1     M         1.499   1.519   1.562   1.700   1.727   1.792   1.602   1.626   1.686
2     S         0.257   0.288   0.179   0.253   0.314   0.140   0.151   0.199   0.014
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     A        -1.561  -1.515  -1.463  -1.635  -1.597  -1.468  -1.301  -1.237  -1.152
5     F         0.257   0.395   0.202   0.422   0.615   0.334   0.151   0.364   0.053
6     V        -0.031  -0.000   0.055  -0.294  -0.228  -0.144  -0.333  -0.279  -0.196
7     T        -1.561  -1.515  -1.463  -1.619  -1.585  -1.453  -1.301  -1.237  -1.152
8     K        -1.561  -1.515  -1.463  -1.635  -1.536  -1.468  -1.301  -1.237  -1.152
9     A         1.499   1.519   1.562   1.510   1.546   1.606   1.602   1.626   1.686
10    E        -1.561  -1.515  -1.463  -1.529  -1.413  -1.365  -1.301  -1.237  -1.152
11    E         0.257   0.288   0.179   0.064   0.093  -0.040   0.151   0.199   0.014
12    M        -0.796  -0.826  -0.800  -0.653  -0.714  -0.696  -0.817  -0.845  -0.794
13    I         0.257   0.395   0.202   0.185   0.406   0.103   0.151   0.364   0.053
14    K        -1.561  -1.515  -1.463  -1.529  -1.420  -1.365  -1.301  -1.237  -1.152
15    S        -0.031   0.003   0.058  -0.217  -0.140  -0.062  -0.333  -0.273  -0.191
16    H         0.257   0.288   0.179   0.478   0.522   0.345   0.151   0.199   0.014
17    P        -0.796  -0.749  -0.771  -0.643  -0.552  -0.613  -0.817  -0.745  -0.758
18    Y        -0.796  -0.749  -0.771  -0.675  -0.598  -0.643  -0.817  -0.745  -0.758
19    F        -0.796  -0.826  -0.800  -0.808  -0.854  -0.831  -0.817  -0.845  -0.794
20    Q         0.257   0.155   0.143   0.490   0.352   0.327   0.151  -0.015  -0.046
21    L         0.257   0.288   0.179   0.198   0.249   0.087   0.151   0.199   0.014
22    S         1.499   1.519   1.562   1.432   1.471   1.530   1.602   1.626   1.686
23    A         0.257   0.155   0.143   0.262   0.094   0.050   0.151  -0.015  -0.046
24    S         0.257   0.308   0.177   0.245   0.336   0.126   0.151   0.230   0.011
25    W         1.499   1.519   1.562   1.600   1.628   1.694   1.602   1.626   1.686
26    C         1.499   1.519   1.562   1.700   1.728   1.792   1.602   1.626   1.686
27    P         1.499   1.519   1.562   1.650   1.681   1.743   1.602   1.626   1.686
28    D         1.499   1.519   1.562   1.510   1.536   1.606   1.602   1.626   1.686
29    C         1.499   1.519   1.562   1.700   1.728   1.792   1.602   1.626   1.686
30    V         0.257   0.155   0.143   0.262   0.142   0.117   0.151  -0.015  -0.046
31    Y         1.499   1.519   1.562   1.613   1.630   1.706   1.602   1.626   1.686
32    A        -0.796  -0.826  -0.800  -0.735  -0.764  -0.740  -0.817  -0.845  -0.794
33    N        -0.796  -0.837  -0.803  -0.643  -0.694  -0.634  -0.817  -0.858  -0.797
34    S         0.257   0.155   0.143   0.160  -0.016  -0.059   0.151  -0.015  -0.046
35    I         1.499   1.519   1.562   1.445   1.463   1.543   1.602   1.626   1.686
36    W         1.499   1.519   1.562   1.600   1.628   1.694   1.602   1.626   1.686
37    N         0.257   0.308   0.177   0.262   0.342   0.115   0.151   0.230   0.011
38    K         0.257   0.155   0.143   0.181   0.040   0.034   0.151  -0.015  -0.046
