1     M         1.287   1.293   1.305   1.480   1.485   1.504   1.346   1.352   1.366
2     L        -0.210  -0.256  -0.274  -0.140  -0.196  -0.215  -0.320  -0.389  -0.416
3     R        -0.210  -0.256  -0.274  -0.312  -0.380  -0.410  -0.320  -0.389  -0.416
4     T        -1.297  -1.286  -1.264  -1.201  -1.183  -1.146  -1.153  -1.135  -1.097
5     T        -0.210  -0.184  -0.253  -0.057  -0.019  -0.117  -0.320  -0.279  -0.383
6     F        -0.343  -0.338  -0.316  -0.125  -0.116  -0.083  -0.528  -0.518  -0.482
7     L        -0.343  -0.338  -0.316  -0.448  -0.438  -0.402  -0.528  -0.518  -0.482
8     R        -0.343  -0.338  -0.316  -0.493  -0.483  -0.446  -0.528  -0.518  -0.482
9     T         1.287   1.293   1.305   1.343   1.350   1.369   1.346   1.352   1.366
10    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    R         1.287   1.293   1.305   1.152   1.162   1.180   1.346   1.352   1.366
12    Q        -0.210  -0.165  -0.245  -0.047   0.026  -0.114  -0.320  -0.249  -0.371
13    L        -0.343  -0.338  -0.316  -0.381  -0.371  -0.336  -0.528  -0.518  -0.482
14    M        -1.297  -1.286  -1.264  -0.839  -0.820  -0.788  -1.153  -1.135  -1.097
15    R        -0.210  -0.256  -0.274  -0.462  -0.552  -0.599  -0.320  -0.389  -0.416
16    K        -1.297  -1.286  -1.264  -1.373  -1.339  -1.316  -1.153  -1.135  -1.097
17    S        -0.210  -0.184  -0.253  -0.075  -0.042  -0.139  -0.320  -0.279  -0.383
18    P        -0.210  -0.184  -0.253  -0.075  -0.031  -0.152  -0.320  -0.279  -0.383
19    R        -1.297  -1.286  -1.264  -0.978  -0.950  -0.926  -1.153  -1.135  -1.097
20    A         1.287   1.293   1.305   1.318   1.325   1.345   1.346   1.352   1.366
21    S        -1.297  -1.286  -1.264  -1.188  -1.164  -1.133  -1.153  -1.135  -1.097
22    F        -0.210  -0.256  -0.274  -0.029  -0.106  -0.151  -0.320  -0.389  -0.416
23    S        -1.297  -1.286  -1.264  -1.002  -0.966  -0.950  -1.153  -1.135  -1.097
24    I        -1.297  -1.286  -1.264  -1.051  -1.047  -0.997  -1.153  -1.135  -1.097
25    V        -0.343  -0.338  -0.316  -0.230  -0.220  -0.186  -0.528  -0.518  -0.482
26    T         1.287   1.293   1.305   1.343   1.350   1.369   1.346   1.352   1.366
27    R         1.287   1.293   1.305   1.152   1.162   1.180   1.346   1.352   1.366
28    A        -1.297  -1.286  -1.264  -1.253  -1.238  -1.197  -1.153  -1.135  -1.097
29    A        -1.297  -1.286  -1.264  -1.162  -1.133  -1.108  -1.153  -1.135  -1.097
30    F         1.287   1.293   1.305   1.460   1.469   1.484   1.346   1.352   1.366
31    -        -0.343  -0.338  -0.316  -0.345  -0.335  -0.300  -0.528  -0.518  -0.482
32    -        -0.343  -0.338  -0.316  -0.646  -0.635  -0.597  -0.528  -0.518  -0.482
33    P        -1.297  -1.286  -1.264  -1.175  -1.158  -1.120  -1.153  -1.135  -1.097
34    H        -0.210  -0.256  -0.274   0.087   0.016  -0.017  -0.320  -0.389  -0.416
35    L        -0.210  -0.256  -0.274  -0.149  -0.206  -0.227  -0.320  -0.389  -0.416
36    K        -0.210  -0.256  -0.274  -0.482  -0.547  -0.556  -0.320  -0.389  -0.416
37    N        -1.297  -1.286  -1.264  -1.266  -1.229  -1.210  -1.153  -1.135  -1.097
38    N        -1.297  -1.286  -1.264  -1.214  -1.186  -1.158  -1.153  -1.135  -1.097
39    Q        -0.210  -0.256  -0.274  -0.178  -0.247  -0.274  -0.320  -0.389  -0.416
40    D        -1.297  -1.286  -1.264  -1.266  -1.238  -1.210  -1.153  -1.135  -1.097
41    E        -1.297  -1.286  -1.264  -1.373  -1.373  -1.316  -1.153  -1.135  -1.097
42    A        -0.210  -0.256  -0.274  -0.121  -0.195  -0.223  -0.320  -0.389  -0.416
43    E        -0.210  -0.256  -0.274  -0.342  -0.430  -0.487  -0.320  -0.389  -0.416
44    K        -0.210  -0.256  -0.274  -0.586  -0.666  -0.686  -0.320  -0.389  -0.416
45    K        -1.297  -1.286  -1.264  -1.292  -1.253  -1.236  -1.153  -1.135  -1.097
46    E        -0.210  -0.256  -0.274  -0.263  -0.339  -0.389  -0.320  -0.389  -0.416
47    Q         1.287   1.293   1.305   1.257   1.263   1.284   1.346   1.352   1.366
48    G        -1.297  -1.286  -1.264  -1.387  -1.371  -1.329  -1.153  -1.135  -1.097
49    L        -0.210  -0.165  -0.245  -0.029   0.050  -0.100  -0.320  -0.249  -0.371
50    F         1.287   1.293   1.305   1.460   1.469   1.484   1.346   1.352   1.366
