1     M         1.432   1.448   1.554   1.682   1.699   1.857   1.533   1.559   1.723
2     P        -1.512  -1.592  -1.432  -1.467  -1.594  -1.370  -1.278  -1.332  -1.122
3     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S         0.544   0.551   0.371   0.690   0.697   0.415   0.492   0.497   0.148
5     F        -0.561  -0.569  -0.481  -0.489  -0.518  -0.385  -0.757  -0.769  -0.637
6     T         1.432   1.448   1.554   1.565   1.580   1.747   1.533   1.559   1.723
7     S         1.432   1.448   1.554   1.507   1.530   1.693   1.533   1.559   1.723
8     I        -0.958  -1.092  -0.984  -0.919  -1.116  -0.981  -0.926  -1.061  -0.908
9     A        -0.488  -0.484  -0.418  -0.623  -0.557  -0.473  -0.692  -0.654  -0.556
10    R        -0.342  -0.316  -0.414  -0.375  -0.396  -0.480  -0.458  -0.479  -0.551
11    I        -1.171  -1.153  -1.022  -1.421  -1.458  -1.238  -1.160  -1.136  -0.946
12    G        -1.042  -1.047  -0.977  -0.974  -1.002  -0.880  -1.043  -1.030  -0.900
13    D        -1.300  -1.440  -1.400  -0.974  -1.198  -1.178  -1.043  -1.184  -1.092
14    Y        -0.958  -0.977  -0.951  -0.840  -0.882  -0.907  -0.926  -0.936  -0.874
15    I         0.690   0.583   0.446   0.787   0.666   0.454   0.713   0.548   0.283
16    L        -0.017  -0.219  -0.353  -0.191  -0.461  -0.645   0.011  -0.265  -0.460
17    K        -0.683  -0.572  -0.885  -0.552  -0.414  -0.876  -0.575  -0.447  -0.794
18    S        -0.700  -0.615  -0.481  -0.782  -0.672  -0.460  -0.926  -0.823  -0.638
19    P         0.690   0.583   0.446   0.875   0.754   0.566   0.713   0.548   0.283
20    V        -1.983  -1.983  -1.774  -1.854  -1.784  -1.513  -1.512  -1.494  -1.245
21    L         1.432   1.448   1.554   1.097   1.125   1.309   1.533   1.559   1.723
22    S        -0.683  -0.803  -0.932  -0.389  -0.559  -0.782  -0.575  -0.726  -0.846
23    K         1.432   1.448   1.554   1.373   1.396   1.567   1.533   1.559   1.723
24    L        -1.171  -1.171  -1.004  -1.338  -1.321  -1.078  -1.160  -1.145  -0.929
25    C        -1.171  -1.120  -0.998  -1.183  -1.209  -0.978  -1.160  -1.102  -0.922
26    V        -1.300  -1.405  -1.398  -1.047  -1.277  -1.306  -1.043  -1.153  -1.090
27    P         1.432   1.448   1.554   1.489   1.518   1.676   1.533   1.559   1.723
28    V        -0.617  -0.613  -0.485  -0.840  -0.857  -0.712  -0.809  -0.809  -0.640
29    A         0.129   0.122   0.258  -0.187  -0.200   0.020  -0.224  -0.251  -0.064
30    N        -1.042  -0.969  -0.958  -0.910  -0.798  -0.729  -1.043  -0.961  -0.884
31    Q        -1.512  -1.549  -1.420  -1.272  -1.342  -1.166  -1.278  -1.301  -1.112
32    F         0.066   0.109   0.260   0.019   0.080   0.302  -0.341  -0.275  -0.060
33    I        -0.488  -0.480  -0.434  -0.550  -0.527  -0.426  -0.692  -0.680  -0.584
34    N        -1.171  -1.163  -1.007  -1.173  -1.130  -0.920  -1.160  -1.135  -0.931
35    L        -1.042  -1.061  -0.973  -1.245  -1.284  -1.098  -1.043  -1.048  -0.899
36    A         0.066   0.100   0.255  -0.277  -0.226   0.020  -0.341  -0.293  -0.070
37    G         1.432   1.448   1.554   1.687   1.711   1.862   1.533   1.559   1.723
38    Y         1.432   1.448   1.554   1.532   1.555   1.717   1.533   1.559   1.723
39    K         0.690   0.833   0.480   0.841   1.009   0.529   0.713   0.917   0.344
40    K        -0.617  -0.610  -0.481  -0.806  -0.794  -0.601  -0.809  -0.806  -0.637
41    L        -0.488  -0.498  -0.415  -0.603  -0.550  -0.447  -0.692  -0.676  -0.555
42    G         1.432   1.448   1.554   1.687   1.711   1.862   1.533   1.559   1.723
43    L         0.690   0.717   0.464   0.482   0.523   0.241   0.713   0.751   0.316
