1     M         0.779   0.784   0.830   1.075   1.068   1.097   0.810   0.819   0.884
2     G         0.779   0.784   0.830   0.930   0.932   0.979   0.810   0.819   0.884
3     R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
4     V         0.779   0.784   0.830   0.710   0.714   0.800   0.810   0.819   0.884
5     R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
6     T         0.779   0.784   0.830   0.786   0.793   0.861   0.810   0.819   0.884
7     K         0.779   0.784   0.830   0.586   0.611   0.699   0.810   0.819   0.884
8     T         0.779   0.784   0.830   0.786   0.793   0.861   0.810   0.819   0.884
9     V        -0.373  -0.476  -0.444  -0.469  -0.647  -0.611  -0.533  -0.710  -0.693
10    K         0.779   0.784   0.830   0.586   0.611   0.699   0.810   0.819   0.884
11    R         0.020  -0.100  -0.411  -0.210  -0.353  -0.827   0.043  -0.127  -0.637
12    A         0.020  -0.100  -0.411   0.256   0.110  -0.401   0.043  -0.127  -0.637
13    S         0.020  -0.100  -0.411   0.208   0.078  -0.417   0.043  -0.127  -0.637
14    K        -0.373  -0.476  -0.444  -0.685  -0.871  -0.860  -0.533  -0.710  -0.693
15    A        -0.605  -0.436  -0.437  -0.814  -0.542  -0.549  -0.917  -0.644  -0.681
16    L        -1.862  -1.860  -1.762  -1.958  -1.926  -1.669  -1.781  -1.753  -1.547
17    I         0.779   0.784   0.830   0.826   0.824   0.894   0.810   0.819   0.884
18    E         0.779   0.784   0.830   0.811   0.808   0.882   0.810   0.819   0.884
19    R        -0.605  -0.616  -0.474  -1.195  -1.215  -0.942  -0.917  -0.948  -0.744
20    Y        -0.373  -0.219  -0.424  -0.117   0.083  -0.264  -0.533  -0.302  -0.659
21    Y         0.779   0.784   0.830   1.003   0.995   1.038   0.810   0.819   0.884
22    P         0.779   0.784   0.830   0.964   0.954   1.007   0.810   0.819   0.884
23    K        -0.373  -0.476  -0.444  -0.685  -0.871  -0.860  -0.533  -0.710  -0.693
24    L         0.779   0.784   0.830   0.658   0.692   0.758   0.810   0.819   0.884
25    T         0.779   0.784   0.830   0.786   0.793   0.861   0.810   0.819   0.884
26    L        -0.373  -0.215  -0.421  -0.435  -0.198  -0.477  -0.533  -0.296  -0.655
27    D         0.779   0.784   0.830   0.875   0.876   0.935   0.810   0.819   0.884
28    F         0.779   0.784   0.830   1.027   1.022   1.058   0.810   0.819   0.884
29    Q        -0.715  -0.656  -0.477  -0.907  -0.817  -0.543  -1.109  -1.019  -0.749
30    T         0.779   0.784   0.830   0.786   0.793   0.861   0.810   0.819   0.884
31    N         0.779   0.784   0.830   0.983   0.991   1.023   0.810   0.819   0.884
32    K         0.779   0.784   0.830   0.586   0.611   0.699   0.810   0.819   0.884
33    R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
34    L        -0.605  -0.653  -0.476  -0.892  -0.965  -0.674  -0.917  -1.014  -0.748
35    C        -1.989  -1.893  -1.768  -1.704  -1.623  -1.491  -1.877  -1.774  -1.553
36    D        -0.373  -0.219  -0.424  -0.293  -0.070  -0.435  -0.533  -0.302  -0.659
37    E         0.779   0.784   0.830   0.811   0.808   0.882   0.810   0.819   0.884
38    I        -0.373  -0.476  -0.444  -0.377  -0.572  -0.566  -0.533  -0.710  -0.693
39    A         0.779   0.784   0.830   0.890   0.896   0.947   0.810   0.819   0.884
40    T        -1.609  -1.469  -1.235  -1.897  -1.659  -1.310  -1.781  -1.601  -1.287
41    I         0.779   0.784   0.830   0.826   0.824   0.894   0.810   0.819   0.884
42    Q        -1.258  -1.233  -1.224  -1.176  -1.172  -1.094  -1.397  -1.382  -1.275
43    S         0.779   0.784   0.830   0.836   0.857   0.902   0.810   0.819   0.884
44    K         0.779   0.784   0.830   0.586   0.611   0.699   0.810   0.819   0.884
45    R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
46    L         0.779   0.784   0.830   0.658   0.692   0.758   0.810   0.819   0.884
47    R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
48    N         0.779   0.784   0.830   0.983   0.991   1.023   0.810   0.819   0.884
