1     M         0.970   0.977   1.022   1.177   1.183   1.237   1.015   1.026   1.091
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -1.210  -1.293  -1.340  -1.075  -1.193  -1.267  -1.090  -1.188  -1.207
5     S        -1.322  -1.348  -1.341  -1.271  -1.301  -1.270  -1.242  -1.277  -1.211
6     R        -0.093  -0.188  -0.165   0.005  -0.180  -0.207  -0.275  -0.441  -0.439
7     K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
8     K         0.258   0.152  -0.079   0.308   0.181  -0.128   0.263   0.107  -0.288
9     N        -1.402  -1.429  -1.367  -1.294  -1.307  -1.202  -1.349  -1.364  -1.235
10    I        -0.871  -0.898  -0.852  -0.926  -0.932  -0.825  -1.027  -1.035  -0.950
11    L         0.970   0.977   1.022   0.911   0.920   0.998   1.015   1.026   1.091
12    K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
13    V         0.970   0.977   1.022   0.863   0.876   0.956   1.015   1.026   1.091
14    I         0.258   0.152  -0.079   0.370   0.238  -0.150   0.263   0.107  -0.288
15    I         0.970   0.977   1.022   0.986   1.004   1.066   1.015   1.026   1.091
16    L         0.970   0.977   1.022   0.911   0.920   0.998   1.015   1.026   1.091
17    G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
18    D         0.258   0.178  -0.079   0.252   0.153  -0.215   0.263   0.145  -0.288
19    S         0.970   0.977   1.022   0.857   0.876   0.950   1.015   1.026   1.091
20    G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
21    V         0.970   0.977   1.022   0.863   0.876   0.956   1.015   1.026   1.091
22    G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
23    K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
24    T         0.258   0.152  -0.079   0.425   0.282  -0.107   0.263   0.107  -0.288
25    S         0.970   0.977   1.022   0.857   0.876   0.950   1.015   1.026   1.091
26    L         0.258   0.178  -0.079   0.313   0.212  -0.164   0.263   0.145  -0.288
27    M         0.970   0.977   1.022   1.177   1.183   1.237   1.015   1.026   1.091
28    H        -1.075  -1.065  -0.887  -1.017  -1.029  -0.791  -1.242  -1.229  -0.992
29    R        -0.280  -0.204  -0.152  -0.318  -0.201  -0.136  -0.597  -0.469  -0.415
30    Y        -0.093  -0.045  -0.113   0.061   0.127  -0.027  -0.275  -0.202  -0.348
31    V         0.970   0.977   1.022   0.863   0.876   0.956   1.015   1.026   1.091
32    N         0.970   0.977   1.022   0.936   0.952   1.021   1.015   1.026   1.091
33    D        -1.853  -1.885  -1.763  -1.823  -1.862  -1.676  -1.564  -1.590  -1.401
34    K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
35    Y        -0.280  -0.204  -0.152  -0.320  -0.207  -0.137  -0.597  -0.469  -0.415
36    S         0.970   0.977   1.022   0.857   0.876   0.950   1.015   1.026   1.091
37    Q        -1.853  -1.930  -1.775  -1.539  -1.661  -1.493  -1.564  -1.621  -1.410
38    Q        -0.420  -0.502  -0.803  -0.211  -0.326  -0.848  -0.382  -0.490  -0.885
39    Y         0.970   0.977   1.022   1.144   1.153   1.208   1.015   1.026   1.091
40    K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
41    A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
42    T         0.970   0.977   1.022   1.041   1.048   1.115   1.015   1.026   1.091
43    I         0.970   0.977   1.022   0.986   1.004   1.066   1.015   1.026   1.091
44    G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
45    A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
