1     M         1.481   1.485   1.545   1.915   1.919   1.969   1.584   1.588   1.674
2     S         0.434   0.415   0.247   0.713   0.690   0.442   0.386   0.356   0.070
3     D         0.072   0.066   0.125  -0.647  -0.688  -0.595  -0.213  -0.225  -0.142
4     E         0.434   0.405   0.263  -0.001  -0.038  -0.155   0.386   0.341   0.098
5     A        -1.888  -1.872  -1.769  -1.752  -1.747  -1.548  -1.411  -1.392  -1.252
6     K         0.304   0.295   0.219   0.349   0.350   0.271   0.180   0.166   0.022
7     -        -0.819  -0.810  -0.717  -0.662  -0.652  -0.502  -0.912  -0.898  -0.764
8     -        -0.819  -0.810  -0.717  -0.570  -0.561  -0.414  -0.912  -0.898  -0.764
9     -         0.149   0.149   0.167   0.138   0.135   0.071  -0.080  -0.080  -0.067
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -         0.149   0.144   0.162   0.642   0.633   0.647  -0.080  -0.089  -0.077
12    -        -0.819  -0.810  -0.717  -0.293  -0.277  -0.148  -0.912  -0.898  -0.764
13    -         1.481   1.485   1.545   1.778   1.780   1.838   1.584   1.588   1.674
14    E         0.434   0.415   0.247   0.003  -0.023  -0.164   0.386   0.356   0.070
15    K        -1.308  -1.320  -1.274  -0.999  -0.983  -0.885  -1.112  -1.120  -1.035
16    R        -0.508  -0.451  -0.609  -0.632  -0.554  -0.813  -0.513  -0.439  -0.629
17    E         0.072   0.073   0.125  -0.305  -0.294  -0.140  -0.213  -0.213  -0.141
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    L        -0.695  -0.626  -0.666  -0.042   0.061   0.002  -0.756  -0.665  -0.701
22    E        -1.421  -1.404  -1.310  -1.416  -1.308  -1.225  -1.224  -1.203  -1.069
23    S        -1.308  -1.277  -1.272  -0.654  -0.600  -0.591  -1.112  -1.077  -1.033
24    Q        -0.508  -0.451  -0.609  -0.917  -0.873  -0.975  -0.513  -0.439  -0.629
25    K        -0.508  -0.537  -0.630  -0.360  -0.378  -0.464  -0.513  -0.549  -0.655
26    E        -0.727  -0.727  -0.681  -0.996  -0.950  -0.852  -0.812  -0.806  -0.724
27    S        -0.727  -0.728  -0.680  -0.929  -0.955  -0.807  -0.812  -0.808  -0.722
28    S        -0.508  -0.459  -0.595   0.063   0.139  -0.081  -0.513  -0.450  -0.611
29    H        -1.421  -1.409  -1.310  -1.155  -1.124  -0.975  -1.224  -1.208  -1.069
30    N        -0.695  -0.715  -0.682  -0.575  -0.622  -0.631  -0.756  -0.779  -0.720
31    K        -1.421  -1.409  -1.310  -0.928  -0.893  -0.757  -1.224  -1.208  -1.069
32    S        -0.695  -0.695  -0.677  -0.713  -0.681  -0.740  -0.756  -0.754  -0.714
33    E         0.030   0.038   0.118  -0.764  -0.724  -0.583  -0.288  -0.274  -0.153
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    K         0.304   0.340   0.230   0.553   0.606   0.389   0.180   0.238   0.041
38    S         0.030   0.037   0.117   0.134   0.181   0.261  -0.288  -0.277  -0.155
39    V        -0.695  -0.715  -0.682  -0.062  -0.060  -0.046  -0.756  -0.779  -0.720
40    E         1.481   1.485   1.545   0.772   0.777   0.874   1.584   1.588   1.674
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    -        -0.695  -0.682  -0.666  -0.275  -0.238  -0.259  -0.756  -0.736  -0.700
58    -        -1.421  -1.411  -1.310  -1.392  -1.356  -1.202  -1.224  -1.209  -1.069
59    -        -0.695  -0.678  -0.674  -0.568  -0.550  -0.492  -0.756  -0.731  -0.711
60    P        -1.888  -1.872  -1.769  -1.407  -1.394  -1.216  -1.411  -1.392  -1.252
61    K        -0.508  -0.537  -0.630  -0.663  -0.701  -0.897  -0.513  -0.549  -0.655
62    P         0.434   0.525   0.272   0.482   0.602   0.317   0.386   0.525   0.113
63    K         1.481   1.485   1.545   1.317   1.336   1.396   1.584   1.588   1.674
