1     M         1.136   1.157   1.217   1.259   1.299   1.371   1.206   1.234   1.326
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     S         0.318   0.383   0.076   0.523   0.596   0.184   0.307   0.401  -0.100
8     T        -1.015  -1.003  -0.806  -1.077  -1.079  -0.811  -1.191  -1.161  -0.896
9     Y         1.136   1.157   1.217   1.239   1.273   1.353   1.206   1.234   1.326
10    D         1.136   1.157   1.217   0.837   0.870   0.993   1.206   1.234   1.326
11    E         0.318   0.460   0.079   0.199   0.386  -0.082   0.307   0.510  -0.096
12    I        -0.057  -0.037  -0.034  -0.234  -0.198  -0.207  -0.292  -0.261  -0.294
13    E         1.136   1.157   1.217   0.892   0.936   1.042   1.206   1.234   1.326
14    I         0.318   0.172   0.054   0.308   0.120  -0.058   0.307   0.083  -0.139
15    E         1.136   1.157   1.217   0.892   0.936   1.042   1.206   1.234   1.326
16    D         1.136   1.157   1.217   0.837   0.870   0.993   1.206   1.234   1.326
17    M        -0.057  -0.097  -0.041  -0.012  -0.078  -0.047  -0.292  -0.366  -0.306
18    T         0.318   0.344   0.072   0.575   0.609   0.150   0.307   0.344  -0.108
19    F         0.318   0.261   0.061   0.479   0.413   0.103   0.307   0.222  -0.127
20    E        -0.452  -0.212  -0.682  -0.575  -0.262  -0.857  -0.442  -0.128  -0.737
21    P        -0.057  -0.111  -0.045  -0.121  -0.229  -0.162  -0.292  -0.391  -0.314
22    E        -1.805  -1.812  -1.718  -1.931  -1.896  -1.764  -1.490  -1.481  -1.319
23    N        -1.954  -1.832  -1.717  -1.500  -1.356  -1.192  -1.640  -1.512  -1.318
24    Q        -0.452  -0.572  -0.715  -0.024  -0.168  -0.391  -0.442  -0.599  -0.779
25    M        -1.410  -1.455  -1.306  -1.356  -1.384  -1.159  -1.341  -1.348  -1.145
26    F        -0.769  -0.809  -0.773  -0.694  -0.764  -0.706  -0.891  -0.949  -0.858
27    T        -0.452  -0.460  -0.700  -0.070  -0.085  -0.458  -0.442  -0.449  -0.760
28    Y         0.318   0.172   0.054   0.521   0.333   0.113   0.307   0.083  -0.139
29    P         1.136   1.157   1.217   1.178   1.207   1.298   1.206   1.234   1.326
30    C         1.136   1.157   1.217   1.229   1.256   1.344   1.206   1.234   1.326
31    P         1.136   1.157   1.217   1.178   1.207   1.298   1.206   1.234   1.326
32    C         1.136   1.157   1.217   1.229   1.256   1.344   1.206   1.234   1.326
33    G         1.136   1.157   1.217   1.320   1.345   1.425   1.206   1.234   1.326
34    D         1.136   1.157   1.217   0.837   0.870   0.993   1.206   1.234   1.326
35    R        -0.057  -0.068  -0.039   0.223   0.193   0.190  -0.292  -0.316  -0.304
36    F         1.136   1.157   1.217   1.188   1.216   1.307   1.206   1.234   1.326
37    Q        -0.769  -0.782  -0.770  -0.750  -0.841  -0.857  -0.891  -0.921  -0.855
38    I         1.136   1.157   1.217   1.021   1.055   1.158   1.206   1.234   1.326
39    Y        -1.410  -1.240  -1.286  -1.302  -1.097  -1.124  -1.341  -1.163  -1.129
40    L         0.318   0.415   0.079   0.464   0.579   0.069   0.307   0.447  -0.096
41    D        -1.164  -1.283  -1.291  -1.334  -1.533  -1.517  -1.041  -1.165  -1.130
42    D         1.136   1.157   1.217   0.837   0.870   0.993   1.206   1.234   1.326
43    M        -0.225  -0.208  -0.057  -0.315  -0.298  -0.073  -0.592  -0.565  -0.335
44    F        -1.410  -1.251  -1.283  -1.124  -0.857  -0.935  -1.341  -1.139  -1.123
45    E        -0.769  -0.804  -0.751  -1.187  -1.187  -1.110  -0.891  -0.904  -0.829
