1     M         1.531   1.564   1.639   1.762   1.819   1.932   1.671   1.710   1.845
2     S        -1.284  -1.245  -1.224  -1.182  -1.186  -1.103  -1.114  -1.069  -0.996
3     F        -1.080  -0.928  -1.153  -0.876  -0.651  -1.030  -0.882  -0.705  -0.923
4     S        -1.015  -0.939  -0.858  -1.108  -0.982  -0.896  -1.057  -0.959  -0.845
5     G         0.682   0.533   0.503   0.766   0.550   0.474   0.639   0.375   0.279
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     K        -0.754  -0.821  -0.781  -0.937  -1.010  -0.945  -0.766  -0.815  -0.762
8     K        -1.080  -1.043  -1.176  -1.068  -1.059  -1.201  -0.882  -0.841  -0.945
9     F         1.531   1.564   1.639   1.557   1.618   1.735   1.671   1.710   1.845
10    R        -0.165  -0.290  -0.277  -0.313  -0.554  -0.517  -0.302  -0.482  -0.461
11    S        -0.165  -0.104  -0.211  -0.056   0.051  -0.104  -0.302  -0.201  -0.359
12    R         0.682   0.773   0.531   0.489   0.618   0.244   0.639   0.775   0.331
13    R         0.225   0.264   0.381  -0.268  -0.216  -0.024  -0.186  -0.127   0.042
14    Q         0.332   0.386   0.424   0.106   0.198   0.211   0.021   0.107   0.128
15    Q         1.531   1.564   1.639   1.571   1.621   1.748   1.671   1.710   1.845
16    L        -0.875  -0.952  -0.850  -1.059  -1.128  -0.971  -0.905  -0.963  -0.834
17    V         0.759   0.879   0.587   0.918   1.065   0.661   0.762   0.939   0.436
18    Y         0.031  -0.143  -0.227   0.281   0.054  -0.074   0.004  -0.243  -0.380
19    E        -0.875  -0.939  -0.835  -0.826  -0.869  -0.735  -0.905  -0.947  -0.818
20    A        -1.015  -1.025  -0.858  -1.239  -1.246  -0.997  -1.057  -1.039  -0.844
21    S         0.245   0.318   0.406   0.229   0.359   0.477  -0.148  -0.022   0.092
22    L        -0.269  -0.259  -0.279  -0.467  -0.471  -0.484  -0.451  -0.450  -0.464
23    A         1.531   1.564   1.639   1.622   1.658   1.797   1.671   1.710   1.845
24    G         0.759   0.631   0.550   0.878   0.707   0.568   0.762   0.543   0.368
25    R         0.145  -0.071  -0.171   0.213  -0.085  -0.260   0.163  -0.141  -0.299
26    Y         1.531   1.564   1.639   1.603   1.657   1.779   1.671   1.710   1.845
27    K        -1.284  -1.206  -1.222  -1.295  -1.219  -1.253  -1.114  -1.036  -0.994
28    K        -0.491  -0.700  -0.760  -0.511  -0.830  -0.899  -0.418  -0.666  -0.731
29    A        -1.284  -1.333  -1.235  -1.167  -1.225  -1.031  -1.114  -1.137  -1.005
30    L        -0.834  -0.856  -0.793  -0.824  -0.819  -0.735  -0.882  -0.882  -0.779
31    S        -1.284  -1.139  -1.193  -1.373  -1.183  -1.232  -1.114  -0.944  -0.965
32    K         1.531   1.564   1.639   1.325   1.379   1.511   1.671   1.710   1.845
33    H        -0.754  -0.866  -0.802  -0.457  -0.630  -0.561  -0.766  -0.873  -0.786
34    P         0.472   0.569   0.511   0.699   0.846   0.744   0.279   0.437   0.294
35    F         1.531   1.564   1.639   1.557   1.618   1.735   1.671   1.710   1.845
36    L         0.472   0.431   0.437   0.313   0.240   0.258   0.279   0.190   0.152
37    F        -0.754  -0.774  -0.779  -0.686  -0.749  -0.736  -0.766  -0.793  -0.763
38    F         0.821   0.659   0.600   0.933   0.727   0.620   0.859   0.591   0.460
39    G         1.531   1.564   1.639   1.603   1.673   1.779   1.671   1.710   1.845
40    L         1.531   1.564   1.639   1.392   1.434   1.575   1.671   1.710   1.845
41    P         1.531   1.564   1.639   1.751   1.803   1.921   1.671   1.710   1.845
