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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    M         1.416   1.443   1.492   1.702   1.738   1.796   1.520   1.558   1.634
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    V         0.162   0.205   0.318  -0.390  -0.287  -0.113  -0.250  -0.182  -0.020
21    N        -1.601  -1.655  -1.525  -1.157  -1.251  -1.055  -1.246  -1.276  -1.115
22    V         0.162   0.225   0.327  -0.335  -0.188  -0.042  -0.250  -0.144  -0.002
23    K        -0.779  -0.697  -0.782  -0.625  -0.543  -0.649  -0.803  -0.734  -0.775
24    V         0.734   0.812   0.515   0.684   0.814   0.346   0.746   0.858   0.350
25    E         0.734   0.673   0.502   0.712   0.645   0.359   0.746   0.646   0.326
26    F         0.734   0.642   0.498   0.979   0.835   0.569   0.746   0.596   0.318
27    L         0.399   0.323   0.363   0.181   0.015   0.132   0.192   0.042   0.066
28    G         1.416   1.443   1.492   1.341   1.382   1.466   1.520   1.558   1.634
29    G         1.416   1.443   1.492   1.341   1.382   1.466   1.520   1.558   1.634
30    L         1.416   1.443   1.492   1.245   1.249   1.378   1.520   1.558   1.634
31    D         0.399   0.323   0.363   0.192   0.057   0.087   0.192   0.042   0.066
32    A        -1.287  -1.326  -1.196  -1.448  -1.518  -1.280  -1.135  -1.151  -0.986
33    I        -0.213  -0.351  -0.313  -0.426  -0.660  -0.564  -0.361  -0.553  -0.504
34    F        -0.465  -0.283  -0.282  -0.491  -0.174  -0.228  -0.692  -0.433  -0.453
35    G        -1.092  -1.115  -1.161  -0.810  -0.874  -0.992  -0.914  -0.932  -0.951
36    K        -0.779  -0.750  -0.784  -0.677  -0.657  -0.706  -0.803  -0.767  -0.779
37    Q        -0.213  -0.179  -0.240  -0.024   0.056  -0.087  -0.361  -0.289  -0.394
38    R         0.219   0.201   0.314   0.282   0.211   0.374  -0.139  -0.190  -0.027
39    V        -1.719  -1.739  -1.543  -1.560  -1.511  -1.213  -1.356  -1.340  -1.128
40    H        -0.213  -0.207  -0.249   0.053   0.041  -0.062  -0.361  -0.328  -0.409
41    K        -1.092  -1.200  -1.176  -0.803  -0.981  -0.989  -0.914  -1.021  -0.965
42    I        -0.779  -0.572  -0.745  -0.879  -0.626  -0.857  -0.803  -0.541  -0.729
43    K        -1.287  -1.126  -1.186  -1.348  -1.106  -1.193  -1.135  -0.987  -0.978
44    M        -0.526  -0.462  -0.711  -0.513  -0.436  -0.818  -0.471  -0.398  -0.689
45    D        -0.526  -0.497  -0.722  -0.116  -0.092  -0.448  -0.471  -0.438  -0.701
46    -        -0.994  -0.949  -0.839  -0.988  -0.937  -0.724  -1.029  -0.975  -0.832
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    K        -2.105  -1.997  -1.815  -1.858  -1.661  -1.460  -1.514  -1.414  -1.214
51    E        -0.671  -0.818  -0.804  -0.736  -1.030  -0.998  -0.647  -0.823  -0.794
52    D        -0.894  -0.923  -0.820  -1.137  -1.165  -1.003  -0.936  -0.945  -0.814
53    P        -0.894  -0.953  -0.818  -0.948  -1.022  -0.810  -0.936  -0.979  -0.814
54    V        -1.253  -1.266  -1.193  -0.993  -1.020  -1.002  -1.081  -1.082  -0.980
55    T        -0.855  -0.930  -0.804  -0.726  -0.805  -0.625  -0.914  -0.958  -0.799
56    V        -0.526  -0.431  -0.726  -0.426  -0.335  -0.689  -0.471  -0.363  -0.705
57    G        -0.526  -0.428  -0.710  -0.424  -0.297  -0.682  -0.471  -0.358  -0.687
58    D        -0.526  -0.747  -0.775  -0.356  -0.630  -0.642  -0.471  -0.730  -0.762
59    L         1.416   1.443   1.492   1.245   1.249   1.378   1.520   1.558   1.634
60    I         0.734   0.646   0.510   0.637   0.534   0.288   0.746   0.603   0.341
61    D        -1.601  -1.531  -1.499  -1.330  -1.231  -1.142  -1.246  -1.172  -1.094
62    H        -0.213  -0.167  -0.276   0.154   0.198   0.048  -0.361  -0.311  -0.453
63    I        -0.213  -0.340  -0.313  -0.334  -0.503  -0.456  -0.361  -0.543  -0.504
64    V        -1.287  -1.253  -1.186  -1.216  -1.099  -1.020  -1.135  -1.078  -0.974
65    S        -1.719  -1.537  -1.511  -1.475  -1.234  -1.180  -1.356  -1.194  -1.106
66    T         0.180   0.260   0.336   0.073   0.214   0.314  -0.214  -0.076   0.015
67    M        -0.347  -0.251  -0.301  -0.720  -0.611  -0.557  -0.582  -0.461  -0.489
68    I         0.399   0.323   0.363   0.261   0.174   0.230   0.192   0.042   0.066
69    N        -1.406  -1.356  -1.207  -1.313  -1.242  -1.012  -1.246  -1.178  -0.995
70    N        -0.779  -0.727  -0.774  -0.745  -0.657  -0.684  -0.803  -0.721  -0.763
71    P        -0.526  -0.465  -0.703  -0.118  -0.042  -0.420  -0.471  -0.402  -0.679
