1     M         0.930   0.948   0.981   1.230   1.245   1.263   0.977   1.002   1.047
2     S         0.930   0.948   0.981   0.972   0.998   1.041   0.977   1.002   1.047
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     E        -2.575  -2.493  -2.179  -2.276  -2.099  -1.755  -2.014  -1.927  -1.580
10    F         0.128  -0.054  -0.157   0.216  -0.029  -0.198   0.098  -0.181  -0.382
11    Y         0.930   0.948   0.981   1.058   1.081   1.115   0.977   1.002   1.047
12    K        -1.568  -1.415  -1.423  -1.573  -1.305  -1.407  -1.514  -1.334  -1.280
13    L         0.128  -0.054  -0.157   0.058  -0.195  -0.357   0.098  -0.181  -0.382
14    A        -0.628  -0.731  -0.880  -0.338  -0.540  -0.847  -0.635  -0.778  -0.959
15    P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
16    V        -1.034  -0.927  -0.919  -1.505  -1.340  -1.245  -1.221  -1.095  -1.012
17    D         0.930   0.948   0.981   1.058   1.080   1.115   0.977   1.002   1.047
18    K        -0.628  -0.533  -0.868  -0.695  -0.559  -0.932  -0.635  -0.506  -0.943
19    K        -0.939  -0.910  -0.912  -1.184  -1.114  -1.057  -1.074  -1.016  -1.001
20    G         0.128   0.208  -0.132   0.132   0.232  -0.217   0.098   0.214  -0.338
21    Q        -1.955  -1.953  -1.826  -1.908  -1.906  -1.745  -1.660  -1.648  -1.451
22    P         0.128  -0.054  -0.157   0.246  -0.017  -0.231   0.098  -0.181  -0.382
23    F        -0.628  -0.766  -0.889  -0.508  -0.733  -0.933  -0.635  -0.819  -0.970
24    P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
25    F         0.128  -0.054  -0.157   0.173  -0.095  -0.305   0.098  -0.181  -0.382
26    D        -2.101  -1.945  -1.836  -2.077  -1.851  -1.685  -1.807  -1.654  -1.460
27    Q        -1.327  -1.429  -1.418  -1.025  -1.177  -1.217  -1.221  -1.332  -1.273
28    L         0.128  -0.054  -0.157   0.083  -0.157  -0.295   0.098  -0.181  -0.382
29    K        -0.939  -1.016  -0.921  -1.274  -1.334  -1.169  -1.074  -1.142  -1.013
30    G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
31    K         0.930   0.948   0.981   0.640   0.686   0.755   0.977   1.002   1.047
32    V         0.930   0.948   0.981   0.919   0.944   0.995   0.977   1.002   1.047
33    V         0.930   0.948   0.981   0.919   0.944   0.995   0.977   1.002   1.047
34    L         0.930   0.948   0.981   0.776   0.803   0.873   0.977   1.002   1.047
35    I        -0.240  -0.206  -0.214  -0.242  -0.200  -0.262  -0.488  -0.433  -0.480
36    V         0.930   0.948   0.981   0.919   0.944   0.995   0.977   1.002   1.047
37    N         0.930   0.948   0.981   1.006   1.029   1.070   0.977   1.002   1.047
38    V         0.128   0.112  -0.145   0.235   0.218  -0.140   0.098   0.076  -0.360
39    A         0.930   0.948   0.981   1.128   1.144   1.175   0.977   1.002   1.047
40    S         0.930   0.948   0.981   0.972   0.998   1.041   0.977   1.002   1.047
41    K         0.930   0.948   0.981   0.640   0.686   0.755   0.977   1.002   1.047
42    C         0.930   0.948   0.981   1.188   1.209   1.227   0.977   1.002   1.047
43    G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
44    F         0.930   0.948   0.981   0.914   0.941   0.991   0.977   1.002   1.047
45    T         0.930   0.948   0.981   1.119   1.138   1.167   0.977   1.002   1.047
46    P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
47    Q         0.930   0.948   0.981   1.034   1.055   1.094   0.977   1.002   1.047
