1     M         1.951   1.975   2.100   2.170   2.205   2.395   2.166   2.203   2.423
2     A         0.939   0.810   0.759   1.000   0.810   0.758   0.957   0.739   0.617
3     -        -0.384  -0.276  -0.287  -0.371  -0.192  -0.236  -0.553  -0.402  -0.422
4     -         0.688   0.647   0.670   0.711   0.632   0.645   0.534   0.452   0.451
5     R        -1.035  -1.029  -0.971  -1.156  -1.168  -1.059  -0.976  -0.958  -0.860
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     P        -0.320  -0.283  -0.279  -0.231  -0.204  -0.178  -0.493  -0.449  -0.424
8     V        -1.035  -1.039  -0.970  -1.221  -1.210  -1.061  -0.976  -0.967  -0.859
9     N        -0.320  -0.390  -0.310  -0.617  -0.721  -0.621  -0.493  -0.571  -0.460
10    T         0.522   0.498   0.567   0.242   0.202   0.300   0.232   0.177   0.251
11    N        -0.320  -0.390  -0.310  -0.604  -0.709  -0.594  -0.493  -0.571  -0.460
12    A         0.939   1.004   0.812   0.833   0.921   0.662   0.957   1.057   0.714
13    E         1.951   1.975   2.100   1.908   1.948   2.134   2.166   2.203   2.423
14    T         0.003  -0.068  -0.176   0.047  -0.037  -0.166  -0.009  -0.115  -0.264
15    E         0.939   0.810   0.759   1.008   0.827   0.745   0.957   0.739   0.617
16    S         0.939   1.061   0.819   0.848   1.008   0.698   0.957   1.146   0.727
17    R        -0.839  -0.902  -0.901  -0.965  -1.059  -1.052  -0.735  -0.805  -0.780
18    G        -0.418  -0.450  -0.319  -0.405  -0.433  -0.249  -0.619  -0.646  -0.471
19    R        -1.040  -1.065  -0.978  -1.223  -1.286  -1.193  -0.967  -0.988  -0.865
20    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    N        -0.384  -0.398  -0.329  -0.756  -0.765  -0.680  -0.553  -0.576  -0.481
44    N        -0.384  -0.398  -0.329  -0.694  -0.688  -0.605  -0.553  -0.576  -0.481
45    N         0.688   0.586   0.626   0.400   0.253   0.295   0.534   0.342   0.367
46    N        -0.384  -0.385  -0.328  -0.678  -0.667  -0.584  -0.553  -0.559  -0.479
47    N        -1.162  -1.106  -1.009  -1.125  -1.005  -0.898  -1.097  -1.028  -0.897
48    N         0.394   0.432   0.552  -0.033   0.053   0.222  -0.009   0.051   0.222
49    N        -0.384  -0.292  -0.297  -0.576  -0.410  -0.490  -0.553  -0.423  -0.437
50    N         0.688   0.760   0.678   0.666   0.814   0.589   0.534   0.653   0.467
51    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    N        -1.663  -1.613  -1.510  -1.665  -1.581  -1.438  -1.315  -1.255  -1.119
61    N        -1.663  -1.613  -1.510  -1.571  -1.490  -1.344  -1.315  -1.255  -1.119
62    G        -0.183  -0.236  -0.238  -0.325  -0.421  -0.428  -0.271  -0.347  -0.353
63    P         0.440   0.440   0.550   0.105   0.122   0.281   0.078   0.066   0.218
64    T        -0.183  -0.236  -0.238  -0.247  -0.319  -0.320  -0.271  -0.347  -0.353
65    S        -1.553  -1.461  -1.448  -1.532  -1.417  -1.391  -1.218  -1.117  -1.065
66    S        -0.320  -0.338  -0.301  -0.494  -0.526  -0.425  -0.493  -0.516  -0.451
