1     M         1.818   1.820   1.849   2.006   2.009   2.053   1.958   1.960   1.996
2     S        -1.132  -1.131  -1.109  -0.825  -0.820  -0.784  -0.995  -0.993  -0.952
3     D        -0.043  -0.042  -0.017  -0.235  -0.234  -0.193  -0.257  -0.255  -0.215
4     T        -0.043  -0.042  -0.017  -0.127  -0.126  -0.085  -0.257  -0.255  -0.215
5     T        -0.043  -0.042  -0.017  -0.194  -0.193  -0.152  -0.257  -0.255  -0.215
6     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     P        -0.043  -0.042  -0.017   0.068   0.069   0.110  -0.257  -0.255  -0.215
9     R        -0.043  -0.042  -0.017  -0.211  -0.210  -0.169  -0.257  -0.255  -0.215
10    Q         1.818   1.820   1.849   1.844   1.846   1.890   1.958   1.960   1.996
11    S         1.818   1.820   1.849   1.676   1.678   1.722   1.958   1.960   1.996
12    S         0.109   0.091   0.066  -0.069  -0.101  -0.144  -0.010  -0.039  -0.080
13    E        -1.132  -1.131  -1.109  -1.287  -1.281  -1.247  -0.995  -0.993  -0.952
14    N        -1.132  -1.131  -1.109  -1.270  -1.271  -1.231  -0.995  -0.993  -0.952
15    D         0.109   0.091   0.066   0.103   0.075   0.042  -0.010  -0.039  -0.080
16    Q        -1.132  -1.131  -1.109  -1.183  -1.185  -1.143  -0.995  -0.993  -0.952
17    D        -1.132  -1.131  -1.109  -0.918  -0.913  -0.878  -0.995  -0.993  -0.952
18    N         0.109   0.091   0.066   0.058   0.026  -0.035  -0.010  -0.039  -0.080
19    N        -1.132  -1.131  -1.109  -0.882  -0.881  -0.842  -0.995  -0.993  -0.952
20    L         0.109   0.123   0.078   0.058   0.082  -0.005  -0.010   0.012  -0.060
21    E        -1.132  -1.131  -1.109  -1.167  -1.160  -1.127  -0.995  -0.993  -0.952
22    R         0.109   0.123   0.078  -0.034  -0.015  -0.074  -0.010   0.012  -0.060
23    T        -1.132  -1.131  -1.109  -1.006  -1.005  -0.967  -0.995  -0.993  -0.952
24    N        -1.132  -1.131  -1.109  -1.175  -1.173  -1.135  -0.995  -0.993  -0.952
25    S        -1.132  -1.131  -1.109  -1.090  -1.083  -1.050  -0.995  -0.993  -0.952
26    L         0.109   0.117   0.080   0.035   0.045  -0.003  -0.010   0.002  -0.057
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -0.043  -0.042  -0.017  -0.304  -0.303  -0.262  -0.257  -0.255  -0.215
30    -         1.818   1.820   1.849   1.874   1.876   1.920   1.958   1.960   1.996
31    K         0.109   0.117   0.080  -0.064  -0.052  -0.105  -0.010   0.002  -0.057
32    S         0.109   0.091   0.066   0.120   0.096   0.075  -0.010  -0.039  -0.080
33    P         1.818   1.820   1.849   2.112   2.116   2.159   1.958   1.960   1.996
34    D         0.109   0.117   0.080   0.192   0.202   0.163  -0.010   0.002  -0.057
35    V         0.109   0.117   0.080   0.170   0.183   0.108  -0.010   0.002  -0.057
36    T         0.109   0.091   0.066   0.035  -0.000  -0.058  -0.010  -0.039  -0.080
37    N         0.109   0.091   0.066   0.296   0.274   0.241  -0.010  -0.039  -0.080
38    N        -1.132  -1.131  -1.109  -0.803  -0.795  -0.763  -0.995  -0.993  -0.952
39    I        -0.043  -0.042  -0.017  -0.221  -0.220  -0.179  -0.257  -0.255  -0.215
40    P         1.818   1.820   1.849   2.112   2.116   2.159   1.958   1.960   1.996
41    S        -1.132  -1.131  -1.109  -1.144  -1.135  -1.104  -0.995  -0.993  -0.952
