1     M         1.793   1.805   1.893   2.006   2.018   2.154   2.039   2.060   2.223
2     E        -0.663  -0.577  -0.590  -0.573  -0.437  -0.461  -0.760  -0.666  -0.653
3     Q        -0.462  -0.530  -0.545  -0.624  -0.743  -0.806  -0.517  -0.604  -0.599
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    -         0.026   0.032   0.014  -0.145  -0.136  -0.152  -0.142  -0.134  -0.185
11    -         0.026   0.027  -0.024   0.236   0.239   0.080  -0.142  -0.141  -0.243
12    -        -0.684  -0.689  -0.589  -0.529  -0.536  -0.405  -0.765  -0.770  -0.646
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    R        -0.140  -0.112  -0.075  -0.355  -0.307  -0.235  -0.395  -0.354  -0.321
17    N        -1.107  -1.073  -1.004  -0.990  -0.952  -0.822  -1.004  -0.972  -0.867
18    N        -0.018   0.007   0.001  -0.165  -0.123  -0.095  -0.273  -0.217  -0.217
19    V        -0.785  -0.763  -0.638  -0.776  -0.741  -0.566  -0.882  -0.856  -0.705
20    F         0.563   0.603   0.656   0.430   0.485   0.572   0.213   0.288   0.335
21    Q         1.793   1.805   1.893   1.660   1.664   1.814   2.039   2.060   2.223
22    A        -1.429  -1.381  -1.347  -1.392  -1.339  -1.251  -1.126  -1.082  -1.008
23    K        -0.018  -0.030   0.003  -0.447  -0.426  -0.379  -0.273  -0.263  -0.213
24    Y         1.793   1.805   1.893   2.039   2.053   2.186   2.039   2.060   2.223
25    N         1.093   1.111   0.909   1.249   1.272   1.000   1.187   1.217   0.842
26    E        -1.429  -1.397  -1.364  -1.135  -1.055  -1.023  -1.126  -1.093  -1.022
27    Y         0.748   0.771   0.711   1.019   1.053   0.942   0.579   0.619   0.449
28    K         0.748   0.696   0.726   0.378   0.290   0.309   0.579   0.473   0.480
29    Q        -0.985  -0.916  -0.973  -0.965  -0.854  -0.892  -0.882  -0.800  -0.833
30    I        -1.307  -1.360  -1.317  -0.988  -1.069  -1.013  -1.004  -1.051  -0.981
31    L         0.748   0.696   0.726   0.606   0.514   0.544   0.579   0.473   0.480
32    E        -0.541  -0.586  -0.572  -0.718  -0.756  -0.707  -0.639  -0.674  -0.633
33    E        -0.541  -0.499  -0.544  -0.741  -0.688  -0.712  -0.639  -0.594  -0.606
34    L         0.748   0.746   0.730   0.606   0.598   0.551   0.579   0.571   0.487
35    Q        -0.462  -0.539  -0.545  -0.404  -0.505  -0.479  -0.517  -0.604  -0.599
36    T        -1.107  -1.074  -1.005  -0.966  -0.933  -0.789  -1.004  -0.972  -0.867
37    K         0.748   0.696   0.726   0.378   0.290   0.309   0.579   0.473   0.480
38    I         0.748   0.696   0.726   0.670   0.570   0.589   0.579   0.473   0.480
39    I        -0.985  -1.053  -1.014  -0.727  -0.813  -0.745  -0.882  -0.943  -0.873
40    E        -0.140  -0.173  -0.082  -0.339  -0.382  -0.258  -0.395  -0.446  -0.332
41    L        -0.018  -0.017  -0.032  -0.203  -0.206  -0.200  -0.273  -0.279  -0.274
42    G        -0.541  -0.586  -0.572  -0.467  -0.529  -0.497  -0.639  -0.674  -0.633
43    H        -1.429  -1.405  -1.367  -0.928  -0.913  -0.868  -1.126  -1.099  -1.023
44    D        -0.140  -0.174  -0.089  -0.309  -0.387  -0.291  -0.395  -0.448  -0.342
45    K        -0.985  -1.055  -1.014  -1.035  -1.104  -1.018  -0.882  -0.944  -0.873
46    D        -0.462  -0.540  -0.553  -0.357  -0.472  -0.502  -0.517  -0.605  -0.609
47    E         1.793   1.805   1.893   1.660   1.680   1.814   2.039   2.060   2.223
