1     M         1.090   1.095   1.169   1.288   1.290   1.388   1.137   1.146   1.250
2     A        -0.830  -0.784  -0.756  -0.859  -0.747  -0.754  -0.990  -0.911  -0.840
3     D        -1.300  -1.283  -1.279  -1.315  -1.274  -1.249  -1.214  -1.192  -1.125
4     Q        -1.426  -1.278  -1.281  -1.537  -1.326  -1.303  -1.349  -1.204  -1.128
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    -        -0.782  -0.745  -0.755  -0.864  -0.812  -0.848  -0.869  -0.826  -0.833
11    E        -1.964  -1.955  -1.702  -2.015  -2.012  -1.643  -1.641  -1.613  -1.310
12    N        -1.964  -1.854  -1.691  -1.932  -1.769  -1.574  -1.641  -1.539  -1.302
13    S        -1.384  -1.342  -1.284  -1.450  -1.422  -1.317  -1.326  -1.264  -1.129
14    P        -1.300  -1.323  -1.288  -1.340  -1.376  -1.307  -1.214  -1.237  -1.133
15    L        -0.214  -0.075  -0.014  -0.469  -0.271  -0.153  -0.542  -0.311  -0.249
16    H        -1.513  -1.525  -1.310  -1.499  -1.544  -1.242  -1.438  -1.434  -1.154
17    T         0.347   0.256   0.029   0.503   0.371  -0.018   0.353   0.218  -0.174
18    V        -0.018  -0.019  -0.028  -0.099  -0.106  -0.169  -0.207  -0.217  -0.274
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    G        -0.018  -0.019  -0.028  -0.032  -0.044  -0.114  -0.207  -0.217  -0.274
21    F         0.347   0.256   0.029   0.297   0.166  -0.146   0.353   0.218  -0.174
22    D         1.090   1.095   1.169   0.958   0.993   1.097   1.137   1.146   1.250
23    A        -0.276  -0.237  -0.075  -0.583  -0.507  -0.257  -0.654  -0.597  -0.356
24    R         1.090   1.095   1.169   1.183   1.177   1.296   1.137   1.146   1.250
25    F         1.090   1.095   1.169   0.932   0.926   1.075   1.137   1.146   1.250
26    P         1.090   1.095   1.169   1.000   1.024   1.135   1.137   1.146   1.250
27    Q         0.347   0.446   0.048   0.431   0.574  -0.020   0.353   0.486  -0.141
28    Q        -0.360  -0.535  -0.731  -0.239  -0.479  -0.766  -0.319  -0.549  -0.802
29    N         1.090   1.095   1.169   1.076   1.109   1.201   1.137   1.146   1.250
30    Q         1.090   1.095   1.169   1.009   1.014   1.142   1.137   1.146   1.250
31    T         0.347   0.308   0.040   0.537   0.487   0.097   0.353   0.294  -0.154
32    K         0.347   0.478   0.065   0.321   0.471  -0.038   0.353   0.529  -0.113
33    H         1.090   1.095   1.169   1.232   1.241   1.339   1.137   1.146   1.250
34    C         1.090   1.095   1.169   1.118   1.124   1.238   1.137   1.146   1.250
35    W        -0.684  -0.763  -0.760  -0.617  -0.748  -0.800  -0.766  -0.862  -0.840
36    Q         1.090   1.095   1.169   1.009   1.014   1.142   1.137   1.146   1.250
37    S        -1.042  -1.003  -0.803  -1.150  -1.074  -0.809  -1.214  -1.164  -0.894
38    Y         1.090   1.095   1.169   1.191   1.195   1.303   1.137   1.146   1.250
39    V         0.347   0.245   0.029   0.462   0.336   0.031   0.353   0.201  -0.174
40    D         1.090   1.095   1.169   0.958   0.993   1.097   1.137   1.146   1.250
41    Y         1.090   1.095   1.169   1.191   1.195   1.303   1.137   1.146   1.250
42    H        -0.018  -0.044  -0.054   0.031  -0.034  -0.141  -0.207  -0.260  -0.319
43    K         0.347   0.245   0.029   0.321   0.196  -0.094   0.353   0.201  -0.174
44    C         1.090   1.095   1.169   1.118   1.124   1.238   1.137   1.146   1.250
45    V        -0.018   0.018  -0.049   0.068   0.120  -0.061  -0.207  -0.156  -0.309
46    N        -0.360  -0.535  -0.731  -0.184  -0.402  -0.748  -0.319  -0.549  -0.802
47    M        -1.025  -0.867  -1.208  -0.712  -0.532  -0.966  -0.878  -0.708  -1.050
48    K         1.090   1.095   1.169   0.941   0.952   1.082   1.137   1.146   1.250
