1     M         1.199   1.200   1.235   1.477   1.496   1.522   1.259   1.260   1.304
2     S         0.063   0.036  -0.061   0.067  -0.007  -0.123  -0.047  -0.089  -0.248
3     -        -0.087  -0.058  -0.099  -0.231  -0.186  -0.255  -0.288  -0.241  -0.311
4     -        -1.021  -1.008  -0.946  -1.012  -1.010  -0.887  -1.062  -1.045  -0.945
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.021  -1.008  -0.946  -0.938  -0.932  -0.815  -1.062  -1.045  -0.945
11    N        -1.602  -1.584  -1.517  -1.499  -1.486  -1.358  -1.352  -1.331  -1.226
12    P         0.063   0.103  -0.050   0.297   0.342   0.128  -0.047   0.015  -0.230
13    C         1.199   1.200   1.235   1.076   1.048   1.134   1.259   1.260   1.304
14    Q        -0.902  -0.942  -0.918  -1.003  -1.038  -0.957  -0.917  -0.965  -0.913
15    K        -0.902  -0.942  -0.918  -0.874  -0.975  -0.940  -0.917  -0.965  -0.913
16    E        -0.902  -0.891  -0.911  -0.840  -0.819  -0.843  -0.917  -0.903  -0.904
17    A         1.199   1.200   1.235   1.304   1.308   1.355   1.259   1.260   1.304
18    C         1.199   1.200   1.235   1.076   1.048   1.134   1.259   1.260   1.304
19    A         0.063   0.036  -0.061   0.217   0.184   0.027  -0.047  -0.089  -0.248
20    I         1.199   1.200   1.235   1.384   1.382   1.432   1.259   1.260   1.304
21    Q         1.199   1.200   1.235   1.256   1.244   1.309   1.259   1.260   1.304
22    D         0.063   0.103  -0.050   0.109   0.151  -0.061  -0.047   0.015  -0.230
23    C         1.199   1.200   1.235   1.076   1.048   1.134   1.259   1.260   1.304
24    L         1.199   1.200   1.235   1.059   1.101   1.118   1.259   1.260   1.304
25    L        -0.902  -0.903  -0.904  -0.952  -0.964  -0.969  -0.917  -0.918  -0.895
26    S        -1.602  -1.584  -1.517  -1.656  -1.622  -1.510  -1.352  -1.331  -1.226
27    H        -0.902  -0.942  -0.918  -0.691  -0.780  -0.710  -0.917  -0.965  -0.913
28    Q        -0.902  -0.888  -0.904  -0.685  -0.669  -0.700  -0.917  -0.900  -0.896
29    Y         1.199   1.200   1.235   1.352   1.346   1.401   1.259   1.260   1.304
30    D         0.063   0.016  -0.056   0.191   0.099  -0.020  -0.047  -0.121  -0.240
31    D         0.063   0.016  -0.056   0.083   0.030  -0.119  -0.047  -0.121  -0.240
32    A         0.063   0.016  -0.056   0.067  -0.038  -0.114  -0.047  -0.121  -0.240
33    K         0.063   0.103  -0.050  -0.151  -0.054  -0.286  -0.047   0.015  -0.230
34    C         1.199   1.200   1.235   1.076   1.048   1.134   1.259   1.260   1.304
35    A        -0.902  -0.888  -0.904  -0.705  -0.691  -0.730  -0.917  -0.900  -0.896
36    K         1.199   1.200   1.235   0.923   0.962   0.986   1.259   1.260   1.304
37    V        -1.602  -1.584  -1.517  -1.508  -1.465  -1.367  -1.352  -1.331  -1.226
38    I         1.199   1.200   1.235   1.384   1.382   1.432   1.259   1.260   1.304
39    D         1.199   1.200   1.235   1.208   1.203   1.262   1.259   1.260   1.304
40    Q        -1.602  -1.584  -1.517  -1.499  -1.495  -1.358  -1.352  -1.331  -1.226
41    L         1.199   1.200   1.235   1.059   1.101   1.118   1.259   1.260   1.304
42    Y         1.199   1.200   1.235   1.352   1.346   1.401   1.259   1.260   1.304
43    I        -1.602  -1.584  -1.517  -1.743  -1.652  -1.595  -1.352  -1.331  -1.226
44    C         1.199   1.200   1.235   1.076   1.048   1.134   1.259   1.260   1.304
45    C         1.199   1.200   1.235   1.076   1.048   1.134   1.259   1.260   1.304
46    S        -0.902  -0.942  -0.918  -1.161  -1.218  -1.144  -0.917  -0.965  -0.913
47    K         0.063   0.103  -0.050  -0.207  -0.108  -0.368  -0.047   0.015  -0.230
48    F         0.063   0.127  -0.039   0.386   0.492   0.211  -0.047   0.053  -0.212
