1     M         0.865   0.867   0.884   1.072   1.071   1.086   0.897   0.901   0.924
2     S         0.865   0.867   0.884   0.669   0.673   0.722   0.897   0.901   0.924
3     A         0.865   0.867   0.884   0.736   0.743   0.782   0.897   0.901   0.924
4     L         0.865   0.867   0.884   0.429   0.433   0.505   0.897   0.901   0.924
5     F         0.865   0.867   0.884   0.834   0.845   0.871   0.897   0.901   0.924
6     N         0.865   0.867   0.884   1.072   1.076   1.086   0.897   0.901   0.924
7     F         0.865   0.867   0.884   0.834   0.845   0.871   0.897   0.901   0.924
8     R        -1.241  -1.202  -1.354  -0.796  -0.752  -0.997  -1.167  -1.126  -1.288
9     S         0.865   0.867   0.884   0.669   0.673   0.722   0.897   0.901   0.924
10    L         0.865   0.867   0.884   0.429   0.433   0.505   0.897   0.901   0.924
11    L         0.865   0.867   0.884   0.429   0.433   0.505   0.897   0.901   0.924
12    Q        -0.244  -0.303  -0.492  -0.028  -0.128  -0.561  -0.282  -0.370  -0.670
13    V         0.865   0.867   0.884   0.915   0.918   0.943   0.897   0.901   0.924
14    I         0.865   0.867   0.884   0.802   0.809   0.841   0.897   0.901   0.924
15    L         0.865   0.867   0.884   0.429   0.433   0.505   0.897   0.901   0.924
16    L         0.865   0.867   0.884   0.429   0.433   0.505   0.897   0.901   0.924
17    L        -0.627  -0.608  -0.543  -1.155  -1.125  -0.962  -0.872  -0.845  -0.752
18    I         0.865   0.867   0.884   0.802   0.809   0.841   0.897   0.901   0.924
19    C         0.865   0.867   0.884   1.026   1.029   1.043   0.897   0.901   0.924
20    S        -0.627  -0.609  -0.542  -0.685  -0.654  -0.589  -0.872  -0.847  -0.750
21    C        -0.244  -0.303  -0.492  -0.035  -0.129  -0.501  -0.282  -0.370  -0.670
22    S        -0.627  -0.647  -0.549  -0.685  -0.754  -0.619  -0.872  -0.909  -0.762
23    Y         0.865   0.867   0.884   1.072   1.075   1.086   0.897   0.901   0.924
24    V        -0.627  -0.564  -0.536  -0.749  -0.634  -0.615  -0.872  -0.774  -0.741
25    H         0.865   0.867   0.884   1.165   1.165   1.169   0.897   0.901   0.924
26    G        -1.241  -1.271  -1.346  -1.240  -1.279  -1.397  -1.167  -1.205  -1.278
27    Q        -0.627  -0.609  -0.542  -0.455  -0.428  -0.348  -0.872  -0.847  -0.750
28    W        -2.087  -2.039  -1.960  -1.705  -1.646  -1.591  -1.757  -1.711  -1.587
29    P         0.865   0.867   0.884   1.088   1.089   1.100   0.897   0.901   0.924
30    S        -1.473  -1.430  -1.374  -1.705  -1.648  -1.502  -1.462  -1.416  -1.311
31    L        -0.627  -0.609  -0.542  -1.063  -1.030  -0.936  -0.872  -0.847  -0.750
32    L        -0.244  -0.303  -0.492  -0.524  -0.600  -0.773  -0.282  -0.370  -0.670
33    D         0.865   0.867   0.884   1.180   1.182   1.183   0.897   0.901   0.924
34    R        -1.241  -1.177  -1.348  -0.857  -0.774  -1.015  -1.167  -1.091  -1.281
35    Y        -1.473  -1.448  -1.376  -1.155  -1.124  -1.032  -1.462  -1.434  -1.313
36    K         0.865   0.867   0.884   1.057   1.061   1.072   0.897   0.901   0.924
