1     M         1.446   1.479   1.555   1.616   1.656   1.785   1.590   1.639   1.767
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     F         0.807   0.792   0.637   0.935   0.922   0.676   0.829   0.803   0.504
5     G         1.446   1.479   1.555   1.513   1.560   1.684   1.590   1.639   1.767
6     P        -0.174  -0.188  -0.157  -0.165  -0.153  -0.149  -0.398  -0.391  -0.367
7     F         0.751   0.626   0.597   0.893   0.726   0.673   0.738   0.520   0.429
8     K        -0.719  -0.801  -0.695  -1.094  -1.203  -1.038  -0.824  -0.899  -0.761
9     L        -1.785  -1.748  -1.648  -1.502  -1.420  -1.309  -1.345  -1.303  -1.165
10    T         0.199   0.043  -0.054   0.309   0.048  -0.139   0.177  -0.049  -0.208
11    S        -0.682  -0.626  -0.664  -0.689  -0.605  -0.639  -0.802  -0.734  -0.730
12    P        -1.054  -1.061  -1.056  -0.902  -0.909  -0.928  -0.966  -0.968  -0.930
13    V        -0.719  -0.668  -0.674  -0.913  -0.874  -0.843  -0.824  -0.773  -0.740
14    A        -1.054  -0.963  -1.050  -0.927  -0.792  -0.944  -0.966  -0.861  -0.924
15    G         1.446   1.479   1.555   1.527   1.574   1.698   1.590   1.639   1.767
16    G         1.446   1.479   1.555   1.527   1.574   1.698   1.590   1.639   1.767
17    L         0.432   0.425   0.468   0.301   0.291   0.342   0.170   0.144   0.177
18    L         0.432   0.373   0.431   0.270   0.162   0.234   0.170   0.043   0.101
19    W         0.751   0.688   0.585   1.052   0.974   0.819   0.738   0.628   0.406
20    K         0.807   0.697   0.628   0.512   0.359   0.237   0.829   0.643   0.489
21    I        -0.610  -0.704  -0.647  -0.468  -0.589  -0.512  -0.693  -0.783  -0.706
22    P        -0.374  -0.469  -0.594  -0.201  -0.363  -0.571  -0.367  -0.488  -0.636
23    W         0.199   0.218  -0.044   0.535   0.564   0.151   0.177   0.203  -0.193
24    R         1.446   1.479   1.555   1.302   1.346   1.478   1.590   1.639   1.767
25    M         0.325   0.304   0.406   0.212   0.136   0.281  -0.041  -0.097   0.049
26    S         0.807   0.774   0.642   0.911   0.865   0.678   0.829   0.773   0.514
27    T        -1.087  -1.158  -1.058  -1.077  -1.183  -1.074  -1.019  -1.071  -0.936
28    H        -1.087  -1.081  -1.055  -1.012  -1.031  -0.972  -1.019  -1.007  -0.934
29    Q         0.807   0.792   0.637   0.990   0.975   0.712   0.829   0.803   0.504
30    K         1.446   1.479   1.555   1.116   1.166   1.296   1.590   1.639   1.767
31    T        -1.087  -0.988  -1.045  -0.913  -0.776  -0.875  -1.019  -0.921  -0.925
32    R         0.199   0.043  -0.054   0.107  -0.121  -0.321   0.177  -0.049  -0.208
33    Q        -0.080  -0.098  -0.144   0.021   0.007  -0.079  -0.258  -0.277  -0.349
34    R         1.446   1.479   1.555   1.302   1.346   1.478   1.590   1.639   1.767
35    E        -1.491  -1.494  -1.382  -1.524  -1.581  -1.374  -1.236  -1.222  -1.074
36    R         1.446   1.479   1.555   1.302   1.346   1.478   1.590   1.639   1.767
37    L         0.325   0.316   0.415   0.139   0.128   0.276  -0.041  -0.072   0.068
38    R         0.271   0.298   0.404  -0.392  -0.353  -0.179  -0.149  -0.109   0.046
39    N        -0.904  -0.807  -0.984  -0.583  -0.440  -0.725  -0.802  -0.685  -0.857
40    V         1.446   1.479   1.555   1.508   1.544   1.679   1.590   1.639   1.767
41    D         1.446   1.479   1.555   1.621   1.669   1.790   1.590   1.639   1.767
