1     M         1.667   1.667   1.688   2.043   2.044   2.076   1.772   1.773   1.799
2     N        -1.068  -1.067  -1.050  -0.893  -0.887  -0.860  -0.955  -0.953  -0.922
3     S        -1.068  -1.067  -1.050  -1.061  -1.049  -1.028  -0.955  -0.953  -0.922
4     Y        -0.059  -0.059  -0.040  -0.205  -0.193  -0.172  -0.273  -0.273  -0.241
5     S        -0.059  -0.059  -0.040  -0.110  -0.108  -0.077  -0.273  -0.273  -0.241
6     L         1.667   1.667   1.688   1.514   1.540   1.547   1.772   1.773   1.799
7     L        -0.059  -0.059  -0.040  -0.193  -0.181  -0.160  -0.273  -0.273  -0.241
8     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     R         1.667   1.667   1.688   1.794   1.791   1.827   1.772   1.773   1.799
10    S        -0.059  -0.059  -0.040  -0.110  -0.120  -0.077  -0.273  -0.273  -0.241
11    F        -0.059  -0.059  -0.040   0.143   0.148   0.176  -0.273  -0.273  -0.241
12    H        -0.059  -0.059  -0.040   0.030   0.022   0.063  -0.273  -0.273  -0.241
13    E        -0.059  -0.059  -0.040  -0.181  -0.193  -0.148  -0.273  -0.273  -0.241
14    S         1.667   1.667   1.688   1.581   1.574   1.614   1.772   1.773   1.799
15    S        -0.059  -0.059  -0.040  -0.266  -0.280  -0.233  -0.273  -0.273  -0.241
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    K         0.082   0.096   0.049  -0.147  -0.126  -0.178  -0.046  -0.023  -0.097
18    P         0.082   0.096   0.050   0.203   0.222   0.149  -0.046  -0.023  -0.096
19    L         0.082   0.096   0.050   0.192   0.220   0.124  -0.046  -0.023  -0.096
20    F         0.082   0.096   0.050   0.029   0.055  -0.010  -0.046  -0.023  -0.096
21    N        -1.068  -1.067  -1.050  -0.972  -0.983  -0.939  -0.955  -0.953  -0.922
22    L        -1.068  -1.067  -1.050  -0.829  -0.823  -0.796  -0.955  -0.953  -0.922
23    A         0.082   0.096   0.050  -0.124  -0.095  -0.178  -0.046  -0.023  -0.096
24    S         0.082   0.096   0.050   0.051   0.074  -0.015  -0.046  -0.023  -0.096
25    T         0.082   0.096   0.050   0.329   0.348   0.284  -0.046  -0.023  -0.096
26    L        -1.068  -1.067  -1.050  -1.024  -1.022  -0.991  -0.955  -0.953  -0.922
27    L         0.082   0.096   0.049   0.095   0.120   0.063  -0.046  -0.023  -0.097
28    K        -1.068  -1.067  -1.050  -1.455  -1.446  -1.422  -0.955  -0.953  -0.922
29    A         0.082   0.096   0.049  -0.159  -0.124  -0.234  -0.046  -0.023  -0.097
30    S        -1.068  -1.067  -1.050  -1.031  -1.032  -0.998  -0.955  -0.953  -0.922
31    K        -1.068  -1.067  -1.050  -1.153  -1.136  -1.120  -0.955  -0.953  -0.922
32    R        -1.068  -1.067  -1.050  -1.255  -1.268  -1.222  -0.955  -0.953  -0.922
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    T        -0.059  -0.059  -0.040   0.143   0.137   0.176  -0.273  -0.273  -0.241
45    Q        -0.059  -0.059  -0.040   0.041   0.045   0.074  -0.273  -0.273  -0.241
46    L        -0.059  -0.059  -0.040  -0.392  -0.382  -0.358  -0.273  -0.273  -0.241
47    R         1.667   1.667   1.688   1.794   1.791   1.827   1.772   1.773   1.799
48    N        -0.059  -0.059  -0.040  -0.316  -0.306  -0.283  -0.273  -0.273  -0.241
49    E        -0.059  -0.059  -0.040  -0.086  -0.096  -0.053  -0.273  -0.273  -0.241
