1     M         1.224   1.224   1.224   1.720   1.720   1.720   1.224   1.224   1.224
2     G        -0.809  -0.809  -0.809  -0.256  -0.256  -0.256  -0.809  -0.809  -0.809
3     E        -0.809  -0.809  -0.809  -1.391  -1.391  -1.391  -0.809  -0.809  -0.809
4     Q         1.224   1.224   1.224   1.408   1.408   1.408   1.224   1.224   1.224
5     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    D         1.224   1.224   1.224   1.344   1.344   1.344   1.224   1.224   1.224
11    V         1.224   1.224   1.224   1.376   1.376   1.376   1.224   1.224   1.224
12    E        -0.809  -0.809  -0.809  -1.045  -1.045  -1.045  -0.809  -0.809  -0.809
13    K         1.224   1.224   1.224   0.979   0.979   0.979   1.224   1.224   1.224
14    L        -0.809  -0.809  -0.809  -0.703  -0.703  -0.703  -0.809  -0.809  -0.809
15    V         1.224   1.224   1.224   1.376   1.376   1.376   1.224   1.224   1.224
16    N        -0.809  -0.809  -0.809  -0.727  -0.727  -0.727  -0.809  -0.809  -0.809
17    S        -0.809  -0.809  -0.809  -0.452  -0.452  -0.452  -0.809  -0.809  -0.809
18    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
19    Q         1.224   1.224   1.224   1.408   1.408   1.408   1.224   1.224   1.224
20    E        -0.809  -0.809  -0.809  -1.097  -1.097  -1.097  -0.809  -0.809  -0.809
21    S        -0.809  -0.809  -0.809  -0.474  -0.474  -0.474  -0.809  -0.809  -0.809
22    F        -0.809  -0.809  -0.809  -0.496  -0.496  -0.496  -0.809  -0.809  -0.809
23    D         1.224   1.224   1.224   1.344   1.344   1.344   1.224   1.224   1.224
24    L        -0.809  -0.809  -0.809  -1.308  -1.308  -1.308  -0.809  -0.809  -0.809
25    D        -0.809  -0.809  -0.809  -1.097  -1.097  -1.097  -0.809  -0.809  -0.809
26    C        -0.809  -0.809  -0.809  -0.256  -0.256  -0.256  -0.809  -0.809  -0.809
27    A        -0.809  -0.809  -0.809  -0.213  -0.213  -0.213  -0.809  -0.809  -0.809
28    Q        -0.809  -0.809  -0.809  -1.045  -1.045  -1.045  -0.809  -0.809  -0.809
29    S         1.224   1.224   1.224   1.408   1.408   1.408   1.224   1.224   1.224
30    V         1.224   1.224   1.224   1.376   1.376   1.376   1.224   1.224   1.224
31    S        -0.809  -0.809  -0.809  -0.680  -0.680  -0.680  -0.809  -0.809  -0.809
32    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
33    F         1.224   1.224   1.224   1.628   1.628   1.628   1.224   1.224   1.224
34    T        -0.809  -0.809  -0.809  -0.407  -0.407  -0.407  -0.809  -0.809  -0.809
35    S        -0.809  -0.809  -0.809  -0.385  -0.385  -0.385  -0.809  -0.809  -0.809
36    K         1.224   1.224   1.224   0.979   0.979   0.979   1.224   1.224   1.224
37    S         1.224   1.224   1.224   1.408   1.408   1.408   1.224   1.224   1.224
38    R         1.224   1.224   1.224   1.566   1.566   1.566   1.224   1.224   1.224
39    S        -0.809  -0.809  -0.809  -0.452  -0.452  -0.452  -0.809  -0.809  -0.809
40    N         1.224   1.224   1.224   1.344   1.344   1.344   1.224   1.224   1.224
41    E        -0.809  -0.809  -0.809  -1.097  -1.097  -1.097  -0.809  -0.809  -0.809
42    A        -0.809  -0.809  -0.809  -0.847  -0.847  -0.847  -0.809  -0.809  -0.809
43    W        -0.809  -0.809  -0.809  -0.657  -0.657  -0.657  -0.809  -0.809  -0.809
44    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
45    E        -0.809  -0.809  -0.809  -1.419  -1.419  -1.419  -0.809  -0.809  -0.809
46    E        -0.809  -0.809  -0.809  -1.097  -1.097  -1.097  -0.809  -0.809  -0.809
47    L        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
48    E        -0.809  -0.809  -0.809  -1.097  -1.097  -1.097  -0.809  -0.809  -0.809
49    N        -0.809  -0.809  -0.809  -1.097  -1.097  -1.097  -0.809  -0.809  -0.809
50    K         1.224   1.224   1.224   0.979   0.979   0.979   1.224   1.224   1.224
51    F         1.224   1.224   1.224   1.628   1.628   1.628   1.224   1.224   1.224
52    K        -0.809  -0.809  -0.809  -0.945  -0.945  -0.945  -0.809  -0.809  -0.809
53    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
54    K         1.224   1.224   1.224   0.979   0.979   0.979   1.224   1.224   1.224
55    D         1.224   1.224   1.224   1.344   1.344   1.344   1.224   1.224   1.224
56    D        -0.809  -0.809  -0.809  -0.995  -0.995  -0.995  -0.809  -0.809  -0.809
57    V        -0.809  -0.809  -0.809  -0.703  -0.703  -0.703  -0.809  -0.809  -0.809
