1     M         1.633   1.649   1.699   1.902   1.923   2.005   1.801   1.820   1.894
2     T         1.633   1.649   1.699   1.608   1.627   1.716   1.801   1.820   1.894
3     E        -0.317  -0.361  -0.408  -0.206  -0.293  -0.380  -0.365  -0.423  -0.481
4     E        -1.670  -1.640  -1.564  -1.657  -1.606  -1.488  -1.293  -1.253  -1.148
5     T        -0.501  -0.431  -0.482  -0.265  -0.140  -0.256  -0.616  -0.516  -0.580
6     I        -1.101  -1.048  -1.040  -1.001  -0.900  -0.898  -0.983  -0.916  -0.884
7     T         1.633   1.649   1.699   1.608   1.627   1.716   1.801   1.820   1.894
8     I        -0.532  -0.486  -0.495  -0.583  -0.480  -0.514  -0.674  -0.609  -0.601
9     D        -0.532  -0.566  -0.488  -0.583  -0.614  -0.503  -0.674  -0.702  -0.592
10    S         0.606   0.514   0.455   0.396   0.247   0.173   0.563   0.407   0.288
11    I        -0.532  -0.476  -0.494  -0.575  -0.490  -0.515  -0.674  -0.598  -0.600
12    S        -0.501  -0.376  -0.450  -0.630  -0.394  -0.562  -0.616  -0.440  -0.537
13    N         0.479   0.560   0.431   0.512   0.643   0.419   0.351   0.485   0.245
14    G         0.210   0.243   0.304  -0.131  -0.112   0.007  -0.133  -0.076   0.014
15    I         1.633   1.649   1.699   1.579   1.592   1.687   1.801   1.820   1.894
16    L        -0.501  -0.533  -0.494  -0.394  -0.400  -0.392  -0.616  -0.660  -0.596
17    N         0.479   0.544   0.427   0.416   0.491   0.333   0.351   0.458   0.238
18    N         0.252   0.232   0.297   0.083   0.040   0.155  -0.055  -0.096   0.000
19    L        -0.317  -0.316  -0.388  -0.272  -0.248  -0.356  -0.365  -0.360  -0.453
20    L        -0.317  -0.318  -0.404  -0.297  -0.300  -0.413  -0.365  -0.368  -0.475
21    T        -0.317  -0.421  -0.451  -0.283  -0.447  -0.494  -0.365  -0.502  -0.539
22    T        -0.532  -0.476  -0.494  -0.846  -0.751  -0.761  -0.674  -0.598  -0.600
23    L        -0.317  -0.184  -0.369  -0.235  -0.039  -0.301  -0.365  -0.178  -0.428
24    I         0.606   0.572   0.475   0.606   0.558   0.397   0.563   0.504   0.323
25    Q        -1.101  -1.114  -1.082  -0.992  -1.011  -0.955  -0.983  -0.990  -0.928
26    D        -0.532  -0.461  -0.494  -0.678  -0.540  -0.632  -0.674  -0.584  -0.600
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    I         0.252   0.232   0.297  -0.104  -0.178  -0.062  -0.055  -0.096   0.000
32    V        -0.317  -0.361  -0.408  -0.125  -0.188  -0.303  -0.365  -0.423  -0.481
33    A        -0.317  -0.342  -0.402  -0.484  -0.536  -0.589  -0.365  -0.399  -0.473
34    R        -0.317  -0.318  -0.404  -0.361  -0.365  -0.493  -0.365  -0.368  -0.475
35    E        -1.101  -1.139  -1.085  -0.932  -0.976  -0.915  -0.983  -1.015  -0.931
36    T        -0.317  -0.421  -0.451  -0.320  -0.486  -0.549  -0.365  -0.502  -0.539
37    T        -1.670  -1.640  -1.564  -1.545  -1.504  -1.378  -1.293  -1.253  -1.148
38    Q        -1.670  -1.640  -1.564  -1.545  -1.448  -1.378  -1.293  -1.253  -1.148
39    Q        -1.670  -1.640  -1.564  -1.695  -1.672  -1.525  -1.293  -1.253  -1.148
40    Q        -0.532  -0.476  -0.494  -0.802  -0.748  -0.724  -0.674  -0.598  -0.600
41    L         0.606   0.572   0.475   0.563   0.522   0.364   0.563   0.504   0.323
42    L         1.633   1.649   1.699   1.550   1.578   1.659   1.801   1.820   1.894
43    K        -1.101  -1.114  -1.082  -1.068  -1.092  -1.044  -0.983  -0.990  -0.928
44    T        -1.101  -1.065  -1.048  -1.286  -1.224  -1.185  -0.983  -0.935  -0.893
45    R        -1.101  -1.139  -1.085  -1.260  -1.337  -1.242  -0.983  -1.015  -0.931
46    Y        -0.501  -0.541  -0.498  -0.377  -0.480  -0.378  -0.616  -0.670  -0.601
47    P         0.327   0.350   0.329   0.439   0.481   0.415   0.082   0.121   0.059
48    D        -0.532  -0.539  -0.482  -0.741  -0.752  -0.650  -0.674  -0.672  -0.584
49    L        -1.670  -1.640  -1.564  -1.510  -1.468  -1.343  -1.293  -1.253  -1.148
50    R        -0.317  -0.342  -0.402  -0.290  -0.340  -0.443  -0.365  -0.399  -0.473
51    S        -1.101  -1.076  -1.056  -1.167  -1.141  -1.065  -0.983  -0.949  -0.901
52    Y        -0.317  -0.421  -0.451  -0.171  -0.339  -0.415  -0.365  -0.502  -0.539
53    Y        -1.101  -1.114  -1.082  -0.793  -0.815  -0.752  -0.983  -0.990  -0.928
54    F        -1.670  -1.640  -1.564  -1.378  -1.345  -1.214  -1.293  -1.253  -1.148
55    D         0.606   0.514   0.455   0.703   0.565   0.464   0.563   0.407   0.288