64    R         0.434   0.525   0.272   0.437   0.562   0.244   0.386   0.525   0.113
65    R         0.434   0.405   0.263   0.875   0.841   0.673   0.386   0.341   0.098
66    R         1.481   1.485   1.545   1.701   1.702   1.764   1.584   1.588   1.674
67    R         1.481   1.485   1.545   1.701   1.702   1.764   1.584   1.588   1.674
68    R         1.481   1.485   1.545   1.701   1.702   1.764   1.584   1.588   1.674
69    N         0.434   0.405   0.263   0.930   0.906   0.705   0.386   0.341   0.098
70    Y         1.481   1.485   1.545   1.902   1.906   1.957   1.584   1.588   1.674
71    D         1.481   1.485   1.545   1.212   1.206   1.296   1.584   1.588   1.674
72    D         0.434   0.442   0.252   0.116   0.117  -0.256   0.386   0.398   0.078
73    Y        -0.695  -0.731  -0.684  -0.375  -0.447  -0.425  -0.756  -0.800  -0.723
74    D         1.481   1.485   1.545   1.207   1.204   1.291   1.584   1.588   1.674
75    A        -0.695  -0.731  -0.684  -0.861  -0.953  -0.927  -0.756  -0.800  -0.723
76    E        -0.508  -0.546  -0.624  -1.151  -1.220  -1.326  -0.513  -0.560  -0.647
77    V        -0.727  -0.730  -0.685  -0.149  -0.147  -0.078  -0.812  -0.810  -0.728
78    A        -1.308  -1.324  -1.272  -0.973  -0.974  -0.922  -1.112  -1.124  -1.033
79    K        -0.508  -0.537  -0.630  -0.572  -0.599  -0.763  -0.513  -0.549  -0.655
80    E         0.434   0.417   0.257  -0.039  -0.064  -0.225   0.386   0.359   0.087
81    E         0.304   0.259   0.209  -0.357  -0.449  -0.510   0.180   0.106   0.006
82    T        -0.695  -0.648  -0.674  -0.603  -0.534  -0.528  -0.756  -0.695  -0.711
83    K         0.304   0.259   0.209   0.247   0.198   0.121   0.180   0.106   0.006
84    A        -1.421  -1.404  -1.310  -1.617  -1.599  -1.418  -1.224  -1.203  -1.069
85    K        -0.695  -0.717  -0.682  -0.661  -0.671  -0.601  -0.756  -0.782  -0.720
86    N        -0.695  -0.717  -0.682  -0.346  -0.366  -0.353  -0.756  -0.782  -0.720
87    G        -0.819  -0.808  -0.717  -0.407  -0.398  -0.258  -0.912  -0.896  -0.764
88    L        -0.819  -0.808  -0.717  -0.447  -0.429  -0.296  -0.912  -0.896  -0.764
89    T        -0.727  -0.729  -0.676  -0.622  -0.628  -0.590  -0.812  -0.810  -0.718
90    K        -0.508  -0.537  -0.630  -0.358  -0.369  -0.461  -0.513  -0.549  -0.655
91    S        -0.508  -0.518  -0.630  -0.185  -0.200  -0.377  -0.513  -0.524  -0.656
92    E         0.434   0.417   0.257   0.003  -0.021  -0.155   0.386   0.359   0.087
93    N        -0.695  -0.735  -0.682  -0.511  -0.595  -0.557  -0.756  -0.805  -0.720
94    N         0.149   0.132   0.154   0.450   0.420   0.425  -0.080  -0.109  -0.090
95    G         0.149   0.136   0.152   0.112   0.073  -0.000  -0.080  -0.103  -0.093
96    T        -0.819  -0.806  -0.717  -1.008  -1.020  -0.834  -0.912  -0.894  -0.764
97    V        -0.819  -0.806  -0.717  -0.373  -0.361  -0.224  -0.912  -0.894  -0.764
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   E        -0.508  -0.516  -0.617  -1.022  -1.040  -1.129  -0.513  -0.522  -0.639
103   D         0.434   0.405   0.263   0.116   0.054  -0.230   0.386   0.341   0.098
104   S        -0.508  -0.525  -0.625  -0.488  -0.537  -0.809  -0.513  -0.533  -0.649
105   E         0.434   0.442   0.252  -0.158  -0.154  -0.439   0.386   0.398   0.078
106   S        -0.508  -0.525  -0.625  -0.488  -0.530  -0.809  -0.513  -0.533  -0.649
107   D        -0.508  -0.546  -0.624  -0.720  -0.793  -0.907  -0.513  -0.560  -0.647
108   M        -1.308  -1.277  -1.272  -1.152  -1.137  -0.956  -1.112  -1.077  -1.033
109   D         0.434   0.405   0.263   0.116   0.054  -0.230   0.386   0.341   0.098
