1     M         1.244   1.267   1.335   1.378   1.404   1.507   1.336   1.365   1.461
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     -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    A        -0.570  -0.641  -0.505  -0.816  -0.915  -0.665  -0.786  -0.859  -0.672
34    V        -0.691  -0.685  -0.538  -1.130  -1.089  -0.841  -0.932  -0.916  -0.712
35    D         0.508   0.343   0.284   0.642   0.382   0.244   0.485   0.213   0.076
36    V         0.019   0.061   0.164  -0.480  -0.402  -0.221  -0.365  -0.295  -0.147
37    P         1.244   1.267   1.335   1.406   1.433   1.533   1.336   1.365   1.461
38    R        -0.557  -0.633  -0.500  -0.506  -0.635  -0.444  -0.790  -0.854  -0.666
39    A         0.508   0.586   0.318   0.642   0.743   0.311   0.485   0.601   0.137
40    V         1.244   1.267   1.335   1.009   1.056   1.166   1.336   1.365   1.461
41    I        -0.184  -0.173  -0.386  -0.217  -0.205  -0.579  -0.223  -0.204  -0.504
42    N        -1.535  -1.519  -1.391  -1.358  -1.365  -1.184  -1.357  -1.322  -1.134
43    K         1.244   1.267   1.335   1.321   1.356   1.455   1.336   1.365   1.461
44    L         1.244   1.267   1.335   1.158   1.200   1.304   1.336   1.365   1.461
45    M        -0.557  -0.630  -0.497  -0.832  -0.933  -0.718  -0.790  -0.851  -0.663
46    L        -0.184  -0.280  -0.427  -0.151  -0.319  -0.593  -0.223  -0.366  -0.560
47    F         1.244   1.267   1.335   1.245   1.282   1.385   1.336   1.365   1.461
48    T         1.244   1.267   1.335   1.245   1.279   1.385   1.336   1.365   1.461
49    A        -0.470  -0.543  -0.482  -0.863  -0.953  -0.870  -0.649  -0.722  -0.641
50    A        -0.184  -0.079  -0.373  -0.239  -0.102  -0.466  -0.223  -0.079  -0.485
51    M         1.244   1.267   1.335   1.378   1.404   1.507   1.336   1.365   1.461
52    V         0.019   0.029   0.151  -0.480  -0.451  -0.232  -0.365  -0.356  -0.172
53    V        -0.184  -0.173  -0.386  -0.363  -0.326  -0.671  -0.223  -0.204  -0.504
54    L        -0.825  -0.864  -0.957  -0.755  -0.825  -0.921  -0.790  -0.841  -0.908
55    P         1.244   1.267   1.335   1.406   1.433   1.533   1.336   1.365   1.461
56    V        -0.557  -0.633  -0.494  -0.998  -1.079  -0.855  -0.790  -0.855  -0.659
57    L        -0.825  -0.947  -0.953  -0.847  -1.021  -1.066  -0.790  -0.930  -0.905
58    T        -0.184  -0.336  -0.419  -0.008  -0.216  -0.302  -0.223  -0.437  -0.549
59    F         0.508   0.343   0.284   0.612   0.404   0.323   0.485   0.213   0.076
60    F         1.244   1.267   1.335   1.245   1.282   1.385   1.336   1.365   1.461
61    I        -1.046  -1.083  -0.984  -1.096  -1.169  -0.950  -1.074  -1.097  -0.941
62    I        -1.401  -1.451  -1.371  -1.400  -1.477  -1.347  -1.216  -1.253  -1.115
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    Q         0.508   0.343   0.284   0.819   0.584   0.466   0.485   0.213   0.076
65    Q        -1.891  -1.857  -1.712  -1.284  -1.231  -1.036  -1.499  -1.451  -1.251
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    F        -0.184  -0.063  -0.385  -0.043   0.131  -0.318  -0.223  -0.054  -0.502
68    T        -0.184  -0.328  -0.429  -0.059  -0.261  -0.414  -0.223  -0.427  -0.564
69    P        -1.401  -1.413  -1.366  -1.061  -1.078  -0.996  -1.216  -1.217  -1.111
70    N         1.244   1.267   1.335   1.434   1.457   1.559   1.336   1.365   1.461
71    T        -0.470  -0.487  -0.488  -0.560  -0.594  -0.609  -0.649  -0.675  -0.650
72    L        -0.557  -0.633  -0.500  -0.847  -0.936  -0.715  -0.790  -0.854  -0.666