42    F         1.531   1.564   1.639   1.557   1.618   1.735   1.671   1.710   1.845
43    C        -0.834  -0.798  -0.787  -0.683  -0.676  -0.618  -0.882  -0.819  -0.770
44    A        -1.610  -1.413  -1.524  -1.313  -1.026  -1.226  -1.230  -1.028  -1.094
45    T        -0.957  -0.861  -0.839  -0.829  -0.719  -0.650  -0.998  -0.886  -0.827
46    I         0.145   0.075  -0.139   0.505   0.391   0.092   0.163   0.048  -0.253
47    V         0.145  -0.026  -0.163   0.313   0.048  -0.183   0.163  -0.082  -0.287
48    L         0.225   0.260   0.379  -0.098  -0.051   0.146  -0.186  -0.135   0.037
49    G         0.145  -0.026  -0.163   0.374   0.150  -0.085   0.163  -0.082  -0.287
50    S         0.821   0.659   0.600   1.016   0.814   0.738   0.859   0.591   0.460
51    F        -1.610  -1.583  -1.565  -1.394  -1.372  -1.371  -1.230  -1.192  -1.128
52    W        -0.834  -0.934  -0.823  -0.573  -0.667  -0.516  -0.882  -0.951  -0.809
53    L         0.821   0.822   0.609   0.764   0.766   0.473   0.859   0.852   0.476
54    S        -1.407  -1.442  -1.263  -1.204  -1.211  -0.973  -1.230  -1.225  -1.028
55    S        -1.407  -1.272  -1.252  -1.513  -1.260  -1.249  -1.230  -1.095  -1.020
56    F        -0.165  -0.256  -0.261  -0.090  -0.215  -0.230  -0.302  -0.428  -0.438
57    T        -0.165  -0.256  -0.261   0.091  -0.065  -0.105  -0.302  -0.428  -0.438
58    A        -0.165  -0.142  -0.232  -0.059  -0.051  -0.187  -0.302  -0.293  -0.398
59    I        -0.165  -0.155  -0.236  -0.076  -0.060  -0.187  -0.302  -0.280  -0.402
60    K         0.285   0.306   0.389  -0.184  -0.161  -0.030  -0.069  -0.045   0.057
61    Y        -0.428  -0.398  -0.313  -0.434  -0.401  -0.295  -0.650  -0.608  -0.505
62    E        -0.491  -0.487  -0.702  -0.391  -0.381  -0.676  -0.418  -0.424  -0.663
63    Q        -0.957  -0.922  -0.839  -1.220  -1.175  -1.016  -0.998  -0.941  -0.825
64    G        -1.610  -1.545  -1.563  -1.436  -1.370  -1.446  -1.230  -1.161  -1.126
65    D         1.531   1.564   1.639   1.632   1.685   1.807   1.671   1.710   1.845
66    R        -0.957  -0.899  -0.837  -1.189  -1.088  -1.004  -0.998  -0.910  -0.824
67    K         0.145   0.044  -0.136   0.067  -0.070  -0.347   0.163   0.009  -0.248
68    V         0.472   0.569   0.511   0.457   0.607   0.495   0.279   0.437   0.294
69    Q        -0.428  -0.469  -0.351  -0.679  -0.808  -0.652  -0.650  -0.704  -0.555
70    E        -0.834  -0.907  -0.819  -0.927  -0.983  -0.857  -0.882  -0.927  -0.804
71    I        -0.957  -0.827  -0.817  -1.017  -0.879  -0.803  -0.998  -0.848  -0.803
72    N        -0.957  -0.788  -0.816  -0.961  -0.698  -0.782  -0.998  -0.791  -0.799
73    E         0.472   0.363   0.421   0.237   0.031   0.099   0.279   0.064   0.122
74    E         0.472   0.428   0.431   0.296   0.229   0.213   0.279   0.184   0.141
75    D        -0.165  -0.205  -0.204  -0.267  -0.292  -0.308  -0.302  -0.330  -0.350
76    I        -1.407  -1.317  -1.257  -1.322  -1.233  -1.153  -1.230  -1.124  -1.024
77    L         0.821   0.929   0.625   0.767   0.899   0.506   0.859   1.012   0.504
78    K        -1.080  -1.155  -1.204  -1.025  -1.135  -1.168  -0.882  -0.956  -0.972
79    I        -0.508  -0.487  -0.353  -0.622  -0.610  -0.400  -0.766  -0.728  -0.558
80    R        -1.284  -1.214  -1.223  -1.218  -1.061  -1.155  -1.114  -1.020  -0.993
81    K        -1.284  -1.173  -1.203  -1.393  -1.236  -1.211  -1.114  -0.986  -0.973
82    N        -0.428  -0.452  -0.351  -0.455  -0.551  -0.415  -0.650  -0.685  -0.555