48    Y         0.930   0.948   0.981   1.058   1.081   1.115   0.977   1.002   1.047
49    K         0.128  -0.054  -0.157  -0.041  -0.253  -0.369   0.098  -0.181  -0.382
50    E        -0.406  -0.316  -0.224  -0.792  -0.623  -0.478  -0.781  -0.624  -0.498
51    L         0.930   0.948   0.981   0.776   0.803   0.873   0.977   1.002   1.047
52    E         0.930   0.948   0.981   0.836   0.868   0.924   0.977   1.002   1.047
53    A        -1.034  -1.114  -0.931  -1.156  -1.299  -1.039  -1.221  -1.281  -1.025
54    L        -0.240  -0.309  -0.233  -0.488  -0.615  -0.482  -0.488  -0.611  -0.514
55    Y        -0.240  -0.176  -0.203  -0.188  -0.089  -0.182  -0.488  -0.381  -0.461
56    K        -0.240  -0.226  -0.218  -0.573  -0.535  -0.493  -0.488  -0.466  -0.487
57    R        -0.628  -0.686  -0.882  -0.737  -0.837  -1.029  -0.635  -0.725  -0.962
58    Y        -0.628  -0.766  -0.889  -0.345  -0.550  -0.786  -0.635  -0.819  -0.970
59    K        -1.327  -1.154  -1.393  -1.398  -1.144  -1.430  -1.221  -1.012  -1.248
60    D         0.128  -0.054  -0.157   0.326   0.059  -0.167   0.098  -0.181  -0.382
61    E        -1.568  -1.478  -1.428  -1.699  -1.557  -1.415  -1.514  -1.406  -1.285
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    G        -0.628  -0.766  -0.889  -0.556  -0.748  -0.914  -0.635  -0.819  -0.970
66    F        -0.628  -0.533  -0.868  -0.536  -0.403  -0.953  -0.635  -0.506  -0.943
67    T        -1.714  -1.735  -1.454  -1.590  -1.649  -1.250  -1.660  -1.648  -1.309
68    I         0.128   0.253  -0.131   0.316   0.465  -0.104   0.098   0.278  -0.337
69    I        -0.406  -0.340  -0.232  -0.706  -0.612  -0.413  -0.781  -0.667  -0.512
70    G         0.128  -0.054  -0.157   0.145  -0.092  -0.226   0.098  -0.181  -0.382
71    F         0.930   0.948   0.981   0.914   0.941   0.991   0.977   1.002   1.047
72    P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
73    C         0.930   0.948   0.981   1.188   1.209   1.227   0.977   1.002   1.047
74    N         0.930   0.948   0.981   1.006   1.029   1.070   0.977   1.002   1.047
75    Q         0.930   0.948   0.981   1.034   1.055   1.094   0.977   1.002   1.047
76    F         0.930   0.948   0.981   0.914   0.941   0.991   0.977   1.002   1.047
77    G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
78    H        -1.034  -1.011  -0.921  -0.982  -0.979  -0.823  -1.221  -1.169  -1.014
79    Q         0.930   0.948   0.981   1.034   1.055   1.094   0.977   1.002   1.047
80    E         0.930   0.948   0.981   0.836   0.868   0.924   0.977   1.002   1.047
81    P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
82    G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
83    S        -0.240  -0.279  -0.225  -0.225  -0.293  -0.223  -0.488  -0.559  -0.500
84    D        -1.955  -1.976  -1.836  -1.618  -1.697  -1.516  -1.660  -1.666  -1.459
85    E         0.128   0.168  -0.140   0.142   0.200  -0.221   0.098   0.157  -0.351
86    E         0.930   0.948   0.981   0.836   0.868   0.924   0.977   1.002   1.047
87    I         0.930   0.948   0.981   1.034   1.050   1.094   0.977   1.002   1.047
88    A        -1.568  -1.610  -1.438  -1.384  -1.446  -1.248  -1.514  -1.531  -1.294
89    Q        -0.406  -0.345  -0.231  -0.546  -0.446  -0.279  -0.781  -0.674  -0.511
90    F         0.930   0.948   0.981   0.914   0.941   0.991   0.977   1.002   1.047
91    C         0.930   0.948   0.981   1.188   1.209   1.227   0.977   1.002   1.047