67    G        -0.320  -0.288  -0.282  -0.454  -0.407  -0.362  -0.493  -0.457  -0.427
68    R        -0.839  -0.912  -0.936  -0.739  -0.866  -0.950  -0.735  -0.816  -0.819
69    T        -1.035  -1.017  -0.971  -1.218  -1.215  -1.124  -0.976  -0.948  -0.860
70    N        -0.320  -0.203  -0.259  -0.554  -0.364  -0.467  -0.493  -0.330  -0.390
71    G        -1.035  -0.955  -0.945  -0.863  -0.775  -0.701  -0.976  -0.886  -0.834
72    K        -0.320  -0.390  -0.310  -0.745  -0.840  -0.720  -0.493  -0.571  -0.460
73    Q         0.939   0.988   0.803   1.038   1.105   0.845   0.957   1.032   0.697
74    R        -0.839  -0.912  -0.936  -0.746  -0.909  -0.961  -0.735  -0.816  -0.819
75    L        -0.320  -0.390  -0.310  -0.432  -0.548  -0.408  -0.493  -0.571  -0.460
76    T        -1.553  -1.551  -1.483  -1.506  -1.559  -1.444  -1.218  -1.203  -1.096
77    A        -0.839  -0.885  -0.900  -0.727  -0.821  -0.842  -0.735  -0.787  -0.779
78    A         0.003  -0.125  -0.200   0.135  -0.066  -0.160  -0.009  -0.191  -0.299
79    Q         0.939   0.810   0.759   1.038   0.858   0.774   0.957   0.739   0.617
80    Q         0.939   0.810   0.759   1.071   0.910   0.836   0.957   0.739   0.617
81    Q         0.003  -0.081  -0.175   0.113  -0.036  -0.196  -0.009  -0.132  -0.262
82    Y         0.003  -0.081  -0.175   0.344   0.220   0.081  -0.009  -0.132  -0.262
83    I        -0.320  -0.357  -0.279  -0.337  -0.380  -0.260  -0.493  -0.521  -0.418
84    K        -0.384  -0.396  -0.328  -0.660  -0.681  -0.569  -0.553  -0.576  -0.479
85    N        -0.384  -0.394  -0.326  -0.314  -0.298  -0.255  -0.553  -0.574  -0.477
86    L         1.951   1.975   2.100   1.875   1.904   2.101   2.166   2.203   2.423
87    I        -0.384  -0.406  -0.329  -0.383  -0.419  -0.356  -0.553  -0.589  -0.481
88    E        -1.553  -1.461  -1.448  -1.705  -1.580  -1.544  -1.218  -1.117  -1.065
89    T        -0.839  -0.820  -0.890  -0.896  -0.881  -0.943  -0.735  -0.714  -0.767
90    H         0.939   0.810   0.759   1.171   1.001   0.912   0.957   0.739   0.617
91    I         0.939   0.810   0.759   1.143   0.978   0.885   0.957   0.739   0.617
92    T        -1.035  -1.029  -0.971  -1.052  -1.054  -0.930  -0.976  -0.958  -0.860
93    D        -0.320  -0.267  -0.268  -0.597  -0.508  -0.487  -0.493  -0.423  -0.403
94    N         0.939   0.810   0.759   0.821   0.672   0.577   0.957   0.739   0.617
95    H        -1.035  -1.017  -0.971  -0.724  -0.694  -0.612  -0.976  -0.948  -0.860
96    P         1.951   1.975   2.100   1.985   2.021   2.210   2.166   2.203   2.423
97    D        -2.072  -2.013  -1.918  -1.750  -1.685  -1.522  -1.460  -1.396  -1.266
98    L        -1.035  -1.029  -0.971  -0.977  -0.951  -0.889  -0.976  -0.958  -0.860
99    R        -1.035  -1.069  -0.948  -0.962  -0.986  -0.823  -0.976  -0.994  -0.837
100   P         0.003  -0.021  -0.168   0.236   0.190  -0.020  -0.009  -0.053  -0.253
101   K         0.003  -0.046  -0.176  -0.150  -0.240  -0.410  -0.009  -0.086  -0.264