50    L         1.667   1.667   1.688   1.514   1.540   1.547   1.772   1.773   1.799
51    I         1.667   1.667   1.688   1.842   1.840   1.875   1.772   1.773   1.799
52    K         1.667   1.667   1.688   1.291   1.296   1.324   1.772   1.773   1.799
53    Q         1.667   1.667   1.688   1.729   1.742   1.762   1.772   1.773   1.799
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    G         1.667   1.667   1.688   1.890   1.888   1.923   1.772   1.773   1.799
56    P         1.667   1.667   1.688   1.756   1.753   1.789   1.772   1.773   1.799
57    K         1.667   1.667   1.688   1.328   1.335   1.361   1.772   1.773   1.799
58    R         1.667   1.667   1.688   1.803   1.803   1.836   1.772   1.773   1.799
59    P         1.667   1.667   1.688   1.756   1.753   1.789   1.772   1.773   1.799
60    T        -1.068  -1.067  -1.050  -0.886  -0.889  -0.853  -0.955  -0.953  -0.922
61    S        -1.068  -1.067  -1.050  -1.031  -1.017  -0.998  -0.955  -0.953  -0.922
62    A         1.667   1.667   1.688   1.625   1.631   1.658   1.772   1.773   1.799
63    Y         0.082   0.096   0.050   0.308   0.328   0.254  -0.046  -0.023  -0.096
64    F        -1.068  -1.067  -1.050  -0.922  -0.933  -0.889  -0.955  -0.953  -0.922
65    L         0.082   0.055   0.041  -0.016  -0.051  -0.073  -0.046  -0.088  -0.111
66    Y         1.667   1.667   1.688   1.803   1.801   1.836   1.772   1.773   1.799
67    L        -1.068  -1.067  -1.050  -0.851  -0.845  -0.817  -0.955  -0.953  -0.922
68    Q        -1.068  -1.067  -1.050  -0.965  -0.977  -0.932  -0.955  -0.953  -0.922
69    D         0.082   0.096   0.050   0.240   0.257   0.199  -0.046  -0.023  -0.096
70    H        -1.068  -1.067  -1.050  -0.726  -0.729  -0.693  -0.955  -0.953  -0.922
71    R         0.082   0.055   0.041   0.339   0.299   0.289  -0.046  -0.088  -0.111
72    S        -1.068  -1.067  -1.050  -1.024  -1.009  -0.991  -0.955  -0.953  -0.922
73    Q        -1.068  -1.067  -1.050  -0.652  -0.650  -0.619  -0.955  -0.953  -0.922
74    F        -1.068  -1.067  -1.050  -0.858  -0.856  -0.824  -0.955  -0.953  -0.922
75    V        -1.068  -1.067  -1.050  -0.503  -0.502  -0.470  -0.955  -0.953  -0.922
76    K         0.082   0.096   0.050  -0.159  -0.124  -0.233  -0.046  -0.023  -0.096
77    E         0.082   0.055   0.041  -0.095  -0.146  -0.175  -0.046  -0.088  -0.111
78    N         0.082   0.055   0.041   0.442   0.401   0.387  -0.046  -0.088  -0.111
79    P         0.082   0.055   0.041   0.235   0.189   0.177  -0.046  -0.088  -0.111
80    T        -1.068  -1.067  -1.050  -0.606  -0.611  -0.573  -0.955  -0.953  -0.922
81    L         0.082   0.055   0.041  -0.153  -0.193  -0.231  -0.046  -0.088  -0.111
82    R        -1.068  -1.067  -1.050  -0.936  -0.929  -0.903  -0.955  -0.953  -0.922
83    P         0.082   0.096   0.049   0.245   0.261   0.202  -0.046  -0.023  -0.097
84    A        -1.068  -1.067  -1.050  -1.153  -1.135  -1.120  -0.955  -0.953  -0.922
85    E         0.082   0.055   0.041  -0.044  -0.091  -0.116  -0.046  -0.088  -0.111
86    I         0.082   0.055   0.041   0.375   0.335   0.323  -0.046  -0.088  -0.111
87    S         1.667   1.667   1.688   1.581   1.574   1.614   1.772   1.773   1.799
