1     M         1.809   1.827   1.898   2.062   2.083   2.206   1.982   2.007   2.122
2     V        -1.330  -1.338  -1.283  -1.228  -1.251  -1.180  -1.065  -1.065  -0.980
3     V        -1.428  -1.398  -1.308  -1.387  -1.331  -1.213  -1.152  -1.116  -1.002
4     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    L         0.678   0.636   0.634   0.497   0.440   0.435   0.513   0.432   0.395
17    T        -1.330  -1.328  -1.261  -1.385  -1.397  -1.301  -1.065  -1.056  -0.961
18    S        -1.330  -1.338  -1.283  -1.246  -1.233  -1.171  -1.065  -1.065  -0.980
19    R        -1.330  -1.338  -1.283  -1.057  -1.076  -1.005  -1.065  -1.065  -0.980
20    K        -0.690  -0.764  -0.776  -0.655  -0.752  -0.799  -0.629  -0.714  -0.712
21    V        -1.330  -1.290  -1.254  -1.271  -1.230  -1.138  -1.065  -1.020  -0.955
22    P        -0.225  -0.283  -0.220  -0.259  -0.327  -0.223  -0.412  -0.478  -0.394
23    L         1.809   1.827   1.898   1.602   1.637   1.751   1.982   2.007   2.122
24    E         0.064   0.044  -0.095   0.115   0.078  -0.154   0.023  -0.011  -0.206
25    E         0.064   0.054  -0.101   0.120   0.109  -0.156   0.023   0.009  -0.215
26    L         0.529   0.537   0.554   0.141   0.156   0.164   0.241   0.248   0.242
27    E         0.529   0.518   0.549   0.355   0.333   0.357   0.241   0.213   0.232
28    D        -0.690  -0.751  -0.764  -0.640  -0.718  -0.760  -0.629  -0.699  -0.698
29    M        -0.690  -0.751  -0.764  -0.721  -0.817  -0.796  -0.629  -0.699  -0.698
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    E         1.809   1.827   1.898   1.812   1.842   1.959   1.982   2.007   2.122
35    K        -0.865  -0.876  -0.815  -0.947  -0.962  -0.853  -0.847  -0.849  -0.759
36    R        -1.330  -1.338  -1.283  -1.300  -1.322  -1.243  -1.065  -1.065  -0.980
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    C        -0.225  -0.181  -0.215  -0.248  -0.209  -0.283  -0.412  -0.365  -0.388
39    F        -0.865  -0.857  -0.814  -0.874  -0.861  -0.806  -0.847  -0.829  -0.757
40    L         0.529   0.511   0.546   0.190   0.161   0.213   0.241   0.199   0.226
41    S        -0.690  -0.646  -0.751  -0.554  -0.484  -0.627  -0.629  -0.576  -0.684
42    T        -1.330  -1.328  -1.261  -1.307  -1.317  -1.208  -1.065  -1.056  -0.961
43    F         0.903   0.808   0.734   0.978   0.829   0.686   0.894   0.734   0.580
44    T        -0.865  -0.866  -0.809  -0.844  -0.842  -0.759  -0.847  -0.839  -0.753
45    Y        -0.401  -0.378  -0.290  -0.586  -0.547  -0.412  -0.629  -0.597  -0.480
46    Q        -1.330  -1.284  -1.261  -1.277  -1.217  -1.184  -1.065  -1.015  -0.961
47    D        -0.690  -0.646  -0.751  -0.586  -0.514  -0.688  -0.629  -0.576  -0.684
48    A         0.529   0.523   0.552   0.466   0.447   0.510   0.241   0.223   0.239
49    F        -0.401  -0.379  -0.286  -0.320  -0.297  -0.157  -0.629  -0.598  -0.474
50    D        -1.330  -1.290  -1.254  -1.286  -1.227  -1.182  -1.065  -1.020  -0.955
