1     M         1.231   1.232   1.252   1.690   1.690   1.709   1.284   1.284   1.307
2     T        -0.225  -0.232  -0.272  -0.440  -0.450  -0.496  -0.352  -0.362  -0.421
3     Y         1.231   1.232   1.252   1.427   1.427   1.451   1.284   1.284   1.307
4     E        -0.225  -0.210  -0.267   0.104   0.125   0.046  -0.352  -0.329  -0.412
5     Q        -1.283  -1.282  -1.244  -1.025  -1.019  -0.956  -1.170  -1.169  -1.103
6     L         1.231   1.232   1.252   0.884   0.885   0.919   1.284   1.284   1.307
7     Y        -0.225  -0.232  -0.272  -0.330  -0.339  -0.388  -0.352  -0.362  -0.421
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    K        -0.225  -0.210  -0.267  -0.066  -0.045  -0.128  -0.352  -0.329  -0.412
11    E        -1.283  -1.282  -1.244  -1.362  -1.365  -1.287  -1.170  -1.169  -1.103
12    F        -1.283  -1.282  -1.244  -1.065  -1.064  -0.995  -1.170  -1.169  -1.103
13    H        -1.283  -1.282  -1.244  -0.881  -0.881  -0.815  -1.170  -1.169  -1.103
14    S        -0.225  -0.210  -0.267  -0.440  -0.418  -0.488  -0.352  -0.329  -0.412
15    S         1.231   1.232   1.252   1.031   1.030   1.063   1.284   1.284   1.307
16    K        -1.283  -1.282  -1.244  -1.147  -1.144  -1.076  -1.170  -1.169  -1.103
17    S        -1.283  -1.282  -1.244  -1.105  -1.109  -1.035  -1.170  -1.169  -1.103
18    F         1.231   1.232   1.252   1.127   1.128   1.157   1.284   1.284   1.307
19    Q        -0.225  -0.210  -0.267   0.064   0.091  -0.020  -0.352  -0.329  -0.412
20    P        -0.225  -0.232  -0.272  -0.107  -0.122  -0.233  -0.352  -0.362  -0.421
21    F        -0.225  -0.232  -0.272  -0.589  -0.602  -0.703  -0.352  -0.362  -0.421
22    I        -0.225  -0.232  -0.272  -0.138  -0.150  -0.224  -0.352  -0.362  -0.421
23    H        -1.283  -1.282  -1.244  -0.781  -0.779  -0.717  -1.170  -1.169  -1.103
24    L         1.231   1.232   1.252   0.884   0.885   0.919   1.284   1.284   1.307
25    D        -1.283  -1.282  -1.244  -1.051  -1.042  -0.982  -1.170  -1.169  -1.103
26    T        -1.283  -1.282  -1.244  -0.920  -0.923  -0.853  -1.170  -1.169  -1.103
27    Q         1.231   1.232   1.252   1.582   1.581   1.603   1.284   1.284   1.307
28    P         1.231   1.232   1.252   1.560   1.560   1.582   1.284   1.284   1.307
29    K        -0.225  -0.232  -0.272  -0.097  -0.109  -0.174  -0.352  -0.362  -0.421
30    F        -0.225  -0.210  -0.267  -0.589  -0.557  -0.689  -0.352  -0.329  -0.412
31    A         1.231   1.232   1.252   1.359   1.360   1.385   1.284   1.284   1.307
32    I        -1.283  -1.282  -1.244  -1.303  -1.296  -1.229  -1.170  -1.169  -1.103
33    C        -1.283  -1.282  -1.244  -0.946  -0.941  -0.879  -1.170  -1.169  -1.103
34    G        -1.283  -1.282  -1.244  -1.303  -1.302  -1.229  -1.170  -1.169  -1.103
35    L         1.231   1.232   1.252   0.884   0.885   0.919   1.284   1.284   1.307
36    I        -0.225  -0.232  -0.272  -0.577  -0.586  -0.622  -0.352  -0.362  -0.421
37    V        -0.225  -0.232  -0.272  -0.601  -0.611  -0.650  -0.352  -0.362  -0.421
38    T        -0.225  -0.232  -0.272  -0.138  -0.147  -0.218  -0.352  -0.362  -0.421
39    L        -0.225  -0.232  -0.272  -0.577  -0.586  -0.622  -0.352  -0.362  -0.421
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    A        -0.225  -0.232  -0.272  -0.589  -0.598  -0.636  -0.352  -0.362  -0.421
46    V        -1.283  -1.282  -1.244  -1.468  -1.470  -1.392  -1.170  -1.169  -1.103
47    L        -0.225  -0.210  -0.267  -0.577  -0.555  -0.615  -0.352  -0.329  -0.412
48    S         1.231   1.232   1.252   1.031   1.030   1.063   1.284   1.284   1.307
49    S        -0.225  -0.210  -0.267  -0.684  -0.654  -0.778  -0.352  -0.329  -0.412
50    A         1.231   1.232   1.252   1.359   1.360   1.385   1.284   1.284   1.307
51    L         1.231   1.232   1.252   0.884   0.885   0.919   1.284   1.284   1.307
