1     M         1.106   1.148   1.211   1.389   1.444   1.529   1.191   1.252   1.348
2     L        -1.386  -1.460  -1.353  -1.527  -1.624  -1.477  -1.290  -1.324  -1.162
3     S        -0.396  -0.432  -0.489  -0.421  -0.534  -0.640  -0.567  -0.629  -0.678
4     R        -0.581  -0.579  -0.532  -0.883  -0.900  -0.798  -0.831  -0.819  -0.733
5     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     I        -1.784  -1.789  -1.651  -1.794  -1.807  -1.597  -1.497  -1.463  -1.273
7     F        -1.386  -1.362  -1.326  -1.363  -1.304  -1.236  -1.290  -1.238  -1.139
8     R         1.106   1.148   1.211   1.044   1.102   1.204   1.191   1.252   1.348
9     N        -1.386  -1.415  -1.337  -1.317  -1.310  -1.199  -1.290  -1.285  -1.149
10    P        -0.917  -0.963  -0.942  -0.997  -1.056  -0.979  -0.980  -1.002  -0.944
11    V        -1.386  -1.390  -1.339  -1.427  -1.415  -1.310  -1.290  -1.266  -1.150
12    I        -1.206  -1.149  -1.299  -1.044  -0.978  -1.149  -1.084  -1.021  -1.113
13    N        -1.675  -1.424  -1.605  -1.344  -0.956  -1.311  -1.394  -1.126  -1.238
14    R        -0.121  -0.135  -0.430  -0.040  -0.048  -0.469  -0.153  -0.165  -0.588
15    T        -1.784  -1.781  -1.645  -1.850  -1.826  -1.651  -1.497  -1.458  -1.269
16    L        -1.386  -1.336  -1.332  -1.486  -1.399  -1.392  -1.290  -1.225  -1.145
17    L        -1.784  -1.786  -1.652  -1.731  -1.709  -1.516  -1.497  -1.462  -1.274
18    R        -1.578  -1.519  -1.366  -1.479  -1.369  -1.170  -1.456  -1.371  -1.173
19    A        -0.653  -0.564  -0.531  -0.997  -0.869  -0.779  -0.926  -0.805  -0.731
20    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    A        -1.024  -1.037  -0.984  -1.157  -1.197  -1.041  -1.105  -1.095  -0.990
24    Y        -1.354  -1.288  -1.334  -1.216  -1.134  -1.143  -1.240  -1.155  -1.146
25    H        -1.354  -1.290  -1.331  -1.339  -1.248  -1.305  -1.240  -1.147  -1.143
26    A        -0.033   0.005   0.102  -0.394  -0.346  -0.161  -0.429  -0.369  -0.226
27    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    R        -1.784  -1.658  -1.627  -1.817  -1.656  -1.546  -1.497  -1.366  -1.257
29    L        -0.699  -0.602  -0.536  -1.170  -1.000  -0.901  -0.980  -0.835  -0.737
30    -        -0.818  -0.829  -0.934  -0.784  -0.782  -0.965  -0.835  -0.845  -0.934
31    -        -0.818  -0.627  -0.909  -0.671  -0.370  -0.888  -0.835  -0.582  -0.905
32    -        -1.497  -1.494  -1.361  -1.416  -1.398  -1.180  -1.382  -1.350  -1.169
33    -        -0.222  -0.202  -0.435  -0.170  -0.146  -0.488  -0.294  -0.258  -0.595
34    -        -1.809  -1.786  -1.646  -1.558  -1.561  -1.362  -1.510  -1.459  -1.269
35    -        -1.809  -1.729  -1.642  -1.659  -1.581  -1.369  -1.510  -1.415  -1.267
36    T        -2.073  -2.029  -1.893  -1.837  -1.781  -1.596  -1.601  -1.534  -1.346
37    K        -1.386  -1.337  -1.322  -1.399  -1.381  -1.289  -1.290  -1.221  -1.137
38    N        -2.073  -2.034  -1.891  -1.758  -1.697  -1.513  -1.601  -1.538  -1.345
39    T        -1.386  -1.394  -1.333  -1.226  -1.270  -1.180  -1.290  -1.275  -1.146
40    F        -1.495  -1.398  -1.344  -1.459  -1.346  -1.214  -1.394  -1.270  -1.155
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    I        -2.073  -2.002  -1.889  -1.867  -1.786  -1.621  -1.601  -1.515  -1.344
