1     M         1.763   1.793   1.920   1.960   2.014   2.208   1.933   1.980   2.206
2     P        -0.259  -0.217  -0.123  -0.263  -0.218  -0.075  -0.549  -0.490  -0.369
3     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     F        -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     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     P        -0.769  -0.756  -0.658  -0.734  -0.733  -0.582  -0.855  -0.830  -0.703
10    T        -1.101  -0.998  -1.028  -0.915  -0.758  -0.768  -0.976  -0.858  -0.853
11    R        -0.769  -0.693  -0.632  -1.056  -0.952  -0.849  -0.855  -0.750  -0.669
12    R        -1.559  -1.491  -1.439  -1.566  -1.461  -1.340  -1.218  -1.149  -1.053
13    Q        -0.295  -0.498  -0.563  -0.192  -0.479  -0.642  -0.248  -0.505  -0.582
14    V        -0.105  -0.075  -0.047  -0.165  -0.108  -0.058  -0.370  -0.303  -0.268
15    L         1.040   0.886   0.854   0.953   0.758   0.701   1.085   0.825   0.728
16    S        -1.434  -1.408  -1.387  -1.077  -1.108  -1.015  -1.097  -1.073  -1.008
17    L         1.040   1.166   0.897   0.982   1.145   0.829   1.085   1.274   0.809
18    Y         1.763   1.793   1.920   1.833   1.884   2.081   1.933   1.980   2.206
19    K         0.495   0.472   0.605   0.026  -0.027   0.184   0.115   0.050   0.233
20    E         0.037  -0.007  -0.006  -0.063  -0.103  -0.151  -0.127  -0.168  -0.197
21    F        -0.230  -0.186  -0.124  -0.469  -0.402  -0.311  -0.491  -0.437  -0.368
22    I         0.495   0.593   0.665   0.172   0.329   0.426   0.115   0.290   0.356
23    K        -0.312  -0.242  -0.120  -0.775  -0.688  -0.495  -0.612  -0.524  -0.367
24    N        -0.563  -0.635  -0.601  -0.662  -0.720  -0.718  -0.612  -0.678  -0.630
25    A         0.037  -0.123  -0.066   0.137  -0.107  -0.026  -0.127  -0.349  -0.291
26    N        -0.162  -0.094  -0.096  -0.311  -0.218  -0.202  -0.441  -0.360  -0.337
27    Q        -0.105  -0.110  -0.059  -0.497  -0.496  -0.414  -0.370  -0.362  -0.289
28    F        -0.295  -0.390  -0.529  -0.024  -0.180  -0.385  -0.248  -0.380  -0.540
29    N        -1.559  -1.535  -1.443  -1.334  -1.311  -1.202  -1.218  -1.186  -1.056
30    N        -0.295  -0.498  -0.563  -0.064  -0.324  -0.421  -0.248  -0.505  -0.582
31    Y         1.763   1.793   1.920   1.833   1.884   2.081   1.933   1.980   2.206
32    N         1.040   0.886   0.854   1.113   0.937   0.882   1.085   0.825   0.728
33    F         1.040   0.886   0.854   1.196   1.013   0.949   1.085   0.825   0.728
34    R         1.040   1.148   0.896   1.043   1.177   0.818   1.085   1.247   0.806
35    E         1.040   1.002   0.867   1.055   1.009   0.811   1.085   1.018   0.753
36    Y         1.040   1.135   0.896   1.209   1.335   1.025   1.085   1.226   0.806
37    F        -0.644  -0.654  -0.604  -0.578  -0.572  -0.492  -0.733  -0.733  -0.643
38    L        -0.312  -0.307  -0.163  -0.784  -0.745  -0.540  -0.612  -0.604  -0.424
39    S         1.040   1.132   0.886   1.082   1.189   0.882   1.085   1.223   0.788
40    K         0.434   0.484   0.617  -0.068   0.026   0.231  -0.006   0.074   0.258
41    T        -0.563  -0.360  -0.539  -0.362  -0.064  -0.328  -0.612  -0.358  -0.559
42    R         0.685   0.799   0.775   0.569   0.732   0.689   0.479   0.672   0.577
43    T        -0.230  -0.077  -0.077  -0.219   0.032  -0.012  -0.491  -0.270  -0.297
44    T        -1.559  -1.582  -1.434  -1.379  -1.473  -1.227  -1.218  -1.218  -1.051
45    F         1.763   1.793   1.920   1.818   1.884   2.067   1.933   1.980   2.206
46    R        -0.105  -0.104  -0.061  -0.420  -0.404  -0.297  -0.370  -0.351  -0.292
47    K         0.037   0.020  -0.047   0.003  -0.075  -0.213  -0.127  -0.193  -0.267
48    N         1.040   0.886   0.854   1.067   0.868   0.779   1.085   0.825   0.728
49    M         0.353   0.376   0.102   0.286   0.313  -0.045   0.358   0.385  -0.026
50    N        -0.563  -0.563  -0.576  -0.543  -0.536  -0.559  -0.612  -0.600  -0.599
51    Q        -0.563  -0.597  -0.598  -0.727  -0.787  -0.795  -0.612  -0.648  -0.634
