1     M         1.011   1.015   1.027   1.336   1.338   1.350   1.046   1.049   1.063
2     S         1.011   1.015   1.027   0.982   0.987   1.008   1.046   1.049   1.063
3     N         1.011   1.015   1.027   1.019   1.023   1.044   1.046   1.049   1.063
4     P         1.011   1.015   1.027   1.144   1.148   1.165   1.046   1.049   1.063
5     F         1.011   1.015   1.027   1.144   1.145   1.165   1.046   1.049   1.063
6     Q        -0.492  -0.441  -0.534  -0.373  -0.274  -0.486  -0.604  -0.524  -0.660
7     N         1.011   1.015   1.027   1.019   1.023   1.044   1.046   1.049   1.063
8     I         1.011   1.015   1.027   1.091   1.097   1.113   1.046   1.049   1.063
9     G         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
10    K        -0.492  -0.544  -0.554  -0.772  -0.855  -0.855  -0.604  -0.679  -0.689
11    N         1.011   1.015   1.027   1.019   1.023   1.044   1.046   1.049   1.063
12    L        -0.492  -0.544  -0.554  -0.488  -0.565  -0.568  -0.604  -0.679  -0.689
13    L        -0.492  -0.544  -0.554  -0.555  -0.639  -0.654  -0.604  -0.679  -0.689
14    Y         1.011   1.015   1.027   1.180   1.184   1.199   1.046   1.049   1.063
15    I        -0.492  -0.544  -0.554  -0.463  -0.553  -0.577  -0.604  -0.679  -0.689
16    S        -0.492  -0.544  -0.554  -0.381  -0.446  -0.432  -0.604  -0.679  -0.689
17    A        -1.584  -1.569  -1.521  -1.574  -1.537  -1.460  -1.428  -1.405  -1.328
18    A        -1.584  -1.569  -1.521  -1.631  -1.605  -1.515  -1.428  -1.405  -1.328
19    G        -0.492  -0.544  -0.554  -0.597  -0.682  -0.695  -0.604  -0.679  -0.689
20    I        -1.584  -1.569  -1.521  -1.376  -1.337  -1.269  -1.428  -1.405  -1.328
21    A        -0.492  -0.441  -0.534  -0.546  -0.458  -0.616  -0.604  -0.524  -0.660
22    S         1.011   1.015   1.027   0.982   0.987   1.008   1.046   1.049   1.063
23    I        -0.492  -0.441  -0.534  -0.463  -0.373  -0.540  -0.604  -0.524  -0.660
24    Y        -0.492  -0.464  -0.539  -0.455  -0.406  -0.512  -0.604  -0.558  -0.666
25    V        -0.492  -0.464  -0.539  -0.455  -0.403  -0.538  -0.604  -0.558  -0.666
26    V         1.011   1.015   1.027   1.000   1.011   1.026   1.046   1.049   1.063
27    K         1.011   1.015   1.027   0.777   0.784   0.810   1.046   1.049   1.063
28    T        -0.492  -0.441  -0.534  -0.301  -0.219  -0.394  -0.604  -0.524  -0.660
29    I        -0.492  -0.544  -0.554  -0.455  -0.542  -0.567  -0.604  -0.679  -0.689
30    V         1.011   1.015   1.027   1.000   1.011   1.026   1.046   1.049   1.063
31    K        -0.492  -0.464  -0.539  -0.693  -0.638  -0.786  -0.604  -0.558  -0.666
32    A        -0.492  -0.544  -0.554  -0.538  -0.624  -0.640  -0.604  -0.679  -0.689
33    R        -0.492  -0.544  -0.554  -0.589  -0.673  -0.684  -0.604  -0.679  -0.689
34    R        -0.492  -0.544  -0.554  -0.693  -0.792  -0.818  -0.604  -0.679  -0.689
35    D        -0.492  -0.544  -0.554  -0.538  -0.622  -0.640  -0.604  -0.679  -0.689
36    A        -0.492  -0.544  -0.554  -0.546  -0.635  -0.650  -0.604  -0.679  -0.689
37    K         1.011   1.015   1.027   0.777   0.784   0.810   1.046   1.049   1.063