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    L         1.818   1.820   1.849   1.676   1.677   1.722   1.958   1.960   1.996
44    F        -1.132  -1.131  -1.109  -0.817  -0.825  -0.777  -0.995  -0.993  -0.952
45    K         0.109   0.091   0.066  -0.087  -0.115  -0.153  -0.010  -0.039  -0.080
46    L         0.109   0.091   0.066  -0.017  -0.047  -0.083  -0.010  -0.039  -0.080
47    A         0.109   0.091   0.066   0.170   0.140   0.095  -0.010  -0.039  -0.080
48    A         0.109   0.091   0.066   0.058   0.023  -0.035  -0.010  -0.039  -0.080
49    E         0.109   0.091   0.066  -0.017  -0.041  -0.070  -0.010  -0.039  -0.080
50    W         1.818   1.820   1.849   2.100   2.103   2.148   1.958   1.960   1.996
51    Q         0.109   0.091   0.066   0.269   0.246   0.219  -0.010  -0.039  -0.080
52    I        -1.132  -1.131  -1.109  -1.287  -1.289  -1.247  -0.995  -0.993  -0.952
53    N        -1.132  -1.131  -1.109  -1.175  -1.175  -1.135  -0.995  -0.993  -0.952
54    N        -1.132  -1.131  -1.109  -0.999  -0.992  -0.959  -0.995  -0.993  -0.952
55    P        -1.132  -1.131  -1.109  -1.006  -1.006  -0.967  -0.995  -0.993  -0.952
56    Q        -1.132  -1.131  -1.109  -1.120  -1.114  -1.081  -0.995  -0.993  -0.952
57    E         0.109   0.091   0.066  -0.140  -0.170  -0.213  -0.010  -0.039  -0.080
58    T         0.109   0.117   0.080   0.035   0.049  -0.029  -0.010   0.002  -0.057
59    F        -1.132  -1.131  -1.109  -0.679  -0.679  -0.638  -0.995  -0.993  -0.952
60    Q         0.109   0.091   0.066   0.080   0.050   0.000  -0.010  -0.039  -0.080
61    N         0.109   0.117   0.080   0.214   0.229   0.169  -0.010   0.002  -0.057
62    H        -1.132  -1.131  -1.109  -0.991  -0.997  -0.952  -0.995  -0.993  -0.952
63    I        -1.132  -1.131  -1.109  -0.768  -0.762  -0.728  -0.995  -0.993  -0.952
64    L         0.109   0.091   0.066   0.109   0.084   0.062  -0.010  -0.039  -0.080
65    E        -1.132  -1.131  -1.109  -1.344  -1.342  -1.305  -0.995  -0.993  -0.952
66    N         0.109   0.091   0.066   0.214   0.188   0.147  -0.010  -0.039  -0.080
67    D         0.109   0.117   0.080  -0.069  -0.056  -0.131  -0.010   0.002  -0.057
68    V         0.109   0.117   0.080   0.371   0.382   0.334  -0.010   0.002  -0.057
69    L         1.818   1.820   1.849   1.676   1.677   1.722   1.958   1.960   1.996
70    K         0.109   0.091   0.066  -0.164  -0.196  -0.243  -0.010  -0.039  -0.080
71    K        -1.132  -1.131  -1.109  -1.222  -1.215  -1.183  -0.995  -0.993  -0.952
72    I         0.109   0.117   0.080   0.192   0.204   0.150  -0.010   0.002  -0.057
73    N        -1.132  -1.131  -1.109  -1.262  -1.261  -1.223  -0.995  -0.993  -0.952
74    E         1.818   1.820   1.849   1.600   1.603   1.646   1.958   1.960   1.996
75    I         1.818   1.820   1.849   1.849   1.852   1.896   1.958   1.960   1.996
76    T         0.109   0.117   0.080   0.069   0.082   0.009  -0.010   0.002  -0.057
77    H        -1.132  -1.131  -1.109  -1.090  -1.094  -1.050  -0.995  -0.993  -0.952
78    L        -1.132  -1.131  -1.109  -1.246  -1.242  -1.207  -0.995  -0.993  -0.952
79    I        -1.132  -1.131  -1.109  -1.036  -1.030  -0.997  -0.995  -0.993  -0.952
80    R        -1.132  -1.131  -1.109  -0.999  -1.004  -0.959  -0.995  -0.993  -0.952
