1     M         1.752   1.791   1.915   1.912   1.963   2.159   1.945   2.005   2.206
2     S        -0.716  -0.696  -0.598  -0.901  -0.898  -0.757  -0.834  -0.807  -0.668
3     A        -0.579  -0.493  -0.526  -0.713  -0.626  -0.619  -0.679  -0.578  -0.587
4     M        -1.439  -1.445  -1.354  -1.210  -1.195  -1.076  -1.142  -1.141  -1.008
5     M        -1.077  -1.040  -0.997  -0.881  -0.819  -0.759  -0.988  -0.946  -0.857
6     V        -1.077  -1.055  -1.002  -1.405  -1.379  -1.286  -0.988  -0.959  -0.861
7     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     G         0.017   0.057   0.030  -0.098  -0.031  -0.133  -0.173  -0.114  -0.177
10    L        -0.680  -0.669  -0.587  -0.906  -0.873  -0.805  -0.778  -0.765  -0.650
11    N        -1.519  -1.511  -1.383  -1.362  -1.355  -1.176  -1.207  -1.191  -1.030
12    K        -1.097  -1.115  -1.009  -1.025  -1.080  -0.907  -0.997  -1.007  -0.865
13    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    L        -0.354  -0.259  -0.427  -0.420  -0.283  -0.497  -0.371  -0.244  -0.453
17    L        -1.439  -1.456  -1.359  -1.537  -1.531  -1.404  -1.142  -1.149  -1.012
18    K         1.004   1.040   0.898   1.123   1.171   1.002   1.019   1.076   0.785
19    P         0.298   0.200   0.117   0.541   0.404   0.273   0.247   0.098  -0.043
20    S        -0.579  -0.496  -0.524  -0.752  -0.659  -0.666  -0.679  -0.577  -0.585
21    A        -0.081  -0.035  -0.011  -0.429  -0.389  -0.360  -0.371  -0.313  -0.260
22    F        -1.800  -1.792  -1.667  -1.596  -1.633  -1.414  -1.297  -1.282  -1.123
23    S        -0.675  -0.698  -0.587  -0.952  -0.951  -0.822  -0.787  -0.805  -0.655
24    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    A        -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    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    S        -1.097  -1.125  -1.020  -1.205  -1.250  -1.128  -0.997  -1.018  -0.876
30    S        -0.675  -0.698  -0.587  -0.707  -0.749  -0.593  -0.787  -0.805  -0.655
31    S        -1.519  -1.507  -1.383  -1.253  -1.192  -1.065  -1.207  -1.188  -1.030
32    R        -0.354  -0.387  -0.473  -0.165  -0.238  -0.369  -0.371  -0.413  -0.511
33    R        -1.077  -1.102  -1.003  -1.067  -1.127  -0.986  -0.988  -1.002  -0.862
34    L        -0.579  -0.569  -0.561  -0.739  -0.706  -0.681  -0.679  -0.670  -0.627
35    L         0.298   0.267   0.133   0.180   0.135  -0.011   0.247   0.191  -0.020
36    F        -0.941  -0.916  -0.936  -0.895  -0.879  -0.873  -0.834  -0.798  -0.792
37    N        -0.218  -0.219  -0.096  -0.406  -0.434  -0.241  -0.525  -0.528  -0.367
38    T        -1.439  -1.438  -1.346  -1.206  -1.168  -1.063  -1.142  -1.135  -1.001
39    A        -1.519  -1.507  -1.383  -1.414  -1.368  -1.229  -1.207  -1.188  -1.030
40    R         0.168   0.088   0.067   0.209   0.073  -0.005   0.054  -0.071  -0.121
41    T        -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    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    K         0.409   0.477   0.153   0.631   0.719   0.288   0.408   0.508   0.011
51    N        -1.411  -1.417  -1.342  -1.045  -1.052  -0.945  -1.128  -1.126  -1.001
