1     M         1.365   1.365   1.365   1.796   1.796   1.796   1.365   1.365   1.365
2     I         1.365   1.365   1.365   1.572   1.572   1.572   1.365   1.365   1.365
3     R         1.365   1.365   1.365   1.521   1.521   1.521   1.365   1.365   1.365
4     R         1.365   1.365   1.365   1.521   1.521   1.521   1.365   1.365   1.365
5     A        -0.727  -0.727  -0.727  -0.524  -0.524  -0.524  -0.727  -0.727  -0.727
6     P        -0.727  -0.727  -0.727  -0.308  -0.308  -0.308  -0.727  -0.727  -0.727
7     T         1.365   1.365   1.365   1.287   1.287   1.287   1.365   1.365   1.365
8     T         1.365   1.365   1.365   1.287   1.287   1.287   1.365   1.365   1.365
9     L         1.365   1.365   1.365   1.313   1.313   1.313   1.365   1.365   1.365
10    Q        -0.727  -0.727  -0.727  -0.712  -0.712  -0.712  -0.727  -0.727  -0.727
11    L         1.365   1.365   1.365   1.313   1.313   1.313   1.365   1.365   1.365
12    S         1.365   1.365   1.365   1.153   1.153   1.153   1.365   1.365   1.365
13    H        -0.727  -0.727  -0.727  -0.397  -0.397  -0.397  -0.727  -0.727  -0.727
14    D        -0.727  -0.727  -0.727  -0.990  -0.990  -0.990  -0.727  -0.727  -0.727
15    D         1.365   1.365   1.365   1.126   1.126   1.126   1.365   1.365   1.365
16    V        -0.727  -0.727  -0.727  -0.361  -0.361  -0.361  -0.727  -0.727  -0.727
17    T        -0.727  -0.727  -0.727  -1.031  -1.031  -1.031  -0.727  -0.727  -0.727
18    S        -0.727  -0.727  -0.727  -1.093  -1.093  -1.093  -0.727  -0.727  -0.727
19    L         1.365   1.365   1.365   1.313   1.313   1.313   1.365   1.365   1.365
20    I        -0.727  -0.727  -0.727  -0.361  -0.361  -0.361  -0.727  -0.727  -0.727
21    D         1.365   1.365   1.365   1.126   1.126   1.126   1.365   1.365   1.365
22    D        -0.727  -0.727  -0.727  -0.849  -0.849  -0.849  -0.727  -0.727  -0.727
23    L         1.365   1.365   1.365   1.313   1.313   1.313   1.365   1.365   1.365
24    N        -0.727  -0.727  -0.727  -0.888  -0.888  -0.888  -0.727  -0.727  -0.727
25    E         1.365   1.365   1.365   1.470   1.470   1.470   1.365   1.365   1.365
26    Q        -0.727  -0.727  -0.727  -0.542  -0.542  -0.542  -0.727  -0.727  -0.727
27    K         1.365   1.365   1.365   1.648   1.648   1.648   1.365   1.365   1.365
28    L         1.365   1.365   1.365   1.313   1.313   1.313   1.365   1.365   1.365
29    K        -0.727  -0.727  -0.727  -0.451  -0.451  -0.451  -0.727  -0.727  -0.727
30    Q        -0.727  -0.727  -0.727  -0.542  -0.542  -0.542  -0.727  -0.727  -0.727
31    Q        -0.727  -0.727  -0.727  -0.506  -0.506  -0.506  -0.727  -0.727  -0.727
32    L        -0.727  -0.727  -0.727  -0.636  -0.636  -0.636  -0.727  -0.727  -0.727
33    N         1.365   1.365   1.365   1.071   1.071   1.071   1.365   1.365   1.365
34    I        -0.727  -0.727  -0.727  -0.397  -0.397  -0.397  -0.727  -0.727  -0.727
35    E        -0.727  -0.727  -0.727  -0.580  -0.580  -0.580  -0.727  -0.727  -0.727
36    K        -0.727  -0.727  -0.727  -0.433  -0.433  -0.433  -0.727  -0.727  -0.727
37    T        -0.727  -0.727  -0.727  -0.990  -0.990  -0.990  -0.727  -0.727  -0.727
38    K        -0.727  -0.727  -0.727  -0.433  -0.433  -0.433  -0.727  -0.727  -0.727
39    Y        -0.727  -0.727  -0.727  -0.221  -0.221  -0.221  -0.727  -0.727  -0.727
40    F        -0.727  -0.727  -0.727  -0.524  -0.524  -0.524  -0.727  -0.727  -0.727
41    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    K        -0.727  -0.727  -0.727  -0.433  -0.433  -0.433  -0.727  -0.727  -0.727