49    K         0.779   0.784   0.830   0.586   0.611   0.699   0.810   0.819   0.884
50    I         0.779   0.784   0.830   0.826   0.824   0.894   0.810   0.819   0.884
51    A         0.779   0.784   0.830   0.890   0.896   0.947   0.810   0.819   0.884
52    G         0.779   0.784   0.830   0.930   0.932   0.979   0.810   0.819   0.884
53    Y         0.779   0.784   0.830   1.003   0.995   1.038   0.810   0.819   0.884
54    T         0.779   0.784   0.830   0.786   0.793   0.861   0.810   0.819   0.884
55    T         0.779   0.784   0.830   0.786   0.793   0.861   0.810   0.819   0.884
56    H         0.779   0.784   0.830   1.104   1.097   1.121   0.810   0.819   0.884
57    L         0.779   0.784   0.830   0.658   0.692   0.758   0.810   0.819   0.884
58    M         0.779   0.784   0.830   1.075   1.068   1.097   0.810   0.819   0.884
59    K         0.020   0.176  -0.397  -0.097   0.110  -0.757   0.043   0.243  -0.613
60    R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
61    I         0.779   0.784   0.830   0.826   0.824   0.894   0.810   0.819   0.884
62    Q         0.779   0.784   0.830   0.890   0.893   0.947   0.810   0.819   0.884
63    K        -0.605  -0.653  -0.476  -1.134  -1.261  -0.941  -0.917  -1.014  -0.748
64    G         0.779   0.784   0.830   0.930   0.932   0.979   0.810   0.819   0.884
65    P         0.779   0.784   0.830   0.964   0.954   1.007   0.810   0.819   0.884
66    V         0.779   0.784   0.830   0.710   0.714   0.800   0.810   0.819   0.884
67    R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
68    G         0.779   0.784   0.830   0.930   0.932   0.979   0.810   0.819   0.884
69    I         0.779   0.784   0.830   0.826   0.824   0.894   0.810   0.819   0.884
70    S         0.779   0.784   0.830   0.836   0.857   0.902   0.810   0.819   0.884
71    F         0.779   0.784   0.830   1.027   1.022   1.058   0.810   0.819   0.884
72    K         0.779   0.784   0.830   0.586   0.611   0.699   0.810   0.819   0.884
73    L         0.779   0.784   0.830   0.658   0.692   0.758   0.810   0.819   0.884
74    Q         0.779   0.784   0.830   0.890   0.893   0.947   0.810   0.819   0.884
75    E         0.779   0.784   0.830   0.811   0.808   0.882   0.810   0.819   0.884
76    E         0.779   0.784   0.830   0.811   0.808   0.882   0.810   0.819   0.884
77    E         0.779   0.784   0.830   0.811   0.808   0.882   0.810   0.819   0.884
78    R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
79    E         0.779   0.784   0.830   0.811   0.808   0.882   0.810   0.819   0.884
80    R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
81    K         0.779   0.784   0.830   0.586   0.611   0.699   0.810   0.819   0.884
82    D         0.779   0.784   0.830   0.875   0.876   0.935   0.810   0.819   0.884
83    Q         0.779   0.784   0.830   0.890   0.893   0.947   0.810   0.819   0.884
84    Y         0.779   0.784   0.830   1.003   0.995   1.038   0.810   0.819   0.884
85    V         0.779   0.784   0.830   0.710   0.714   0.800   0.810   0.819   0.884
86    P         0.779   0.784   0.830   0.964   0.954   1.007   0.810   0.819   0.884
87    E        -0.373  -0.215  -0.421  -0.345  -0.127  -0.459  -0.533  -0.296  -0.655
88    V         0.020   0.062  -0.406   0.074   0.121  -0.527   0.043   0.096  -0.629
89    S         0.779   0.784   0.830   0.836   0.857   0.902   0.810   0.819   0.884
90    A        -0.373  -0.476  -0.444  -0.286  -0.469  -0.474  -0.533  -0.710  -0.693
91    L         0.779   0.784   0.830   0.658   0.692   0.758   0.810   0.819   0.884
92    D        -0.373  -0.476  -0.444  -0.300  -0.487  -0.484  -0.533  -0.710  -0.693
93    L        -0.113  -0.382  -0.446  -0.147  -0.484  -0.562  -0.142  -0.557  -0.697
94    S        -0.113  -0.382  -0.446  -0.001  -0.385  -0.551  -0.142  -0.557  -0.697
95    R        -0.952  -1.043  -1.215  -0.538  -0.716  -1.142  -0.935  -1.090  -1.262