46    D         0.970   0.977   1.022   0.850   0.863   0.945   1.015   1.026   1.091
47    F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
48    L         0.970   0.977   1.022   0.911   0.920   0.998   1.015   1.026   1.091
49    T         0.258   0.152  -0.079   0.436   0.296  -0.076   0.263   0.107  -0.288
50    K         0.258   0.255  -0.072   0.308   0.305  -0.118   0.263   0.257  -0.277
51    E         0.970   0.977   1.022   0.983   0.991   1.063   1.015   1.026   1.091
52    V        -0.731  -0.782  -0.830  -0.784  -0.849  -0.936  -0.812  -0.864  -0.920
53    T        -1.322  -1.261  -1.345  -1.191  -1.140  -1.273  -1.242  -1.195  -1.213
54    V        -0.731  -0.706  -0.828  -0.799  -0.781  -0.943  -0.812  -0.794  -0.921
55    D        -0.420  -0.482  -0.793  -0.345  -0.431  -0.878  -0.382  -0.469  -0.871
56    G        -1.023  -0.967  -0.888  -1.259  -1.191  -1.032  -1.186  -1.124  -0.993
57    D        -0.731  -0.782  -0.830  -0.798  -0.856  -0.929  -0.812  -0.864  -0.920
58    K        -0.093  -0.152  -0.156  -0.148  -0.242  -0.242  -0.275  -0.380  -0.423
59    V        -1.322  -1.360  -1.357  -1.329  -1.390  -1.397  -1.242  -1.278  -1.226
60    A        -0.093  -0.005  -0.114  -0.254  -0.117  -0.315  -0.275  -0.136  -0.349
61    T         0.258   0.152  -0.079   0.436   0.296  -0.076   0.263   0.107  -0.288
62    M        -0.280  -0.275  -0.178  -0.290  -0.299  -0.188  -0.597  -0.595  -0.462
63    Q         0.970   0.977   1.022   1.020   1.031   1.096   1.015   1.026   1.091
64    V        -1.075  -1.065  -0.887  -1.298  -1.279  -1.012  -1.242  -1.229  -0.992
65    W         0.970   0.977   1.022   1.225   1.234   1.280   1.015   1.026   1.091
66    D         0.970   0.977   1.022   0.850   0.863   0.945   1.015   1.026   1.091
67    T         0.970   0.977   1.022   1.041   1.048   1.115   1.015   1.026   1.091
68    A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
69    G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
70    Q         0.970   0.977   1.022   1.020   1.031   1.096   1.015   1.026   1.091
71    E         0.970   0.977   1.022   0.983   0.991   1.063   1.015   1.026   1.091
72    R         0.970   0.977   1.022   1.123   1.129   1.189   1.015   1.026   1.091
73    F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
74    Q         0.970   0.977   1.022   1.020   1.031   1.096   1.015   1.026   1.091
75    S         0.970   0.977   1.022   0.857   0.876   0.950   1.015   1.026   1.091
76    L         0.970   0.977   1.022   0.911   0.920   0.998   1.015   1.026   1.091
77    G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
78    V         0.258   0.152  -0.079   0.254   0.119  -0.234   0.263   0.107  -0.288
79    A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
80    F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
81    Y         0.970   0.977   1.022   1.144   1.153   1.208   1.015   1.026   1.091
82    R         0.970   0.977   1.022   1.123   1.129   1.189   1.015   1.026   1.091
83    G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
84    A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
85    D         0.970   0.977   1.022   0.850   0.863   0.945   1.015   1.026   1.091
86    C         0.970   0.977   1.022   1.162   1.171   1.224   1.015   1.026   1.091
87    C         0.970   0.977   1.022   1.162   1.171   1.224   1.015   1.026   1.091
88    V         0.970   0.977   1.022   0.863   0.876   0.956   1.015   1.026   1.091
89    L         0.970   0.977   1.022   0.911   0.920   0.998   1.015   1.026   1.091
