1     M         1.142   1.158   1.223   1.537   1.562   1.650   1.200   1.223   1.317
2     S         1.142   1.158   1.223   1.293   1.323   1.424   1.200   1.223   1.317
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     D        -0.517  -0.461  -0.293  -0.532  -0.480  -0.271  -0.845  -0.758  -0.502
6     S        -0.935  -1.004  -1.126  -1.391  -1.455  -1.440  -0.845  -0.944  -1.049
7     I        -2.041  -1.923  -1.788  -1.855  -1.838  -1.556  -1.755  -1.625  -1.399
8     I        -1.279  -1.347  -1.164  -0.483  -0.568  -0.404  -1.300  -1.351  -1.095
9     S         1.142   1.158   1.223   1.293   1.323   1.424   1.200   1.223   1.317
10    F         0.064   0.194  -0.187   0.804   0.938   0.444   0.064   0.244  -0.330
11    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
12    A         0.064   0.084  -0.194  -0.618  -0.570  -0.805   0.064   0.091  -0.340
13    F        -0.382  -0.238  -0.248  -0.034   0.137   0.095  -0.618  -0.392  -0.429
14    I         1.142   1.158   1.223   1.416   1.437   1.538   1.200   1.223   1.317
15    L         1.142   1.158   1.223   1.243   1.271   1.377   1.200   1.223   1.317
16    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
17    D         1.142   1.158   1.223   1.184   1.213   1.322   1.200   1.223   1.317
18    A         0.064  -0.142  -0.225  -0.647  -0.860  -0.897   0.064  -0.241  -0.391
19    G        -0.382  -0.294  -0.259  -0.317  -0.197  -0.221  -0.618  -0.481  -0.446
20    L        -1.832  -1.848  -1.789  -0.827  -0.873  -0.805  -1.527  -1.540  -1.399
21    E         0.064   0.084  -0.194   0.214   0.231  -0.131   0.064   0.091  -0.340
22    I         0.064   0.084  -0.194   0.648   0.661   0.305   0.064   0.091  -0.340
23    T         1.142   1.158   1.223   1.473   1.496   1.591   1.200   1.223   1.317
24    S        -0.382  -0.436  -0.296  -0.533  -0.768  -0.726  -0.618  -0.715  -0.508
25    D        -0.382  -0.266  -0.270  -0.277  -0.115  -0.209  -0.618  -0.435  -0.465
26    N        -0.517  -0.461  -0.293  -0.030   0.010   0.194  -0.845  -0.758  -0.502
27    L         0.064  -0.142  -0.225   0.474   0.242   0.112   0.064  -0.241  -0.391
28    L        -0.382  -0.403  -0.295   0.043   0.015   0.151  -0.618  -0.660  -0.506
29    T        -0.382  -0.294  -0.259  -0.349  -0.189  -0.366  -0.618  -0.481  -0.446
30    I        -0.382  -0.295  -0.264   0.032   0.135   0.102  -0.618  -0.483  -0.454
31    T         0.064  -0.142  -0.225   0.698   0.455   0.294   0.064  -0.241  -0.391
32    K         1.142   1.158   1.223   1.367   1.379   1.493   1.200   1.223   1.317
33    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
34    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
35    G         0.064  -0.142  -0.225   0.364   0.131   0.007   0.064  -0.241  -0.391
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    A         0.064  -0.142  -0.225  -0.687  -0.926  -0.999   0.064  -0.241  -0.391
38    N        -1.279  -1.359  -1.160  -0.532  -0.667  -0.522  -1.300  -1.367  -1.091
39    V         0.064   0.084  -0.194   0.667   0.682   0.314   0.064   0.091  -0.340
40    D        -0.382  -0.418  -0.293  -0.277  -0.372  -0.257  -0.618  -0.686  -0.502
41    N        -1.832  -1.848  -1.789  -0.607  -0.648  -0.682  -1.527  -1.540  -1.399
42    V         0.064  -0.142  -0.225   0.667   0.425   0.269   0.064  -0.241  -0.391
43    W         1.142   1.158   1.223   1.592   1.616   1.702   1.200   1.223   1.317
44    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
45    D        -0.935  -1.093  -1.136  -0.429  -0.641  -0.796  -0.845  -1.044  -1.061
46    V        -0.935  -1.093  -1.136  -0.090  -0.318  -0.437  -0.845  -1.044  -1.061
47    Y        -0.517  -0.451  -0.288   0.042   0.107   0.267  -0.845  -0.740  -0.495
48    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
49    K         1.142   1.158   1.223   1.367   1.379   1.493   1.200   1.223   1.317
50    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
51    L         0.064   0.141  -0.189   0.479   0.559   0.170   0.064   0.172  -0.332
52    E         1.142   1.158   1.223   1.028   1.052   1.178   1.200   1.223   1.317
53    G         1.142   1.158   1.223   1.141   1.174   1.283   1.200   1.223   1.317
54    K         1.142   1.158   1.223   1.367   1.379   1.493   1.200   1.223   1.317
55    D         0.064   0.141  -0.189   0.442   0.523   0.169   0.064   0.172  -0.332
56    L        -1.832  -1.892  -1.784  -0.876  -0.962  -0.870  -1.527  -1.582  -1.395
57    K         1.142   1.158   1.223   1.367   1.379   1.493   1.200   1.223   1.317