102   S        -0.839  -0.902  -0.901  -0.618  -0.712  -0.742  -0.735  -0.805  -0.780
103   H        -0.839  -0.885  -0.900  -0.564  -0.638  -0.701  -0.735  -0.787  -0.779
104   P         0.939   0.810   0.759   1.085   0.899   0.818   0.957   0.739   0.617
105   M         0.394   0.425   0.546   0.301   0.349   0.534  -0.009   0.038   0.211
106   D         0.939   0.810   0.759   1.110   0.930   0.812   0.957   0.739   0.617
107   F         1.951   1.975   2.100   2.026   2.069   2.251   2.166   2.203   2.423
108   E        -0.839  -0.912  -0.936  -0.660  -0.757  -0.820  -0.735  -0.816  -0.819
109   E        -1.035  -0.959  -0.941  -0.987  -0.872  -0.850  -0.976  -0.884  -0.829
110   Y         0.003  -0.081  -0.175   0.330   0.199   0.059  -0.009  -0.132  -0.262
111   T         0.003  -0.068  -0.176   0.009  -0.088  -0.226  -0.009  -0.115  -0.264
112   D        -0.320  -0.362  -0.273  -0.267  -0.320  -0.204  -0.493  -0.528  -0.413
113   A         0.003   0.036  -0.137   0.154   0.198  -0.050  -0.009   0.038  -0.208
114   F        -0.839  -0.912  -0.936  -0.595  -0.744  -0.792  -0.735  -0.816  -0.819
115   L         0.939   1.061   0.819   0.980   1.129   0.838   0.957   1.146   0.727
116   R         0.003   0.023  -0.173   0.160   0.193  -0.114  -0.009   0.019  -0.260
117   R        -0.320  -0.191  -0.259  -0.599  -0.432  -0.492  -0.493  -0.319  -0.390
118   Y         1.951   1.975   2.100   2.078   2.121   2.304   2.166   2.203   2.423
119   K         0.003   0.023  -0.173  -0.224  -0.197  -0.528  -0.009   0.019  -0.260
120   D        -0.839  -0.912  -0.936  -0.666  -0.811  -0.908  -0.735  -0.816  -0.819
121   H        -1.035  -1.048  -0.952  -0.968  -1.001  -0.874  -0.976  -0.975  -0.841
122   F        -0.320  -0.390  -0.310  -0.131  -0.211  -0.091  -0.493  -0.571  -0.460
123   Q        -0.320  -0.365  -0.282  -0.324  -0.390  -0.297  -0.493  -0.533  -0.422
124   L         0.939   0.933   0.789   0.979   0.972   0.791   0.957   0.945   0.672
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   D        -0.839  -0.840  -0.894  -0.878  -0.861  -0.960  -0.735  -0.736  -0.771
127   V        -1.035  -1.029  -0.971  -0.812  -0.823  -0.743  -0.976  -0.958  -0.860
128   P         0.939   0.933   0.789   1.057   1.049   0.818   0.957   0.945   0.672
129   D        -0.839  -0.912  -0.936  -0.551  -0.690  -0.739  -0.735  -0.816  -0.819
130   N        -1.553  -1.539  -1.482  -1.420  -1.397  -1.277  -1.218  -1.193  -1.095
131   L         0.003   0.086  -0.127   0.192   0.288   0.052  -0.009   0.105  -0.194
132   T         0.394   0.424   0.546   0.054   0.104   0.285  -0.009   0.036   0.211
133   L         0.522   0.588   0.604   0.387   0.487   0.505   0.232   0.346   0.324
134   Q         0.394   0.436   0.558   0.027   0.094   0.261  -0.009   0.058   0.234
135   G         0.939   0.933   0.789   1.097   1.113   0.858   0.957   0.945   0.672
136   Y         0.003   0.023  -0.173   0.384   0.418   0.146  -0.009   0.019  -0.260
137   L         0.522   0.545   0.601   0.387   0.419   0.500   0.232   0.265   0.319