90    V        -0.093  -0.045  -0.113  -0.156  -0.092  -0.179  -0.275  -0.202  -0.348
91    Y         0.258   0.287  -0.065   0.548   0.580   0.061   0.263   0.302  -0.263
92    D         0.970   0.977   1.022   0.850   0.863   0.945   1.015   1.026   1.091
93    V         0.970   0.977   1.022   0.863   0.876   0.956   1.015   1.026   1.091
94    T        -0.280  -0.310  -0.185  -0.397  -0.476  -0.288  -0.597  -0.659  -0.474
95    N         0.970   0.977   1.022   0.936   0.952   1.021   1.015   1.026   1.091
96    A        -1.525  -1.419  -1.367  -1.644  -1.483  -1.390  -1.457  -1.343  -1.234
97    S         0.258   0.364  -0.062   0.269   0.397  -0.207   0.263   0.407  -0.260
98    S         0.970   0.977   1.022   0.857   0.876   0.950   1.015   1.026   1.091
99    F        -0.093  -0.045  -0.113  -0.103  -0.036  -0.180  -0.275  -0.202  -0.348
100   E        -1.075  -1.037  -0.871  -1.298  -1.252  -0.993  -1.242  -1.198  -0.974
101   N        -0.731  -0.843  -0.856  -0.734  -0.913  -0.933  -0.812  -0.960  -0.955
102   I        -0.731  -0.600  -0.823  -0.748  -0.555  -0.908  -0.812  -0.634  -0.911
103   K        -1.525  -1.511  -1.380  -1.639  -1.633  -1.421  -1.457  -1.449  -1.247
104   S         0.258   0.152  -0.079   0.248   0.118  -0.239   0.263   0.107  -0.288
105   W         0.970   0.977   1.022   1.225   1.234   1.280   1.015   1.026   1.091
106   R        -0.280  -0.227  -0.170  -0.350  -0.257  -0.220  -0.597  -0.510  -0.448
107   D         0.970   0.977   1.022   0.850   0.863   0.945   1.015   1.026   1.091
108   E         0.970   0.977   1.022   0.983   0.991   1.063   1.015   1.026   1.091
109   F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
110   L         0.970   0.977   1.022   0.911   0.920   0.998   1.015   1.026   1.091
111   V        -0.871  -0.938  -0.855  -1.022  -1.104  -0.966  -1.027  -1.094  -0.956
112   H        -0.871  -0.898  -0.852  -0.745  -0.782  -0.736  -1.027  -1.035  -0.950
113   A        -0.093  -0.045  -0.113  -0.252  -0.180  -0.314  -0.275  -0.202  -0.348
114   N        -0.093  -0.138  -0.154  -0.187  -0.264  -0.342  -0.275  -0.356  -0.420
115   V        -0.871  -0.820  -0.857  -0.888  -0.818  -0.825  -1.027  -0.987  -0.958
116   N        -0.731  -0.696  -0.836  -0.731  -0.703  -0.867  -0.812  -0.800  -0.930
117   S        -1.075  -1.070  -0.888  -1.366  -1.358  -1.082  -1.242  -1.235  -0.993
118   P         0.970   0.977   1.022   1.171   1.177   1.232   1.015   1.026   1.091
119   E        -0.731  -0.697  -0.824  -0.669  -0.623  -0.845  -0.812  -0.764  -0.912
120   T        -1.525  -1.471  -1.371  -1.571  -1.508  -1.369  -1.457  -1.411  -1.238
121   F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
122   P         0.970   0.977   1.022   1.171   1.177   1.232   1.015   1.026   1.091
123   F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
124   V        -0.280  -0.275  -0.178  -0.528  -0.521  -0.368  -0.597  -0.595  -0.462
125   I        -0.731  -0.843  -0.856  -0.714  -0.899  -0.957  -0.812  -0.960  -0.955
126   L        -0.280  -0.281  -0.178  -0.486  -0.496  -0.335  -0.597  -0.607  -0.463
127   G         0.258   0.302  -0.067   0.390   0.444  -0.110   0.263   0.323  -0.267
128   N         0.970   0.977   1.022   0.936   0.952   1.021   1.015   1.026   1.091
129   K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
130   I        -0.340  -0.318  -0.185  -0.624  -0.594  -0.377  -0.704  -0.674  -0.475
131   D         0.970   0.977   1.022   0.850   0.863   0.945   1.015   1.026   1.091