81    E        -1.132  -1.131  -1.109  -1.344  -1.336  -1.305  -0.995  -0.993  -0.952
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    S        -1.132  -1.131  -1.109  -1.270  -1.270  -1.231  -0.995  -0.993  -0.952
85    Y        -1.132  -1.131  -1.109  -1.067  -1.071  -1.027  -0.995  -0.993  -0.952
86    K        -1.132  -1.131  -1.109  -1.262  -1.260  -1.223  -0.995  -0.993  -0.952
87    D         0.109   0.091   0.066   0.063   0.036  -0.004  -0.010  -0.039  -0.080
88    L        -0.043  -0.042  -0.017  -0.107  -0.106  -0.065  -0.257  -0.255  -0.215
89    S        -0.043  -0.042  -0.017  -0.082  -0.081  -0.040  -0.257  -0.255  -0.215
90    S        -0.043  -0.042  -0.017  -0.185  -0.184  -0.143  -0.257  -0.255  -0.215
91    Q        -0.043  -0.042  -0.017  -0.211  -0.210  -0.169  -0.257  -0.255  -0.215
92    D         1.818   1.820   1.849   1.719   1.721   1.765   1.958   1.960   1.996
93    G        -0.043  -0.042  -0.017  -0.120  -0.119  -0.078  -0.257  -0.255  -0.215
94    M        -0.043  -0.042  -0.017   0.201   0.203   0.244  -0.257  -0.255  -0.215
95    M        -0.043  -0.042  -0.017   0.031   0.032   0.073  -0.257  -0.255  -0.215
96    S        -0.043  -0.042  -0.017  -0.250  -0.249  -0.209  -0.257  -0.255  -0.215
97    K         0.109   0.091   0.066  -0.064  -0.090  -0.126  -0.010  -0.039  -0.080
98    Q        -1.132  -1.131  -1.109  -1.206  -1.205  -1.167  -0.995  -0.993  -0.952
99    Q        -1.132  -1.131  -1.109  -0.734  -0.729  -0.693  -0.995  -0.993  -0.952
100   Q        -1.132  -1.131  -1.109  -0.962  -0.958  -0.922  -0.995  -0.993  -0.952
101   E        -1.132  -1.131  -1.109  -1.167  -1.157  -1.127  -0.995  -0.993  -0.952
102   K        -1.132  -1.131  -1.109  -1.120  -1.113  -1.081  -0.995  -0.993  -0.952
103   M         0.109   0.123   0.078   0.052   0.071   0.014  -0.010   0.012  -0.060
104   D         0.109   0.117   0.080   0.063   0.076   0.019  -0.010   0.002  -0.057
105   W         1.818   1.820   1.849   2.100   2.103   2.148   1.958   1.960   1.996
106   D         0.109   0.091   0.066  -0.069  -0.103  -0.158  -0.010  -0.039  -0.080
107   L        -1.132  -1.131  -1.109  -1.254  -1.254  -1.215  -0.995  -0.993  -0.952
108   F        -1.132  -1.131  -1.109  -0.699  -0.700  -0.659  -0.995  -0.993  -0.952
109   C         0.109   0.123   0.078   0.450   0.470   0.411  -0.010   0.012  -0.060
110   T        -1.132  -1.131  -1.109  -1.238  -1.241  -1.199  -0.995  -0.993  -0.952
111   V         1.818   1.820   1.849   1.970   1.971   2.017   1.958   1.960   1.996
112   P        -1.132  -1.131  -1.109  -0.825  -0.822  -0.784  -0.995  -0.993  -0.952
113   V         0.109   0.123   0.078   0.225   0.246   0.179  -0.010   0.012  -0.060
114   N        -1.132  -1.131  -1.109  -1.270  -1.269  -1.231  -0.995  -0.993  -0.952
115   I         0.109   0.117   0.080   0.058   0.071  -0.002  -0.010   0.002  -0.057
116   I         0.109   0.123   0.078   0.280   0.305   0.224  -0.010   0.012  -0.060
117   E         0.109   0.123   0.078  -0.069  -0.045  -0.134  -0.010   0.012  -0.060
118   Q         1.818   1.820   1.849   1.837   1.841   1.883   1.958   1.960   1.996
119   Y         1.818   1.820   1.849   2.041   2.043   2.088   1.958   1.960   1.996
120   T         0.109   0.123   0.078  -0.017   0.004  -0.064  -0.010   0.012  -0.060