138   L         1.951   1.975   2.100   1.848   1.880   2.074   2.166   2.203   2.423
139   G        -0.320  -0.338  -0.301  -0.417  -0.456  -0.452  -0.493  -0.516  -0.451
140   S         0.939   0.810   0.759   0.864   0.709   0.636   0.957   0.739   0.617
141   K        -0.839  -0.840  -0.894  -0.709  -0.714  -0.819  -0.735  -0.736  -0.771
142   L        -0.320  -0.357  -0.279  -0.220  -0.233  -0.125  -0.493  -0.521  -0.418
143   G         1.951   1.975   2.100   2.026   2.085   2.251   2.166   2.203   2.423
144   A         0.939   1.004   0.812   0.727   0.806   0.559   0.957   1.057   0.714
145   K         0.003   0.172  -0.098  -0.079   0.137  -0.191  -0.009   0.227  -0.153
146   T         1.951   1.975   2.100   1.949   1.987   2.175   2.166   2.203   2.423
147   Y        -0.839  -0.830  -0.876  -0.325  -0.298  -0.352  -0.735  -0.726  -0.751
148   S         0.939   0.988   0.803   0.848   0.919   0.673   0.957   1.032   0.697
149   Y        -0.320  -0.288  -0.271  -0.312  -0.266  -0.273  -0.493  -0.438  -0.411
150   K         0.939   0.933   0.789   0.739   0.733   0.544   0.957   0.945   0.672
151   R        -0.839  -0.912  -0.936  -0.699  -0.796  -0.891  -0.735  -0.816  -0.819
152   N         0.003  -0.125  -0.200  -0.110  -0.279  -0.444  -0.009  -0.191  -0.299
153   T        -1.035  -0.925  -0.944  -1.050  -0.920  -0.862  -0.976  -0.859  -0.833
154   Q        -1.040  -0.934  -0.975  -1.358  -1.188  -1.278  -0.967  -0.837  -0.862
155   G        -1.162  -1.106  -1.009  -1.369  -1.253  -1.141  -1.097  -1.028  -0.897
156   Q        -0.384  -0.400  -0.326  -0.347  -0.426  -0.322  -0.553  -0.578  -0.477
157   H        -0.384  -0.400  -0.326  -0.199  -0.232  -0.122  -0.553  -0.578  -0.477
158   D        -0.384  -0.385  -0.328  -0.297  -0.309  -0.230  -0.553  -0.559  -0.479
159   K        -1.162  -1.106  -1.009  -1.111  -1.006  -0.884  -1.097  -1.028  -0.897
160   R         0.939   0.988   0.803   0.983   1.060   0.754   0.957   1.032   0.697
161   I         0.522   0.507   0.569   0.597   0.578   0.659   0.232   0.193   0.256
162   H        -1.035  -1.039  -0.970  -1.084  -1.112  -0.975  -0.976  -0.967  -0.859
163   K         1.951   1.975   2.100   1.627   1.659   1.852   2.166   2.203   2.423
164   R        -1.553  -1.439  -1.447  -1.268  -1.107  -1.115  -1.218  -1.096  -1.064
165   D         0.939   1.004   0.812   1.041   1.130   0.888   0.957   1.057   0.714
166   L         0.003   0.086  -0.127   0.116   0.222  -0.059  -0.009   0.105  -0.194
167   A         0.939   0.988   0.803   0.950   0.999   0.738   0.957   1.032   0.697
168   N        -0.320  -0.264  -0.273  -0.724  -0.634  -0.677  -0.493  -0.428  -0.416
169   V        -2.072  -2.013  -1.918  -1.779  -1.688  -1.552  -1.460  -1.396  -1.266
170   V        -0.839  -0.830  -0.876  -0.441  -0.464  -0.521  -0.735  -0.726  -0.751
171   R         0.522   0.596   0.636   0.136   0.248   0.304   0.232   0.360   0.385
172   R        -0.839  -0.758  -0.851  -0.980  -0.869  -0.998  -0.735  -0.634  -0.722
