1     M         1.602   1.617   1.753   1.864   1.876   2.098   1.763   1.787   2.014
2     S         0.006   0.004  -0.102   0.001  -0.016  -0.177  -0.096  -0.104  -0.273
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S         0.006  -0.021  -0.103   0.108   0.073  -0.093  -0.096  -0.139  -0.274
5     L        -0.157  -0.195  -0.171  -0.530  -0.557  -0.499  -0.361  -0.406  -0.379
6     S         0.909   0.840   0.715   0.974   0.881   0.717   0.950   0.837   0.583
7     L         0.909   0.852   0.721   0.665   0.612   0.402   0.950   0.857   0.593
8     Y         1.602   1.617   1.753   1.730   1.742   1.965   1.763   1.787   2.014
9     T        -0.191  -0.236  -0.168  -0.266  -0.347  -0.235  -0.444  -0.496  -0.389
10    V         0.567   0.599   0.612   0.469   0.498   0.502   0.369   0.419   0.385
11    Q        -1.268  -1.240  -1.161  -1.244  -1.198  -1.094  -1.141  -1.110  -0.977
12    A         1.602   1.617   1.753   1.648   1.659   1.883   1.763   1.787   2.014
13    V        -0.373  -0.459  -0.610  -0.131  -0.270  -0.442  -0.328  -0.438  -0.611
14    L         0.909   0.862   0.719   0.666   0.624   0.401   0.950   0.874   0.591
15    I         0.909   0.852   0.721   0.909   0.827   0.583   0.950   0.857   0.593
16    L         1.602   1.617   1.753   1.283   1.323   1.519   1.763   1.787   2.014
17    D         0.909   0.862   0.719   0.957   0.892   0.680   0.950   0.874   0.591
18    Q        -1.268  -1.229  -1.159  -1.210  -1.164  -1.056  -1.141  -1.103  -0.976
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    Q        -0.828  -0.836  -0.739  -0.939  -0.957  -0.821  -0.909  -0.909  -0.769
21    G         1.602   1.617   1.753   1.703   1.738   1.938   1.763   1.787   2.014
22    E        -1.268  -1.212  -1.150  -1.271  -1.206  -1.073  -1.141  -1.088  -0.969
23    R         1.602   1.617   1.753   1.817   1.829   2.052   1.763   1.787   2.014
24    I        -0.191  -0.113  -0.160  -0.644  -0.537  -0.568  -0.444  -0.366  -0.379
25    Y         0.385   0.443   0.523   0.366   0.463   0.564   0.021   0.125   0.207
26    A        -0.389  -0.395  -0.250  -0.575  -0.594  -0.370  -0.676  -0.684  -0.492
27    K         1.602   1.617   1.753   1.596   1.613   1.831   1.763   1.787   2.014
28    Y         1.602   1.617   1.753   1.730   1.742   1.965   1.763   1.787   2.014
29    Y         0.909   0.968   0.736   1.139   1.205   0.919   0.950   1.040   0.622
30    Q        -2.224  -2.182  -2.048  -1.836  -1.802  -1.596  -1.490  -1.457  -1.284
31    P        -0.055   0.026  -0.109   0.127   0.251   0.005  -0.212  -0.088  -0.294
32    P         0.248   0.290  -0.018   0.604   0.650   0.194   0.253   0.309  -0.147
33    H         0.248   0.290  -0.018   0.600   0.656   0.126   0.253   0.309  -0.147
34    R        -1.147  -1.113  -1.095  -1.057  -1.031  -1.009  -1.025  -0.995  -0.919
35    S        -1.614  -1.567  -1.494  -1.574  -1.520  -1.417  -1.272  -1.232  -1.105
36    D        -1.250  -1.248  -1.139  -1.352  -1.364  -1.197  -1.120  -1.113  -0.959
37    E        -0.885  -0.868  -0.752  -0.985  -0.923  -0.774  -0.968  -0.943  -0.783
38    G        -1.112  -1.032  -1.094  -1.001  -0.899  -1.019  -0.968  -0.890  -0.911
39    H        -1.250  -1.248  -1.140  -0.953  -0.945  -0.802  -1.120  -1.114  -0.959
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    Q        -1.270  -1.217  -1.150  -1.244  -1.173  -1.075  -1.128  -1.080  -0.966