51    D         1.287   1.293   1.305   1.110   1.116   1.139   1.346   1.352   1.366
52    S        -1.297  -1.286  -1.264  -1.226  -1.212  -1.171  -1.153  -1.135  -1.097
53    N         1.287   1.293   1.305   1.339   1.348   1.365   1.346   1.352   1.366
54    K        -0.210  -0.184  -0.253  -0.513  -0.479  -0.566  -0.320  -0.279  -0.383
55    K         1.287   1.293   1.305   0.937   0.938   0.968   1.346   1.352   1.366
56    R        -1.297  -1.286  -1.264  -1.601  -1.595  -1.542  -1.153  -1.135  -1.097
57    L         1.287   1.293   1.305   1.215   1.225   1.243   1.346   1.352   1.366
58    D        -0.210  -0.165  -0.245  -0.263  -0.176  -0.333  -0.320  -0.249  -0.371
59    T        -1.297  -1.286  -1.264  -1.162  -1.138  -1.108  -1.153  -1.135  -1.097
60    L         1.287   1.293   1.305   1.215   1.225   1.243   1.346   1.352   1.366
61    E         1.287   1.293   1.305   1.277   1.292   1.304   1.346   1.352   1.366
62    H         1.287   1.293   1.305   1.499   1.506   1.523   1.346   1.352   1.366
63    G        -0.210  -0.256  -0.274  -0.131  -0.216  -0.266  -0.320  -0.389  -0.416
64    K        -0.210  -0.256  -0.274  -0.472  -0.540  -0.544  -0.320  -0.389  -0.416
65    N        -1.297  -1.286  -1.264  -1.319  -1.330  -1.262  -1.153  -1.135  -1.097
66    -         1.287   1.293   1.305   1.338   1.345   1.364   1.346   1.352   1.366
67    -        -0.343  -0.338  -0.316  -0.794  -0.783  -0.744  -0.528  -0.518  -0.482
68    -        -0.343  -0.338  -0.316  -0.504  -0.494  -0.457  -0.528  -0.518  -0.482
69    P        -0.210  -0.184  -0.253   0.025   0.061  -0.035  -0.320  -0.279  -0.383
70    D        -0.210  -0.165  -0.245  -0.206  -0.124  -0.278  -0.320  -0.249  -0.371
71    Y         1.287   1.293   1.305   1.519   1.525   1.543   1.346   1.352   1.366
72    K         1.287   1.293   1.305   0.937   0.938   0.968   1.346   1.352   1.366
73    Q        -0.343  -0.338  -0.316  -0.476  -0.466  -0.429  -0.528  -0.518  -0.482
74    P         1.287   1.293   1.305   1.311   1.318   1.337   1.346   1.352   1.366
75    G        -0.343  -0.338  -0.316  -0.251  -0.242  -0.207  -0.528  -0.518  -0.482
76    M        -1.297  -1.286  -1.264  -0.919  -0.916  -0.868  -1.153  -1.135  -1.097
77    E        -1.297  -1.286  -1.264  -1.513  -1.509  -1.455  -1.153  -1.135  -1.097
78    D        -0.210  -0.256  -0.274  -0.312  -0.381  -0.397  -0.320  -0.389  -0.416
79    L         1.287   1.293   1.305   1.215   1.225   1.243   1.346   1.352   1.366
80    K        -0.210  -0.184  -0.253  -0.565  -0.527  -0.628  -0.320  -0.279  -0.383
81    K        -1.297  -1.286  -1.264  -1.414  -1.376  -1.357  -1.153  -1.135  -1.097
82    K         1.287   1.293   1.305   0.937   0.938   0.968   1.346   1.352   1.366
83    G         1.287   1.293   1.305   1.420   1.429   1.445   1.346   1.352   1.366
84    D        -1.297  -1.286  -1.264  -1.513  -1.505  -1.455  -1.153  -1.135  -1.097
85    D        -0.210  -0.184  -0.253  -0.312  -0.272  -0.368  -0.320  -0.279  -0.383
86    A         1.287   1.293   1.305   1.318   1.325   1.345   1.346   1.352   1.366
87    R        -0.210  -0.256  -0.274  -0.244  -0.304  -0.326  -0.320  -0.389  -0.416
88    I         1.287   1.293   1.305   1.499   1.503   1.523   1.346   1.352   1.366
89    E        -0.210  -0.256  -0.274  -0.342  -0.430  -0.487  -0.320  -0.389  -0.416
90    Q         1.287   1.293   1.305   1.257   1.263   1.284   1.346   1.352   1.366
91    N        -0.210  -0.256  -0.274  -0.029  -0.089  -0.114  -0.320  -0.389  -0.416
92    R         1.287   1.293   1.305   1.152   1.162   1.180   1.346   1.352   1.366
93    P        -0.210  -0.256  -0.274  -0.057  -0.133  -0.167  -0.320  -0.389  -0.416
94    D         1.287   1.293   1.305   1.110   1.116   1.139   1.346   1.352   1.366
95    D         1.287   1.293   1.305   1.110   1.116   1.139   1.346   1.352   1.366
96    G         1.287   1.293   1.305   1.420   1.429   1.445   1.346   1.352   1.366
97    V         1.287   1.293   1.305   1.440   1.443   1.464   1.346   1.352   1.366
98    Y         1.287   1.293   1.305   1.519   1.525   1.543   1.346   1.352   1.366
* 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/Q12497
Output conservation file - output/Q12497
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