92    Q        -0.240  -0.176  -0.203  -0.223  -0.124  -0.216  -0.488  -0.381  -0.461
93    L         0.128   0.112  -0.145   0.012  -0.007  -0.449   0.098   0.076  -0.360
94    N         0.930   0.948   0.981   1.006   1.029   1.070   0.977   1.002   1.047
95    Y         0.930   0.948   0.981   1.058   1.081   1.115   0.977   1.002   1.047
96    G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
97    V         0.930   0.948   0.981   0.919   0.944   0.995   0.977   1.002   1.047
98    T        -0.406  -0.389  -0.241  -0.464  -0.454  -0.237  -0.781  -0.755  -0.528
99    F         0.930   0.948   0.981   0.914   0.941   0.991   0.977   1.002   1.047
100   P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
101   I        -0.406  -0.384  -0.239  -0.589  -0.563  -0.327  -0.781  -0.745  -0.526
102   M        -0.240  -0.277  -0.228  -0.364  -0.416  -0.297  -0.488  -0.554  -0.505
103   K        -1.327  -1.298  -1.408  -1.340  -1.283  -1.355  -1.221  -1.175  -1.264
104   K         0.930   0.948   0.981   0.640   0.686   0.755   0.977   1.002   1.047
105   I        -0.406  -0.389  -0.241  -0.566  -0.559  -0.323  -0.781  -0.755  -0.528
106   D        -1.180  -1.177  -0.955  -1.271  -1.300  -0.967  -1.367  -1.351  -1.053
107   V         0.930   0.948   0.981   0.919   0.944   0.995   0.977   1.002   1.047
108   N         0.930   0.948   0.981   1.006   1.029   1.070   0.977   1.002   1.047
109   G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
110   G        -1.327  -1.110  -1.394  -1.040  -0.737  -1.220  -1.221  -0.963  -1.249
111   N        -1.327  -1.154  -1.392  -1.152  -0.892  -1.351  -1.221  -1.012  -1.247
112   E        -1.568  -1.467  -1.428  -1.333  -1.192  -1.199  -1.514  -1.391  -1.284
113   D         0.930   0.948   0.981   1.058   1.080   1.115   0.977   1.002   1.047
114   P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
115   V         0.128  -0.054  -0.157   0.178  -0.092  -0.302   0.098  -0.181  -0.382
116   Y         0.930   0.948   0.981   1.058   1.081   1.115   0.977   1.002   1.047
117   K        -1.955  -1.980  -1.836  -2.034  -2.079  -1.794  -1.660  -1.671  -1.459
118   F        -1.034  -1.114  -0.931  -1.009  -1.073  -0.795  -1.221  -1.281  -1.025
119   L         0.128  -0.054  -0.157   0.113  -0.111  -0.219   0.098  -0.181  -0.382
120   K         0.930   0.948   0.981   0.640   0.686   0.755   0.977   1.002   1.047
121   S        -1.568  -1.513  -1.435  -1.549  -1.477  -1.394  -1.514  -1.449  -1.292
122   Q        -0.406  -0.389  -0.241  -0.616  -0.604  -0.373  -0.781  -0.755  -0.528
123   K         0.930   0.948   0.981   0.640   0.686   0.755   0.977   1.002   1.047
124   S        -1.955  -2.006  -1.835  -1.819  -1.918  -1.727  -1.660  -1.693  -1.458
125   G         0.930   0.948   0.981   0.820   0.843   0.910   0.977   1.002   1.047
126   M        -1.327  -1.225  -1.401  -1.216  -1.096  -1.273  -1.221  -1.096  -1.256
127   L         0.128  -0.054  -0.157   0.113  -0.111  -0.219   0.098  -0.181  -0.382
128   G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
129   L        -0.240  -0.152  -0.206  -0.490  -0.348  -0.441  -0.488  -0.341  -0.467
130   R        -2.101  -2.037  -1.840  -1.990  -1.943  -1.621  -1.807  -1.726  -1.462
131   G        -0.406  -0.329  -0.228  -0.474  -0.313  -0.217  -0.781  -0.645  -0.506
132   I         0.930   0.948   0.981   1.034   1.050   1.094   0.977   1.002   1.047
