1     -         1.621   1.672   1.784   1.819   1.893   2.075   1.783   1.859   2.059
2     -        -0.379  -0.540  -0.424  -0.300  -0.610  -0.478  -0.491  -0.715  -0.567
3     -        -1.183  -1.219  -1.038  -1.307  -1.351  -1.053  -1.141  -1.170  -0.942
4     -        -0.599  -0.473  -0.419  -0.948  -0.774  -0.686  -0.816  -0.639  -0.563
5     -        -0.379  -0.540  -0.424  -0.445  -0.711  -0.556  -0.491  -0.715  -0.567
6     -        -1.183  -1.219  -1.038  -1.228  -1.277  -1.027  -1.141  -1.170  -0.942
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    -         0.568   0.746   0.526   0.773   1.027   0.665   0.483   0.766   0.354
13    -        -0.379  -0.540  -0.424  -0.588  -0.887  -0.737  -0.491  -0.715  -0.567
14    -        -0.379  -0.097  -0.331  -0.495  -0.069  -0.470  -0.491  -0.094  -0.436
15    -        -1.183  -1.193  -1.031  -1.262  -1.289  -1.059  -1.141  -1.146  -0.934
16    -        -0.379  -0.540  -0.424  -0.177  -0.471  -0.340  -0.491  -0.715  -0.567
17    -         0.568   0.680   0.514   0.493   0.662   0.426   0.483   0.661   0.332
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -0.379  -0.540  -0.424  -0.056  -0.308  -0.142  -0.491  -0.715  -0.567
63    M        -2.150  -2.040  -1.877  -1.827  -1.696  -1.454  -1.601  -1.496  -1.286
64    V        -1.664  -1.532  -1.460  -1.649  -1.374  -1.375  -1.375  -1.241  -1.115
65    T        -0.430  -0.355  -0.374  -0.451  -0.276  -0.297  -0.628  -0.549  -0.513
66    T        -0.430  -0.260  -0.350  -0.537  -0.288  -0.393  -0.628  -0.411  -0.481
67    L        -1.297  -1.218  -1.036  -1.631  -1.537  -1.268  -1.263  -1.168  -0.940
68    T         0.229   0.229   0.370   0.042  -0.033   0.187  -0.121  -0.141   0.055
69    P         1.621   1.672   1.784   1.627   1.685   1.889   1.783   1.859   2.059
70    V        -0.274  -0.420  -0.380  -0.407  -0.624  -0.529  -0.374  -0.561  -0.511
71    I        -1.524  -1.338  -1.428  -1.311  -0.997  -1.135  -1.263  -1.059  -1.086
72    C        -0.430  -0.333  -0.368  -0.469  -0.335  -0.304  -0.628  -0.512  -0.503
73    E        -2.026  -2.029  -1.832  -2.045  -1.981  -1.714  -1.516  -1.491  -1.255
74    S        -1.524  -1.348  -1.428  -1.363  -1.082  -1.198  -1.263  -1.065  -1.087
75    A         0.438   0.425   0.437   0.091   0.064   0.073   0.260   0.222   0.187
76    P         0.673   0.565   0.502   0.688   0.491   0.343   0.655   0.469   0.309
77    A        -0.932  -0.993  -0.976  -0.945  -1.054  -1.090  -0.882  -0.948  -0.878
78    A        -0.932  -0.890  -0.942  -0.910  -0.796  -0.904  -0.882  -0.801  -0.839
79    A         0.073  -0.139  -0.282  -0.037  -0.352  -0.535   0.133  -0.153  -0.367
80    A         0.229   0.233   0.375  -0.180  -0.203   0.070  -0.121  -0.133   0.067
81    S        -0.430  -0.516  -0.402  -0.656  -0.770  -0.625  -0.628  -0.711  -0.545
82    Y         1.621   1.672   1.784   1.799   1.864   2.055   1.783   1.859   2.059
83    S         0.438   0.425   0.437   0.296   0.310   0.266   0.260   0.222   0.187
84    H         0.229   0.305   0.397   0.303   0.416   0.552  -0.121   0.004   0.108