88    K         0.082   0.096   0.049  -0.301  -0.272  -0.350  -0.046  -0.023  -0.097
89    I         0.082   0.096   0.049   0.324   0.342   0.277  -0.046  -0.023  -0.097
90    A         0.082   0.096   0.049  -0.061  -0.028  -0.124  -0.046  -0.023  -0.097
91    G         1.667   1.667   1.688   1.930   1.930   1.963   1.772   1.773   1.799
92    E         0.082   0.055   0.041  -0.182  -0.238  -0.275  -0.046  -0.088  -0.111
93    K         0.082   0.055   0.041  -0.241  -0.278  -0.295  -0.046  -0.088  -0.111
94    W         1.667   1.667   1.688   2.032   2.034   2.065   1.772   1.773   1.799
95    Q         0.082   0.096   0.050   0.198   0.218   0.143  -0.046  -0.023  -0.096
96    N        -1.068  -1.067  -1.050  -0.972  -0.983  -0.939  -0.955  -0.953  -0.922
97    L         1.667   1.667   1.688   1.540   1.550   1.573   1.772   1.773   1.799
98    E         0.082   0.096   0.050  -0.135  -0.109  -0.191  -0.046  -0.023  -0.096
99    A         0.082   0.096   0.050  -0.044  -0.021  -0.100  -0.046  -0.023  -0.096
100   D        -1.068  -1.067  -1.050  -0.914  -0.927  -0.881  -0.955  -0.953  -0.922
101   I         0.082   0.096   0.050   0.062   0.079   0.019  -0.046  -0.023  -0.096
102   K         1.667   1.667   1.688   1.328   1.335   1.361   1.772   1.773   1.799
103   E         0.082   0.055   0.041   0.012  -0.035  -0.052  -0.046  -0.088  -0.111
104   K         0.082   0.096   0.049  -0.235  -0.213  -0.276  -0.046  -0.023  -0.097
105   Y         1.667   1.667   1.688   1.803   1.801   1.836   1.772   1.773   1.799
106   I        -1.068  -1.067  -1.050  -0.679  -0.682  -0.646  -0.955  -0.953  -0.922
107   S        -1.068  -1.067  -1.050  -0.951  -0.942  -0.917  -0.955  -0.953  -0.922
108   E        -1.068  -1.067  -1.050  -1.378  -1.370  -1.345  -0.955  -0.953  -0.922
109   R        -1.068  -1.067  -1.050  -0.907  -0.915  -0.874  -0.955  -0.953  -0.922
110   K         0.082   0.096   0.049  -0.241  -0.217  -0.283  -0.046  -0.023  -0.097
111   K        -1.068  -1.067  -1.050  -1.192  -1.188  -1.159  -0.955  -0.953  -0.922
112   L         0.082   0.096   0.049  -0.101  -0.068  -0.157  -0.046  -0.023  -0.097
113   Y        -1.068  -1.067  -1.050  -0.994  -0.990  -0.961  -0.955  -0.953  -0.922
114   S         0.082   0.096   0.050  -0.095  -0.071  -0.158  -0.046  -0.023  -0.096
115   E         0.082   0.055   0.041  -0.182  -0.238  -0.275  -0.046  -0.088  -0.111
116   Y         1.667   1.667   1.688   1.803   1.801   1.836   1.772   1.773   1.799
117   Q        -1.068  -1.067  -1.050  -1.353  -1.351  -1.320  -0.955  -0.953  -0.922
118   K        -1.068  -1.067  -1.050  -1.145  -1.142  -1.112  -0.955  -0.953  -0.922
119   A         0.082   0.096   0.049  -0.159  -0.124  -0.234  -0.046  -0.023  -0.097
120   K         0.082   0.055   0.041  -0.211  -0.247  -0.261  -0.046  -0.088  -0.111
121   K        -1.068  -1.067  -1.050  -1.296  -1.296  -1.263  -0.955  -0.953  -0.922
122   E         0.082   0.055   0.041  -0.044  -0.091  -0.116  -0.046  -0.088  -0.111
123   F         0.082   0.055   0.041   0.308   0.259   0.238  -0.046  -0.088  -0.111
124   D        -1.068  -1.067  -1.050  -0.972  -0.978  -0.939  -0.955  -0.953  -0.922
125   E        -1.068  -1.067  -1.050  -1.378  -1.384  -1.345  -0.955  -0.953  -0.922