44    K         0.066   0.105   0.257  -0.220  -0.160   0.084  -0.341  -0.284  -0.066
45    F        -0.683  -0.846  -0.940  -0.217  -0.471  -0.654  -0.575  -0.772  -0.855
46    D         0.129   0.167   0.276   0.070   0.128   0.281  -0.224  -0.166  -0.030
47    D         1.432   1.448   1.554   1.521   1.546   1.707   1.533   1.559   1.723
48    L         1.432   1.448   1.554   1.097   1.125   1.309   1.533   1.559   1.723
49    I        -0.342  -0.400  -0.404  -0.442  -0.495  -0.541  -0.458  -0.524  -0.535
50    A        -1.641  -1.583  -1.426  -2.015  -1.925  -1.686  -1.395  -1.330  -1.117
51    E         1.432   1.448   1.554   1.305   1.336   1.504   1.533   1.559   1.723
52    E         1.432   1.448   1.554   1.305   1.336   1.504   1.533   1.559   1.723
53    N         0.129   0.167   0.276   0.128   0.185   0.328  -0.224  -0.166  -0.030
54    P        -0.342  -0.445  -0.428  -0.333  -0.491  -0.514  -0.458  -0.593  -0.571
55    I        -1.854  -1.864  -1.768  -1.626  -1.634  -1.534  -1.395  -1.401  -1.239
56    M        -0.683  -0.803  -0.932  -0.227  -0.414  -0.671  -0.575  -0.726  -0.846
57    Q         0.690   0.583   0.446   0.923   0.767   0.485   0.713   0.548   0.283
58    T        -0.958  -1.024  -0.977  -0.938  -1.084  -1.102  -0.926  -0.998  -0.902
59    A         1.432   1.448   1.554   1.294   1.323   1.493   1.533   1.559   1.723
60    L         0.324   0.366   0.352  -0.079  -0.008  -0.036   0.128   0.190   0.113
61    R        -1.171  -1.188  -1.009  -1.174  -1.192  -0.930  -1.160  -1.163  -0.935
62    R         1.432   1.448   1.554   1.500   1.515   1.686   1.533   1.559   1.723
63    L         1.432   1.448   1.554   1.097   1.125   1.309   1.533   1.559   1.723
64    P         0.690   0.583   0.446   0.848   0.717   0.501   0.713   0.548   0.283
65    E        -1.983  -1.914  -1.777  -1.968  -1.845  -1.666  -1.512  -1.443  -1.247
66    D        -1.983  -1.954  -1.789  -1.728  -1.707  -1.416  -1.512  -1.475  -1.255
67    E         0.690   0.682   0.462   0.606   0.603   0.227   0.713   0.700   0.312
68    S        -0.017   0.039  -0.309   0.234   0.306  -0.190   0.011   0.081  -0.399
69    Y         1.432   1.448   1.554   1.532   1.555   1.717   1.533   1.559   1.723
70    A        -0.488  -0.484  -0.436  -0.678  -0.644  -0.539  -0.692  -0.687  -0.586
71    R         1.432   1.448   1.554   1.500   1.515   1.686   1.533   1.559   1.723
72    A        -1.171  -1.089  -1.010  -1.132  -1.039  -0.935  -1.160  -1.092  -0.935
73    Y         0.690   0.682   0.462   0.916   0.910   0.624   0.713   0.700   0.312
74    R         1.432   1.448   1.554   1.500   1.515   1.686   1.533   1.559   1.723
75    I        -0.017   0.071  -0.294   0.116   0.240  -0.313   0.011   0.124  -0.378
76    I        -0.342  -0.433  -0.429  -0.402  -0.568  -0.611  -0.458  -0.604  -0.572
77    R        -0.342  -0.245  -0.378  -0.206  -0.088  -0.249  -0.458  -0.337  -0.499
78    A         1.432   1.448   1.554   1.294   1.323   1.493   1.533   1.559   1.723
79    H        -0.342  -0.464  -0.433  -0.010  -0.193  -0.172  -0.458  -0.622  -0.578
80    Q         1.432   1.448   1.554   1.618   1.641   1.797   1.533   1.559   1.723
81    T        -1.300  -1.035  -1.314  -1.222  -0.902  -1.153  -1.043  -0.768  -1.012
82    E        -0.342  -0.215  -0.345  -0.366  -0.144  -0.406  -0.458  -0.268  -0.451
83    L         0.690   0.584   0.448   0.443   0.313   0.124   0.713   0.549   0.287
84    T        -0.488  -0.527  -0.432  -0.515  -0.571  -0.440  -0.692  -0.721  -0.579
85    H        -0.017  -0.007  -0.300   0.421   0.430  -0.024   0.011   0.009  -0.386
86    H        -0.700  -0.625  -0.477  -0.713  -0.638  -0.411  -0.926  -0.827  -0.631