51    L         1.809   1.827   1.898   1.602   1.637   1.751   1.982   2.007   2.122
52    G         1.809   1.827   1.898   1.790   1.811   1.937   1.982   2.007   2.122
53    T        -0.690  -0.682  -0.754  -0.598  -0.593  -0.688  -0.629  -0.620  -0.687
54    Y        -1.330  -1.282  -1.258  -1.271  -1.197  -1.165  -1.065  -1.011  -0.958
55    I        -0.401  -0.379  -0.286  -0.645  -0.611  -0.465  -0.629  -0.598  -0.474
56    R         1.809   1.827   1.898   1.911   1.934   2.057   1.982   2.007   2.122
57    N        -1.330  -1.282  -1.258  -1.233  -1.162  -1.130  -1.065  -1.011  -0.958
58    A        -0.690  -0.649  -0.749  -0.819  -0.753  -0.906  -0.629  -0.579  -0.682
59    V        -0.865  -0.859  -0.817  -0.889  -0.875  -0.812  -0.847  -0.833  -0.760
60    K        -0.401  -0.379  -0.286  -0.821  -0.770  -0.630  -0.629  -0.598  -0.474
61    E         0.415   0.442   0.525   0.098   0.153   0.274   0.023   0.068   0.186
62    N        -1.428  -1.396  -1.308  -1.327  -1.297  -1.153  -1.152  -1.114  -1.002
63    F        -0.313  -0.348  -0.265  -0.356  -0.423  -0.291  -0.525  -0.561  -0.449
64    P         0.064  -0.064  -0.130   0.345   0.146   0.028   0.023  -0.158  -0.257
65    E        -1.330  -1.282  -1.258  -1.138  -1.079  -1.038  -1.065  -1.011  -0.958
66    K         0.903   0.808   0.734   0.909   0.782   0.651   0.894   0.734   0.580
67    P         0.064   0.065  -0.084   0.373   0.375   0.148   0.023   0.023  -0.192
68    V         0.415   0.442   0.525   0.147   0.188   0.319   0.023   0.068   0.186
69    A        -0.865  -0.857  -0.814  -1.016  -1.009  -0.953  -0.847  -0.829  -0.757
70    I         1.809   1.827   1.898   1.773   1.800   1.920   1.982   2.007   2.122
71    D         0.529   0.580   0.572   0.423   0.511   0.484   0.241   0.329   0.277
72    I         1.809   1.827   1.898   1.773   1.800   1.920   1.982   2.007   2.122
73    S         0.415   0.442   0.525   0.151   0.209   0.338   0.023   0.068   0.186
74    L         0.903   0.858   0.739   0.765   0.712   0.537   0.894   0.817   0.589
75    P        -0.870  -0.809  -0.803  -0.854  -0.760  -0.762  -0.838  -0.763  -0.742
76    N         0.064   0.086  -0.083   0.282   0.315   0.034   0.023   0.052  -0.190
77    G         0.903   0.964   0.769   0.936   1.016   0.739   0.894   0.988   0.643
78    H         0.064   0.086  -0.083   0.343   0.362   0.081   0.023   0.052  -0.190
79    C        -1.330  -1.343  -1.269  -1.007  -1.033  -0.908  -1.065  -1.069  -0.968
80    L         0.064  -0.064  -0.130   0.022  -0.145  -0.221   0.023  -0.158  -0.257
81    F         0.903   0.964   0.769   1.051   1.132   0.872   0.894   0.988   0.643
82    R        -0.225  -0.190  -0.202  -0.076  -0.033  -0.041  -0.412  -0.367  -0.370
83    T        -0.690  -0.740  -0.762  -0.659  -0.771  -0.837  -0.629  -0.688  -0.696
84    V         0.415   0.442   0.525   0.160   0.193   0.332   0.023   0.068   0.186