48    H         1.793   1.805   1.893   2.082   2.096   2.229   2.039   2.060   2.223
49    T        -0.985  -0.972  -0.986  -1.075  -1.054  -1.050  -0.882  -0.858  -0.845
50    I        -0.018   0.044  -0.018  -0.182  -0.114  -0.166  -0.273  -0.206  -0.252
51    V         1.793   1.805   1.893   1.793   1.807   1.945   2.039   2.060   2.223
52    I        -0.462  -0.470  -0.525  -0.408  -0.424  -0.469  -0.517  -0.539  -0.575
53    K        -0.985  -0.993  -0.972  -1.197  -1.215  -1.145  -0.882  -0.890  -0.833
54    T         1.093   1.020   0.902   1.219   1.134   0.986   1.187   1.066   0.830
55    L         1.793   1.805   1.893   1.695   1.708   1.849   2.039   2.060   2.223
56    K        -1.429  -1.459  -1.352  -1.420  -1.433  -1.269  -1.126  -1.141  -1.012
57    D        -1.429  -1.350  -1.336  -0.956  -0.842  -0.849  -1.126  -1.059  -1.000
58    A        -1.107  -1.060  -1.021  -0.940  -0.872  -0.805  -1.004  -0.959  -0.880
59    E        -0.541  -0.487  -0.547  -0.367  -0.279  -0.355  -0.639  -0.578  -0.609
60    P        -0.785  -0.755  -0.913  -0.264  -0.214  -0.503  -0.639  -0.605  -0.767
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    T        -0.985  -0.960  -0.948  -0.786  -0.737  -0.735  -0.882  -0.859  -0.809
66    R         1.793   1.805   1.893   1.978   1.991   2.127   2.039   2.060   2.223
67    K         1.093   1.075   0.900   0.936   0.926   0.716   1.187   1.158   0.826
68    C         1.793   1.805   1.893   2.103   2.116   2.250   2.039   2.060   2.223
69    Y         0.563   0.635   0.697   0.727   0.847   0.924   0.213   0.352   0.420
70    R         0.748   0.696   0.726   0.794   0.688   0.679   0.579   0.473   0.480
71    M         1.793   1.805   1.893   2.006   2.018   2.154   2.039   2.060   2.223
72    I         1.093   1.162   0.916   1.191   1.272   0.956   1.187   1.298   0.856
73    G         0.119   0.148   0.037   0.395   0.450   0.275  -0.030   0.025  -0.164
74    G         0.748   0.841   0.787   0.940   1.073   0.983   0.579   0.751   0.604
75    A         0.563   0.635   0.697   0.449   0.567   0.649   0.213   0.352   0.420
76    L         1.093   1.070   0.902   1.093   1.064   0.840   1.187   1.151   0.830
77    V         1.793   1.805   1.893   1.793   1.807   1.945   2.039   2.060   2.223
78    E         0.748   0.772   0.709   0.596   0.639   0.518   0.579   0.621   0.445
79    S        -0.663  -0.586  -0.589  -0.793  -0.693  -0.649  -0.760  -0.671  -0.651
80    D        -0.663  -0.689  -0.621  -0.564  -0.596  -0.503  -0.760  -0.787  -0.688
81    V         1.093   1.020   0.902   1.191   1.099   0.935   1.187   1.066   0.830
82    Q        -0.985  -0.974  -0.977  -1.117  -1.067  -1.094  -0.882  -0.874  -0.838
83    T        -0.140  -0.174  -0.089  -0.278  -0.341  -0.232  -0.395  -0.448  -0.342
84    S         0.119   0.248   0.065   0.169   0.358   0.106  -0.030   0.168  -0.111
85    L        -0.203  -0.198  -0.417  -0.035  -0.035  -0.393  -0.152  -0.146  -0.431
86    P         0.119   0.053  -0.004   0.271   0.133  -0.043  -0.030  -0.137  -0.227
87    I        -0.203  -0.166  -0.417   0.053   0.102  -0.247  -0.152  -0.104  -0.431
88    L         1.793   1.805   1.893   1.695   1.708   1.849   2.039   2.060   2.223
89    E        -1.107  -1.037  -1.015  -1.310  -1.206  -1.165  -1.004  -0.943  -0.876
90    T         0.119   0.125   0.034   0.181   0.173   0.057  -0.030  -0.046  -0.161
