1     M         1.456   1.456   1.469   1.785   1.785   1.805   1.531   1.531   1.547
2     D         1.456   1.456   1.469   1.380   1.381   1.400   1.531   1.531   1.547
3     A        -0.041  -0.059  -0.087   0.029   0.001  -0.045  -0.159  -0.187  -0.230
4     F         1.456   1.456   1.469   1.738   1.738   1.758   1.531   1.531   1.547
5     S         1.456   1.456   1.469   1.423   1.423   1.444   1.531   1.531   1.547
6     L         1.456   1.456   1.469   1.251   1.251   1.272   1.531   1.531   1.547
7     K         1.456   1.456   1.469   1.245   1.248   1.266   1.531   1.531   1.547
8     K        -0.041  -0.059  -0.087  -0.253  -0.280  -0.324  -0.159  -0.187  -0.230
9     D        -0.041  -0.059  -0.087  -0.200  -0.232  -0.288  -0.159  -0.187  -0.230
10    N         1.456   1.456   1.469   1.511   1.511   1.531   1.531   1.531   1.547
11    R         1.456   1.456   1.469   1.543   1.540   1.564   1.531   1.531   1.547
12    K        -0.041  -0.059  -0.087  -0.205  -0.231  -0.269  -0.159  -0.187  -0.230
13    K        -0.041  -0.059  -0.087  -0.205  -0.231  -0.269  -0.159  -0.187  -0.230
14    F         1.456   1.456   1.469   1.744   1.744   1.764   1.531   1.531   1.547
15    Q         1.456   1.456   1.469   1.543   1.542   1.564   1.531   1.531   1.547
16    D         1.456   1.456   1.469   1.380   1.381   1.400   1.531   1.531   1.547
17    K         1.456   1.456   1.469   1.245   1.248   1.266   1.531   1.531   1.547
18    Q        -0.041  -0.036  -0.090  -0.046  -0.038  -0.146  -0.159  -0.151  -0.235
19    K        -0.041  -0.059  -0.087  -0.205  -0.231  -0.269  -0.159  -0.187  -0.230
20    L         1.456   1.456   1.469   1.324   1.326   1.345   1.531   1.531   1.547
21    K         1.456   1.456   1.469   1.245   1.248   1.266   1.531   1.531   1.547
22    R         1.456   1.456   1.469   1.543   1.540   1.564   1.531   1.531   1.547
23    K        -0.041  -0.059  -0.087  -0.226  -0.251  -0.294  -0.159  -0.187  -0.230
24    H         1.456   1.456   1.469   1.702   1.700   1.722   1.531   1.531   1.547
25    A        -0.041  -0.059  -0.087   0.029   0.001  -0.045  -0.159  -0.187  -0.230
26    T         1.456   1.456   1.469   1.489   1.488   1.510   1.531   1.531   1.547
27    P         1.456   1.456   1.469   1.554   1.552   1.574   1.531   1.531   1.547
28    S         1.456   1.456   1.469   1.446   1.445   1.466   1.531   1.531   1.547
29    D         1.456   1.456   1.469   1.380   1.381   1.400   1.531   1.531   1.547
30    R         1.456   1.456   1.469   1.543   1.540   1.564   1.531   1.531   1.547
31    K         1.456   1.456   1.469   1.245   1.248   1.266   1.531   1.531   1.547
32    Y         1.456   1.456   1.469   1.754   1.753   1.774   1.531   1.531   1.547
33    R         1.456   1.456   1.469   1.543   1.540   1.564   1.531   1.531   1.547
34    L        -0.174  -0.174  -0.159  -0.460  -0.461  -0.435  -0.370  -0.370  -0.345
35    L         1.456   1.456   1.469   1.251   1.251   1.272   1.531   1.531   1.547
36    N         1.456   1.456   1.469   1.515   1.515   1.535   1.531   1.531   1.547
37    R        -0.174  -0.174  -0.159  -0.366  -0.367  -0.342  -0.370  -0.370  -0.345
38    Q        -0.174  -0.174  -0.159  -0.378  -0.379  -0.353  -0.370  -0.370  -0.345
39    K        -0.174  -0.174  -0.159  -0.472  -0.473  -0.447  -0.370  -0.370  -0.345
40    E         1.456   1.456   1.469   1.330   1.330   1.351   1.531   1.531   1.547