38    F         1.011   1.015   1.027   1.144   1.145   1.165   1.046   1.049   1.063
39    I        -1.584  -1.569  -1.521  -1.678  -1.641  -1.561  -1.428  -1.405  -1.328
40    P         1.011   1.015   1.027   1.144   1.148   1.165   1.046   1.049   1.063
41    K        -1.584  -1.569  -1.521  -1.323  -1.290  -1.217  -1.428  -1.405  -1.328
42    A        -0.492  -0.544  -0.554  -0.530  -0.616  -0.629  -0.604  -0.679  -0.689
43    R        -0.492  -0.464  -0.539  -0.580  -0.528  -0.660  -0.604  -0.558  -0.666
44    G        -1.584  -1.569  -1.521  -1.643  -1.614  -1.527  -1.428  -1.405  -1.328
45    N        -0.492  -0.464  -0.539  -0.580  -0.533  -0.648  -0.604  -0.558  -0.666
46    N        -0.492  -0.464  -0.539  -0.530  -0.481  -0.603  -0.604  -0.558  -0.666
47    G        -0.492  -0.464  -0.539  -0.463  -0.421  -0.554  -0.604  -0.558  -0.666
48    E        -1.584  -1.569  -1.521  -1.666  -1.664  -1.549  -1.428  -1.405  -1.328
49    V        -1.584  -1.569  -1.521  -1.750  -1.736  -1.630  -1.428  -1.405  -1.328
50    N        -1.584  -1.569  -1.521  -1.597  -1.571  -1.482  -1.428  -1.405  -1.328
51    E        -0.492  -0.464  -0.539  -0.488  -0.445  -0.552  -0.604  -0.558  -0.666
52    K        -1.584  -1.569  -1.521  -1.551  -1.533  -1.438  -1.428  -1.405  -1.328
53    N        -1.584  -1.569  -1.521  -1.597  -1.573  -1.482  -1.428  -1.405  -1.328
54    Y         1.011   1.015   1.027   1.180   1.184   1.199   1.046   1.049   1.063
55    Y         1.011   1.015   1.027   1.180   1.184   1.199   1.046   1.049   1.063
56    D        -0.492  -0.544  -0.554  -0.538  -0.624  -0.640  -0.604  -0.679  -0.689
57    N         1.011   1.015   1.027   1.019   1.023   1.044   1.046   1.049   1.063
58    L        -0.492  -0.544  -0.554  -0.488  -0.563  -0.568  -0.604  -0.679  -0.689
59    A         1.011   1.015   1.027   1.000   1.007   1.026   1.046   1.049   1.063
60    Q        -0.492  -0.544  -0.554  -0.285  -0.383  -0.421  -0.604  -0.679  -0.689
61    V         1.011   1.015   1.027   1.000   1.011   1.026   1.046   1.049   1.063
62    K         1.011   1.015   1.027   0.777   0.784   0.810   1.046   1.049   1.063
63    P         1.011   1.015   1.027   1.144   1.148   1.165   1.046   1.049   1.063
64    G         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
65    F         1.011   1.015   1.027   1.144   1.145   1.165   1.046   1.049   1.063
66    P         1.011   1.015   1.027   1.144   1.148   1.165   1.046   1.049   1.063
67    I        -1.584  -1.569  -1.521  -1.344  -1.297  -1.238  -1.428  -1.405  -1.328
68    P        -0.492  -0.544  -0.554  -0.504  -0.612  -0.652  -0.604  -0.679  -0.689
69    K         1.011   1.015   1.027   0.777   0.784   0.810   1.046   1.049   1.063
70    D        -1.584  -1.569  -1.521  -1.666  -1.626  -1.549  -1.428  -1.405  -1.328
71    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    I        -0.626  -0.621  -0.580  -0.725  -0.715  -0.640  -0.810  -0.798  -0.730
76    D         1.011   1.015   1.027   0.956   0.962   0.983   1.046   1.049   1.063
77    C        -0.626  -0.621  -0.580  -0.631  -0.622  -0.550  -0.810  -0.798  -0.730
78    S        -1.584  -1.569  -1.521  -1.540  -1.512  -1.427  -1.428  -1.405  -1.328