42    Q        -1.087  -1.067  -1.053  -0.841  -0.815  -0.791  -1.019  -0.980  -0.929
43    V         0.493   0.513   0.507   0.511   0.529   0.514   0.285   0.313   0.254
44    I        -0.682  -0.703  -0.665  -0.592  -0.605  -0.560  -0.802  -0.811  -0.732
45    K        -1.087  -1.031  -1.051  -1.226  -1.110  -1.105  -1.019  -0.964  -0.930
46    Q        -0.793  -0.716  -0.694  -0.772  -0.673  -0.616  -0.910  -0.815  -0.761
47    L         0.493   0.488   0.466   0.428   0.430   0.375   0.285   0.265   0.172
48    T        -1.198  -1.138  -1.088  -1.339  -1.263  -1.215  -1.128  -1.059  -0.963
49    L        -1.380  -1.454  -1.384  -1.337  -1.429  -1.377  -1.128  -1.182  -1.074
50    G        -0.316  -0.338  -0.251  -0.385  -0.427  -0.313  -0.584  -0.614  -0.503
51    L         0.807   0.697   0.628   0.855   0.725   0.622   0.829   0.643   0.489
52    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    A        -0.165  -0.147  -0.189  -0.165  -0.128  -0.301  -0.358  -0.329  -0.412
67    M         0.305   0.317   0.407   0.083   0.102   0.248  -0.080  -0.071   0.051
68    E        -0.165  -0.147  -0.189  -0.031  -0.009  -0.089  -0.358  -0.329  -0.412
69    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    Y        -1.785  -1.798  -1.668  -1.312  -1.326  -1.149  -1.345  -1.337  -1.178
74    K        -0.374  -0.394  -0.582  -0.543  -0.561  -0.812  -0.367  -0.387  -0.620
75    P        -0.793  -0.849  -0.720  -1.032  -1.130  -0.963  -0.910  -0.951  -0.788
76    R        -1.087  -1.111  -1.067  -1.147  -1.158  -1.074  -1.019  -1.033  -0.944
77    S        -1.198  -1.183  -1.087  -1.149  -1.125  -0.967  -1.128  -1.095  -0.962
78    K        -1.198  -1.143  -1.086  -1.389  -1.286  -1.197  -1.128  -1.067  -0.961
79    S        -1.785  -1.781  -1.659  -1.458  -1.459  -1.275  -1.345  -1.326  -1.173
80    L        -0.610  -0.421  -0.611  -0.912  -0.641  -0.860  -0.693  -0.452  -0.662
81    R        -0.610  -0.683  -0.665  -0.909  -1.015  -0.982  -0.693  -0.768  -0.725
82    L        -0.206  -0.179  -0.179  -0.235  -0.185  -0.189  -0.475  -0.436  -0.412
83    L        -0.793  -0.849  -0.720  -0.786  -0.818  -0.642  -0.910  -0.951  -0.788
84    N        -1.491  -1.502  -1.403  -1.400  -1.478  -1.340  -1.236  -1.226  -1.089
85    K        -1.087  -1.158  -1.078  -1.319  -1.354  -1.207  -1.019  -1.071  -0.953
86    P        -1.785  -1.798  -1.664  -1.684  -1.675  -1.559  -1.345  -1.337  -1.176
87    S        -1.198  -1.193  -1.094  -1.119  -1.103  -0.955  -1.128  -1.106  -0.968
88    V        -1.380  -1.221  -1.324  -1.027  -0.796  -0.963  -1.128  -0.962  -1.024
89    F        -0.374  -0.494  -0.613  -0.052  -0.194  -0.348  -0.367  -0.516  -0.659
90    P         0.807   0.792   0.637   0.944   0.932   0.715   0.829   0.803   0.504
91    K        -0.080  -0.130  -0.180  -0.433  -0.512  -0.553  -0.258  -0.349  -0.407
92    E         0.807   0.697   0.628   1.015   0.861   0.750   0.829   0.643   0.489
93    N        -1.491  -1.379  -1.375  -1.208  -1.080  -1.036  -1.236  -1.132  -1.069
94    Q        -0.206  -0.261  -0.183  -0.164  -0.219  -0.111  -0.475  -0.522  -0.417
95    M         1.446   1.479   1.555   1.616   1.656   1.785   1.590   1.639   1.767
96    S        -0.316  -0.341  -0.245  -0.488  -0.549  -0.416  -0.584  -0.619  -0.494