85    A         1.621   1.672   1.784   1.317   1.382   1.589   1.783   1.859   2.059
86    M        -0.567  -0.538  -0.421  -0.705  -0.723  -0.528  -0.755  -0.723  -0.565
87    K         1.621   1.672   1.784   1.552   1.634   1.817   1.783   1.859   2.059
88    V        -0.932  -1.059  -0.987  -1.143  -1.390  -1.240  -0.882  -1.012  -0.892
89    N        -0.274  -0.400  -0.374  -0.192  -0.396  -0.342  -0.374  -0.559  -0.508
90    N        -0.274  -0.193  -0.317  -0.198  -0.091  -0.320  -0.374  -0.236  -0.420
91    L        -1.021  -1.022  -0.964  -1.043  -1.013  -1.004  -1.009  -0.987  -0.870
92    I         0.828   0.693   0.571   0.884   0.719   0.529   0.894   0.682   0.437
93    F         0.438   0.463   0.418   0.617   0.654   0.544   0.260   0.291   0.149
94    L        -0.430  -0.354  -0.382  -0.512  -0.422  -0.395  -0.628  -0.548  -0.522
95    S         1.621   1.672   1.784   1.509   1.620   1.775   1.783   1.859   2.059
96    G         1.621   1.672   1.784   1.706   1.743   1.965   1.783   1.859   2.059
97    Q         1.621   1.672   1.784   1.757   1.825   2.016   1.783   1.859   2.059
98    I         0.073  -0.139  -0.282   0.147  -0.178  -0.465   0.133  -0.153  -0.367
99    P         0.828   0.773   0.584   0.913   0.827   0.525   0.894   0.808   0.462
100   V        -1.021  -1.101  -0.973  -0.942  -1.075  -0.839  -1.009  -1.054  -0.876
101   T        -0.205  -0.463  -0.398   0.064  -0.353  -0.273  -0.248  -0.609  -0.531
102   P        -0.932  -0.942  -0.953  -0.935  -0.955  -1.043  -0.882  -0.876  -0.858
103   D         0.073   0.049  -0.252   0.435   0.403  -0.041   0.133   0.106  -0.325
104   N         0.162   0.244   0.390  -0.029   0.101   0.339  -0.248  -0.112   0.095
105   K        -0.274  -0.444  -0.372  -0.309  -0.546  -0.482  -0.374  -0.598  -0.503
106   L        -1.524  -1.623  -1.464  -1.414  -1.550  -1.352  -1.263  -1.327  -1.120
107   V        -0.932  -0.937  -0.941  -0.969  -0.940  -0.920  -0.882  -0.856  -0.837
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   E        -0.638  -0.503  -0.867  -0.365  -0.203  -0.728  -0.501  -0.337  -0.751
111   G         0.073   0.318  -0.231   0.324   0.605  -0.164   0.133   0.465  -0.295
112   S         0.162   0.208   0.370  -0.082   0.005   0.245  -0.248  -0.182   0.055
113   I         0.073  -0.050  -0.270   0.188   0.021  -0.347   0.133  -0.036  -0.350
114   A        -1.524  -1.287  -1.417  -1.408  -1.012  -1.255  -1.263  -1.009  -1.078
115   D         0.162   0.227   0.375   0.032   0.097   0.352  -0.248  -0.146   0.066
116   K        -0.430  -0.287  -0.356  -0.398  -0.201  -0.236  -0.628  -0.449  -0.485
117   A         0.162   0.244   0.390  -0.220  -0.040   0.190  -0.248  -0.112   0.095
118   E        -0.932  -1.086  -0.999  -0.813  -1.064  -0.988  -0.882  -1.036  -0.903
119   Q         0.073  -0.042  -0.254   0.367   0.208  -0.178   0.133  -0.018  -0.327
120   V        -0.932  -0.912  -0.958  -0.914  -0.903  -0.923  -0.882  -0.859  -0.860
121   I         0.438   0.381   0.404   0.332   0.233   0.223   0.260   0.143   0.122
122   Q        -0.932  -1.013  -0.989  -0.711  -0.882  -0.855  -0.882  -0.975  -0.894