83    Q        -0.428  -0.399  -0.315  -0.804  -0.786  -0.648  -0.650  -0.615  -0.508
84    R         1.531   1.564   1.639   1.457   1.499   1.639   1.671   1.710   1.845
85    E        -1.733  -1.629  -1.580  -1.780  -1.665  -1.526  -1.346  -1.235  -1.141
86    F         0.285   0.401   0.439   0.100   0.309   0.338  -0.069   0.135   0.156
87    D         1.531   1.564   1.639   1.632   1.685   1.807   1.671   1.710   1.845
88    I        -0.754  -0.833  -0.796  -0.629  -0.730  -0.702  -0.766  -0.831  -0.774
89    K         0.145  -0.071  -0.171   0.089  -0.201  -0.359   0.163  -0.141  -0.299
90    E         0.472   0.569   0.511   0.327   0.481   0.387   0.279   0.437   0.294
91    E         0.472   0.569   0.511   0.296   0.455   0.348   0.279   0.437   0.294
92    Y         0.821   0.822   0.609   0.976   0.988   0.671   0.859   0.852   0.476
93    Y         1.531   1.564   1.639   1.603   1.657   1.779   1.671   1.710   1.845
94    R         1.531   1.564   1.639   1.457   1.499   1.639   1.671   1.710   1.845
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    L         1.531   1.564   1.639   1.392   1.434   1.575   1.671   1.710   1.845
98    Q         0.145  -0.071  -0.171   0.382   0.098  -0.081   0.163  -0.141  -0.299
99    G        -0.165  -0.290  -0.277  -0.090  -0.276  -0.284  -0.302  -0.482  -0.461
100   L         0.821   0.771   0.606   0.730   0.655   0.393   0.859   0.772   0.471
101   S        -1.733  -1.706  -1.594  -1.598  -1.534  -1.365  -1.346  -1.300  -1.151
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   E        -1.284  -1.294  -1.235  -1.275  -1.271  -1.177  -1.114  -1.107  -1.005
112   E        -0.304  -0.225  -0.260  -0.503  -0.393  -0.404  -0.534  -0.441  -0.446
113   D         0.145  -0.071  -0.171   0.387   0.074  -0.106   0.163  -0.141  -0.299
114   W         0.285   0.292   0.390   0.312   0.309   0.433  -0.069  -0.072   0.061
115   E         1.531   1.564   1.639   1.404   1.465   1.587   1.671   1.710   1.845
116   P        -0.957  -1.008  -0.854  -0.764  -0.830  -0.629  -0.998  -1.023  -0.840
117   V         0.225   0.267   0.381  -0.194  -0.145   0.045  -0.186  -0.120   0.043
118   R         1.531   1.564   1.639   1.457   1.499   1.639   1.671   1.710   1.845
119   V         0.821   0.929   0.625   0.976   1.110   0.724   0.859   1.012   0.504
120   A        -1.407  -1.300  -1.243  -1.502  -1.389  -1.269  -1.230  -1.122  -1.013
121   R         1.531   1.564   1.639   1.457   1.499   1.639   1.671   1.710   1.845
122   L        -1.284  -1.157  -1.200  -1.410  -1.211  -1.298  -1.114  -0.963  -0.971
123   K         1.531   1.564   1.639   1.325   1.379   1.511   1.671   1.710   1.845
124   D         0.682   0.826   0.573   0.810   1.024   0.639   0.639   0.858   0.409
125   E         1.531   1.564   1.639   1.404   1.465   1.587   1.671   1.710   1.845
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   S         0.472   0.569   0.511   0.494   0.640   0.532   0.279   0.437   0.294
133   E        -0.304  -0.400  -0.280  -0.502  -0.605  -0.417  -0.534  -0.628  -0.470
134   N        -0.754  -0.866  -0.804  -0.466  -0.622  -0.563  -0.766  -0.865  -0.784
135   V         0.145  -0.071  -0.171   0.268  -0.078  -0.297   0.163  -0.141  -0.299
136   W        -0.754  -0.886  -0.808  -0.578  -0.813  -0.776  -0.766  -0.890  -0.793
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     *
* 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/P47081
Output conservation file - output/P47081
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
