1     M         1.524   1.524   1.524   1.775   1.775   1.775   1.524   1.524   1.524
2     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     A        -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    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    A        -0.651  -0.651  -0.651  -0.874  -0.874  -0.874  -0.651  -0.651  -0.651
23    L        -0.651  -0.651  -0.651  -0.748  -0.748  -0.748  -0.651  -0.651  -0.651
24    S        -0.651  -0.651  -0.651  -0.566  -0.566  -0.566  -0.651  -0.651  -0.651
25    L         1.524   1.524   1.524   1.616   1.616   1.616   1.524   1.524   1.524
26    Q        -0.651  -0.651  -0.651  -0.748  -0.748  -0.748  -0.651  -0.651  -0.651
27    R        -0.651  -0.651  -0.651  -0.258  -0.258  -0.258  -0.651  -0.651  -0.651
28    R         1.524   1.524   1.524   1.749   1.749   1.749   1.524   1.524   1.524
29    S        -0.651  -0.651  -0.651  -0.982  -0.982  -0.982  -0.651  -0.651  -0.651
30    Q        -0.651  -0.651  -0.651  -0.315  -0.315  -0.315  -0.651  -0.651  -0.651
31    E        -0.651  -0.651  -0.651  -0.687  -0.687  -0.687  -0.651  -0.651  -0.651
32    F         1.524   1.524   1.524   1.589   1.589   1.589   1.524   1.524   1.524
33    A        -0.651  -0.651  -0.651  -0.853  -0.853  -0.853  -0.651  -0.651  -0.651
34    T        -0.651  -0.651  -0.651  -0.526  -0.526  -0.526  -0.651  -0.651  -0.651
35    S        -0.651  -0.651  -0.651  -0.626  -0.626  -0.626  -0.651  -0.651  -0.651
36    W         1.524   1.524   1.524   1.775   1.775   1.775   1.524   1.524   1.524
37    I        -0.651  -0.651  -0.651  -0.315  -0.315  -0.315  -0.651  -0.651  -0.651
38    S         1.524   1.524   1.524   1.313   1.313   1.313   1.524   1.524   1.524
39    M        -0.651  -0.651  -0.651  -0.391  -0.391  -0.391  -0.651  -0.651  -0.651
40    T        -0.651  -0.651  -0.651  -0.626  -0.626  -0.626  -0.651  -0.651  -0.651
41    Y         1.524   1.524   1.524   1.507   1.507   1.507   1.524   1.524   1.524
42    S        -0.651  -0.651  -0.651  -0.961  -0.961  -0.961  -0.651  -0.651  -0.651
43    Q        -0.651  -0.651  -0.651  -0.646  -0.646  -0.646  -0.651  -0.651  -0.651
44    S        -0.651  -0.651  -0.651  -0.546  -0.546  -0.546  -0.651  -0.651  -0.651
45    Y        -0.651  -0.651  -0.651  -0.728  -0.728  -0.728  -0.651  -0.651  -0.651
46    G        -0.651  -0.651  -0.651  -0.982  -0.982  -0.982  -0.651  -0.651  -0.651
47    D         1.524   1.524   1.524   1.199   1.199   1.199   1.524   1.524   1.524
48    L         1.524   1.524   1.524   1.616   1.616   1.616   1.524   1.524   1.524
49    A         1.524   1.524   1.524   1.452   1.452   1.452   1.524   1.524   1.524
50    Q        -0.651  -0.651  -0.651  -0.333  -0.333  -0.333  -0.651  -0.651  -0.651
51    N        -0.651  -0.651  -0.651  -0.646  -0.646  -0.646  -0.651  -0.651  -0.651
52    W         1.524   1.524   1.524   1.775   1.775   1.775   1.524   1.524   1.524
