1     M         1.299   1.320   1.385   1.416   1.444   1.538   1.391   1.427   1.526
2     S         0.649   0.484   0.415   0.573   0.355   0.235   0.652   0.380   0.226
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.475  -1.367  -1.254  -1.549  -1.389  -1.224  -1.311  -1.208  -1.063
12    -         0.436   0.347   0.350   0.421   0.258   0.274   0.310   0.139   0.103
13    S        -0.792  -0.910  -0.835  -0.841  -0.989  -0.849  -0.826  -0.947  -0.848
14    E        -0.551  -0.691  -0.796  -0.441  -0.667  -0.875  -0.509  -0.700  -0.800
15    R         1.299   1.320   1.385   1.302   1.303   1.432   1.391   1.427   1.526
16    A         1.299   1.320   1.385   1.307   1.333   1.437   1.391   1.427   1.526
17    C         1.299   1.320   1.385   1.348   1.383   1.475   1.391   1.427   1.526
18    M         0.649   0.484   0.415   0.839   0.613   0.477   0.652   0.380   0.226
19    L         0.031  -0.212  -0.298   0.129  -0.217  -0.387   0.019  -0.331  -0.466
20    C         1.299   1.320   1.385   1.348   1.383   1.475   1.391   1.427   1.526
21    G         0.649   0.555   0.417   0.601   0.480   0.240   0.652   0.498   0.228
22    I         0.649   0.756   0.450   0.765   0.886   0.471   0.652   0.807   0.289
23    V         0.330   0.393   0.348   0.179   0.274   0.195   0.124   0.222   0.100
24    Q         0.031  -0.212  -0.298   0.262  -0.087  -0.240   0.019  -0.331  -0.466
25    T        -0.380  -0.252  -0.348  -0.505  -0.315  -0.455  -0.615  -0.455  -0.545
26    T        -1.575  -1.613  -1.545  -1.175  -1.216  -1.125  -1.248  -1.279  -1.166
27    N        -1.389  -1.350  -1.224  -1.338  -1.313  -1.126  -1.248  -1.196  -1.039
28    E        -1.575  -1.613  -1.545  -1.474  -1.561  -1.484  -1.248  -1.279  -1.166
29    F         1.299   1.320   1.385   1.428   1.446   1.549   1.391   1.427   1.526
30    N        -1.688  -1.635  -1.539  -1.576  -1.535  -1.402  -1.354  -1.301  -1.161
31    R        -0.865  -0.871  -0.838  -0.965  -0.967  -0.902  -0.931  -0.920  -0.850
32    D        -1.986  -1.774  -1.782  -1.681  -1.369  -1.410  -1.459  -1.294  -1.233
33    G         1.299   1.320   1.385   1.196   1.230   1.333   1.391   1.427   1.526
34    C         1.299   1.320   1.385   1.348   1.383   1.475   1.391   1.427   1.526
35    P         1.299   1.320   1.385   1.290   1.323   1.421   1.391   1.427   1.526
36    N         1.299   1.320   1.385   1.422   1.441   1.544   1.391   1.427   1.526
37    C         1.299   1.320   1.385   1.335   1.365   1.463   1.391   1.427   1.526
38    Q        -0.432  -0.363  -0.370  -0.559  -0.447  -0.463  -0.677  -0.577  -0.570
39    G        -0.348  -0.345  -0.330  -0.637  -0.603  -0.597  -0.539  -0.521  -0.511
40    I        -0.902  -0.934  -0.869  -0.938  -0.985  -0.896  -0.953  -0.987  -0.883
41    F         0.122   0.239   0.295  -0.073   0.117   0.198  -0.264  -0.061  -0.001
42    E        -0.432  -0.363  -0.370  -0.443  -0.288  -0.328  -0.677  -0.577  -0.570
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    E        -1.276  -1.336  -1.242  -1.221  -1.326  -1.195  -1.142  -1.185  -1.053
47    A        -1.276  -1.345  -1.238  -1.338  -1.478  -1.326  -1.142  -1.191  -1.050