50    L        -0.845  -0.791  -0.738  -1.137  -1.025  -0.939  -0.922  -0.865  -0.767
51    L        -0.339  -0.286  -0.213  -0.808  -0.725  -0.618  -0.616  -0.553  -0.443
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -0.849  -0.844  -0.738  -0.715  -0.699  -0.551  -0.913  -0.908  -0.764
56    -        -0.849  -0.875  -0.769  -0.762  -0.815  -0.671  -0.913  -0.943  -0.800
57    F        -0.259  -0.254  -0.181  -0.307  -0.301  -0.239  -0.509  -0.498  -0.400
58    N        -1.614  -1.572  -1.490  -1.382  -1.312  -1.216  -1.272  -1.232  -1.102
59    S        -0.389  -0.364  -0.248  -0.593  -0.565  -0.398  -0.676  -0.645  -0.488
60    V        -0.828  -0.844  -0.740  -1.081  -1.104  -0.990  -0.909  -0.919  -0.771
61    K        -0.373  -0.385  -0.610  -0.170  -0.188  -0.515  -0.328  -0.345  -0.612
62    K        -1.147  -1.234  -1.156  -1.107  -1.234  -1.149  -1.025  -1.098  -0.972
63    Q         0.909   0.840   0.715   1.087   1.016   0.802   0.950   0.837   0.583
64    K        -1.147  -1.139  -1.119  -1.198  -1.178  -1.101  -1.025  -1.016  -0.938
65    E        -1.586  -1.528  -1.485  -1.353  -1.258  -1.194  -1.257  -1.205  -1.099
66    F         1.602   1.617   1.753   1.767   1.784   2.002   1.763   1.787   2.014
67    E         1.602   1.617   1.753   1.589   1.601   1.824   1.763   1.787   2.014
68    K         0.909   0.968   0.736   0.978   1.050   0.729   0.950   1.040   0.622
69    Q        -1.147  -0.985  -1.105  -1.023  -0.773  -0.955  -1.025  -0.867  -0.924
70    L         1.602   1.617   1.753   1.283   1.323   1.519   1.763   1.787   2.014
71    Y        -0.373  -0.402  -0.598  -0.078  -0.140  -0.481  -0.328  -0.370  -0.597
72    R        -1.268  -1.203  -1.149  -1.197  -1.111  -1.015  -1.141  -1.083  -0.968
73    K         1.602   1.617   1.753   1.596   1.613   1.831   1.763   1.787   2.014
74    T         0.909   0.944   0.743   1.094   1.126   0.854   0.950   1.003   0.635
75    H        -0.949  -1.013  -1.090  -0.402  -0.496  -0.625  -0.793  -0.863  -0.907
76    K         0.248   0.239  -0.022   0.428   0.416   0.072   0.253   0.234  -0.152
77    Q        -0.373  -0.403  -0.609  -0.087  -0.117  -0.459  -0.328  -0.369  -0.610
78    D        -1.147  -1.155  -1.104  -0.948  -0.933  -0.845  -1.025  -1.018  -0.922
79    S        -0.828  -0.865  -0.752  -0.856  -0.876  -0.723  -0.909  -0.942  -0.783
80    E         0.567   0.688   0.644   0.458   0.645   0.553   0.369   0.580   0.446
81    I         0.909   0.852   0.721   0.953   0.873   0.683   0.950   0.857   0.593
82    L        -0.055  -0.027  -0.122  -0.355  -0.315  -0.423  -0.212  -0.188  -0.315
83    I        -0.191  -0.226  -0.163  -0.616  -0.637  -0.530  -0.444  -0.478  -0.381
84    F        -0.191  -0.124  -0.157  -0.150  -0.060  -0.095  -0.444  -0.357  -0.370
85    E         0.909   1.003   0.742   0.959   1.071   0.723   0.950   1.092   0.632
86    D        -0.191  -0.191  -0.155  -0.273  -0.232  -0.183  -0.444  -0.419  -0.361
87    H        -0.191  -0.160  -0.175  -0.189  -0.181  -0.239  -0.444  -0.422  -0.397
88    L         0.567   0.511   0.542   0.173   0.088   0.098   0.369   0.256   0.244
89    V         0.567   0.599   0.612   0.469   0.498   0.502   0.369   0.419   0.385
90    L        -1.147  -1.113  -1.127  -1.387  -1.334  -1.312  -1.025  -0.999  -0.948
91    Y         0.909   0.840   0.715   1.153   1.064   0.918   0.950   0.837   0.583
