1     M         1.622   1.622   1.646   1.976   1.976   2.014   1.723   1.723   1.753
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -         1.622   1.622   1.646   1.680   1.678   1.718   1.723   1.723   1.753
5     D        -1.116  -1.116  -1.093  -1.000  -1.001  -0.959  -0.996  -0.996  -0.955
6     C        -1.116  -1.116  -1.093  -0.735  -0.736  -0.694  -0.996  -0.996  -0.955
7     P        -1.116  -1.116  -1.093  -0.930  -0.931  -0.888  -0.996  -0.996  -0.955
8     S         0.035   0.033  -0.001   0.157   0.153   0.099  -0.090  -0.094  -0.147
9     N        -1.116  -1.116  -1.093  -1.021  -1.021  -0.979  -0.996  -0.996  -0.955
10    V         0.035   0.033  -0.001   0.050   0.046  -0.016  -0.090  -0.094  -0.147
11    V        -1.116  -1.116  -1.093  -0.850  -0.848  -0.809  -0.996  -0.996  -0.955
12    L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
13    L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
14    L         0.035   0.033  -0.003  -0.550  -0.554  -0.595  -0.090  -0.094  -0.150
15    L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
16    Q         1.622   1.622   1.646   1.712   1.713   1.750   1.723   1.723   1.753
17    L         0.035   0.041  -0.001  -0.247  -0.235  -0.356  -0.090  -0.081  -0.147
18    V        -1.116  -1.116  -1.093  -1.427  -1.428  -1.385  -0.996  -0.996  -0.955
19    L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
20    Q         0.035   0.033  -0.001   0.142   0.139   0.090  -0.090  -0.094  -0.147
21    R         0.035   0.041  -0.001   0.408   0.417   0.345  -0.090  -0.081  -0.147
22    Q         1.622   1.622   1.646   1.712   1.713   1.750   1.723   1.723   1.753
23    Q         1.622   1.622   1.646   1.712   1.713   1.750   1.723   1.723   1.753
24    T        -1.116  -1.116  -1.093  -1.042  -1.043  -1.000  -0.996  -0.996  -0.955
25    L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
26    A         0.035   0.033  -0.003   0.225   0.221   0.151  -0.090  -0.094  -0.150
27    H         0.035   0.033  -0.003   0.444   0.440   0.383  -0.090  -0.094  -0.150
28    R        -1.116  -1.116  -1.093  -0.841  -0.841  -0.799  -0.996  -0.996  -0.955
29    D         0.035   0.033  -0.003   0.173   0.169   0.102  -0.090  -0.094  -0.150
30    K         0.035   0.033  -0.001   0.096   0.091   0.035  -0.090  -0.094  -0.147
31    S         0.035   0.033  -0.003   0.157   0.153   0.096  -0.090  -0.094  -0.150
32    V         0.035   0.041  -0.001  -0.541  -0.533  -0.583  -0.090  -0.081  -0.147
33    D         0.035   0.033  -0.001   0.188   0.183   0.122  -0.090  -0.094  -0.147
34    L         0.035   0.033  -0.003  -0.550  -0.554  -0.595  -0.090  -0.094  -0.150
35    Q        -1.116  -1.116  -1.093  -0.990  -0.989  -0.949  -0.996  -0.996  -0.955
36    T        -1.116  -1.116  -1.093  -1.062  -1.064  -1.021  -0.996  -0.996  -0.955
37    L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
38    L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
39    K         0.035   0.041  -0.001   0.066   0.076   0.002  -0.090  -0.081  -0.147
40    D         0.035   0.041  -0.001   0.050   0.058  -0.004  -0.090  -0.081  -0.147
41    P         1.622   1.622   1.646   1.878   1.879   1.916   1.723   1.723   1.753
42    V         0.035   0.033  -0.001   0.050   0.046  -0.016  -0.090  -0.094  -0.147
43    I         0.035   0.033  -0.001   0.042   0.038  -0.022  -0.090  -0.094  -0.147
44    D         1.622   1.622   1.646   1.829   1.830   1.867   1.723   1.723   1.753
45    N         0.035   0.033  -0.003   0.066   0.061  -0.004  -0.090  -0.094  -0.150
46    D        -1.116  -1.116  -1.093  -1.000  -1.001  -0.959  -0.996  -0.996  -0.955
47    V         1.622   1.622   1.646   1.712   1.713   1.750   1.723   1.723   1.753
48    L        -1.116  -1.116  -1.093  -1.289  -1.284  -1.247  -0.996  -0.996  -0.955