132   A        -1.058  -0.910  -1.305  -0.881  -0.693  -1.222  -0.919  -0.756  -1.171
133   E        -0.093  -0.045  -0.113  -0.143  -0.073  -0.225  -0.275  -0.202  -0.348
134   E        -0.280  -0.227  -0.170  -0.494  -0.399  -0.344  -0.597  -0.510  -0.448
135   S         0.258   0.178  -0.079   0.264   0.173  -0.194   0.263   0.145  -0.288
136   K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
137   K        -0.280  -0.310  -0.185  -0.434  -0.482  -0.273  -0.597  -0.659  -0.474
138   I        -1.402  -1.487  -1.360  -1.397  -1.498  -1.292  -1.349  -1.416  -1.229
139   V        -0.731  -0.697  -0.824  -0.696  -0.651  -0.810  -0.812  -0.764  -0.912
140   S         0.970   0.977   1.022   0.857   0.876   0.950   1.015   1.026   1.091
141   E        -2.304  -2.326  -2.098  -2.192  -2.255  -1.934  -1.779  -1.786  -1.519
142   K        -1.322  -1.274  -1.348  -1.290  -1.251  -1.300  -1.242  -1.203  -1.218
143   S        -1.525  -1.454  -1.375  -1.588  -1.480  -1.364  -1.457  -1.393  -1.243
144   A        -0.731  -0.623  -0.814  -0.799  -0.657  -0.912  -0.812  -0.680  -0.900
145   Q        -0.871  -0.867  -0.859  -0.883  -0.887  -0.812  -1.027  -1.023  -0.960
146   E        -1.525  -1.524  -1.381  -1.560  -1.586  -1.348  -1.457  -1.454  -1.248
147   L        -1.525  -1.419  -1.367  -1.527  -1.362  -1.291  -1.457  -1.343  -1.234
148   A        -1.075  -1.023  -0.874  -1.137  -1.031  -0.833  -1.242  -1.178  -0.976
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   K        -0.994  -0.989  -0.872  -1.133  -1.129  -0.955  -1.134  -1.132  -0.974
152   S        -0.994  -1.016  -0.874  -1.187  -1.241  -1.021  -1.134  -1.168  -0.977
153   L        -1.649  -1.763  -1.748  -1.330  -1.498  -1.452  -1.349  -1.462  -1.388
154   G         0.970   0.977   1.022   1.004   1.016   1.082   1.015   1.026   1.091
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   D        -0.731  -0.706  -0.818  -0.753  -0.687  -0.894  -0.812  -0.762  -0.905
158   I        -0.994  -0.911  -0.847  -1.022  -0.888  -0.829  -1.134  -1.028  -0.941
159   P         0.970   0.977   1.022   1.171   1.177   1.232   1.015   1.026   1.091
160   L        -1.075  -1.023  -0.874  -1.176  -1.074  -0.879  -1.242  -1.178  -0.976
161   F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
162   L        -0.731  -0.600  -0.823  -0.681  -0.488  -0.832  -0.812  -0.634  -0.911
163   T         0.970   0.977   1.022   1.041   1.048   1.115   1.015   1.026   1.091
164   S         0.970   0.977   1.022   0.857   0.876   0.950   1.015   1.026   1.091
165   A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
166   K         0.970   0.977   1.022   0.885   0.898   0.976   1.015   1.026   1.091
167   N        -1.402  -1.270  -1.357  -1.473  -1.296  -1.396  -1.349  -1.229  -1.226
168   A        -1.322  -1.343  -1.348  -1.374  -1.407  -1.424  -1.242  -1.256  -1.217
169   I        -0.420  -0.496  -0.789  -0.212  -0.308  -0.772  -0.382  -0.486  -0.867
170   N         0.258   0.152  -0.079   0.341   0.213  -0.135   0.263   0.107  -0.288
171   V         0.970   0.977   1.022   0.863   0.876   0.956   1.015   1.026   1.091
172   D        -1.075  -1.065  -0.891  -1.258  -1.250  -0.976  -1.242  -1.230  -0.997
173   T        -2.304  -2.258  -2.090  -2.089  -2.035  -1.852  -1.779  -1.738  -1.514
174   A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
175   F         0.970   0.977   1.022   1.004   1.012   1.082   1.015   1.026   1.091