41    E        -0.174  -0.174  -0.159  -0.366  -0.367  -0.342  -0.370  -0.370  -0.345
42    K        -0.174  -0.174  -0.159  -0.581  -0.582  -0.556  -0.370  -0.370  -0.345
43    A         1.456   1.456   1.469   1.469   1.469   1.490   1.531   1.531   1.547
44    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    E        -1.127  -1.127  -1.111  -1.272  -1.274  -1.246  -1.003  -1.003  -0.976
47    E        -1.127  -1.127  -1.111  -1.101  -1.098  -1.075  -1.003  -1.003  -0.976
48    K        -1.127  -1.127  -1.111  -1.108  -1.102  -1.082  -1.003  -1.003  -0.976
49    D        -0.041  -0.027  -0.081  -0.242  -0.221  -0.310  -0.159  -0.138  -0.221
50    Q        -0.041  -0.036  -0.090  -0.046  -0.038  -0.146  -0.159  -0.151  -0.235
51    D        -1.127  -1.127  -1.111  -1.157  -1.154  -1.131  -1.003  -1.003  -0.976
52    Q        -1.127  -1.127  -1.111  -1.108  -1.107  -1.082  -1.003  -1.003  -0.976
53    E        -0.041  -0.036  -0.090  -0.163  -0.158  -0.234  -0.159  -0.151  -0.235
54    Q        -1.127  -1.127  -1.111  -1.143  -1.150  -1.117  -1.003  -1.003  -0.976
55    P        -1.127  -1.127  -1.111  -0.947  -0.954  -0.921  -1.003  -1.003  -0.976
56    A        -1.127  -1.127  -1.111  -0.960  -0.960  -0.934  -1.003  -1.003  -0.976
57    L         1.456   1.456   1.469   1.324   1.326   1.345   1.531   1.531   1.547
58    K        -1.127  -1.127  -1.111  -1.264  -1.258  -1.238  -1.003  -1.003  -0.976
59    S         1.456   1.456   1.469   1.446   1.445   1.466   1.531   1.531   1.547
60    N         1.456   1.456   1.469   1.511   1.511   1.531   1.531   1.531   1.547
61    E        -0.041  -0.059  -0.087  -0.086  -0.113  -0.141  -0.159  -0.187  -0.230
62    D        -1.127  -1.127  -1.111  -1.080  -1.086  -1.055  -1.003  -1.003  -0.976
63    R         1.456   1.456   1.469   1.543   1.540   1.564   1.531   1.531   1.547
64    Y         1.456   1.456   1.469   1.754   1.753   1.774   1.531   1.531   1.547
65    Y        -1.127  -1.127  -1.111  -0.806  -0.811  -0.781  -1.003  -1.003  -0.976
66    E        -1.127  -1.127  -1.111  -1.250  -1.249  -1.224  -1.003  -1.003  -0.976
67    D        -1.127  -1.127  -1.111  -1.087  -1.080  -1.062  -1.003  -1.003  -0.976
68    P        -0.041  -0.036  -0.090  -0.021  -0.012  -0.119  -0.159  -0.151  -0.235
69    V        -1.127  -1.127  -1.111  -0.940  -0.937  -0.915  -1.003  -1.003  -0.976
70    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    E         1.456   1.456   1.469   1.330   1.330   1.351   1.531   1.531   1.547
72    D        -0.174  -0.174  -0.159  -0.448  -0.449  -0.424  -0.370  -0.370  -0.345
73    P         1.456   1.456   1.469   1.605   1.605   1.625   1.531   1.531   1.547
74    H        -0.041  -0.027  -0.081  -0.006   0.013  -0.056  -0.159  -0.138  -0.221
75    S        -1.127  -1.127  -1.111  -1.020  -1.019  -0.994  -1.003  -1.003  -0.976
76    A        -0.041  -0.027  -0.081   0.203   0.226   0.128  -0.159  -0.138  -0.221
77    V        -1.127  -1.127  -1.111  -1.115  -1.124  -1.089  -1.003  -1.003  -0.976
78    A        -1.127  -1.127  -1.111  -0.947  -0.949  -0.921  -1.003  -1.003  -0.976
79    N        -1.127  -1.127  -1.111  -0.953  -0.948  -0.928  -1.003  -1.003  -0.976
80    A        -1.127  -1.127  -1.111  -1.143  -1.142  -1.117  -1.003  -1.003  -0.976
81    E        -1.127  -1.127  -1.111  -1.272  -1.274  -1.246  -1.003  -1.003  -0.976
