1     M         0.651   0.678   0.724   0.927   0.921   0.945   0.663   0.696   0.757
2     T        -0.922  -1.109  -0.873  -0.857  -1.284  -1.004  -1.109  -1.408  -1.073
3     R         0.651   0.678   0.724   0.503   0.549   0.656   0.663   0.696   0.757
4     S        -2.050  -1.844  -1.785  -1.791  -1.529  -1.538  -2.075  -1.788  -1.659
5     S         0.651   0.678   0.724   0.670   0.700   0.770   0.663   0.696   0.757
6     V         0.651   0.678   0.724   0.366   0.433   0.563   0.663   0.696   0.757
7     L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
8     A        -0.128  -0.307  -0.830   0.116  -0.028  -0.751  -0.035  -0.244  -1.005
9     D         0.651   0.678   0.724   0.788   0.806   0.850   0.663   0.696   0.757
10    A        -0.591  -0.884  -0.846  -0.359  -0.714  -0.699  -0.626  -1.052  -1.030
11    L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
12    N        -0.891  -0.876  -1.768  -0.459  -0.432  -1.622  -0.679  -0.640  -1.640
13    A        -2.354  -2.220  -1.794  -2.454  -2.216  -1.648  -2.505  -2.209  -1.669
14    I         0.651   0.678   0.724   0.352   0.441   0.553   0.663   0.696   0.757
15    N        -1.760  -1.952  -1.797  -1.516  -1.892  -1.718  -1.699  -1.902  -1.672
16    N         0.651   0.678   0.724   0.693   0.728   0.786   0.663   0.696   0.757
17    A         0.651   0.678   0.724   0.675   0.734   0.773   0.663   0.696   0.757
18    E         0.651   0.678   0.724   0.757   0.782   0.829   0.663   0.696   0.757
19    K        -0.591  -0.884  -0.846  -0.647  -1.062  -1.041  -0.626  -1.052  -1.030
20    T        -2.050  -2.193  -1.800  -1.854  -2.162  -1.679  -2.075  -2.176  -1.675
21    G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
22    K        -0.591  -0.884  -0.846  -0.647  -1.062  -1.041  -0.626  -1.052  -1.030
23    R         0.651   0.678   0.724   0.503   0.549   0.656   0.663   0.696   0.757
24    Q         0.651   0.678   0.724   0.811   0.816   0.866   0.663   0.696   0.757
25    V         0.651   0.678   0.724   0.366   0.433   0.563   0.663   0.696   0.757
26    L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
27    L        -0.128   0.134  -0.820  -0.238   0.081  -1.076  -0.035   0.262  -0.990
28    R         0.651   0.678   0.724   0.503   0.549   0.656   0.663   0.696   0.757
29    P         0.651   0.678   0.724   0.945   0.937   0.957   0.663   0.696   0.757
30    S        -0.128  -0.160  -0.824   0.095   0.075  -0.823  -0.035  -0.064  -0.995
31    S         0.651   0.678   0.724   0.670   0.700   0.770   0.663   0.696   0.757
32    K         0.651   0.678   0.724   0.480   0.551   0.640   0.663   0.696   0.757
33    V         0.651   0.678   0.724   0.366   0.433   0.563   0.663   0.696   0.757
34    I         0.651   0.678   0.724   0.352   0.441   0.553   0.663   0.696   0.757
35    I        -0.922  -0.998  -0.872  -1.287  -1.415  -1.224  -1.109  -1.231  -1.071
36    K         0.651   0.678   0.724   0.480   0.551   0.640   0.663   0.696   0.757
37    F         0.651   0.678   0.724   0.811   0.824   0.866   0.663   0.696   0.757
38    L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
39    Q        -1.448  -1.157  -0.871  -1.620  -1.162  -0.785  -1.968  -1.487  -1.071
40    V         0.651   0.678   0.724   0.366   0.433   0.563   0.663   0.696   0.757
41    M         0.651   0.678   0.724   0.927   0.921   0.945   0.663   0.696   0.757
42    Q         0.651   0.678   0.724   0.811   0.816   0.866   0.663   0.696   0.757
43    K        -1.335  -0.849  -1.759  -1.204  -0.581  -1.713  -1.216  -0.610  -1.630
44    H         0.651   0.678   0.724   0.878   0.888   0.912   0.663   0.696   0.757
