1     M         1.347   1.348   1.363   1.628   1.630   1.650   1.410   1.412   1.428
2     G         1.347   1.348   1.363   1.412   1.418   1.435   1.410   1.412   1.428
3     A        -1.192  -1.190  -1.169  -1.103  -1.101  -1.063  -1.072  -1.068  -1.032
4     V        -0.124  -0.119  -0.172  -0.151  -0.145  -0.252  -0.244  -0.236  -0.317
5     L         1.347   1.348   1.363   1.161   1.163   1.186   1.410   1.412   1.428
6     S         1.347   1.348   1.363   1.200   1.203   1.224   1.410   1.412   1.428
7     C         1.347   1.348   1.363   1.663   1.665   1.685   1.410   1.412   1.428
8     C         1.347   1.348   1.363   1.663   1.665   1.685   1.410   1.412   1.428
9     R        -1.192  -1.190  -1.169  -0.884  -0.873  -0.845  -1.072  -1.068  -1.032
10    N        -1.192  -1.190  -1.169  -1.235  -1.225  -1.194  -1.072  -1.068  -1.032
11    H        -1.192  -1.190  -1.169  -0.977  -0.981  -0.938  -1.072  -1.068  -1.032
12    S        -1.192  -1.190  -1.169  -1.390  -1.378  -1.348  -1.072  -1.068  -1.032
13    G        -1.192  -1.190  -1.169  -1.080  -1.081  -1.040  -1.072  -1.068  -1.032
14    E        -0.124  -0.153  -0.174  -0.308  -0.353  -0.388  -0.244  -0.288  -0.321
15    E         1.347   1.348   1.363   1.187   1.191   1.212   1.410   1.412   1.428
16    N         1.347   1.348   1.363   1.319   1.317   1.342   1.410   1.412   1.428
17    E        -0.124  -0.153  -0.174  -0.308  -0.353  -0.388  -0.244  -0.288  -0.321
18    A        -0.124  -0.095  -0.165   0.093   0.144   0.018  -0.244  -0.199  -0.306
19    L         1.347   1.348   1.363   1.161   1.163   1.186   1.410   1.412   1.428
20    L        -0.124  -0.119  -0.172  -0.291  -0.284  -0.358  -0.244  -0.236  -0.317
21    R        -1.192  -1.190  -1.169  -1.103  -1.101  -1.063  -1.072  -1.068  -1.032
22    E        -0.124  -0.119  -0.172  -0.369  -0.356  -0.455  -0.244  -0.236  -0.317
23    Q        -0.124  -0.119  -0.172  -0.174  -0.166  -0.255  -0.244  -0.236  -0.317
24    Q        -0.124  -0.153  -0.174  -0.179  -0.228  -0.266  -0.244  -0.288  -0.321
25    A        -0.124  -0.095  -0.165  -0.049  -0.001  -0.117  -0.244  -0.199  -0.306
26    G         1.347   1.348   1.363   1.366   1.368   1.389   1.410   1.412   1.428
27    Y         1.347   1.348   1.363   1.605   1.604   1.626   1.410   1.412   1.428
28    G         1.347   1.348   1.363   1.412   1.418   1.435   1.410   1.412   1.428
29    S        -0.124  -0.119  -0.172  -0.255  -0.244  -0.324  -0.244  -0.236  -0.317
30    Q        -0.124  -0.119  -0.172  -0.243  -0.233  -0.338  -0.244  -0.236  -0.317
31    G         1.347   1.348   1.363   1.366   1.368   1.389   1.410   1.412   1.428
32    N        -0.255  -0.254  -0.235  -0.364  -0.363  -0.329  -0.451  -0.450  -0.417
33    A        -0.124  -0.119  -0.172  -0.060  -0.048  -0.140  -0.244  -0.236  -0.317
34    N        -0.124  -0.153  -0.174  -0.168  -0.217  -0.255  -0.244  -0.288  -0.321
35    D        -1.192  -1.190  -1.169  -1.118  -1.122  -1.078  -1.072  -1.068  -1.032
36    E        -0.124  -0.153  -0.174  -0.308  -0.353  -0.388  -0.244  -0.288  -0.321
37    Y        -0.124  -0.119  -0.172   0.017   0.026  -0.090  -0.244  -0.236  -0.317
38    D        -1.192  -1.190  -1.169  -1.035  -1.034  -0.996  -1.072  -1.068  -1.032
39    A        -1.192  -1.190  -1.169  -1.332  -1.330  -1.290  -1.072  -1.068  -1.032
40    E        -1.192  -1.190  -1.169  -1.110  -1.090  -1.070  -1.072  -1.068  -1.032
41    Q        -1.192  -1.190  -1.169  -1.415  -1.413  -1.373  -1.072  -1.068  -1.032
42    M        -0.124  -0.095  -0.165  -0.038   0.002  -0.086  -0.244  -0.199  -0.306