72    N        -1.092  -1.118  -1.161  -0.742  -0.786  -0.873  -0.914  -0.935  -0.951
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    D        -0.025  -0.269  -0.278  -0.004  -0.354  -0.371  -0.069  -0.414  -0.448
77    V        -0.779  -0.800  -0.798  -0.829  -0.831  -0.819  -0.803  -0.840  -0.794
78    S        -1.406  -1.265  -1.206  -1.338  -1.176  -1.069  -1.246  -1.108  -0.995
79    I        -0.465  -0.500  -0.372  -0.920  -1.024  -0.815  -0.692  -0.740  -0.577
80    F         1.416   1.443   1.492   1.619   1.656   1.720   1.520   1.558   1.634
81    I        -0.213  -0.285  -0.293  -0.506  -0.625  -0.676  -0.361  -0.455  -0.476
82    E        -0.213  -0.351  -0.313  -0.367  -0.624  -0.522  -0.361  -0.553  -0.504
83    D        -0.855  -0.801  -0.783  -0.976  -0.897  -0.878  -0.914  -0.847  -0.780
84    D        -0.347  -0.352  -0.298  -0.683  -0.654  -0.577  -0.582  -0.554  -0.483
85    S        -0.347  -0.364  -0.314  -0.363  -0.383  -0.324  -0.582  -0.583  -0.507
86    I        -0.347  -0.333  -0.291  -0.758  -0.684  -0.646  -0.582  -0.531  -0.473
87    R         1.416   1.443   1.492   1.702   1.744   1.796   1.520   1.558   1.634
88    P         1.416   1.443   1.492   1.651   1.686   1.750   1.520   1.558   1.634
89    G         1.416   1.443   1.492   1.341   1.382   1.466   1.520   1.558   1.634
90    I         0.734   0.646   0.510   0.648   0.560   0.313   0.746   0.603   0.341
91    I         0.219   0.261   0.332  -0.271  -0.224  -0.084  -0.139  -0.076   0.007
92    T        -0.347  -0.333  -0.291  -0.473  -0.398  -0.312  -0.582  -0.531  -0.473
93    L         1.416   1.443   1.492   1.245   1.249   1.378   1.520   1.558   1.634
94    I         0.734   0.642   0.498   0.648   0.554   0.291   0.746   0.596   0.318
95    N         1.416   1.443   1.492   1.580   1.617   1.685   1.520   1.558   1.634
96    D         1.416   1.443   1.492   1.334   1.390   1.460   1.520   1.558   1.634
97    T        -0.526  -0.747  -0.775  -0.137  -0.422  -0.460  -0.471  -0.730  -0.762
98    D         1.416   1.443   1.492   1.334   1.390   1.460   1.520   1.558   1.634
99    W         1.416   1.443   1.492   1.746   1.782   1.837   1.520   1.558   1.634
100   E         1.416   1.443   1.492   1.341   1.395   1.466   1.520   1.558   1.634
101   L         1.416   1.443   1.492   1.245   1.249   1.378   1.520   1.558   1.634
102   E         0.734   0.642   0.498   0.699   0.572   0.321   0.746   0.596   0.318
103   G        -0.213  -0.185  -0.285  -0.354  -0.375  -0.465  -0.361  -0.365  -0.466
104   E        -0.213  -0.183  -0.254  -0.217  -0.154  -0.249  -0.361  -0.294  -0.415
105   K        -0.542  -0.524  -0.372  -0.835  -0.822  -0.586  -0.803  -0.771  -0.577
106   D        -0.779  -0.820  -0.781  -0.815  -0.811  -0.754  -0.803  -0.821  -0.773
107   Y         1.416   1.443   1.492   1.714   1.755   1.808   1.520   1.558   1.634
108   I        -0.213  -0.302  -0.287  -0.398  -0.504  -0.516  -0.361  -0.474  -0.468
109   L        -0.213   0.011  -0.238  -0.527  -0.197  -0.575  -0.361  -0.046  -0.397
110   E         0.399   0.323   0.363   0.317   0.205   0.274   0.192   0.042   0.066
111   D        -0.974  -0.974  -0.840  -1.051  -1.023  -0.831  -1.024  -1.001  -0.835
112   G         0.734   0.646   0.510   0.767   0.665   0.494   0.746   0.603   0.341
113   D         1.416   1.443   1.492   1.334   1.390   1.460   1.520   1.558   1.634
114   I        -0.526  -0.607  -0.747  -0.520  -0.621  -0.891  -0.471  -0.571  -0.730
115   I        -0.779  -0.628  -0.773  -1.010  -0.790  -0.998  -0.803  -0.646  -0.767
116   S        -1.287  -1.367  -1.217  -1.268  -1.457  -1.272  -1.135  -1.177  -1.002
117   F         1.416   1.443   1.492   1.619   1.656   1.720   1.520   1.558   1.634
118   T        -0.526  -0.747  -0.775  -0.278  -0.603  -0.725  -0.471  -0.730  -0.762
119   S         1.416   1.443   1.492   1.567   1.598   1.673   1.520   1.558   1.634
120   T         1.416   1.443   1.492   1.541   1.596   1.649   1.520   1.558   1.634
121   L         1.416   1.443   1.492   1.245   1.249   1.378   1.520   1.558   1.634
122   H         1.416   1.443   1.492   1.689   1.722   1.785   1.520   1.558   1.634
123   G         1.416   1.443   1.492   1.341   1.382   1.466   1.520   1.558   1.634
124   G         0.734   0.642   0.498   0.744   0.628   0.425   0.746   0.596   0.318
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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/P40554
Output conservation file - output/P40554
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