79    E         1.011   1.015   1.027   1.109   1.105   1.131   1.046   1.049   1.063
80    D        -1.584  -1.569  -1.521  -1.365  -1.337  -1.258  -1.428  -1.405  -1.328
81    H        -1.584  -1.569  -1.521  -1.129  -1.110  -1.031  -1.428  -1.405  -1.328
82    Q        -1.584  -1.569  -1.521  -1.365  -1.346  -1.258  -1.428  -1.405  -1.328
83    L        -0.492  -0.464  -0.539  -0.463  -0.411  -0.549  -0.604  -0.558  -0.666
84    V        -0.492  -0.544  -0.554  -0.640  -0.738  -0.772  -0.604  -0.679  -0.689
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    R         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
91    K         1.011   1.015   1.027   0.777   0.784   0.810   1.046   1.049   1.063
92    S         1.011   1.015   1.027   0.982   0.987   1.008   1.046   1.049   1.063
93    K        -0.492  -0.544  -0.554  -0.693  -0.769  -0.753  -0.604  -0.679  -0.689
94    Y        -0.492  -0.544  -0.554  -0.309  -0.396  -0.412  -0.604  -0.679  -0.689
95    E         1.011   1.015   1.027   1.109   1.105   1.131   1.046   1.049   1.063
96    G        -0.492  -0.441  -0.534  -0.589  -0.503  -0.651  -0.604  -0.524  -0.660
97    S        -1.584  -1.569  -1.521  -1.643  -1.613  -1.527  -1.428  -1.405  -1.328
98    G         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
99    L        -0.492  -0.441  -0.534  -0.555  -0.465  -0.621  -0.604  -0.524  -0.660
100   S         1.011   1.015   1.027   0.982   0.987   1.008   1.046   1.049   1.063
101   A        -0.492  -0.544  -0.554  -0.455  -0.530  -0.533  -0.604  -0.679  -0.689
102   V        -0.492  -0.544  -0.554  -0.530  -0.612  -0.629  -0.604  -0.679  -0.689
103   T         1.011   1.015   1.027   1.267   1.263   1.284   1.046   1.049   1.063
104   R         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
105   K         1.011   1.015   1.027   0.777   0.784   0.810   1.046   1.049   1.063
106   R         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
107   G         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
108   D         1.011   1.015   1.027   1.000   1.007   1.026   1.046   1.049   1.063
109   K        -0.492  -0.464  -0.539  -0.693  -0.638  -0.786  -0.604  -0.558  -0.666
110   L         1.011   1.015   1.027   0.982   0.990   1.008   1.046   1.049   1.063
111   G         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
112   F         1.011   1.015   1.027   1.144   1.145   1.165   1.046   1.049   1.063
113   L         1.011   1.015   1.027   0.982   0.990   1.008   1.046   1.049   1.063
114   D         1.011   1.015   1.027   1.000   1.007   1.026   1.046   1.049   1.063
115   R         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
116   R         1.011   1.015   1.027   0.946   0.952   0.973   1.046   1.049   1.063
117   R        -1.584  -1.569  -1.521  -1.631  -1.607  -1.515  -1.428  -1.405  -1.328
118   N         1.011   1.015   1.027   1.019   1.023   1.044   1.046   1.049   1.063
119   E        -0.492  -0.441  -0.534  -0.438  -0.359  -0.515  -0.604  -0.524  -0.660
* 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/Q3E6R5
Output conservation file - output/Q3E6R5
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
