1     M         1.088   1.137   1.172   1.315   1.379   1.408   1.097   1.172   1.226
2     S         0.164   0.167  -0.135   0.162   0.209  -0.237   0.176   0.177  -0.297
3     L        -1.257  -0.954  -1.035  -1.405  -1.120  -1.101  -1.309  -1.004  -1.002
4     D         1.088   1.137   1.172   0.972   1.073   1.140   1.097   1.172   1.226
5     F         0.164   0.167  -0.135   0.213   0.254  -0.196   0.176   0.177  -0.297
6     N        -0.717  -0.779  -1.001  -0.500  -0.621  -0.997  -0.613  -0.744  -0.959
7     T        -1.302  -0.880  -1.010  -1.423  -0.858  -0.999  -1.403  -0.892  -0.975
8     L        -1.121  -1.054  -1.019  -1.381  -1.234  -1.157  -1.140  -1.030  -0.981
9     A         1.088   1.137   1.172   1.118   1.159   1.254   1.097   1.172   1.226
10    Q        -1.992  -1.539  -1.598  -2.104  -1.397  -1.463  -1.797  -1.282  -1.270
11    N        -1.121  -0.493  -0.964  -1.238  -0.375  -0.985  -1.140  -0.368  -0.915
12    F         1.088   1.137   1.172   1.000   1.102   1.162   1.097   1.172   1.226
13    T        -1.302  -1.291  -1.044  -1.202  -1.213  -0.849  -1.403  -1.309  -1.012
14    Q        -2.153  -1.916  -1.639  -2.208  -1.861  -1.514  -1.929  -1.618  -1.308
15    F         0.164  -0.155  -0.167   0.247  -0.133  -0.156   0.176  -0.294  -0.349
16    Y         1.088   1.137   1.172   1.132   1.215   1.265   1.097   1.172   1.226
17    Y         1.088   1.137   1.172   1.132   1.215   1.265   1.097   1.172   1.226
18    N        -1.302  -1.295  -1.034  -1.566  -1.529  -1.173  -1.403  -1.315  -1.000
19    Q        -0.535  -0.392  -0.220  -0.954  -0.694  -0.397  -0.876  -0.676  -0.436
20    F         1.088   1.137   1.172   1.000   1.102   1.162   1.097   1.172   1.226
21    D         1.088   1.137   1.172   0.972   1.073   1.140   1.097   1.172   1.226
22    T        -0.292  -0.094  -0.207  -0.480  -0.161  -0.369  -0.482  -0.200  -0.414
23    D         1.088   1.137   1.172   0.972   1.073   1.140   1.097   1.172   1.226
24    R         1.088   1.137   1.172   1.221   1.300   1.334   1.097   1.172   1.226
25    S        -1.121  -1.069  -1.024  -1.171  -1.033  -0.986  -1.140  -1.047  -0.988
26    Q         0.164  -0.155  -0.167   0.095  -0.303  -0.343   0.176  -0.294  -0.349
27    L         1.088   1.137   1.172   0.779   0.886   0.989   1.097   1.172   1.226
28    G        -0.717  -1.008  -1.022  -0.454  -0.954  -0.997  -0.613  -0.979  -0.984
29    N        -0.717  -1.008  -1.022  -0.492  -0.907  -1.014  -0.613  -0.979  -0.984
30    L         1.088   1.137   1.172   0.779   0.886   0.989   1.097   1.172   1.226
31    Y         1.088   1.137   1.172   1.132   1.215   1.265   1.097   1.172   1.226
32    R         1.088   1.137   1.172   1.221   1.300   1.334   1.097   1.172   1.226
33    N        -1.567  -1.136  -1.045  -1.794  -1.156  -1.040  -1.666  -1.144  -1.012
34    E        -1.888  -1.811  -1.634  -1.723  -1.579  -1.405  -1.666  -1.523  -1.303
35    S         1.088   1.137   1.172   0.951   1.068   1.123   1.097   1.172   1.226
36    M         1.088   1.137   1.172   1.315   1.379   1.408   1.097   1.172   1.226
37    L         1.088   1.137   1.172   0.779   0.886   0.989   1.097   1.172   1.226
38    T         0.164   0.167  -0.135   0.278   0.272  -0.198   0.176   0.177  -0.297
39    F         1.088   1.137   1.172   1.000   1.102   1.162   1.097   1.172   1.226
40    E         0.164   0.165  -0.133   0.394   0.406  -0.076   0.176   0.175  -0.295
41    T        -0.535  -0.392  -0.220  -0.748  -0.575  -0.269  -0.876  -0.676  -0.436
42    S        -1.463  -1.277  -1.065  -1.704  -1.433  -1.101  -1.534  -1.294  -1.034
