1     M         1.345   1.347   1.364   1.516   1.517   1.544   1.409   1.411   1.431
2     K         1.345   1.347   1.364   1.293   1.291   1.323   1.409   1.411   1.431
3     S        -1.225  -1.223  -1.196  -1.293  -1.292  -1.241  -1.100  -1.097  -1.051
4     F         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
5     Q        -1.225  -1.223  -1.196  -1.205  -1.191  -1.154  -1.100  -1.097  -1.051
6     K        -1.225  -1.223  -1.196  -1.252  -1.252  -1.201  -1.100  -1.097  -1.051
7     S        -1.225  -1.223  -1.196  -1.178  -1.179  -1.128  -1.100  -1.097  -1.051
8     Y        -1.225  -1.223  -1.196  -1.011  -1.004  -0.962  -1.100  -1.097  -1.051
9     E        -1.225  -1.223  -1.196  -1.391  -1.383  -1.338  -1.100  -1.097  -1.051
10    F         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
11    D        -1.225  -1.223  -1.196  -1.018  -1.015  -0.968  -1.100  -1.097  -1.051
12    Y         1.345   1.347   1.364   1.527   1.528   1.555   1.409   1.411   1.431
13    P        -0.144  -0.133  -0.190  -0.053  -0.033  -0.146  -0.264  -0.246  -0.333
14    W        -0.144  -0.126  -0.186   0.066   0.094  -0.009  -0.264  -0.236  -0.327
15    E         1.345   1.347   1.364   1.282   1.286   1.312   1.409   1.411   1.431
16    K        -1.225  -1.223  -1.196  -1.185  -1.184  -1.134  -1.100  -1.097  -1.051
17    V         1.345   1.347   1.364   1.216   1.216   1.247   1.409   1.411   1.431
18    T        -0.144  -0.168  -0.197  -0.316  -0.358  -0.414  -0.264  -0.301  -0.344
19    T        -0.144  -0.126  -0.186  -0.316  -0.284  -0.383  -0.264  -0.236  -0.327
20    A         1.345   1.347   1.364   1.314   1.320   1.344   1.409   1.411   1.431
21    N        -0.144  -0.126  -0.186  -0.019   0.005  -0.078  -0.264  -0.236  -0.327
22    W         1.345   1.347   1.364   1.558   1.559   1.586   1.409   1.411   1.431
23    M        -1.225  -1.223  -1.196  -1.018  -1.010  -0.968  -1.100  -1.097  -1.051
24    K         1.345   1.347   1.364   1.293   1.291   1.323   1.409   1.411   1.431
25    Y         1.345   1.347   1.364   1.527   1.528   1.555   1.409   1.411   1.431
26    P        -0.144  -0.133  -0.190   0.103   0.119   0.037  -0.264  -0.246  -0.333
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    N         1.345   1.347   1.364   1.411   1.410   1.440   1.409   1.411   1.431
30    K        -0.144  -0.168  -0.197  -0.255  -0.296  -0.346  -0.264  -0.301  -0.344
31    I        -1.225  -1.223  -1.196  -1.068  -1.067  -1.018  -1.100  -1.097  -1.051
32    S        -0.144  -0.126  -0.186  -0.265  -0.233  -0.334  -0.264  -0.236  -0.327
33    T         1.345   1.347   1.364   1.205   1.207   1.236   1.409   1.411   1.431
34    H         1.345   1.347   1.364   1.548   1.549   1.575   1.409   1.411   1.431
35    V         1.345   1.347   1.364   1.216   1.216   1.247   1.409   1.411   1.431
36    I        -0.144  -0.133  -0.190  -0.160  -0.140  -0.252  -0.264  -0.246  -0.333
37    A         1.345   1.347   1.364   1.314   1.320   1.344   1.409   1.411   1.431
38    V         1.345   1.347   1.364   1.216   1.216   1.247   1.409   1.411   1.431
39    D         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
40    V        -0.144  -0.168  -0.197  -0.362  -0.405  -0.457  -0.264  -0.301  -0.344