92    K         0.248   0.227  -0.023   0.360   0.314  -0.068   0.253   0.217  -0.155
93    E        -0.828  -0.857  -0.752  -0.793  -0.815  -0.638  -0.909  -0.935  -0.783
94    Y        -0.828  -0.857  -0.752  -0.812  -0.894  -0.728  -0.909  -0.935  -0.783
95    I        -1.268  -1.287  -1.161  -1.236  -1.254  -1.058  -1.141  -1.147  -0.977
96    D         1.602   1.617   1.753   1.575   1.590   1.810   1.763   1.787   2.014
97    I        -0.055   0.016  -0.116  -0.169  -0.065  -0.337  -0.212  -0.104  -0.305
98    T        -1.147  -1.145  -1.119  -1.146  -1.166  -1.173  -1.025  -1.024  -0.941
99    I        -0.191  -0.224  -0.159  -0.603  -0.616  -0.507  -0.444  -0.475  -0.377
100   Y         0.248   0.374   0.027   0.561   0.701   0.271   0.253   0.426  -0.079
101   L        -0.055  -0.162  -0.169  -0.408  -0.564  -0.585  -0.212  -0.370  -0.382
102   V         0.909   0.968   0.736   0.974   1.030   0.724   0.950   1.040   0.622
103   A         0.385   0.456   0.530   0.268   0.410   0.478   0.021   0.151   0.221
104   S        -0.949  -0.939  -1.066  -0.707  -0.701  -0.862  -0.793  -0.784  -0.883
105   L        -0.949  -1.048  -1.105  -0.994  -1.094  -1.149  -0.793  -0.902  -0.922
106   E        -0.630  -0.601  -0.674  -0.648  -0.619  -0.732  -0.676  -0.645  -0.698
107   E         1.602   1.617   1.753   1.589   1.601   1.824   1.763   1.787   2.014
108   N         1.602   1.617   1.753   1.689   1.705   1.924   1.763   1.787   2.014
109   E         1.602   1.617   1.753   1.589   1.601   1.824   1.763   1.787   2.014
110   I        -0.389  -0.346  -0.223  -0.681  -0.623  -0.433  -0.676  -0.618  -0.453
111   V        -0.389  -0.389  -0.250  -0.735  -0.718  -0.501  -0.676  -0.676  -0.491
112   L         0.909   0.932   0.729   0.662   0.713   0.409   0.950   0.984   0.609
113   Q         0.385   0.470   0.550   0.320   0.475   0.570   0.021   0.177   0.261
114   Q        -0.828  -0.846  -0.737  -0.881  -0.896  -0.750  -0.909  -0.921  -0.767
115   G        -1.586  -1.544  -1.475  -1.566  -1.505  -1.369  -1.257  -1.220  -1.093
116   F        -1.147  -1.170  -1.142  -1.074  -1.170  -1.101  -1.025  -1.048  -0.961
117   S        -1.586  -1.622  -1.495  -1.490  -1.545  -1.360  -1.257  -1.276  -1.106
118   A        -0.828  -0.855  -0.741  -0.835  -0.871  -0.713  -0.909  -0.929  -0.772
119   I        -0.389  -0.335  -0.233  -0.801  -0.723  -0.557  -0.676  -0.610  -0.468
120   R        -0.708  -0.672  -0.680  -0.582  -0.532  -0.508  -0.793  -0.753  -0.709
121   G        -0.311  -0.211  -0.160  -0.474  -0.316  -0.258  -0.560  -0.419  -0.360
122   A         0.385   0.421   0.512   0.179   0.235   0.349   0.021   0.082   0.184
123   L         1.602   1.617   1.753   1.283   1.323   1.519   1.763   1.787   2.014
124   D        -1.147  -1.101  -1.105  -1.032  -0.949  -0.925  -1.025  -0.966  -0.923
125   L        -0.191  -0.222  -0.177  -0.580  -0.589  -0.484  -0.444  -0.479  -0.399
126   I         0.385   0.470   0.550  -0.151   0.012   0.098   0.021   0.177   0.261
127   L         0.567   0.505   0.540   0.235   0.160   0.198   0.369   0.244   0.241
128   N        -0.389  -0.317  -0.219  -0.619  -0.516  -0.369  -0.676  -0.585  -0.449
129   S        -1.586  -1.614  -1.511  -1.311  -1.318  -1.158  -1.257  -1.270  -1.118
130   G        -0.828  -0.865  -0.752  -0.842  -0.914  -0.756  -0.909  -0.942  -0.783
