1     M         1.240   1.273   1.320   1.563   1.593   1.649   1.331   1.377   1.446
2     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     F         1.240   1.273   1.320   1.450   1.485   1.544   1.331   1.377   1.446
5     G         1.240   1.273   1.320   1.216   1.268   1.327   1.331   1.377   1.446
6     L         0.358   0.256   0.144  -0.004  -0.119  -0.234   0.330   0.164  -0.042
7     G         1.240   1.273   1.320   1.216   1.268   1.327   1.331   1.377   1.446
8     R        -0.740  -0.788  -0.715  -0.511  -0.567  -0.451  -0.872  -0.913  -0.802
9     L         0.358   0.256   0.144  -0.087  -0.233  -0.407   0.330   0.164  -0.042
10    F        -0.006  -0.030   0.030  -0.167  -0.283  -0.244  -0.271  -0.325  -0.244
11    Y         1.240   1.273   1.320   1.583   1.623   1.668   1.331   1.377   1.446
12    V         1.240   1.273   1.320   1.161   1.215   1.276   1.331   1.377   1.446
13    I        -0.740  -0.765  -0.693  -0.922  -0.961  -0.821  -0.872  -0.886  -0.776
14    L        -0.458  -0.429  -0.647  -0.922  -0.864  -1.204  -0.471  -0.427  -0.711
15    L         1.240   1.273   1.320   0.771   0.828   0.914   1.331   1.377   1.446
16    L        -0.458  -0.429  -0.647  -0.830  -0.769  -1.041  -0.471  -0.427  -0.711
17    I        -0.458  -0.553  -0.655  -0.672  -0.868  -1.085  -0.471  -0.595  -0.722
18    N         1.240   1.273   1.320   1.419   1.460   1.515   1.331   1.377   1.446
19    A        -0.740  -0.763  -0.711  -0.643  -0.679  -0.612  -0.872  -0.884  -0.796
20    V        -0.117  -0.071   0.026  -0.553  -0.481  -0.305  -0.471  -0.401  -0.251
21    A         1.240   1.273   1.320   1.471   1.508   1.563   1.331   1.377   1.446
22    V         0.358   0.256   0.144   0.312   0.161  -0.051   0.330   0.164  -0.042
23    L         1.240   1.273   1.320   0.771   0.828   0.914   1.331   1.377   1.446
24    S         1.240   1.273   1.320   1.345   1.379   1.447   1.331   1.377   1.446
25    E         1.240   1.273   1.320   1.522   1.571   1.611   1.331   1.377   1.446
26    E        -0.117  -0.065   0.029   0.089   0.175   0.302  -0.471  -0.390  -0.247
27    R         1.240   1.273   1.320   1.377   1.416   1.476   1.331   1.377   1.446
28    F         1.240   1.273   1.320   1.450   1.485   1.544   1.331   1.377   1.446
29    L         1.240   1.273   1.320   0.771   0.828   0.914   1.331   1.377   1.446
30    R        -1.363  -1.302  -1.258  -1.190  -1.120  -1.037  -1.272  -1.198  -1.096
31    R         1.240   1.273   1.320   1.377   1.416   1.476   1.331   1.377   1.446
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    I         0.358   0.298   0.151   0.249   0.156  -0.074   0.330   0.233  -0.028
42    G         1.240   1.273   1.320   1.216   1.268   1.327   1.331   1.377   1.446
43    L        -0.117  -0.065   0.029  -0.379  -0.222  -0.077  -0.471  -0.390  -0.247
44    G         0.358   0.256   0.144   0.419   0.285   0.106   0.330   0.164  -0.042
45    R        -0.740  -0.693  -0.672  -0.611  -0.512  -0.469  -0.872  -0.781  -0.745
46    S        -0.458  -0.491  -0.641  -0.165  -0.215  -0.411  -0.471  -0.512  -0.703
47    N        -1.815  -1.717  -1.682  -1.471  -1.334  -1.278  -1.473  -1.372  -1.275
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    D        -0.825  -0.707  -0.710  -0.672  -0.540  -0.471  -0.976  -0.834  -0.797
53    E        -0.795  -0.824  -0.737  -0.662  -0.740  -0.637  -0.922  -0.952  -0.827
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    T        -1.815  -1.737  -1.673  -1.330  -1.224  -1.130  -1.473  -1.383  -1.268
64    P        -1.815  -1.841  -1.696  -1.459  -1.608  -1.375  -1.473  -1.468  -1.285
65    V        -1.363  -1.251  -1.244  -1.391  -1.238  -1.155  -1.272  -1.149  -1.083
66    F        -0.458  -0.429  -0.647  -0.195  -0.154  -0.563  -0.471  -0.427  -0.711