85    T        -0.690  -0.756  -0.758  -0.519  -0.626  -0.641  -0.629  -0.705  -0.692
86    Y        -0.979  -0.954  -0.864  -0.995  -0.958  -0.824  -0.956  -0.922  -0.806
87    G        -0.865  -0.857  -0.814  -0.992  -0.987  -0.915  -0.847  -0.829  -0.757
88    G         0.903   0.964   0.769   0.948   1.027   0.759   0.894   0.988   0.643
89    S        -0.225  -0.194  -0.214  -0.333  -0.300  -0.334  -0.412  -0.378  -0.386
90    A        -0.690  -0.658  -0.732  -0.664  -0.610  -0.739  -0.629  -0.588  -0.662
91    L        -0.690  -0.756  -0.758  -0.746  -0.834  -0.822  -0.629  -0.705  -0.692
92    D         1.809   1.827   1.898   1.812   1.845   1.959   1.982   2.007   2.122
93    N         1.809   1.827   1.898   1.960   1.987   2.105   1.982   2.007   2.122
94    D         0.903   0.858   0.739   0.990   0.936   0.766   0.894   0.817   0.589
95    F        -1.795  -1.762  -1.671  -1.478  -1.443  -1.303  -1.282  -1.246  -1.132
96    W         0.903   0.808   0.734   1.279   1.144   1.017   0.894   0.734   0.580
97    I         0.529   0.532   0.553   0.347   0.348   0.368   0.241   0.239   0.240
98    Q        -0.690  -0.690  -0.732  -0.609  -0.620  -0.669  -0.629  -0.629  -0.662
99    R         1.809   1.827   1.898   1.911   1.934   2.057   1.982   2.007   2.122
100   K         1.809   1.827   1.898   1.767   1.808   1.914   1.982   2.007   2.122
101   K        -0.690  -0.764  -0.776  -0.615  -0.711  -0.745  -0.629  -0.714  -0.712
102   K        -0.865  -0.859  -0.817  -0.857  -0.847  -0.772  -0.847  -0.833  -0.760
103   T         0.903   0.858   0.739   1.030   0.964   0.776   0.894   0.817   0.589
104   A         0.529   0.590   0.603   0.401   0.508   0.507   0.241   0.348   0.336
105   L        -0.225  -0.287  -0.227  -0.520  -0.591  -0.489  -0.412  -0.483  -0.402
106   R         1.809   1.827   1.898   1.911   1.934   2.057   1.982   2.007   2.122
107   F         1.809   1.827   1.898   1.873   1.898   2.019   1.982   2.007   2.122
108   G         0.064   0.012  -0.102   0.134   0.050  -0.124   0.023  -0.053  -0.217
109   H        -0.865  -0.913  -0.833  -0.711  -0.756  -0.642  -0.847  -0.883  -0.776
110   S         1.809   1.827   1.898   1.762   1.794   1.909   1.982   2.007   2.122
111   S         1.809   1.827   1.898   1.762   1.794   1.909   1.982   2.007   2.122
112   F         0.064   0.023  -0.088   0.291   0.231   0.086   0.023  -0.039  -0.198
113   Y         0.064  -0.064  -0.130   0.328   0.130   0.016   0.023  -0.158  -0.257
114   M        -0.225  -0.223  -0.211  -0.230  -0.219  -0.241  -0.412  -0.395  -0.377
115   G         0.903   0.964   0.769   0.956   1.033   0.772   0.894   0.988   0.643
116   -        -0.282  -0.326  -0.258  -0.298  -0.389  -0.288  -0.466  -0.526  -0.437
117   -        -0.282  -0.326  -0.258  -0.256  -0.312  -0.210  -0.466  -0.526  -0.437
118   C        -0.865  -0.793  -0.808  -0.836  -0.701  -0.709  -0.847  -0.766  -0.751
119   K        -0.225  -0.190  -0.214  -0.305  -0.272  -0.308  -0.412  -0.374  -0.386