52    V        -0.976  -0.899  -0.959  -0.879  -0.735  -0.874  -0.892  -0.807  -0.821
53    A        -1.095  -1.071  -1.007  -1.136  -1.094  -1.019  -1.010  -0.982  -0.867
54    S         0.409   0.400   0.137   0.495   0.502   0.148   0.408   0.398  -0.014
55    E        -0.659  -0.586  -0.558  -0.449  -0.327  -0.280  -0.773  -0.685  -0.621
56    M        -1.728  -1.744  -1.643  -1.204  -1.210  -1.087  -1.246  -1.250  -1.107
57    N        -1.095  -1.091  -1.005  -1.373  -1.368  -1.213  -1.010  -0.994  -0.866
58    T         0.409   0.432   0.187   0.495   0.542   0.221   0.408   0.444   0.064
59    K        -1.728  -1.689  -1.637  -1.218  -1.131  -1.092  -1.246  -1.206  -1.103
60    A        -0.779  -0.667  -0.871  -0.639  -0.518  -0.723  -0.655  -0.521  -0.724
61    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    A        -0.462  -0.526  -0.498  -0.142  -0.203  -0.192  -0.537  -0.597  -0.546
64    E         0.726   0.778   0.730   0.780   0.856   0.702   0.527   0.612   0.452
65    E        -1.411  -1.413  -1.353  -1.073  -1.089  -1.028  -1.128  -1.121  -1.008
66    Q        -0.976  -0.976  -0.971  -0.711  -0.773  -0.729  -0.892  -0.893  -0.835
67    I        -0.462  -0.427  -0.485  -0.472  -0.403  -0.523  -0.537  -0.485  -0.536
68    L         1.752   1.791   1.915   1.426   1.473   1.664   1.945   2.005   2.206
69    N        -0.223  -0.233  -0.100  -0.359  -0.399  -0.209  -0.537  -0.548  -0.372
70    K        -0.146  -0.077  -0.034  -0.246  -0.122  -0.109  -0.419  -0.316  -0.276
71    Q         1.752   1.791   1.915   1.854   1.905   2.099   1.945   2.005   2.206
72    R         1.752   1.791   1.915   1.759   1.805   2.003   1.945   2.005   2.206
73    A        -0.540  -0.606  -0.541  -0.672  -0.805  -0.713  -0.655  -0.713  -0.606
74    K        -0.976  -0.939  -0.972  -0.750  -0.669  -0.758  -0.892  -0.847  -0.834
75    R         1.752   1.791   1.915   1.759   1.805   2.003   1.945   2.005   2.206
76    P         1.752   1.791   1.915   1.826   1.875   2.071   1.945   2.005   2.206
77    I        -0.659  -0.676  -0.596  -0.700  -0.703  -0.578  -0.773  -0.789  -0.667
78    S         1.752   1.791   1.915   1.674   1.719   1.916   1.945   2.005   2.206
79    P         1.752   1.791   1.915   1.826   1.875   2.071   1.945   2.005   2.206
80    H         1.752   1.791   1.915   1.888   1.940   2.135   1.945   2.005   2.206
81    L         1.752   1.791   1.915   1.426   1.473   1.664   1.945   2.005   2.206
82    T        -0.208  -0.210  -0.438   0.030   0.039  -0.211  -0.182  -0.191  -0.467
83    I         1.752   1.791   1.915   1.742   1.792   1.985   1.945   2.005   2.206
84    Y         1.752   1.791   1.915   1.791   1.845   2.036   1.945   2.005   2.206
85    Q         0.109   0.038   0.021   0.381   0.316   0.286  -0.064  -0.149  -0.203
86    P         1.064   1.117   0.930   1.212   1.281   1.007   1.118   1.199   0.845
87    Q         1.064   0.953   0.883   1.296   1.167   1.078   1.118   0.928   0.756
88    L         1.064   0.953   0.883   0.872   0.744   0.666   1.118   0.928   0.756
89    T         1.752   1.791   1.915   1.609   1.667   1.850   1.945   2.005   2.206
90    W         1.064   1.117   0.930   1.378   1.442   1.240   1.118   1.199   0.845
