1     M         1.472   1.474   1.498   1.801   1.804   1.835   1.555   1.557   1.585
2     Q        -1.256  -1.253  -1.218  -0.665  -0.647  -0.606  -1.115  -1.110  -1.050
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    L         1.472   1.474   1.498   1.580   1.585   1.617   1.555   1.557   1.585
11    -        -0.249  -0.248  -0.216  -0.255  -0.250  -0.200  -0.448  -0.445  -0.391
12    L        -0.108  -0.088  -0.142  -0.248  -0.212  -0.294  -0.225  -0.193  -0.274
13    R        -1.256  -1.253  -1.218  -0.960  -0.954  -0.898  -1.115  -1.110  -1.050
14    C        -0.108  -0.135  -0.157  -0.071  -0.132  -0.218  -0.225  -0.266  -0.299
15    F        -0.108  -0.088  -0.142   0.032   0.068  -0.019  -0.225  -0.193  -0.274
16    S        -0.108  -0.095  -0.143  -0.346  -0.321  -0.388  -0.225  -0.204  -0.276
17    I        -0.108  -0.095  -0.143  -0.200  -0.177  -0.240  -0.225  -0.204  -0.276
18    F        -0.108  -0.095  -0.143   0.177   0.201   0.127  -0.225  -0.204  -0.276
19    S        -1.256  -1.253  -1.218  -1.219  -1.206  -1.155  -1.115  -1.110  -1.050
20    V        -1.256  -1.253  -1.218  -1.172  -1.149  -1.108  -1.115  -1.110  -1.050
21    I        -0.108  -0.135  -0.157  -0.511  -0.568  -0.635  -0.225  -0.266  -0.299
22    A        -1.256  -1.253  -1.218  -0.760  -0.749  -0.700  -1.115  -1.110  -1.050
23    S        -0.108  -0.095  -0.143  -0.321  -0.298  -0.360  -0.225  -0.204  -0.276
24    V         1.472   1.474   1.498   1.505   1.509   1.542   1.555   1.557   1.585
25    L        -0.249  -0.248  -0.216  -0.553  -0.547  -0.495  -0.448  -0.445  -0.391
26    A        -0.108  -0.088  -0.142  -0.236  -0.204  -0.260  -0.225  -0.193  -0.274
27    Q        -1.256  -1.253  -1.218  -1.203  -1.222  -1.139  -1.115  -1.110  -1.050
28    E        -1.256  -1.253  -1.218  -1.187  -1.175  -1.123  -1.115  -1.110  -1.050
29    L        -1.256  -1.253  -1.218  -1.079  -1.064  -1.016  -1.115  -1.110  -1.050
30    T        -0.108  -0.135  -0.157  -0.710  -0.762  -0.798  -0.225  -0.266  -0.299
31    T         1.472   1.474   1.498   1.030   1.024   1.072   1.555   1.557   1.585
32    I        -0.108  -0.135  -0.157  -0.421  -0.468  -0.526  -0.225  -0.266  -0.299
33    C         1.472   1.474   1.498   1.777   1.781   1.811   1.555   1.557   1.585
34    E        -0.108  -0.095  -0.143   0.100   0.120   0.047  -0.225  -0.204  -0.276
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    Q        -0.108  -0.088  -0.142  -0.421  -0.400  -0.437  -0.225  -0.193  -0.274
37    I         1.472   1.474   1.498   1.325   1.329   1.364   1.555   1.557   1.585
38    P         1.472   1.474   1.498   1.728   1.732   1.763   1.555   1.557   1.585
39    S        -1.256  -1.253  -1.218  -1.187  -1.171  -1.123  -1.115  -1.110  -1.050
40    P        -0.108  -0.095  -0.143   0.210   0.234   0.156  -0.225  -0.204  -0.276
41    T        -0.108  -0.135  -0.157  -0.472  -0.509  -0.512  -0.225  -0.266  -0.299
42    L         1.472   1.474   1.498   1.580   1.585   1.617   1.555   1.557   1.585
43    E         1.472   1.474   1.498   1.630   1.631   1.666   1.555   1.557   1.585
44    S        -0.108  -0.088  -0.142  -0.710  -0.678  -0.770  -0.225  -0.193  -0.274
45    T         1.472   1.474   1.498   1.030   1.024   1.072   1.555   1.557   1.585
46    P         1.472   1.474   1.498   1.728   1.732   1.763   1.555   1.557   1.585
47    Y        -0.108  -0.135  -0.157  -0.082  -0.131  -0.194  -0.225  -0.266  -0.299
48    S         1.472   1.474   1.498   1.219   1.224   1.259   1.555   1.557   1.585
49    L        -1.256  -1.253  -1.218  -1.684  -1.693  -1.615  -1.115  -1.110  -1.050
50    S        -0.108  -0.135  -0.157  -0.200  -0.226  -0.234  -0.225  -0.266  -0.299
51    T         1.472   1.474   1.498   1.030   1.024   1.072   1.555   1.557   1.585