123   N         1.621   1.672   1.784   1.616   1.711   1.879   1.783   1.859   2.059
124   I        -0.430  -0.251  -0.355  -0.685  -0.365  -0.525  -0.628  -0.374  -0.479
125   K        -1.159  -1.090  -0.985  -1.278  -1.151  -1.031  -1.136  -1.030  -0.890
126   N        -0.274  -0.336  -0.366  -0.275  -0.374  -0.478  -0.374  -0.457  -0.491
127   V         0.162   0.209   0.369  -0.276  -0.239   0.046  -0.248  -0.179   0.055
128   L         0.828   0.693   0.571   0.889   0.747   0.532   0.894   0.682   0.437
129   E        -1.297  -1.366  -1.415  -0.950  -1.089  -1.149  -1.009  -1.076  -1.073
130   A        -0.932  -0.935  -0.962  -1.100  -1.169  -1.093  -0.882  -0.897  -0.867
131   S         0.162   0.244   0.390  -0.396  -0.265  -0.042  -0.248  -0.112   0.095
132   N         0.162   0.244   0.390  -0.029   0.101   0.339  -0.248  -0.112   0.095
133   S         1.621   1.672   1.784   1.509   1.620   1.775   1.783   1.859   2.059
134   S         0.828   0.996   0.605   0.860   1.099   0.604   0.894   1.139   0.499
135   L         0.073  -0.112  -0.280   0.283   0.094  -0.159   0.133  -0.118  -0.365
136   D        -1.159  -1.104  -1.004  -1.098  -1.034  -0.867  -1.136  -1.082  -0.910
137   R        -0.567  -0.350  -0.377  -0.503  -0.187  -0.218  -0.755  -0.448  -0.502
138   V        -0.274  -0.316  -0.335  -0.362  -0.426  -0.492  -0.374  -0.417  -0.452
139   V         1.621   1.672   1.784   1.422   1.465   1.691   1.783   1.859   2.059
140   K         1.621   1.672   1.784   1.552   1.634   1.817   1.783   1.859   2.059
141   V         0.438   0.612   0.497   0.111   0.361   0.159   0.260   0.547   0.300
142   N         0.828   0.693   0.571   0.962   0.822   0.639   0.894   0.682   0.437
143   I         0.828   0.803   0.582   0.849   0.819   0.460   0.894   0.856   0.458
144   F         0.828   0.693   0.571   1.106   0.978   0.784   0.894   0.682   0.437
145   L         0.828   0.693   0.571   0.869   0.712   0.481   0.894   0.682   0.437
146   A         0.229   0.331   0.398  -0.012   0.168   0.215  -0.121   0.051   0.111
147   D         1.621   1.672   1.784   1.768   1.833   2.026   1.783   1.859   2.059
148   I         0.438   0.463   0.418   0.573   0.644   0.459   0.260   0.291   0.149
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   N        -2.026  -1.975  -1.857  -1.762  -1.670  -1.554  -1.516  -1.454  -1.273
151   H        -1.661  -1.637  -1.475  -1.337  -1.314  -1.065  -1.390  -1.343  -1.129
152   F         1.621   1.672   1.784   1.752   1.856   2.011   1.783   1.859   2.059
153   A        -0.274  -0.188  -0.354  -0.476  -0.405  -0.545  -0.374  -0.283  -0.480
154   E        -0.430  -0.331  -0.380  -0.648  -0.593  -0.534  -0.628  -0.526  -0.519
155   F        -0.932  -1.058  -0.994  -0.666  -0.824  -0.811  -0.882  -1.013  -0.899
156   N         1.621   1.672   1.784   1.616   1.711   1.879   1.783   1.859   2.059
157   S        -1.021  -0.845  -0.946  -1.060  -0.805  -0.936  -1.009  -0.814  -0.852
158   V         0.828   0.803   0.582   0.753   0.699   0.442   0.894   0.856   0.458