173   H         1.951   1.975   2.100   2.061   2.103   2.286   2.166   2.203   2.423
174   F         1.951   1.975   2.100   2.026   2.069   2.251   2.166   2.203   2.423
175   D        -1.553  -1.539  -1.482  -1.298  -1.252  -1.222  -1.218  -1.193  -1.095
176   E        -1.035  -0.950  -0.936  -1.194  -1.071  -1.044  -0.976  -0.880  -0.826
177   H        -0.839  -0.840  -0.894  -0.600  -0.621  -0.647  -0.735  -0.736  -0.771
178   S        -0.320  -0.203  -0.259  -0.384  -0.193  -0.277  -0.493  -0.330  -0.390
179   I        -1.035  -0.999  -0.949  -0.645  -0.594  -0.493  -0.976  -0.925  -0.837
180   K         0.394   0.426   0.548  -0.036   0.026   0.206  -0.009   0.040   0.214
181   E         1.951   1.975   2.100   1.908   1.948   2.134   2.166   2.203   2.423
182   T        -1.035  -1.029  -0.971  -1.160  -1.173  -1.070  -0.976  -0.958  -0.860
183   D         0.522   0.551   0.584   0.447   0.494   0.529   0.232   0.277   0.284
184   C         0.394   0.436   0.558   0.481   0.538   0.714  -0.009   0.058   0.234
185   I         0.939   1.030   0.817   1.125   1.257   0.950   0.957   1.099   0.724
186   P        -0.839  -0.912  -0.936  -0.513  -0.621  -0.650  -0.735  -0.816  -0.819
187   Q        -1.035  -1.070  -0.960  -1.003  -1.001  -0.861  -0.976  -0.995  -0.849
188   F         1.951   1.975   2.100   2.026   2.069   2.251   2.166   2.203   2.423
189   I         0.003  -0.125  -0.200   0.310   0.143   0.018  -0.009  -0.191  -0.299
190   Y         1.951   1.975   2.100   2.078   2.121   2.304   2.166   2.203   2.423
191   K         0.003  -0.081  -0.175  -0.123  -0.260  -0.365  -0.009  -0.132  -0.262
192   V         1.951   1.975   2.100   2.130   2.167   2.356   2.166   2.203   2.423
193   K        -0.320  -0.209  -0.238  -0.581  -0.432  -0.440  -0.493  -0.339  -0.364
194   N         0.939   0.933   0.789   0.847   0.867   0.670   0.957   0.945   0.672
195   Q         0.003  -0.081  -0.175   0.217   0.108  -0.029  -0.009  -0.132  -0.262
196   K         0.394   0.436   0.558   0.050   0.148   0.333  -0.009   0.058   0.234
197   K         0.939   0.988   0.803   0.740   0.802   0.566   0.957   1.032   0.697
198   K        -0.839  -0.912  -0.936  -0.884  -1.008  -0.982  -0.735  -0.816  -0.819
199   F         1.951   1.975   2.100   2.026   2.069   2.251   2.166   2.203   2.423
200   K         0.939   1.030   0.817   0.739   0.855   0.586   0.957   1.099   0.724
201   M         0.394   0.436   0.558   0.301   0.334   0.526  -0.009   0.058   0.234
202   E        -0.839  -0.912  -0.936  -0.686  -0.801  -0.858  -0.735  -0.816  -0.819
203   F         1.951   1.975   2.100   2.026   2.069   2.251   2.166   2.203   2.423
204   R        -1.035  -1.070  -0.958  -1.218  -1.274  -1.110  -0.976  -0.995  -0.847
205   G         0.688   0.557   0.626   0.762   0.545   0.637   0.534   0.288   0.367
* 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/P38429
Output conservation file - output/P38429
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
