1     M         1.088   1.133   1.193   1.209   1.266   1.357   1.158   1.219   1.304
2     F        -0.761  -0.902  -0.995  -0.600  -0.794  -0.998  -0.734  -0.900  -0.966
3     L        -1.601  -1.575  -1.418  -1.638  -1.589  -1.402  -1.458  -1.401  -1.188
4     P        -0.406  -0.330  -0.535  -0.301  -0.182  -0.541  -0.524  -0.404  -0.697
5     K        -1.601  -1.520  -1.410  -1.605  -1.476  -1.330  -1.458  -1.346  -1.181
6     F         0.058   0.087   0.088  -0.180  -0.139  -0.151  -0.215  -0.169  -0.213
7     N        -1.052  -1.082  -1.033  -1.068  -1.109  -1.008  -1.084  -1.095  -1.007
8     P        -1.601  -1.532  -1.410  -1.555  -1.439  -1.277  -1.458  -1.357  -1.181
9     I        -1.203  -1.139  -1.046  -1.224  -1.121  -0.990  -1.271  -1.177  -1.022
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    R        -0.771  -0.739  -0.590  -0.990  -0.947  -0.727  -1.038  -0.978  -0.772
20    S        -1.923  -1.894  -1.712  -1.964  -1.914  -1.651  -1.587  -1.525  -1.291
21    F        -1.453  -1.359  -1.390  -1.484  -1.339  -1.406  -1.313  -1.184  -1.164
22    S        -1.582  -1.531  -1.408  -1.612  -1.521  -1.354  -1.450  -1.369  -1.180
23    P        -0.558  -0.586  -0.561  -0.637  -0.660  -0.648  -0.764  -0.773  -0.735
24    I        -1.582  -1.526  -1.409  -1.724  -1.638  -1.432  -1.450  -1.364  -1.181
25    L        -1.453  -1.458  -1.396  -1.422  -1.421  -1.312  -1.313  -1.288  -1.169
26    R        -0.558  -0.537  -0.561  -0.623  -0.602  -0.679  -0.764  -0.731  -0.736
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    A        -1.599  -1.498  -1.408  -1.600  -1.458  -1.306  -1.469  -1.344  -1.181
29    K        -1.784  -1.766  -1.696  -1.585  -1.547  -1.433  -1.469  -1.430  -1.279
30    T        -0.179  -0.053  -0.483  -0.006   0.172  -0.440  -0.208  -0.027  -0.625
31    L        -0.284  -0.164  -0.496  -0.148   0.027  -0.529  -0.352  -0.176  -0.643
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    L        -1.923  -1.817  -1.704  -1.921  -1.750  -1.609  -1.587  -1.460  -1.285
39    R        -1.923  -1.885  -1.717  -1.735  -1.713  -1.456  -1.587  -1.523  -1.294
40    Y        -1.897  -1.777  -1.696  -1.801  -1.625  -1.506  -1.574  -1.443  -1.281
41    Q        -1.002  -1.097  -1.018  -0.884  -0.994  -0.874  -1.049  -1.121  -0.993
42    N        -1.002  -0.831  -0.999  -0.861  -0.613  -0.846  -1.049  -0.824  -0.973
43    R        -2.196  -2.140  -1.964  -2.027  -1.983  -1.721  -1.679  -1.603  -1.368
44    M         0.439   0.509   0.186   0.594   0.693   0.234   0.422   0.527  -0.031
45    Y        -0.463  -0.581  -0.539  -0.364  -0.504  -0.451  -0.629  -0.757  -0.704
46    L        -0.590  -0.527  -0.547  -0.784  -0.744  -0.681  -0.839  -0.760  -0.721
47    S         1.088   1.133   1.193   1.062   1.111   1.221   1.158   1.219   1.304
48    T        -0.179  -0.077  -0.480   0.012   0.148  -0.426  -0.208  -0.063  -0.621
49    E        -0.179  -0.385  -0.504  -0.279  -0.557  -0.743  -0.208  -0.494  -0.654
50    I        -0.463  -0.340  -0.523  -0.473  -0.288  -0.611  -0.629  -0.450  -0.684
51    R        -0.052  -0.065   0.064  -0.190  -0.238  -0.028  -0.418  -0.453  -0.258
52    K        -0.776  -0.771  -0.596  -0.875  -0.882  -0.607  -1.049  -1.022  -0.778