45    Q        -0.988  -0.909  -0.952  -0.894  -0.791  -0.824  -1.084  -0.978  -0.959
46    S        -0.917  -0.985  -0.955  -0.702  -0.842  -0.766  -0.980  -1.040  -0.961
47    R         1.106   1.148   1.211   1.044   1.102   1.204   1.191   1.252   1.348
48    K        -1.024  -1.070  -0.990  -0.926  -0.989  -0.874  -1.105  -1.129  -0.997
49    Y        -0.121  -0.335  -0.454   0.109  -0.204  -0.452  -0.153  -0.452  -0.622
50    S         1.106   1.148   1.211   1.191   1.242   1.343   1.191   1.252   1.348
51    D        -0.988  -0.967  -0.966  -1.037  -0.990  -1.062  -1.084  -1.025  -0.972
52    A        -0.581  -0.500  -0.519  -0.725  -0.608  -0.555  -0.831  -0.740  -0.717
53    H         1.106   1.148   1.211   1.381   1.436   1.522   1.191   1.252   1.348
54    D        -0.581  -0.459  -0.512  -0.526  -0.298  -0.490  -0.831  -0.645  -0.704
55    E         0.477   0.299   0.224   0.394   0.187   0.087   0.468   0.173   0.008
56    E         0.477   0.299   0.224   0.351   0.114  -0.031   0.468   0.173   0.008
57    T         0.477   0.299   0.224   0.664   0.427   0.279   0.468   0.173   0.008
58    F         0.477   0.299   0.224   0.560   0.283   0.137   0.468   0.173   0.008
59    E         0.477   0.525   0.240   0.373   0.458   0.055   0.468   0.539   0.037
60    E         1.106   1.148   1.211   0.921   0.995   1.089   1.191   1.252   1.348
61    F         0.477   0.299   0.224   0.600   0.350   0.247   0.468   0.173   0.008
62    T         0.477   0.299   0.224   0.671   0.438   0.299   0.468   0.173   0.008
63    A         0.168   0.089   0.121  -0.046  -0.169  -0.121  -0.049  -0.206  -0.189
64    R         0.477   0.299   0.224   0.492   0.252   0.127   0.468   0.173   0.008
65    Y         0.168   0.237   0.149   0.220   0.330   0.131  -0.049   0.066  -0.134
66    E         0.477   0.299   0.224   0.378   0.161   0.042   0.468   0.173   0.008
67    K        -0.121  -0.231  -0.432   0.102  -0.061  -0.355  -0.153  -0.318  -0.590
68    E         0.477   0.299   0.224   0.362   0.131  -0.002   0.468   0.173   0.008
69    F         1.106   1.148   1.211   1.139   1.178   1.293   1.191   1.252   1.348
70    D        -0.519  -0.613  -0.502  -0.751  -0.836  -0.668  -0.773  -0.855  -0.695
71    E        -0.396  -0.489  -0.499  -0.602  -0.728  -0.754  -0.567  -0.696  -0.691
72    A         0.168   0.064   0.116  -0.097  -0.296  -0.217  -0.049  -0.254  -0.198
73    Y         0.168   0.064   0.116   0.259   0.071   0.132  -0.049  -0.254  -0.198
74    D         1.106   1.148   1.211   1.216   1.273   1.366   1.191   1.252   1.348
75    L        -0.121  -0.335  -0.454  -0.103  -0.389  -0.584  -0.153  -0.452  -0.622
76    F         1.106   1.148   1.211   1.139   1.178   1.293   1.191   1.252   1.348
77    E         1.106   1.148   1.211   0.921   0.995   1.089   1.191   1.252   1.348
78    V         0.168   0.064   0.116   0.013  -0.211  -0.153  -0.049  -0.254  -0.198
79    Q         1.106   1.148   1.211   1.263   1.301   1.411   1.191   1.252   1.348
80    R         1.106   1.148   1.211   1.044   1.102   1.204   1.191   1.252   1.348
81    V        -0.917  -1.030  -0.972  -0.817  -0.949  -0.828  -0.980  -1.075  -0.978
82    L         1.106   1.148   1.211   0.998   1.063   1.161   1.191   1.252   1.348