44    N        -0.727  -0.727  -0.727  -1.031  -1.031  -1.031  -0.727  -0.727  -0.727
45    G        -0.727  -0.727  -0.727  -0.731  -0.731  -0.731  -0.727  -0.727  -0.727
46    G        -0.727  -0.727  -0.727  -0.636  -0.636  -0.636  -0.727  -0.727  -0.727
47    S        -0.727  -0.727  -0.727  -0.693  -0.693  -0.693  -0.727  -0.727  -0.727
48    L         1.365   1.365   1.365   1.313   1.313   1.313   1.365   1.365   1.365
49    H        -0.727  -0.727  -0.727  -0.415  -0.415  -0.415  -0.727  -0.727  -0.727
50    S         1.365   1.365   1.365   1.153   1.153   1.153   1.365   1.365   1.365
51    N        -0.727  -0.727  -0.727  -0.790  -0.790  -0.790  -0.727  -0.727  -0.727
52    T        -0.727  -0.727  -0.727  -0.969  -0.969  -0.969  -0.727  -0.727  -0.727
53    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    Q        -0.727  -0.727  -0.727  -0.580  -0.580  -0.580  -0.727  -0.727  -0.727
56    D         1.365   1.365   1.365   1.126   1.126   1.126   1.365   1.365   1.365
57    T         1.365   1.365   1.365   1.287   1.287   1.287   1.365   1.365   1.365
58    S        -0.727  -0.727  -0.727  -0.790  -0.790  -0.790  -0.727  -0.727  -0.727
59    Q        -0.727  -0.727  -0.727  -0.693  -0.693  -0.693  -0.727  -0.727  -0.727
60    N        -0.727  -0.727  -0.727  -0.809  -0.809  -0.809  -0.727  -0.727  -0.727
61    I        -0.727  -0.727  -0.727  -0.751  -0.751  -0.751  -0.727  -0.727  -0.727
62    E        -0.727  -0.727  -0.727  -0.561  -0.561  -0.561  -0.727  -0.727  -0.727
63    D         1.365   1.365   1.365   1.126   1.126   1.126   1.365   1.365   1.365
64    N         1.365   1.365   1.365   1.071   1.071   1.071   1.365   1.365   1.365
65    N         1.365   1.365   1.365   1.071   1.071   1.071   1.365   1.365   1.365
66    N        -0.727  -0.727  -0.727  -1.157  -1.157  -1.157  -0.727  -0.727  -0.727
67    D         1.365   1.365   1.365   1.126   1.126   1.126   1.365   1.365   1.365
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    N         1.365   1.365   1.365   1.071   1.071   1.071   1.365   1.365   1.365
75    D        -0.727  -0.727  -0.727  -1.157  -1.157  -1.157  -0.727  -0.727  -0.727
76    N        -0.727  -0.727  -0.727  -0.790  -0.790  -0.790  -0.727  -0.727  -0.727
77    D         1.365   1.365   1.365   1.126   1.126   1.126   1.365   1.365   1.365
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    I         1.365   1.365   1.365   1.572   1.572   1.572   1.365   1.365   1.365
87    D         1.365   1.365   1.365   1.126   1.126   1.126   1.365   1.365   1.365
88    E        -0.727  -0.727  -0.727  -0.829  -0.829  -0.829  -0.727  -0.727  -0.727
89    D        -0.727  -0.727  -0.727  -0.655  -0.655  -0.655  -0.727  -0.727  -0.727
90    D        -0.727  -0.727  -0.727  -0.770  -0.770  -0.770  -0.727  -0.727  -0.727
91    D        -0.727  -0.727  -0.727  -1.157  -1.157  -1.157  -0.727  -0.727  -0.727
92    M        -0.727  -0.727  -0.727  -0.290  -0.290  -0.290  -0.727  -0.727  -0.727
93    S         1.365   1.365   1.365   1.153   1.153   1.153   1.365   1.365   1.365
94    S        -0.727  -0.727  -0.727  -0.598  -0.598  -0.598  -0.727  -0.727  -0.727
95    Y        -0.727  -0.727  -0.727  -0.487  -0.487  -0.487  -0.727  -0.727  -0.727
96    N        -0.727  -0.727  -0.727  -1.157  -1.157  -1.157  -0.727  -0.727  -0.727
97    D        -0.727  -0.727  -0.727  -1.157  -1.157  -1.157  -0.727  -0.727  -0.727
98    K         1.365   1.365   1.365   1.648   1.648   1.648   1.365   1.365   1.365