37    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    H        -1.473  -1.485  -1.373  -1.365  -1.353  -1.178  -1.462  -1.470  -1.309
39    E        -0.244  -0.306  -0.490   0.064  -0.017  -0.282  -0.282  -0.375  -0.666
40    V        -2.087  -2.106  -1.968  -1.919  -1.934  -1.738  -1.757  -1.773  -1.594
41    L         0.865   0.867   0.884   0.429   0.433   0.505   0.897   0.901   0.924
42    G        -0.244  -0.222  -0.485  -0.051  -0.020  -0.500  -0.282  -0.252  -0.659
43    A        -1.241  -1.331  -1.354  -1.114  -1.268  -1.353  -1.167  -1.277  -1.288
44    F         0.865   0.867   0.884   0.834   0.845   0.871   0.897   0.901   0.924
45    W         0.865   0.867   0.884   1.149   1.151   1.155   0.897   0.901   0.924
46    K         0.865   0.867   0.884   1.057   1.061   1.072   0.897   0.901   0.924
47    M        -1.241  -1.331  -1.354  -1.104  -1.236  -1.277  -1.167  -1.277  -1.288
48    A         0.865   0.867   0.884   0.736   0.743   0.782   0.897   0.901   0.924
49    R         0.865   0.867   0.884   0.994   0.998   1.015   0.897   0.901   0.924
50    V        -0.244  -0.306  -0.490  -0.198  -0.282  -0.558  -0.282  -0.375  -0.666
51    G         0.865   0.867   0.884   1.010   1.014   1.029   0.897   0.901   0.924
52    E         0.865   0.867   0.884   1.149   1.148   1.155   0.897   0.901   0.924
53    R         0.865   0.867   0.884   0.994   0.998   1.015   0.897   0.901   0.924
54    A        -0.627  -0.609  -0.542  -1.218  -1.191  -1.027  -0.872  -0.847  -0.750
55    S         0.865   0.867   0.884   0.669   0.673   0.722   0.897   0.901   0.924
56    P         0.865   0.867   0.884   1.088   1.089   1.100   0.897   0.901   0.924
57    Y         0.865   0.867   0.884   1.072   1.075   1.086   0.897   0.901   0.924
58    V         0.865   0.867   0.884   0.915   0.918   0.943   0.897   0.901   0.924
59    S        -0.627  -0.596  -0.536  -1.003  -0.950  -0.838  -0.872  -0.825  -0.741
60    L        -0.244  -0.188  -0.481  -0.599  -0.524  -0.905  -0.282  -0.204  -0.652
61    A        -1.473  -1.486  -1.381  -1.415  -1.429  -1.250  -1.462  -1.471  -1.318
62    C         0.865   0.867   0.884   1.026   1.029   1.043   0.897   0.901   0.924
63    I        -0.627  -0.596  -0.536  -0.829  -0.772  -0.680  -0.872  -0.825  -0.741
64    L        -1.241  -1.271  -1.346  -1.387  -1.455  -1.621  -1.167  -1.205  -1.278
65    M         0.865   0.867   0.884   1.072   1.071   1.086   0.897   0.901   0.924
66    A         0.865   0.867   0.884   0.736   0.743   0.782   0.897   0.901   0.924
67    I        -1.473  -1.488  -1.375  -1.495  -1.515  -1.346  -1.462  -1.473  -1.312
68    S        -0.627  -0.596  -0.536  -0.800  -0.760  -0.633  -0.872  -0.825  -0.741
69    Q        -2.087  -2.068  -1.976  -1.571  -1.546  -1.453  -1.757  -1.737  -1.601
70    F        -0.627  -0.609  -0.542  -1.155  -1.127  -0.961  -0.872  -0.847  -0.750
71    N        -2.087  -2.068  -1.976  -1.807  -1.793  -1.719  -1.757  -1.737  -1.601
72    S        -0.244  -0.303  -0.492  -0.267  -0.341  -0.545  -0.282  -0.370  -0.670
* 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/Q8TGJ3
Output conservation file - output/Q8TGJ3
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