91    Y        -0.208  -0.237  -0.419   0.103   0.070  -0.201  -0.182  -0.224  -0.443
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    L        -0.027  -0.098  -0.002  -0.220  -0.301  -0.163  -0.301  -0.375  -0.245
94    S         1.752   1.791   1.915   1.674   1.719   1.916   1.945   2.005   2.206
95    S         0.109   0.047   0.054   0.042  -0.052  -0.078  -0.064  -0.134  -0.149
96    L        -0.462  -0.488  -0.511  -0.587  -0.597  -0.604  -0.537  -0.562  -0.566
97    H         1.064   0.953   0.883   1.332   1.205   1.117   1.118   0.928   0.756
98    R         1.752   1.791   1.915   1.759   1.805   2.003   1.945   2.005   2.206
99    I         0.544   0.609   0.687   0.372   0.483   0.571   0.172   0.285   0.365
100   S         0.544   0.575   0.655   0.246   0.298   0.383   0.172   0.217   0.297
101   L         0.409   0.400   0.137   0.526   0.521   0.130   0.408   0.398  -0.014
102   V        -0.208  -0.330  -0.461  -0.052  -0.241  -0.462  -0.182  -0.338  -0.496
103   L        -1.411  -1.465  -1.344  -1.457  -1.534  -1.383  -1.128  -1.159  -1.002
104   M        -0.540  -0.608  -0.539  -0.567  -0.635  -0.553  -0.655  -0.715  -0.605
105   G        -0.027  -0.096  -0.005  -0.287  -0.379  -0.245  -0.301  -0.372  -0.247
106   L         0.109   0.168   0.068  -0.008   0.088  -0.105  -0.064   0.026  -0.129
107   G        -0.146  -0.138  -0.070  -0.506  -0.510  -0.417  -0.419  -0.408  -0.328
108   F         0.544   0.542   0.648   0.259   0.223   0.337   0.172   0.150   0.283
109   Y         1.752   1.791   1.915   1.791   1.845   2.036   1.945   2.005   2.206
110   L         0.409   0.400   0.137   0.282   0.251  -0.148   0.408   0.398  -0.014
111   F        -0.462  -0.511  -0.529  -0.631  -0.697  -0.705  -0.537  -0.594  -0.590
112   T         0.109   0.103   0.008  -0.112  -0.159  -0.368  -0.064  -0.100  -0.224
113   I        -0.540  -0.606  -0.554  -0.260  -0.342  -0.258  -0.655  -0.713  -0.621
114   L        -0.223  -0.215  -0.089  -0.697  -0.713  -0.542  -0.537  -0.525  -0.358
115   F         0.487   0.512   0.639   0.345   0.383   0.563   0.054   0.087   0.264
116   G        -0.223  -0.233  -0.104  -0.697  -0.741  -0.560  -0.537  -0.548  -0.378
117   V        -0.027  -0.019  -0.015  -0.383  -0.388  -0.382  -0.301  -0.284  -0.265
118   S        -0.659  -0.592  -0.580  -0.925  -0.848  -0.814  -0.773  -0.696  -0.648
119   G        -0.976  -0.932  -0.965  -0.780  -0.687  -0.770  -0.892  -0.835  -0.824
120   L        -0.976  -0.890  -0.937  -1.130  -1.008  -1.089  -0.892  -0.794  -0.797
121   L        -0.462  -0.465  -0.522  -0.700  -0.721  -0.789  -0.537  -0.557  -0.585
122   G         0.109   0.182   0.056   0.131   0.222   0.063  -0.064   0.033  -0.151
123   L        -0.579  -0.640  -0.581  -0.589  -0.659  -0.577  -0.679  -0.741  -0.648
124   G        -0.659  -0.654  -0.587  -0.557  -0.538  -0.444  -0.773  -0.762  -0.655
125   L        -0.659  -0.583  -0.558  -0.797  -0.713  -0.631  -0.773  -0.683  -0.623
126   T        -0.779  -0.848  -0.941  -0.229  -0.306  -0.486  -0.655  -0.730  -0.798
127   T         0.109   0.100   0.047  -0.025  -0.046  -0.159  -0.064  -0.092  -0.163