41    L        -0.144  -0.133  -0.190  -0.214  -0.195  -0.281  -0.264  -0.246  -0.333
42    R        -1.225  -1.223  -1.196  -1.205  -1.202  -1.154  -1.100  -1.097  -1.051
43    R         1.345   1.347   1.364   1.336   1.338   1.365   1.409   1.411   1.431
44    E        -1.225  -1.223  -1.196  -1.335  -1.330  -1.282  -1.100  -1.097  -1.051
45    L        -0.144  -0.168  -0.197  -0.331  -0.374  -0.422  -0.264  -0.301  -0.344
46    K        -1.225  -1.223  -1.196  -1.232  -1.231  -1.181  -1.100  -1.097  -1.051
47    E        -1.225  -1.223  -1.196  -1.081  -1.082  -1.031  -1.100  -1.097  -1.051
48    H        -0.277  -0.276  -0.252  -0.225  -0.223  -0.182  -0.473  -0.471  -0.430
49    G        -1.225  -1.223  -1.196  -1.178  -1.172  -1.128  -1.100  -1.097  -1.051
50    D        -0.144  -0.168  -0.197  -0.019  -0.059  -0.107  -0.264  -0.301  -0.344
51    V        -0.144  -0.133  -0.190  -0.255  -0.239  -0.319  -0.264  -0.246  -0.333
52    L         1.345   1.347   1.364   1.260   1.263   1.290   1.409   1.411   1.431
53    L        -1.225  -1.223  -1.196  -1.152  -1.154  -1.102  -1.100  -1.097  -1.051
54    T         1.345   1.347   1.364   1.205   1.207   1.236   1.409   1.411   1.431
55    E         1.345   1.347   1.364   1.282   1.286   1.312   1.409   1.411   1.431
56    R         1.345   1.347   1.364   1.336   1.338   1.365   1.409   1.411   1.431
57    L         1.345   1.347   1.364   1.260   1.263   1.290   1.409   1.411   1.431
58    I         1.345   1.347   1.364   1.422   1.424   1.450   1.409   1.411   1.431
59    T         1.345   1.347   1.364   1.205   1.207   1.236   1.409   1.411   1.431
60    I        -0.144  -0.168  -0.197   0.103   0.061   0.004  -0.264  -0.301  -0.344
61    R        -0.144  -0.126  -0.186  -0.086  -0.060  -0.142  -0.264  -0.236  -0.327
62    Q         1.345   1.347   1.364   1.495   1.500   1.524   1.409   1.411   1.431
63    N        -0.144  -0.168  -0.197  -0.170  -0.206  -0.252  -0.264  -0.301  -0.344
64    T        -1.225  -1.223  -1.196  -1.370  -1.364  -1.317  -1.100  -1.097  -1.051
65    P         1.345   1.347   1.364   1.516   1.517   1.544   1.409   1.411   1.431
66    H        -1.225  -1.223  -1.196  -1.126  -1.114  -1.076  -1.100  -1.097  -1.051
67    W         1.345   1.347   1.364   1.558   1.559   1.586   1.409   1.411   1.431
68    M        -1.225  -1.223  -1.196  -1.107  -1.097  -1.056  -1.100  -1.097  -1.051
69    S        -1.225  -1.223  -1.196  -1.349  -1.345  -1.296  -1.100  -1.097  -1.051
70    I        -1.225  -1.223  -1.196  -1.245  -1.238  -1.194  -1.100  -1.097  -1.051
71    L        -0.144  -0.133  -0.190  -0.170  -0.152  -0.228  -0.264  -0.246  -0.333
72    V        -1.225  -1.223  -1.196  -1.133  -1.138  -1.082  -1.100  -1.097  -1.051
73    G        -0.144  -0.126  -0.186  -0.019   0.010  -0.089  -0.264  -0.236  -0.327
74    N        -0.144  -0.168  -0.197  -0.033  -0.075  -0.125  -0.264  -0.301  -0.344
75    T        -1.225  -1.223  -1.196  -1.239  -1.237  -1.187  -1.100  -1.097  -1.051
76    N        -1.225  -1.223  -1.196  -0.974  -0.974  -0.925  -1.100  -1.097  -1.051
77    L        -0.144  -0.168  -0.197  -0.120  -0.165  -0.224  -0.264  -0.301  -0.344
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    A        -1.225  -1.223  -1.196  -1.113  -1.111  -1.063  -1.100  -1.097  -1.051