45    G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
46    Y         0.651   0.678   0.724   0.901   0.914   0.927   0.663   0.696   0.757
47    I         0.651   0.678   0.724   0.352   0.441   0.553   0.663   0.696   0.757
48    G        -1.335  -1.637  -1.786  -1.162  -1.531  -1.686  -1.216  -1.583  -1.660
49    E         0.651   0.678   0.724   0.757   0.782   0.829   0.663   0.696   0.757
50    F         0.651   0.678   0.724   0.811   0.824   0.866   0.663   0.696   0.757
51    E        -0.922  -1.075  -0.873  -0.775  -1.049  -0.813  -1.109  -1.354  -1.073
52    Y        -0.922  -1.109  -0.873  -0.642  -1.019  -0.757  -1.109  -1.408  -1.073
53    I        -0.922  -0.940  -0.869  -1.287  -1.310  -1.219  -1.109  -1.140  -1.067
54    D         0.651   0.678   0.724   0.788   0.806   0.850   0.663   0.696   0.757
55    D         0.651   0.678   0.724   0.788   0.806   0.850   0.663   0.696   0.757
56    H         0.651   0.678   0.724   0.878   0.888   0.912   0.663   0.696   0.757
57    R         0.651   0.678   0.724   0.503   0.549   0.656   0.663   0.696   0.757
58    S         0.651   0.678   0.724   0.670   0.700   0.770   0.663   0.696   0.757
59    G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
60    K         0.651   0.678   0.724   0.480   0.551   0.640   0.663   0.696   0.757
61    I         0.651   0.678   0.724   0.352   0.441   0.553   0.663   0.696   0.757
62    V         0.651   0.678   0.724   0.366   0.433   0.563   0.663   0.696   0.757
63    V        -0.591  -0.884  -0.846  -0.787  -1.217  -1.172  -0.626  -1.052  -1.030
64    Q        -0.128  -0.160  -0.824   0.243   0.195  -0.711  -0.035  -0.064  -0.995
65    L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
66    N         0.651   0.678   0.724   0.693   0.728   0.786   0.663   0.696   0.757
67    G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
68    R         0.651   0.678   0.724   0.503   0.549   0.656   0.663   0.696   0.757
69    L        -1.335  -1.758  -1.792  -1.207  -1.780  -1.760  -1.216  -1.700  -1.667
70    N         0.651   0.678   0.724   0.693   0.728   0.786   0.663   0.696   0.757
71    K         0.651   0.678   0.724   0.480   0.551   0.640   0.663   0.696   0.757
72    C         0.651   0.678   0.724   1.060   1.026   1.035   0.663   0.696   0.757
73    G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
74    V         0.651   0.678   0.724   0.366   0.433   0.563   0.663   0.696   0.757
75    I         0.651   0.678   0.724   0.352   0.441   0.553   0.663   0.696   0.757
76    S        -0.591  -0.168  -0.821  -0.405   0.076  -0.767  -0.626  -0.073  -0.992
77    P         0.651   0.678   0.724   0.945   0.937   0.957   0.663   0.696   0.757
78    R         0.651   0.678   0.724   0.503   0.549   0.656   0.663   0.696   0.757
79    F        -0.128  -0.307  -0.830   0.254   0.065  -0.666  -0.035  -0.244  -1.005
80    N         0.651   0.678   0.724   0.693   0.728   0.786   0.663   0.696   0.757
81    V         0.651   0.678   0.724   0.366   0.433   0.563   0.663   0.696   0.757
82    K        -0.128  -0.307  -0.830  -0.109  -0.258  -1.013  -0.035  -0.244  -1.005
83    I        -2.050  -1.823  -1.795  -2.365  -2.112  -1.999  -2.075  -1.846  -1.670
84    G        -3.987  -3.474  -2.982  -3.937  -3.234  -2.556  -3.364  -2.747  -2.170
85    D        -0.128  -0.307  -0.830   0.220   0.029  -0.734  -0.035  -0.244  -1.005
86    I        -2.968  -2.572  -2.459  -3.157  -2.503  -2.343  -2.773  -2.191  -1.980
87    E         0.651   0.678   0.724   0.757   0.782   0.829   0.663   0.696   0.757
88    K        -1.161  -0.635  -0.837  -1.518  -0.680  -1.025  -1.485  -0.684  -1.016