48    G        -1.276  -1.322  -1.235  -1.356  -1.443  -1.266  -1.142  -1.176  -1.048
49    V        -1.276  -1.189  -1.223  -1.336  -1.216  -1.222  -1.142  -1.060  -1.037
50    S        -0.865  -0.871  -0.838  -0.985  -0.951  -0.899  -0.931  -0.920  -0.850
51    T        -0.865  -0.806  -0.830  -0.927  -0.858  -0.854  -0.931  -0.857  -0.843
52    M        -1.276  -1.261  -1.222  -1.150  -1.145  -1.118  -1.142  -1.116  -1.035
53    E        -0.865  -0.950  -0.855  -0.980  -1.086  -0.949  -0.931  -0.995  -0.868
54    C         0.649   0.484   0.415   0.792   0.584   0.467   0.652   0.380   0.226
55    T         1.299   1.320   1.385   1.382   1.392   1.507   1.391   1.427   1.526
56    S         1.299   1.320   1.385   1.154   1.196   1.294   1.391   1.427   1.526
57    P         0.649   0.555   0.417   0.729   0.615   0.405   0.652   0.498   0.228
58    S         0.330   0.212   0.267   0.086  -0.129  -0.064   0.124  -0.113  -0.055
59    F         1.299   1.320   1.385   1.428   1.446   1.549   1.391   1.427   1.526
60    E         1.299   1.320   1.385   1.296   1.341   1.426   1.391   1.427   1.526
61    G         1.299   1.320   1.385   1.196   1.230   1.333   1.391   1.427   1.526
62    L        -0.253  -0.310  -0.360  -0.264  -0.386  -0.423  -0.404  -0.526  -0.560
63    V         0.031  -0.212  -0.298   0.089  -0.238  -0.366   0.019  -0.331  -0.466
64    G        -0.380  -0.342  -0.336  -0.560  -0.431  -0.430  -0.615  -0.529  -0.523
65    M        -0.380  -0.406  -0.368  -0.428  -0.439  -0.395  -0.615  -0.632  -0.571
66    C        -0.792  -0.923  -0.846  -0.760  -0.927  -0.846  -0.826  -0.962  -0.858
67    K        -1.276  -1.322  -1.235  -1.205  -1.301  -1.179  -1.142  -1.176  -1.048
68    P         0.031   0.116  -0.231   0.142   0.262  -0.259   0.019   0.128  -0.370
69    T        -0.792  -0.748  -0.808  -0.727  -0.658  -0.758  -0.826  -0.772  -0.819
70    K        -0.551  -0.582  -0.761  -0.337  -0.390  -0.713  -0.509  -0.569  -0.760
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    S         1.299   1.320   1.385   1.154   1.196   1.294   1.391   1.427   1.526
73    W         0.649   0.672   0.440   0.924   0.946   0.599   0.652   0.682   0.271
74    V         0.649   0.672   0.440   0.613   0.647   0.302   0.652   0.682   0.271
75    A         0.031   0.081  -0.233   0.126   0.197  -0.313   0.019   0.081  -0.372
76    K        -0.380  -0.346  -0.342  -0.447  -0.406  -0.383  -0.615  -0.577  -0.542
77    W         0.649   0.672   0.440   0.926   0.943   0.603   0.652   0.682   0.271
78    L        -0.253  -0.267  -0.353  -0.241  -0.301  -0.377  -0.404  -0.481  -0.551
79    S         0.159   0.320   0.337  -0.126   0.164   0.180  -0.193   0.089   0.080
80    V        -0.253  -0.168  -0.267  -0.277  -0.120  -0.302  -0.404  -0.267  -0.421
81    D         1.299   1.320   1.385   1.255   1.262   1.388   1.391   1.427   1.526
82    H        -1.276  -1.166  -1.201  -1.334  -1.208  -1.170  -1.142  -1.059  -1.020
83    S        -0.792  -0.552  -0.806  -0.604  -0.304  -0.648  -0.826  -0.585  -0.818
84    I        -0.978  -0.934  -0.861  -1.035  -1.002  -0.858  -1.037  -0.993  -0.876
85    A        -0.380  -0.387  -0.346  -0.504  -0.470  -0.417  -0.615  -0.602  -0.544