43    Q         1.088   1.137   1.172   0.887   0.993   1.073   1.097   1.172   1.226
44    L        -0.717  -1.009  -1.025  -0.772  -1.177  -1.122  -0.613  -0.980  -0.987
45    Q         0.164  -0.155  -0.167   0.049  -0.421  -0.475   0.176  -0.294  -0.349
46    G         1.088   1.137   1.172   1.139   1.177   1.270   1.097   1.172   1.226
47    A         0.164   0.167  -0.135   0.325   0.298  -0.128   0.176   0.177  -0.297
48    K        -1.121  -0.936  -1.037  -0.916  -0.893  -0.946  -1.140  -0.993  -1.005
49    D        -1.888  -1.737  -1.633  -1.899  -1.753  -1.546  -1.666  -1.503  -1.303
50    I         1.088   1.137   1.172   1.173   1.240   1.297   1.097   1.172   1.226
51    V         0.164  -0.155  -0.167   0.256  -0.189  -0.233   0.176  -0.294  -0.349
52    E         1.088   1.137   1.172   1.187   1.270   1.308   1.097   1.172   1.226
53    K         1.088   1.137   1.172   1.322   1.361   1.413   1.097   1.172   1.226
54    L         1.088   1.137   1.172   0.779   0.886   0.989   1.097   1.172   1.226
55    V        -0.717  -0.753  -0.997  -0.520  -0.657  -0.958  -0.613  -0.719  -0.954
56    S         0.082  -0.075  -0.196   0.058  -0.126  -0.325   0.066  -0.171  -0.397
57    L         1.088   1.137   1.172   0.786   0.898   0.994   1.097   1.172   1.226
58    P         1.088   1.137   1.172   1.263   1.330   1.367   1.097   1.172   1.226
59    F         1.088   1.137   1.172   0.997   1.099   1.159   1.097   1.172   1.226
60    Q         0.082  -0.075  -0.196   0.002  -0.192  -0.363   0.066  -0.171  -0.397
61    K        -0.717  -0.740  -0.985  -0.266  -0.344  -0.798  -0.613  -0.636  -0.940
62    V         1.088   1.137   1.172   1.049   1.138   1.200   1.097   1.172   1.226
63    Q        -1.888  -1.890  -1.639  -1.766  -1.765  -1.431  -1.666  -1.597  -1.308
64    H         1.088   1.137   1.172   1.362   1.407   1.445   1.097   1.172   1.226
65    R        -0.717  -1.009  -1.025  -0.302  -0.727  -0.784  -0.613  -0.980  -0.987
66    I         0.164  -0.155  -0.167   0.386  -0.068  -0.130   0.176  -0.294  -0.349
67    T        -1.302  -1.218  -1.025  -1.523  -1.342  -1.056  -1.403  -1.220  -0.989
68    T        -0.717  -1.009  -1.025  -0.474  -0.910  -0.966  -0.613  -0.980  -0.987
69    L        -0.717  -1.009  -1.025  -0.751  -1.108  -1.073  -0.613  -0.980  -0.987
70    D         1.088   1.137   1.172   0.972   1.073   1.140   1.097   1.172   1.226
71    A         1.088   1.137   1.172   1.118   1.159   1.254   1.097   1.172   1.226
72    Q         1.088   1.137   1.172   0.887   0.993   1.073   1.097   1.172   1.226
73    P         1.088   1.137   1.172   1.261   1.326   1.366   1.097   1.172   1.226
74    A        -1.121  -0.933  -1.034  -1.048  -0.968  -0.977  -1.140  -0.990  -1.002
75    S        -0.717  -1.008  -1.022  -0.610  -1.028  -1.038  -0.613  -0.979  -0.984
76    P        -1.463  -1.273  -1.065  -1.439  -1.274  -0.966  -1.534  -1.290  -1.034
77    N        -0.866  -1.112  -1.051  -0.739  -1.141  -1.124  -0.793  -1.091  -1.018
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    G         1.088   1.137   1.172   1.139   1.177   1.270   1.097   1.172   1.226
80    D        -0.717  -1.008  -1.022  -0.617  -1.043  -1.092  -0.613  -0.979  -0.984
81    V        -0.535  -0.399  -0.243  -0.766  -0.561  -0.320  -0.876  -0.687  -0.473
82    L        -0.535  -0.392  -0.220  -1.004  -0.680  -0.393  -0.876  -0.676  -0.436
83    V         0.164  -0.155  -0.167   0.268  -0.157  -0.199   0.176  -0.294  -0.349
84    M        -0.292  -0.388  -0.242  -0.224  -0.548  -0.379  -0.482  -0.669  -0.473
85    I        -0.535  -0.131  -0.171  -0.766  -0.120  -0.206  -0.876  -0.256  -0.356