176   E         0.970   0.977   1.022   0.983   0.991   1.063   1.015   1.026   1.091
177   E        -1.075  -1.079  -0.889  -1.240  -1.250  -0.954  -1.242  -1.247  -0.994
178   I        -0.280  -0.303  -0.184  -0.484  -0.542  -0.368  -0.597  -0.646  -0.473
179   A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
180   R        -0.340  -0.323  -0.185  -0.506  -0.485  -0.271  -0.704  -0.682  -0.476
181   S        -1.525  -1.556  -1.384  -1.529  -1.575  -1.321  -1.457  -1.479  -1.250
182   A         0.970   0.977   1.022   0.869   0.879   0.962   1.015   1.026   1.091
183   L         0.258   0.152  -0.079   0.341   0.214  -0.085   0.263   0.107  -0.288
184   Q        -1.058  -1.217  -1.346  -0.728  -0.964  -1.173  -0.919  -1.102  -1.213
185   Q         0.258   0.178  -0.079   0.415   0.314  -0.093   0.263   0.145  -0.288
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   N         0.024   0.026  -0.144  -0.044  -0.050  -0.365  -0.086  -0.087  -0.402
190   Q        -0.825  -0.870  -0.881  -0.815  -0.903  -1.002  -0.911  -0.973  -0.985
191   A        -2.304  -2.313  -2.079  -2.200  -2.206  -1.870  -1.779  -1.778  -1.507
192   D        -0.731  -0.697  -0.824  -0.802  -0.749  -0.929  -0.812  -0.764  -0.912
193   T        -1.525  -1.399  -1.368  -1.622  -1.452  -1.367  -1.457  -1.332  -1.236
194   E        -1.525  -1.459  -1.364  -1.519  -1.454  -1.256  -1.457  -1.397  -1.233
195   A        -0.871  -0.823  -0.846  -1.091  -1.004  -0.999  -1.027  -0.953  -0.942
196   F        -1.525  -1.553  -1.373  -1.452  -1.484  -1.225  -1.457  -1.475  -1.241
197   E        -1.853  -1.919  -1.766  -1.760  -1.868  -1.665  -1.564  -1.614  -1.404
198   D        -0.420  -0.502  -0.803  -0.353  -0.465  -0.912  -0.382  -0.490  -0.885
199   D         0.970   0.977   1.022   0.850   0.863   0.945   1.015   1.026   1.091
200   Y        -0.871  -0.798  -0.841  -0.808  -0.716  -0.767  -1.027  -0.934  -0.938
201   N        -1.649  -1.753  -1.750  -1.414  -1.580  -1.617  -1.349  -1.453  -1.391
202   D         0.258   0.302  -0.067   0.252   0.306  -0.195   0.263   0.323  -0.267
203   A        -0.731  -0.853  -0.856  -0.680  -0.847  -0.815  -0.812  -0.967  -0.955
204   I         0.970   0.977   1.022   0.986   1.004   1.066   1.015   1.026   1.091
205   N         0.258   0.178  -0.079   0.374   0.287  -0.044   0.263   0.145  -0.288
206   I         0.258   0.178  -0.079   0.377   0.281  -0.132   0.263   0.145  -0.288
207   R        -1.322  -1.256  -1.350  -0.950  -0.869  -1.061  -1.242  -1.168  -1.218
208   L        -0.420  -0.502  -0.803  -0.243  -0.346  -0.748  -0.382  -0.490  -0.885
209   D        -0.340  -0.323  -0.185  -0.636  -0.615  -0.384  -0.704  -0.682  -0.475
210   G        -1.075  -1.059  -0.883  -1.260  -1.245  -0.995  -1.242  -1.222  -0.987
211   E        -0.731  -0.776  -0.838  -0.701  -0.762  -0.890  -0.812  -0.861  -0.933
212   N        -2.631  -2.595  -2.368  -2.321  -2.285  -1.958  -1.886  -1.859  -1.594
213   N        -1.853  -1.821  -1.741  -1.809  -1.751  -1.639  -1.564  -1.525  -1.383
214   S        -1.322  -1.360  -1.357  -1.328  -1.380  -1.384  -1.242  -1.278  -1.226
215   C         0.970   0.977   1.022   1.162   1.171   1.224   1.015   1.026   1.091
216   S        -1.853  -1.806  -1.748  -1.788  -1.699  -1.599  -1.564  -1.512  -1.389
217   C         0.970   0.977   1.022   1.162   1.171   1.224   1.015   1.026   1.091
* 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/P32939
Output conservation file - output/P32939
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