39    L        -0.796  -0.675  -0.761  -0.675  -0.473  -0.625  -0.817  -0.652  -0.746
40    N        -0.796  -0.749  -0.771  -0.643  -0.563  -0.590  -0.817  -0.745  -0.758
41    V         1.499   1.519   1.562   1.393   1.441   1.492   1.602   1.626   1.686
42    Q        -1.561  -1.515  -1.463  -1.551  -1.515  -1.387  -1.301  -1.237  -1.152
43    D        -0.796  -0.837  -0.803  -0.825  -0.929  -0.853  -0.817  -0.858  -0.797
44    K         0.257   0.288   0.179   0.181   0.227   0.086   0.151   0.199   0.014
45    V         0.257   0.395   0.202   0.220   0.422   0.129   0.151   0.364   0.053
46    F        -0.796  -0.837  -0.803  -0.589  -0.642  -0.574  -0.817  -0.858  -0.797
47    V        -0.796  -0.826  -0.800  -0.842  -0.876  -0.834  -0.817  -0.845  -0.794
48    F        -0.796  -0.826  -0.800  -0.686  -0.745  -0.685  -0.817  -0.845  -0.794
49    D         0.257   0.155   0.143   0.236   0.045   0.011   0.151  -0.015  -0.046
50    I         0.257   0.155   0.143   0.215   0.039   0.017   0.151  -0.015  -0.046
51    G        -0.796  -0.826  -0.800  -0.713  -0.749  -0.714  -0.817  -0.845  -0.794
52    S        -0.796  -0.826  -0.800  -0.977  -1.037  -1.007  -0.817  -0.845  -0.794
53    L        -0.796  -0.826  -0.800  -0.871  -0.892  -0.865  -0.817  -0.845  -0.794
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    P        -0.796  -0.675  -0.761  -0.686  -0.499  -0.623  -0.817  -0.652  -0.746
57    R        -0.796  -0.837  -0.803  -0.686  -0.733  -0.704  -0.817  -0.858  -0.797
58    N        -0.796  -0.749  -0.771  -0.859  -0.776  -0.830  -0.817  -0.745  -0.758
59    E         0.257   0.288   0.179   0.042   0.069  -0.070   0.151   0.199   0.014
60    Q        -0.796  -0.826  -0.800  -0.579  -0.623  -0.586  -0.817  -0.845  -0.794
61    E        -0.796  -0.749  -0.771  -0.941  -0.878  -0.875  -0.817  -0.745  -0.758
62    K        -0.031  -0.000   0.055  -0.493  -0.460  -0.345  -0.333  -0.279  -0.196
63    W        -0.796  -0.826  -0.800  -0.719  -0.786  -0.746  -0.817  -0.845  -0.794
64    R         0.257   0.155   0.143   0.299   0.113   0.069   0.151  -0.015  -0.046
65    I        -0.796  -0.775  -0.783  -0.819  -0.810  -0.809  -0.817  -0.786  -0.773
66    A         1.499   1.519   1.562   1.510   1.546   1.606   1.602   1.626   1.686
67    F         1.499   1.519   1.562   1.523   1.556   1.619   1.602   1.626   1.686
68    Q        -0.796  -0.837  -0.803  -0.713  -0.784  -0.752  -0.817  -0.858  -0.797
69    K        -0.031   0.003   0.058  -0.493  -0.454  -0.341  -0.333  -0.273  -0.191
70    V        -0.796  -0.826  -0.800  -0.842  -0.873  -0.834  -0.817  -0.845  -0.794
71    V        -1.561  -1.515  -1.463  -1.507  -1.399  -1.343  -1.301  -1.237  -1.152
72    G         1.499   1.519   1.562   1.510   1.546   1.606   1.602   1.626   1.686
73    S        -0.796  -0.837  -0.803  -0.802  -0.829  -0.802  -0.817  -0.858  -0.797
74    R         0.257   0.155   0.143   0.324   0.152   0.107   0.151  -0.015  -0.046
75    N         0.257   0.155   0.143   0.349   0.202   0.181   0.151  -0.015  -0.046
76    L         0.257   0.155   0.143   0.155   0.001  -0.035   0.151  -0.015  -0.046