86    G         1.299   1.320   1.385   1.196   1.230   1.333   1.391   1.427   1.526
87    M        -0.865  -0.950  -0.855  -0.873  -0.987  -0.866  -0.931  -0.995  -0.868
88    Y         1.299   1.320   1.385   1.461   1.479   1.580   1.391   1.427   1.526
89    A         1.299   1.320   1.385   1.307   1.333   1.437   1.391   1.427   1.526
90    I        -0.253  -0.225  -0.347  -0.329  -0.348  -0.452  -0.404  -0.438  -0.542
91    K         0.649   0.484   0.415   0.814   0.591   0.460   0.652   0.380   0.226
92    V         0.330   0.404   0.307   0.179   0.291   0.124   0.124   0.240   0.022
93    D        -0.865  -0.950  -0.855  -0.886  -0.989  -0.856  -0.931  -0.995  -0.868
94    G         1.299   1.320   1.385   1.196   1.230   1.333   1.391   1.427   1.526
95    R        -0.865  -0.950  -0.855  -0.867  -0.976  -0.836  -0.931  -0.995  -0.868
96    L         1.299   1.320   1.385   1.278   1.314   1.410   1.391   1.427   1.526
97    P         0.649   0.484   0.415   0.734   0.524   0.415   0.652   0.380   0.226
98    A        -1.575  -1.536  -1.510  -1.408  -1.390  -1.336  -1.248  -1.222  -1.139
99    E        -0.865  -0.730  -0.812  -0.941  -0.730  -0.819  -0.931  -0.769  -0.820
100   V         0.159   0.218   0.274  -0.115  -0.022   0.067  -0.193  -0.102  -0.042
101   V        -0.792  -0.752  -0.813  -0.835  -0.794  -0.843  -0.826  -0.782  -0.822
102   E        -1.090  -1.069  -1.194  -0.947  -0.912  -1.149  -0.931  -0.915  -1.010
103   L        -1.276  -1.322  -1.235  -1.309  -1.399  -1.257  -1.142  -1.176  -1.048
104   L         1.299   1.320   1.385   1.278   1.314   1.410   1.391   1.427   1.526
105   P        -1.276  -1.299  -1.227  -1.231  -1.259  -1.145  -1.142  -1.157  -1.040
106   -        -0.997  -0.898  -0.852  -1.243  -1.099  -1.024  -1.041  -0.939  -0.863
107   -        -0.997  -0.983  -0.878  -1.069  -1.085  -0.924  -1.041  -1.029  -0.891
108   -         0.139   0.249   0.292  -0.094   0.084   0.148  -0.231  -0.043  -0.007
109   -         0.139   0.246   0.284  -0.115   0.077   0.116  -0.231  -0.048  -0.024
110   H        -1.575  -1.613  -1.545  -1.215  -1.312  -1.284  -1.248  -1.279  -1.166
111   Y         1.299   1.320   1.385   1.461   1.479   1.580   1.391   1.427   1.526
112   K        -0.380  -0.342  -0.336  -0.455  -0.381  -0.359  -0.615  -0.529  -0.523
113   P         1.299   1.320   1.385   1.290   1.323   1.421   1.391   1.427   1.526
114   R         1.299   1.320   1.385   1.302   1.303   1.432   1.391   1.427   1.526
115   D         0.649   0.484   0.415   0.699   0.464   0.384   0.652   0.380   0.226
116   G         1.299   1.320   1.385   1.196   1.230   1.333   1.391   1.427   1.526
117   S         0.649   0.484   0.415   0.592   0.387   0.281   0.652   0.380   0.226
118   Q        -0.380  -0.393  -0.339  -0.488  -0.489  -0.428  -0.615  -0.596  -0.526
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   V        -1.276  -1.336  -1.242  -1.247  -1.272  -1.127  -1.142  -1.185  -1.053
122   E         0.330   0.536   0.424   0.215   0.514   0.354   0.124   0.467   0.241
* 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/P32914
Output conservation file - output/P32914
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
