1     M         2.125   2.129   2.191   2.496   2.503   2.603   2.432   2.439   2.543
2     S        -0.158  -0.128  -0.148  -0.506  -0.465  -0.492  -0.319  -0.276  -0.305
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -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     -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    M         0.727   0.741   0.744   0.772   0.801   0.762   0.475   0.501   0.481
59    Q        -0.158  -0.120  -0.153  -0.405  -0.363  -0.378  -0.319  -0.264  -0.312
60    I         2.125   2.129   2.191   2.011   2.014   2.115   2.432   2.439   2.543
61    E         0.890   0.878   0.834   0.879   0.864   0.766   0.781   0.758   0.656
62    I        -0.158  -0.171  -0.158  -0.362  -0.385  -0.365  -0.319  -0.338  -0.319
63    K        -0.158  -0.135  -0.149  -0.343  -0.307  -0.332  -0.319  -0.287  -0.307
64    D         0.890   0.859   0.829   0.844   0.783   0.693   0.781   0.724   0.646
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    G        -0.800  -0.777  -0.796  -0.875  -0.858  -0.836  -0.738  -0.712  -0.718
67    R        -0.800  -0.817  -0.800  -0.497  -0.533  -0.521  -0.738  -0.756  -0.722
68    S        -0.800  -0.832  -0.814  -0.949  -0.974  -0.930  -0.738  -0.774  -0.738
69    D        -1.409  -1.402  -1.360  -1.385  -1.365  -1.311  -1.090  -1.083  -1.020
70    N         1.026   1.014   0.932   1.139   1.127   0.997   1.023   1.002   0.840
71    S        -0.800  -0.832  -0.814  -0.766  -0.791  -0.726  -0.738  -0.774  -0.738
72    P         2.125   2.129   2.191   2.444   2.450   2.551   2.432   2.439   2.543
73    L         0.038   0.017  -0.048   0.081   0.053  -0.034  -0.033  -0.064  -0.160
74    P        -0.191  -0.179  -0.168  -0.330  -0.326  -0.281  -0.385  -0.370  -0.344
75    E        -0.800  -0.763  -0.793  -0.369  -0.309  -0.351  -0.738  -0.694  -0.714
76    R        -0.800  -0.777  -0.796  -0.635  -0.625  -0.626  -0.738  -0.712  -0.718
77    K         0.038   0.043  -0.031   0.188   0.194   0.115  -0.033  -0.026  -0.135
78    L         1.026   1.014   0.932   0.937   0.924   0.780   1.023   1.002   0.840
79    V        -0.800  -0.794  -0.792  -0.969  -0.971  -0.964  -0.738  -0.731  -0.714
80    T        -1.409  -1.402  -1.360  -1.416  -1.416  -1.341  -1.090  -1.083  -1.020
81    L        -0.191  -0.193  -0.172  -0.419  -0.416  -0.369  -0.385  -0.385  -0.348
82    I         1.026   1.014   0.931   0.929   0.911   0.771   1.023   1.002   0.839
83    Q        -1.409  -1.402  -1.360  -1.234  -1.233  -1.158  -1.090  -1.083  -1.020
84    E         0.647   0.643   0.682   0.282   0.270   0.300   0.319   0.309   0.358
85    S        -1.409  -1.402  -1.360  -1.398  -1.369  -1.323  -1.090  -1.083  -1.020
86    Y        -0.800  -0.794  -0.788  -0.357  -0.359  -0.335  -0.738  -0.732  -0.709
87    D        -0.158  -0.137  -0.150  -0.580  -0.551  -0.563  -0.319  -0.290  -0.308
88    S        -0.158  -0.135  -0.148  -0.625  -0.591  -0.610  -0.319  -0.286  -0.305
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   T         0.727   0.747   0.746   0.556   0.596   0.547   0.475   0.512   0.484
101   E        -0.800  -0.777  -0.796  -0.780  -0.762  -0.787  -0.738  -0.712  -0.718
102   S        -0.800  -0.794  -0.792  -0.895  -0.878  -0.911  -0.738  -0.731  -0.714
103   T        -0.800  -0.777  -0.796  -0.531  -0.490  -0.539  -0.738  -0.712  -0.718
104   S        -0.800  -0.817  -0.793  -1.082  -1.110  -1.058  -0.738  -0.756  -0.714
