1     M         1.808   1.880   2.030   1.940   2.038   2.293   2.034   2.157   2.435
2     L         0.622   0.725   0.742   0.347   0.509   0.525   0.357   0.527   0.488
3     Y         1.808   1.880   2.030   2.012   2.110   2.366   2.034   2.157   2.435
4     E         1.808   1.880   2.030   1.874   1.978   2.226   2.034   2.157   2.435
5     L         1.061   1.040   0.921   0.907   0.901   0.728   1.135   1.097   0.849
6     I        -0.810  -0.736  -0.684  -0.934  -0.830  -0.712  -0.919  -0.838  -0.734
7     G        -0.681  -0.624  -0.625  -0.631  -0.546  -0.505  -0.791  -0.725  -0.668
8     L         0.350   0.568   0.153   0.299   0.607   0.003   0.365   0.684   0.059
9     V        -0.597  -0.636  -0.633  -0.565  -0.658  -0.648  -0.663  -0.711  -0.675
10    R         1.061   1.019   0.915   1.041   1.000   0.835   1.135   1.063   0.837
11    I        -0.253  -0.261  -0.146  -0.534  -0.541  -0.371  -0.534  -0.559  -0.405
12    T        -1.154  -1.156  -1.084  -1.165  -1.150  -1.087  -1.048  -1.025  -0.910
13    N        -1.154  -1.192  -1.117  -0.889  -0.961  -0.833  -1.048  -1.065  -0.942
14    S        -0.940  -1.062  -1.078  -0.676  -0.891  -0.955  -0.791  -0.925  -0.899
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    N        -0.655  -0.686  -0.670  -0.771  -0.831  -0.746  -0.705  -0.756  -0.709
19    A        -1.286  -1.255  -1.160  -1.251  -1.273  -1.101  -1.162  -1.121  -0.982
20    P        -1.286  -1.213  -1.166  -1.195  -1.163  -1.034  -1.162  -1.085  -0.987
21    K        -1.657  -1.633  -1.520  -1.351  -1.311  -1.170  -1.320  -1.283  -1.125
22    L        -1.154  -1.074  -1.083  -1.183  -1.061  -1.092  -1.048  -0.955  -0.908
23    E         0.350   0.149   0.063   0.530   0.221   0.048   0.365   0.067  -0.082
24    A         1.061   1.040   0.921   1.170   1.137   0.986   1.135   1.097   0.849
25    K         0.023  -0.011  -0.011  -0.045  -0.069  -0.084  -0.149  -0.179  -0.203
26    E        -0.597  -0.696  -0.637  -0.514  -0.635  -0.566  -0.663  -0.756  -0.672
27    L        -0.124  -0.148  -0.074  -0.600  -0.618  -0.510  -0.406  -0.427  -0.312
28    S        -0.124  -0.005  -0.040  -0.264  -0.141  -0.139  -0.406  -0.274  -0.271
29    S        -0.681  -0.762  -0.646  -0.848  -0.971  -0.831  -0.791  -0.851  -0.691
30    T         0.350   0.149   0.063   0.565   0.299   0.170   0.365   0.067  -0.082
31    I        -0.940  -0.988  -1.073  -0.898  -0.936  -1.097  -0.791  -0.843  -0.895
32    G         1.808   1.880   2.030   1.868   1.964   2.219   2.034   2.157   2.435
33    K         0.496   0.509   0.649   0.127   0.113   0.310   0.108   0.093   0.291
34    L         0.023  -0.087  -0.046  -0.178  -0.330  -0.261  -0.149  -0.302  -0.264
35    I         1.808   1.880   2.030   1.625   1.743   1.972   2.034   2.157   2.435
36    I         0.434   0.505   0.655  -0.189  -0.072   0.135  -0.021   0.085   0.306
37    Q        -1.154  -1.156  -1.104  -0.897  -0.891  -0.814  -1.048  -1.024  -0.929
38    N         1.061   1.040   0.921   1.288   1.269   1.115   1.135   1.097   0.849
39    R         0.350   0.167   0.060   0.396   0.139  -0.044   0.365   0.093  -0.087
40    G         1.808   1.880   2.030   1.868   1.964   2.219   2.034   2.157   2.435
41    V         0.693   0.826   0.804   0.575   0.779   0.700   0.493   0.718   0.617
42    V         0.496   0.565   0.673   0.179   0.274   0.404   0.108   0.208   0.343
43    R         1.061   0.943   0.902   1.052   0.903   0.837   1.135   0.930   0.812
