1     M         0.994   0.994   0.994   1.311   1.311   1.311   0.994   0.994   0.994
2     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    M        -0.994  -0.994  -0.994  -0.684  -0.684  -0.684  -0.994  -0.994  -0.994
33    R         0.994   0.994   0.994   1.135   1.135   1.135   0.994   0.994   0.994
34    K        -0.994  -0.994  -0.994  -0.812  -0.812  -0.812  -0.994  -0.994  -0.994
35    N        -0.994  -0.994  -0.994  -0.790  -0.790  -0.790  -0.994  -0.994  -0.994
36    T        -0.994  -0.994  -0.994  -1.366  -1.366  -1.366  -0.994  -0.994  -0.994
37    L        -0.994  -0.994  -0.994  -0.834  -0.834  -0.834  -0.994  -0.994  -0.994
38    D         0.994   0.994   0.994   1.015   1.015   1.015   0.994   0.994   0.994
39    M        -0.994  -0.994  -0.994  -0.769  -0.769  -0.769  -0.994  -0.994  -0.994
40    V         0.994   0.994   0.994   0.923   0.923   0.923   0.994   0.994   0.994
41    T         0.994   0.994   0.994   0.639   0.639   0.639   0.994   0.994   0.994
42    I         0.994   0.994   0.994   1.075   1.075   1.075   0.994   0.994   0.994
43    G         0.994   0.994   0.994   0.799   0.799   0.799   0.994   0.994   0.994
44    I        -0.994  -0.994  -0.994  -0.944  -0.944  -0.944  -0.994  -0.994  -0.994
45    A        -0.994  -0.994  -0.994  -0.877  -0.877  -0.877  -0.994  -0.994  -0.994
46    C        -0.994  -0.994  -0.994  -0.642  -0.642  -0.642  -0.994  -0.994  -0.994
47    L         0.994   0.994   0.994   0.923   0.923   0.923   0.994   0.994   0.994
48    V         0.994   0.994   0.994   0.923   0.923   0.923   0.994   0.994   0.994
49    G         0.994   0.994   0.994   0.799   0.799   0.799   0.994   0.994   0.994
50    V        -0.994  -0.994  -0.994  -0.944  -0.944  -0.944  -0.994  -0.994  -0.994
51    Y         0.994   0.994   0.994   1.311   1.311   1.311   0.994   0.994   0.994
52    T         0.994   0.994   0.994   0.639   0.639   0.639   0.994   0.994   0.994
53    G         0.994   0.994   0.994   0.799   0.799   0.799   0.994   0.994   0.994
54    T        -0.994  -0.994  -0.994  -1.079  -1.079  -1.079  -0.994  -0.994  -0.994
55    R         0.994   0.994   0.994   1.135   1.135   1.135   0.994   0.994   0.994
56    F         0.994   0.994   0.994   1.223   1.223   1.223   0.994   0.994   0.994
57    F         0.994   0.994   0.994   1.223   1.223   1.223   0.994   0.994   0.994
58    E         0.994   0.994   0.994   1.253   1.253   1.253   0.994   0.994   0.994
59    P         0.994   0.994   0.994   0.830   0.830   0.830   0.994   0.994   0.994
60    I         0.994   0.994   0.994   1.075   1.075   1.075   0.994   0.994   0.994
61    V         0.994   0.994   0.994   0.923   0.923   0.923   0.994   0.994   0.994
62    I        -0.994  -0.994  -0.994  -0.944  -0.944  -0.944  -0.994  -0.994  -0.994
63    D        -0.994  -0.994  -0.994  -1.079  -1.079  -1.079  -0.994  -0.994  -0.994
64    R        -0.994  -0.994  -0.994  -0.663  -0.663  -0.663  -0.994  -0.994  -0.994
65    L         0.994   0.994   0.994   0.923   0.923   0.923   0.994   0.994   0.994
66    R        -0.994  -0.994  -0.994  -0.663  -0.663  -0.663  -0.994  -0.994  -0.994
67    K         0.994   0.994   0.994   1.105   1.105   1.105   0.994   0.994   0.994
68    D         0.994   0.994   0.994   1.015   1.015   1.015   0.994   0.994   0.994
69    G         0.994   0.994   0.994   0.799   0.799   0.799   0.994   0.994   0.994
70    N        -0.994  -0.994  -0.994  -0.642  -0.642  -0.642  -0.994  -0.994  -0.994
71    L         0.994   0.994   0.994   0.923   0.923   0.923   0.994   0.994   0.994
72    R         0.994   0.994   0.994   1.135   1.135   1.135   0.994   0.994   0.994