58    E         1.224   1.224   1.224   0.841   0.841   0.841   1.224   1.224   1.224
59    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
60    D        -0.809  -0.809  -0.809  -0.385  -0.385  -0.385  -0.809  -0.809  -0.809
61    D        -0.809  -0.809  -0.809  -0.680  -0.680  -0.680  -0.809  -0.809  -0.809
62    V        -0.809  -0.809  -0.809  -0.995  -0.995  -0.995  -0.809  -0.809  -0.809
63    E        -0.809  -0.809  -0.809  -0.774  -0.774  -0.774  -0.809  -0.809  -0.809
64    N        -0.809  -0.809  -0.809  -1.097  -1.097  -1.097  -0.809  -0.809  -0.809
65    L        -0.809  -0.809  -0.809  -0.970  -0.970  -0.970  -0.809  -0.809  -0.809
66    R        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
67    A        -0.809  -0.809  -0.809  -0.320  -0.320  -0.320  -0.809  -0.809  -0.809
68    E         1.224   1.224   1.224   0.841   0.841   0.841   1.224   1.224   1.224
69    I        -0.809  -0.809  -0.809  -0.542  -0.542  -0.542  -0.809  -0.809  -0.809
70    D        -0.809  -0.809  -0.809  -0.680  -0.680  -0.680  -0.809  -0.809  -0.809
71    M        -0.809  -0.809  -0.809  -0.452  -0.452  -0.452  -0.809  -0.809  -0.809
72    K         1.224   1.224   1.224   0.979   0.979   0.979   1.224   1.224   1.224
73    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
74    N        -0.809  -0.809  -0.809  -0.680  -0.680  -0.680  -0.809  -0.809  -0.809
75    M        -0.809  -0.809  -0.809  -0.798  -0.798  -0.798  -0.809  -0.809  -0.809
76    L        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
77    E        -0.809  -0.809  -0.809  -0.920  -0.920  -0.920  -0.809  -0.809  -0.809
78    D        -0.809  -0.809  -0.809  -0.727  -0.727  -0.727  -0.809  -0.809  -0.809
79    K         1.224   1.224   1.224   0.979   0.979   0.979   1.224   1.224   1.224
80    V         1.224   1.224   1.224   1.376   1.376   1.376   1.224   1.224   1.224
81    S        -0.809  -0.809  -0.809  -1.045  -1.045  -1.045  -0.809  -0.809  -0.809
82    Y         1.224   1.224   1.224   1.597   1.597   1.597   1.224   1.224   1.224
83    Y         1.224   1.224   1.224   1.597   1.597   1.597   1.224   1.224   1.224
84    E         1.224   1.224   1.224   0.841   0.841   0.841   1.224   1.224   1.224
85    R        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
86    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
87    Y        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
88    K        -0.809  -0.809  -0.809  -0.703  -0.703  -0.703  -0.809  -0.809  -0.809
89    E         1.224   1.224   1.224   0.841   0.841   0.841   1.224   1.224   1.224
90    L         1.224   1.224   1.224   0.945   0.945   0.945   1.224   1.224   1.224
91    E         1.224   1.224   1.224   0.841   0.841   0.841   1.224   1.224   1.224
92    E         1.224   1.224   1.224   0.841   0.841   0.841   1.224   1.224   1.224
93    F        -0.809  -0.809  -0.809  -0.298  -0.298  -0.298  -0.809  -0.809  -0.809
94    Q         1.224   1.224   1.224   1.408   1.408   1.408   1.224   1.224   1.224
95    N        -0.809  -0.809  -0.809  -0.995  -0.995  -0.995  -0.809  -0.809  -0.809
96    E         1.224   1.224   1.224   0.841   0.841   0.841   1.224   1.224   1.224
97    I        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
98    K        -0.809  -0.809  -0.809  -1.391  -1.391  -1.391  -0.809  -0.809  -0.809
99    I        -0.809  -0.809  -0.809  -0.519  -0.519  -0.519  -0.809  -0.809  -0.809
100   K        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
101   T        -0.809  -0.809  -0.809  -0.277  -0.277  -0.277  -0.809  -0.809  -0.809
102   V        -0.809  -0.809  -0.809  -0.970  -0.970  -0.970  -0.809  -0.809  -0.809
103   V        -0.809  -0.809  -0.809  -0.995  -0.995  -0.995  -0.809  -0.809  -0.809
104   N        -0.809  -0.809  -0.809  -0.703  -0.703  -0.703  -0.809  -0.809  -0.809
105   N        -0.809  -0.809  -0.809  -0.680  -0.680  -0.680  -0.809  -0.809  -0.809
106   R        -0.809  -0.809  -0.809  -0.822  -0.822  -0.822  -0.809  -0.809  -0.809
107   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   P        -0.809  -0.809  -0.809  -0.342  -0.342  -0.342  -0.809  -0.809  -0.809
113   K         1.224   1.224   1.224   0.979   0.979   0.979   1.224   1.224   1.224
* 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/P35727
Output conservation file - output/P35727
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