67    G        -0.458  -0.429  -0.647  -0.236  -0.185  -0.432  -0.471  -0.427  -0.711
68    Q        -1.192  -1.244  -1.249  -0.678  -0.751  -0.774  -1.072  -1.117  -1.086
69    D        -2.268  -2.173  -2.040  -1.578  -1.474  -1.264  -1.673  -1.576  -1.401
70    Q        -1.815  -1.743  -1.673  -1.244  -1.146  -1.049  -1.473  -1.388  -1.268
71    N        -1.192  -1.244  -1.249  -0.811  -0.873  -0.899  -1.072  -1.117  -1.086
72    T        -0.117  -0.071   0.020  -0.182  -0.122   0.031  -0.471  -0.401  -0.262
73    T        -0.740  -0.788  -0.715  -0.808  -0.914  -0.820  -0.872  -0.913  -0.802
74    K         1.240   1.273   1.320   1.563   1.602   1.649   1.331   1.377   1.446
75    S        -0.006   0.027   0.045   0.011   0.046   0.072  -0.271  -0.223  -0.216
76    K        -0.006  -0.030   0.030   0.199   0.130   0.192  -0.271  -0.325  -0.244
77    V        -1.363  -1.353  -1.251  -1.788  -1.793  -1.543  -1.272  -1.234  -1.089
78    V        -0.740  -0.788  -0.715  -1.162  -1.280  -1.194  -0.872  -0.913  -0.802
79    Q        -0.740  -0.788  -0.715  -0.400  -0.448  -0.333  -0.872  -0.913  -0.802
80    L         1.240   1.273   1.320   0.771   0.828   0.914   1.331   1.377   1.446
81    I         1.240   1.273   1.320   1.083   1.119   1.204   1.331   1.377   1.446
82    G        -0.740  -0.788  -0.715  -0.777  -0.830  -0.699  -0.872  -0.913  -0.802
83    A         1.240   1.273   1.320   1.471   1.508   1.563   1.331   1.377   1.446
84    V         0.358   0.256   0.144   0.312   0.161  -0.051   0.330   0.164  -0.042
85    Q        -0.117  -0.065   0.029  -0.070  -0.005   0.141  -0.471  -0.390  -0.247
86    T         1.240   1.273   1.320   1.398   1.429   1.496   1.331   1.377   1.446
87    L         0.358   0.256   0.144  -0.070  -0.204  -0.370   0.330   0.164  -0.042
88    L        -0.117  -0.065   0.029  -0.461  -0.314  -0.158  -0.471  -0.390  -0.247
89    R         0.358   0.256   0.144   0.589   0.443   0.265   0.330   0.164  -0.042
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   I        -1.192  -1.153  -1.219  -1.395  -1.331  -1.469  -1.072  -1.026  -1.056
107   P         0.358   0.298   0.151   0.864   0.789   0.550   0.330   0.233  -0.028
108   L         0.358   0.298   0.151   0.023  -0.032  -0.171   0.330   0.233  -0.028
109   I         0.358   0.298   0.151   0.171   0.060  -0.235   0.330   0.233  -0.028
110   G        -1.363  -1.353  -1.251  -1.353  -1.288  -1.112  -1.272  -1.234  -1.089
111   I        -0.006  -0.004   0.034  -0.344  -0.355  -0.290  -0.271  -0.278  -0.236
112   N         0.358   0.298   0.151   0.514   0.408   0.076   0.330   0.233  -0.028
113   I        -1.192  -1.304  -1.238  -1.415  -1.633  -1.534  -1.072  -1.180  -1.076
114   L        -1.363  -1.279  -1.236  -1.900  -1.665  -1.555  -1.272  -1.158  -1.074
115   V        -0.458  -0.491  -0.641  -0.452  -0.490  -0.738  -0.471  -0.512  -0.703
116   I         1.240   1.273   1.320   1.083   1.119   1.204   1.331   1.377   1.446
117   V        -0.740  -0.731  -0.707  -0.955  -0.947  -0.857  -0.872  -0.854  -0.793
118   Y         0.358   0.298   0.151   0.824   0.747   0.516   0.330   0.233  -0.028
119   E        -0.458  -0.611  -0.652   0.008  -0.202  -0.288  -0.471  -0.670  -0.719
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   L         1.240   1.273   1.320   0.771   0.828   0.914   1.331   1.377   1.446
129   L        -1.363  -1.318  -1.252  -1.890  -1.687  -1.594  -1.272  -1.198  -1.090
130   L         0.358   0.298   0.151  -0.016  -0.079  -0.248   0.330   0.233  -0.028
131   G         0.358   0.298   0.151   0.419   0.346   0.119   0.330   0.233  -0.028
* 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/Q3E834
Output conservation file - output/Q3E834
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