80    Y        -0.144  -0.133  -0.190   0.061   0.080  -0.014  -0.264  -0.246  -0.333
81    V        -0.144  -0.126  -0.186  -0.255  -0.229  -0.313  -0.264  -0.236  -0.327
82    R        -0.144  -0.133  -0.190  -0.135  -0.118  -0.204  -0.264  -0.246  -0.333
83    E         1.345   1.347   1.364   1.282   1.286   1.312   1.409   1.411   1.431
84    V        -0.144  -0.168  -0.197  -0.362  -0.405  -0.457  -0.264  -0.301  -0.344
85    S         1.345   1.347   1.364   1.260   1.262   1.290   1.409   1.411   1.431
86    T        -0.144  -0.168  -0.197  -0.067  -0.114  -0.181  -0.264  -0.301  -0.344
87    V         1.345   1.347   1.364   1.216   1.216   1.247   1.409   1.411   1.431
88    D         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
89    R        -1.225  -1.223  -1.196  -1.159  -1.155  -1.108  -1.100  -1.097  -1.051
90    R        -0.144  -0.168  -0.197  -0.224  -0.268  -0.312  -0.264  -0.301  -0.344
91    D        -1.225  -1.223  -1.196  -1.252  -1.241  -1.201  -1.100  -1.097  -1.051
92    R        -0.144  -0.133  -0.190  -0.204  -0.186  -0.286  -0.264  -0.246  -0.333
93    S        -0.144  -0.168  -0.197  -0.341  -0.382  -0.432  -0.264  -0.301  -0.344
94    L        -0.144  -0.133  -0.190  -0.310  -0.290  -0.395  -0.264  -0.246  -0.333
95    T         1.345   1.347   1.364   1.205   1.207   1.236   1.409   1.411   1.431
96    M        -0.144  -0.126  -0.186  -0.053  -0.020  -0.139  -0.264  -0.236  -0.327
97    R        -1.225  -1.223  -1.196  -1.349  -1.342  -1.296  -1.100  -1.097  -1.051
98    S        -0.144  -0.126  -0.186  -0.316  -0.283  -0.394  -0.264  -0.236  -0.327
99    C        -1.225  -1.223  -1.196  -1.178  -1.162  -1.128  -1.100  -1.097  -1.051
100   N         1.345   1.347   1.364   1.411   1.410   1.440   1.409   1.411   1.431
101   M        -1.225  -1.223  -1.196  -1.107  -1.096  -1.056  -1.100  -1.097  -1.051
102   T         1.345   1.347   1.364   1.205   1.207   1.236   1.409   1.411   1.431
103   F        -0.144  -0.133  -0.190   0.014   0.030  -0.051  -0.264  -0.246  -0.333
104   P        -0.144  -0.168  -0.197  -0.170  -0.204  -0.238  -0.264  -0.301  -0.344
105   H        -1.225  -1.223  -1.196  -0.986  -0.981  -0.937  -1.100  -1.097  -1.051
106   I        -1.225  -1.223  -1.196  -1.218  -1.210  -1.167  -1.100  -1.097  -1.051
107   L         1.345   1.347   1.364   1.260   1.263   1.290   1.409   1.411   1.431
108   K        -1.225  -1.223  -1.196  -1.205  -1.207  -1.154  -1.100  -1.097  -1.051
109   C        -0.144  -0.168  -0.197  -0.165  -0.198  -0.222  -0.264  -0.301  -0.344
110   Y        -1.225  -1.223  -1.196  -0.949  -0.943  -0.900  -1.100  -1.097  -1.051
111   E         1.345   1.347   1.364   1.282   1.286   1.312   1.409   1.411   1.431
112   T         1.345   1.347   1.364   1.205   1.207   1.236   1.409   1.411   1.431
113   V         1.345   1.347   1.364   1.216   1.216   1.247   1.409   1.411   1.431
114   R        -1.225  -1.223  -1.196  -1.384  -1.377  -1.331  -1.100  -1.097  -1.051
115   Y         1.345   1.347   1.364   1.527   1.528   1.555   1.409   1.411   1.431
116   V        -0.144  -0.168  -0.197  -0.310  -0.354  -0.408  -0.264  -0.301  -0.344
117   P         1.345   1.347   1.364   1.516   1.517   1.544   1.409   1.411   1.431
118   H        -0.144  -0.133  -0.190  -0.024  -0.003  -0.119  -0.264  -0.246  -0.333