133   K         0.930   0.948   0.981   0.640   0.686   0.755   0.977   1.002   1.047
134   W         0.930   0.948   0.981   1.243   1.259   1.274   0.977   1.002   1.047
135   N         0.930   0.948   0.981   1.006   1.029   1.070   0.977   1.002   1.047
136   F         0.930   0.948   0.981   0.914   0.941   0.991   0.977   1.002   1.047
137   E         0.930   0.948   0.981   0.836   0.868   0.924   0.977   1.002   1.047
138   K         0.930   0.948   0.981   0.640   0.686   0.755   0.977   1.002   1.047
139   F         0.930   0.948   0.981   0.914   0.941   0.991   0.977   1.002   1.047
140   L         0.930   0.948   0.981   0.776   0.803   0.873   0.977   1.002   1.047
141   V        -0.406  -0.395  -0.241  -0.589  -0.581  -0.328  -0.781  -0.766  -0.529
142   D        -0.628  -0.812  -0.894  -0.367  -0.658  -0.841  -0.635  -0.875  -0.976
143   K        -0.628  -0.620  -0.875  -0.695  -0.661  -0.939  -0.635  -0.618  -0.952
144   K        -2.101  -2.121  -1.848  -2.000  -1.967  -1.566  -1.807  -1.793  -1.469
145   G         0.930   0.948   0.981   0.826   0.851   0.915   0.977   1.002   1.047
146   K        -1.327  -1.231  -1.405  -1.356  -1.219  -1.377  -1.221  -1.102  -1.260
147   V         0.930   0.948   0.981   0.919   0.944   0.995   0.977   1.002   1.047
148   Y        -1.568  -1.553  -1.436  -1.533  -1.564  -1.386  -1.514  -1.481  -1.292
149   E        -0.628  -0.765  -0.889  -0.576  -0.789  -0.969  -0.635  -0.819  -0.970
150   R         0.930   0.948   0.981   1.211   1.231   1.247   0.977   1.002   1.047
151   Y        -0.628  -0.766  -0.889  -0.303  -0.485  -0.703  -0.635  -0.819  -0.970
152   S        -0.240  -0.309  -0.233  -0.222  -0.339  -0.229  -0.488  -0.611  -0.514
153   S         0.930   0.948   0.981   0.972   0.998   1.041   0.977   1.002   1.047
154   L        -0.628  -0.812  -0.894  -0.580  -0.825  -0.905  -0.635  -0.875  -0.976
155   T        -0.628  -0.619  -0.877  -0.348  -0.337  -0.847  -0.635  -0.618  -0.954
156   K        -0.628  -0.570  -0.870  -0.729  -0.632  -0.999  -0.635  -0.553  -0.946
157   P         0.930   0.948   0.981   0.977   1.003   1.045   0.977   1.002   1.047
158   S        -1.180  -1.061  -0.937  -1.308  -1.133  -0.936  -1.367  -1.201  -1.031
159   S        -0.628  -0.619  -0.877  -0.401  -0.384  -0.771  -0.635  -0.618  -0.954
160   L         0.128   0.167  -0.141   0.079   0.130  -0.279   0.098   0.156  -0.353
161   S        -1.955  -1.921  -1.828  -2.054  -2.056  -1.943  -1.660  -1.619  -1.452
162   E        -1.568  -1.528  -1.434  -1.552  -1.487  -1.310  -1.514  -1.448  -1.290
163   T        -1.955  -1.980  -1.833  -1.601  -1.647  -1.525  -1.660  -1.672  -1.456
164   I         0.930   0.948   0.981   1.034   1.050   1.094   0.977   1.002   1.047
165   E         0.128  -0.054  -0.157   0.094  -0.168  -0.368   0.098  -0.181  -0.382
166   E        -1.568  -1.567  -1.439  -1.750  -1.764  -1.504  -1.514  -1.498  -1.295
167   L        -0.628  -0.812  -0.894  -0.663  -0.943  -1.076  -0.635  -0.875  -0.976
168   L         0.930   0.948   0.981   0.776   0.803   0.873   0.977   1.002   1.047
169   K        -0.767  -0.825  -0.906  -0.990  -1.107  -1.161  -0.818  -0.902  -0.992
170   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   E        -1.048  -1.006  -0.930  -1.419  -1.341  -1.196  -1.217  -1.147  -1.023
* 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/P40581
Output conservation file - output/P40581
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
