1     M         0.803   0.824   0.862   1.105   1.132   1.141   0.828   0.858   0.914
2     G        -1.296  -1.100  -1.160  -1.630  -1.333  -1.366  -1.472  -1.224  -1.209
3     K         0.803   0.824   0.862   0.473   0.498   0.627   0.828   0.858   0.914
4     G         0.803   0.824   0.862   0.648   0.688   0.769   0.828   0.858   0.914
5     T         0.803   0.824   0.862   0.702   0.717   0.813   0.828   0.858   0.914
6     P        -1.697  -1.914  -1.710  -1.172  -1.573  -1.402  -1.568  -1.771  -1.497
7     S         0.803   0.824   0.862   0.702   0.749   0.813   0.828   0.858   0.914
8     F        -0.349  -0.174  -0.379  -0.057   0.164  -0.174  -0.513  -0.257  -0.612
9     G         0.803   0.824   0.862   0.648   0.688   0.769   0.828   0.858   0.914
10    K        -0.349  -0.246  -0.376  -0.587  -0.462  -0.546  -0.513  -0.366  -0.607
11    R         0.044  -0.160  -0.358  -0.134  -0.411  -0.760   0.062  -0.235  -0.577
12    H         0.803   0.824   0.862   0.959   0.997   1.022   0.828   0.858   0.914
13    N        -0.349  -0.546  -0.426  -0.155  -0.565  -0.448  -0.513  -0.860  -0.692
14    K         0.803   0.824   0.862   0.473   0.498   0.627   0.828   0.858   0.914
15    S         0.044  -0.167  -0.371   0.062  -0.209  -0.558   0.062  -0.246  -0.598
16    H         0.803   0.824   0.862   0.959   0.997   1.022   0.828   0.858   0.914
17    T        -0.684  -0.795  -1.136  -0.524  -0.731  -1.134  -0.609  -0.772  -1.179
18    L        -0.349  -0.246  -0.376   0.039   0.150  -0.073  -0.513  -0.366  -0.607
19    C         0.803   0.824   0.862   0.974   0.995   1.034   0.828   0.858   0.914
20    N        -1.840  -1.853  -1.705  -1.866  -1.996  -1.818  -1.759  -1.748  -1.493
21    R         0.803   0.824   0.862   0.537   0.586   0.679   0.828   0.858   0.914
22    C         0.803   0.824   0.862   0.974   0.995   1.034   0.828   0.858   0.914
23    G         0.803   0.824   0.862   0.648   0.688   0.769   0.828   0.858   0.914
24    R        -0.691  -0.630  -0.432  -1.402  -1.322  -0.925  -1.088  -1.007  -0.703
25    R         0.044   0.128  -0.351  -0.105   0.015  -0.647   0.062   0.169  -0.565
26    S         0.803   0.824   0.862   0.702   0.749   0.813   0.828   0.858   0.914
27    F        -0.684  -0.817  -1.134  -0.147  -0.332  -0.774  -0.609  -0.797  -1.176
28    H         0.803   0.824   0.862   0.959   0.997   1.022   0.828   0.858   0.914
29    V        -1.840  -2.001  -1.710  -1.239  -1.459  -1.131  -1.759  -1.868  -1.498
30    Q         0.803   0.824   0.862   1.098   1.123   1.135   0.828   0.858   0.914
31    K         0.803   0.824   0.862   0.473   0.498   0.627   0.828   0.858   0.914
32    K        -1.043  -0.888  -1.136  -1.290  -1.091  -1.337  -1.088  -0.896  -1.178
33    T         0.044  -0.167  -0.371   0.116  -0.146  -0.373   0.062  -0.246  -0.598
34    C         0.803   0.824   0.862   0.974   0.995   1.034   0.828   0.858   0.914
35    S        -0.582  -0.377  -0.400  -0.821  -0.453  -0.566  -0.897  -0.576  -0.649
36    S        -0.349  -0.246  -0.376  -0.403  -0.253  -0.446  -0.513  -0.366  -0.607
37    C         0.803   0.824   0.862   0.974   0.995   1.034   0.828   0.858   0.914
38    G         0.803   0.824   0.862   0.648   0.688   0.769   0.828   0.858   0.914
39    Y         0.803   0.824   0.862   1.083   1.106   1.123   0.828   0.858   0.914
40    P         0.803   0.824   0.862   1.120   1.140   1.152   0.828   0.858   0.914
41    A        -0.349  -0.372  -0.401  -0.413  -0.444  -0.567  -0.513  -0.567  -0.650
42    A         0.803   0.824   0.862   0.771   0.827   0.869   0.828   0.858   0.914
43    K         0.803   0.824   0.862   0.473   0.498   0.627   0.828   0.858   0.914
44    T        -1.697  -1.659  -1.691  -1.385  -1.346  -1.267  -1.568  -1.516  -1.479
45    R         0.803   0.824   0.862   0.537   0.586   0.679   0.828   0.858   0.914
46    S         0.044  -0.167  -0.371   0.033  -0.256  -0.658   0.062  -0.246  -0.598
