1     M         1.290   1.305   1.380   1.536   1.559   1.667   1.394   1.415   1.526
2     M        -1.334  -1.332  -1.254  -1.317  -1.284  -1.138  -1.203  -1.194  -1.062
3     F        -1.669  -1.667  -1.572  -1.666  -1.704  -1.554  -1.340  -1.331  -1.184
4     N        -1.669  -1.649  -1.565  -1.520  -1.511  -1.341  -1.340  -1.315  -1.179
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    I        -0.179  -0.199  -0.308  -0.254  -0.297  -0.493  -0.281  -0.310  -0.466
20    Y        -1.207  -1.199  -1.225  -1.092  -1.104  -1.105  -1.067  -1.054  -1.033
21    L        -0.058  -0.008  -0.271  -0.155  -0.076  -0.496  -0.110  -0.037  -0.412
22    F        -1.334  -1.357  -1.263  -1.357  -1.374  -1.226  -1.203  -1.216  -1.068
23    V        -1.334  -1.371  -1.260  -1.416  -1.454  -1.254  -1.203  -1.226  -1.066
24    T        -1.669  -1.667  -1.572  -1.593  -1.612  -1.468  -1.340  -1.331  -1.185
25    F         0.595   0.546   0.409   0.775   0.704   0.473   0.573   0.494   0.230
26    F        -0.872  -0.826  -0.857  -0.926  -0.866  -0.870  -0.930  -0.868  -0.863
27    S        -1.669  -1.634  -1.562  -1.643  -1.591  -1.475  -1.340  -1.304  -1.177
28    T        -1.669  -1.642  -1.566  -1.435  -1.395  -1.293  -1.340  -1.310  -1.180
29    I        -0.410  -0.436  -0.383  -0.714  -0.758  -0.665  -0.657  -0.677  -0.582
30    -        -0.470  -0.494  -0.417  -0.480  -0.527  -0.403  -0.699  -0.731  -0.620
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    L        -1.207  -1.270  -1.234  -1.088  -1.205  -1.189  -1.067  -1.124  -1.041
53    A         0.595   0.522   0.407   0.719   0.621   0.420   0.573   0.454   0.226
54    G        -0.872  -0.850  -0.854  -0.958  -0.938  -0.933  -0.930  -0.902  -0.861
55    -        -0.496  -0.495  -0.413  -0.669  -0.652  -0.533  -0.750  -0.741  -0.617
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    S        -0.422  -0.474  -0.395  -0.567  -0.644  -0.505  -0.653  -0.715  -0.595
61    L        -0.179  -0.196  -0.308  -0.261  -0.285  -0.459  -0.281  -0.305  -0.466
62    S        -0.813  -0.721  -0.830  -0.733  -0.564  -0.773  -0.839  -0.721  -0.829
63    D        -0.961  -0.921  -0.879  -1.196  -1.130  -1.052  -1.025  -0.980  -0.887
64    L         1.290   1.305   1.380   1.146   1.176   1.290   1.394   1.415   1.526
65    E        -0.872  -0.858  -0.857  -0.828  -0.805  -0.822  -0.930  -0.912  -0.865
66    I        -0.058  -0.008  -0.271  -0.026   0.036  -0.343  -0.110  -0.037  -0.412
67    G        -0.328  -0.389  -0.371  -0.584  -0.682  -0.628  -0.520  -0.600  -0.564
68    I         0.277   0.254   0.266   0.078   0.021   0.021   0.027  -0.019  -0.039
69    I        -0.872  -0.903  -0.867  -0.996  -1.029  -0.951  -0.930  -0.953  -0.874
70    K        -0.058  -0.082  -0.270   0.059   0.036  -0.232  -0.110  -0.145  -0.412
71    R        -0.998  -0.988  -0.896  -1.111  -1.084  -0.925  -1.067  -1.049  -0.905
72    I         0.150   0.151   0.242  -0.178  -0.198  -0.034  -0.214  -0.217  -0.086
73    P         0.443   0.475   0.335   0.531   0.576   0.319   0.322   0.375   0.092
74    V        -0.965  -0.960  -0.893  -1.129  -1.121  -1.010  -1.018  -1.006  -0.899