82    L        -1.127  -1.127  -1.111  -0.837  -0.831  -0.812  -1.003  -1.003  -0.976
83    N        -1.127  -1.127  -1.111  -1.006  -1.006  -0.981  -1.003  -1.003  -0.976
84    K        -1.127  -1.127  -1.111  -1.384  -1.382  -1.358  -1.003  -1.003  -0.976
85    V        -0.041  -0.059  -0.087   0.009  -0.027  -0.084  -0.159  -0.187  -0.230
86    L        -0.041  -0.027  -0.081  -0.081  -0.057  -0.160  -0.159  -0.138  -0.221
87    K        -0.041  -0.036  -0.090  -0.226  -0.216  -0.298  -0.159  -0.151  -0.235
88    D        -0.041  -0.027  -0.081  -0.285  -0.260  -0.352  -0.159  -0.138  -0.221
89    V        -0.041  -0.036  -0.090   0.175   0.179   0.103  -0.159  -0.151  -0.235
90    L        -1.127  -1.127  -1.111  -1.250  -1.243  -1.224  -1.003  -1.003  -0.976
91    K        -0.174  -0.174  -0.159  -0.581  -0.582  -0.556  -0.370  -0.370  -0.345
92    N        -0.174  -0.174  -0.159  -0.056  -0.057  -0.033  -0.370  -0.370  -0.345
93    R        -0.174  -0.174  -0.159  -0.320  -0.321  -0.296  -0.370  -0.370  -0.345
94    L         1.456   1.456   1.469   1.251   1.251   1.272   1.531   1.531   1.547
95    Q        -0.174  -0.174  -0.159  -0.164  -0.165  -0.140  -0.370  -0.370  -0.345
96    Q        -0.174  -0.174  -0.159  -0.378  -0.379  -0.353  -0.370  -0.370  -0.345
97    N        -0.174  -0.174  -0.159  -0.046  -0.047  -0.022  -0.370  -0.370  -0.345
98    D         1.456   1.456   1.469   1.361   1.361   1.382   1.531   1.531   1.547
99    D        -0.174  -0.174  -0.159  -0.448  -0.449  -0.424  -0.370  -0.370  -0.345
100   A        -0.041  -0.036  -0.090   0.029   0.038  -0.050  -0.159  -0.151  -0.235
101   T        -0.041  -0.036  -0.090   0.024   0.030  -0.054  -0.159  -0.151  -0.235
102   A        -1.127  -1.127  -1.111  -0.863  -0.864  -0.837  -1.003  -1.003  -0.976
103   V        -1.127  -1.127  -1.111  -1.192  -1.199  -1.166  -1.003  -1.003  -0.976
104   N        -1.127  -1.127  -1.111  -1.122  -1.119  -1.096  -1.003  -1.003  -0.976
105   N        -1.127  -1.127  -1.111  -0.908  -0.905  -0.882  -1.003  -1.003  -0.976
106   V        -1.127  -1.127  -1.111  -0.960  -0.963  -0.934  -1.003  -1.003  -0.976
107   A        -0.041  -0.036  -0.090   0.004   0.013  -0.079  -0.159  -0.151  -0.235
108   N        -1.127  -1.127  -1.111  -0.837  -0.835  -0.812  -1.003  -1.003  -0.976
109   K        -1.127  -1.127  -1.111  -1.101  -1.097  -1.075  -1.003  -1.003  -0.976
110   D        -0.041  -0.059  -0.087  -0.200  -0.232  -0.288  -0.159  -0.187  -0.230
111   T        -0.041  -0.059  -0.087   0.093   0.065   0.030  -0.159  -0.187  -0.230
112   L        -1.127  -1.127  -1.111  -1.094  -1.091  -1.068  -1.003  -1.003  -0.976
113   K        -1.127  -1.127  -1.111  -1.108  -1.105  -1.082  -1.003  -1.003  -0.976
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -0.174  -0.174  -0.159   0.111   0.110   0.134  -0.370  -0.370  -0.345
116   -         1.456   1.456   1.469   1.444   1.444   1.465   1.531   1.531   1.547
117   I        -1.127  -1.127  -1.111  -1.074  -1.076  -1.048  -1.003  -1.003  -0.976
118   K        -0.041  -0.059  -0.087  -0.205  -0.231  -0.269  -0.159  -0.187  -0.230
119   D        -0.041  -0.027  -0.081  -0.006   0.017  -0.082  -0.159  -0.138  -0.221
120   L        -0.041  -0.059  -0.087  -0.061  -0.084  -0.117  -0.159  -0.187  -0.230
121   K        -1.127  -1.127  -1.111  -1.272  -1.265  -1.246  -1.003  -1.003  -0.976