46    G         1.136   1.157   1.217   1.320   1.345   1.425   1.206   1.234   1.326
47    E         0.318   0.261   0.061   0.199   0.152  -0.108   0.307   0.222  -0.127
48    K        -1.164  -0.945  -1.243  -1.288  -0.989  -1.379  -1.041  -0.780  -1.081
49    V        -0.225  -0.202  -0.060  -0.517  -0.471  -0.240  -0.592  -0.554  -0.341
50    A         1.136   1.157   1.217   1.105   1.129   1.233   1.206   1.234   1.326
51    V         0.318   0.172   0.054   0.521   0.341   0.176   0.307   0.083  -0.139
52    C         1.136   1.157   1.217   1.229   1.256   1.344   1.206   1.234   1.326
53    P         1.136   1.157   1.217   1.178   1.207   1.298   1.206   1.234   1.326
54    S         1.136   1.157   1.217   1.218   1.236   1.335   1.206   1.234   1.326
55    C         1.136   1.157   1.217   1.229   1.256   1.344   1.206   1.234   1.326
56    S         1.136   1.157   1.217   1.218   1.236   1.335   1.206   1.234   1.326
57    L         1.136   1.157   1.217   1.208   1.223   1.325   1.206   1.234   1.326
58    M         0.318   0.172   0.054   0.515   0.320   0.065   0.307   0.083  -0.139
59    I        -0.225  -0.209  -0.059  -0.517  -0.474  -0.232  -0.592  -0.566  -0.339
60    D        -1.559  -1.445  -1.316  -1.414  -1.180  -1.022  -1.490  -1.355  -1.157
61    V         1.136   1.157   1.217   1.198   1.223   1.316   1.206   1.234   1.326
62    V        -0.057   0.072   0.001  -0.234  -0.027  -0.150  -0.292  -0.078  -0.232
63    F         0.318   0.172   0.054   0.479   0.291   0.092   0.307   0.083  -0.139
64    D        -0.225  -0.181  -0.056  -0.874  -0.781  -0.567  -0.592  -0.516  -0.334
65    K        -1.410  -1.494  -1.314  -1.207  -1.366  -1.163  -1.341  -1.393  -1.154
66    E        -0.057  -0.140  -0.052  -0.503  -0.672  -0.553  -0.292  -0.443  -0.327
67    D        -0.452  -0.641  -0.731  -0.582  -0.845  -0.936  -0.442  -0.686  -0.801
68    L         0.318   0.172   0.054   0.491   0.284   0.088   0.307   0.083  -0.139
69    A        -2.348  -2.258  -2.070  -2.438  -2.228  -2.008  -1.790  -1.692  -1.444
70    E        -0.452  -0.495  -0.707  -0.450  -0.474  -0.713  -0.442  -0.492  -0.770
71    Y        -1.164  -1.310  -1.296  -0.871  -1.090  -1.134  -1.041  -1.192  -1.136
72    Y        -1.805  -1.873  -1.730  -1.668  -1.838  -1.697  -1.490  -1.532  -1.328
73    E        -1.164  -1.260  -1.285  -1.205  -1.316  -1.345  -1.041  -1.142  -1.124
74    E        -0.758  -0.897  -0.783  -1.073  -1.330  -1.177  -0.849  -1.025  -0.867
75    A         1.136   1.157   1.217   1.037   1.060   1.172   1.206   1.234   1.326
76    G        -1.520  -1.531  -1.333  -1.282  -1.355  -1.060  -1.437  -1.428  -1.171
77    I        -0.937  -0.955  -0.802  -1.019  -1.033  -0.795  -1.088  -1.107  -0.891
78    H        -0.937  -0.768  -0.769  -1.041  -0.778  -0.797  -1.088  -0.855  -0.850
79    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    P        -0.758  -0.740  -0.753  -0.668  -0.642  -0.652  -0.849  -0.822  -0.829
83    I         1.136   1.157   1.217   1.051   1.083   1.184   1.206   1.234   1.326
84    A         0.138   0.020   0.007   0.043  -0.152  -0.197   0.032  -0.164  -0.221
85    A        -0.967  -0.972  -0.787  -1.188  -1.184  -0.905  -1.143  -1.123  -0.873
86    A         0.138   0.068   0.017   0.084  -0.026  -0.102   0.032  -0.085  -0.203
87    A        -1.164  -1.042  -1.246  -0.940  -0.777  -1.054  -1.041  -0.888  -1.084
* 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/Q3E840
Output conservation file - output/Q3E840
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
