1     M         1.260   1.294   1.354   1.489   1.529   1.611   1.341   1.389   1.485
2     G         1.260   1.294   1.354   1.301   1.337   1.436   1.341   1.389   1.485
3     K         1.260   1.294   1.354   1.120   1.164   1.267   1.341   1.389   1.485
4     R         1.260   1.294   1.354   1.377   1.412   1.507   1.341   1.389   1.485
5     K         1.260   1.294   1.354   1.120   1.164   1.267   1.341   1.389   1.485
6     K        -0.449  -0.474  -0.418  -0.785  -0.801  -0.708  -0.682  -0.690  -0.603
7     S         0.599   0.515   0.374   0.403   0.324   0.087   0.596   0.459   0.192
8     T        -0.319  -0.219  -0.375  -0.505  -0.393  -0.543  -0.469  -0.364  -0.542
9     R         0.470   0.412   0.323   0.556   0.464   0.289   0.395   0.289   0.098
10    K        -0.867  -0.831  -0.861  -0.845  -0.802  -0.821  -0.894  -0.825  -0.843
11    P         0.599   0.515   0.374   0.828   0.702   0.470   0.596   0.459   0.192
12    T        -1.360  -1.250  -1.265  -1.056  -0.966  -0.915  -1.214  -1.111  -1.054
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    K         0.599   0.466   0.354   0.588   0.427   0.288   0.596   0.380   0.155
15    R         0.045   0.096   0.204  -0.160  -0.082   0.082  -0.362  -0.284  -0.127
16    L        -1.057  -0.943  -0.920  -0.856  -0.733  -0.678  -1.107  -0.991  -0.909
17    V        -0.942  -1.024  -0.909  -0.942  -1.056  -0.865  -1.001  -1.048  -0.896
18    Q        -0.030  -0.248  -0.348   0.238  -0.081  -0.281  -0.043  -0.345  -0.498
19    K        -1.057  -0.979  -0.925  -0.976  -0.855  -0.746  -1.107  -1.021  -0.915
20    L         1.260   1.294   1.354   1.320   1.363   1.454   1.341   1.389   1.485
21    D        -0.030  -0.152  -0.340  -0.127  -0.270  -0.499  -0.043  -0.218  -0.487
22    T         0.599   0.678   0.385   0.826   0.925   0.538   0.596   0.709   0.213
23    K        -1.664  -1.516  -1.585  -1.342  -1.130  -1.325  -1.320  -1.180  -1.178
24    F         1.260   1.294   1.354   1.406   1.451   1.533   1.341   1.389   1.485
25    N        -0.942  -0.834  -0.883  -0.815  -0.647  -0.767  -1.001  -0.859  -0.869
26    C         1.260   1.294   1.354   1.330   1.369   1.463   1.341   1.389   1.485
27    L         1.260   1.294   1.354   1.320   1.363   1.454   1.341   1.389   1.485
28    F         1.260   1.294   1.354   1.406   1.451   1.533   1.341   1.389   1.485
29    C         1.260   1.294   1.354   1.330   1.369   1.463   1.341   1.389   1.485
30    N         1.260   1.294   1.354   1.340   1.387   1.472   1.341   1.389   1.485
31    H         1.260   1.294   1.354   1.448   1.489   1.572   1.341   1.389   1.485
32    E         0.599   0.626   0.370   0.589   0.646   0.298   0.596   0.632   0.185
33    K        -0.319  -0.334  -0.401  -0.401  -0.435  -0.546  -0.469  -0.499  -0.578
34    S         1.260   1.294   1.354   0.978   1.055   1.135   1.341   1.389   1.485
35    V         1.260   1.294   1.354   1.287   1.321   1.423   1.341   1.389   1.485
36    S        -0.449  -0.419  -0.416  -0.641  -0.560  -0.523  -0.682  -0.640  -0.600
37    C         0.274   0.251   0.234   0.335   0.275   0.217   0.063   0.007  -0.068
38    T        -0.319  -0.460  -0.420  -0.287  -0.540  -0.570  -0.469  -0.655  -0.603
39    L        -0.319  -0.217  -0.371  -0.093   0.034  -0.159  -0.469  -0.327  -0.535
40    D         1.260   1.294   1.354   0.947   1.010   1.106   1.341   1.389   1.485
41    K         1.260   1.294   1.354   1.120   1.164   1.267   1.341   1.389   1.485
42    K         0.599   0.515   0.374   0.582   0.484   0.303   0.596   0.459   0.192