120   K        -0.865  -0.792  -0.809  -0.838  -0.710  -0.735  -0.847  -0.764  -0.752
121   G        -0.225  -0.257  -0.211  -0.369  -0.391  -0.323  -0.412  -0.438  -0.376
122   D        -0.225  -0.158  -0.180  -0.311  -0.210  -0.209  -0.412  -0.315  -0.334
123   K        -0.690  -0.740  -0.762  -0.581  -0.656  -0.679  -0.629  -0.688  -0.696
124   T         0.064   0.168  -0.076   0.240   0.387   0.021   0.023   0.170  -0.180
125   P        -0.401  -0.379  -0.285  -0.499  -0.474  -0.330  -0.629  -0.599  -0.473
126   E        -0.225  -0.285  -0.216  -0.222  -0.298  -0.185  -0.412  -0.480  -0.389
127   E         0.064   0.044  -0.095   0.126   0.087  -0.137   0.023  -0.011  -0.206
128   K         0.415   0.433   0.517   0.082   0.111   0.243   0.023   0.050   0.170
129   F        -0.865  -0.792  -0.809  -0.820  -0.694  -0.739  -0.847  -0.764  -0.752
130   F         0.064  -0.064  -0.130   0.185  -0.020  -0.145   0.023  -0.158  -0.257
131   V         0.903   0.952   0.759   1.011   1.083   0.789   0.894   0.969   0.625
132   D        -0.225  -0.257  -0.211  -0.353  -0.373  -0.304  -0.412  -0.438  -0.376
133   S        -0.865  -0.913  -0.809  -0.868  -0.948  -0.792  -0.847  -0.883  -0.753
134   K        -0.865  -0.913  -0.833  -0.988  -1.042  -0.926  -0.847  -0.883  -0.776
135   E         0.415   0.440   0.523   0.131   0.178   0.304   0.023   0.063   0.181
136   Y         1.809   1.827   1.898   1.976   2.002   2.121   1.982   2.007   2.122
137   A         0.903   0.808   0.734   0.931   0.783   0.672   0.894   0.734   0.580
138   F        -0.865  -0.792  -0.809  -0.920  -0.824  -0.838  -0.847  -0.764  -0.752
139   H         0.903   0.808   0.734   1.196   1.061   0.938   0.894   0.734   0.580
140   G         1.809   1.827   1.898   1.790   1.811   1.937   1.982   2.007   2.122
141   G         1.809   1.827   1.898   1.790   1.811   1.937   1.982   2.007   2.122
142   A        -0.401  -0.368  -0.282  -0.705  -0.658  -0.520  -0.629  -0.584  -0.470
143   V        -0.225  -0.219  -0.224  -0.290  -0.296  -0.300  -0.412  -0.414  -0.400
144   L         0.903   0.973   0.764   1.103   1.205   0.864   0.894   1.003   0.634
145   I         0.903   0.952   0.759   0.878   0.951   0.636   0.894   0.969   0.625
146   Q        -0.690  -0.682  -0.754  -0.499  -0.507  -0.616  -0.629  -0.620  -0.687
147   S        -0.690  -0.632  -0.716  -0.854  -0.755  -0.902  -0.629  -0.558  -0.644
148   E        -1.330  -1.337  -1.288  -1.255  -1.250  -1.198  -1.065  -1.064  -0.985
149   R        -0.313  -0.268  -0.242  -0.383  -0.336  -0.271  -0.525  -0.468  -0.421
150   S        -0.690  -0.646  -0.751  -0.666  -0.603  -0.772  -0.629  -0.576  -0.684
151   D         0.064  -0.064  -0.130   0.126  -0.072  -0.199   0.023  -0.158  -0.257
152   Y        -0.225  -0.257  -0.211  -0.300  -0.355  -0.280  -0.412  -0.438  -0.376
153   P        -0.690  -0.679  -0.756  -0.419  -0.408  -0.549  -0.629  -0.617  -0.689
154   Y         0.064   0.073  -0.091   0.149   0.157  -0.074   0.023   0.033  -0.201