58    E         0.064  -0.142  -0.225   0.214  -0.040  -0.177   0.064  -0.241  -0.391
59    I        -0.517  -0.461  -0.293  -0.208  -0.161   0.030  -0.845  -0.758  -0.502
60    L         1.142   1.158   1.223   1.243   1.271   1.377   1.200   1.223   1.317
61    S        -0.382  -0.294  -0.259   0.010   0.115   0.120  -0.618  -0.481  -0.446
62    G        -1.279  -1.347  -1.164  -0.760  -0.801  -0.617  -1.300  -1.351  -1.095
63    F         0.064  -0.142  -0.225   0.672   0.440   0.280   0.064  -0.241  -0.391
64    H        -1.279  -1.347  -1.164  -1.031  -1.130  -1.064  -1.300  -1.351  -1.095
65    N        -1.832  -1.775  -1.778  -1.831  -1.775  -1.495  -1.527  -1.472  -1.389
66    A         0.064  -0.142  -0.225  -0.658  -0.876  -0.925   0.064  -0.241  -0.391
67    G        -0.382  -0.294  -0.259  -0.690  -0.521  -0.674  -0.618  -0.481  -0.446
68    P         0.064  -0.142  -0.225   0.565   0.208  -0.176   0.064  -0.241  -0.391
69    V         0.064   0.194  -0.187  -0.579  -0.426  -0.713   0.064   0.244  -0.330
70    A        -0.935  -0.743  -1.086  -1.323  -1.119  -1.320  -0.845  -0.607  -1.002
71    G        -0.469  -0.467  -0.297  -0.951  -1.074  -0.895  -0.764  -0.768  -0.510
72    A        -1.383  -1.263  -1.163  -1.434  -1.151  -1.141  -1.418  -1.271  -1.094
73    G        -0.935  -0.812  -1.093  -1.334  -1.184  -1.340  -0.845  -0.693  -1.010
74    A         0.064   0.155  -0.181  -0.658  -0.531  -0.884   0.064   0.191  -0.320
75    A        -0.382  -0.294  -0.259  -1.182  -1.060  -0.946  -0.618  -0.481  -0.446
76    S        -1.488  -1.395  -1.184  -1.729  -1.528  -1.369  -1.527  -1.406  -1.116
77    G        -0.382  -0.238  -0.248  -1.182  -0.994  -0.941  -0.618  -0.392  -0.429
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    A        -0.469  -0.454  -0.297  -0.953  -0.998  -0.874  -0.764  -0.746  -0.509
80    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
81    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
82    A        -0.935  -1.093  -1.136  -1.426  -1.591  -1.503  -0.845  -1.044  -1.061
83    G         0.064   0.215  -0.184   0.141   0.349  -0.446   0.064   0.272  -0.324
84    G        -2.041  -1.999  -1.795  -1.772  -1.922  -1.653  -1.755  -1.696  -1.405
85    D        -2.594  -2.392  -2.281  -2.770  -2.607  -2.287  -1.982  -1.787  -1.588
86    A        -1.279  -1.138  -1.142  -1.475  -1.244  -1.279  -1.300  -1.120  -1.071
87    A         0.064  -0.142  -0.225  -0.687  -0.926  -0.999   0.064  -0.241  -0.391
88    A         1.142   1.158   1.223   0.184   0.237   0.394   1.200   1.223   1.317
89    E        -1.279  -1.338  -1.159  -1.832  -1.833  -1.509  -1.300  -1.340  -1.089
90    E         0.064  -0.142  -0.225   0.024  -0.335  -0.672   0.064  -0.241  -0.391
91    E         0.064   0.141  -0.189   0.024   0.123  -0.571   0.064   0.172  -0.332
92    K        -1.279  -1.318  -1.155  -1.697  -1.790  -1.483  -1.300  -1.314  -1.084
93    E        -2.047  -1.980  -1.801  -1.706  -1.568  -1.510  -1.746  -1.670  -1.410
94    E         0.064  -0.142  -0.225   0.268   0.042  -0.046   0.064  -0.241  -0.391
95    E         0.064   0.084  -0.194   0.237   0.254  -0.080   0.064   0.091  -0.340
96    A        -0.382  -0.275  -0.271  -0.809  -0.608  -0.827  -0.618  -0.451  -0.466
97    A        -0.382  -0.436  -0.296  -1.042  -1.028  -0.721  -0.618  -0.715  -0.508
98    E         1.142   1.158   1.223   1.028   1.052   1.178   1.200   1.223   1.317
99    E         1.142   1.158   1.223   1.028   1.052   1.178   1.200   1.223   1.317
100   S         1.142   1.158   1.223   1.293   1.323   1.424   1.200   1.223   1.317
101   D         1.142   1.158   1.223   1.184   1.213   1.322   1.200   1.223   1.317
102   D        -0.935  -1.036  -1.125  -0.467  -0.643  -0.851  -0.845  -0.979  -1.047
103   D         1.142   1.158   1.223   1.184   1.213   1.322   1.200   1.223   1.317
104   M         1.142   1.158   1.223   1.537   1.562   1.650   1.200   1.223   1.317
105   G         1.142   1.158   1.223   1.141   1.174   1.283   1.200   1.223   1.317
106   F         0.064   0.155  -0.181   0.691   0.787   0.382   0.064   0.191  -0.320
107   G         1.142   1.158   1.223   1.141   1.174   1.283   1.200   1.223   1.317
108   L         1.142   1.158   1.223   1.243   1.271   1.377   1.200   1.223   1.317
109   F         1.142   1.158   1.223   1.441   1.471   1.561   1.200   1.223   1.317
110   D         1.142   1.158   1.223   1.184   1.213   1.322   1.200   1.223   1.317
* 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/P10622
Output conservation file - output/P10622
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