83    N         1.106   1.148   1.211   1.244   1.289   1.392   1.191   1.252   1.348
84    N         1.106   1.148   1.211   1.244   1.289   1.392   1.191   1.252   1.348
85    C         0.477   0.454   0.235   0.810   0.774   0.366   0.468   0.429   0.027
86    F         1.106   1.148   1.211   1.139   1.178   1.293   1.191   1.252   1.348
87    S        -0.050   0.013   0.113  -0.394  -0.312  -0.145  -0.463  -0.352  -0.204
88    Y         1.106   1.148   1.211   1.236   1.297   1.385   1.191   1.252   1.348
89    D         1.106   1.148   1.211   1.216   1.273   1.366   1.191   1.252   1.348
90    L         0.477   0.299   0.224   0.460   0.238   0.124   0.468   0.173   0.008
91    V         1.106   1.148   1.211   1.069   1.113   1.228   1.191   1.252   1.348
92    P         1.106   1.148   1.211   1.240   1.294   1.388   1.191   1.252   1.348
93    A         0.168   0.064   0.116  -0.055  -0.230  -0.141  -0.049  -0.254  -0.198
94    P         0.477   0.299   0.224   0.688   0.442   0.300   0.468   0.173   0.008
95    A        -0.396  -0.552  -0.505  -0.555  -0.758  -0.672  -0.567  -0.761  -0.698
96    V         1.106   1.148   1.211   1.069   1.113   1.228   1.191   1.252   1.348
97    I         0.477   0.454   0.235   0.701   0.664   0.283   0.468   0.429   0.027
98    E         0.477   0.454   0.235   0.331   0.320  -0.066   0.468   0.429   0.027
99    K        -0.121  -0.335  -0.454   0.065  -0.246  -0.483  -0.153  -0.452  -0.622
100   A         1.106   1.148   1.211   0.934   0.994   1.101   1.191   1.252   1.348
101   L         1.106   1.148   1.211   0.998   1.063   1.161   1.191   1.252   1.348
102   R        -0.519  -0.509  -0.502  -0.621  -0.599  -0.555  -0.773  -0.730  -0.696
103   A         1.106   1.148   1.211   0.934   0.994   1.101   1.191   1.252   1.348
104   A         0.003   0.073   0.115  -0.213  -0.110  -0.015  -0.360  -0.237  -0.199
105   R         1.106   1.148   1.211   1.044   1.102   1.204   1.191   1.252   1.348
106   R         0.477   0.594   0.248   0.492   0.642   0.167   0.468   0.642   0.052
107   V         1.106   1.148   1.211   1.069   1.113   1.228   1.191   1.252   1.348
108   N         1.106   1.148   1.211   1.244   1.289   1.392   1.191   1.252   1.348
109   D         1.106   1.148   1.211   1.216   1.273   1.366   1.191   1.252   1.348
110   L        -0.699  -0.607  -0.523  -0.942  -0.773  -0.642  -0.980  -0.840  -0.719
111   P         1.106   1.148   1.211   1.240   1.294   1.388   1.191   1.252   1.348
112   T         1.106   1.148   1.211   1.216   1.278   1.366   1.191   1.252   1.348
113   A         1.106   1.148   1.211   0.934   0.994   1.101   1.191   1.252   1.348
114   I         0.477   0.586   0.260   0.531   0.655   0.242   0.468   0.630   0.074
115   R         1.106   1.148   1.211   1.044   1.102   1.204   1.191   1.252   1.348
116   V        -0.396  -0.485  -0.487  -0.405  -0.513  -0.511  -0.567  -0.662  -0.671
117   F         1.106   1.148   1.211   1.139   1.178   1.293   1.191   1.252   1.348
118   E         1.106   1.148   1.211   0.921   0.995   1.089   1.191   1.252   1.348
119   A         0.003  -0.009   0.101  -0.239  -0.233  -0.030  -0.360  -0.396  -0.227
120   L         0.168   0.064   0.116   0.037  -0.124  -0.038  -0.049  -0.254  -0.198
121   K         0.477   0.594   0.248   0.615   0.762   0.243   0.468   0.642   0.052