53    A         1.088   1.133   1.193   1.012   1.083   1.175   1.158   1.219   1.304
54    I         0.119   0.044   0.084   0.007  -0.161  -0.135  -0.103  -0.248  -0.221
55    E        -0.052   0.007   0.073  -0.402  -0.309  -0.184  -0.418  -0.316  -0.242
56    D        -1.897  -1.872  -1.706  -1.690  -1.661  -1.425  -1.574  -1.518  -1.287
57    A         1.088   1.133   1.193   1.012   1.083   1.175   1.158   1.219   1.304
58    I        -0.106  -0.053   0.068  -0.341  -0.251  -0.063  -0.524  -0.432  -0.251
59    E        -1.599  -1.602  -1.409  -1.799  -1.762  -1.472  -1.469  -1.433  -1.181
60    S        -0.463  -0.573  -0.536  -0.534  -0.730  -0.694  -0.629  -0.746  -0.701
61    A        -0.463  -0.579  -0.533  -0.544  -0.683  -0.635  -0.629  -0.754  -0.697
62    P         0.439   0.516   0.196   0.525   0.634   0.171   0.422   0.538  -0.013
63    V         0.439   0.230   0.177   0.552   0.264   0.151   0.422   0.084  -0.046
64    V         1.088   1.133   1.193   1.124   1.189   1.278   1.158   1.219   1.304
65    L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
66    F         1.088   1.133   1.193   1.103   1.176   1.260   1.158   1.219   1.304
67    M         1.088   1.133   1.193   1.209   1.266   1.357   1.158   1.219   1.304
68    K         1.088   1.133   1.193   1.128   1.175   1.282   1.158   1.219   1.304
69    G         1.088   1.133   1.193   1.070   1.139   1.229   1.158   1.219   1.304
70    T         1.088   1.133   1.193   1.124   1.186   1.278   1.158   1.219   1.304
71    P         1.088   1.133   1.193   1.091   1.159   1.248   1.158   1.219   1.304
72    E         0.439   0.230   0.177   0.296   0.022  -0.059   0.422   0.084  -0.046
73    F        -0.179  -0.385  -0.504  -0.016  -0.293  -0.498  -0.208  -0.494  -0.654
74    P         1.088   1.133   1.193   1.091   1.159   1.248   1.158   1.219   1.304
75    K        -0.179  -0.341  -0.495   0.023  -0.204  -0.436  -0.208  -0.440  -0.641
76    C         1.088   1.133   1.193   1.316   1.382   1.456   1.158   1.219   1.304
77    G         1.088   1.133   1.193   1.070   1.139   1.229   1.158   1.219   1.304
78    F         1.088   1.133   1.193   1.103   1.176   1.260   1.158   1.219   1.304
79    S         1.088   1.133   1.193   1.062   1.111   1.221   1.158   1.219   1.304
80    R         0.439   0.230   0.177   0.558   0.253   0.118   0.422   0.084  -0.046
81    A         0.439   0.230   0.177   0.446   0.169   0.071   0.422   0.084  -0.046
82    T        -0.179  -0.385  -0.504  -0.028  -0.340  -0.561  -0.208  -0.494  -0.654
83    I         1.088   1.133   1.193   1.087   1.143   1.244   1.158   1.219   1.304
84    G        -0.761  -0.567  -0.969  -0.539  -0.274  -0.868  -0.734  -0.479  -0.937
85    L        -1.187  -1.162  -1.044  -1.207  -1.192  -1.026  -1.259  -1.210  -1.021
86    L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
87    G         0.439   0.230   0.177   0.495   0.206   0.095   0.422   0.084  -0.046
88    N        -1.002  -0.992  -1.021  -0.918  -0.985  -0.921  -1.049  -1.043  -0.998
89    Q         0.439   0.230   0.177   0.529   0.214   0.071   0.422   0.084  -0.046
90    G         0.439   0.230   0.177   0.518   0.251   0.157   0.422   0.084  -0.046
91    V         1.088   1.133   1.193   1.124   1.189   1.278   1.158   1.219   1.304