43    R         1.347   1.348   1.363   1.424   1.426   1.447   1.410   1.412   1.428
44    L        -0.124  -0.153  -0.174  -0.332  -0.379  -0.411  -0.244  -0.288  -0.321
45    K         1.347   1.348   1.363   1.461   1.461   1.484   1.410   1.412   1.428
46    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    H        -0.255  -0.254  -0.235  -0.138  -0.136  -0.104  -0.451  -0.450  -0.417
48    E         1.347   1.348   1.363   1.162   1.163   1.186   1.410   1.412   1.428
49    H        -0.255  -0.254  -0.235  -0.315  -0.314  -0.281  -0.451  -0.450  -0.417
50    E         1.347   1.348   1.363   1.162   1.163   1.186   1.410   1.412   1.428
51    Q        -1.192  -1.190  -1.169  -1.299  -1.298  -1.258  -1.072  -1.068  -1.032
52    K        -0.124  -0.153  -0.174  -0.010  -0.059  -0.096  -0.244  -0.288  -0.321
53    L        -0.124  -0.153  -0.174  -0.279  -0.323  -0.347  -0.244  -0.288  -0.321
54    L        -0.124  -0.119  -0.172  -0.185  -0.179  -0.234  -0.244  -0.236  -0.317
55    A         1.347   1.348   1.363   1.412   1.416   1.435   1.410   1.412   1.428
56    R         1.347   1.348   1.363   1.424   1.426   1.447   1.410   1.412   1.428
57    E         1.347   1.348   1.363   1.187   1.191   1.212   1.410   1.412   1.428
58    Q        -0.124  -0.153  -0.174  -0.255  -0.310  -0.356  -0.244  -0.288  -0.321
59    E        -0.124  -0.119  -0.172  -0.308  -0.298  -0.384  -0.244  -0.236  -0.317
60    L         1.347   1.348   1.363   1.161   1.163   1.186   1.410   1.412   1.428
61    R        -0.124  -0.153  -0.174  -0.005  -0.049  -0.081  -0.244  -0.288  -0.321
62    D        -0.124  -0.153  -0.174  -0.243  -0.296  -0.342  -0.244  -0.288  -0.321
63    I         1.347   1.348   1.363   1.412   1.413   1.435   1.410   1.412   1.428
64    V         1.347   1.348   1.363   1.436   1.435   1.459   1.410   1.412   1.428
65    A        -1.192  -1.190  -1.169  -1.235  -1.230  -1.194  -1.072  -1.068  -1.032
66    N        -0.124  -0.119  -0.172  -0.168  -0.160  -0.251  -0.244  -0.236  -0.317
67    T         1.347   1.348   1.363   1.509   1.511   1.532   1.410   1.412   1.428
68    N         1.347   1.348   1.363   1.338   1.339   1.362   1.410   1.412   1.428
69    D         1.347   1.348   1.363   1.326   1.327   1.349   1.410   1.412   1.428
70    K         1.347   1.348   1.363   1.461   1.461   1.484   1.410   1.412   1.428
71    L         1.347   1.348   1.363   1.161   1.163   1.186   1.410   1.412   1.428
72    I         1.347   1.348   1.363   1.412   1.413   1.435   1.410   1.412   1.428
73    D         1.347   1.348   1.363   1.326   1.327   1.349   1.410   1.412   1.428
74    I         1.347   1.348   1.363   1.412   1.413   1.435   1.410   1.412   1.428
75    S        -0.124  -0.153  -0.174  -0.255  -0.295  -0.328  -0.244  -0.288  -0.321
76    M         1.347   1.348   1.363   1.628   1.630   1.650   1.410   1.412   1.428
77    I         1.347   1.348   1.363   1.412   1.413   1.435   1.410   1.412   1.428
78    N        -0.124  -0.095  -0.165  -0.291  -0.243  -0.354  -0.244  -0.199  -0.306
79    N         1.347   1.348   1.363   1.338   1.339   1.362   1.410   1.412   1.428
80    S         1.347   1.348   1.363   1.200   1.203   1.224   1.410   1.412   1.428
81    G         1.347   1.348   1.363   1.412   1.418   1.435   1.410   1.412   1.428
82    I         1.347   1.348   1.363   1.412   1.413   1.435   1.410   1.412   1.428
83    V         1.347   1.348   1.363   1.436   1.435   1.459   1.410   1.412   1.428
84    I        -1.192  -1.190  -1.169  -0.999  -0.994  -0.959  -1.072  -1.068  -1.032
85    Q        -1.192  -1.190  -1.169  -1.110  -1.110  -1.070  -1.072  -1.068  -1.032