122   Q        -1.127  -1.127  -1.111  -1.006  -1.009  -0.981  -1.003  -1.003  -0.976
123   M         1.456   1.456   1.469   1.785   1.785   1.805   1.531   1.531   1.547
124   N        -1.127  -1.127  -1.111  -0.901  -0.898  -0.876  -1.003  -1.003  -0.976
125   T        -0.041  -0.036  -0.090   0.039   0.044  -0.037  -0.159  -0.151  -0.235
126   D        -0.041  -0.036  -0.090  -0.127  -0.118  -0.209  -0.159  -0.151  -0.235
127   E         1.456   1.456   1.469   1.290   1.289   1.311   1.531   1.531   1.547
128   L         1.456   1.456   1.469   1.324   1.326   1.345   1.531   1.531   1.547
129   N         1.456   1.456   1.469   1.511   1.511   1.531   1.531   1.531   1.547
130   R        -1.127  -1.127  -1.111  -1.108  -1.109  -1.082  -1.003  -1.003  -0.976
131   W        -0.041  -0.027  -0.081   0.014   0.032  -0.025  -0.159  -0.138  -0.221
132   L         1.456   1.456   1.469   1.324   1.326   1.345   1.531   1.531   1.547
133   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   Q        -1.127  -1.127  -1.111  -1.060  -1.060  -1.034  -1.003  -1.003  -0.976
136   N         1.456   1.456   1.469   1.511   1.511   1.531   1.531   1.531   1.547
137   T        -1.127  -1.127  -1.111  -0.980  -0.982  -0.954  -1.003  -1.003  -0.976
138   T        -0.041  -0.059  -0.087   0.039   0.008  -0.032  -0.159  -0.187  -0.230
139   S        -0.041  -0.027  -0.081   0.064   0.083  -0.010  -0.159  -0.138  -0.221
140   A        -1.127  -1.127  -1.111  -0.876  -0.872  -0.850  -1.003  -1.003  -0.976
141   I        -1.127  -1.127  -1.111  -0.882  -0.884  -0.857  -1.003  -1.003  -0.976
142   T        -1.127  -1.127  -1.111  -0.953  -0.954  -0.928  -1.003  -1.003  -0.976
143   A        -0.041  -0.027  -0.081  -0.184  -0.165  -0.244  -0.159  -0.138  -0.221
144   A        -1.127  -1.127  -1.111  -1.108  -1.104  -1.082  -1.003  -1.003  -0.976
145   E        -1.127  -1.127  -1.111  -1.178  -1.179  -1.152  -1.003  -1.003  -0.976
146   P        -1.127  -1.127  -1.111  -1.080  -1.084  -1.055  -1.003  -1.003  -0.976
147   E        -1.127  -1.127  -1.111  -1.294  -1.288  -1.268  -1.003  -1.003  -0.976
148   S         1.456   1.456   1.469   1.446   1.445   1.466   1.531   1.531   1.547
149   L        -0.174  -0.174  -0.159  -0.643  -0.644  -0.618  -0.370  -0.370  -0.345
150   V        -0.174  -0.174  -0.159   0.059   0.058   0.083  -0.370  -0.370  -0.345
151   V        -0.174  -0.174  -0.159  -0.110  -0.111  -0.086  -0.370  -0.370  -0.345
152   P         1.456   1.456   1.469   1.605   1.605   1.625   1.531   1.531   1.547
153   I        -0.174  -0.174  -0.159  -0.241  -0.242  -0.217  -0.370  -0.370  -0.345
154   H        -0.041  -0.036  -0.090   0.117   0.126   0.013  -0.159  -0.151  -0.235
155   V        -0.041  -0.036  -0.090   0.184   0.188   0.114  -0.159  -0.151  -0.235
156   Q        -1.127  -1.127  -1.111  -0.980  -0.981  -0.954  -1.003  -1.003  -0.976
157   G        -1.127  -1.127  -1.111  -1.026  -1.026  -1.001  -1.003  -1.003  -0.976
158   D        -1.127  -1.127  -1.111  -1.250  -1.252  -1.224  -1.003  -1.003  -0.976
159   H        -0.041  -0.036  -0.090   0.301   0.307   0.228  -0.159  -0.151  -0.235
160   D        -1.127  -1.127  -1.111  -1.384  -1.385  -1.358  -1.003  -1.003  -0.976
161   R        -0.041  -0.036  -0.090   0.024   0.030  -0.065  -0.159  -0.151  -0.235
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -0.174  -0.174  -0.159  -0.265  -0.266  -0.241  -0.370  -0.370  -0.345