126   K        -1.068  -1.067  -1.050  -0.879  -0.872  -0.846  -0.955  -0.953  -0.922
127   L         1.667   1.667   1.688   1.540   1.550   1.573   1.772   1.773   1.799
128   P         1.667   1.667   1.688   1.756   1.753   1.789   1.772   1.773   1.799
129   P         1.667   1.667   1.688   1.756   1.753   1.789   1.772   1.773   1.799
130   K         1.667   1.667   1.688   1.328   1.335   1.361   1.772   1.773   1.799
131   K         1.667   1.667   1.688   1.328   1.335   1.361   1.772   1.773   1.799
132   P         1.667   1.667   1.688   1.756   1.753   1.789   1.772   1.773   1.799
133   A         0.082   0.096   0.049  -0.061  -0.028  -0.124  -0.046  -0.023  -0.097
134   G        -1.068  -1.067  -1.050  -0.843  -0.838  -0.810  -0.955  -0.953  -0.922
135   P         0.082   0.055   0.041   0.051  -0.003  -0.034  -0.046  -0.088  -0.111
136   F         1.667   1.667   1.688   1.895   1.896   1.928   1.772   1.773   1.799
137   I        -1.068  -1.067  -1.050  -0.886  -0.877  -0.853  -0.955  -0.953  -0.922
138   K        -1.068  -1.067  -1.050  -1.498  -1.484  -1.465  -0.955  -0.953  -0.922
139   Y         0.082   0.096   0.050   0.308   0.328   0.254  -0.046  -0.023  -0.096
140   A        -1.068  -1.067  -1.050  -1.296  -1.287  -1.263  -0.955  -0.953  -0.922
141   N         0.082   0.055   0.041   0.122   0.065   0.020  -0.046  -0.088  -0.111
142   E         1.667   1.667   1.688   1.600   1.600   1.633   1.772   1.773   1.799
143   V         0.082   0.055   0.041   0.133   0.074   0.030  -0.046  -0.088  -0.111
144   R         0.082   0.055   0.041   0.095   0.043   0.009  -0.046  -0.088  -0.111
145   S        -1.068  -1.067  -1.050  -1.168  -1.166  -1.135  -0.955  -0.953  -0.922
146   Q         0.082   0.096   0.049   0.079   0.100   0.016  -0.046  -0.023  -0.097
147   V        -1.068  -1.067  -1.050  -0.886  -0.895  -0.853  -0.955  -0.953  -0.922
148   F        -1.068  -1.067  -1.050  -1.061  -1.056  -1.028  -0.955  -0.953  -0.922
149   A        -1.068  -1.067  -1.050  -1.031  -1.017  -0.998  -0.955  -0.953  -0.922
150   Q         0.082   0.055   0.041   0.079   0.025  -0.000  -0.046  -0.088  -0.111
151   H         0.082   0.096   0.050   0.442   0.460   0.400  -0.046  -0.023  -0.096
152   P         1.667   1.667   1.688   1.756   1.753   1.789   1.772   1.773   1.799
153   D        -1.068  -1.067  -1.050  -0.836  -0.831  -0.803  -0.955  -0.953  -0.922
154   K         0.082   0.096   0.050  -0.241  -0.203  -0.313  -0.046  -0.023  -0.096
155   S         1.667   1.667   1.688   1.515   1.521   1.548   1.772   1.773   1.799
156   Q         0.082   0.096   0.049   0.214   0.231   0.168  -0.046  -0.023  -0.097
157   L        -1.068  -1.067  -1.050  -0.886  -0.881  -0.853  -0.955  -0.953  -0.922
158   D         0.082   0.055   0.041   0.272   0.217   0.186  -0.046  -0.088  -0.111
159   L         0.082   0.055   0.041   0.007  -0.027  -0.048  -0.046  -0.088  -0.111
160   M        -1.068  -1.067  -1.050  -0.951  -0.954  -0.917  -0.955  -0.953  -0.922
161   K         0.082   0.096   0.049  -0.355  -0.325  -0.412  -0.046  -0.023  -0.097
162   I         0.082   0.096   0.050   0.007   0.034  -0.035  -0.046  -0.023  -0.096
163   I         0.082   0.055   0.041   0.187   0.138   0.107  -0.046  -0.088  -0.111