110   D         0.434   0.405   0.263   0.116   0.054  -0.230   0.386   0.341   0.098
111   A        -1.308  -1.325  -1.280  -1.255  -1.291  -1.267  -1.112  -1.125  -1.041
112   K        -0.508  -0.525  -0.625  -0.265  -0.264  -0.329  -0.513  -0.533  -0.649
113   L         0.072   0.070   0.127  -0.065  -0.089  -0.058  -0.213  -0.218  -0.139
114   D         0.434   0.442   0.252   0.378   0.381   0.200   0.386   0.398   0.078
115   A        -1.888  -1.872  -1.769  -1.009  -0.966  -0.835  -1.411  -1.392  -1.252
116   L        -0.508  -0.518  -0.630   0.047   0.042  -0.150  -0.513  -0.524  -0.656
117   M        -0.695  -0.701  -0.674  -0.354  -0.362  -0.382  -0.756  -0.761  -0.711
118   G        -1.308  -1.320  -1.274  -0.933  -0.951  -0.910  -1.112  -1.120  -1.035
119   N        -1.308  -1.325  -1.280  -0.913  -0.934  -0.909  -1.112  -1.125  -1.041
120   E         1.481   1.485   1.545   0.866   0.865   0.964   1.584   1.588   1.674
121   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   E         0.072   0.066   0.125  -0.762  -0.784  -0.644  -0.213  -0.225  -0.142
123   E         0.434   0.405   0.263   0.003  -0.034  -0.148   0.386   0.341   0.098
124   E         1.481   1.485   1.545   0.866   0.865   0.964   1.584   1.588   1.674
125   E         1.481   1.485   1.545   0.866   0.865   0.964   1.584   1.588   1.674
126   D         1.481   1.485   1.545   1.212   1.206   1.296   1.584   1.588   1.674
127   D         0.434   0.442   0.252   0.116   0.117  -0.256   0.386   0.398   0.078
128   L         1.481   1.485   1.545   1.809   1.811   1.868   1.584   1.588   1.674
129   A        -0.727  -0.730  -0.685  -0.333  -0.322  -0.261  -0.812  -0.810  -0.728
130   E         1.481   1.485   1.545   0.866   0.865   0.964   1.584   1.588   1.674
131   I         1.481   1.485   1.545   1.775   1.774   1.835   1.584   1.588   1.674
132   D         1.481   1.485   1.545   1.212   1.206   1.296   1.584   1.588   1.674
133   T        -1.308  -1.325  -1.280  -0.930  -0.950  -0.918  -1.112  -1.125  -1.041
134   S         1.481   1.485   1.545   1.618   1.619   1.685   1.584   1.588   1.674
135   N         1.481   1.485   1.545   1.782   1.792   1.842   1.584   1.588   1.674
136   I         1.481   1.485   1.545   1.775   1.774   1.835   1.584   1.588   1.674
137   I         1.481   1.485   1.545   1.775   1.774   1.835   1.584   1.588   1.674
138   T         1.481   1.485   1.545   1.742   1.744   1.803   1.584   1.588   1.674
139   S        -0.508  -0.459  -0.595   0.022   0.088  -0.100  -0.513  -0.450  -0.611
140   G         1.481   1.485   1.545   1.755   1.755   1.816   1.584   1.588   1.674
141   R         1.481   1.485   1.545   1.701   1.702   1.764   1.584   1.588   1.674
142   R         1.481   1.485   1.545   1.701   1.702   1.764   1.584   1.588   1.674
143   T         1.481   1.485   1.545   1.742   1.744   1.803   1.584   1.588   1.674
144   R         1.481   1.485   1.545   1.701   1.702   1.764   1.584   1.588   1.674
145   G         1.481   1.485   1.545   1.755   1.755   1.816   1.584   1.588   1.674
146   K         1.481   1.485   1.545   1.317   1.336   1.396   1.584   1.588   1.674
147   V         0.072   0.066   0.125   0.434   0.424   0.491  -0.213  -0.225  -0.142
148   I         1.481   1.485   1.545   1.775   1.774   1.835   1.584   1.588   1.674
149   D         1.481   1.485   1.545   1.212   1.206   1.296   1.584   1.588   1.674
150   Y         0.072   0.070   0.127   0.572   0.569   0.634  -0.213  -0.218  -0.139
151   K        -0.508  -0.525  -0.625  -0.372  -0.373  -0.475  -0.513  -0.533  -0.649
152   K         1.481   1.485   1.545   1.317   1.336   1.396   1.584   1.588   1.674