165   -        -0.174  -0.174  -0.159  -0.078  -0.079  -0.055  -0.370  -0.370  -0.345
166   -        -0.174  -0.174  -0.159  -0.313  -0.314  -0.289  -0.370  -0.370  -0.345
167   -        -0.174  -0.174  -0.159  -0.194  -0.195  -0.170  -0.370  -0.370  -0.345
168   -        -0.174  -0.174  -0.159  -0.374  -0.375  -0.350  -0.370  -0.370  -0.345
169   -        -0.174  -0.174  -0.159  -0.217  -0.218  -0.193  -0.370  -0.370  -0.345
170   -        -0.174  -0.174  -0.159  -0.182  -0.183  -0.158  -0.370  -0.370  -0.345
171   -        -0.174  -0.174  -0.159  -0.325  -0.326  -0.301  -0.370  -0.370  -0.345
172   -        -0.174  -0.174  -0.159  -0.337  -0.338  -0.313  -0.370  -0.370  -0.345
173   -        -0.174  -0.174  -0.159  -0.386  -0.387  -0.362  -0.370  -0.370  -0.345
174   -        -0.174  -0.174  -0.159  -0.194  -0.195  -0.170  -0.370  -0.370  -0.345
175   A        -1.127  -1.127  -1.111  -0.960  -0.960  -0.934  -1.003  -1.003  -0.976
176   G        -1.127  -1.127  -1.111  -0.914  -0.920  -0.889  -1.003  -1.003  -0.976
177   K        -1.127  -1.127  -1.111  -1.115  -1.110  -1.089  -1.003  -1.003  -0.976
178   K        -1.127  -1.127  -1.111  -1.067  -1.065  -1.041  -1.003  -1.003  -0.976
179   I        -1.127  -1.127  -1.111  -0.831  -0.834  -0.806  -1.003  -1.003  -0.976
180   S        -0.041  -0.027  -0.081  -0.006   0.017  -0.077  -0.159  -0.138  -0.221
181   A        -1.127  -1.127  -1.111  -1.279  -1.279  -1.253  -1.003  -1.003  -0.976
182   P         1.456   1.456   1.469   1.554   1.552   1.574   1.531   1.531   1.547
183   S        -0.174  -0.174  -0.159  -0.460  -0.461  -0.435  -0.370  -0.370  -0.345
184   T        -0.041  -0.027  -0.081  -0.046  -0.025  -0.112  -0.159  -0.138  -0.221
185   D        -1.127  -1.127  -1.111  -1.060  -1.062  -1.034  -1.003  -1.003  -0.976
186   L        -1.127  -1.127  -1.111  -0.940  -0.938  -0.915  -1.003  -1.003  -0.976
187   P         1.456   1.456   1.469   1.554   1.552   1.574   1.531   1.531   1.547
188   E        -0.041  -0.036  -0.090  -0.189  -0.184  -0.264  -0.159  -0.151  -0.235
189   E        -0.041  -0.036  -0.090  -0.158  -0.153  -0.228  -0.159  -0.151  -0.235
190   L         1.456   1.456   1.469   1.324   1.326   1.345   1.531   1.531   1.547
191   E        -1.127  -1.127  -1.111  -1.301  -1.294  -1.275  -1.003  -1.003  -0.976
192   T        -1.127  -1.127  -1.111  -1.006  -1.003  -0.981  -1.003  -1.003  -0.976
193   D         1.456   1.456   1.469   1.380   1.381   1.400   1.531   1.531   1.547
194   Q        -0.041  -0.027  -0.081  -0.163  -0.146  -0.221  -0.159  -0.138  -0.221
195   D        -1.127  -1.127  -1.111  -0.953  -0.946  -0.928  -1.003  -1.003  -0.976
196   F         1.456   1.456   1.469   1.744   1.744   1.764   1.531   1.531   1.547
197   L         1.456   1.456   1.469   1.324   1.326   1.345   1.531   1.531   1.547
198   D         1.456   1.456   1.469   1.380   1.381   1.400   1.531   1.531   1.547
199   G        -0.041  -0.027  -0.081   0.059   0.076   0.006  -0.159  -0.138  -0.221
200   L        -0.041  -0.027  -0.081   0.107   0.133   0.022  -0.159  -0.138  -0.221
201   L        -0.041  -0.036  -0.090  -0.061  -0.053  -0.121  -0.159  -0.151  -0.235
* 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/P40022
Output conservation file - output/P40022
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
