1     M         1.694   1.704   1.785   1.870   1.878   2.011   1.896   1.912   2.044
2     L        -0.280  -0.264  -0.239  -0.430  -0.409  -0.364  -0.477  -0.440  -0.400
3     R        -0.730  -0.753  -0.774  -0.653  -0.723  -0.748  -0.693  -0.721  -0.724
4     T        -1.351  -1.311  -1.277  -1.282  -1.249  -1.169  -1.124  -1.084  -1.010
5     S        -0.730  -0.810  -0.818  -0.624  -0.683  -0.739  -0.693  -0.786  -0.775
6     L        -0.901  -0.855  -0.845  -1.057  -0.997  -0.958  -0.908  -0.861  -0.810
7     T        -1.351  -1.392  -1.313  -1.256  -1.344  -1.217  -1.124  -1.158  -1.042
8     K        -0.730  -0.784  -0.801  -0.603  -0.670  -0.728  -0.693  -0.756  -0.756
9     G        -0.730  -0.675  -0.766  -0.867  -0.790  -0.930  -0.693  -0.628  -0.715
10    A         0.001  -0.056  -0.166  -0.139  -0.225  -0.417  -0.045  -0.128  -0.290
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    R        -1.802  -1.778  -1.680  -1.752  -1.752  -1.568  -1.340  -1.316  -1.183
24    L        -0.280  -0.291  -0.275  -0.331  -0.363  -0.334  -0.477  -0.498  -0.457
25    T        -1.351  -1.281  -1.281  -1.308  -1.192  -1.201  -1.124  -1.054  -1.013
26    G        -1.351  -1.284  -1.286  -1.327  -1.260  -1.208  -1.124  -1.057  -1.018
27    T        -1.351  -1.392  -1.313  -1.499  -1.553  -1.473  -1.124  -1.158  -1.042
28    R        -0.901  -0.895  -0.852  -1.103  -1.109  -1.016  -0.908  -0.895  -0.815
29    F        -0.280  -0.221  -0.245  -0.328  -0.246  -0.252  -0.477  -0.384  -0.409
30    V        -1.351  -1.357  -1.283  -1.228  -1.192  -1.117  -1.124  -1.126  -1.015
31    Q        -0.901  -0.898  -0.856  -1.105  -1.107  -1.024  -0.908  -0.898  -0.820
32    T        -1.351  -1.392  -1.313  -1.342  -1.386  -1.285  -1.124  -1.158  -1.042
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -0.906  -0.883  -0.838  -1.088  -1.054  -0.974  -0.900  -0.874  -0.798
40    -        -0.906  -0.950  -0.880  -1.091  -1.176  -1.085  -0.900  -0.948  -0.844
41    K        -1.351  -1.392  -1.313  -1.153  -1.218  -1.092  -1.124  -1.158  -1.042
42    A        -0.730  -0.810  -0.818  -0.738  -0.851  -0.834  -0.693  -0.786  -0.775
43    L         0.341   0.361   0.450   0.056   0.090   0.241  -0.045  -0.013   0.118
44    S         0.815   0.764   0.664   0.783   0.753   0.535   0.817   0.731   0.530
45    K        -0.730  -0.788  -0.807  -0.536  -0.637  -0.693  -0.693  -0.760  -0.762
46    A         0.341   0.361   0.450  -0.067  -0.017   0.117  -0.045  -0.013   0.118
47    T        -0.280  -0.264  -0.239  -0.302  -0.286  -0.232  -0.477  -0.440  -0.400
48    L         0.001   0.150  -0.126   0.009   0.195  -0.161  -0.045   0.166  -0.231
49    T        -1.802  -1.778  -1.680  -1.724  -1.685  -1.541  -1.340  -1.316  -1.183
50    D        -0.280  -0.210  -0.251  -0.167  -0.071  -0.125  -0.477  -0.401  -0.424
51    L         0.452   0.430   0.477   0.222   0.170   0.256   0.170   0.123   0.171
52    P        -0.280  -0.260  -0.251  -0.303  -0.265  -0.251  -0.477  -0.447  -0.423
53    E        -0.280  -0.221  -0.245  -0.464  -0.314  -0.398  -0.477  -0.384  -0.409
54    R         1.694   1.704   1.785   1.727   1.735   1.870   1.896   1.912   2.044
55    W         1.694   1.704   1.785   1.853   1.863   1.995   1.896   1.912   2.044
56    E         0.001   0.003  -0.136   0.049   0.052  -0.168  -0.045  -0.045  -0.247