128   E        -0.223  -0.178  -0.093  -0.450  -0.403  -0.287  -0.537  -0.477  -0.364
129   K        -0.462  -0.468  -0.535  -0.413  -0.435  -0.480  -0.537  -0.560  -0.600
130   V         0.109   0.105   0.025  -0.146  -0.150  -0.261  -0.064  -0.072  -0.195
131   S        -0.027   0.023  -0.006  -0.202  -0.140  -0.192  -0.301  -0.246  -0.253
132   N        -1.411  -1.415  -1.340  -1.103  -1.137  -1.001  -1.128  -1.124  -0.999
133   W        -0.976  -0.915  -0.976  -1.005  -0.936  -1.014  -0.892  -0.828  -0.838
134   Y        -0.540  -0.606  -0.554  -0.472  -0.574  -0.505  -0.655  -0.713  -0.621
135   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   Q        -0.976  -0.912  -0.966  -0.891  -0.822  -0.826  -0.892  -0.825  -0.829
137   K        -1.411  -1.386  -1.341  -1.221  -1.197  -1.111  -1.128  -1.099  -1.000
138   F        -0.540  -0.500  -0.531  -0.728  -0.681  -0.672  -0.655  -0.611  -0.597
139   S         0.726   0.733   0.722   0.769   0.772   0.708   0.527   0.528   0.436
140   K        -1.411  -1.375  -1.332  -1.333  -1.240  -1.222  -1.128  -1.090  -0.993
141   I        -1.411  -1.374  -1.332  -1.135  -1.117  -1.011  -1.128  -1.089  -0.993
142   T        -0.779  -0.762  -0.636  -1.029  -0.987  -0.830  -0.892  -0.868  -0.706
143   E        -0.462  -0.370  -0.519  -0.099   0.013  -0.135  -0.537  -0.433  -0.576
144   W        -1.292  -1.349  -1.314  -1.159  -1.219  -1.131  -1.010  -1.057  -0.975
145   S        -1.411  -1.371  -1.336  -1.346  -1.311  -1.252  -1.128  -1.087  -0.996
146   I        -0.659  -0.669  -0.588  -1.010  -1.051  -0.907  -0.773  -0.779  -0.658
147   K         1.752   1.791   1.915   1.837   1.887   2.082   1.945   2.005   2.206
148   G         0.109   0.050   0.010  -0.074  -0.183  -0.210  -0.064  -0.166  -0.221
149   S        -1.411  -1.384  -1.339  -1.545  -1.517  -1.455  -1.128  -1.097  -0.998
150   F        -0.976  -0.944  -0.971  -0.669  -0.640  -0.620  -0.892  -0.860  -0.833
151   A         1.064   1.087   0.899   0.898   0.905   0.680   1.118   1.151   0.786
152   Y         0.109   0.027   0.014   0.268   0.185   0.144  -0.064  -0.167  -0.214
153   L         0.109   0.132   0.019   0.118   0.169  -0.093  -0.064  -0.022  -0.202
154   F         1.064   1.087   0.899   1.152   1.182   0.891   1.118   1.151   0.786
155   A        -0.223  -0.199  -0.099  -0.605  -0.569  -0.442  -0.537  -0.504  -0.371
156   I         0.109   0.159   0.084   0.220   0.304   0.192  -0.064   0.021  -0.100
157   H         1.752   1.791   1.915   1.888   1.940   2.135   1.945   2.005   2.206
158   Y        -0.659  -0.608  -0.588  -0.783  -0.734  -0.656  -0.773  -0.717  -0.658
159   G        -0.027  -0.090  -0.003  -0.076  -0.140  -0.029  -0.301  -0.362  -0.248
160   G         0.409   0.400   0.137   0.754   0.752   0.354   0.408   0.398  -0.014
161   A         0.409   0.400   0.137   0.487   0.477   0.049   0.408   0.398  -0.014
162   I         0.544   0.549   0.667   0.372   0.368   0.530   0.172   0.163   0.323
163   R         1.752   1.791   1.915   1.759   1.805   2.003   1.945   2.005   2.206
164   H         1.752   1.791   1.915   1.888   1.940   2.135   1.945   2.005   2.206