119   P        -0.144  -0.133  -0.190  -0.053  -0.033  -0.146  -0.264  -0.246  -0.333
120   K        -1.225  -1.223  -1.196  -1.218  -1.217  -1.167  -1.100  -1.097  -1.051
121   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   S        -0.277  -0.276  -0.252  -0.552  -0.551  -0.507  -0.473  -0.471  -0.430
124   N        -1.225  -1.223  -1.196  -1.081  -1.077  -1.031  -1.100  -1.097  -1.051
125   V        -1.225  -1.223  -1.196  -1.212  -1.211  -1.161  -1.100  -1.097  -1.051
126   T         1.345   1.347   1.364   1.205   1.207   1.236   1.409   1.411   1.431
127   L        -1.225  -1.223  -1.196  -1.377  -1.375  -1.324  -1.100  -1.097  -1.051
128   F         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
129   K        -1.225  -1.223  -1.196  -1.024  -1.027  -0.974  -1.100  -1.097  -1.051
130   Q         1.345   1.347   1.364   1.495   1.500   1.524   1.409   1.411   1.431
131   D        -0.144  -0.168  -0.197  -0.184  -0.220  -0.262  -0.264  -0.301  -0.344
132   A         1.345   1.347   1.364   1.314   1.320   1.344   1.409   1.411   1.431
133   K        -0.144  -0.126  -0.186  -0.224  -0.198  -0.294  -0.264  -0.236  -0.327
134   F        -0.144  -0.168  -0.197  -0.057  -0.097  -0.143  -0.264  -0.301  -0.344
135   L        -1.225  -1.223  -1.196  -1.391  -1.384  -1.338  -1.100  -1.097  -1.051
136   S        -0.144  -0.168  -0.197  -0.239  -0.278  -0.336  -0.264  -0.301  -0.344
137   G        -0.144  -0.168  -0.197  -0.194  -0.229  -0.268  -0.264  -0.301  -0.344
138   V        -0.144  -0.168  -0.197  -0.260  -0.301  -0.360  -0.264  -0.301  -0.344
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   P        -1.225  -1.223  -1.196  -0.876  -0.874  -0.828  -1.100  -1.097  -1.051
141   T        -1.225  -1.223  -1.196  -1.055  -1.062  -1.006  -1.100  -1.097  -1.051
142   K        -0.144  -0.133  -0.190  -0.150  -0.134  -0.212  -0.264  -0.246  -0.333
143   T        -0.144  -0.168  -0.197  -0.244  -0.289  -0.348  -0.264  -0.301  -0.344
144   F        -1.225  -1.223  -1.196  -1.152  -1.144  -1.102  -1.100  -1.097  -1.051
145   S        -0.144  -0.133  -0.190  -0.275  -0.256  -0.353  -0.264  -0.246  -0.333
146   E        -0.144  -0.168  -0.197  -0.140  -0.185  -0.240  -0.264  -0.301  -0.344
147   K        -1.225  -1.223  -1.196  -1.349  -1.344  -1.296  -1.100  -1.097  -1.051
148   V        -0.144  -0.168  -0.197  -0.160  -0.206  -0.267  -0.264  -0.301  -0.344
149   E         1.345   1.347   1.364   1.282   1.286   1.312   1.409   1.411   1.431
150   N        -1.225  -1.223  -1.196  -1.018  -1.016  -0.968  -1.100  -1.097  -1.051
151   W        -0.144  -0.133  -0.190  -0.038  -0.017  -0.138  -0.264  -0.246  -0.333
152   G        -1.225  -1.223  -1.196  -1.239  -1.226  -1.187  -1.100  -1.097  -1.051
153   V         1.345   1.347   1.364   1.216   1.216   1.247   1.409   1.411   1.431
154   K        -0.144  -0.126  -0.186  -0.174  -0.150  -0.236  -0.264  -0.236  -0.327
155   R        -0.144  -0.126  -0.186  -0.125  -0.097  -0.187  -0.264  -0.236  -0.327
156   F         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
157   S        -1.225  -1.223  -1.196  -1.192  -1.192  -1.141  -1.100  -1.097  -1.051
158   D        -1.225  -1.223  -1.196  -1.218  -1.211  -1.167  -1.100  -1.097  -1.051