43    N        -0.623  -0.811  -0.876  -0.300  -0.602  -0.722  -0.575  -0.799  -0.859
44    S        -1.360  -1.108  -1.249  -1.241  -0.861  -1.068  -1.214  -0.946  -1.038
45    I        -0.563  -0.562  -0.459  -0.481  -0.521  -0.377  -0.788  -0.792  -0.652
46    G         1.260   1.294   1.354   1.301   1.337   1.436   1.341   1.389   1.485
47    T        -1.779  -1.704  -1.603  -1.622  -1.487  -1.312  -1.427  -1.346  -1.192
48    L         1.260   1.294   1.354   1.320   1.363   1.454   1.341   1.389   1.485
49    S        -0.449  -0.477  -0.409  -0.562  -0.562  -0.544  -0.682  -0.681  -0.589
50    C         1.260   1.294   1.354   1.330   1.369   1.463   1.341   1.389   1.485
51    K         1.260   1.294   1.354   1.120   1.164   1.267   1.341   1.389   1.485
52    I         0.599   0.626   0.370   0.823   0.855   0.493   0.596   0.632   0.185
53    C         1.260   1.294   1.354   1.330   1.369   1.463   1.341   1.389   1.485
54    G         1.260   1.294   1.354   1.301   1.337   1.436   1.341   1.389   1.485
55    Q         1.260   1.294   1.354   1.363   1.408   1.494   1.341   1.389   1.485
56    S         0.599   0.466   0.354   0.403   0.255   0.054   0.596   0.380   0.155
57    F         0.599   0.515   0.374   0.878   0.782   0.581   0.596   0.459   0.192
58    Q         1.260   1.294   1.354   1.363   1.408   1.494   1.341   1.389   1.485
59    T        -0.319  -0.391  -0.419  -0.134  -0.285  -0.321  -0.469  -0.594  -0.603
60    R        -1.360  -1.432  -1.302  -1.107  -1.233  -1.077  -1.214  -1.249  -1.084
61    I         0.599   0.466   0.354   0.823   0.649   0.466   0.596   0.380   0.155
62    N        -0.319  -0.339  -0.376  -0.093  -0.107  -0.174  -0.469  -0.478  -0.539
63    S        -0.867  -0.914  -0.899  -0.950  -1.001  -0.906  -0.894  -0.948  -0.887
64    L         1.260   1.294   1.354   1.320   1.363   1.454   1.341   1.389   1.485
65    S         0.599   0.466   0.354   0.377   0.220  -0.013   0.596   0.380   0.155
66    Q         0.100   0.093   0.204   0.049  -0.030   0.155  -0.256  -0.289  -0.127
67    P         0.599   0.466   0.354   0.847   0.652   0.481   0.596   0.380   0.155
68    V         0.274   0.242   0.240   0.321   0.252   0.238   0.063  -0.010  -0.058
69    D         1.260   1.294   1.354   0.947   1.010   1.106   1.341   1.389   1.485
70    V         0.599   0.669   0.386   0.750   0.824   0.471   0.596   0.696   0.213
71    Y         1.260   1.294   1.354   1.434   1.464   1.559   1.341   1.389   1.485
72    S         1.260   1.294   1.354   0.978   1.055   1.135   1.341   1.389   1.485
73    D        -0.030  -0.152  -0.340  -0.176  -0.333  -0.611  -0.043  -0.218  -0.487
74    W         1.260   1.294   1.354   1.503   1.542   1.624   1.341   1.389   1.485
75    F        -0.449  -0.455  -0.406  -0.305  -0.293  -0.241  -0.682  -0.647  -0.582
76    D         1.260   1.294   1.354   0.947   1.010   1.106   1.341   1.389   1.485
77    A         1.260   1.294   1.354   1.258   1.260   1.396   1.341   1.389   1.485
78    V        -0.449  -0.455  -0.406  -0.416  -0.412  -0.342  -0.682  -0.647  -0.582
79    E         0.274   0.172   0.226   0.031  -0.176  -0.150   0.063  -0.140  -0.085
80    E        -0.638  -0.527  -0.438  -0.978  -0.788  -0.669  -0.894  -0.740  -0.623
81    V         0.274   0.357   0.292   0.304   0.410   0.302   0.063   0.194   0.042
82    N         0.100   0.250   0.263   0.000   0.195   0.237  -0.256   0.004  -0.013
83    S        -0.867  -0.922  -0.875  -0.948  -0.929  -0.914  -0.894  -0.925  -0.858
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    G        -0.449  -0.420  -0.389  -0.547  -0.466  -0.419  -0.682  -0.603  -0.559