49    V        -1.116  -1.116  -1.093  -1.104  -1.105  -1.063  -0.996  -0.996  -0.955
50    E        -1.116  -1.116  -1.093  -1.094  -1.094  -1.052  -0.996  -0.996  -0.955
51    F         0.035   0.033  -0.003   0.507   0.503   0.453  -0.090  -0.094  -0.150
52    K        -1.116  -1.116  -1.093  -1.021  -1.020  -0.979  -0.996  -0.996  -0.955
53    T         0.035   0.041  -0.001   0.135   0.143   0.073  -0.090  -0.081  -0.147
54    H         0.035   0.033  -0.003   0.336   0.331   0.259  -0.090  -0.094  -0.150
55    K        -1.116  -1.116  -1.093  -0.990  -0.990  -0.949  -0.996  -0.996  -0.955
56    L        -1.116  -1.116  -1.093  -1.083  -1.078  -1.042  -0.996  -0.996  -0.955
57    V         0.035   0.033  -0.003  -0.231  -0.236  -0.344  -0.090  -0.094  -0.150
58    Q         0.035   0.033  -0.003   0.066   0.062  -0.001  -0.090  -0.094  -0.150
59    L         0.035   0.033  -0.001  -0.550  -0.554  -0.593  -0.090  -0.094  -0.147
60    Y         0.035   0.033  -0.003   0.233   0.228   0.160  -0.090  -0.094  -0.150
61    G         0.035   0.041  -0.001   0.372   0.380   0.322  -0.090  -0.081  -0.147
62    P         1.622   1.622   1.646   1.878   1.879   1.916   1.723   1.723   1.753
63    Q        -1.116  -1.116  -1.093  -1.073  -1.073  -1.031  -0.996  -0.996  -0.955
64    Y        -1.116  -1.116  -1.093  -1.346  -1.348  -1.304  -0.996  -0.996  -0.955
65    C        -1.116  -1.116  -1.093  -0.707  -0.708  -0.665  -0.996  -0.996  -0.955
66    R        -1.116  -1.116  -1.093  -0.850  -0.851  -0.809  -0.996  -0.996  -0.955
67    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    I         0.035   0.041  -0.001  -0.550  -0.542  -0.593  -0.090  -0.081  -0.147
69    S        -1.116  -1.116  -1.093  -0.990  -0.990  -0.949  -0.996  -0.996  -0.955
70    L        -1.116  -1.116  -1.093  -1.486  -1.482  -1.444  -0.996  -0.996  -0.955
71    R         1.622   1.622   1.646   1.895   1.895   1.933   1.723   1.723   1.753
72    G        -1.116  -1.116  -1.093  -0.831  -0.833  -0.789  -0.996  -0.996  -0.955
73    L         0.035   0.033  -0.001  -0.550  -0.554  -0.593  -0.090  -0.094  -0.147
74    K         0.035   0.033  -0.003   0.157   0.153   0.102  -0.090  -0.094  -0.150
75    T        -1.116  -1.116  -1.093  -0.651  -0.649  -0.609  -0.996  -0.996  -0.955
76    M         0.035   0.041  -0.001  -0.400  -0.393  -0.422  -0.090  -0.081  -0.147
77    V         0.035   0.033  -0.001   0.050   0.046  -0.016  -0.090  -0.094  -0.147
78    T        -1.116  -1.116  -1.093  -1.042  -1.043  -1.000  -0.996  -0.996  -0.955
79    D         0.035   0.033  -0.003   0.135   0.130   0.058  -0.090  -0.094  -0.150
80    I        -1.116  -1.116  -1.093  -1.201  -1.201  -1.159  -0.996  -0.996  -0.955
81    F         0.035   0.033  -0.003   0.073   0.067  -0.048  -0.090  -0.094  -0.150
82    A        -1.116  -1.116  -1.093  -0.890  -0.891  -0.848  -0.996  -0.996  -0.955
83    N         0.035   0.033  -0.003   0.042   0.037  -0.030  -0.090  -0.094  -0.150
84    G         1.622   1.622   1.646   2.019   2.019   2.057   1.723   1.723   1.753
85    I         1.622   1.622   1.646   1.756   1.756   1.794   1.723   1.723   1.753
86    P         1.622   1.622   1.646   1.877   1.877   1.915   1.723   1.723   1.753
87    K        -0.106  -0.106  -0.082  -0.203  -0.203  -0.162  -0.317  -0.317  -0.278
88    N        -0.106  -0.106  -0.082  -0.239  -0.239  -0.199  -0.317  -0.317  -0.278
89    A        -0.106  -0.106  -0.082   0.093   0.093   0.133  -0.317  -0.317  -0.278
90    Q        -0.106  -0.106  -0.082  -0.203  -0.203  -0.162  -0.317  -0.317  -0.278
91    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    S        -0.106  -0.106  -0.082  -0.106  -0.107  -0.065  -0.317  -0.317  -0.278
93    G        -0.106  -0.106  -0.082   0.052   0.052   0.093  -0.317  -0.317  -0.278