105   N        -1.409  -1.402  -1.360  -1.428  -1.436  -1.354  -1.090  -1.083  -1.020
106   L        -0.800  -0.763  -0.793  -0.748  -0.682  -0.766  -0.738  -0.694  -0.714
107   L         0.038  -0.004  -0.049  -0.206  -0.281  -0.397  -0.033  -0.096  -0.160
108   I         1.026   1.014   0.931   0.985   0.967   0.848   1.023   1.002   0.839
109   K        -1.409  -1.402  -1.360  -1.102  -1.082  -1.025  -1.090  -1.083  -1.020
110   L        -0.191  -0.178  -0.170  -0.378  -0.357  -0.326  -0.385  -0.368  -0.347
111   V         0.647   0.664   0.695   0.390   0.413   0.462   0.319   0.351   0.384
112   L         1.026   1.014   0.932   1.024   1.013   0.899   1.023   1.002   0.840
113   E         0.038  -0.004  -0.049   0.219   0.158   0.089  -0.033  -0.096  -0.160
114   K        -1.409  -1.402  -1.360  -1.183  -1.153  -1.107  -1.090  -1.083  -1.020
115   L         2.125   2.129   2.191   2.041   2.055   2.145   2.432   2.439   2.543
116   E        -0.191  -0.155  -0.166  -0.358  -0.307  -0.314  -0.385  -0.343  -0.342
117   K        -0.191  -0.207  -0.176  -0.338  -0.349  -0.303  -0.385  -0.403  -0.353
118   H        -0.800  -0.832  -0.814  -0.617  -0.681  -0.678  -0.738  -0.774  -0.738
119   S         2.125   2.129   2.191   1.787   1.793   1.889   2.432   2.439   2.543
120   S         1.026   0.986   0.913   0.690   0.628   0.505   1.023   0.952   0.805
121   L        -1.409  -1.402  -1.360  -1.071  -1.049  -0.993  -1.090  -1.083  -1.020
122   Y         0.647   0.642   0.682   0.862   0.854   0.914   0.319   0.307   0.359
123   K         2.125   2.129   2.191   2.064   2.073   2.168   2.432   2.439   2.543
124   Y         0.647   0.676   0.703   0.830   0.879   0.918   0.319   0.374   0.399
125   I         0.038  -0.005  -0.054  -0.001  -0.070  -0.143  -0.033  -0.096  -0.169
126   A         1.026   1.092   0.947   1.240   1.326   1.135   1.023   1.135   0.868
127   S        -0.800  -0.832  -0.814  -0.870  -0.897  -0.842  -0.738  -0.774  -0.738
128   V         0.647   0.635   0.679   0.321   0.274   0.329   0.319   0.292   0.352
129   T         2.125   2.129   2.191   2.316   2.324   2.422   2.432   2.439   2.543
130   T        -0.800  -0.794  -0.792  -1.168  -1.173  -1.151  -0.738  -0.731  -0.714
131   L         0.038   0.021  -0.045  -0.048  -0.071  -0.191  -0.033  -0.059  -0.156
132   N        -0.800  -0.817  -0.800  -0.631  -0.653  -0.625  -0.738  -0.756  -0.722
133   I        -0.800  -0.832  -0.814  -0.771  -0.817  -0.774  -0.738  -0.774  -0.738
134   E        -1.409  -1.402  -1.360  -1.162  -1.152  -1.085  -1.090  -1.083  -1.020
135   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   N         0.727   0.732   0.737   0.678   0.687   0.687   0.475   0.483   0.467
138   E        -0.158  -0.185  -0.172  -0.136  -0.179  -0.162  -0.319  -0.358  -0.340
139   E        -0.919  -0.913  -0.868  -1.164  -1.151  -1.088  -0.870  -0.863  -0.797
140   N        -1.409  -1.402  -1.360  -1.517  -1.499  -1.443  -1.090  -1.083  -1.020
141   A        -0.800  -0.817  -0.800  -0.639  -0.661  -0.658  -0.738  -0.756  -0.722
142   N        -0.800  -0.777  -0.796  -0.729  -0.681  -0.731  -0.738  -0.712  -0.718
143   F        -0.800  -0.817  -0.800  -0.369  -0.400  -0.366  -0.738  -0.756  -0.722
144   S        -0.800  -0.817  -0.800  -0.880  -0.891  -0.845  -0.738  -0.756  -0.722
145   L         0.038   0.079  -0.020  -0.056   0.009  -0.155  -0.033   0.025  -0.119
146   K        -0.191  -0.196  -0.166  -0.271  -0.276  -0.218  -0.385  -0.390  -0.341
