1     M         1.315   1.410   1.509   1.338   1.449   1.620   1.414   1.553   1.712
2     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L         0.039   0.201   0.265  -0.198   0.108   0.126  -0.352  -0.086  -0.021
5     G         1.315   1.410   1.509   1.167   1.348   1.459   1.414   1.553   1.712
6     F        -0.103  -0.071  -0.350  -0.037  -0.006  -0.353  -0.116  -0.097  -0.457
7     G         1.315   1.410   1.509   1.167   1.348   1.459   1.414   1.553   1.712
8     G         0.524   0.314   0.327   0.464   0.194   0.133   0.491   0.120   0.097
9     G        -1.694  -1.592  -1.466  -1.823  -1.689  -1.498  -1.515  -1.377  -1.177
10    Q        -1.692  -1.514  -1.438  -1.753  -1.444  -1.334  -1.528  -1.312  -1.155
11    P         1.315   1.410   1.509   1.494   1.605   1.768   1.414   1.553   1.712
12    Q         0.589   0.590   0.404   0.524   0.564   0.255   0.590   0.585   0.239
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    L        -1.232  -1.187  -1.024  -1.201  -1.099  -0.836  -1.293  -1.191  -0.967
15    S        -0.103  -0.400  -0.420   0.037  -0.382  -0.383  -0.116  -0.525  -0.554
16    S         0.231   0.169   0.245   0.089  -0.068   0.029   0.002  -0.148  -0.061
17    Q        -0.421  -0.599  -0.481  -0.489  -0.730  -0.539  -0.587  -0.820  -0.646
18    Q         0.589   0.456   0.385   0.521   0.359   0.214   0.590   0.366   0.204
19    K         0.589   0.460   0.394   0.547   0.373   0.258   0.590   0.373   0.221
20    I        -0.021   0.095   0.233  -0.289  -0.115   0.108  -0.469  -0.289  -0.084
21    Q        -1.024  -0.988  -1.011  -1.167  -1.146  -1.162  -1.058  -1.015  -0.955
22    A         0.589   0.460   0.394   0.601   0.431   0.336   0.590   0.373   0.221
23    A         0.589   0.456   0.385   0.594   0.414   0.302   0.590   0.366   0.204
24    E         1.315   1.410   1.509   1.197   1.301   1.487   1.414   1.553   1.712
25    A        -0.103  -0.400  -0.420  -0.055  -0.495  -0.576  -0.116  -0.525  -0.554
26    E         1.315   1.410   1.509   1.197   1.301   1.487   1.414   1.553   1.712
27    L         0.589   0.460   0.394   0.549   0.384   0.277   0.590   0.373   0.221
28    D        -0.103  -0.400  -0.420   0.092  -0.386  -0.454  -0.116  -0.525  -0.554
29    L        -0.564  -0.526  -0.439  -0.720  -0.614  -0.495  -0.822  -0.709  -0.586
30    V         0.589   0.460   0.394   0.668   0.491   0.396   0.590   0.373   0.221
31    T        -0.103  -0.400  -0.420   0.120  -0.343  -0.408  -0.116  -0.525  -0.554
32    D        -0.421  -0.377  -0.412  -0.415  -0.335  -0.449  -0.587  -0.491  -0.545
33    M         0.589   0.460   0.394   0.730   0.549   0.470   0.590   0.373   0.221
34    F         0.589   0.456   0.385   0.745   0.628   0.493   0.590   0.366   0.204
35    N         0.589   0.456   0.385   0.587   0.423   0.285   0.590   0.366   0.204
36    K        -1.024  -0.596  -0.924  -0.926  -0.284  -0.813  -1.058  -0.517  -0.856
37    L         0.589   0.456   0.385   0.556   0.389   0.281   0.590   0.366   0.204
38    V         1.315   1.410   1.509   1.286   1.406   1.571   1.414   1.553   1.712
39    N        -2.026  -1.910  -1.780  -1.989  -1.880  -1.628  -1.646  -1.495  -1.283
40    N        -1.566  -1.647  -1.455  -1.556  -1.606  -1.344  -1.411  -1.417  -1.169
41    C         1.315   1.410   1.509   1.360   1.479   1.640   1.414   1.553   1.712
42    Y        -0.421  -0.342  -0.399  -0.138  -0.021  -0.120  -0.587  -0.443  -0.526
43    K        -1.566  -1.477  -1.418  -1.583  -1.513  -1.386  -1.411  -1.270  -1.137
44    K         1.315   1.410   1.509   1.182   1.308   1.473   1.414   1.553   1.712
45    C         1.315   1.410   1.509   1.360   1.479   1.640   1.414   1.553   1.712
46    I         1.315   1.410   1.509   1.418   1.516   1.695   1.414   1.553   1.712
47    N        -1.358  -1.511  -1.438  -1.241  -1.507  -1.408  -1.175  -1.305  -1.154
48    T        -1.900  -1.703  -1.762  -1.760  -1.497  -1.566  -1.528  -1.323  -1.268
49    S        -1.900  -1.730  -1.747  -1.672  -1.520  -1.462  -1.528  -1.344  -1.257