94    N        -0.106  -0.106  -0.082  -0.160  -0.162  -0.119  -0.317  -0.317  -0.278
95    D        -0.106  -0.106  -0.082  -0.233  -0.235  -0.192  -0.317  -0.317  -0.278
96    Q         0.035   0.041  -0.001  -0.005   0.004  -0.067  -0.090  -0.081  -0.147
97    P         0.035   0.033  -0.003   0.180   0.175   0.102  -0.090  -0.094  -0.150
98    V        -1.116  -1.116  -1.093  -1.021  -1.020  -0.979  -0.996  -0.996  -0.955
99    T         0.035   0.033  -0.001   0.127   0.123   0.061  -0.090  -0.094  -0.147
100   V        -1.116  -1.116  -1.093  -1.486  -1.488  -1.444  -0.996  -0.996  -0.955
101   V         0.035   0.041  -0.001   0.042   0.051  -0.022  -0.090  -0.081  -0.147
102   D         0.035   0.041  -0.001   0.173   0.182   0.113  -0.090  -0.081  -0.147
103   L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
104   A         1.622   1.622   1.646   1.895   1.895   1.933   1.723   1.723   1.753
105   N         1.622   1.622   1.646   1.729   1.729   1.767   1.723   1.723   1.753
106   Y         0.035   0.033  -0.001   0.357   0.354   0.306  -0.090  -0.094  -0.147
107   Y         1.622   1.622   1.646   1.895   1.895   1.933   1.723   1.723   1.753
108   Y         1.622   1.622   1.646   1.895   1.895   1.933   1.723   1.723   1.753
109   M         0.035   0.041  -0.001   0.225   0.233   0.176  -0.090  -0.081  -0.147
110   Q        -1.116  -1.116  -1.093  -1.104  -1.105  -1.063  -0.996  -0.996  -0.955
111   R         1.622   1.622   1.646   1.895   1.895   1.933   1.723   1.723   1.753
112   I         0.035   0.033  -0.001  -0.247  -0.254  -0.356  -0.090  -0.094  -0.147
113   N         1.622   1.622   1.646   1.729   1.729   1.767   1.723   1.723   1.753
114   E         0.035   0.033  -0.001   0.081   0.076   0.031  -0.090  -0.094  -0.147
115   L         1.622   1.622   1.646   1.071   1.072   1.110   1.723   1.723   1.753
116   Q         0.035   0.033  -0.003   0.027   0.022  -0.045  -0.090  -0.094  -0.150
117   N         0.035   0.041  -0.001   0.003   0.011  -0.058  -0.090  -0.081  -0.147
118   T        -1.116  -1.116  -1.093  -1.062  -1.064  -1.021  -0.996  -0.996  -0.955
119   E         0.035   0.033  -0.001   0.003  -0.002  -0.058  -0.090  -0.094  -0.147
120   L         0.035   0.033  -0.001  -0.550  -0.554  -0.593  -0.090  -0.094  -0.147
121   P         1.622   1.622   1.646   1.878   1.879   1.916   1.723   1.723   1.753
122   Q        -1.116  -1.116  -1.093  -1.073  -1.073  -1.031  -0.996  -0.996  -0.955
123   L         0.035   0.033  -0.003  -0.550  -0.554  -0.595  -0.090  -0.094  -0.150
124   K        -1.116  -1.116  -1.093  -0.960  -0.960  -0.918  -0.996  -0.996  -0.955
125   E        -1.116  -1.116  -1.093  -1.083  -1.083  -1.042  -0.996  -0.996  -0.955
126   A        -1.116  -1.116  -1.093  -1.000  -1.002  -0.959  -0.996  -0.996  -0.955
127   L        -1.116  -1.116  -1.093  -1.168  -1.163  -1.127  -0.996  -0.996  -0.955
128   L         0.035   0.041  -0.001  -0.214  -0.201  -0.324  -0.090  -0.081  -0.147
129   T        -1.116  -1.116  -1.093  -1.000  -1.001  -0.959  -0.996  -0.996  -0.955
130   R        -1.116  -1.116  -1.093  -1.392  -1.396  -1.350  -0.996  -0.996  -0.955
131   L        -1.116  -1.116  -1.093  -1.136  -1.131  -1.094  -0.996  -0.996  -0.955
132   E        -1.116  -1.116  -1.093  -0.930  -0.928  -0.888  -0.996  -0.996  -0.955
133   H        -1.116  -1.116  -1.093  -0.773  -0.774  -0.732  -0.996  -0.996  -0.955
134   M         0.035   0.041  -0.001  -0.400  -0.393  -0.422  -0.090  -0.081  -0.147
135   I        -1.116  -1.116  -1.093  -0.960  -0.959  -0.918  -0.996  -0.996  -0.955
136   -        -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/Q06707
Output conservation file - output/Q06707
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
