1     M         1.248   1.257   1.343   1.576   1.582   1.701   1.339   1.355   1.490
2     I         0.497   0.397   0.208   0.508   0.392   0.091   0.524   0.369   0.032
3     F        -0.891  -0.962  -1.123  -0.310  -0.435  -0.703  -0.757  -0.850  -0.997
4     L         1.248   1.257   1.343   1.297   1.316   1.449   1.339   1.355   1.490
5     K         1.248   1.257   1.343   1.101   1.132   1.272   1.339   1.355   1.490
6     S        -0.545  -0.601  -0.626  -0.473  -0.560  -0.621  -0.640  -0.717  -0.734
7     V        -1.728  -1.613  -1.587  -1.669  -1.505  -1.434  -1.455  -1.351  -1.235
8     I        -0.070  -0.026   0.077  -0.347  -0.264  -0.125  -0.408  -0.344  -0.205
9     K        -0.133  -0.083   0.065  -0.517  -0.399  -0.162  -0.524  -0.450  -0.227
10    V         0.128   0.030   0.080  -0.123  -0.274  -0.145  -0.058  -0.243  -0.200
11    I         1.248   1.257   1.343   1.180   1.212   1.344   1.339   1.355   1.490
12    D         1.248   1.257   1.343   1.374   1.390   1.518   1.339   1.355   1.490
13    N         1.248   1.257   1.343   1.352   1.375   1.498   1.339   1.355   1.490
14    S         1.248   1.257   1.343   1.341   1.355   1.489   1.339   1.355   1.490
15    G         1.248   1.257   1.343   1.247   1.273   1.404   1.339   1.355   1.490
16    A         1.248   1.257   1.343   1.247   1.247   1.404   1.339   1.355   1.490
17    Q        -0.891  -1.104  -1.156  -0.480  -0.822  -0.966  -0.757  -1.008  -1.032
18    L        -0.545  -0.331  -0.574  -0.676  -0.340  -0.760  -0.640  -0.370  -0.661
19    A        -0.070  -0.078   0.061  -0.477  -0.554  -0.307  -0.408  -0.439  -0.235
20    E         1.248   1.257   1.343   1.508   1.517   1.639   1.339   1.355   1.490
21    C         1.248   1.257   1.343   1.492   1.509   1.625   1.339   1.355   1.490
22    I         0.497   0.389   0.205   0.501   0.368   0.068   0.524   0.358   0.027
23    K        -0.218  -0.375  -0.572  -0.197  -0.394  -0.659  -0.175  -0.391  -0.655
24    V         1.248   1.257   1.343   1.020   1.033   1.200   1.339   1.355   1.490
25    I        -0.823  -0.775  -0.655  -1.158  -1.119  -0.942  -0.990  -0.940  -0.768
26    R        -0.070  -0.012   0.076  -0.371  -0.275  -0.139  -0.408  -0.319  -0.208
27    K        -1.168  -1.216  -1.174  -1.139  -1.194  -1.075  -1.106  -1.141  -1.052
28    G        -0.338  -0.405  -0.595  -0.283  -0.375  -0.730  -0.334  -0.438  -0.686
29    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    P         1.248   1.257   1.343   1.471   1.478   1.605   1.339   1.355   1.490
31    K         0.431   0.490   0.200   0.321   0.414  -0.022   0.426   0.508   0.018
32    S        -1.168  -1.271  -1.177  -1.140  -1.326  -1.214  -1.106  -1.209  -1.057
33    P        -1.728  -1.759  -1.613  -1.183  -1.206  -0.990  -1.455  -1.470  -1.255
34    A         0.128   0.299   0.161   0.015   0.275   0.042  -0.058   0.216  -0.053
35    M        -2.204  -2.063  -1.951  -2.067  -1.870  -1.678  -1.688  -1.563  -1.373
36    V        -0.693  -0.699  -0.625  -1.144  -1.132  -0.960  -0.873  -0.867  -0.737
37    G         1.248   1.257   1.343   1.247   1.273   1.404   1.339   1.355   1.490
38    D         1.248   1.257   1.343   1.374   1.390   1.518   1.339   1.355   1.490
39    R        -0.823  -0.784  -0.668  -1.034  -0.985  -0.802  -0.990  -0.943  -0.784
40    I         0.497   0.435   0.214   0.468   0.395  -0.001   0.524   0.428   0.042
41    V         0.128   0.227   0.145  -0.151  -0.001  -0.099  -0.058   0.098  -0.080
42    C        -0.070  -0.068   0.063  -0.253  -0.297  -0.119  -0.408  -0.421  -0.231
43    V         1.248   1.257   1.343   1.020   1.033   1.200   1.339   1.355   1.490
44    I         0.128   0.258   0.169  -0.231  -0.019  -0.163  -0.058   0.149  -0.038
45    Q        -0.070  -0.029   0.074  -0.348  -0.271  -0.089  -0.408  -0.349  -0.212
46    K        -0.545  -0.546  -0.601  -0.669  -0.656  -0.724  -0.640  -0.627  -0.697
