1     M         1.143   1.188   1.227   1.266   1.324   1.376   1.212   1.273   1.329
2     G         0.165   0.103   0.005   0.262   0.173   0.007   0.069  -0.035  -0.219
3     N         1.143   1.188   1.227   1.150   1.211   1.269   1.212   1.273   1.329
4     I        -0.211  -0.152  -0.059  -0.169  -0.069   0.049  -0.574  -0.474  -0.333
5     M         1.143   1.188   1.227   1.280   1.388   1.389   1.212   1.273   1.329
6     S         1.143   1.188   1.227   1.113   1.170   1.235   1.212   1.273   1.329
7     A        -1.460  -1.415  -1.341  -1.292  -1.236  -1.087  -1.360  -1.290  -1.162
8     S         1.143   1.188   1.227   1.143   1.191   1.262   1.212   1.273   1.329
9     F         0.263   0.072   0.037   0.473   0.263   0.163   0.220  -0.085  -0.163
10    A         0.263   0.072   0.037   0.241  -0.065  -0.065   0.220  -0.085  -0.163
11    P        -0.552  -0.622  -0.731  -0.289  -0.390  -0.614  -0.574  -0.673  -0.787
12    E         1.143   1.188   1.227   0.834   0.919   0.975   1.212   1.273   1.329
13    C         1.143   1.188   1.227   1.192   1.216   1.308   1.212   1.273   1.329
14    T         1.143   1.188   1.227   1.221   1.287   1.335   1.212   1.273   1.329
15    D        -1.455  -1.329  -1.316  -1.551  -1.272  -1.347  -1.368  -1.209  -1.139
16    L        -0.211  -0.095  -0.035  -0.456  -0.351  -0.189  -0.574  -0.373  -0.290
17    K         1.143   1.188   1.227   0.770   0.834   0.916   1.212   1.273   1.329
18    T        -1.284  -1.061  -1.271  -1.311  -0.986  -1.224  -1.170  -0.896  -1.093
19    K        -0.833  -0.766  -0.768  -1.221  -1.091  -1.045  -0.971  -0.856  -0.837
20    Y         1.143   1.188   1.227   1.221   1.261   1.335   1.212   1.273   1.329
21    D         1.143   1.188   1.227   1.113   1.182   1.234   1.212   1.273   1.329
22    S        -1.906  -1.817  -1.749  -1.780  -1.684  -1.598  -1.567  -1.454  -1.325
23    C         1.143   1.188   1.227   1.192   1.216   1.308   1.212   1.273   1.329
24    F         1.143   1.188   1.227   1.202   1.287   1.317   1.212   1.273   1.329
25    N         1.143   1.188   1.227   1.152   1.263   1.271   1.212   1.273   1.329
26    E        -1.455  -1.389  -1.321  -1.637  -1.432  -1.412  -1.368  -1.252  -1.143
27    W         1.143   1.188   1.227   1.318   1.376   1.425   1.212   1.273   1.329
28    Y         1.143   1.188   1.227   1.221   1.261   1.335   1.212   1.273   1.329
29    S        -1.284  -1.260  -1.310  -0.981  -1.045  -1.026  -1.170  -1.137  -1.132
30    E         0.263   0.072   0.037   0.086  -0.125  -0.195   0.220  -0.085  -0.163
31    K         1.143   1.188   1.227   0.770   0.834   0.916   1.212   1.273   1.329
32    F         1.143   1.188   1.227   1.202   1.287   1.317   1.212   1.273   1.329
33    L         1.143   1.188   1.227   1.123   1.141   1.243   1.212   1.273   1.329
34    K         0.263   0.288   0.061   0.052   0.096  -0.155   0.220   0.257  -0.123
35    G         1.143   1.188   1.227   1.172   1.365   1.289   1.212   1.273   1.329
36    K        -0.833  -0.913  -0.785  -1.282  -1.353  -1.152  -0.971  -1.034  -0.857
37    S         0.263   0.072   0.037   0.387   0.095   0.054   0.220  -0.085  -0.163
38    V        -1.906  -1.869  -1.756  -1.263  -1.176  -1.077  -1.567  -1.494  -1.330
39    E         0.263   0.072   0.037   0.086  -0.125  -0.195   0.220  -0.085  -0.163
40    N         0.263   0.072   0.037   0.442   0.254   0.160   0.220  -0.085  -0.163
41    E         0.263   0.072   0.037   0.078  -0.155  -0.214   0.220  -0.085  -0.163
42    C         1.143   1.188   1.227   1.192   1.216   1.308   1.212   1.273   1.329
43    S        -1.906  -1.832  -1.745  -1.519  -1.483  -1.319  -1.567  -1.466  -1.321
44    K        -1.455  -1.321  -1.319  -1.744  -1.492  -1.453  -1.368  -1.187  -1.142
45    Q        -0.833  -0.574  -0.741  -0.778  -0.437  -0.678  -0.971  -0.603  -0.800