86    G        -0.124  -0.153  -0.174  -0.156  -0.206  -0.258  -0.244  -0.288  -0.321
87    T        -1.192  -1.190  -1.169  -0.870  -0.861  -0.831  -1.072  -1.068  -1.032
88    D         1.347   1.348   1.363   1.326   1.327   1.349   1.410   1.412   1.428
89    L        -0.124  -0.119  -0.172  -0.279  -0.273  -0.344  -0.244  -0.236  -0.317
90    Q        -1.192  -1.190  -1.169  -1.243  -1.231  -1.202  -1.072  -1.068  -1.032
91    E        -1.192  -1.190  -1.169  -1.267  -1.261  -1.226  -1.072  -1.068  -1.032
92    A        -0.124  -0.153  -0.174  -0.156  -0.208  -0.258  -0.244  -0.288  -0.321
93    L        -0.255  -0.254  -0.235  -0.305  -0.307  -0.270  -0.451  -0.450  -0.417
94    D        -1.192  -1.190  -1.169  -1.141  -1.136  -1.101  -1.072  -1.068  -1.032
95    K        -1.192  -1.190  -1.169  -1.126  -1.127  -1.086  -1.072  -1.068  -1.032
96    R        -0.124  -0.095  -0.165  -0.134  -0.088  -0.197  -0.244  -0.199  -0.306
97    Q        -0.124  -0.119  -0.172  -0.094  -0.086  -0.161  -0.244  -0.236  -0.317
98    Q        -1.192  -1.190  -1.169  -1.235  -1.225  -1.194  -1.072  -1.068  -1.032
99    E         1.347   1.348   1.363   1.187   1.191   1.212   1.410   1.412   1.428
100   E        -0.255  -0.254  -0.235  -0.502  -0.501  -0.466  -0.451  -0.450  -0.417
101   G        -0.255  -0.254  -0.235  -0.352  -0.351  -0.317  -0.451  -0.450  -0.417
102   G        -0.255  -0.254  -0.235  -0.291  -0.290  -0.257  -0.451  -0.450  -0.417
103   D        -0.255  -0.254  -0.235  -0.515  -0.513  -0.479  -0.451  -0.450  -0.417
104   S        -0.255  -0.254  -0.235  -0.672  -0.671  -0.635  -0.451  -0.450  -0.417
105   R        -0.255  -0.254  -0.235  -0.340  -0.338  -0.305  -0.451  -0.450  -0.417
106   E         1.347   1.348   1.363   1.162   1.163   1.186   1.410   1.412   1.428
107   D        -0.255  -0.254  -0.235  -0.364  -0.363  -0.329  -0.451  -0.450  -0.417
108   E        -0.255  -0.254  -0.235  -0.528  -0.526  -0.492  -0.451  -0.450  -0.417
109   R         1.347   1.348   1.363   1.416   1.418   1.439   1.410   1.412   1.428
110   S         1.347   1.348   1.363   1.144   1.146   1.169   1.410   1.412   1.428
111   A        -0.255  -0.254  -0.235  -0.528  -0.526  -0.492  -0.451  -0.450  -0.417
112   G        -0.255  -0.254  -0.235  -0.377  -0.375  -0.342  -0.451  -0.450  -0.417
113   D        -0.255  -0.254  -0.235  -0.291  -0.290  -0.257  -0.451  -0.450  -0.417
114   D         1.347   1.348   1.363   1.366   1.368   1.389   1.410   1.412   1.428
115   N        -0.255  -0.254  -0.235  -0.364  -0.363  -0.329  -0.451  -0.450  -0.417
116   L        -0.255  -0.254  -0.235  -0.352  -0.351  -0.317  -0.451  -0.450  -0.417
117   S        -0.124  -0.153  -0.174  -0.255  -0.298  -0.328  -0.244  -0.288  -0.321
118   G        -1.192  -1.190  -1.169  -1.149  -1.152  -1.108  -1.072  -1.068  -1.032
119   H        -0.124  -0.119  -0.172   0.126   0.136   0.036  -0.244  -0.236  -0.317
120   S        -1.192  -1.190  -1.169  -1.243  -1.233  -1.202  -1.072  -1.068  -1.032
121   V         1.347   1.348   1.363   1.436   1.435   1.459   1.410   1.412   1.428
122   P         1.347   1.348   1.363   1.563   1.563   1.585   1.410   1.412   1.428
123   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   F        -1.192  -1.190  -1.169  -0.948  -0.962  -0.909  -1.072  -1.068  -1.032
142   T         1.347   1.348   1.363   1.509   1.511   1.532   1.410   1.412   1.428
143   L        -1.192  -1.190  -1.169  -1.088  -1.078  -1.048  -1.072  -1.068  -1.032
144   L         1.347   1.348   1.363   1.161   1.163   1.186   1.410   1.412   1.428