91    K        -0.663  -0.656  -0.586  -0.893  -0.858  -0.769  -0.760  -0.748  -0.648
92    K        -1.751  -1.772  -1.661  -1.394  -1.428  -1.319  -1.247  -1.256  -1.126
93    E        -0.785  -0.756  -0.900  -0.702  -0.668  -0.895  -0.639  -0.609  -0.753
94    N        -1.107  -1.074  -1.015  -1.045  -1.004  -0.939  -1.004  -0.970  -0.875
95    I         0.748   0.773   0.718   0.606   0.641   0.530   0.579   0.622   0.463
96    E        -0.541  -0.554  -0.551  -0.896  -0.902  -0.892  -0.639  -0.641  -0.609
97    G        -1.107  -1.047  -1.004  -1.332  -1.237  -1.150  -1.004  -0.950  -0.867
98    T        -0.785  -0.763  -0.644  -0.886  -0.858  -0.675  -0.882  -0.856  -0.711
99    I        -1.751  -1.771  -1.661  -1.530  -1.546  -1.420  -1.247  -1.256  -1.126
100   S        -1.107  -1.113  -1.013  -1.011  -1.020  -0.889  -1.004  -1.001  -0.874
101   K        -0.785  -0.772  -0.922  -0.801  -0.774  -0.981  -0.639  -0.624  -0.776
102   M         0.119   0.172   0.080   0.177   0.258   0.163  -0.030   0.065  -0.087
103   K        -1.307  -1.385  -1.357  -1.276  -1.356  -1.288  -1.004  -1.072  -1.015
104   E        -1.429  -1.350  -1.325  -1.498  -1.410  -1.330  -1.126  -1.059  -0.992
105   T        -0.018   0.027  -0.013  -0.318  -0.268  -0.290  -0.273  -0.224  -0.248
106   L         0.563   0.561   0.639   0.421   0.418   0.544   0.213   0.202   0.299
107   I        -1.307  -1.385  -1.357  -1.170  -1.304  -1.324  -1.004  -1.072  -1.015
108   Q        -0.462  -0.497  -0.510  -0.758  -0.801  -0.831  -0.517  -0.552  -0.560
109   T        -1.307  -1.385  -1.357  -1.137  -1.253  -1.278  -1.004  -1.072  -1.015
110   A        -0.663  -0.688  -0.621  -0.614  -0.659  -0.595  -0.760  -0.785  -0.688
111   K        -0.018  -0.002  -0.000  -0.416  -0.360  -0.344  -0.273  -0.234  -0.228
112   E         1.093   1.020   0.902   1.017   0.923   0.723   1.187   1.066   0.830
113   F        -0.140  -0.175  -0.110   0.015  -0.059  -0.006  -0.395  -0.449  -0.373
114   E        -0.203  -0.238  -0.466  -0.193  -0.242  -0.644  -0.152  -0.197  -0.494
115   K         0.119   0.052   0.010  -0.056  -0.139  -0.176  -0.030  -0.138  -0.197
116   W         1.093   1.075   0.900   1.541   1.521   1.303   1.187   1.158   0.826
117   K        -0.462  -0.550  -0.545  -0.681  -0.799  -0.764  -0.517  -0.620  -0.602
118   K         0.425   0.329   0.159   0.311   0.196  -0.054   0.457   0.314   0.041
119   D        -0.018  -0.071  -0.030  -0.231  -0.306  -0.267  -0.273  -0.335  -0.272
120   N         1.793   1.805   1.893   1.850   1.864   2.001   2.039   2.060   2.223
121   K         0.563   0.560   0.640   0.153   0.157   0.274   0.213   0.201   0.300
122   I         0.748   0.744   0.730   0.701   0.689   0.642   0.579   0.567   0.490
123   Q         0.563   0.541   0.633   0.100   0.032   0.159   0.213   0.161   0.286
124   V         0.748   0.696   0.726   0.701   0.610   0.633   0.579   0.473   0.480
125   V         1.793   1.805   1.893   1.793   1.807   1.945   2.039   2.060   2.223
126   K        -0.140  -0.129  -0.084  -0.482  -0.465  -0.380  -0.395  -0.380  -0.336
127   N        -0.462  -0.445  -0.511  -0.382  -0.374  -0.417  -0.517  -0.512  -0.557
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -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/P40005
Output conservation file - output/P40005
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