44    D         0.023   0.101   0.018   0.044   0.191  -0.024  -0.149  -0.009  -0.159
45    I         1.061   0.943   0.902   0.969   0.830   0.756   1.135   0.930   0.812
46    V        -1.284  -1.194  -1.136  -1.235  -1.109  -1.012  -1.176  -1.067  -0.961
47    P        -0.681  -0.715  -0.651  -0.613  -0.632  -0.504  -0.791  -0.797  -0.695
48    M        -0.253  -0.214  -0.116  -0.277  -0.208  -0.075  -0.534  -0.490  -0.362
49    G         1.061   1.019   0.915   1.196   1.138   0.980   1.135   1.063   0.837
50    I        -2.314  -2.217  -2.116  -2.138  -2.031  -1.866  -1.561  -1.473  -1.321
51    R        -0.597  -0.488  -0.572  -0.664  -0.471  -0.618  -0.663  -0.506  -0.598
52    Y        -1.627  -1.540  -1.483  -1.493  -1.383  -1.257  -1.305  -1.216  -1.097
53    L         1.808   1.880   2.030   1.561   1.676   1.906   2.034   2.157   2.435
54    P         1.061   0.943   0.902   1.248   1.094   1.031   1.135   0.930   0.812
55    K        -0.253  -0.230  -0.137  -0.509  -0.481  -0.365  -0.534  -0.509  -0.392
56    I         0.023   0.020  -0.049  -0.131  -0.159  -0.233  -0.149  -0.201  -0.273
57    M         0.023   0.136   0.004  -0.117   0.038  -0.138  -0.149  -0.000  -0.189
58    K        -0.124  -0.017  -0.048  -0.380  -0.231  -0.250  -0.406  -0.270  -0.275
59    K         0.350   0.234   0.087   0.421   0.269   0.041   0.365   0.196  -0.044
60    D        -0.940  -1.101  -1.079  -0.618  -0.905  -0.882  -0.791  -0.962  -0.901
61    Q         1.061   0.943   0.902   1.252   1.112   1.055   1.135   0.930   0.812
62    E         0.023  -0.107  -0.062   0.079  -0.149  -0.097  -0.149  -0.355  -0.292
63    K        -0.597  -0.441  -0.607  -0.702  -0.546  -0.738  -0.663  -0.527  -0.645
64    H         0.693   0.609   0.689   0.898   0.743   0.847   0.493   0.298   0.377
65    F        -0.320  -0.557  -0.585   0.041  -0.324  -0.390  -0.277  -0.578  -0.604
66    R        -0.597  -0.729  -0.642  -0.510  -0.698  -0.598  -0.663  -0.802  -0.683
67    A         0.693   0.857   0.794   0.679   0.918   0.804   0.493   0.775   0.596
68    Y        -0.597  -0.641  -0.639  -0.240  -0.327  -0.286  -0.663  -0.730  -0.683
69    H        -0.597  -0.671  -0.643  -0.242  -0.349  -0.307  -0.663  -0.759  -0.686
70    F         1.061   0.943   0.902   1.356   1.226   1.194   1.135   0.930   0.812
71    L        -0.940  -1.101  -1.079  -0.994  -1.224  -1.213  -0.791  -0.962  -0.901
72    M         1.061   1.173   0.946   1.257   1.407   1.083   1.135   1.315   0.898
73    L        -1.154  -1.263  -1.135  -1.334  -1.484  -1.311  -1.048  -1.126  -0.959
74    F         1.061   1.040   0.921   1.340   1.330   1.187   1.135   1.097   0.849
75    D         1.061   0.943   0.902   1.305   1.169   1.122   1.135   0.930   0.812
76    S        -0.320  -0.363  -0.526  -0.121  -0.173  -0.391  -0.277  -0.332  -0.528
77    S         1.061   0.943   0.902   1.111   0.974   0.918   1.135   0.930   0.812
78    A        -0.810  -0.641  -0.650  -0.946  -0.679  -0.723  -0.919  -0.716  -0.693
79    A        -1.284  -1.307  -1.148  -1.149  -1.199  -0.952  -1.176  -1.167  -0.972
80    V         0.350   0.234   0.087   0.525   0.358   0.140   0.365   0.196  -0.044
81    Q         1.061   1.040   0.921   1.266   1.263   1.119   1.135   1.097   0.849
82    S        -0.940  -0.939  -1.049  -0.744  -0.750  -0.905  -0.791  -0.784  -0.869
83    E         0.693   0.819   0.756   0.707   0.897   0.770   0.493   0.706   0.519
84    I         0.023   0.067   0.014  -0.267  -0.163  -0.303  -0.149  -0.067  -0.164