73    T        -0.994  -0.994  -0.994  -1.126  -1.126  -1.126  -0.994  -0.994  -0.994
74    D         0.994   0.994   0.994   1.015   1.015   1.015   0.994   0.994   0.994
75    I        -0.994  -0.994  -0.994  -0.944  -0.944  -0.944  -0.994  -0.994  -0.994
76    P        -0.994  -0.994  -0.994  -0.944  -0.944  -0.944  -0.994  -0.994  -0.994
77    I        -0.994  -0.994  -0.994  -0.944  -0.944  -0.944  -0.994  -0.994  -0.994
78    P         0.994   0.994   0.994   0.830   0.830   0.830   0.994   0.994   0.994
79    E        -0.994  -0.994  -0.994  -0.684  -0.684  -0.684  -0.994  -0.994  -0.994
80    Y         0.994   0.994   0.994   1.311   1.311   1.311   0.994   0.994   0.994
81    D         0.994   0.994   0.994   1.015   1.015   1.015   0.994   0.994   0.994
82    E         0.994   0.994   0.994   1.253   1.253   1.253   0.994   0.994   0.994
83    D         0.994   0.994   0.994   1.015   1.015   1.015   0.994   0.994   0.994
84    G         0.994   0.994   0.994   0.799   0.799   0.799   0.994   0.994   0.994
85    N         0.994   0.994   0.994   1.075   1.075   1.075   0.994   0.994   0.994
86    L         0.994   0.994   0.994   0.923   0.923   0.923   0.994   0.994   0.994
87    L        -0.994  -0.994  -0.994  -1.057  -1.057  -1.057  -0.994  -0.994  -0.994
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    K        -0.994  -0.994  -0.994  -0.748  -0.748  -0.748  -0.994  -0.994  -0.994
97    V        -0.994  -0.994  -0.994  -1.268  -1.268  -1.268  -0.994  -0.994  -0.994
98    T        -0.994  -0.994  -0.994  -1.079  -1.079  -1.079  -0.994  -0.994  -0.994
99    P         0.994   0.994   0.994   0.830   0.830   0.830   0.994   0.994   0.994
100   S        -0.994  -0.994  -0.994  -0.790  -0.790  -0.790  -0.994  -0.994  -0.994
101   L        -0.994  -0.994  -0.994  -0.944  -0.944  -0.944  -0.994  -0.994  -0.994
102   S        -0.994  -0.994  -0.994  -0.855  -0.855  -0.855  -0.994  -0.994  -0.994
103   S         0.994   0.994   0.994   1.045   1.045   1.045   0.994   0.994   0.994
104   T         0.994   0.994   0.994   0.639   0.639   0.639   0.994   0.994   0.994
105   P        -0.994  -0.994  -0.994  -1.220  -1.220  -1.220  -0.994  -0.994  -0.994
106   A        -0.994  -0.994  -0.994  -1.079  -1.079  -1.079  -0.994  -0.994  -0.994
107   A        -0.994  -0.994  -0.994  -0.966  -0.966  -0.966  -0.994  -0.994  -0.994
108   P        -0.994  -0.994  -0.994  -1.341  -1.341  -1.341  -0.994  -0.994  -0.994
109   P        -0.994  -0.994  -0.994  -1.341  -1.341  -1.341  -0.994  -0.994  -0.994
110   T         0.994   0.994   0.994   0.639   0.639   0.639   0.994   0.994   0.994
111   P        -0.994  -0.994  -0.994  -1.034  -1.034  -1.034  -0.994  -0.994  -0.994
112   P        -0.994  -0.994  -0.994  -1.341  -1.341  -1.341  -0.994  -0.994  -0.994
113   T        -0.994  -0.994  -0.994  -1.173  -1.173  -1.173  -0.994  -0.994  -0.994
114   P        -0.994  -0.994  -0.994  -1.341  -1.341  -1.341  -0.994  -0.994  -0.994
115   P         0.994   0.994   0.994   0.830   0.830   0.830   0.994   0.994   0.994
116   T        -0.994  -0.994  -0.994  -1.149  -1.149  -1.149  -0.994  -0.994  -0.994
117   P         0.994   0.994   0.994   0.830   0.830   0.830   0.994   0.994   0.994
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   P        -0.994  -0.994  -0.994  -1.057  -1.057  -1.057  -0.994  -0.994  -0.994
132   Q        -0.994  -0.994  -0.994  -0.726  -0.726  -0.726  -0.994  -0.994  -0.994
133   Q        -0.994  -0.994  -0.994  -1.011  -1.011  -1.011  -0.994  -0.994  -0.994
* 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/Q06011
Output conservation file - output/Q06011
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