92    D         0.439   0.230   0.177   0.603   0.299   0.174   0.422   0.084  -0.046
93    P         0.439   0.230   0.177   0.516   0.226   0.113   0.422   0.084  -0.046
94    A        -1.784  -1.792  -1.700  -1.758  -1.735  -1.575  -1.469  -1.451  -1.282
95    K         1.088   1.133   1.193   1.128   1.175   1.282   1.158   1.219   1.304
96    F         0.439   0.230   0.177   0.512   0.214   0.079   0.422   0.084  -0.046
97    A         0.439   0.230   0.177   0.446   0.173   0.069   0.422   0.084  -0.046
98    A         0.439   0.230   0.177   0.446   0.172   0.069   0.422   0.084  -0.046
99    Y         0.119   0.171   0.096   0.258   0.344   0.140  -0.103  -0.018  -0.197
100   N         1.088   1.133   1.193   1.217   1.276   1.364   1.158   1.219   1.304
101   V         1.088   1.133   1.193   1.124   1.189   1.278   1.158   1.219   1.304
102   L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
103   E         0.439   0.230   0.177   0.287   0.001  -0.085   0.422   0.084  -0.046
104   D         0.439   0.230   0.177   0.631   0.350   0.253   0.422   0.084  -0.046
105   P        -1.300  -1.368  -1.384  -1.182  -1.279  -1.383  -1.154  -1.212  -1.159
106   E         1.088   1.133   1.193   0.863   0.932   1.038   1.158   1.219   1.304
107   L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
108   R         1.088   1.133   1.193   1.148   1.216   1.301   1.158   1.219   1.304
109   E        -0.179  -0.129  -0.477  -0.248  -0.170  -0.631  -0.208  -0.130  -0.617
110   G         1.088   1.133   1.193   1.070   1.139   1.229   1.158   1.219   1.304
111   I         1.088   1.133   1.193   1.087   1.143   1.244   1.158   1.219   1.304
112   K         1.088   1.133   1.193   1.128   1.175   1.282   1.158   1.219   1.304
113   E         1.088   1.133   1.193   0.863   0.932   1.038   1.158   1.219   1.304
114   F        -0.590  -0.473  -0.541  -0.582  -0.417  -0.490  -0.839  -0.681  -0.712
115   S         1.088   1.133   1.193   1.062   1.111   1.221   1.158   1.219   1.304
116   E        -1.486  -1.388  -1.396  -1.536  -1.373  -1.329  -1.364  -1.256  -1.170
117   W         1.088   1.133   1.193   1.348   1.410   1.485   1.158   1.219   1.304
118   P         1.088   1.133   1.193   1.091   1.159   1.248   1.158   1.219   1.304
119   T         1.088   1.133   1.193   1.124   1.186   1.278   1.158   1.219   1.304
120   I         1.088   1.133   1.193   1.087   1.143   1.244   1.158   1.219   1.304
121   P         1.088   1.133   1.193   1.091   1.159   1.248   1.158   1.219   1.304
122   Q         1.088   1.133   1.193   1.132   1.194   1.286   1.158   1.219   1.304
123   L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
124   Y         1.088   1.133   1.193   1.297   1.360   1.438   1.158   1.219   1.304
125   V        -0.052  -0.063   0.065  -0.226  -0.272  -0.069  -0.418  -0.450  -0.257
126   N         0.439   0.457   0.182   0.659   0.687   0.277   0.422   0.450  -0.037
127   K         0.119   0.044   0.084   0.086  -0.071  -0.035  -0.103  -0.248  -0.221
128   E         1.088   1.133   1.193   0.863   0.932   1.038   1.158   1.219   1.304
129   F         1.088   1.133   1.193   1.103   1.176   1.260   1.158   1.219   1.304
130   I        -0.106  -0.057   0.064  -0.341  -0.258  -0.071  -0.524  -0.438  -0.258