52    F        -1.283  -1.282  -1.244  -1.188  -1.186  -1.117  -1.170  -1.169  -1.103
53    A        -1.283  -1.282  -1.244  -1.078  -1.074  -1.009  -1.170  -1.169  -1.103
54    V        -1.283  -1.282  -1.244  -1.105  -1.104  -1.035  -1.170  -1.169  -1.103
55    G        -0.225  -0.232  -0.272  -0.036  -0.046  -0.118  -0.352  -0.362  -0.421
56    S        -0.225  -0.232  -0.272  -0.385  -0.395  -0.429  -0.352  -0.362  -0.421
57    K        -1.283  -1.282  -1.244  -1.274  -1.268  -1.201  -1.170  -1.169  -1.103
58    S        -0.225  -0.232  -0.272  -0.276  -0.291  -0.390  -0.352  -0.362  -0.421
59    S        -1.283  -1.282  -1.244  -1.133  -1.133  -1.062  -1.170  -1.169  -1.103
60    Y        -1.283  -1.282  -1.244  -1.259  -1.254  -1.187  -1.170  -1.169  -1.103
61    I        -0.225  -0.232  -0.272  -0.159  -0.171  -0.237  -0.352  -0.362  -0.421
62    K        -0.225  -0.210  -0.267  -0.026  -0.005  -0.081  -0.352  -0.329  -0.412
63    K        -0.225  -0.232  -0.272  -0.036  -0.047  -0.101  -0.352  -0.362  -0.421
64    L        -0.225  -0.232  -0.272  -0.589  -0.602  -0.703  -0.352  -0.362  -0.421
65    F        -1.283  -1.282  -1.244  -1.515  -1.519  -1.438  -1.170  -1.169  -1.103
66    F        -1.283  -1.282  -1.244  -1.288  -1.290  -1.215  -1.170  -1.169  -1.103
67    Y         1.231   1.232   1.252   1.427   1.427   1.451   1.284   1.284   1.307
68    T        -0.225  -0.232  -0.272  -0.066  -0.074  -0.137  -0.352  -0.362  -0.421
69    I        -0.225  -0.232  -0.272  -0.341  -0.355  -0.470  -0.352  -0.362  -0.421
70    L         1.231   1.232   1.252   0.884   0.885   0.919   1.284   1.284   1.307
71    S        -1.283  -1.282  -1.244  -1.347  -1.348  -1.273  -1.170  -1.169  -1.103
72    V        -0.225  -0.210  -0.267  -0.170  -0.145  -0.240  -0.352  -0.329  -0.412
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    I         1.231   1.232   1.252   1.382   1.382   1.407   1.284   1.284   1.307
79    G         1.231   1.232   1.252   1.449   1.450   1.473   1.284   1.284   1.307
80    S         1.231   1.232   1.252   1.031   1.030   1.063   1.284   1.284   1.307
81    L         1.231   1.232   1.252   0.884   0.885   0.919   1.284   1.284   1.307
82    F         1.231   1.232   1.252   1.127   1.128   1.157   1.284   1.284   1.307
83    A        -0.225  -0.232  -0.272  -0.362  -0.372  -0.428  -0.352  -0.362  -0.421
84    G         1.231   1.232   1.252   1.449   1.450   1.473   1.284   1.284   1.307
85    L        -0.225  -0.232  -0.272  -0.341  -0.355  -0.470  -0.352  -0.362  -0.421
86    T        -1.283  -1.282  -1.244  -1.303  -1.304  -1.229  -1.170  -1.169  -1.103
87    T        -0.225  -0.232  -0.272  -0.118  -0.126  -0.199  -0.352  -0.362  -0.421
88    V         1.231   1.232   1.252   1.336   1.335   1.362   1.284   1.284   1.307
89    F         1.231   1.232   1.252   1.127   1.128   1.157   1.284   1.284   1.307
90    A        -0.225  -0.232  -0.272  -0.589  -0.598  -0.636  -0.352  -0.362  -0.421
91    S        -0.225  -0.232  -0.272  -0.440  -0.450  -0.496  -0.352  -0.362  -0.421
92    N         1.231   1.232   1.252   1.647   1.647   1.667   1.284   1.284   1.307
93    S         1.231   1.232   1.252   1.031   1.030   1.063   1.284   1.284   1.307
94    F         1.231   1.232   1.252   1.127   1.128   1.157   1.284   1.284   1.307
95    G         1.231   1.232   1.252   1.449   1.450   1.473   1.284   1.284   1.307
96    V         1.231   1.232   1.252   1.336   1.335   1.362   1.284   1.284   1.307
97    Y         1.231   1.232   1.252   1.427   1.427   1.451   1.284   1.284   1.307
98    V         1.231   1.232   1.252   1.336   1.335   1.362   1.284   1.284   1.307
* 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/Q92316
Output conservation file - output/Q92316
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