49    G         1.090   1.095   1.169   1.142   1.151   1.260   1.137   1.146   1.250
50    E         1.090   1.095   1.169   1.051   1.066   1.179   1.137   1.146   1.250
51    D        -0.214  -0.186  -0.072  -0.536  -0.471  -0.312  -0.542  -0.505  -0.351
52    F         1.090   1.095   1.169   0.932   0.926   1.075   1.137   1.146   1.250
53    A        -0.830  -0.867  -0.770  -0.937  -0.978  -0.827  -0.990  -1.018  -0.856
54    P         1.090   1.095   1.169   1.000   1.024   1.135   1.137   1.146   1.250
55    C         1.090   1.095   1.169   1.118   1.124   1.238   1.137   1.146   1.250
56    K        -0.360  -0.419  -0.706  -0.313  -0.394  -0.796  -0.319  -0.402  -0.770
57    V        -0.959  -0.985  -0.799  -1.042  -1.114  -0.833  -1.102  -1.141  -0.889
58    F         1.090   1.095   1.169   0.932   0.926   1.075   1.137   1.146   1.250
59    W         0.347   0.308   0.040   0.495   0.442  -0.002   0.353   0.294  -0.154
60    K        -1.025  -1.139  -1.272  -0.849  -1.000  -1.128  -0.878  -1.013  -1.116
61    T        -0.684  -0.713  -0.768  -0.564  -0.654  -0.718  -0.766  -0.835  -0.853
62    Y        -0.018  -0.019  -0.028  -0.008  -0.031  -0.111  -0.207  -0.217  -0.274
63    N        -1.983  -1.961  -1.713  -1.813  -1.776  -1.452  -1.662  -1.618  -1.318
64    A         0.347   0.446   0.048   0.542   0.677   0.092   0.353   0.486  -0.141
65    L         1.090   1.095   1.169   1.216   1.222   1.325   1.137   1.146   1.250
66    C         1.090   1.095   1.169   1.118   1.124   1.238   1.137   1.146   1.250
67    P         1.090   1.095   1.169   1.000   1.024   1.135   1.137   1.146   1.250
68    L        -1.854  -1.881  -1.693  -1.594  -1.614  -1.361  -1.550  -1.558  -1.303
69    D        -0.684  -0.744  -0.754  -0.776  -0.833  -0.863  -0.766  -0.837  -0.835
70    W         1.090   1.095   1.169   1.150   1.161   1.267   1.137   1.146   1.250
71    I        -0.684  -0.681  -0.750  -0.589  -0.573  -0.671  -0.766  -0.748  -0.829
72    E        -0.360  -0.419  -0.706  -0.241  -0.321  -0.801  -0.319  -0.402  -0.770
73    K        -0.018  -0.110  -0.061  -0.170  -0.321  -0.231  -0.207  -0.371  -0.332
74    W         1.090   1.095   1.169   1.150   1.161   1.267   1.137   1.146   1.250
75    D         0.347   0.375   0.044   0.323   0.387  -0.098   0.353   0.390  -0.147
76    D        -0.830  -0.775  -0.763  -1.034  -0.944  -0.873  -0.990  -0.933  -0.848
77    Q         1.090   1.095   1.169   1.009   1.014   1.142   1.137   1.146   1.250
78    R         1.090   1.095   1.169   1.183   1.177   1.296   1.137   1.146   1.250
79    E        -0.360  -0.258  -0.686  -0.191  -0.070  -0.653  -0.319  -0.203  -0.745
80    K        -1.384  -1.298  -1.283  -1.489  -1.347  -1.309  -1.326  -1.235  -1.129
81    G         1.090   1.095   1.169   1.142   1.151   1.260   1.137   1.146   1.250
82    I        -1.513  -1.525  -1.310  -1.488  -1.517  -1.218  -1.438  -1.434  -1.154
83    F         1.090   1.095   1.169   0.932   0.926   1.075   1.137   1.146   1.250
84    A        -0.276  -0.210  -0.058  -0.583  -0.466  -0.235  -0.654  -0.549  -0.327
85    G        -1.300  -1.365  -1.289  -1.132  -1.256  -1.134  -1.214  -1.285  -1.135
86    D        -1.300  -1.411  -1.301  -1.386  -1.527  -1.410  -1.214  -1.319  -1.145
87    I        -0.830  -0.831  -0.761  -0.690  -0.687  -0.564  -0.990  -0.984  -0.846
88    N        -1.426  -1.415  -1.302  -1.486  -1.495  -1.292  -1.349  -1.337  -1.146
89    S        -0.782  -0.825  -0.786  -0.807  -0.906  -0.833  -0.869  -0.947  -0.872
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    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q01519
Output conservation file - output/Q01519
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