122   Y        -1.206  -1.284  -1.327  -0.944  -1.113  -1.192  -1.084  -1.155  -1.139
123   K         1.106   1.148   1.211   1.187   1.237   1.339   1.191   1.252   1.348
124   V         0.477   0.299   0.224   0.490   0.219   0.074   0.468   0.173   0.008
125   E        -0.121  -0.274  -0.440  -0.158  -0.343  -0.575  -0.153  -0.373  -0.602
126   N         0.168   0.104   0.124   0.252   0.126   0.126  -0.049  -0.179  -0.183
127   E        -0.988  -0.862  -0.954  -1.101  -0.865  -0.948  -1.084  -0.920  -0.959
128   D        -0.988  -0.967  -0.966  -1.064  -1.022  -0.970  -1.084  -1.025  -0.972
129   Q         1.106   1.148   1.211   1.263   1.301   1.411   1.191   1.252   1.348
130   Y         1.106   1.148   1.211   1.236   1.297   1.385   1.191   1.252   1.348
131   K        -0.699  -0.645  -0.536  -0.868  -0.774  -0.643  -0.980  -0.890  -0.736
132   A         0.477   0.454   0.235   0.394   0.373   0.078   0.468   0.429   0.027
133   Y         1.106   1.148   1.211   1.236   1.297   1.385   1.191   1.252   1.348
134   L         0.477   0.299   0.224   0.428   0.181   0.038   0.468   0.173   0.008
135   D        -0.917  -1.030  -0.972  -0.952  -1.103  -1.104  -0.980  -1.075  -0.978
136   E         0.477   0.525   0.240   0.331   0.417  -0.056   0.468   0.539   0.037
137   L         1.106   1.148   1.211   0.998   1.063   1.161   1.191   1.252   1.348
138   K         1.106   1.148   1.211   1.187   1.237   1.339   1.191   1.252   1.348
139   D        -0.396  -0.397  -0.494  -0.325  -0.361  -0.535  -0.567  -0.611  -0.683
140   V        -0.396  -0.361  -0.474  -0.434  -0.383  -0.570  -0.567  -0.492  -0.652
141   R         0.477   0.299   0.224   0.523   0.308   0.212   0.468   0.173   0.008
142   Q        -0.917  -0.950  -0.954  -0.994  -1.015  -0.978  -0.980  -0.993  -0.960
143   E         1.106   1.148   1.211   0.921   0.995   1.089   1.191   1.252   1.348
144   L         1.106   1.148   1.211   0.998   1.063   1.161   1.191   1.252   1.348
145   G         1.106   1.148   1.211   1.350   1.386   1.492   1.191   1.252   1.348
146   V         0.168   0.304   0.201   0.240   0.450   0.243  -0.049   0.182  -0.036
147   P        -1.097  -1.150  -0.996  -1.044  -1.126  -0.911  -1.187  -1.205  -1.003
148   L         1.106   1.148   1.211   0.998   1.063   1.161   1.191   1.252   1.348
149   K         1.106   1.148   1.211   1.187   1.237   1.339   1.191   1.252   1.348
150   E         1.106   1.148   1.211   0.921   0.995   1.089   1.191   1.252   1.348
151   E         0.168   0.293   0.187   0.133   0.351   0.096  -0.049   0.163  -0.062
152   L         1.106   1.148   1.211   0.998   1.063   1.161   1.191   1.252   1.348
153   F         0.003   0.050   0.110  -0.125  -0.061   0.031  -0.360  -0.281  -0.211
154   P        -0.341  -0.249  -0.479  -0.243  -0.102  -0.562  -0.463  -0.323  -0.658
155   S        -1.112  -1.059  -0.988  -1.222  -1.158  -1.000  -1.198  -1.116  -0.994
156   S        -1.112  -1.069  -0.990  -1.354  -1.295  -1.171  -1.198  -1.126  -0.996
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   S        -1.784  -1.754  -1.641  -1.546  -1.519  -1.360  -1.497  -1.439  -1.266
* 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/P00427
Output conservation file - output/P00427
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