85    L        -0.320  -0.557  -0.585  -0.357  -0.679  -0.734  -0.277  -0.578  -0.604
86    R         1.808   1.880   2.030   1.707   1.817   2.056   2.034   2.157   2.435
87    T         0.350   0.149   0.063   0.503   0.204   0.035   0.365   0.067  -0.082
88    L         0.350   0.234   0.087   0.280   0.139  -0.073   0.365   0.196  -0.044
89    K        -0.124  -0.115  -0.051  -0.398  -0.353  -0.262  -0.406  -0.369  -0.277
90    K        -0.810  -0.843  -0.695  -1.102  -1.169  -0.959  -0.919  -0.934  -0.744
91    D         1.061   0.943   0.902   1.285   1.140   1.077   1.135   0.930   0.812
92    P         1.808   1.880   2.030   1.904   2.011   2.257   2.034   2.157   2.435
93    R         1.061   0.943   0.902   1.041   0.891   0.812   1.135   0.930   0.812
94    V         0.350   0.353   0.112   0.448   0.438   0.023   0.365   0.367  -0.005
95    I         0.496   0.537   0.664  -0.039   0.014   0.164   0.108   0.151   0.323
96    R         1.808   1.880   2.030   1.707   1.817   2.056   2.034   2.157   2.435
97    S        -0.597  -0.664  -0.633  -0.569  -0.673  -0.604  -0.663  -0.753  -0.675
98    S        -1.154  -1.243  -1.106  -1.003  -1.109  -0.900  -1.048  -1.105  -0.932
99    I         0.350   0.234   0.087   0.395   0.273   0.093   0.365   0.196  -0.044
100   V         0.023   0.239   0.038  -0.025   0.314  -0.011  -0.149   0.185  -0.131
101   K         1.808   1.880   2.030   1.720   1.830   2.068   2.034   2.157   2.435
102   V        -1.497  -1.380  -1.444  -1.527  -1.376  -1.451  -1.176  -1.056  -1.059
103   D        -1.154  -1.159  -1.106  -0.935  -0.972  -0.881  -1.048  -1.047  -0.934
104   L        -0.283  -0.224  -0.128  -0.620  -0.548  -0.388  -0.596  -0.516  -0.381
105   D        -1.264  -1.112  -1.125  -1.080  -0.885  -0.877  -1.153  -0.999  -0.951
106   K        -0.940  -0.988  -1.073  -0.754  -0.822  -0.934  -0.791  -0.843  -0.895
107   Q        -0.940  -0.809  -1.004  -0.778  -0.608  -0.873  -0.791  -0.637  -0.821
108   L         1.061   1.019   0.915   0.894   0.859   0.688   1.135   1.063   0.837
109   D        -1.627  -1.653  -1.522  -1.396  -1.478  -1.277  -1.305  -1.298  -1.127
110   R        -1.286  -1.143  -1.134  -1.396  -1.151  -1.211  -1.162  -1.002  -0.956
111   A        -0.828  -0.676  -0.691  -1.020  -0.860  -0.826  -0.934  -0.762  -0.737
112   S         0.434   0.505   0.650   0.101   0.208   0.420  -0.021   0.084   0.294
113   S         0.088  -0.015  -0.040   0.048  -0.136  -0.218  -0.021  -0.189  -0.243
114   L        -0.197  -0.092  -0.091  -0.400  -0.231  -0.316  -0.477  -0.339  -0.331
115   H         0.088   0.045  -0.039   0.261   0.160   0.065  -0.021  -0.105  -0.241
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   R         0.088   0.147  -0.019   0.008   0.083  -0.189  -0.021   0.065  -0.209
121   S         0.434   0.505   0.650   0.136   0.243   0.454  -0.021   0.084   0.294
122   L        -0.076   0.113  -0.035  -0.331  -0.057  -0.275  -0.267   0.014  -0.236
123   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   Q        -1.627  -1.575  -1.491  -1.417  -1.340  -1.225  -1.305  -1.244  -1.103
137   S        -1.627  -1.489  -1.488  -1.609  -1.457  -1.422  -1.305  -1.163  -1.101
138   I        -1.284  -1.301  -1.145  -1.599  -1.564  -1.369  -1.176  -1.162  -0.970
* 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/P28778
Output conservation file - output/P28778
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
