1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    M         1.421   1.447   1.518   1.652   1.684   1.787   1.560   1.599   1.712
17    V        -0.825  -0.884  -0.876  -0.697  -0.811  -0.785  -0.811  -0.881  -0.848
18    S         0.680   0.721   0.485   0.761   0.818   0.493   0.689   0.750   0.332
19    Q        -1.739  -1.715  -1.626  -1.568  -1.547  -1.421  -1.344  -1.315  -1.185
20    E        -1.381  -1.268  -1.289  -1.254  -1.116  -1.101  -1.199  -1.092  -1.054
21    T        -0.887  -0.888  -0.875  -0.853  -0.870  -0.844  -0.908  -0.909  -0.852
22    I        -0.887  -0.877  -0.873  -0.868  -0.826  -0.833  -0.908  -0.894  -0.850
23    K        -1.400  -1.333  -1.300  -1.422  -1.342  -1.265  -1.207  -1.136  -1.061
24    H        -0.825  -0.831  -0.876  -0.701  -0.701  -0.708  -0.811  -0.814  -0.849
25    V        -0.018  -0.036  -0.259   0.087   0.054  -0.295  -0.037  -0.061  -0.384
26    K        -0.887  -0.846  -0.857  -0.986  -0.930  -0.922  -0.908  -0.853  -0.832
27    D        -1.246  -1.275  -1.278  -1.042  -1.098  -1.115  -1.053  -1.078  -1.042
28    L        -0.018  -0.102  -0.265   0.010  -0.113  -0.314  -0.037  -0.159  -0.392
29    I         0.680   0.568   0.473   0.689   0.548   0.396   0.689   0.502   0.310
30    A        -0.529  -0.457  -0.392  -0.772  -0.652  -0.552  -0.763  -0.662  -0.574
31    E        -1.381  -1.319  -1.299  -1.303  -1.207  -1.204  -1.199  -1.127  -1.061
32    N        -0.887  -0.765  -0.850  -0.882  -0.671  -0.806  -0.908  -0.751  -0.820
33    E        -1.381  -1.426  -1.305  -1.289  -1.372  -1.208  -1.199  -1.222  -1.066
34    I         0.340   0.377   0.362   0.226   0.278   0.227   0.108   0.168   0.102
35    F         0.340   0.272   0.318   0.429   0.280   0.328   0.108  -0.029   0.016
36    V         0.340   0.466   0.402   0.226   0.424   0.302   0.108   0.327   0.178
37    A         0.340   0.272   0.318   0.257   0.146   0.227   0.108  -0.029   0.016
38    S         0.680   0.568   0.473   0.739   0.588   0.429   0.689   0.502   0.310
39    K         1.421   1.447   1.518   1.230   1.266   1.377   1.560   1.599   1.712
40    T         0.340   0.377   0.362   0.276   0.336   0.289   0.108   0.168   0.102
41    Y         1.421   1.447   1.518   1.562   1.593   1.699   1.560   1.599   1.712
42    C         1.421   1.447   1.518   1.620   1.655   1.756   1.560   1.599   1.712
43    P         1.421   1.447   1.518   1.588   1.625   1.724   1.560   1.599   1.712
44    Y         1.421   1.447   1.518   1.562   1.593   1.699   1.560   1.599   1.712
45    C         1.421   1.447   1.518   1.620   1.655   1.756   1.560   1.599   1.712
46    H        -1.381  -1.317  -1.296  -1.259  -1.127  -1.130  -1.199  -1.130  -1.060
47    A        -0.665  -0.616  -0.799  -0.582  -0.515  -0.798  -0.618  -0.556  -0.760
48    A         0.680   0.682   0.486   0.793   0.804   0.502   0.689   0.690   0.334
49    L        -0.307  -0.376  -0.350  -0.548  -0.637  -0.612  -0.473  -0.553  -0.519
50    N        -1.023  -0.952  -0.909  -1.107  -1.039  -0.936  -1.053  -0.982  -0.888
51    T        -0.665  -0.776  -0.840  -0.488  -0.659  -0.812  -0.618  -0.751  -0.807