121   K         0.109   0.091   0.066  -0.064  -0.091  -0.126  -0.010  -0.039  -0.080
122   D        -1.132  -1.131  -1.109  -1.238  -1.234  -1.199  -0.995  -0.993  -0.952
123   M         0.109   0.091   0.066   0.334   0.305   0.264  -0.010  -0.039  -0.080
124   D         0.109   0.117   0.080  -0.069  -0.056  -0.131  -0.010   0.002  -0.057
125   E         0.109   0.117   0.080  -0.099  -0.085  -0.143  -0.010   0.002  -0.057
126   I         0.109   0.091   0.066   0.058   0.024  -0.029  -0.010  -0.039  -0.080
127   Y         0.109   0.123   0.078   0.069   0.087   0.033  -0.010   0.012  -0.060
128   E         0.109   0.123   0.078   0.058   0.084  -0.010  -0.010   0.012  -0.060
129   K        -1.132  -1.131  -1.109  -1.403  -1.398  -1.364  -0.995  -0.993  -0.952
130   M         0.109   0.123   0.078   0.052   0.071   0.014  -0.010   0.012  -0.060
131   E         0.109   0.123   0.078  -0.069  -0.045  -0.134  -0.010   0.012  -0.060
132   R        -1.132  -1.131  -1.109  -1.270  -1.273  -1.231  -0.995  -0.993  -0.952
133   L         0.109   0.117   0.080   0.035   0.045  -0.003  -0.010   0.002  -0.057
134   A         0.109   0.123   0.078   0.328   0.351   0.273  -0.010   0.012  -0.060
135   K         0.109   0.091   0.066  -0.034  -0.061  -0.092  -0.010  -0.039  -0.080
136   Q         0.109   0.123   0.078  -0.087  -0.065  -0.134  -0.010   0.012  -0.060
137   Q         0.109   0.117   0.080   0.264   0.276   0.231  -0.010   0.002  -0.057
138   R        -1.132  -1.131  -1.109  -0.692  -0.691  -0.652  -0.995  -0.993  -0.952
139   L         0.109   0.117   0.080   0.052   0.063   0.016  -0.010   0.002  -0.057
140   W         1.818   1.820   1.849   2.100   2.103   2.148   1.958   1.960   1.996
141   C         0.109   0.123   0.078   0.269   0.289   0.235  -0.010   0.012  -0.060
142   E         0.109   0.091   0.066  -0.140  -0.170  -0.213  -0.010  -0.039  -0.080
143   S         0.109   0.117   0.080  -0.005   0.006  -0.048  -0.010   0.002  -0.057
144   A         1.818   1.820   1.849   1.886   1.888   1.932   1.958   1.960   1.996
145   F         0.109   0.091   0.066   0.440   0.410   0.366  -0.010  -0.039  -0.080
146   Q        -1.132  -1.131  -1.109  -1.136  -1.137  -1.096  -0.995  -0.993  -0.952
147   I         0.109   0.091   0.066   0.058   0.024  -0.029  -0.010  -0.039  -0.080
148   D         1.818   1.820   1.849   1.751   1.752   1.797   1.958   1.960   1.996
149   V         0.109   0.123   0.078   0.035   0.054  -0.005  -0.010   0.012  -0.060
150   E        -1.132  -1.131  -1.109  -0.825  -0.816  -0.784  -0.995  -0.993  -0.952
151   R         0.109   0.091   0.066   0.120   0.084   0.026  -0.010  -0.039  -0.080
152   C         0.109   0.123   0.078   0.492   0.510   0.451  -0.010   0.012  -0.060
153   G         0.109   0.123   0.078   0.280   0.299   0.241  -0.010   0.012  -0.060
154   D         0.109   0.123   0.078   0.103   0.126   0.045  -0.010   0.012  -0.060
155   S        -1.132  -1.131  -1.109  -1.074  -1.072  -1.035  -0.995  -0.993  -0.952
156   I         1.818   1.820   1.849   1.849   1.852   1.896   1.958   1.960   1.996
157   L        -1.132  -1.131  -1.109  -0.962  -0.956  -0.922  -0.995  -0.993  -0.952
158   N         0.109   0.091   0.066   0.214   0.188   0.147  -0.010  -0.039  -0.080
159   A         0.109   0.091   0.066   0.092   0.058   0.004  -0.010  -0.039  -0.080