77    P         1.499   1.519   1.562   1.650   1.681   1.743   1.602   1.626   1.686
78    T         1.499   1.519   1.562   1.536   1.565   1.631   1.602   1.626   1.686
79    I         0.257   0.308   0.177   0.215   0.286   0.079   0.151   0.230   0.011
80    V        -0.796  -0.826  -0.800  -0.763  -0.785  -0.740  -0.817  -0.845  -0.794
81    V         0.257   0.155   0.143   0.211   0.081   0.041   0.151  -0.015  -0.046
82    N        -0.796  -0.775  -0.783  -0.643  -0.600  -0.607  -0.817  -0.786  -0.773
83    G         1.499   1.519   1.562   1.510   1.546   1.606   1.602   1.626   1.686
84    K         1.499   1.519   1.562   1.327   1.350   1.427   1.602   1.626   1.686
85    F        -0.796  -0.775  -0.783  -0.836  -0.797  -0.803  -0.817  -0.786  -0.773
86    W         0.257   0.155   0.143   0.365   0.195   0.154   0.151  -0.015  -0.046
87    G         1.499   1.519   1.562   1.510   1.546   1.606   1.602   1.626   1.686
88    T         1.499   1.519   1.562   1.536   1.565   1.631   1.602   1.626   1.686
89    E         1.499   1.519   1.562   1.246   1.254   1.348   1.602   1.626   1.686
90    S        -0.796  -0.837  -0.803  -0.882  -0.970  -0.898  -0.817  -0.858  -0.797
91    Q        -1.561  -1.515  -1.463  -1.428  -1.359  -1.266  -1.301  -1.237  -1.152
92    L         1.499   1.519   1.562   1.380   1.408   1.479   1.602   1.626   1.686
93    H        -0.796  -0.826  -0.800  -0.648  -0.726  -0.683  -0.817  -0.845  -0.794
94    R         0.257   0.288   0.179   0.299   0.349   0.142   0.151   0.199   0.014
95    F        -0.796  -0.837  -0.803  -0.713  -0.751  -0.722  -0.817  -0.858  -0.797
96    E         0.257   0.155   0.143   0.073  -0.090  -0.082   0.151  -0.015  -0.046
97    A        -1.561  -1.515  -1.463  -1.449  -1.392  -1.287  -1.301  -1.237  -1.152
98    K        -0.796  -0.775  -0.783  -0.906  -0.901  -0.908  -0.817  -0.786  -0.773
99    G         1.499   1.519   1.562   1.510   1.546   1.606   1.602   1.626   1.686
100   T        -0.796  -0.837  -0.803  -0.802  -0.883  -0.833  -0.817  -0.858  -0.797
101   L         1.499   1.519   1.562   1.380   1.408   1.479   1.602   1.626   1.686
102   E        -0.796  -0.675  -0.761  -0.977  -0.752  -0.929  -0.817  -0.652  -0.746
103   E         0.257   0.288   0.179   0.064   0.093  -0.040   0.151   0.199   0.014
104   E         0.257   0.155   0.143   0.042  -0.135  -0.128   0.151  -0.015  -0.046
105   L         0.257   0.155   0.143   0.198   0.050   0.029   0.151  -0.015  -0.046
106   T        -0.796  -0.826  -0.800  -0.719  -0.785  -0.728  -0.817  -0.845  -0.794
107   K         0.257   0.155   0.143   0.142  -0.012  -0.024   0.151  -0.015  -0.046
108   I        -0.796  -0.837  -0.803  -0.719  -0.784  -0.706  -0.817  -0.858  -0.797
109   G         0.257   0.155   0.143   0.373   0.237   0.217   0.151  -0.015  -0.046
110   L         0.257   0.288   0.179   0.198   0.249   0.087   0.151   0.199   0.014
111   L        -1.561  -1.515  -1.463  -1.666  -1.572  -1.499  -1.301  -1.237  -1.152
112   P        -1.561  -1.515  -1.463  -1.378  -1.311  -1.218  -1.301  -1.237  -1.152
* 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/Q05926
Output conservation file - output/Q05926
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