50    Y         1.315   1.410   1.509   1.453   1.578   1.729   1.414   1.553   1.712
51    S        -1.024  -1.182  -1.016  -0.987  -1.158  -0.919  -1.058  -1.184  -0.960
52    E        -0.421  -0.288  -0.408  -0.492  -0.320  -0.475  -0.587  -0.370  -0.542
53    G        -0.421  -0.283  -0.435  -0.578  -0.373  -0.621  -0.587  -0.422  -0.584
54    E        -0.421  -0.084  -0.382  -0.411   0.078  -0.396  -0.587  -0.103  -0.506
55    L        -0.103   0.243  -0.319  -0.045   0.382  -0.325  -0.116   0.357  -0.412
56    N        -0.564  -0.608  -0.474  -0.756  -0.794  -0.578  -0.822  -0.836  -0.637
57    K         0.589   0.590   0.404   0.547   0.552   0.275   0.590   0.585   0.239
58    N        -0.690  -0.594  -0.499  -1.001  -0.843  -0.758  -0.940  -0.820  -0.668
59    E         1.315   1.410   1.509   1.197   1.301   1.487   1.414   1.553   1.712
60    S        -0.421  -0.254  -0.403  -0.520  -0.255  -0.527  -0.587  -0.319  -0.536
61    S        -1.566  -1.242  -1.416  -1.579  -1.172  -1.342  -1.411  -1.095  -1.138
62    C         1.315   1.410   1.509   1.360   1.479   1.640   1.414   1.553   1.712
63    L         0.231   0.247   0.266   0.089   0.092   0.126   0.002  -0.002  -0.019
64    D         1.315   1.410   1.509   1.367   1.483   1.647   1.414   1.553   1.712
65    R         1.315   1.410   1.509   1.446   1.563   1.722   1.414   1.553   1.712
66    C         1.315   1.410   1.509   1.360   1.479   1.640   1.414   1.553   1.712
67    V         0.589   0.456   0.385   0.651   0.460   0.336   0.590   0.366   0.204
68    A         0.589   0.460   0.394   0.587   0.408   0.300   0.590   0.373   0.221
69    K         1.315   1.410   1.509   1.182   1.308   1.473   1.414   1.553   1.712
70    Y         0.589   0.456   0.385   0.834   0.666   0.528   0.590   0.366   0.204
71    F         1.315   1.410   1.509   1.338   1.506   1.620   1.414   1.553   1.712
72    E         0.589   0.590   0.404   0.583   0.571   0.343   0.590   0.585   0.239
73    T        -0.103  -0.290  -0.394   0.127  -0.159  -0.344  -0.116  -0.372  -0.518
74    N         0.589   0.456   0.385   0.628   0.493   0.390   0.590   0.366   0.204
75    V        -0.421  -0.533  -0.481  -0.459  -0.698  -0.596  -0.587  -0.754  -0.646
76    Q        -0.564  -0.529  -0.443  -0.870  -0.762  -0.654  -0.822  -0.714  -0.593
77    V        -0.103  -0.400  -0.420   0.047  -0.392  -0.431  -0.116  -0.525  -0.554
78    G         0.231   0.123   0.237   0.023  -0.169  -0.031   0.002  -0.235  -0.076
79    E        -0.103  -0.400  -0.420  -0.053  -0.501  -0.531  -0.116  -0.525  -0.554
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   N        -1.024  -1.152  -1.010  -0.984  -1.161  -0.953  -1.058  -1.161  -0.955
126   M        -0.103  -0.293  -0.400   0.098  -0.198  -0.356  -0.116  -0.377  -0.526
127   Q         0.589   0.590   0.404   0.534   0.571   0.279   0.590   0.585   0.239
128   K        -0.103   0.008  -0.346  -0.054   0.097  -0.394  -0.116   0.035  -0.451
129   M        -1.024  -1.117  -0.996  -1.043  -1.174  -0.974  -1.058  -1.109  -0.939
130   G         0.231   0.167   0.240   0.069  -0.012   0.061   0.002  -0.151  -0.070
131   Q         0.589   0.590   0.404   0.541   0.579   0.298   0.590   0.585   0.239
132   S        -1.566  -1.524  -1.429  -1.554  -1.577  -1.350  -1.411  -1.331  -1.148
133   F        -1.566  -1.647  -1.455  -1.432  -1.459  -1.238  -1.411  -1.417  -1.169
134   N        -1.673  -1.673  -1.464  -1.768  -1.697  -1.443  -1.507  -1.439  -1.176
135   A        -1.566  -1.556  -1.439  -1.527  -1.496  -1.344  -1.411  -1.347  -1.155
136   A        -1.232  -1.076  -0.995  -1.197  -0.942  -0.862  -1.293  -1.063  -0.935
137   G         0.524   0.467   0.350   0.486   0.425   0.299   0.491   0.385   0.139
138   K        -1.147  -1.218  -1.041  -1.077  -1.156  -0.857  -1.199  -1.223  -0.985
139   F        -0.909  -0.866  -0.999  -0.736  -0.764  -0.946  -0.892  -0.854  -0.939
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P87108
Output conservation file - output/P87108
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