52    Q        -1.101  -1.083  -1.042  -1.037  -1.021  -1.001  -0.976  -0.952  -0.871
53    D         0.495   0.600   0.661   0.392   0.591   0.638   0.115   0.304   0.348
54    P        -0.895  -0.766  -0.969  -0.521  -0.348  -0.698  -0.733  -0.589  -0.790
55    K        -1.559  -1.497  -1.428  -1.532  -1.424  -1.362  -1.218  -1.152  -1.046
56    V        -1.101  -1.020  -1.045  -1.298  -1.197  -1.207  -0.976  -0.890  -0.875
57    L        -0.295  -0.399  -0.531  -0.029  -0.190  -0.433  -0.248  -0.388  -0.542
58    M        -1.434  -1.245  -1.379  -1.338  -1.065  -1.298  -1.097  -0.910  -1.002
59    N        -0.769  -0.714  -0.651  -0.916  -0.861  -0.763  -0.855  -0.797  -0.696
60    L        -0.563  -0.651  -0.603  -0.622  -0.715  -0.645  -0.612  -0.695  -0.633
61    F        -1.227  -1.141  -1.099  -1.156  -1.021  -0.994  -1.097  -1.006  -0.923
62    K        -0.769  -0.636  -0.625  -1.103  -0.917  -0.886  -0.855  -0.704  -0.664
63    E        -0.895  -1.018  -1.034  -0.722  -0.924  -0.944  -0.733  -0.867  -0.857
64    A        -0.105  -0.184  -0.077  -0.100  -0.210  -0.043  -0.370  -0.448  -0.312
65    K        -1.101  -0.984  -1.033  -1.181  -1.011  -1.143  -0.976  -0.843  -0.858
66    N        -0.644  -0.587  -0.604  -0.933  -0.860  -0.879  -0.733  -0.661  -0.644
67    D        -1.101  -1.187  -1.087  -1.023  -1.194  -1.072  -0.976  -1.038  -0.911
68    L         1.763   1.793   1.920   1.584   1.642   1.833   1.933   1.980   2.206
69    G        -0.563  -0.635  -0.601  -0.400  -0.528  -0.499  -0.612  -0.678  -0.630
70    V        -0.563  -0.595  -0.606  -0.455  -0.504  -0.528  -0.612  -0.650  -0.644
71    L         1.040   0.886   0.854   0.967   0.779   0.733   1.085   0.825   0.728
72    K         0.037   0.069  -0.041  -0.219  -0.203  -0.344  -0.127  -0.115  -0.260
73    R         1.763   1.793   1.920   1.710   1.747   1.959   1.933   1.980   2.206
74    Q         1.763   1.793   1.920   1.702   1.757   1.951   1.933   1.980   2.206
75    S         0.495   0.552   0.635   0.374   0.455   0.577   0.115   0.209   0.296
76    V        -0.230  -0.193  -0.102  -0.275  -0.238  -0.101  -0.491  -0.445  -0.338
77    I         1.763   1.793   1.920   1.861   1.905   2.110   1.933   1.980   2.206
78    S         1.040   0.886   0.854   1.152   0.941   0.887   1.085   0.825   0.728
79    Q         0.353   0.300   0.099   0.467   0.398   0.116   0.358   0.262  -0.031
80    M         0.353   0.412   0.120   0.683   0.774   0.317   0.358   0.437   0.000
81    Y         1.040   1.135   0.896   1.209   1.335   1.025   1.085   1.226   0.806
82    T        -0.295  -0.498  -0.563   0.025  -0.285  -0.431  -0.248  -0.505  -0.582
83    F        -0.295  -0.498  -0.563  -0.076  -0.398  -0.540  -0.248  -0.505  -0.582
84    D         0.353   0.155   0.055   0.642   0.345   0.161   0.358   0.069  -0.099
85    R        -0.563  -0.692  -0.620  -0.746  -0.919  -0.798  -0.612  -0.749  -0.658
86    L         1.040   1.135   0.896   0.953   1.084   0.768   1.085   1.226   0.806
87    V         1.763   1.793   1.920   1.768   1.816   2.017   1.933   1.980   2.206
88    V         1.763   1.793   1.920   1.768   1.816   2.017   1.933   1.980   2.206
89    E         1.763   1.793   1.920   1.695   1.743   1.944   1.933   1.980   2.206
90    P         0.037  -0.080  -0.067   0.324   0.135   0.169  -0.127  -0.310  -0.296
91    L        -0.895  -1.018  -1.034  -0.789  -0.964  -0.966  -0.733  -0.867  -0.857
92    Q        -1.101  -1.053  -1.069  -1.251  -1.145  -1.200  -0.976  -0.931  -0.897
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   G        -1.322  -1.277  -1.135  -1.136  -1.077  -0.879  -1.170  -1.117  -0.953
108   R        -1.208  -1.118  -1.094  -1.230  -1.092  -1.008  -1.075  -0.978  -0.916
109   K        -1.101  -1.187  -1.087  -1.001  -1.112  -0.932  -0.976  -1.038  -0.911
110   H        -1.559  -1.570  -1.435  -1.275  -1.315  -1.109  -1.218  -1.210  -1.051
* 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/Q6Q560
Output conservation file - output/Q6Q560
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