145   T        -1.192  -1.190  -1.169  -0.948  -0.941  -0.909  -1.072  -1.068  -1.032
146   S        -0.124  -0.119  -0.172  -0.255  -0.245  -0.324  -0.244  -0.236  -0.317
147   P        -1.192  -1.190  -1.169  -1.126  -1.133  -1.086  -1.072  -1.068  -1.032
148   D        -1.192  -1.190  -1.169  -1.211  -1.201  -1.170  -1.072  -1.068  -1.032
149   S        -1.192  -1.190  -1.169  -1.187  -1.175  -1.147  -1.072  -1.068  -1.032
150   A        -1.192  -1.190  -1.169  -1.156  -1.148  -1.116  -1.072  -1.068  -1.032
151   K        -1.192  -1.190  -1.169  -1.073  -1.074  -1.033  -1.072  -1.068  -1.032
152   I        -1.192  -1.190  -1.169  -0.991  -0.993  -0.952  -1.072  -1.068  -1.032
153   S        -0.124  -0.095  -0.165  -0.066  -0.011  -0.152  -0.244  -0.199  -0.306
154   K        -1.192  -1.190  -1.169  -1.006  -1.005  -0.967  -1.072  -1.068  -1.032
155   E        -1.192  -1.190  -1.169  -1.103  -1.090  -1.063  -1.072  -1.068  -1.032
156   Q        -0.124  -0.153  -0.174  -0.139  -0.184  -0.219  -0.244  -0.288  -0.321
157   L        -0.124  -0.153  -0.174  -0.291  -0.335  -0.361  -0.244  -0.288  -0.321
158   K        -1.192  -1.190  -1.169  -1.073  -1.074  -1.033  -1.072  -1.068  -1.032
159   K        -1.192  -1.190  -1.169  -1.299  -1.301  -1.258  -1.072  -1.068  -1.032
160   L        -1.192  -1.190  -1.169  -1.065  -1.044  -1.026  -1.072  -1.068  -1.032
161   H         1.347   1.348   1.363   1.616   1.619   1.638   1.410   1.412   1.428
162   S        -0.124  -0.153  -0.174  -0.232  -0.273  -0.300  -0.244  -0.288  -0.321
163   N        -1.192  -1.190  -1.169  -1.058  -1.053  -1.018  -1.072  -1.068  -1.032
164   I        -1.192  -1.190  -1.169  -1.088  -1.077  -1.048  -1.072  -1.068  -1.032
165   L        -0.124  -0.095  -0.165   0.039   0.095  -0.055  -0.244  -0.199  -0.306
166   N        -1.192  -1.190  -1.169  -1.156  -1.149  -1.116  -1.072  -1.068  -1.032
167   E        -1.192  -1.190  -1.169  -1.299  -1.288  -1.258  -1.072  -1.068  -1.032
168   I        -0.124  -0.095  -0.165  -0.291  -0.247  -0.347  -0.244  -0.199  -0.306
169   F        -1.192  -1.190  -1.169  -0.955  -0.959  -0.916  -1.072  -1.068  -1.032
170   S        -0.124  -0.153  -0.174  -0.232  -0.273  -0.300  -0.244  -0.288  -0.321
171   Q        -1.192  -1.190  -1.169  -1.299  -1.292  -1.258  -1.072  -1.068  -1.032
172   S        -0.124  -0.095  -0.165  -0.393  -0.342  -0.465  -0.244  -0.199  -0.306
173   Q        -1.192  -1.190  -1.169  -1.187  -1.174  -1.147  -1.072  -1.068  -1.032
174   V         1.347   1.348   1.363   1.436   1.435   1.459   1.410   1.412   1.428
175   N        -1.192  -1.190  -1.169  -1.235  -1.235  -1.194  -1.072  -1.068  -1.032
176   K        -1.192  -1.190  -1.169  -0.814  -0.807  -0.776  -1.072  -1.068  -1.032
177   P        -1.192  -1.190  -1.169  -0.941  -0.945  -0.902  -1.072  -1.068  -1.032
178   G        -0.124  -0.153  -0.174  -0.038  -0.081  -0.118  -0.244  -0.288  -0.321
179   P        -0.124  -0.119  -0.172   0.056   0.064  -0.039  -0.244  -0.236  -0.317
180   L         1.347   1.348   1.363   1.161   1.163   1.186   1.410   1.412   1.428
181   T        -0.124  -0.095  -0.165   0.006   0.048  -0.056  -0.244  -0.199  -0.306
182   V        -0.124  -0.153  -0.174  -0.038  -0.088  -0.123  -0.244  -0.288  -0.321
183   P        -0.124  -0.095  -0.165  -0.049  -0.008  -0.101  -0.244  -0.199  -0.306
184   F        -1.192  -1.190  -1.169  -1.065  -1.068  -1.026  -1.072  -1.068  -1.032
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -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/Q02205
Output conservation file - output/Q02205
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