86    T         1.088   1.137   1.172   1.091   1.147   1.233   1.097   1.172   1.226
87    G         1.088   1.137   1.172   1.139   1.177   1.270   1.097   1.172   1.226
88    D        -1.302  -1.218  -1.025  -1.452  -1.286  -1.057  -1.403  -1.220  -0.989
89    L         1.088   1.137   1.172   0.779   0.886   0.989   1.097   1.172   1.226
90    L        -1.121  -1.118  -1.036  -1.273  -1.230  -0.998  -1.140  -1.131  -1.004
91    I        -1.121  -1.145  -1.045  -1.078  -1.226  -1.120  -1.140  -1.170  -1.013
92    D         1.088   1.137   1.172   0.972   1.073   1.140   1.097   1.172   1.226
93    E        -1.302  -1.146  -1.028  -1.401  -1.178  -0.999  -1.403  -1.171  -0.995
94    E         0.164   0.165  -0.133   0.377   0.393  -0.118   0.176   0.175  -0.295
95    Q         1.088   1.137   1.172   0.882   0.988   1.070   1.097   1.172   1.226
96    N        -0.717  -1.008  -1.022  -0.418  -0.781  -0.841  -0.613  -0.979  -0.984
97    P        -0.535  -0.282  -0.221  -0.610  -0.226  -0.180  -0.876  -0.495  -0.438
98    Q        -0.292  -0.388  -0.242  -0.646  -0.884  -0.641  -0.482  -0.669  -0.473
99    R        -0.717  -1.009  -1.025  -0.319  -0.772  -0.825  -0.613  -0.980  -0.987
100   F        -0.535  -0.131  -0.171  -0.785  -0.091  -0.219  -0.876  -0.256  -0.356
101   S         0.164   0.165  -0.133   0.162   0.208  -0.234   0.176   0.175  -0.295
102   Q         1.088   1.137   1.172   0.887   0.993   1.073   1.097   1.172   1.226
103   V         0.164  -0.155  -0.167   0.260  -0.185  -0.221   0.176  -0.294  -0.349
104   F         1.088   1.137   1.172   1.000   1.102   1.162   1.097   1.172   1.226
105   H         0.164  -0.155  -0.167   0.540   0.019  -0.093   0.176  -0.294  -0.349
106   L         1.088   1.137   1.172   0.779   0.886   0.989   1.097   1.172   1.226
107   I        -1.546  -1.578  -1.620  -1.157  -1.350  -1.385  -1.271  -1.320  -1.290
108   P        -0.717  -1.008  -1.022  -0.346  -0.846  -0.953  -0.613  -0.979  -0.984
109   D        -0.717  -0.487  -0.967  -0.584  -0.281  -0.935  -0.613  -0.348  -0.919
110   G        -1.121  -1.202  -1.042  -1.030  -1.200  -0.977  -1.140  -1.201  -1.009
111   N        -1.567  -1.176  -1.042  -1.851  -1.244  -1.074  -1.666  -1.169  -1.008
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   S        -0.717  -1.008  -1.022  -0.656  -1.087  -1.148  -0.613  -0.979  -0.984
114   Y         0.164  -0.155  -0.167   0.395   0.007  -0.022   0.176  -0.294  -0.349
115   Y         0.164  -0.155  -0.167   0.326  -0.131  -0.211   0.176  -0.294  -0.349
116   V         1.088   1.137   1.172   1.049   1.138   1.200   1.097   1.172   1.226
117   F        -0.717  -0.487  -0.967  -0.618  -0.327  -1.048  -0.613  -0.348  -0.919
118   N         1.088   1.137   1.172   1.098   1.219   1.238   1.097   1.172   1.226
119   D         1.088   1.137   1.172   0.972   1.073   1.140   1.097   1.172   1.226
120   I         0.164   0.167  -0.135   0.337   0.332  -0.200   0.176   0.177  -0.297
121   F         1.088   1.137   1.172   1.000   1.102   1.162   1.097   1.172   1.226
122   R         0.164  -0.155  -0.167   0.460   0.038  -0.023   0.176  -0.294  -0.349
123   L         1.088   1.137   1.172   0.779   0.886   0.989   1.097   1.172   1.226
124   N         0.164  -0.155  -0.167   0.299  -0.114  -0.215   0.176  -0.294  -0.349
125   Y         0.082  -0.260  -0.196   0.183  -0.410  -0.369   0.066  -0.460  -0.397
126   S        -1.546  -1.766  -1.641  -1.432  -1.872  -1.649  -1.271  -1.481  -1.309
127   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P33331
Output conservation file - output/P33331
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