147   N         0.647   0.676   0.703   0.139   0.182   0.222   0.319   0.374   0.399
148   D        -0.800  -0.817  -0.793  -0.818  -0.859  -0.824  -0.738  -0.756  -0.714
149   I        -0.191  -0.209  -0.170  -0.182  -0.202  -0.137  -0.385  -0.405  -0.347
150   G         1.026   1.014   0.932   1.396   1.378   1.265   1.023   1.002   0.840
151   A         0.038  -0.004  -0.049   0.246   0.172   0.080  -0.033  -0.096  -0.160
152   S         0.038  -0.005  -0.054  -0.236  -0.297  -0.367  -0.033  -0.096  -0.169
153   W         2.125   2.129   2.191   2.465   2.470   2.572   2.432   2.439   2.543
154   E         0.038   0.079  -0.015   0.150   0.215   0.064  -0.033   0.025  -0.111
155   S        -0.800  -0.763  -0.793  -0.711  -0.637  -0.716  -0.738  -0.694  -0.714
156   K         1.026   0.986   0.913   1.007   0.953   0.837   1.023   0.952   0.805
157   K         1.026   1.014   0.931   0.900   0.882   0.718   1.023   1.002   0.839
158   D         2.125   2.129   2.191   2.230   2.236   2.335   2.432   2.439   2.543
159   G         2.125   2.129   2.191   2.423   2.428   2.529   2.432   2.439   2.543
160   I        -1.409  -1.402  -1.360  -0.963  -0.948  -0.885  -1.090  -1.083  -1.020
161   F        -0.191  -0.209  -0.170  -0.122  -0.143  -0.076  -0.385  -0.405  -0.347
162   N        -0.800  -0.803  -0.791  -0.734  -0.743  -0.725  -0.738  -0.741  -0.712
163   Y         0.038   0.043  -0.031   0.407   0.412   0.289  -0.033  -0.026  -0.135
164   K        -0.191  -0.179  -0.168  -0.201  -0.183  -0.161  -0.385  -0.370  -0.344
165   L         0.727   0.698   0.723   0.392   0.339   0.363   0.475   0.417   0.439
166   E         0.727   0.698   0.723   0.742   0.701   0.737   0.475   0.417   0.439
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   D        -0.800  -0.832  -0.814  -0.418  -0.459  -0.411  -0.738  -0.774  -0.738
172   K        -0.800  -0.832  -0.814  -0.808  -0.868  -0.822  -0.738  -0.774  -0.738
173   N        -0.800  -0.803  -0.791  -0.488  -0.493  -0.459  -0.738  -0.741  -0.712
174   N        -0.800  -0.817  -0.793  -0.600  -0.627  -0.582  -0.738  -0.756  -0.714
175   N        -0.191  -0.178  -0.166  -0.282  -0.267  -0.230  -0.385  -0.368  -0.342
176   E        -0.800  -0.817  -0.793  -0.604  -0.622  -0.589  -0.738  -0.756  -0.714
177   C        -0.800  -0.777  -0.796  -0.702  -0.687  -0.677  -0.738  -0.712  -0.718
178   Y        -0.800  -0.777  -0.796  -0.613  -0.592  -0.582  -0.738  -0.712  -0.718
179   L         0.038   0.043  -0.031  -0.048  -0.041  -0.167  -0.033  -0.026  -0.135
180   I         0.647   0.664   0.692   0.457   0.488   0.515   0.319   0.351   0.379
181   T         0.647   0.664   0.692   0.214   0.235   0.288   0.319   0.351   0.379
182   I         0.647   0.651   0.685   0.390   0.391   0.446   0.319   0.325   0.363
183   L        -0.191  -0.156  -0.169  -0.022   0.037   0.006  -0.385  -0.344  -0.345
184   W         2.125   2.129   2.191   2.465   2.470   2.572   2.432   2.439   2.543
185   L         0.647   0.676   0.703   0.258   0.316   0.340   0.319   0.374   0.399
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   H         0.038   0.079  -0.020  -0.221  -0.174  -0.299  -0.033   0.025  -0.119
189   K        -0.800  -0.832  -0.814  -0.959  -1.014  -0.994  -0.738  -0.774  -0.738
* 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/P40045
Output conservation file - output/P40045
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