49    Y         1.199   1.200   1.235   1.352   1.346   1.401   1.259   1.260   1.304
50    N        -0.902  -0.942  -0.918  -0.751  -0.790  -0.749  -0.917  -0.965  -0.913
51    D        -1.602  -1.584  -1.517  -1.685  -1.653  -1.538  -1.352  -1.331  -1.226
52    N        -0.902  -0.891  -0.911  -0.924  -0.929  -0.972  -0.917  -0.903  -0.904
53    G         1.199   1.200   1.235   1.415   1.449   1.462   1.259   1.260   1.304
54    K        -1.602  -1.584  -1.517  -1.685  -1.678  -1.538  -1.352  -1.331  -1.226
55    D         1.199   1.200   1.235   1.208   1.203   1.262   1.259   1.260   1.304
56    S        -0.902  -0.888  -0.904  -0.988  -0.975  -1.025  -0.917  -0.900  -0.896
57    R        -0.902  -0.830  -0.905  -0.778  -0.650  -0.802  -0.917  -0.826  -0.897
58    S         0.063   0.127  -0.039   0.114   0.175  -0.020  -0.047   0.053  -0.212
59    P        -0.902  -0.903  -0.904  -0.556  -0.551  -0.559  -0.917  -0.918  -0.895
60    C         0.063   0.036  -0.061  -0.073  -0.164  -0.275  -0.047  -0.089  -0.248
61    C         1.199   1.200   1.235   1.076   1.048   1.134   1.259   1.260   1.304
62    P         1.199   1.200   1.235   1.368   1.360   1.417   1.259   1.260   1.304
63    L         0.063   0.016  -0.056  -0.264  -0.301  -0.463  -0.047  -0.121  -0.240
64    P        -0.201  -0.189  -0.140  -0.077  -0.069   0.017  -0.482  -0.460  -0.381
65    S        -0.902  -0.903  -0.904  -0.960  -0.982  -0.997  -0.917  -0.918  -0.895
66    L         1.199   1.200   1.235   1.059   1.101   1.118   1.259   1.260   1.304
67    L         1.199   1.200   1.235   1.059   1.101   1.118   1.259   1.260   1.304
68    E        -0.902  -0.942  -0.918  -1.010  -1.090  -1.070  -0.917  -0.965  -0.913
69    L         1.199   1.200   1.235   1.059   1.101   1.118   1.259   1.260   1.304
70    K         1.199   1.200   1.235   0.923   0.962   0.986   1.259   1.260   1.304
71    M        -0.902  -0.942  -0.918  -0.867  -0.891  -0.838  -0.917  -0.965  -0.913
72    K         0.063   0.036  -0.061  -0.196  -0.214  -0.368  -0.047  -0.089  -0.248
73    Q         1.199   1.200   1.235   1.256   1.244   1.309   1.259   1.260   1.304
74    R         1.199   1.200   1.235   1.384   1.429   1.432   1.259   1.260   1.304
75    K        -0.902  -0.903  -0.904  -1.062  -1.060  -1.089  -0.917  -0.918  -0.895
76    L         0.063   0.036  -0.061  -0.089  -0.112  -0.290  -0.047  -0.089  -0.248
77    T        -0.902  -0.942  -0.918  -0.771  -0.816  -0.830  -0.917  -0.965  -0.913
78    P        -1.602  -1.584  -1.517  -1.665  -1.612  -1.519  -1.352  -1.331  -1.226
79    G        -0.902  -0.942  -0.918  -0.588  -0.630  -0.601  -0.917  -0.965  -0.913
80    D         1.199   1.200   1.235   1.208   1.203   1.262   1.259   1.260   1.304
81    S         0.063   0.016  -0.056   0.150   0.055  -0.063  -0.047  -0.121  -0.240
82    -        -1.021  -1.008  -0.946  -1.194  -1.160  -1.063  -1.062  -1.045  -0.945
83    -        -1.021  -1.008  -0.946  -0.889  -0.896  -0.768  -1.062  -1.045  -0.945
84    -        -0.087  -0.058  -0.099  -0.183  -0.141  -0.175  -0.288  -0.241  -0.311
85    -        -0.087  -0.058  -0.099  -0.212  -0.167  -0.232  -0.288  -0.241  -0.311
86    -        -1.021  -1.008  -0.946  -0.913  -0.887  -0.791  -1.062  -1.045  -0.945
87    -        -0.087  -0.115  -0.113   0.006  -0.051  -0.053  -0.288  -0.336  -0.335
88    -        -0.087  -0.065  -0.098  -0.391  -0.358  -0.376  -0.288  -0.253  -0.310
89    -        -0.087  -0.115  -0.113  -0.135  -0.202  -0.245  -0.288  -0.336  -0.335
* 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/Q3E7A9
Output conservation file - output/Q3E7A9
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