153   T         0.072   0.070   0.127   0.279   0.280   0.339  -0.213  -0.218  -0.139
154   A         1.481   1.485   1.545   1.625   1.642   1.691   1.584   1.588   1.674
155   E         0.434   0.417   0.257  -0.127  -0.152  -0.378   0.386   0.359   0.087
156   E         0.072   0.063   0.124  -0.688  -0.691  -0.561  -0.213  -0.230  -0.143
157   L         1.481   1.485   1.545   1.809   1.811   1.868   1.584   1.588   1.674
158   D        -0.508  -0.546  -0.624  -0.889  -0.971  -1.158  -0.513  -0.560  -0.647
159   K        -0.508  -0.545  -0.613  -0.414  -0.441  -0.519  -0.513  -0.559  -0.634
160   K        -1.308  -1.277  -1.272  -1.555  -1.491  -1.385  -1.112  -1.077  -1.033
161   E        -1.308  -1.325  -1.280  -1.249  -1.236  -1.051  -1.112  -1.125  -1.041
162   P        -1.308  -1.277  -1.272  -0.815  -0.789  -0.774  -1.112  -1.077  -1.033
163   S        -1.308  -1.281  -1.258  -0.793  -0.743  -0.739  -1.112  -1.082  -1.020
164   T        -0.695  -0.731  -0.684  -0.156  -0.193  -0.129  -0.756  -0.800  -0.723
165   G        -1.421  -1.404  -1.310  -1.309  -1.298  -1.122  -1.224  -1.203  -1.069
166   S        -0.695  -0.731  -0.684  -0.908  -1.018  -0.989  -0.756  -0.800  -0.723
167   K        -1.888  -1.872  -1.769  -1.952  -1.879  -1.739  -1.411  -1.392  -1.252
168   D         0.434   0.417   0.257   0.312   0.285   0.095   0.386   0.359   0.087
169   D        -0.508  -0.516  -0.617  -0.725  -0.745  -0.904  -0.513  -0.522  -0.639
170   V        -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   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   G        -0.819  -0.806  -0.717  -0.960  -0.973  -0.787  -0.912  -0.894  -0.764
174   E         0.149   0.132   0.154  -0.300  -0.308  -0.192  -0.080  -0.109  -0.090
175   K        -0.819  -0.806  -0.717  -1.153  -1.125  -0.972  -0.912  -0.894  -0.764
176   E         0.149   0.132   0.154  -0.455  -0.475  -0.377  -0.080  -0.109  -0.090
177   E        -0.727  -0.727  -0.681  -1.353  -1.328  -1.188  -0.812  -0.806  -0.724
178   D         0.072   0.097   0.142  -0.762  -0.732  -0.624  -0.213  -0.170  -0.112
179   D         0.434   0.442   0.252   0.116   0.117  -0.256   0.386   0.398   0.078
180   E        -0.727  -0.715  -0.682  -1.508  -1.478  -1.376  -0.812  -0.795  -0.724
181   D         0.434   0.525   0.272  -0.158  -0.033  -0.404   0.386   0.525   0.113
182   E        -0.508  -0.516  -0.617  -0.952  -0.972  -1.031  -0.513  -0.522  -0.639
183   E        -0.727  -0.728  -0.680  -1.274  -1.251  -1.092  -0.812  -0.808  -0.722
184   D         1.481   1.485   1.545   1.212   1.206   1.296   1.584   1.588   1.674
185   D        -1.308  -1.336  -1.278  -1.453  -1.497  -1.369  -1.112  -1.137  -1.039
186   D         0.072   0.063   0.124  -0.647  -0.697  -0.597  -0.213  -0.230  -0.143
187   F         1.481   1.485   1.545   1.921   1.924   1.975   1.584   1.588   1.674
188   K         1.481   1.485   1.545   1.317   1.336   1.396   1.584   1.588   1.674
189   E         0.434   0.415   0.247  -0.158  -0.195  -0.447   0.386   0.356   0.070
190   -        -0.819  -0.810  -0.717  -0.792  -0.751  -0.627  -0.912  -0.898  -0.764
191   -         0.149   0.149   0.167   0.396   0.397   0.426  -0.080  -0.080  -0.067
192   -        -0.819  -0.810  -0.717  -0.629  -0.606  -0.470  -0.912  -0.898  -0.764
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -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     *
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   -         0.149   0.149   0.167   0.138   0.141   0.190  -0.080  -0.080  -0.067
* 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/P40019
Output conservation file - output/P40019
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