164   G         0.082   0.055   0.041   0.214   0.160   0.123  -0.046  -0.088  -0.111
165   D        -1.068  -1.067  -1.050  -0.914  -0.926  -0.881  -0.955  -0.953  -0.922
166   K         0.082   0.096   0.049  -0.211  -0.188  -0.250  -0.046  -0.023  -0.097
167   W         1.667   1.667   1.688   2.032   2.034   2.065   1.772   1.773   1.799
168   Q         0.082   0.096   0.050  -0.241  -0.217  -0.282  -0.046  -0.023  -0.096
169   S         1.667   1.667   1.688   1.515   1.521   1.548   1.772   1.773   1.799
170   L         1.667   1.667   1.688   1.540   1.550   1.573   1.772   1.773   1.799
171   D         0.082   0.096   0.049   0.416   0.436   0.366  -0.046  -0.023  -0.097
172   Q        -1.068  -1.067  -1.050  -1.107  -1.110  -1.074  -0.955  -0.953  -0.922
173   S         0.082   0.096   0.049  -0.038  -0.016  -0.083  -0.046  -0.023  -0.097
174   I        -1.068  -1.067  -1.050  -0.843  -0.842  -0.810  -0.955  -0.953  -0.922
175   K         1.667   1.667   1.688   1.328   1.335   1.361   1.772   1.773   1.799
176   D        -1.068  -1.067  -1.050  -1.153  -1.155  -1.120  -0.955  -0.953  -0.922
177   K         0.082   0.055   0.041  -0.241  -0.278  -0.295  -0.046  -0.088  -0.111
178   Y         1.667   1.667   1.688   1.803   1.801   1.836   1.772   1.773   1.799
179   I        -1.068  -1.067  -1.050  -0.843  -0.852  -0.810  -0.955  -0.953  -0.922
180   Q        -1.068  -1.067  -1.050  -0.713  -0.714  -0.680  -0.955  -0.953  -0.922
181   E        -1.068  -1.067  -1.050  -1.255  -1.268  -1.222  -0.955  -0.953  -0.922
182   Y         1.667   1.667   1.688   1.803   1.801   1.836   1.772   1.773   1.799
183   K        -1.068  -1.067  -1.050  -1.239  -1.225  -1.206  -0.955  -0.953  -0.922
184   K         0.082   0.096   0.050  -0.182  -0.155  -0.256  -0.046  -0.023  -0.096
185   A        -1.068  -1.067  -1.050  -0.781  -0.775  -0.748  -0.955  -0.953  -0.922
186   I        -1.068  -1.067  -1.050  -1.264  -1.259  -1.230  -0.955  -0.953  -0.922
187   Q        -1.068  -1.067  -1.050  -1.161  -1.158  -1.128  -0.955  -0.953  -0.922
188   E         0.082   0.096   0.049  -0.095  -0.071  -0.159  -0.046  -0.023  -0.097
189   Y         0.082   0.096   0.049   0.329   0.345   0.289  -0.046  -0.023  -0.097
190   N        -1.068  -1.067  -1.050  -0.886  -0.889  -0.853  -0.955  -0.953  -0.922
191   A        -1.068  -1.067  -1.050  -1.280  -1.288  -1.246  -0.955  -0.953  -0.922
192   R        -1.068  -1.067  -1.050  -0.879  -0.877  -0.846  -0.955  -0.953  -0.922
193   Y        -1.068  -1.067  -1.050  -0.619  -0.620  -0.586  -0.955  -0.953  -0.922
194   P        -1.068  -1.067  -1.050  -0.822  -0.824  -0.789  -0.955  -0.953  -0.922
195   L        -1.068  -1.067  -1.050  -1.031  -1.028  -0.998  -0.955  -0.953  -0.922
196   N        -1.068  -1.067  -1.050  -1.084  -1.081  -1.051  -0.955  -0.953  -0.922
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   -        -0.059  -0.059  -0.040  -0.588  -0.590  -0.555  -0.273  -0.273  -0.241
202   -        -0.059  -0.059  -0.040  -0.368  -0.369  -0.334  -0.273  -0.273  -0.241
* 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/Q02486
Output conservation file - output/Q02486
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