57    N        -1.802  -1.778  -1.680  -1.539  -1.482  -1.358  -1.340  -1.316  -1.183
58    M         0.452   0.536   0.545   0.409   0.562   0.548   0.170   0.325   0.304
59    P         0.815   0.764   0.664   0.837   0.789   0.606   0.817   0.731   0.530
60    N        -1.351  -1.392  -1.313  -1.240  -1.296  -1.168  -1.124  -1.158  -1.042
61    L        -0.280  -0.266  -0.252  -0.420  -0.400  -0.382  -0.477  -0.457  -0.426
62    E         0.452   0.536   0.545   0.365   0.500   0.509   0.170   0.325   0.304
63    Q         0.001  -0.076  -0.167   0.133   0.015  -0.138  -0.045  -0.157  -0.291
64    K        -1.802  -1.778  -1.680  -1.709  -1.665  -1.527  -1.340  -1.316  -1.183
65    E        -0.901  -0.925  -0.848  -0.920  -0.944  -0.810  -0.908  -0.926  -0.812
66    I        -0.280  -0.206  -0.252  -0.391  -0.322  -0.320  -0.477  -0.393  -0.424
67    A        -0.730  -0.773  -0.802  -0.546  -0.623  -0.674  -0.693  -0.742  -0.757
68    D        -1.351  -1.349  -1.289  -0.975  -0.972  -0.890  -1.124  -1.121  -1.020
69    N        -1.351  -1.392  -1.313  -1.221  -1.277  -1.150  -1.124  -1.158  -1.042
70    L         1.694   1.704   1.785   1.562   1.565   1.707   1.896   1.912   2.044
71    T        -0.901  -0.922  -0.855  -0.926  -0.939  -0.824  -0.908  -0.923  -0.819
72    E        -1.351  -1.308  -1.285  -1.339  -1.258  -1.245  -1.124  -1.082  -1.017
73    R         1.694   1.704   1.785   1.727   1.735   1.870   1.896   1.912   2.044
74    Q         0.341   0.357   0.448   0.254   0.265   0.415  -0.045  -0.020   0.115
75    K         0.452   0.536   0.545   0.244   0.410   0.387   0.170   0.325   0.304
76    L        -0.730  -0.810  -0.818  -0.715  -0.845  -0.830  -0.693  -0.786  -0.775
77    P         0.452   0.430   0.477   0.341   0.312   0.373   0.170   0.123   0.171
78    W         1.694   1.704   1.785   1.853   1.863   1.995   1.896   1.912   2.044
79    K        -1.351  -1.392  -1.313  -1.376  -1.446  -1.362  -1.124  -1.158  -1.042
80    T        -0.450  -0.428  -0.331  -0.571  -0.528  -0.379  -0.693  -0.664  -0.527
81    L         1.694   1.704   1.785   1.562   1.565   1.707   1.896   1.912   2.044
82    N         0.001  -0.041  -0.158   0.065   0.003  -0.173  -0.045  -0.107  -0.279
83    N        -0.901  -0.906  -0.854  -0.973  -0.982  -0.873  -0.908  -0.907  -0.818
84    E        -0.280  -0.306  -0.272  -0.544  -0.588  -0.512  -0.477  -0.513  -0.453
85    E         1.694   1.704   1.785   1.657   1.675   1.801   1.896   1.912   2.044
86    I         0.815   0.824   0.672   0.848   0.876   0.652   0.817   0.831   0.545
87    K         0.815   0.782   0.664   0.841   0.813   0.627   0.817   0.761   0.530
88    A         1.694   1.704   1.785   1.508   1.512   1.654   1.896   1.912   2.044
89    A         1.694   1.704   1.785   1.508   1.512   1.654   1.896   1.912   2.044
90    W         0.452   0.444   0.480   0.547   0.530   0.570   0.170   0.150   0.178
91    Y         0.815   0.764   0.664   1.096   1.030   0.887   0.817   0.731   0.530
92    I         1.694   1.704   1.785   1.773   1.776   1.916   1.896   1.912   2.044
93    S         0.452   0.423   0.477   0.164   0.137   0.160   0.170   0.110   0.172
94    Y         0.452   0.444   0.480   0.504   0.489   0.535   0.170   0.150   0.178
95    G         1.694   1.704   1.785   1.709   1.715   1.853   1.896   1.912   2.044
96    E         0.452   0.430   0.477   0.258   0.224   0.270   0.170   0.123   0.171