159   N        -0.144  -0.126  -0.186  -0.135  -0.108  -0.214  -0.264  -0.236  -0.327
160   A         1.345   1.347   1.364   1.314   1.320   1.344   1.409   1.411   1.431
161   V        -1.225  -1.223  -1.196  -1.363  -1.359  -1.310  -1.100  -1.097  -1.051
162   K        -0.144  -0.126  -0.186  -0.224  -0.198  -0.294  -0.264  -0.236  -0.327
163   G         1.345   1.347   1.364   1.464   1.466   1.492   1.409   1.411   1.431
164   K         1.345   1.347   1.364   1.293   1.291   1.323   1.409   1.411   1.431
165   V        -0.144  -0.168  -0.197  -0.290  -0.333  -0.389  -0.264  -0.301  -0.344
166   G         1.345   1.347   1.364   1.464   1.466   1.492   1.409   1.411   1.431
167   F         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
168   D        -0.144  -0.168  -0.197  -0.184  -0.220  -0.262  -0.264  -0.301  -0.344
169   S         1.345   1.347   1.364   1.260   1.262   1.290   1.409   1.411   1.431
170   I        -0.144  -0.168  -0.197  -0.255  -0.293  -0.330  -0.264  -0.301  -0.344
171   L         1.345   1.347   1.364   1.260   1.263   1.290   1.409   1.411   1.431
172   A        -0.144  -0.126  -0.186  -0.229  -0.194  -0.304  -0.264  -0.236  -0.327
173   M        -0.144  -0.126  -0.186  -0.038  -0.008  -0.122  -0.264  -0.236  -0.327
174   F        -1.225  -1.223  -1.196  -1.152  -1.146  -1.102  -1.100  -1.097  -1.051
175   N        -0.144  -0.133  -0.190  -0.116  -0.099  -0.198  -0.264  -0.246  -0.333
176   D        -0.277  -0.276  -0.252  -0.335  -0.334  -0.292  -0.473  -0.471  -0.430
177   I        -0.277  -0.276  -0.252  -0.449  -0.448  -0.405  -0.473  -0.471  -0.430
178   W        -0.277  -0.276  -0.252  -0.192  -0.190  -0.150  -0.473  -0.471  -0.430
179   K        -0.277  -0.276  -0.252  -0.461  -0.459  -0.416  -0.473  -0.471  -0.430
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     *
187   -         1.345   1.347   1.364   1.533   1.535   1.561   1.409   1.411   1.431
188   -        -0.277  -0.276  -0.252  -0.395  -0.394  -0.351  -0.473  -0.471  -0.430
189   -        -0.277  -0.276  -0.252  -0.521  -0.520  -0.476  -0.473  -0.471  -0.430
190   -        -0.277  -0.276  -0.252  -0.263  -0.261  -0.220  -0.473  -0.471  -0.430
191   -        -0.277  -0.276  -0.252  -0.339  -0.338  -0.296  -0.473  -0.471  -0.430
192   -        -0.277  -0.276  -0.252  -0.628  -0.626  -0.582  -0.473  -0.471  -0.430
193   -        -0.277  -0.276  -0.252  -0.339  -0.338  -0.296  -0.473  -0.471  -0.430
194   -        -0.277  -0.276  -0.252  -0.328  -0.327  -0.285  -0.473  -0.471  -0.430
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -         1.345   1.347   1.364   1.443   1.444   1.471   1.409   1.411   1.431
197   -        -0.277  -0.276  -0.252  -0.373  -0.371  -0.329  -0.473  -0.471  -0.430
198   -        -0.277  -0.276  -0.252  -0.407  -0.405  -0.362  -0.473  -0.471  -0.430
199   N        -1.225  -1.223  -1.196  -1.212  -1.205  -1.161  -1.100  -1.097  -1.051
200   A        -0.144  -0.133  -0.190  -0.120  -0.100  -0.182  -0.264  -0.246  -0.333
201   N        -1.225  -1.223  -1.196  -1.272  -1.263  -1.221  -1.100  -1.097  -1.051
202   E        -0.144  -0.168  -0.197  -0.229  -0.267  -0.324  -0.264  -0.301  -0.344
* 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/Q04006
Output conservation file - output/Q04006
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