46    W         0.263   0.072   0.037   0.576   0.320   0.235   0.220  -0.085  -0.163
47    Y        -1.284  -1.412  -1.332  -0.904  -1.166  -0.998  -1.170  -1.279  -1.153
48    A        -0.833  -0.667  -0.751  -1.115  -0.850  -0.945  -0.971  -0.715  -0.813
49    Y         1.143   1.188   1.227   1.221   1.261   1.335   1.212   1.273   1.329
50    T        -1.906  -1.891  -1.761  -1.643  -1.730  -1.491  -1.567  -1.508  -1.334
51    T        -1.455  -1.480  -1.329  -1.432  -1.416  -1.214  -1.368  -1.345  -1.152
52    C         1.143   1.188   1.227   1.192   1.216   1.308   1.212   1.273   1.329
53    V         0.263   0.072   0.037   0.504   0.264   0.154   0.220  -0.085  -0.163
54    N        -1.284  -1.349  -1.310  -1.063  -1.195  -1.148  -1.170  -1.221  -1.132
55    A        -0.552  -0.713  -0.761  -0.550  -0.887  -0.893  -0.574  -0.779  -0.825
56    A         0.263   0.404   0.072   0.241   0.372  -0.011   0.220   0.429  -0.103
57    L         1.143   1.188   1.227   1.123   1.141   1.243   1.212   1.273   1.329
58    V        -0.833  -0.921  -0.789  -0.845  -1.077  -0.880  -0.971  -1.045  -0.863
59    K        -0.100  -0.142  -0.061  -0.440  -0.473  -0.309  -0.376  -0.457  -0.336
60    Q        -0.100  -0.149  -0.060  -0.164  -0.344  -0.230  -0.376  -0.470  -0.334
61    G        -0.100  -0.142  -0.061  -0.276  -0.320  -0.327  -0.376  -0.457  -0.336
62    I         0.263   0.243   0.060   0.578   0.596   0.288   0.220   0.188  -0.124
63    K        -0.552  -0.746  -0.749  -0.698  -0.909  -0.911  -0.574  -0.820  -0.809
64    P         0.263   0.243   0.060   0.419   0.453   0.040   0.220   0.188  -0.124
65    A        -0.833  -0.921  -0.789  -0.814  -0.925  -0.698  -0.971  -1.045  -0.863
66    L         0.263   0.243   0.060   0.405   0.354   0.152   0.220   0.188  -0.124
67    D         0.263   0.072   0.037   0.302   0.012  -0.095   0.220  -0.085  -0.163
68    E        -0.552  -0.713  -0.761  -0.772  -1.039  -1.143  -0.574  -0.779  -0.825
69    A         1.143   1.188   1.227   0.991   1.008   1.121   1.212   1.273   1.329
70    R         1.143   1.188   1.227   1.347   1.409   1.451   1.212   1.273   1.329
71    E        -0.100   0.008  -0.034  -0.635  -0.447  -0.536  -0.376  -0.194  -0.287
72    E        -0.552  -0.578  -0.730  -0.602  -0.598  -0.784  -0.574  -0.593  -0.785
73    A        -0.552  -0.713  -0.761  -0.449  -0.711  -0.703  -0.574  -0.779  -0.825
74    P         1.143   1.188   1.227   1.232   1.303   1.345   1.212   1.273   1.329
75    F         1.143   1.188   1.227   1.198   1.257   1.313   1.212   1.273   1.329
76    E         0.165   0.076  -0.007  -0.066  -0.183  -0.281   0.069  -0.079  -0.241
77    N        -0.713  -0.646  -0.771  -0.516  -0.459  -0.600  -0.789  -0.699  -0.837
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    G        -0.713  -0.748  -0.779  -0.602  -0.679  -0.743  -0.789  -0.822  -0.848
85    G         1.143   1.188   1.227   1.141   1.205   1.260   1.212   1.273   1.329
86    K         0.165   0.076  -0.007  -0.063  -0.120  -0.260   0.069  -0.079  -0.241
87    L        -0.713  -0.748  -0.779  -0.508  -0.569  -0.617  -0.789  -0.822  -0.848
88    K        -1.460  -1.300  -1.331  -1.370  -1.083  -1.243  -1.360  -1.169  -1.152
89    E        -0.888  -0.811  -0.794  -1.079  -0.985  -0.900  -1.021  -0.908  -0.866
90    V        -1.565  -1.467  -1.351  -1.829  -1.714  -1.498  -1.468  -1.332  -1.171
91    D         0.044   0.001  -0.024   0.117   0.050   0.010  -0.128  -0.206  -0.271
92    K        -0.888  -0.814  -0.789  -1.126  -1.001  -1.042  -1.021  -0.910  -0.860
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -         0.044   0.120   0.008  -0.363  -0.236  -0.451  -0.128  -0.007  -0.214
95    -        -1.565  -1.486  -1.351  -1.348  -1.244  -1.052  -1.468  -1.350  -1.171
* 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/O60200
Output conservation file - output/O60200
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