160   E         1.818   1.820   1.849   1.600   1.603   1.646   1.958   1.960   1.996
161   T        -1.132  -1.131  -1.109  -1.067  -1.071  -1.027  -0.995  -0.993  -0.952
162   W         1.818   1.820   1.849   2.100   2.103   2.148   1.958   1.960   1.996
163   M         0.109   0.091   0.066   0.285   0.255   0.207  -0.010  -0.039  -0.080
164   K         1.818   1.820   1.849   1.613   1.615   1.659   1.958   1.960   1.996
165   K        -1.132  -1.131  -1.109  -1.403  -1.401  -1.364  -0.995  -0.993  -0.952
166   K         1.818   1.820   1.849   1.613   1.615   1.659   1.958   1.960   1.996
167   E         1.818   1.820   1.849   1.600   1.603   1.646   1.958   1.960   1.996
168   R         0.109   0.123   0.078   0.214   0.236   0.167  -0.010   0.012  -0.060
169   H        -1.132  -1.131  -1.109  -0.740  -0.743  -0.700  -0.995  -0.993  -0.952
170   L         1.818   1.820   1.849   1.676   1.677   1.722   1.958   1.960   1.996
171   E         0.109   0.117   0.080  -0.099  -0.085  -0.143  -0.010   0.002  -0.057
172   Y         1.818   1.820   1.849   2.041   2.043   2.088   1.958   1.960   1.996
173   K         0.109   0.117   0.080  -0.075  -0.064  -0.118  -0.010   0.002  -0.057
174   N        -1.132  -1.131  -1.109  -0.955  -0.952  -0.915  -0.995  -0.993  -0.952
175   I        -1.132  -1.131  -1.109  -1.151  -1.145  -1.112  -0.995  -0.993  -0.952
176   E         1.818   1.820   1.849   1.600   1.603   1.646   1.958   1.960   1.996
177   M         0.109   0.123   0.078   0.052   0.071   0.014  -0.010   0.012  -0.060
178   E        -1.132  -1.131  -1.109  -1.167  -1.160  -1.127  -0.995  -0.993  -0.952
179   R         0.109   0.117   0.080   0.231   0.243   0.180  -0.010   0.002  -0.057
180   S         1.818   1.820   1.849   1.676   1.678   1.722   1.958   1.960   1.996
181   A         1.818   1.820   1.849   1.886   1.888   1.932   1.958   1.960   1.996
182   N        -1.132  -1.131  -1.109  -0.999  -0.992  -0.959  -0.995  -0.993  -0.952
183   E         0.109   0.117   0.080  -0.034  -0.023  -0.070  -0.010   0.002  -0.057
184   I         1.818   1.820   1.849   1.849   1.852   1.896   1.958   1.960   1.996
185   K         1.818   1.820   1.849   1.613   1.615   1.659   1.958   1.960   1.996
186   E        -1.132  -1.131  -1.109  -1.113  -1.106  -1.073  -0.995  -0.993  -0.952
187   T         0.109   0.091   0.066   0.165   0.135   0.093  -0.010  -0.039  -0.080
188   I         0.109   0.091   0.066   0.058   0.024  -0.029  -0.010  -0.039  -0.080
189   Q        -1.132  -1.131  -1.109  -1.344  -1.344  -1.305  -0.995  -0.993  -0.952
190   R         0.109   0.117   0.080   0.181   0.194   0.124  -0.010   0.002  -0.057
191   L         1.818   1.820   1.849   1.676   1.677   1.722   1.958   1.960   1.996
192   T         0.109   0.123   0.078  -0.017   0.004  -0.064  -0.010   0.012  -0.060
193   D        -1.132  -1.131  -1.109  -1.230  -1.226  -1.191  -0.995  -0.993  -0.952
194   D        -0.043  -0.042  -0.017  -0.440  -0.439  -0.399  -0.257  -0.255  -0.215
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   R         0.109   0.091   0.066   0.148   0.113   0.058  -0.010  -0.039  -0.080
* 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/Q06201
Output conservation file - output/Q06201
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