75    E        -0.965  -0.985  -0.896  -1.082  -1.150  -1.006  -1.018  -1.035  -0.902
76    D        -0.998  -1.022  -0.897  -1.062  -1.051  -0.882  -1.067  -1.079  -0.906
77    C         0.595   0.522   0.407   0.880   0.768   0.540   0.573   0.454   0.226
78    L        -0.328  -0.328  -0.367  -0.426  -0.422  -0.502  -0.520  -0.521  -0.557
79    I        -1.334  -1.270  -1.252  -1.346  -1.241  -1.217  -1.203  -1.141  -1.060
80    K         0.595   0.522   0.407   0.647   0.561   0.371   0.573   0.454   0.226
81    A        -0.328  -0.333  -0.370  -0.319  -0.347  -0.396  -0.520  -0.545  -0.562
82    M        -1.334  -1.310  -1.255  -1.283  -1.237  -1.156  -1.203  -1.175  -1.062
83    P        -0.872  -0.933  -0.865  -0.842  -0.921  -0.825  -0.930  -0.982  -0.872
84    G         1.290   1.305   1.380   1.103   1.110   1.248   1.394   1.415   1.526
85    D         1.290   1.305   1.380   1.347   1.401   1.485   1.394   1.415   1.526
86    K        -2.004  -1.992  -1.847  -1.736  -1.693  -1.501  -1.477  -1.460  -1.277
87    V         0.277   0.279   0.290   0.087   0.080   0.075   0.027   0.027   0.007
88    K        -0.058  -0.120  -0.288   0.000  -0.086  -0.358  -0.110  -0.196  -0.437
89    V         1.290   1.305   1.380   1.250   1.270   1.391   1.394   1.415   1.526
90    H         1.290   1.305   1.380   1.560   1.588   1.691   1.394   1.415   1.526
91    Y         1.290   1.305   1.380   1.526   1.547   1.658   1.394   1.415   1.526
92    T        -0.663  -0.730  -0.814  -0.483  -0.599  -0.753  -0.657  -0.736  -0.810
93    G         1.290   1.305   1.380   1.103   1.110   1.248   1.394   1.415   1.526
94    S        -0.328  -0.374  -0.366  -0.466  -0.529  -0.539  -0.520  -0.570  -0.554
95    L         1.290   1.305   1.380   1.146   1.176   1.290   1.394   1.415   1.526
96    L        -1.057  -1.044  -0.919  -1.165  -1.138  -0.948  -1.118  -1.098  -0.926
97    E        -0.663  -0.749  -0.815  -0.480  -0.591  -0.715  -0.657  -0.758  -0.811
98    S        -0.410  -0.387  -0.378  -0.513  -0.474  -0.414  -0.657  -0.627  -0.576
99    G         1.290   1.305   1.380   1.103   1.110   1.248   1.394   1.415   1.526
100   T        -0.410  -0.382  -0.377  -0.510  -0.472  -0.439  -0.657  -0.618  -0.575
101   V        -0.663  -0.749  -0.815  -0.645  -0.779  -0.900  -0.657  -0.758  -0.811
102   F         1.290   1.305   1.380   1.428   1.447   1.563   1.394   1.415   1.526
103   D         1.290   1.305   1.380   1.347   1.401   1.485   1.394   1.415   1.526
104   S         0.595   0.522   0.407   0.638   0.534   0.365   0.573   0.454   0.226
105   S         1.290   1.305   1.380   1.271   1.286   1.411   1.394   1.415   1.526
106   Y        -0.058   0.026  -0.261   0.208   0.331  -0.163  -0.110   0.010  -0.399
107   S        -1.207  -1.189  -1.226  -1.033  -1.010  -1.030  -1.067  -1.043  -1.034
108   R         1.290   1.305   1.380   1.452   1.476   1.587   1.394   1.415   1.526
109   G         0.595   0.630   0.420   0.504   0.534   0.299   0.573   0.628   0.251
110   S        -1.334  -1.336  -1.254  -1.236  -1.238  -1.123  -1.203  -1.196  -1.061