97    W         0.452   0.423   0.477   0.577   0.526   0.611   0.170   0.110   0.172
98    G         1.694   1.704   1.785   1.709   1.715   1.853   1.896   1.912   2.044
99    P         1.694   1.704   1.785   1.663   1.689   1.807   1.896   1.912   2.044
100   R         1.694   1.704   1.785   1.727   1.735   1.870   1.896   1.912   2.044
101   R        -0.901  -0.863  -0.841  -1.109  -1.061  -1.005  -0.908  -0.867  -0.807
102   P         0.718   0.651   0.602   0.783   0.692   0.609   0.653   0.534   0.413
103   V        -0.280  -0.318  -0.276  -0.450  -0.499  -0.430  -0.477  -0.526  -0.457
104   H        -0.280  -0.247  -0.241  -0.050   0.014   0.006  -0.477  -0.418  -0.403
105   G        -1.351  -1.372  -1.294  -1.237  -1.272  -1.156  -1.124  -1.141  -1.025
106   K         0.718   0.709   0.612   0.688   0.674   0.511   0.653   0.637   0.434
107   G         1.694   1.704   1.785   1.714   1.726   1.858   1.896   1.912   2.044
108   D        -0.280  -0.306  -0.263  -0.246  -0.267  -0.242  -0.477  -0.506  -0.441
109   V        -0.730  -0.607  -0.772  -0.576  -0.393  -0.650  -0.693  -0.543  -0.722
110   A        -0.901  -0.878  -0.848  -1.144  -1.078  -1.054  -0.908  -0.881  -0.813
111   F        -0.730  -0.726  -0.768  -0.649  -0.637  -0.705  -0.693  -0.687  -0.718
112   I         0.452   0.444   0.480   0.430   0.402   0.451   0.170   0.150   0.178
113   T         0.001  -0.021  -0.153   0.172   0.131  -0.102  -0.045  -0.077  -0.271
114   K        -0.730  -0.773  -0.802  -0.536  -0.612  -0.695  -0.693  -0.742  -0.757
115   G         0.001   0.024  -0.136   0.174   0.198  -0.012  -0.045  -0.014  -0.246
116   V        -0.280  -0.270  -0.250  -0.341  -0.333  -0.279  -0.477  -0.452  -0.420
117   F        -0.730  -0.714  -0.773  -0.525  -0.511  -0.604  -0.693  -0.672  -0.723
118   L        -0.901  -0.863  -0.841  -1.051  -1.030  -0.957  -0.908  -0.867  -0.807
119   G         0.815   0.876   0.684   0.958   1.026   0.809   0.817   0.917   0.568
120   L         0.001   0.024  -0.136   0.009   0.027  -0.176  -0.045  -0.014  -0.246
121   G        -1.351  -1.372  -1.294  -1.263  -1.327  -1.185  -1.124  -1.141  -1.025
122   I        -0.901  -0.855  -0.835  -1.079  -1.013  -0.983  -0.908  -0.862  -0.800
123   S         0.452   0.478   0.493   0.258   0.341   0.308   0.170   0.215   0.204
124   F         0.452   0.446   0.477   0.451   0.433   0.471   0.170   0.155   0.171
125   G        -0.730  -0.675  -0.766  -0.622  -0.540  -0.715  -0.693  -0.628  -0.715
126   L         0.452   0.430   0.477   0.222   0.170   0.256   0.170   0.123   0.171
127   F         1.694   1.704   1.785   1.819   1.831   1.961   1.896   1.912   2.044
128   G        -0.280  -0.215  -0.252  -0.431  -0.337  -0.384  -0.477  -0.388  -0.426
129   L        -0.730  -0.633  -0.767  -0.736  -0.620  -0.784  -0.693  -0.576  -0.716
130   V        -1.351  -1.325  -1.277  -1.005  -0.966  -0.887  -1.124  -1.097  -1.009
131   R         0.815   0.782   0.664   0.887   0.832   0.644   0.817   0.761   0.530
132   L        -1.351  -1.292  -1.284  -1.406  -1.363  -1.291  -1.124  -1.065  -1.016
133   L        -0.280  -0.318  -0.276  -0.331  -0.406  -0.341  -0.477  -0.526  -0.457
134   A         0.815   0.782   0.664   0.704   0.650   0.496   0.817   0.761   0.530
135   N        -1.351  -1.350  -1.284  -1.427  -1.400  -1.313  -1.124  -1.120  -1.016
