1     M         0.536   0.551   0.577   1.101   1.065   1.024   0.555   0.575   0.609
2     V         0.536   0.551   0.577   0.699   0.684   0.721   0.555   0.575   0.609
3     N         0.536   0.551   0.577   1.085   1.039   1.011   0.555   0.575   0.609
4     V        -1.043  -1.107  -0.983  -0.731  -0.881  -0.709  -1.333  -1.444  -1.265
5     P         0.536   0.551   0.577   1.043   0.993   0.980   0.555   0.575   0.609
6     K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
7     T         0.536   0.551   0.577   0.628   0.652   0.668   0.555   0.575   0.609
8     R         0.536   0.551   0.577   0.682   0.684   0.708   0.555   0.575   0.609
9     K        -1.530  -1.153  -1.865  -2.171  -1.655  -2.150  -1.490  -1.015  -1.854
10    T         0.536   0.551   0.577   0.628   0.652   0.668   0.555   0.575   0.609
11    Y         0.536   0.551   0.577   0.924   0.901   0.891   0.555   0.575   0.609
12    C         0.536   0.551   0.577   0.847   0.836   0.832   0.555   0.575   0.609
13    K        -1.530  -1.933  -1.888  -2.164  -2.497  -2.100  -1.490  -1.979  -1.880
14    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
15    K        -0.522  -0.670  -0.956  -1.386  -1.461  -1.660  -0.546  -0.756  -1.219
16    T        -3.357  -3.181  -3.044  -2.234  -2.143  -2.121  -2.906  -2.700  -2.389
17    C         0.536   0.551   0.577   0.847   0.836   0.832   0.555   0.575   0.609
18    R        -0.522  -0.670  -0.956  -0.208  -0.434  -0.963  -0.546  -0.756  -1.219
19    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
20    H         0.536   0.551   0.577   0.916   0.897   0.884   0.555   0.575   0.609
21    T        -0.522  -0.352  -0.947  -0.232  -0.045  -0.889  -0.546  -0.315  -1.204
22    Q        -1.530  -1.933  -1.888  -1.127  -1.692  -1.724  -1.490  -1.979  -1.880
23    H         0.536   0.551   0.577   0.916   0.897   0.884   0.555   0.575   0.609
24    K        -0.522  -0.852  -0.961  -1.386  -1.702  -1.661  -0.546  -1.031  -1.227
25    V         0.536   0.551   0.577   0.699   0.684   0.721   0.555   0.575   0.609
26    T         0.536   0.551   0.577   0.628   0.652   0.668   0.555   0.575   0.609
27    Q         0.536   0.551   0.577   0.593   0.644   0.641   0.555   0.575   0.609
28    Y         0.536   0.551   0.577   0.924   0.901   0.891   0.555   0.575   0.609
29    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
30    A        -0.522  -0.852  -0.961  -0.266  -0.872  -1.398  -0.546  -1.031  -1.227
31    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
32    K        -0.522  -0.852  -0.961  -1.321  -1.585  -1.455  -0.546  -1.031  -1.227
33    A        -0.522  -0.852  -0.961  -0.055  -0.478  -0.687  -0.546  -1.031  -1.227
34    S         0.536   0.551   0.577   1.018   0.976   0.961   0.555   0.575   0.609
35    L        -1.530  -1.933  -1.888  -1.181  -1.973  -2.142  -1.490  -1.979  -1.880
36    F        -1.992  -2.039  -1.889  -1.400  -1.547  -1.471  -2.119  -2.108  -1.882
37    A         0.536   0.551   0.577   0.760   0.768   0.767   0.555   0.575   0.609
38    Q         0.536   0.551   0.577   0.593   0.644   0.641   0.555   0.575   0.609
39    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
40    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
41    R         0.536   0.551   0.577   0.682   0.684   0.708   0.555   0.575   0.609
42    R         0.536   0.551   0.577   0.682   0.684   0.708   0.555   0.575   0.609
43    Y         0.536   0.551   0.577   0.924   0.901   0.891   0.555   0.575   0.609
44    D         0.536   0.551   0.577   1.076   1.036   1.005   0.555   0.575   0.609
45    R         0.536   0.551   0.577   0.682   0.684   0.708   0.555   0.575   0.609
46    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
47    Q         0.536   0.551   0.577   0.593   0.644   0.641   0.555   0.575   0.609
48    S        -0.522  -0.293  -0.947  -0.004   0.227  -1.156  -0.546  -0.239  -1.204
49    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
50    F        -1.410  -1.229  -0.984  -1.199  -0.992  -0.707  -1.962  -1.651  -1.266
51    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
52    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
53    Q         0.536   0.551   0.577   0.593   0.644   0.641   0.555   0.575   0.609
54    T         0.536   0.551   0.577   0.628   0.652   0.668   0.555   0.575   0.609