47    A         0.497   0.389   0.205   0.605   0.455   0.219   0.524   0.358   0.027
48    K         0.128   0.274   0.154  -0.048   0.191  -0.048  -0.058   0.175  -0.064
49    P        -0.545  -0.616  -0.624  -0.363  -0.477  -0.549  -0.640  -0.728  -0.729
50    L        -1.514  -1.624  -1.594  -1.299  -1.524  -1.461  -1.222  -1.336  -1.238
51    T        -1.690  -1.739  -1.621  -1.346  -1.433  -1.271  -1.398  -1.447  -1.260
52    Q        -0.480  -0.606  -0.638  -0.299  -0.540  -0.667  -0.524  -0.711  -0.744
53    N        -1.401  -1.354  -1.213  -1.328  -1.287  -1.064  -1.352  -1.302  -1.091
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    I        -0.480  -0.583  -0.635  -0.463  -0.598  -0.669  -0.524  -0.682  -0.740
56    T        -0.891  -1.104  -1.156  -0.566  -0.895  -1.032  -0.757  -1.008  -1.032
57    G        -0.218  -0.375  -0.572  -0.089  -0.311  -0.633  -0.175  -0.391  -0.655
58    T        -1.383  -1.353  -1.192  -1.330  -1.326  -1.106  -1.339  -1.297  -1.072
59    A        -0.545  -0.489  -0.579  -0.504  -0.396  -0.551  -0.640  -0.550  -0.666
60    N        -1.728  -1.585  -1.584  -1.689  -1.509  -1.467  -1.455  -1.311  -1.231
61    T        -0.823  -0.763  -0.671  -0.885  -0.818  -0.691  -0.990  -0.925  -0.788
62    N        -0.218  -0.409  -0.577   0.069  -0.179  -0.438  -0.175  -0.436  -0.663
63    R        -0.070  -0.090   0.061  -0.449  -0.529  -0.268  -0.408  -0.461  -0.235
64    V         0.497   0.397   0.208   0.340   0.198  -0.065   0.524   0.369   0.032
65    K         0.497   0.397   0.208   0.419   0.296  -0.002   0.524   0.369   0.032
66    K        -0.133  -0.087   0.064  -0.609  -0.523  -0.256  -0.524  -0.457  -0.230
67    G         0.128   0.227   0.145   0.010   0.178   0.005  -0.058   0.098  -0.080
68    D         0.497   0.397   0.208   0.732   0.607   0.332   0.524   0.369   0.032
69    I         1.248   1.257   1.343   1.180   1.212   1.344   1.339   1.355   1.490
70    C        -1.514  -1.585  -1.583  -1.177  -1.328  -1.421  -1.222  -1.303  -1.229
71    H        -0.545  -0.492  -0.613  -0.239  -0.203  -0.411  -0.640  -0.589  -0.717
72    A         1.248   1.257   1.343   1.247   1.247   1.404   1.339   1.355   1.490
73    I        -0.133  -0.088   0.063  -0.709  -0.633  -0.357  -0.524  -0.458  -0.231
74    V         0.128   0.050   0.087  -0.231  -0.378  -0.318  -0.058  -0.206  -0.188
75    V         1.248   1.257   1.343   1.020   1.033   1.200   1.339   1.355   1.490
76    R         1.248   1.257   1.343   1.230   1.238   1.389   1.339   1.355   1.490
77    S         0.497   0.585   0.230   0.746   0.867   0.343   0.524   0.645   0.071
78    K         0.497   0.567   0.227   0.419   0.523   0.031   0.524   0.620   0.064
79    Q        -1.168  -1.170  -1.168  -0.999  -1.037  -1.090  -1.106  -1.108  -1.047
80    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    N        -1.253  -1.313  -1.185  -1.136  -1.202  -1.029  -1.222  -1.256  -1.064
82    M        -2.204  -2.052  -1.950  -1.995  -1.908  -1.629  -1.688  -1.557  -1.372
83    C        -2.204  -2.057  -1.942  -2.082  -1.875  -1.655  -1.688  -1.561  -1.367
84    R         1.248   1.257   1.343   1.230   1.238   1.389   1.339   1.355   1.490
85    K        -0.823  -0.745  -0.670  -0.932  -0.802  -0.765  -0.990  -0.893  -0.786
86    D         1.248   1.257   1.343   1.374   1.390   1.518   1.339   1.355   1.490
87    G         1.248   1.257   1.343   1.247   1.273   1.404   1.339   1.355   1.490
88    S         0.497   0.435   0.214   0.660   0.574   0.214   0.524   0.428   0.042
89    T        -1.383  -1.298  -1.195  -1.316  -1.227  -1.018  -1.339  -1.264  -1.075
90    V        -0.070  -0.010   0.080  -0.598  -0.490  -0.330  -0.408  -0.314  -0.200
91    A        -1.168  -1.046  -1.150  -1.173  -0.989  -1.101  -1.106  -0.962  -1.027
92    F         1.248   1.257   1.343   1.581   1.594   1.705   1.339   1.355   1.490
