -0.456  -0.547  -0.338  -0.283  -0.441  -0.606  -0.556  -0.664
61    M        -0.040  -0.055   0.086  -0.268  -0.305  -0.098  -0.382  -0.412  -0.213
62    D        -0.494  -0.491  -0.550  -0.367  -0.371  -0.471  -0.606  -0.610  -0.667
63    Q        -0.181  -0.148  -0.492   0.168   0.206  -0.277  -0.159  -0.118  -0.586
64    I         0.502   0.518   0.233   0.481   0.504   0.102   0.512   0.535   0.053
65    F        -0.040  -0.055   0.086   0.009  -0.017   0.181  -0.382  -0.412  -0.213
66    V        -0.040  -0.007   0.092  -0.330  -0.262  -0.132  -0.382  -0.324  -0.201
67    R         1.218   1.219   1.300   1.054   1.053   1.200   1.295   1.297   1.420
68    G         1.218   1.219   1.300   1.088   1.086   1.230   1.295   1.297   1.420
69    S         1.218   1.219   1.300   1.234   1.238   1.363   1.295   1.297   1.420
70    Q        -1.089  -1.077  -1.088  -0.822  -0.800  -0.841  -1.053  -1.035  -0.998
71    I         0.148   0.127   0.139   0.030  -0.009  -0.033  -0.047  -0.086  -0.115
72    K         0.148   0.141   0.128  -0.066  -0.080  -0.107  -0.047  -0.061  -0.135
73    F         0.502   0.472   0.230   0.735   0.698   0.295   0.512   0.468   0.048
74    I        -1.295  -1.300  -1.123  -1.346  -1.351  -1.129  -1.277  -1.278  -1.036
75    V        -1.295  -1.284  -1.125  -1.449  -1.435  -1.167  -1.277  -1.269  -1.039
76    V         0.502   0.464   0.227   0.481   0.436   0.092   0.512   0.456   0.043
77    P         1.218   1.219   1.300   1.188   1.195   1.321   1.295   1.297   1.420
78    D         0.148   0.142   0.114   0.206   0.195   0.102  -0.047  -0.060  -0.160
79    L        -0.494  -0.454  -0.547  -0.479  -0.414  -0.600  -0.606  -0.550  -0.662
80    L         1.218   1.219   1.300   1.101   1.103   1.243   1.295   1.297   1.420
81    K         0.148   0.130   0.139   0.051   0.019  -0.026  -0.047  -0.081  -0.115
82    N         0.502   0.472   0.230   0.662   0.630   0.301   0.512   0.468   0.048
83    A         1.218   1.219   1.300   1.324   1.323   1.445   1.295   1.297   1.420
84    P         1.218   1.219   1.300   1.188   1.195   1.321   1.295   1.297   1.420
85    L        -0.040  -0.024   0.090  -0.268  -0.236  -0.087  -0.382  -0.355  -0.206
86    F         1.218   1.219   1.300   1.376   1.379   1.491   1.295   1.297   1.420
87    K        -0.760  -0.751  -0.604  -0.887  -0.879  -0.674  -0.941  -0.931  -0.736
88    K        -1.624  -1.649  -1.515  -1.545  -1.576  -1.416  -1.388  -1.406  -1.203
89    N        -2.079  -2.104  -1.856  -1.948  -1.985  -1.655  -1.612  -1.626  -1.330
90    S        -1.954  -1.943  -1.832  -1.660  -1.646  -1.494  -1.500  -1.491  -1.313
91    S        -1.295  -1.299  -1.123  -1.556  -1.565  -1.292  -1.277  -1.276  -1.036
92    -        -0.789  -0.802  -0.632  -0.995  -1.030  -0.748  -0.995  -1.007  -0.773
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    R        -1.170  -1.203  -1.099  -1.282  -1.315  -1.125  -1.165  -1.191  -1.013
95    P        -1.419  -1.422  -1.489  -1.230  -1.241  -1.372  -1.165  -1.171  -1.180
96    M        -1.295  -1.276  -1.117  -1.431  -1.402  -1.150  -1.277  -1.259  -1.029
97    P        -0.824  -0.884  -1.065  -0.736  -0.826  -1.201  -0.718  -0.789  -0.973
98    P        -0.181  -0.218  -0.505  -0.068  -0.112  -0.572  -0.159  -0.209  -0.603
99    I        -1.624  -1.641  -1.503  -1.580  -1.589  -1.388  -1.388  -1.396  -1.194
100   R         1.218   1.219   1.300   1.054   1.053   1.200   1.295   1.297   1.420
101   G         1.218   1.219   1.300   1.088   1.086   1.230   1.295   1.297   1.420
102   P        -0.040  -0.055   0.086  -0.364  -0.398  -0.184  -0.382  -0.412  -0.213
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   K        -1.211  -1.211  -1.108  -1.396  -1.404  -1.277  -1.188  -1.189  -1.022
116   R        -0.977  -1.026  -1.080  -0.994  -1.084  -1.162  -0.896  -0.956  -0.989
117   R        -0.181  -0.131  -0.494  -0.172  -0.112  -0.598  -0.159  -0.094  -0.588
* 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/P43321
Output conservation file - output/P43321
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