131   M        -1.466  -1.472  -1.456  -1.263  -1.273  -1.255  -1.141  -1.146  -1.074
132   D         1.602   1.617   1.753   1.575   1.590   1.810   1.763   1.787   2.014
133   K         1.602   1.617   1.753   1.596   1.613   1.831   1.763   1.787   2.014
134   K        -0.630  -0.520  -0.638  -0.428  -0.238  -0.447  -0.676  -0.529  -0.648
135   N        -0.311  -0.235  -0.193  -0.369  -0.262  -0.226  -0.560  -0.456  -0.410
136   I        -0.055  -0.121  -0.148  -0.184  -0.304  -0.411  -0.212  -0.302  -0.352
137   Q        -0.191  -0.174  -0.154  -0.551  -0.502  -0.487  -0.444  -0.398  -0.361
138   E         0.909   0.932   0.729   0.971   0.994   0.712   0.950   0.984   0.609
139   N        -0.191  -0.170  -0.165  -0.113  -0.087  -0.060  -0.444  -0.420  -0.384
140   Y         0.909   0.852   0.721   1.139   1.063   0.895   0.950   0.857   0.593
141   D         1.602   1.617   1.753   1.575   1.590   1.810   1.763   1.787   2.014
142   M        -0.191  -0.241  -0.172  -0.297  -0.394  -0.315  -0.444  -0.503  -0.393
143   V         0.909   0.840   0.715   0.934   0.819   0.596   0.950   0.837   0.583
144   L        -1.147  -1.127  -1.112  -1.142  -1.123  -1.100  -1.025  -1.008  -0.935
145   L         0.909   0.840   0.715   0.662   0.592   0.386   0.950   0.837   0.583
146   A         0.248   0.205  -0.014   0.481   0.406   0.133   0.253   0.187  -0.141
147   I         0.909   0.840   0.715   0.953   0.856   0.673   0.950   0.837   0.583
148   D         1.602   1.617   1.753   1.575   1.590   1.810   1.763   1.787   2.014
149   E         1.602   1.617   1.753   1.589   1.601   1.824   1.763   1.787   2.014
150   T        -1.147  -1.091  -1.097  -1.041  -0.991  -0.995  -1.025  -0.976  -0.921
151   I         0.567   0.511   0.542   0.453   0.340   0.354   0.369   0.256   0.244
152   D         1.602   1.617   1.753   1.575   1.590   1.810   1.763   1.787   2.014
153   N        -0.055  -0.010  -0.081  -0.085  -0.008  -0.132  -0.212  -0.127  -0.244
154   G         1.602   1.617   1.753   1.703   1.738   1.938   1.763   1.787   2.014
155   V         0.385   0.421   0.517   0.128   0.173   0.309   0.021   0.082   0.193
156   I         0.567   0.599   0.569   0.453   0.492   0.406   0.369   0.420   0.298
157   L         0.909   0.932   0.729   0.662   0.713   0.409   0.950   0.984   0.609
158   E         1.602   1.617   1.753   1.589   1.601   1.824   1.763   1.787   2.014
159   T        -0.055  -0.057  -0.141   0.030  -0.001  -0.135  -0.212  -0.225  -0.342
160   D         0.909   0.840   0.715   0.959   0.864   0.679   0.950   0.837   0.583
161   S         0.909   1.003   0.742   1.199   1.308   0.953   0.950   1.092   0.632
162   N        -0.949  -0.898  -1.059  -0.710  -0.664  -0.906  -0.793  -0.744  -0.876
163   T        -0.630  -0.731  -0.698  -0.622  -0.820  -0.825  -0.676  -0.790  -0.726
164   I         1.602   1.617   1.753   1.568   1.584   1.803   1.763   1.787   2.014
165   A        -0.055  -0.076  -0.118  -0.053  -0.095  -0.178  -0.212  -0.235  -0.300
166   S        -0.055  -0.087  -0.133  -0.079  -0.123  -0.205  -0.212  -0.254  -0.330
167   R         1.602   1.617   1.753   1.817   1.829   2.052   1.763   1.787   2.014
168   V         0.909   0.862   0.719   1.027   0.957   0.818   0.950   0.874   0.591
169   S         0.385   0.431   0.521   0.237   0.309   0.424   0.021   0.102   0.201
170   K        -0.055  -0.084  -0.117  -0.018  -0.052  -0.088  -0.212  -0.246  -0.299