99    A        -0.727  -0.727  -0.727  -0.655  -0.655  -0.655  -0.727  -0.727  -0.727
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   A        -0.727  -0.727  -0.727  -0.433  -0.433  -0.433  -0.727  -0.727  -0.727
116   S         1.365   1.365   1.365   1.153   1.153   1.153   1.365   1.365   1.365
117   V        -0.727  -0.727  -0.727  -0.255  -0.255  -0.255  -0.727  -0.727  -0.727
118   A         1.365   1.365   1.365   1.572   1.572   1.572   1.365   1.365   1.365
119   H        -0.727  -0.727  -0.727  -0.397  -0.397  -0.397  -0.727  -0.727  -0.727
120   T        -0.727  -0.727  -0.727  -1.031  -1.031  -1.031  -0.727  -0.727  -0.727
121   R        -0.727  -0.727  -0.727  -0.693  -0.693  -0.693  -0.727  -0.727  -0.727
122   V        -0.727  -0.727  -0.727  -0.561  -0.561  -0.561  -0.727  -0.727  -0.727
123   L        -0.727  -0.727  -0.727  -0.949  -0.949  -0.949  -0.727  -0.727  -0.727
124   N         1.365   1.365   1.365   1.071   1.071   1.071   1.365   1.365   1.365
125   S         1.365   1.365   1.365   1.153   1.153   1.153   1.365   1.365   1.365
126   L        -0.727  -0.727  -0.727  -1.010  -1.010  -1.010  -0.727  -0.727  -0.727
127   H        -0.727  -0.727  -0.727  -0.135  -0.135  -0.135  -0.727  -0.727  -0.727
128   L        -0.727  -0.727  -0.727  -0.693  -0.693  -0.693  -0.727  -0.727  -0.727
129   S        -0.727  -0.727  -0.727  -0.731  -0.731  -0.731  -0.727  -0.727  -0.727
130   T        -0.727  -0.727  -0.727  -1.031  -1.031  -1.031  -0.727  -0.727  -0.727
131   D        -0.727  -0.727  -0.727  -1.093  -1.093  -1.093  -0.727  -0.727  -0.727
132   S        -0.727  -0.727  -0.727  -0.809  -0.809  -0.809  -0.727  -0.727  -0.727
133   N        -0.727  -0.727  -0.727  -1.136  -1.136  -1.136  -0.727  -0.727  -0.727
134   T        -0.727  -0.727  -0.727  -0.636  -0.636  -0.636  -0.727  -0.727  -0.727
135   A        -0.727  -0.727  -0.727  -0.655  -0.655  -0.655  -0.727  -0.727  -0.727
136   H        -0.727  -0.727  -0.727  -0.636  -0.636  -0.636  -0.727  -0.727  -0.727
137   E         1.365   1.365   1.365   1.470   1.470   1.470   1.365   1.365   1.365
138   T         1.365   1.365   1.365   1.287   1.287   1.287   1.365   1.365   1.365
139   S        -0.727  -0.727  -0.727  -0.829  -0.829  -0.829  -0.727  -0.727  -0.727
140   N        -0.727  -0.727  -0.727  -0.809  -0.809  -0.809  -0.727  -0.727  -0.727
141   A        -0.727  -0.727  -0.727  -0.433  -0.433  -0.433  -0.727  -0.727  -0.727
142   N        -0.727  -0.727  -0.727  -1.136  -1.136  -1.136  -0.727  -0.727  -0.727
143   D        -0.727  -0.727  -0.727  -0.990  -0.990  -0.990  -0.727  -0.727  -0.727
144   N        -0.727  -0.727  -0.727  -0.868  -0.868  -0.868  -0.727  -0.727  -0.727
145   H        -0.727  -0.727  -0.727  -0.636  -0.636  -0.636  -0.727  -0.727  -0.727
146   N         1.365   1.365   1.365   1.071   1.071   1.071   1.365   1.365   1.365
147   P         1.365   1.365   1.365   1.772   1.772   1.772   1.365   1.365   1.365
148   F         1.365   1.365   1.365   1.722   1.722   1.722   1.365   1.365   1.365
149   Y         1.365   1.365   1.365   1.772   1.772   1.772   1.365   1.365   1.365
150   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   E        -0.727  -0.727  -0.727  -0.561  -0.561  -0.561  -0.727  -0.727  -0.727
153   E        -0.727  -0.727  -0.727  -0.506  -0.506  -0.506  -0.727  -0.727  -0.727
* 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/P14724
Output conservation file - output/P14724
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