55    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
56    P        -1.322  -1.024  -0.973  -1.095  -0.661  -0.763  -1.805  -1.305  -1.248
57    V        -1.322  -1.024  -0.973  -1.111  -0.769  -0.707  -1.805  -1.305  -1.248
58    F         0.536   0.551   0.577   0.907   0.893   0.878   0.555   0.575   0.609
59    H         0.536   0.551   0.577   0.916   0.897   0.884   0.555   0.575   0.609
60    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
61    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
62    A         0.536   0.551   0.577   0.760   0.768   0.767   0.555   0.575   0.609
63    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
64    T        -0.522  -0.852  -0.961  -0.241  -0.695  -0.940  -0.546  -1.031  -1.227
65    T         0.536   0.551   0.577   0.628   0.652   0.668   0.555   0.575   0.609
66    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
67    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
68    V         0.536   0.551   0.577   0.699   0.684   0.721   0.555   0.575   0.609
69    V         0.536   0.551   0.577   0.699   0.684   0.721   0.555   0.575   0.609
70    L         0.536   0.551   0.577   0.717   0.726   0.734   0.555   0.575   0.609
71    R         0.536   0.551   0.577   0.682   0.684   0.708   0.555   0.575   0.609
72    L         0.536   0.551   0.577   0.717   0.726   0.734   0.555   0.575   0.609
73    E         0.536   0.551   0.577   0.984   0.962   0.935   0.555   0.575   0.609
74    C         0.536   0.551   0.577   0.847   0.836   0.832   0.555   0.575   0.609
75    V        -1.530  -1.512  -1.874  -0.904  -0.960  -1.372  -1.490  -1.463  -1.865
76    K        -3.173  -2.717  -2.541  -3.180  -2.534  -2.310  -3.063  -2.546  -2.200
77    C         0.536   0.551   0.577   0.847   0.836   0.832   0.555   0.575   0.609
78    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
79    T        -2.479  -2.660  -2.540  -1.902  -2.211  -2.130  -2.277  -2.444  -2.199
80    R        -0.522  -0.258  -0.945  -1.386  -0.978  -1.657  -0.546  -0.194  -1.201
81    A        -3.357  -3.326  -3.047  -2.679  -2.857  -2.581  -2.906  -2.805  -2.391
82    Q         0.536   0.551   0.577   0.593   0.644   0.641   0.555   0.575   0.609
83    L         0.536   0.551   0.577   0.717   0.726   0.734   0.555   0.575   0.609
84    T        -3.843  -3.479  -3.047  -3.099  -2.741  -2.232  -3.378  -2.928  -2.390
85    L         0.536   0.551   0.577   0.717   0.726   0.734   0.555   0.575   0.609
86    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
87    R         0.536   0.551   0.577   0.682   0.684   0.708   0.555   0.575   0.609
88    C         0.536   0.551   0.577   0.847   0.836   0.832   0.555   0.575   0.609
89    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
90    H         0.536   0.551   0.577   0.916   0.897   0.884   0.555   0.575   0.609
91    F         0.536   0.551   0.577   0.907   0.893   0.878   0.555   0.575   0.609
92    E         0.536   0.551   0.577   0.984   0.962   0.935   0.555   0.575   0.609
93    L         0.536   0.551   0.577   0.717   0.726   0.734   0.555   0.575   0.609
94    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
95    G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
96    E        -1.410  -1.229  -0.984  -1.039  -0.852  -0.588  -1.962  -1.651  -1.266
97    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
98    K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
99    Q        -1.043  -1.197  -0.985  -0.999  -1.288  -1.037  -1.333  -1.597  -1.267
100   K         0.536   0.551   0.577  -0.502  -0.361  -0.183   0.555   0.575   0.609
101   G         0.536   0.551   0.577   0.557   0.572   0.614   0.555   0.575   0.609
102   Q        -1.043  -1.197  -0.985  -0.956  -1.219  -0.964  -1.333  -1.597  -1.267
103   A         0.536   0.551   0.577   0.760   0.768   0.767   0.555   0.575   0.609
104   L        -0.522  -0.852  -0.961  -0.089  -0.503  -0.685  -0.546  -1.031  -1.227
105   Q        -0.522  -0.670  -0.956  -0.276  -0.448  -0.954  -0.546  -0.756  -1.219
106   F         0.536   0.551   0.577   0.907   0.893   0.878   0.555   0.575   0.609
* 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/P0CX27
Output conservation file - output/P0CX27
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