171   P        -0.191  -0.241  -0.172  -0.125  -0.210  -0.099  -0.444  -0.503  -0.393
172   P         1.602   1.617   1.753   1.817   1.829   2.052   1.763   1.787   2.014
173   T        -1.466  -1.464  -1.470  -1.252  -1.275  -1.261  -1.141  -1.142  -1.085
174   N        -0.949  -0.918  -0.770  -1.085  -1.056  -0.837  -1.025  -0.991  -0.801
175   E        -0.708  -0.672  -0.681  -0.833  -0.792  -0.787  -0.793  -0.752  -0.711
176   P        -2.224  -2.182  -2.048  -1.861  -1.855  -1.621  -1.490  -1.457  -1.284
177   Q        -1.466  -1.480  -1.469  -1.118  -1.141  -1.142  -1.141  -1.152  -1.085
178   M        -1.147  -1.094  -1.116  -1.289  -1.212  -1.184  -1.025  -0.983  -0.938
179   A        -1.905  -1.886  -1.779  -1.651  -1.663  -1.492  -1.373  -1.356  -1.200
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   L        -1.147  -1.205  -1.137  -1.376  -1.430  -1.369  -1.025  -1.065  -0.954
186   D        -0.055  -0.103  -0.142  -0.076  -0.149  -0.208  -0.212  -0.279  -0.344
187   L        -0.311  -0.357  -0.247  -0.709  -0.745  -0.581  -0.560  -0.631  -0.486
188   -        -0.845  -0.850  -0.746  -0.928  -0.926  -0.774  -0.922  -0.922  -0.775
189   D         0.567   0.688   0.644   0.468   0.653   0.560   0.369   0.580   0.446
190   K        -0.055  -0.162  -0.169  -0.004  -0.150  -0.150  -0.212  -0.370  -0.382
191   G         0.909   0.852   0.721   1.104   1.048   0.852   0.950   0.857   0.593
192   F        -0.630  -0.709  -0.693  -0.864  -0.956  -0.920  -0.676  -0.763  -0.720
193   L        -1.147  -1.234  -1.156  -1.216  -1.282  -1.146  -1.025  -1.098  -0.972
194   G        -0.055   0.091  -0.077   0.028   0.252  -0.017  -0.212   0.005  -0.238
195   A        -0.373  -0.531  -0.653  -0.239  -0.500  -0.777  -0.328  -0.526  -0.664
196   W        -1.147  -1.234  -1.156  -0.935  -1.070  -0.968  -1.025  -1.098  -0.972
197   G        -0.389  -0.346  -0.223  -0.513  -0.416  -0.271  -0.676  -0.618  -0.453
198   F        -0.055  -0.153  -0.169   0.010  -0.176  -0.282  -0.212  -0.362  -0.381
199   A         0.248   0.142  -0.044   0.499   0.364   0.125   0.253   0.100  -0.187
200   K        -0.191  -0.237  -0.177  -0.327  -0.386  -0.269  -0.444  -0.496  -0.399
201   S        -1.147  -1.234  -1.156  -1.131  -1.252  -1.137  -1.025  -1.098  -0.972
202   K         0.909   0.852   0.721   1.013   0.943   0.784   0.950   0.857   0.593
203   F        -0.373  -0.420  -0.608  -0.500  -0.559  -0.822  -0.328  -0.394  -0.610
204   Q        -0.828  -0.766  -0.731  -0.764  -0.665  -0.622  -0.909  -0.845  -0.761
205   E         0.248   0.142  -0.044   0.362   0.208  -0.093   0.253   0.100  -0.187
206   R         0.248   0.142  -0.044   0.674   0.535   0.294   0.253   0.100  -0.187
207   L         0.248   0.122  -0.052   0.083  -0.064  -0.330   0.253   0.071  -0.198
208   Q        -0.373  -0.531  -0.653  -0.139  -0.361  -0.636  -0.328  -0.526  -0.664
209   Q         0.847   0.745   0.671   1.016   0.880   0.735   0.853   0.678   0.499
210   G         1.602   1.617   1.753   1.706   1.720   1.941   1.763   1.787   2.014
211   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
212   L         0.847   0.745   0.671   0.596   0.472   0.371   0.853   0.678   0.499
* 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/P53600
Output conservation file - output/P53600
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