136   P         0.815   0.782   0.664   0.812   0.775   0.564   0.817   0.761   0.530
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   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   T        -0.730  -0.788  -0.807  -0.764  -0.844  -0.929  -0.693  -0.760  -0.762
141   P         0.815   0.782   0.664   0.823   0.786   0.582   0.817   0.761   0.530
142   K        -1.351  -1.281  -1.281  -1.322  -1.219  -1.231  -1.124  -1.054  -1.013
143   T         1.694   1.704   1.785   1.645   1.648   1.789   1.896   1.912   2.044
144   M         0.001   0.066  -0.128   0.244   0.332   0.020  -0.045   0.042  -0.235
145   N        -0.280  -0.285  -0.256  -0.357  -0.360  -0.315  -0.477  -0.476  -0.429
146   R        -0.280  -0.294  -0.260  -0.341  -0.352  -0.301  -0.477  -0.492  -0.436
147   E         1.694   1.704   1.785   1.657   1.675   1.801   1.896   1.912   2.044
148   W         1.694   1.704   1.785   1.853   1.863   1.995   1.896   1.912   2.044
149   Q         1.694   1.704   1.785   1.738   1.747   1.882   1.896   1.912   2.044
150   L         0.815   0.824   0.672   0.817   0.833   0.591   0.817   0.831   0.545
151   K         0.001   0.024  -0.136   0.012   0.053  -0.216  -0.045  -0.014  -0.246
152   S         0.815   0.788   0.667   0.810   0.819   0.587   0.817   0.772   0.535
153   D         0.341   0.361   0.450   0.334   0.361   0.500  -0.045  -0.013   0.118
154   E         0.815   0.876   0.684   0.884   0.968   0.722   0.817   0.917   0.568
155   Y         0.001  -0.056  -0.166   0.322   0.240   0.067  -0.045  -0.128  -0.290
156   L         0.815   0.764   0.664   0.785   0.710   0.595   0.817   0.731   0.530
157   K         1.694   1.704   1.785   1.645   1.676   1.789   1.896   1.912   2.044
158   S        -0.280  -0.313  -0.281  -0.503  -0.525  -0.524  -0.477  -0.524  -0.465
159   K        -0.730  -0.810  -0.818  -0.601  -0.703  -0.713  -0.693  -0.786  -0.775
160   N        -0.280  -0.316  -0.282  -0.284  -0.351  -0.305  -0.477  -0.527  -0.466
161   A         0.001  -0.071  -0.171  -0.085  -0.186  -0.339  -0.045  -0.149  -0.297
162   N         0.815   0.788   0.667   1.054   1.017   0.857   0.817   0.772   0.535
163   P         1.694   1.704   1.785   1.663   1.689   1.807   1.896   1.912   2.044
164   W        -0.730  -0.784  -0.801  -0.494  -0.590  -0.622  -0.693  -0.756  -0.756
165   G         0.001  -0.041  -0.158   0.035  -0.029  -0.219  -0.045  -0.107  -0.279
166   G         0.815   0.782   0.664   0.886   0.830   0.655   0.817   0.761   0.530
167   Y         0.001  -0.071  -0.171   0.236   0.122  -0.076  -0.045  -0.149  -0.297
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   S        -0.280  -0.316  -0.282  -0.380  -0.401  -0.359  -0.477  -0.527  -0.466
177   Q         0.815   0.788   0.667   0.981   0.944   0.801   0.817   0.772   0.535
178   V         0.341   0.352   0.445   0.221   0.226   0.381  -0.045  -0.030   0.108
179   Q         0.815   0.764   0.664   0.912   0.846   0.679   0.817   0.731   0.530
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   S        -0.335  -0.315  -0.277  -0.404  -0.373  -0.318  -0.531  -0.503  -0.450
199   K        -0.335  -0.315  -0.282  -0.623  -0.590  -0.564  -0.531  -0.503  -0.458
* 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/P00425
Output conservation file - output/P00425
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