165   L         0.409   0.432   0.187   0.302   0.336   0.025   0.408   0.444   0.064
166   I         0.109   0.069   0.032   0.109   0.057  -0.056  -0.064  -0.100  -0.185
167   W         1.064   0.953   0.883   1.358   1.219   1.126   1.118   0.928   0.756
168   D         1.752   1.791   1.915   1.963   2.015   2.211   1.945   2.005   2.206
169   T        -0.027  -0.101  -0.013  -0.187  -0.295  -0.206  -0.301  -0.381  -0.262
170   A        -0.146  -0.126  -0.072  -0.412  -0.388  -0.362  -0.419  -0.391  -0.331
171   K         1.064   0.953   0.883   1.265   1.130   1.031   1.118   0.928   0.756
172   E         1.064   0.953   0.883   1.319   1.180   1.074   1.118   0.928   0.756
173   L         1.064   0.953   0.883   0.859   0.723   0.635   1.118   0.928   0.756
174   T         0.726   0.669   0.696   0.557   0.464   0.460   0.527   0.404   0.383
175   L        -0.462  -0.479  -0.502  -0.622  -0.631  -0.658  -0.537  -0.546  -0.551
176   K         0.409   0.361   0.143   0.675   0.590   0.281   0.408   0.330  -0.005
177   G         1.064   0.953   0.883   1.095   0.953   0.839   1.118   0.928   0.756
178   V         1.064   0.953   0.883   1.118   0.984   0.886   1.118   0.928   0.756
179   Y         1.064   0.953   0.883   1.220   1.089   0.987   1.118   0.928   0.756
180   R         1.064   0.953   0.883   1.202   1.069   0.987   1.118   0.928   0.756
181   T         1.752   1.791   1.915   1.609   1.667   1.850   1.945   2.005   2.206
182   G         1.752   1.791   1.915   1.685   1.733   1.927   1.945   2.005   2.206
183   Y         1.064   0.953   0.883   1.247   1.126   1.047   1.118   0.928   0.756
184   A        -0.779  -0.829  -0.893  -0.775  -0.849  -0.949  -0.655  -0.710  -0.747
185   L         0.409   0.291   0.132   0.509   0.359   0.083   0.408   0.233  -0.020
186   I        -0.208  -0.300  -0.413  -0.242  -0.341  -0.502  -0.182  -0.301  -0.436
187   G         0.487   0.510   0.641   0.056   0.076   0.279   0.054   0.084   0.268
188   F         0.109   0.076   0.023  -0.227  -0.300  -0.384  -0.064  -0.120  -0.202
189   T         0.544   0.542   0.648   0.246   0.237   0.371   0.172   0.150   0.283
190   A         0.109   0.033   0.013  -0.094  -0.202  -0.231  -0.064  -0.157  -0.213
191   V        -0.223  -0.197  -0.085  -0.502  -0.453  -0.324  -0.537  -0.502  -0.352
192   L        -2.044  -2.035  -1.913  -1.908  -1.912  -1.731  -1.364  -1.349  -1.192
193   G         0.409   0.474   0.156   0.498   0.585   0.106   0.408   0.504   0.017
194   T        -0.976  -1.023  -0.988  -1.014  -1.078  -1.073  -0.892  -0.933  -0.849
195   Y         1.064   1.149   0.908   1.213   1.324   1.009   1.118   1.250   0.802
196   L         0.409   0.405   0.149   0.297   0.297  -0.038   0.408   0.405   0.006
197   L        -0.462  -0.433  -0.505  -0.705  -0.663  -0.759  -0.537  -0.491  -0.559
198   T        -0.462  -0.455  -0.534  -0.283  -0.248  -0.352  -0.537  -0.516  -0.593
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   L        -1.095  -1.075  -0.996  -0.822  -0.781  -0.689  -1.010  -0.982  -0.859
* 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/P33421
Output conservation file - output/P33421
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