52    L         0.187   0.214   0.299  -0.181  -0.133  -0.010  -0.182  -0.141  -0.021
53    F        -1.381  -1.381  -1.303  -1.184  -1.205  -1.093  -1.199  -1.189  -1.066
54    E        -1.739  -1.704  -1.640  -1.566  -1.513  -1.436  -1.344  -1.307  -1.195
55    K        -1.381  -1.338  -1.301  -1.433  -1.380  -1.296  -1.199  -1.145  -1.063
56    L        -0.887  -0.866  -0.854  -0.984  -0.947  -0.929  -0.908  -0.862  -0.825
57    K        -0.665  -0.776  -0.840  -0.688  -0.860  -0.967  -0.618  -0.751  -0.807
58    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    K        -0.307  -0.160  -0.296  -0.509  -0.286  -0.497  -0.473  -0.256  -0.439
63    V        -0.665  -0.694  -0.814  -0.475  -0.518  -0.656  -0.618  -0.649  -0.777
64    L        -1.739  -1.760  -1.649  -1.477  -1.551  -1.407  -1.344  -1.347  -1.202
65    V        -0.394  -0.398  -0.372  -0.526  -0.512  -0.460  -0.618  -0.607  -0.552
66    L        -0.307  -0.289  -0.349  -0.393  -0.374  -0.434  -0.473  -0.480  -0.521
67    Q         0.187   0.196   0.292  -0.013  -0.004   0.140  -0.182  -0.177  -0.034
68    L         0.680   0.568   0.473   0.597   0.451   0.298   0.689   0.502   0.310
69    N         0.187   0.205   0.294   0.030   0.042   0.188  -0.182  -0.160  -0.031
70    D        -0.887  -0.956  -0.891  -0.885  -0.998  -0.906  -0.908  -0.971  -0.868
71    M        -1.023  -1.004  -0.910  -0.991  -0.922  -0.813  -1.053  -1.019  -0.887
72    K        -1.381  -1.428  -1.302  -1.315  -1.380  -1.207  -1.199  -1.224  -1.065
73    E        -0.018  -0.135  -0.268   0.142  -0.023  -0.220  -0.037  -0.204  -0.397
74    G         1.421   1.447   1.518   1.409   1.444   1.551   1.560   1.599   1.712
75    A        -0.394  -0.450  -0.360  -0.543  -0.611  -0.470  -0.618  -0.669  -0.540
76    D         0.187   0.205   0.294  -0.017   0.008   0.138  -0.182  -0.160  -0.031
77    I        -0.018  -0.036  -0.259   0.029   0.014  -0.349  -0.037  -0.061  -0.384
78    Q         1.421   1.447   1.518   1.409   1.442   1.551   1.560   1.599   1.712
79    A        -1.023  -1.038  -0.910  -1.103  -1.118  -0.931  -1.053  -1.052  -0.888
80    A         0.680   0.568   0.473   0.705   0.565   0.446   0.689   0.502   0.310
81    L         1.421   1.447   1.518   1.251   1.290   1.398   1.560   1.599   1.712
82    Y        -0.529  -0.476  -0.413  -0.728  -0.655  -0.547  -0.763  -0.687  -0.602
83    E         0.340   0.272   0.318   0.194   0.054   0.085   0.108  -0.029   0.016
84    I        -0.307  -0.381  -0.348  -0.488  -0.601  -0.593  -0.473  -0.561  -0.519
85    N         0.680   0.682   0.486   0.818   0.828   0.552   0.689   0.690   0.334
86    G         1.421   1.447   1.518   1.409   1.444   1.551   1.560   1.599   1.712
87    Q         1.421   1.447   1.518   1.409   1.442   1.551   1.560   1.599   1.712
88    R         0.340   0.434   0.361   0.452   0.612   0.419   0.108   0.270   0.099
89    T         1.421   1.447   1.518   1.449   1.492   1.590   1.560   1.599   1.712
90    V         1.421   1.447   1.518   1.389   1.416   1.531   1.560   1.599   1.712
