1     M         1.033   1.035   1.087   1.421   1.423   1.492   1.079   1.084   1.156
2     K         1.033   1.035   1.087   1.200   1.201   1.287   1.079   1.084   1.156
3     Y         0.067   0.035  -0.200   0.720   0.682   0.370   0.049   0.001  -0.375
4     L         1.033   1.035   1.087   0.993   1.001   1.095   1.079   1.084   1.156
5     A         1.033   1.035   1.087   0.478   0.493   0.617   1.079   1.084   1.156
6     A         1.033   1.035   1.087   0.478   0.493   0.617   1.079   1.084   1.156
7     Y         1.033   1.035   1.087   1.435   1.439   1.505   1.079   1.084   1.156
8     L         1.033   1.035   1.087   0.993   1.001   1.095   1.079   1.084   1.156
9     L         1.033   1.035   1.087   0.993   1.001   1.095   1.079   1.084   1.156
10    L         0.067  -0.000  -0.203   0.261   0.187  -0.052   0.049  -0.051  -0.380
11    V        -1.817  -1.841  -1.655  -1.220  -1.294  -1.132  -1.598  -1.613  -1.361
12    Q        -0.827  -0.900  -1.036  -0.257  -0.382  -0.759  -0.774  -0.869  -1.017
13    G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
14    G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
15    N         0.067  -0.000  -0.203   0.684   0.600   0.276   0.049  -0.051  -0.380
16    A        -1.135  -1.096  -1.067  -1.001  -0.959  -1.099  -1.186  -1.146  -1.058
17    A        -0.332  -0.322  -0.278  -0.510  -0.505  -0.562  -0.569  -0.558  -0.505
18    P         1.033   1.035   1.087   1.421   1.423   1.492   1.079   1.084   1.156
19    S         0.067   0.140  -0.188   0.207   0.306  -0.312   0.049   0.151  -0.355
20    A         1.033   1.035   1.087   0.478   0.493   0.617   1.079   1.084   1.156
21    A        -1.135  -1.154  -1.073  -1.336  -1.340  -1.125  -1.186  -1.203  -1.064
22    D         0.067  -0.000  -0.203   0.352   0.255  -0.148   0.049  -0.051  -0.380
23    I        -0.332  -0.360  -0.286   0.080   0.022   0.076  -0.569  -0.622  -0.518
24    K        -0.827  -0.764  -1.019  -0.279  -0.232  -0.566  -0.774  -0.705  -0.996
25    A        -0.827  -0.821  -1.025  -0.944  -0.926  -1.047  -0.774  -0.774  -1.004
26    V        -0.332  -0.299  -0.273  -0.123  -0.079  -0.122  -0.569  -0.520  -0.497
27    V        -0.827  -0.725  -1.014  -0.441  -0.333  -0.654  -0.774  -0.651  -0.991
28    E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
29    S        -0.827  -0.929  -1.039  -0.505  -0.666  -0.921  -0.774  -0.905  -1.021
30    V         1.033   1.035   1.087   1.284   1.285   1.365   1.079   1.084   1.156
31    G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
32    A        -1.322  -1.296  -1.103  -1.237  -1.229  -0.983  -1.392  -1.363  -1.098
33    E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
34    V        -0.332  -0.332  -0.283  -0.726  -0.720  -0.565  -0.569  -0.575  -0.514
35    D        -0.332  -0.305  -0.276  -0.300  -0.260  -0.324  -0.569  -0.530  -0.502
36    E        -1.631  -1.722  -1.648  -1.345  -1.444  -1.296  -1.392  -1.489  -1.353
37    A        -1.817  -1.830  -1.659  -2.126  -2.148  -1.951  -1.598  -1.604  -1.364
38    R         0.067  -0.000  -0.203   0.704   0.617   0.271   0.049  -0.051  -0.380
39    I        -1.135  -1.140  -1.069  -0.687  -0.686  -0.654  -1.186  -1.184  -1.059
40    N        -1.817  -1.830  -1.659  -0.985  -1.024  -0.887  -1.598  -1.604  -1.364
41    E        -1.135  -1.116  -1.066  -1.657  -1.615  -1.477  -1.186  -1.156  -1.055
42    L         1.033   1.035   1.087   0.993   1.001   1.095   1.079   1.084   1.156
43    L         0.067   0.035  -0.200   0.261   0.227  -0.048   0.049   0.001  -0.375
44    S        -1.135  -1.154  -1.073  -0.755  -0.777  -0.666  -1.186  -1.203  -1.064
45    S        -1.817  -1.777  -1.652  -1.694  -1.641  -1.633  -1.598  -1.560  -1.358
46    L         1.033   1.035   1.087   0.993   1.001   1.095   1.079   1.084   1.156
47    E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
48    G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
49    K         1.033   1.035   1.087   1.200   1.201   1.287   1.079   1.084   1.156
50    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    S        -1.817  -1.843  -1.660  -1.163  -1.182  -0.967  -1.598  -1.615  -1.364
52    L        -0.827  -0.929  -1.039  -0.441  -0.561  -0.679  -0.774  -0.905  -1.021
53    E        -2.313  -2.282  -2.106  -1.701  -1.699  -1.596  -1.804  -1.777  -1.537
54    E         0.067   0.012  -0.201  -0.014  -0.078  -0.328   0.049  -0.033  -0.378
55    I         0.067   0.110  -0.188   0.261   0.308  -0.033   0.049   0.108  -0.355
56    I         0.067  -0.000  -0.203   0.611   0.527   0.216   0.049  -0.051  -0.380