56    P        -0.317  -0.421  -0.451   0.009  -0.145  -0.227  -0.365  -0.502  -0.539
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    N        -0.532  -0.562  -0.485  -0.793  -0.840  -0.699  -0.674  -0.697  -0.588
60    G         0.252   0.296   0.330  -0.107  -0.046   0.027  -0.055   0.022   0.060
61    S        -1.101  -1.076  -1.056  -1.297  -1.267  -1.206  -0.983  -0.949  -0.901
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    L        -0.317  -0.421  -0.451  -0.308  -0.451  -0.498  -0.365  -0.502  -0.539
76    D         0.606   0.514   0.455   0.703   0.565   0.464   0.563   0.407   0.288
77    I         0.606   0.514   0.455   0.566   0.409   0.294   0.563   0.407   0.288
78    N        -1.101  -1.129  -1.082  -0.855  -0.899  -0.848  -0.983  -1.004  -0.928
79    G         0.606   0.514   0.455   0.723   0.590   0.480   0.563   0.407   0.288
80    L        -1.101  -0.987  -1.070  -1.088  -0.880  -1.047  -0.983  -0.847  -0.916
81    Q        -1.101  -0.987  -1.070  -0.868  -0.685  -0.807  -0.983  -0.847  -0.916
82    K         1.633   1.649   1.699   1.654   1.660   1.762   1.801   1.820   1.894
83    Q         0.606   0.514   0.455   0.612   0.473   0.338   0.563   0.407   0.288
84    Q        -0.532  -0.486  -0.495  -0.575  -0.496  -0.495  -0.674  -0.609  -0.601
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    E         0.252   0.307   0.333   0.190   0.301   0.322  -0.055   0.043   0.066
90    S         0.252   0.232   0.297  -0.171  -0.207  -0.082  -0.055  -0.096   0.000
91    S         0.606   0.654   0.486   0.433   0.489   0.280   0.563   0.639   0.343
92    Q        -1.101  -1.139  -1.085  -1.006  -1.058  -0.977  -0.983  -1.015  -0.931
93    Y         1.633   1.649   1.699   1.757   1.789   1.862   1.801   1.820   1.894
94    I         0.252   0.296   0.330   0.251   0.338   0.374  -0.055   0.022   0.060
95    H        -1.670  -1.640  -1.564  -1.395  -1.345  -1.231  -1.293  -1.253  -1.148
96    C         1.633   1.649   1.699   1.824   1.846   1.929   1.801   1.820   1.894
97    E        -0.317  -0.361  -0.408  -0.196  -0.267  -0.365  -0.365  -0.423  -0.481
98    N         0.606   0.654   0.486   0.686   0.743   0.531   0.563   0.639   0.343
99    C         1.633   1.649   1.699   1.824   1.846   1.929   1.801   1.820   1.894
100   G         1.633   1.649   1.699   1.712   1.738   1.818   1.801   1.820   1.894
101   R         1.633   1.649   1.699   1.538   1.568   1.647   1.801   1.820   1.894
102   D        -1.101  -1.129  -1.082  -1.063  -1.134  -1.063  -0.983  -1.004  -0.928
103   V         0.252   0.232   0.297   0.213   0.165   0.257  -0.055  -0.096   0.000
104   S         0.252   0.232   0.297  -0.086  -0.104   0.016  -0.055  -0.096   0.000
105   A         0.606   0.678   0.495   0.757   0.866   0.599   0.563   0.677   0.358
106   N         0.252   0.232   0.297   0.096   0.057   0.171  -0.055  -0.096   0.000
107   R         1.633   1.649   1.699   1.538   1.568   1.647   1.801   1.820   1.894
108   L         0.606   0.678   0.495   0.864   0.971   0.676   0.563   0.677   0.358
109   A         1.633   1.649   1.699   1.746   1.772   1.851   1.801   1.820   1.894
110   A        -0.317  -0.421  -0.451  -0.235  -0.415  -0.505  -0.365  -0.502  -0.539
111   H         1.633   1.649   1.699   1.858   1.886   1.961   1.801   1.820   1.894
112   L        -0.317  -0.421  -0.451  -0.272  -0.411  -0.445  -0.365  -0.502  -0.539
113   Q        -1.101  -1.139  -1.085  -1.088  -1.164  -1.073  -0.983  -1.015  -0.931
114   R         0.252   0.232   0.297  -0.008  -0.041   0.069  -0.055  -0.096   0.000
115   C         1.633   1.649   1.699   1.824   1.846   1.929   1.801   1.820   1.894
116   L         1.633   1.649   1.699   1.550   1.578   1.659   1.801   1.820   1.894
117   S        -0.532  -0.461  -0.494  -0.750  -0.612  -0.667  -0.674  -0.584  -0.600
118   R         1.633   1.649   1.699   1.538   1.568   1.647   1.801   1.820   1.894
119   G        -0.317  -0.421  -0.451  -0.221  -0.385  -0.463  -0.365  -0.502  -0.539
120   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   R         1.633   1.649   1.699   1.538   1.568   1.647   1.801   1.820   1.894
122   R         0.252   0.232   0.297  -0.008  -0.041   0.069  -0.055  -0.096   0.000
* 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/Q03067
Output conservation file - output/Q03067
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