91    P         1.421   1.447   1.518   1.588   1.625   1.724   1.560   1.599   1.712
92    N         1.421   1.447   1.518   1.469   1.492   1.609   1.560   1.599   1.712
93    I         0.187   0.254   0.314  -0.076   0.039   0.118  -0.182  -0.064   0.008
94    Y         0.680   0.682   0.486   0.963   0.961   0.704   0.689   0.690   0.334
95    I         1.421   1.447   1.518   1.334   1.379   1.478   1.560   1.599   1.712
96    N        -0.307  -0.376  -0.350  -0.226  -0.310  -0.258  -0.473  -0.553  -0.519
97    G        -0.018  -0.169  -0.280   0.104  -0.115  -0.320  -0.037  -0.249  -0.415
98    K        -0.394  -0.318  -0.364  -0.601  -0.514  -0.531  -0.618  -0.530  -0.544
99    H         1.421   1.447   1.518   1.626   1.657   1.762   1.560   1.599   1.712
100   I         0.680   0.568   0.473   0.689   0.548   0.396   0.689   0.502   0.310
101   G         1.421   1.447   1.518   1.409   1.444   1.551   1.560   1.599   1.712
102   G         1.421   1.447   1.518   1.409   1.444   1.551   1.560   1.599   1.712
103   N         1.421   1.447   1.518   1.469   1.492   1.609   1.560   1.599   1.712
104   D         0.680   0.682   0.486   0.753   0.760   0.479   0.689   0.690   0.334
105   D         1.421   1.447   1.518   1.402   1.434   1.544   1.560   1.599   1.712
106   L        -0.307  -0.311  -0.319  -0.417  -0.392  -0.393  -0.473  -0.455  -0.472
107   Q         0.680   0.643   0.480   0.765   0.719   0.479   0.689   0.627   0.322
108   E        -0.394  -0.357  -0.356  -0.547  -0.497  -0.472  -0.618  -0.567  -0.535
109   L         0.680   0.643   0.480   0.606   0.563   0.329   0.689   0.627   0.322
110   R        -2.097  -2.051  -1.929  -1.719  -1.628  -1.488  -1.489  -1.443  -1.289
111   E        -1.381  -1.319  -1.299  -1.373  -1.304  -1.242  -1.199  -1.127  -1.061
112   T        -1.381  -1.346  -1.287  -1.353  -1.315  -1.203  -1.199  -1.154  -1.053
113   G         0.187   0.254   0.314  -0.006   0.107   0.188  -0.182  -0.064   0.008
114   E        -0.394  -0.333  -0.357  -0.610  -0.510  -0.519  -0.618  -0.541  -0.535
115   L         0.680   0.643   0.480   0.620   0.578   0.358   0.689   0.627   0.322
116   E        -0.887  -0.880  -0.857  -0.866  -0.850  -0.826  -0.908  -0.888  -0.833
117   E        -1.023  -1.004  -0.909  -1.159  -1.130  -0.983  -1.053  -1.022  -0.887
118   L         0.187   0.196   0.292  -0.252  -0.248  -0.095  -0.182  -0.177  -0.034
119   L        -0.307  -0.376  -0.350  -0.404  -0.476  -0.449  -0.473  -0.553  -0.519
120   E        -0.297  -0.412  -0.377  -0.466  -0.644  -0.595  -0.432  -0.597  -0.552
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   P        -0.665  -0.803  -0.840  -0.493  -0.690  -0.717  -0.618  -0.782  -0.807
128   I        -1.246  -1.237  -1.264  -1.135  -1.127  -1.175  -1.053  -1.042  -1.028
129   L         0.680   0.568   0.473   0.595   0.445   0.293   0.689   0.502   0.310
130   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   N        -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/P25373
Output conservation file - output/P25373
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