57    A         1.033   1.035   1.087   0.478   0.493   0.617   1.079   1.084   1.156
58    E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
59    G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
60    Q        -0.827  -0.743  -1.015  -0.074   0.002  -0.393  -0.774  -0.678  -0.993
61    K        -1.631  -1.567  -1.628  -0.773  -0.720  -0.875  -1.392  -1.329  -1.335
62    K         1.033   1.035   1.087   1.200   1.201   1.287   1.079   1.084   1.156
63    F        -0.332  -0.274  -0.261  -0.190  -0.121  -0.090  -0.569  -0.479  -0.477
64    A         1.033   1.035   1.087   0.478   0.493   0.617   1.079   1.084   1.156
65    T         0.067   0.110  -0.188   0.385   0.428   0.079   0.049   0.108  -0.355
66    V         1.033   1.035   1.087   1.284   1.285   1.365   1.079   1.084   1.156
67    P         1.033   1.035   1.087   1.421   1.423   1.492   1.079   1.084   1.156
68    T        -1.817  -1.790  -1.653  -1.363  -1.374  -1.258  -1.598  -1.571  -1.359
69    G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
70    G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
71    A         1.033   1.035   1.087   0.478   0.493   0.617   1.079   1.084   1.156
72    S        -0.332  -0.338  -0.282  -0.820  -0.823  -0.685  -0.569  -0.584  -0.513
73    S        -1.135  -1.171  -1.073  -1.511  -1.547  -1.377  -1.186  -1.226  -1.065
74    A        -1.135  -1.088  -1.059  -1.474  -1.395  -1.256  -1.186  -1.118  -1.046
75    A        -0.453  -0.433  -0.294  -1.083  -1.066  -0.840  -0.774  -0.746  -0.533
76    A         0.067   0.012  -0.201  -0.362  -0.427  -0.729   0.049  -0.033  -0.378
77    G        -1.322  -1.282  -1.102  -1.692  -1.697  -1.415  -1.392  -1.348  -1.095
78    A        -1.135  -1.166  -1.078  -1.511  -1.514  -1.373  -1.186  -1.226  -1.070
79    A        -0.827  -0.775  -1.022  -1.134  -1.080  -1.381  -0.774  -0.719  -1.000
80    G         0.067   0.110  -0.188  -0.362  -0.300  -0.708   0.049   0.108  -0.355
81    A        -0.332  -0.232  -0.254  -0.940  -0.781  -0.807  -0.569  -0.411  -0.465
82    A        -1.135  -1.161  -1.071  -1.589  -1.609  -1.425  -1.186  -1.214  -1.062
83    A         0.067   0.012  -0.201  -0.362  -0.427  -0.729   0.049  -0.033  -0.378
84    G        -1.817  -1.839  -1.658  -2.017  -1.981  -1.725  -1.598  -1.610  -1.363
85    G        -0.453  -0.433  -0.294  -1.083  -1.066  -0.840  -0.774  -0.746  -0.532
86    D        -1.631  -1.661  -1.636  -1.643  -1.743  -1.828  -1.392  -1.427  -1.342
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    A        -0.332  -0.332  -0.283  -0.877  -0.892  -0.896  -0.569  -0.575  -0.514
90    A        -0.332  -0.364  -0.287  -1.018  -1.079  -0.948  -0.569  -0.629  -0.521
91    E        -1.322  -1.287  -1.103  -1.729  -1.648  -1.427  -1.392  -1.353  -1.097
92    E         0.067   0.035  -0.200  -0.016  -0.054  -0.330   0.049   0.001  -0.375
93    E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
94    K        -0.453  -0.422  -0.289  -0.627  -0.624  -0.422  -0.774  -0.727  -0.524
95    E        -0.453  -0.422  -0.289  -0.627  -0.547  -0.374  -0.774  -0.727  -0.524
96    E         0.067   0.035  -0.200   0.003  -0.034  -0.288   0.049   0.001  -0.375
97    E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
98    A        -0.453  -0.422  -0.289  -1.208  -1.123  -0.918  -0.774  -0.727  -0.524
99    K         0.067   0.140  -0.188   0.296   0.391  -0.233   0.049   0.151  -0.355
100   E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
101   E         1.033   1.035   1.087   0.751   0.758   0.870   1.079   1.084   1.156
102   S         1.033   1.035   1.087   1.113   1.117   1.206   1.079   1.084   1.156
103   D         1.033   1.035   1.087   1.207   1.214   1.294   1.079   1.084   1.156
104   D        -0.332  -0.360  -0.286  -0.300  -0.377  -0.354  -0.569  -0.622  -0.518
105   D         1.033   1.035   1.087   1.207   1.214   1.294   1.079   1.084   1.156
106   M         1.033   1.035   1.087   1.421   1.423   1.492   1.079   1.084   1.156
107   G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
108   F         0.067   0.012  -0.201   0.689   0.624   0.318   0.049  -0.033  -0.378
109   G         1.033   1.035   1.087   0.894   0.904   1.003   1.079   1.084   1.156
110   L         1.033   1.035   1.087   0.993   1.001   1.095   1.079   1.084   1.156
111   F         1.033   1.035   1.087   1.421   1.426   1.492   1.079   1.084   1.156
112   D         1.033   1.035   1.087   1.207   1.214   1.294   1.079   1.084   1.156
* 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/P02400
Output conservation file - output/P02400
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