131   G         1.088   1.133   1.193   1.070   1.139   1.229   1.158   1.219   1.304
132   G         1.088   1.133   1.193   1.070   1.139   1.229   1.158   1.219   1.304
133   C         0.439   0.230   0.177   0.740   0.444   0.305   0.422   0.084  -0.046
134   D         1.088   1.133   1.193   1.185   1.241   1.335   1.158   1.219   1.304
135   V         0.119   0.214   0.114   0.063   0.206   0.019  -0.103   0.056  -0.164
136   I        -0.590  -0.693  -0.542  -0.729  -0.886  -0.654  -0.839  -0.921  -0.711
137   T        -1.075  -1.171  -1.026  -1.028  -1.170  -0.956  -1.154  -1.212  -1.003
138   S         0.439   0.572   0.191   0.509   0.663   0.172   0.422   0.619  -0.021
139   M         1.088   1.133   1.193   1.209   1.266   1.357   1.158   1.219   1.304
140   A        -0.463  -0.503  -0.547  -0.453  -0.502  -0.540  -0.629  -0.709  -0.717
141   R        -0.463  -0.581  -0.539  -0.409  -0.571  -0.534  -0.629  -0.757  -0.704
142   S        -0.463  -0.330  -0.530  -0.449  -0.278  -0.539  -0.629  -0.443  -0.694
143   G         1.088   1.133   1.193   1.070   1.139   1.229   1.158   1.219   1.304
144   E         1.088   1.133   1.193   0.863   0.932   1.038   1.158   1.219   1.304
145   L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
146   A        -0.179  -0.335  -0.486  -0.081  -0.265  -0.483  -0.208  -0.432  -0.629
147   D        -0.776  -0.703  -0.590  -0.993  -0.873  -0.730  -1.049  -0.935  -0.771
148   L        -0.761  -0.833  -0.984  -0.705  -0.841  -1.001  -0.734  -0.824  -0.954
149   L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
150   E        -0.179  -0.325  -0.487  -0.258  -0.464  -0.669  -0.208  -0.420  -0.630
151   E        -0.179  -0.064  -0.474  -0.279  -0.112  -0.697  -0.208  -0.041  -0.613
152   A        -1.897  -1.900  -1.712  -1.817  -1.821  -1.517  -1.574  -1.536  -1.291
153   Q        -1.075  -0.998  -1.013  -1.010  -0.892  -0.940  -1.154  -1.047  -0.991
154   A        -0.761  -0.676  -0.976  -0.648  -0.515  -0.952  -0.734  -0.610  -0.945
155   L         1.088   1.133   1.193   0.949   1.001   1.117   1.158   1.219   1.304
156   V        -0.703  -0.701  -0.580  -0.853  -0.870  -0.701  -0.944  -0.932  -0.759
157   P         0.439   0.457   0.182   0.525   0.561   0.148   0.422   0.450  -0.037
158   E         0.439   0.457   0.182   0.288   0.328  -0.073   0.422   0.450  -0.037
159   E         0.439   0.230   0.177   0.297   0.025  -0.056   0.422   0.084  -0.046
160   E        -0.761  -0.819  -0.988  -0.787  -0.886  -1.064  -0.734  -0.809  -0.959
161   E        -0.558  -0.666  -0.550  -0.839  -0.977  -0.789  -0.764  -0.878  -0.721
162   E        -1.052  -1.088  -1.030  -1.220  -1.258  -1.159  -1.084  -1.112  -1.004
163   T        -1.052  -1.095  -1.029  -1.047  -1.138  -1.070  -1.084  -1.120  -1.003
164   K        -0.654  -0.630  -0.569  -0.882  -0.896  -0.769  -0.897  -0.862  -0.746
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.207  -1.099  -1.039  -1.170  -1.003  -0.933  -1.263  -1.113  -1.013
182   D        -1.203  -1.135  -1.041  -1.157  -1.060  -0.907  -1.271  -1.168  -1.017
183   R        -1.486  -1.373  -1.386  -1.441  -1.264  -1.290  -1.364  -1.225  -1.162
* 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/Q02784
Output conservation file - output/Q02784
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