86    R        -0.563  -0.385  -0.421  -0.623  -0.404  -0.453  -0.788  -0.540  -0.601
87    G        -1.360  -1.267  -1.267  -1.229  -1.112  -1.079  -1.214  -1.094  -1.052
88    S        -1.057  -1.070  -0.927  -1.364  -1.360  -1.133  -1.107  -1.096  -0.916
89    D        -1.664  -1.669  -1.593  -1.673  -1.694  -1.534  -1.320  -1.309  -1.184
90    T        -1.475  -1.398  -1.298  -1.666  -1.570  -1.377  -1.320  -1.229  -1.081
91    D        -1.360  -1.315  -1.280  -1.342  -1.268  -1.249  -1.214  -1.163  -1.066
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    D        -1.171  -1.286  -1.271  -1.112  -1.261  -1.162  -1.001  -1.111  -1.056
97    E        -1.171  -1.286  -1.271  -0.923  -1.090  -1.022  -1.001  -1.111  -1.056
98    G        -1.360  -1.341  -1.282  -1.402  -1.434  -1.356  -1.214  -1.173  -1.066
99    S        -1.664  -1.709  -1.609  -1.595  -1.581  -1.456  -1.320  -1.339  -1.196
100   D        -0.030  -0.248  -0.348  -0.226  -0.528  -0.743  -0.043  -0.345  -0.498
101   S        -1.360  -1.365  -1.288  -1.352  -1.315  -1.167  -1.214  -1.198  -1.072
102   D        -1.057  -1.085  -0.930  -1.224  -1.232  -0.995  -1.107  -1.110  -0.918
103   Y        -0.867  -0.928  -0.901  -0.709  -0.835  -0.853  -0.894  -0.957  -0.890
104   E        -1.327  -1.390  -1.304  -1.361  -1.526  -1.392  -1.162  -1.211  -1.085
105   S        -0.136  -0.269  -0.372  -0.247  -0.393  -0.530  -0.189  -0.385  -0.531
106   D         0.541   0.372   0.319   0.302   0.084   0.018   0.507   0.221   0.091
107   S        -0.980  -1.025  -0.924  -1.414  -1.438  -1.299  -1.023  -1.055  -0.911
108   E        -0.980  -1.005  -0.914  -1.216  -1.192  -1.037  -1.023  -1.029  -0.902
109   Q        -1.805  -1.713  -1.604  -1.299  -1.169  -1.055  -1.440  -1.347  -1.192
110   D        -1.327  -1.166  -1.245  -1.195  -0.984  -1.152  -1.162  -0.987  -1.031
111   A        -0.406  -0.366  -0.415  -0.248  -0.241  -0.275  -0.567  -0.515  -0.591
112   K        -1.076  -0.914  -0.911  -1.283  -1.043  -1.030  -1.112  -0.924  -0.897
113   T        -1.076  -0.914  -0.911  -1.128  -0.924  -0.868  -1.112  -0.924  -0.897
114   Q        -0.590  -0.588  -0.451  -0.539  -0.548  -0.361  -0.839  -0.822  -0.641
115   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -         0.470   0.411   0.329   0.614   0.510   0.331   0.395   0.288   0.111
153   E        -1.171  -1.191  -1.262  -1.002  -1.041  -1.138  -1.001  -1.016  -1.047
154   V        -1.360  -1.317  -1.279  -1.238  -1.192  -1.190  -1.214  -1.151  -1.064
155   D        -0.449  -0.487  -0.410  -0.837  -0.847  -0.710  -0.682  -0.711  -0.594
156   S        -0.623  -0.811  -0.876  -0.673  -0.896  -1.023  -0.575  -0.799  -0.859
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   D         1.260   1.294   1.354   0.920   0.976   1.081   1.341   1.389   1.485
159   E         0.470   0.511   0.305   0.323   0.381   0.005   0.395   0.452   0.066
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   D        -0.136  -0.233  -0.344  -0.283  -0.391  -0.549  -0.189  -0.326  -0.491
176   S        -0.416  -0.505  -0.429  -0.859  -0.978  -0.909  -0.606  -0.721  -0.616
177   D         0.274   0.262   0.252  -0.092  -0.101  -0.148   0.063   0.026  -0.035
178   D        -1.664  -1.665  -1.591  -1.626  -1.591  -1.473  -1.320  -1.307  -1.183
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   E        -0.623  -0.655  -0.843  -0.494  -0.566  -0.806  -0.575  -0.619  -0.821
* 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/P36053
Output conservation file - output/P36053
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