111   P         1.290   1.305   1.380   1.408   1.427   1.543   1.394   1.415   1.526
112   I         0.277   0.219   0.262   0.037  -0.093  -0.048   0.027  -0.087  -0.047
113   A        -1.207  -1.255  -1.233  -0.899  -0.965  -0.949  -1.067  -1.110  -1.040
114   F         1.290   1.305   1.380   1.428   1.447   1.563   1.394   1.415   1.526
115   E        -1.669  -1.673  -1.575  -1.408  -1.402  -1.238  -1.340  -1.336  -1.187
116   L         0.595   0.522   0.407   0.493   0.397   0.205   0.573   0.454   0.226
117   G         1.290   1.305   1.380   1.103   1.110   1.248   1.394   1.415   1.526
118   V        -2.004  -1.992  -1.847  -1.851  -1.854  -1.612  -1.477  -1.460  -1.277
119   G        -0.058  -0.084  -0.276  -0.184  -0.237  -0.519  -0.110  -0.145  -0.420
120   R         0.277   0.322   0.290   0.370   0.444   0.365   0.027   0.105   0.008
121   V         1.290   1.305   1.380   1.250   1.270   1.391   1.394   1.415   1.526
122   I         1.290   1.305   1.380   1.235   1.249   1.376   1.394   1.415   1.526
123   K        -1.669  -1.625  -1.562  -1.511  -1.449  -1.336  -1.340  -1.296  -1.177
124   G         0.595   0.546   0.409   0.504   0.431   0.283   0.573   0.494   0.230
125   W         1.290   1.305   1.380   1.584   1.608   1.714   1.394   1.415   1.526
126   D         0.595   0.630   0.420   0.713   0.793   0.455   0.573   0.628   0.251
127   Q         0.277   0.219   0.262   0.335   0.227   0.261   0.027  -0.087  -0.047
128   G         1.290   1.305   1.380   1.103   1.110   1.248   1.394   1.415   1.526
129   V        -0.410  -0.394  -0.383  -0.767  -0.748  -0.702  -0.657  -0.631  -0.582
130   A        -0.328  -0.286  -0.350  -0.499  -0.428  -0.504  -0.520  -0.453  -0.532
131   G        -0.058  -0.060  -0.272  -0.132  -0.146  -0.417  -0.110  -0.113  -0.414
132   M         1.290   1.305   1.380   1.536   1.559   1.667   1.394   1.415   1.526
133   C         0.595   0.522   0.407   0.907   0.807   0.597   0.573   0.454   0.226
134   V        -0.328  -0.276  -0.353  -0.544  -0.461  -0.603  -0.520  -0.441  -0.535
135   G         1.290   1.305   1.380   1.103   1.110   1.248   1.394   1.415   1.526
136   E         1.290   1.305   1.380   1.358   1.392   1.495   1.394   1.415   1.526
137   K         0.595   0.630   0.418   0.605   0.663   0.303   0.573   0.627   0.246
138   R         1.290   1.305   1.380   1.452   1.476   1.587   1.394   1.415   1.526
139   K        -0.328  -0.349  -0.358  -0.378  -0.392  -0.412  -0.520  -0.536  -0.543
140   L         1.290   1.305   1.380   1.146   1.176   1.290   1.394   1.415   1.526
141   Q        -0.872  -0.889  -0.860  -0.608  -0.625  -0.553  -0.930  -0.938  -0.867
142   I         0.595   0.546   0.409   0.635   0.568   0.403   0.573   0.494   0.230
143   P        -0.058  -0.178  -0.294   0.194   0.029  -0.139  -0.110  -0.277  -0.445
144   S         0.134   0.158   0.242  -0.047  -0.007   0.120  -0.247  -0.204  -0.087
145   S        -0.872  -0.889  -0.860  -0.650  -0.657  -0.631  -0.930  -0.938  -0.867
146   L         0.595   0.546   0.409   0.493   0.432   0.209   0.573   0.494   0.230
147   A         0.595   0.630   0.418   0.692   0.746   0.385   0.573   0.627   0.246