89    W         0.651   0.678   0.724   1.069   1.039   1.041   0.663   0.696   0.757
90    T        -1.864  -1.755  -1.785  -1.853  -1.866  -1.862  -1.968  -1.806  -1.659
91    A        -3.801  -3.518  -2.984  -3.498  -3.106  -2.478  -3.256  -2.769  -2.171
92    N        -1.335  -1.758  -1.792  -0.965  -1.538  -1.662  -1.216  -1.700  -1.667
93    L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
94    L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
95    P         0.651   0.678   0.724   0.945   0.937   0.957   0.663   0.696   0.757
96    A        -1.161  -1.154  -0.873  -1.268  -1.302  -0.908  -1.485  -1.482  -1.072
97    R         0.651   0.678   0.724   0.503   0.549   0.656   0.663   0.696   0.757
98    Q         0.651   0.678   0.724   0.811   0.816   0.866   0.663   0.696   0.757
99    F        -0.591  -0.884  -0.846  -0.337  -0.838  -0.906  -0.626  -1.052  -1.030
100   G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
101   Y        -0.591  -0.884  -0.846  -0.248  -0.752  -0.854  -0.626  -1.052  -1.030
102   V        -1.161  -1.154  -0.873  -1.687  -1.720  -1.226  -1.485  -1.482  -1.072
103   I        -0.591  -0.884  -0.846  -0.799  -1.212  -1.174  -0.626  -1.052  -1.030
104   L         0.651   0.678   0.724   0.494   0.563   0.650   0.663   0.696   0.757
105   T         0.651   0.678   0.724   0.784   0.826   0.847   0.663   0.696   0.757
106   T         0.651   0.678   0.724   0.784   0.826   0.847   0.663   0.696   0.757
107   S         0.651   0.678   0.724   0.670   0.700   0.770   0.663   0.696   0.757
108   A        -0.591  -0.884  -0.846  -0.452  -0.884  -0.929  -0.626  -1.052  -1.030
109   G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
110   I         0.651   0.678   0.724   0.352   0.441   0.553   0.663   0.696   0.757
111   M         0.651   0.678   0.724   0.927   0.921   0.945   0.663   0.696   0.757
112   D        -0.591  -0.884  -0.846  -0.311  -0.763  -0.796  -0.626  -1.052  -1.030
113   H         0.651   0.678   0.724   0.878   0.888   0.912   0.663   0.696   0.757
114   E        -0.591  -0.884  -0.846  -0.339  -0.775  -0.805  -0.626  -1.052  -1.030
115   E         0.651   0.678   0.724   0.757   0.782   0.829   0.663   0.696   0.757
116   A         0.651   0.678   0.724   0.675   0.734   0.773   0.663   0.696   0.757
117   R        -0.591  -0.151  -0.820  -0.560  -0.050  -0.835  -0.626  -0.052  -0.990
118   R        -0.591  -0.884  -0.846  -0.595  -0.995  -0.955  -0.626  -1.052  -1.030
119   K        -0.591  -0.555  -0.846  -0.647  -0.571  -1.041  -0.626  -0.573  -1.030
120   H        -0.591  -0.884  -0.846  -0.203  -0.648  -0.698  -0.626  -1.052  -1.030
121   V        -0.591  -0.884  -0.846  -0.732  -1.107  -1.033  -0.626  -1.052  -1.030
122   S        -2.243  -2.165  -1.799  -2.297  -2.210  -1.734  -2.344  -2.144  -1.675
123   G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
124   K         0.651   0.678   0.724   0.480   0.551   0.640   0.663   0.696   0.757
125   I         0.651   0.678   0.724   0.352   0.441   0.553   0.663   0.696   0.757
126   L        -0.128  -0.307  -0.830  -0.106  -0.260  -1.065  -0.035  -0.244  -1.005
127   G         0.651   0.678   0.724   0.480   0.558   0.640   0.663   0.696   0.757
128   F         0.651   0.678   0.724   0.811   0.824   0.866   0.663   0.696   0.757
129   V        -1.323  -1.143  -0.857  -1.761  -1.370  -0.934  -1.753  -1.465  -1.048
130   Y         0.651   0.678   0.724   0.901   0.914   0.927   0.663   0.696   0.757
* 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/Q3E7Y3
Output conservation file - output/Q3E7Y3
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