159   Y         1.621   1.672   1.784   1.799   1.864   2.055   1.783   1.859   2.059
160   A        -1.297  -1.304  -1.403  -1.277  -1.310  -1.402  -1.009  -1.006  -1.061
161   K         0.438   0.425   0.437   0.344   0.315   0.314   0.260   0.222   0.187
162   Y        -0.638  -0.739  -0.918  -0.122  -0.243  -0.518  -0.501  -0.612  -0.809
163   F         0.438   0.425   0.437   0.515   0.519   0.451   0.260   0.222   0.187
164   N        -1.661  -1.681  -1.486  -1.547  -1.510  -1.248  -1.390  -1.372  -1.139
165   T        -1.641  -1.568  -1.483  -1.393  -1.296  -1.177  -1.366  -1.282  -1.135
166   H         0.438   0.425   0.437   0.671   0.638   0.601   0.260   0.222   0.187
167   K         0.073  -0.139  -0.282   0.289   0.070  -0.128   0.133  -0.153  -0.367
168   P         0.828   0.693   0.571   0.913   0.711   0.499   0.894   0.682   0.437
169   A         1.621   1.672   1.784   1.317   1.382   1.589   1.783   1.859   2.059
170   R         1.621   1.672   1.784   1.834   1.960   2.090   1.783   1.859   2.059
171   S         0.438   0.337   0.402   0.336   0.201   0.272   0.260   0.063   0.118
172   C         0.438   0.337   0.402   0.690   0.498   0.570   0.260   0.063   0.118
173   V         0.828   0.693   0.571   0.742   0.542   0.395   0.894   0.682   0.437
174   A         0.828   0.693   0.571   0.658   0.483   0.352   0.894   0.682   0.437
175   V         0.828   0.773   0.584   0.706   0.604   0.330   0.894   0.808   0.462
176   A        -1.021  -1.071  -0.966  -1.189  -1.248  -1.022  -1.009  -1.029  -0.872
177   A        -1.297  -1.304  -1.404  -1.229  -1.257  -1.327  -1.009  -1.006  -1.063
178   L         0.073   0.022  -0.273   0.193   0.151  -0.349   0.133   0.067  -0.354
179   P         1.621   1.672   1.784   1.627   1.685   1.889   1.783   1.859   2.059
180   L         0.828   0.803   0.582   0.887   0.895   0.548   0.894   0.856   0.458
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   G         1.621   1.672   1.784   1.706   1.743   1.965   1.783   1.859   2.059
185   V         0.073  -0.139  -0.282   0.127  -0.164  -0.311   0.133  -0.153  -0.367
186   D        -0.932  -0.972  -0.972  -0.681  -0.768  -0.753  -0.882  -0.929  -0.874
187   M        -1.159  -1.119  -1.019  -1.284  -1.274  -1.061  -1.136  -1.093  -0.924
188   E         1.621   1.672   1.784   1.637   1.688   1.899   1.783   1.859   2.059
189   M         0.162   0.208   0.370   0.013   0.099   0.323  -0.248  -0.182   0.055
190   E         0.828   0.693   0.571   0.987   0.807   0.669   0.894   0.682   0.437
191   A        -0.657  -0.616  -0.454  -0.903  -0.833  -0.625  -0.882  -0.820  -0.609
192   I         0.438   0.429   0.413   0.285   0.241   0.160   0.260   0.230   0.139
193   A         0.828   0.693   0.571   0.615   0.421   0.242   0.894   0.682   0.437
194   A        -1.159  -0.992  -0.982  -1.360  -1.106  -1.093  -1.136  -0.950  -0.886
195   E         0.828   0.803   0.582   0.967   0.922   0.638   0.894   0.856   0.458
196   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P40037
Output conservation file - output/P40037
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