96    S        -1.404  -1.478  -1.234  -1.522  -1.570  -1.204  -1.569  -1.617  -1.286
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    N        -2.323  -2.387  -2.188  -2.064  -2.185  -1.981  -1.973  -2.002  -1.718
100   G        -1.258  -1.217  -1.214  -1.146  -1.116  -1.060  -1.397  -1.357  -1.264
101   V        -1.862  -1.884  -1.760  -1.942  -1.956  -1.875  -1.781  -1.751  -1.545
102   L        -0.708  -0.895  -1.187  -0.624  -0.848  -1.312  -0.629  -0.865  -1.229
103   N        -1.719  -1.655  -1.756  -1.373  -1.265  -1.488  -1.589  -1.495  -1.541
104   V         0.020   0.134  -0.399   0.074   0.201  -0.515   0.043   0.189  -0.617
105   D         0.779   0.784   0.830   0.875   0.876   0.935   0.810   0.819   0.884
106   N        -2.532  -2.362  -2.193  -2.263  -2.074  -1.829  -2.164  -2.013  -1.722
107   Q        -1.527  -1.407  -1.225  -1.595  -1.411  -1.169  -1.685  -1.523  -1.276
108   T         0.779   0.784   0.830   0.786   0.793   0.861   0.810   0.819   0.884
109   S        -1.258  -1.155  -1.220  -1.356  -1.302  -1.298  -1.397  -1.317  -1.271
110   D         0.020   0.108  -0.399   0.238   0.333  -0.400   0.043   0.156  -0.617
111   L        -0.373  -0.476  -0.444  -0.435  -0.559  -0.505  -0.533  -0.710  -0.693
112   V        -0.715  -0.660  -0.472  -1.153  -1.051  -0.736  -1.109  -1.027  -0.741
113   K         0.020   0.108  -0.399  -0.030   0.088  -0.539   0.043   0.156  -0.617
114   S        -1.719  -1.783  -1.755  -1.476  -1.514  -1.499  -1.589  -1.629  -1.541
115   L         0.779   0.784   0.830   0.658   0.692   0.758   0.810   0.819   0.884
116   G         0.779   0.784   0.830   0.930   0.932   0.979   0.810   0.819   0.884
117   L        -1.527  -1.465  -1.226  -1.534  -1.398  -1.096  -1.685  -1.596  -1.276
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   K        -1.258  -1.331  -1.219  -1.485  -1.529  -1.302  -1.397  -1.468  -1.269
120   L        -0.715  -0.606  -0.467  -1.057  -0.836  -0.643  -1.109  -0.931  -0.732
121   P         0.779   0.784   0.830   0.964   0.954   1.007   0.810   0.819   0.884
122   L        -1.862  -1.792  -1.757  -2.022  -1.914  -1.779  -1.781  -1.700  -1.543
123   S        -2.867  -2.883  -2.546  -2.698  -2.754  -2.355  -2.260  -2.227  -1.838
124   V        -0.373  -0.219  -0.424  -0.469  -0.245  -0.576  -0.533  -0.302  -0.659
125   I        -1.862  -1.814  -1.755  -1.929  -1.860  -1.737  -1.781  -1.708  -1.542
126   N        -2.532  -2.384  -2.187  -2.180  -1.956  -1.687  -2.164  -1.996  -1.717
127   V        -1.862  -1.885  -1.757  -1.853  -1.839  -1.604  -1.781  -1.752  -1.542
128   S        -0.708  -0.927  -1.189  -0.426  -0.696  -1.140  -0.629  -0.905  -1.231
129   A        -0.522  -0.623  -0.476  -0.506  -0.700  -0.497  -0.776  -0.960  -0.749
130   Q        -0.952  -1.133  -1.218  -0.700  -0.986  -1.178  -0.935  -1.189  -1.266
131   R        -0.820  -0.899  -1.200  -0.917  -1.006  -1.367  -0.769  -0.877  -1.244
132   -        -1.420  -1.272  -1.223  -1.338  -1.109  -1.078  -1.565  -1.365  -1.273
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   D        -2.532  -2.526  -2.196  -2.272  -2.265  -1.807  -2.164  -2.114  -1.724
137   R         0.020  -0.098  -0.407  -0.180  -0.315  -0.719   0.043  -0.124  -0.630
138   R         0.020  -0.064  -0.406  -0.159  -0.246  -0.648   0.043  -0.076  -0.629
139   Y         0.020   0.173  -0.398   0.412   0.567  -0.213   0.043   0.239  -0.615
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   R        -1.401  -1.301  -1.739  -1.413  -1.284  -1.776  -1.205  -1.106  -1.525
144   K        -1.066  -1.228  -1.221  -1.275  -1.548  -1.466  -1.109  -1.325  -1.271
145   R         0.779   0.784   0.830   0.459   0.478   0.596   0.810   0.819   0.884
146   N        -1.401  -1.661  -1.758  -0.841  -1.186  -1.381  -1.205  -1.490  -1.543
* 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/P14127
Output conservation file - output/P14127
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