155   A         0.415   0.433   0.517   0.098   0.113   0.260   0.023   0.050   0.170
156   C        -1.330  -1.217  -1.251  -1.144  -0.978  -1.033  -1.065  -0.946  -0.952
157   L         0.064  -0.064  -0.130  -0.045  -0.225  -0.328   0.023  -0.158  -0.257
158   T         0.903   0.808   0.734   1.091   0.968   0.874   0.894   0.734   0.580
159   I         0.529   0.537   0.554   0.347   0.357   0.369   0.241   0.248   0.242
160   S         1.809   1.827   1.898   1.762   1.794   1.909   1.982   2.007   2.122
161   G         1.809   1.827   1.898   1.790   1.811   1.937   1.982   2.007   2.122
162   L         1.809   1.827   1.898   1.602   1.637   1.751   1.982   2.007   2.122
163   K        -0.865  -0.913  -0.833  -0.902  -0.951  -0.821  -0.847  -0.883  -0.776
164   Q         1.809   1.827   1.898   1.971   1.991   2.116   1.982   2.007   2.122
165   E        -0.690  -0.756  -0.758  -0.566  -0.681  -0.672  -0.629  -0.705  -0.692
166   E         0.903   0.808   0.734   0.990   0.863   0.758   0.894   0.734   0.580
167   D         1.809   1.827   1.898   1.812   1.845   1.959   1.982   2.007   2.122
168   H         1.809   1.827   1.898   2.040   2.068   2.185   1.982   2.007   2.122
169   L         0.064  -0.064  -0.130   0.018  -0.146  -0.228   0.023  -0.158  -0.257
170   M        -0.225  -0.149  -0.190  -0.433  -0.329  -0.349  -0.412  -0.308  -0.354
171   A         0.064  -0.064  -0.130   0.115  -0.093  -0.201   0.023  -0.158  -0.257
172   V        -0.865  -0.913  -0.833  -0.891  -0.959  -0.830  -0.847  -0.883  -0.776
173   S        -1.330  -1.338  -1.283  -1.198  -1.203  -1.126  -1.065  -1.065  -0.980
174   S        -0.225  -0.223  -0.211  -0.291  -0.266  -0.233  -0.412  -0.395  -0.377
175   L        -0.225  -0.204  -0.202  -0.550  -0.520  -0.499  -0.412  -0.390  -0.370
176   I        -1.330  -1.337  -1.288  -1.300  -1.319  -1.239  -1.065  -1.064  -0.985
177   A        -1.330  -1.269  -1.253  -1.275  -1.180  -1.167  -1.065  -0.999  -0.953
178   F         0.064   0.179  -0.048   0.245   0.405   0.082   0.023   0.185  -0.140
179   A        -0.225  -0.181  -0.215  -0.518  -0.477  -0.527  -0.412  -0.365  -0.388
180   N        -1.330  -1.337  -1.288  -1.189  -1.208  -1.163  -1.065  -1.064  -0.985
181   E        -0.870  -0.791  -0.802  -0.848  -0.707  -0.757  -0.838  -0.743  -0.741
182   S        -0.870  -0.910  -0.840  -0.996  -1.064  -0.975  -0.838  -0.876  -0.782
183   L        -0.282  -0.247  -0.223  -0.383  -0.317  -0.317  -0.466  -0.416  -0.389
184   E        -0.282  -0.316  -0.264  -0.601  -0.670  -0.625  -0.466  -0.513  -0.445
185   E        -0.282  -0.258  -0.228  -0.512  -0.468  -0.446  -0.466  -0.431  -0.395
186   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   D        -0.865  -0.838  -0.811  -0.812  -0.772  -0.718  -0.847  -0.812  -0.754
* 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/P38276
Output conservation file - output/P38276
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