93    G        -0.070   0.062   0.118  -0.243   0.011   0.060  -0.408  -0.184  -0.130
94    D         1.248   1.257   1.343   1.374   1.390   1.518   1.339   1.355   1.490
95    T         0.497   0.585   0.230   0.696   0.814   0.316   0.524   0.645   0.071
96    A         1.248   1.257   1.343   1.247   1.247   1.404   1.339   1.355   1.490
97    C         1.248   1.257   1.343   1.492   1.509   1.625   1.339   1.355   1.490
98    V         1.248   1.257   1.343   1.020   1.033   1.200   1.339   1.355   1.490
99    L         1.248   1.257   1.343   1.297   1.316   1.449   1.339   1.355   1.490
100   I         0.497   0.435   0.214   0.468   0.395  -0.001   0.524   0.428   0.042
101   N         1.248   1.257   1.343   1.352   1.375   1.498   1.339   1.355   1.490
102   K         0.497   0.397   0.208   0.440   0.326   0.053   0.524   0.369   0.032
103   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   T        -1.383  -1.353  -1.192  -1.367  -1.340  -1.064  -1.339  -1.297  -1.072
105   G        -0.218  -0.369  -0.563  -0.045  -0.237  -0.521  -0.175  -0.382  -0.644
106   E         0.128   0.119   0.097   0.307   0.277   0.182  -0.058  -0.086  -0.168
107   P         1.248   1.257   1.343   1.486   1.501   1.620   1.339   1.355   1.490
108   L        -0.218  -0.409  -0.577  -0.103  -0.400  -0.755  -0.175  -0.436  -0.663
109   G         1.248   1.257   1.343   1.247   1.273   1.404   1.339   1.355   1.490
110   T        -0.545  -0.610  -0.622  -0.414  -0.501  -0.565  -0.640  -0.721  -0.729
111   R         1.248   1.257   1.343   1.230   1.238   1.389   1.339   1.355   1.490
112   I        -0.218  -0.230  -0.542  -0.202  -0.207  -0.736  -0.175  -0.205  -0.615
113   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   D        -1.383  -1.362  -1.201  -1.387  -1.358  -1.118  -1.339  -1.305  -1.080
117   G        -0.070  -0.027   0.076  -0.305  -0.229  -0.072  -0.408  -0.345  -0.207
118   C         0.497   0.585   0.230   0.377   0.481   0.065   0.524   0.645   0.071
119   V         1.248   1.257   1.343   1.020   1.033   1.200   1.339   1.355   1.490
120   D        -0.823  -0.713  -0.650  -1.018  -0.862  -0.762  -0.990  -0.851  -0.762
121   R        -1.253  -1.293  -1.179  -1.445  -1.462  -1.232  -1.222  -1.237  -1.058
122   T         0.128   0.258   0.169   0.319   0.517   0.339  -0.058   0.149  -0.038
123   L         0.497   0.397   0.208   0.587   0.443   0.090   0.524   0.369   0.032
124   K        -0.070   0.032   0.094  -0.449  -0.253  -0.180  -0.408  -0.238  -0.174
125   D        -1.253  -1.300  -1.168  -1.129  -1.195  -1.011  -1.222  -1.246  -1.048
126   K        -0.545  -0.546  -0.601  -0.750  -0.728  -0.822  -0.640  -0.627  -0.697
127   G        -1.514  -1.515  -1.583  -1.270  -1.293  -1.355  -1.222  -1.230  -1.229
128   Y        -1.168  -1.264  -1.171  -0.613  -0.736  -0.603  -1.106  -1.200  -1.051
129   N        -0.545  -0.685  -0.642  -0.445  -0.658  -0.604  -0.640  -0.832  -0.754
130   K         1.248   1.257   1.343   1.101   1.132   1.272   1.339   1.355   1.490
131   I         0.497   0.397   0.208   0.468   0.337  -0.013   0.524   0.369   0.032
132   C        -1.383  -1.381  -1.202  -1.508  -1.540  -1.269  -1.339  -1.322  -1.081
133   S         0.497   0.567   0.227   0.662   0.748   0.244   0.524   0.620   0.064
134   L         0.497   0.389   0.205   0.666   0.538   0.291   0.524   0.358   0.027
135   A         1.248   1.257   1.343   1.247   1.247   1.404   1.339   1.355   1.490
136   S        -0.070   0.062   0.118  -0.095   0.148   0.193  -0.408  -0.184  -0.130
137   R        -0.693  -0.739  -0.630  -0.978  -1.003  -0.764  -0.873  -0.915  -0.742
138   V        -1.253  -1.200  -1.170  -1.392  -1.302  -1.202  -1.222  -1.165  -1.051
139   I        -1.383  -1.367  -1.192  -1.419  -1.409  -1.144  -1.339  -1.305  -1.071
* 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/P35996
Output conservation file - output/P35996
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