97    S        -0.610  -0.527  -0.623  -0.530  -0.394  -0.554  -0.693  -0.570  -0.676
98    K         0.199   0.218  -0.024  -0.056  -0.030  -0.394   0.177   0.204  -0.163
99    D         1.446   1.479   1.555   1.621   1.669   1.790   1.590   1.639   1.767
100   K         1.446   1.479   1.555   1.116   1.166   1.296   1.590   1.639   1.767
101   Y         1.446   1.479   1.555   1.600   1.643   1.769   1.590   1.639   1.767
102   W         0.199   0.329  -0.017   0.400   0.558   0.099   0.177   0.365  -0.152
103   T        -0.682  -0.683  -0.668  -0.637  -0.640  -0.573  -0.802  -0.788  -0.734
104   F         1.446   1.479   1.555   1.519   1.566   1.690   1.590   1.639   1.767
105   D        -0.610  -0.715  -0.654  -0.414  -0.574  -0.503  -0.693  -0.801  -0.717
106   K         0.271   0.298   0.405  -0.392  -0.344  -0.170  -0.149  -0.110   0.048
107   K        -0.374  -0.468  -0.573  -0.478  -0.591  -0.690  -0.367  -0.487  -0.609
108   A        -1.087  -1.137  -1.051  -0.913  -0.963  -0.839  -1.019  -1.047  -0.929
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   V        -0.374  -0.251  -0.546  -0.592  -0.407  -0.845  -0.367  -0.208  -0.576
115   G        -0.374  -0.353  -0.580  -0.152  -0.120  -0.479  -0.367  -0.335  -0.618
116   Y         0.807   0.792   0.637   1.031   1.015   0.785   0.829   0.803   0.504
117   R         1.446   1.479   1.555   1.302   1.346   1.478   1.590   1.639   1.767
118   K         1.446   1.479   1.555   1.116   1.166   1.296   1.590   1.639   1.767
119   G        -0.080  -0.149  -0.167  -0.050  -0.163  -0.216  -0.258  -0.357  -0.389
120   I         0.325   0.304   0.406   0.295   0.224   0.374  -0.041  -0.097   0.049
121   H         1.446   1.479   1.555   1.695   1.734   1.862   1.590   1.639   1.767
122   K         0.325   0.316   0.415  -0.301  -0.326  -0.168  -0.041  -0.072   0.068
123   V         0.199   0.189  -0.061   0.356   0.338  -0.058   0.177   0.165  -0.219
124   P         1.446   1.479   1.555   1.503   1.548   1.674   1.590   1.639   1.767
125   K         0.807   0.697   0.628   0.561   0.428   0.345   0.829   0.643   0.489
126   W         0.807   0.697   0.628   1.104   0.962   0.841   0.829   0.643   0.489
127   T         1.446   1.479   1.555   1.508   1.540   1.679   1.590   1.639   1.767
128   K         0.493   0.498   0.475   0.020   0.026  -0.053   0.285   0.285   0.190
129   I        -1.087  -1.125  -1.058  -1.015  -1.065  -0.975  -1.019  -1.033  -0.934
130   S         0.493   0.423   0.457   0.450   0.309   0.346   0.285   0.140   0.153
131   I        -1.198  -1.121  -1.086  -0.984  -0.883  -0.814  -1.128  -1.049  -0.962
132   R         1.446   1.479   1.555   1.302   1.346   1.478   1.590   1.639   1.767
133   K        -0.904  -0.874  -0.742  -1.297  -1.253  -1.076  -1.019  -0.976  -0.810
134   A         0.807   0.893   0.652   1.056   1.160   0.846   0.829   0.962   0.533
135   P         1.446   1.479   1.555   1.503   1.548   1.674   1.590   1.639   1.767
136   K        -1.380  -1.365  -1.362  -1.633  -1.611  -1.587  -1.128  -1.106  -1.056
137   F        -0.793  -0.697  -0.693  -0.737  -0.592  -0.567  -0.910  -0.791  -0.758
138   F         0.807   0.842   0.634   0.962   1.012   0.729   0.829   0.882   0.499
* 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/P14063
Output conservation file - output/P14063
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