87    L         0.690   0.584   0.448   0.443   0.313   0.124   0.713   0.549   0.287
88    L         0.690   0.717   0.464   0.423   0.464   0.104   0.713   0.751   0.316
89    P         0.690   0.717   0.464   0.859   0.900   0.557   0.713   0.751   0.316
90    R        -1.171  -1.050  -0.986  -1.294  -1.116  -0.980  -1.160  -1.021  -0.907
91    N        -0.683  -0.727  -0.903  -0.314  -0.393  -0.703  -0.575  -0.634  -0.814
92    E        -0.958  -0.861  -0.951  -1.018  -0.885  -0.973  -0.926  -0.818  -0.874
93    W        -0.342  -0.292  -0.392  -0.093  -0.021  -0.246  -0.458  -0.392  -0.518
94    I        -0.488  -0.334  -0.411  -0.457  -0.244  -0.335  -0.692  -0.509  -0.552
95    K         0.690   0.583   0.446   0.743   0.612   0.424   0.713   0.548   0.283
96    A        -0.342  -0.299  -0.361  -0.319  -0.202  -0.339  -0.458  -0.377  -0.474
97    Q         0.324   0.490   0.400   0.192   0.435   0.310   0.128   0.398   0.200
98    E         0.324   0.451   0.364   0.159   0.355   0.210   0.128   0.334   0.134
99    D         1.432   1.448   1.554   1.521   1.546   1.707   1.533   1.559   1.723
100   V        -1.512  -1.469  -1.412  -1.273  -1.227  -1.139  -1.278  -1.235  -1.105
101   P        -0.488  -0.480  -0.434  -0.389  -0.365  -0.266  -0.692  -0.680  -0.584
102   Y         1.432   1.448   1.554   1.532   1.555   1.717   1.533   1.559   1.723
103   L         1.432   1.448   1.554   1.097   1.125   1.309   1.533   1.559   1.723
104   L        -1.641  -1.509  -1.433  -1.767  -1.529  -1.392  -1.395  -1.273  -1.123
105   P         1.432   1.448   1.554   1.489   1.518   1.676   1.533   1.559   1.723
106   Y        -0.017  -0.219  -0.353   0.202  -0.101  -0.377   0.011  -0.265  -0.460
107   I         0.324   0.307   0.307   0.137   0.103  -0.004   0.128   0.088   0.030
108   L        -0.017  -0.219  -0.353  -0.209  -0.487  -0.687   0.011  -0.265  -0.460
109   E        -0.017  -0.102  -0.329   0.059  -0.042  -0.345   0.011  -0.109  -0.427
110   A        -0.342  -0.464  -0.433  -0.452  -0.627  -0.576  -0.458  -0.622  -0.578
111   E         0.690   0.584   0.448   0.653   0.524   0.314   0.713   0.549   0.287
112   A         0.324   0.366   0.352   0.098   0.166   0.113   0.128   0.190   0.113
113   A        -0.342  -0.136  -0.346  -0.485  -0.161  -0.449  -0.458  -0.170  -0.453
114   A        -0.017  -0.051  -0.318   0.029  -0.021  -0.379   0.011  -0.046  -0.412
115   K        -0.488  -0.534  -0.442  -0.560  -0.618  -0.488  -0.692  -0.731  -0.591
116   E         1.432   1.448   1.554   1.305   1.336   1.504   1.533   1.559   1.723
117   K         0.324   0.307   0.298   0.217   0.180   0.145   0.128   0.087   0.013
118   D        -0.700  -0.652  -0.481  -1.027  -0.947  -0.690  -0.926  -0.866  -0.637
119   E        -0.488  -0.393  -0.430  -0.810  -0.709  -0.678  -0.692  -0.604  -0.579
120   L         0.690   0.584   0.448   0.482   0.364   0.218   0.713   0.549   0.287
121   D         1.432   1.448   1.554   1.521   1.546   1.707   1.533   1.559   1.723
122   N        -0.017  -0.219  -0.353   0.315   0.026  -0.229   0.011  -0.265  -0.460
123   I         0.129   0.201   0.285  -0.407  -0.281  -0.145  -0.224  -0.104  -0.013
124   E        -0.017  -0.219  -0.353  -0.014  -0.296  -0.544   0.011  -0.265  -0.460
125   V         0.690   0.822   0.480   0.836   1.005   0.475   0.713   0.900   0.344
126   S        -1.641  -1.516  -1.421  -1.633  -1.471  -1.331  -1.395  -1.282  -1.114
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   K        -0.958  -1.046  -0.977  -0.880  -0.989  -0.875  -0.926  -1.019  -0.902
* 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/P00128
Output conservation file - output/P00128
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