47    Y        -0.582  -0.432  -0.408  -0.418  -0.191  -0.245  -0.897  -0.665  -0.662
48    N         0.803   0.824   0.862   1.033   1.062   1.082   0.828   0.858   0.914
49    W         0.803   0.824   0.862   1.191   1.208   1.210   0.828   0.858   0.914
50    G        -1.235  -1.279  -1.167  -1.472  -1.500  -1.346  -1.376  -1.385  -1.217
51    A        -2.301  -2.246  -2.124  -1.855  -1.772  -1.586  -1.951  -1.906  -1.660
52    K         0.803   0.824   0.862   0.473   0.498   0.627   0.828   0.858   0.914
53    A         0.803   0.824   0.862   0.771   0.827   0.869   0.828   0.858   0.914
54    K         0.803   0.824   0.862   0.473   0.498   0.627   0.828   0.858   0.914
55    R         0.803   0.824   0.862   0.537   0.586   0.679   0.828   0.858   0.914
56    R         0.803   0.824   0.862   0.537   0.586   0.679   0.828   0.858   0.914
57    H        -1.235  -1.326  -1.166  -1.507  -1.646  -1.406  -1.376  -1.451  -1.216
58    T         0.803   0.824   0.862   0.702   0.717   0.813   0.828   0.858   0.914
59    T         0.803   0.824   0.862   0.702   0.717   0.813   0.828   0.858   0.914
60    G         0.803   0.824   0.862   0.648   0.688   0.769   0.828   0.858   0.914
61    T         0.803   0.824   0.862   0.702   0.717   0.813   0.828   0.858   0.914
62    G         0.803   0.824   0.862   0.648   0.688   0.769   0.828   0.858   0.914
63    R         0.803   0.824   0.862   0.537   0.586   0.679   0.828   0.858   0.914
64    M         0.044  -0.167  -0.371   0.512   0.253  -0.106   0.062  -0.246  -0.598
65    R        -1.362  -1.144  -1.150  -1.720  -1.376  -1.396  -1.472  -1.199  -1.195
66    Y         0.044  -0.160  -0.358   0.444   0.164  -0.253   0.062  -0.235  -0.577
67    L         0.803   0.824   0.862   1.091   1.102   1.129   0.828   0.858   0.914
68    K         0.044  -0.167  -0.371  -0.170  -0.455  -0.729   0.062  -0.246  -0.598
69    H        -1.697  -1.914  -1.710  -1.477  -1.820  -1.592  -1.568  -1.771  -1.497
70    V         0.803   0.824   0.862   1.120   1.136   1.152   0.828   0.858   0.914
71    S        -2.301  -2.119  -2.113  -2.048  -1.782  -1.779  -1.951  -1.787  -1.651
72    R         0.803   0.824   0.862   0.537   0.586   0.679   0.828   0.858   0.914
73    R        -1.362  -1.393  -1.176  -1.841  -2.002  -1.601  -1.472  -1.531  -1.228
74    F         0.803   0.824   0.862   1.025   1.049   1.076   0.828   0.858   0.914
75    K         0.044  -0.160  -0.358  -0.192  -0.482  -0.781   0.062  -0.235  -0.577
76    N         0.803   0.824   0.862   1.033   1.062   1.082   0.828   0.858   0.914
77    G         0.803   0.824   0.862   0.648   0.688   0.769   0.828   0.858   0.914
78    F         0.803   0.824   0.862   1.025   1.049   1.076   0.828   0.858   0.914
79    Q        -0.420  -0.362  -0.392  -0.266  -0.197  -0.394  -0.627  -0.551  -0.634
80    T        -1.317  -1.223  -1.164  -1.570  -1.432  -1.318  -1.476  -1.349  -1.215
81    G         0.803   0.824   0.862   0.650   0.691   0.771   0.828   0.858   0.914
82    S        -2.447  -2.147  -2.126  -2.160  -1.774  -1.779  -2.083  -1.810  -1.661
83    A        -1.235  -1.353  -1.169  -1.179  -1.319  -1.094  -1.376  -1.493  -1.220
84    S        -2.301  -2.150  -2.118  -2.451  -2.208  -2.114  -1.951  -1.785  -1.655
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    K        -1.505  -1.462  -1.186  -1.763  -1.681  -1.232  -1.663  -1.607  -1.239
90    A        -1.235  -1.279  -1.167  -1.108  -1.113  -0.938  -1.376  -1.385  -1.217
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    S        -0.684  -0.840  -1.131  -0.569  -0.779  -1.253  -0.609  -0.823  -1.172
94    A         0.044  -0.160  -0.358   0.200  -0.005  -0.260   0.062  -0.235  -0.577
* 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/P49166
Output conservation file - output/P49166
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