52    T        -0.108  -0.135  -0.157  -0.371  -0.403  -0.392  -0.225  -0.266  -0.299
53    T        -0.108  -0.095  -0.143  -0.421  -0.409  -0.438  -0.225  -0.204  -0.276
54    I        -0.108  -0.135  -0.157  -0.141  -0.170  -0.189  -0.225  -0.266  -0.299
55    L        -1.256  -1.253  -1.218  -1.485  -1.497  -1.418  -1.115  -1.110  -1.050
56    A        -0.108  -0.135  -0.157   0.032  -0.018  -0.098  -0.225  -0.266  -0.299
57    N         1.472   1.474   1.498   1.777   1.781   1.811   1.555   1.557   1.585
58    G         1.472   1.474   1.498   1.801   1.805   1.835   1.555   1.557   1.585
59    K        -0.108  -0.135  -0.157   0.166   0.128   0.075  -0.225  -0.266  -0.299
60    A        -1.256  -1.253  -1.218  -1.172  -1.186  -1.108  -1.115  -1.110  -1.050
61    M        -0.108  -0.135  -0.157   0.231   0.191   0.142  -0.225  -0.266  -0.299
62    Q        -0.108  -0.088  -0.142  -0.152  -0.120  -0.184  -0.225  -0.193  -0.274
63    G         1.472   1.474   1.498   1.801   1.805   1.835   1.555   1.557   1.585
64    V        -0.108  -0.135  -0.157  -0.200  -0.246  -0.305  -0.225  -0.266  -0.299
65    F        -0.108  -0.135  -0.157  -0.164  -0.226  -0.307  -0.225  -0.266  -0.299
66    E        -0.108  -0.095  -0.143   0.122   0.143   0.073  -0.225  -0.204  -0.276
67    Y        -0.108  -0.135  -0.157  -0.002  -0.046  -0.097  -0.225  -0.266  -0.299
68    Y         1.472   1.474   1.498   1.630   1.632   1.666   1.555   1.557   1.585
69    K        -1.256  -1.253  -1.218  -0.705  -0.693  -0.646  -1.115  -1.110  -1.050
70    S         1.472   1.474   1.498   1.219   1.224   1.259   1.555   1.557   1.585
71    V        -0.108  -0.088  -0.142  -0.284  -0.247  -0.336  -0.225  -0.193  -0.274
72    T        -0.108  -0.095  -0.143  -0.434  -0.419  -0.453  -0.225  -0.204  -0.276
73    F        -0.108  -0.088  -0.142   0.078   0.112   0.024  -0.225  -0.193  -0.274
74    V        -0.108  -0.095  -0.143  -0.200  -0.172  -0.276  -0.225  -0.204  -0.276
75    S         1.472   1.474   1.498   1.219   1.224   1.259   1.555   1.557   1.585
76    N        -0.108  -0.088  -0.142   0.210   0.242   0.158  -0.225  -0.193  -0.274
77    C         1.472   1.474   1.498   1.777   1.781   1.811   1.555   1.557   1.585
78    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    S        -0.249  -0.248  -0.216  -0.608  -0.603  -0.549  -0.448  -0.445  -0.391
83    T         1.472   1.474   1.498   0.947   0.950   0.990   1.555   1.557   1.585
84    T        -1.256  -1.253  -1.218  -1.300  -1.282  -1.235  -1.115  -1.110  -1.050
85    S        -1.256  -1.253  -1.218  -1.187  -1.169  -1.123  -1.115  -1.110  -1.050
86    K        -0.108  -0.135  -0.157   0.166   0.128   0.075  -0.225  -0.266  -0.299
87    G        -1.256  -1.253  -1.218  -0.844  -0.837  -0.783  -1.115  -1.110  -1.050
88    S        -1.256  -1.253  -1.218  -1.187  -1.173  -1.123  -1.115  -1.110  -1.050
89    P        -1.256  -1.253  -1.218  -1.019  -1.009  -0.956  -1.115  -1.110  -1.050
90    I        -1.256  -1.253  -1.218  -1.665  -1.673  -1.596  -1.115  -1.110  -1.050
91    N        -1.256  -1.253  -1.218  -1.094  -1.101  -1.031  -1.115  -1.110  -1.050
92    T         1.472   1.474   1.498   1.030   1.024   1.072   1.555   1.557   1.585
93    Q        -1.256  -1.253  -1.218  -0.873  -0.864  -0.812  -1.115  -1.110  -1.050
94    Y        -1.256  -1.253  -1.218  -1.267  -1.257  -1.202  -1.115  -1.110  -1.050
95    V        -0.108  -0.088  -0.142  -0.284  -0.247  -0.336  -0.225  -0.193  -0.274
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    F        -0.108  -0.135  -0.157   0.242   0.210   0.184  -0.225  -0.266  -0.299
* 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/P32781
Output conservation file - output/P32781
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