148   Y         1.290   1.305   1.380   1.526   1.547   1.658   1.394   1.415   1.526
149   G         1.290   1.305   1.380   1.103   1.110   1.248   1.394   1.415   1.526
150   E        -1.207  -1.183  -1.221  -1.085  -1.032  -1.090  -1.067  -1.038  -1.029
151   R         0.277   0.284   0.276   0.364   0.375   0.335   0.027   0.036  -0.021
152   G         0.595   0.522   0.407   0.470   0.359   0.209   0.573   0.454   0.226
153   V        -0.410  -0.437  -0.382  -0.592  -0.634  -0.539  -0.657  -0.678  -0.581
154   P         0.595   0.614   0.412   0.478   0.487   0.232   0.573   0.601   0.236
155   G        -0.872  -0.818  -0.850  -1.025  -0.977  -0.953  -0.930  -0.870  -0.856
156   V         0.443   0.355   0.339   0.325   0.184   0.130   0.322   0.166   0.100
157   I         1.290   1.305   1.380   1.235   1.249   1.376   1.394   1.415   1.526
158   P         1.290   1.305   1.380   1.408   1.427   1.543   1.394   1.415   1.526
159   P         0.277   0.266   0.280   0.287   0.262   0.258   0.027   0.003  -0.012
160   S        -0.872  -0.809  -0.847  -0.731  -0.607  -0.712  -0.930  -0.850  -0.852
161   A         0.277   0.271   0.272   0.213   0.199   0.156   0.027   0.011  -0.029
162   D        -0.872  -0.883  -0.860  -0.835  -0.834  -0.821  -0.930  -0.933  -0.867
163   L         1.290   1.305   1.380   1.146   1.176   1.290   1.394   1.415   1.526
164   V        -0.328  -0.280  -0.349  -0.496  -0.420  -0.521  -0.520  -0.448  -0.529
165   F         1.290   1.305   1.380   1.428   1.447   1.563   1.394   1.415   1.526
166   D        -0.998  -0.972  -0.894  -1.050  -0.993  -0.886  -1.067  -1.037  -0.903
167   V        -0.537  -0.527  -0.427  -0.673  -0.659  -0.508  -0.793  -0.776  -0.633
168   E         1.290   1.305   1.380   1.358   1.392   1.495   1.394   1.415   1.526
169   L         1.290   1.305   1.380   1.146   1.176   1.290   1.394   1.415   1.526
170   V         0.595   0.546   0.409   0.595   0.523   0.302   0.573   0.494   0.230
171   D        -0.058  -0.072  -0.280   0.027   0.019  -0.367  -0.110  -0.133  -0.425
172   V         0.595   0.614   0.412   0.582   0.600   0.299   0.573   0.601   0.236
173   K        -0.872  -0.832  -0.857  -0.852  -0.793  -0.814  -0.930  -0.890  -0.865
174   S        -0.872  -0.813  -0.857  -0.967  -0.917  -0.893  -0.930  -0.858  -0.863
175   A        -1.669  -1.596  -1.562  -1.540  -1.429  -1.363  -1.340  -1.269  -1.177
176   A        -1.352  -1.348  -1.267  -1.355  -1.332  -1.242  -1.211  -1.201  -1.070
177   -        -0.319  -0.292  -0.359  -0.403  -0.357  -0.491  -0.482  -0.441  -0.539
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.057  -1.050  -0.919  -1.015  -1.017  -0.803  -1.118  -1.103  -0.926
188   -         1.290   1.305   1.380   1.316   1.339   1.455   1.394   1.415   1.526
189   -         1.290   1.305   1.380   1.351   1.372   1.489   1.394   1.415   1.526
190   -         1.290   1.305   1.380   1.129   1.153   1.274   1.394   1.415   1.526
* 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/P32472
Output conservation file - output/P32472
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