73    I        -0.184  -0.284  -0.429  -0.147  -0.282  -0.521  -0.223  -0.371  -0.564
74    S         0.508   0.343   0.284   0.642   0.375   0.244   0.485   0.213   0.076
75    G         1.244   1.267   1.335   1.424   1.444   1.551   1.336   1.365   1.461
76    G         0.508   0.343   0.284   0.717   0.445   0.310   0.485   0.213   0.076
77    L        -0.470  -0.548  -0.486  -0.757  -0.833  -0.790  -0.649  -0.728  -0.646
78    A         0.508   0.530   0.314   0.391   0.407   0.142   0.485   0.515   0.130
79    A         1.244   1.267   1.335   1.049   1.065   1.203   1.336   1.365   1.461
80    A        -1.046  -1.106  -0.993  -1.335  -1.417  -1.232  -1.074  -1.114  -0.950
81    M        -0.470  -0.370  -0.457  -0.591  -0.435  -0.624  -0.649  -0.523  -0.607
82    A         1.244   1.267   1.335   1.049   1.065   1.203   1.336   1.365   1.461
83    N         1.244   1.267   1.335   1.434   1.457   1.559   1.336   1.365   1.461
84    V        -0.184  -0.117  -0.394  -0.363  -0.247  -0.685  -0.223  -0.129  -0.516
85    V         1.244   1.267   1.335   1.009   1.056   1.166   1.336   1.365   1.461
86    L         1.244   1.267   1.335   1.158   1.200   1.304   1.336   1.365   1.461
87    I         0.508   0.590   0.322   0.472   0.576   0.157   0.485   0.606   0.144
88    V        -0.825  -0.635  -0.909  -0.639  -0.352  -0.854  -0.790  -0.552  -0.855
89    Y         1.244   1.267   1.335   1.498   1.518   1.619   1.336   1.365   1.461
90    I         0.019   0.051   0.157  -0.442  -0.384  -0.210  -0.365  -0.313  -0.160
91    V         0.171   0.222   0.189  -0.098  -0.014  -0.126  -0.082   0.003  -0.099
92    V        -0.470  -0.383  -0.463  -0.849  -0.700  -0.793  -0.649  -0.526  -0.616
93    A         1.244   1.267   1.335   1.049   1.065   1.203   1.336   1.365   1.461
94    F         0.508   0.343   0.284   0.592   0.373   0.276   0.485   0.213   0.076
95    R        -1.891  -1.877  -1.714  -1.706  -1.746  -1.428  -1.499  -1.465  -1.253
96    E         1.244   1.267   1.335   1.350   1.377   1.481   1.336   1.365   1.461
97    D         1.244   1.267   1.335   1.350   1.381   1.481   1.336   1.365   1.461
98    T        -0.825  -0.910  -0.949  -0.711  -0.818  -0.909  -0.790  -0.890  -0.900
99    E        -1.046  -1.019  -0.985  -0.992  -0.949  -0.859  -1.074  -1.038  -0.943
100   D        -1.535  -1.438  -1.379  -1.460  -1.308  -1.232  -1.357  -1.252  -1.124
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   H        -1.555  -1.401  -1.381  -1.132  -0.905  -0.888  -1.365  -1.197  -1.124
103   K        -0.312  -0.203  -0.414  -0.221  -0.055  -0.432  -0.401  -0.245  -0.543
104   V        -1.555  -1.501  -1.394  -1.416  -1.304  -1.195  -1.365  -1.300  -1.135
105   D         0.001   0.042   0.156  -0.134  -0.063   0.116  -0.401  -0.331  -0.162
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   G        -0.825  -0.721  -0.915  -0.552  -0.404  -0.685  -0.790  -0.656  -0.862
115   N        -1.535  -1.499  -1.385  -1.358  -1.297  -1.104  -1.357  -1.308  -1.129
116   K         0.508   0.590   0.322   0.663   0.773   0.394   0.485   0.606   0.144
117   K         1.244   1.267   1.335   1.321   1.356   1.455   1.336   1.365   1.461
118   E        -1.046  -1.007  -0.988  -0.931  -0.877  -0.831  -1.074  -1.025  -0.946
119   D        -2.246  -2.174  -1.990  -1.883  -1.789  -1.515  -1.641  -1.564  -1.339
* 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/P41806
Output conservation file - output/P41806
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