53    Q        -0.651  -0.651  -0.651  -0.546  -0.546  -0.546  -0.651  -0.651  -0.651
54    N        -0.651  -0.651  -0.651  -0.687  -0.687  -0.687  -0.651  -0.651  -0.651
55    D        -0.651  -0.651  -0.651  -0.961  -0.961  -0.961  -0.651  -0.651  -0.651
56    E        -0.651  -0.651  -0.651  -0.448  -0.448  -0.448  -0.651  -0.651  -0.651
57    G        -0.651  -0.651  -0.651  -0.586  -0.586  -0.586  -0.651  -0.651  -0.651
58    G        -0.651  -0.651  -0.651  -0.982  -0.982  -0.982  -0.651  -0.651  -0.651
59    A        -0.651  -0.651  -0.651  -0.853  -0.853  -0.853  -0.651  -0.651  -0.651
60    G        -0.651  -0.651  -0.651  -0.982  -0.982  -0.982  -0.651  -0.651  -0.651
61    N        -0.651  -0.651  -0.651  -0.646  -0.646  -0.646  -0.651  -0.651  -0.651
62    F        -0.651  -0.651  -0.651  -0.526  -0.526  -0.526  -0.651  -0.651  -0.651
63    D        -0.651  -0.651  -0.651  -0.728  -0.728  -0.728  -0.651  -0.651  -0.651
64    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    A        -0.651  -0.651  -0.651  -0.546  -0.546  -0.546  -0.651  -0.651  -0.651
67    E         1.524   1.524   1.524   1.562   1.562   1.562   1.524   1.524   1.524
68    E         1.524   1.524   1.524   1.562   1.562   1.562   1.524   1.524   1.524
69    K        -0.651  -0.651  -0.651  -0.391  -0.391  -0.391  -0.651  -0.651  -0.651
70    L        -0.651  -0.651  -0.651  -0.315  -0.315  -0.315  -0.651  -0.651  -0.651
71    Q        -0.651  -0.651  -0.651  -0.429  -0.429  -0.429  -0.651  -0.651  -0.651
72    N        -0.651  -0.651  -0.651  -0.961  -0.961  -0.961  -0.651  -0.651  -0.651
73    F         1.524   1.524   1.524   1.589   1.589   1.589   1.524   1.524   1.524
74    F        -0.651  -0.651  -0.651  -0.333  -0.333  -0.333  -0.651  -0.651  -0.651
75    S        -0.651  -0.651  -0.651  -0.874  -0.874  -0.874  -0.651  -0.651  -0.651
76    G        -0.651  -0.651  -0.651  -0.874  -0.874  -0.874  -0.651  -0.651  -0.651
77    N         1.524   1.524   1.524   1.313   1.313   1.313   1.524   1.524   1.524
78    R        -0.651  -0.651  -0.651  -0.626  -0.626  -0.626  -0.651  -0.651  -0.651
79    D        -0.651  -0.651  -0.651  -1.071  -1.071  -1.071  -0.651  -0.651  -0.651
80    W        -0.651  -0.651  -0.651  -0.391  -0.391  -0.391  -0.651  -0.651  -0.651
81    K         1.524   1.524   1.524   1.722   1.722   1.722   1.524   1.524   1.524
82    Y         1.524   1.524   1.524   1.507   1.507   1.507   1.524   1.524   1.524
83    C         1.524   1.524   1.524   1.801   1.801   1.801   1.524   1.524   1.524
84    F        -0.651  -0.651  -0.651  -0.429  -0.429  -0.429  -0.651  -0.651  -0.651
85    A        -0.651  -0.651  -0.651  -0.769  -0.769  -0.769  -0.651  -0.651  -0.651
86    A        -0.651  -0.651  -0.651  -0.448  -0.448  -0.448  -0.651  -0.651  -0.651
87    E        -0.651  -0.651  -0.651  -0.687  -0.687  -0.687  -0.651  -0.651  -0.651
88    D        -0.651  -0.651  -0.651  -0.728  -0.728  -0.728  -0.651  -0.651  -0.651
89    T        -0.651  -0.651  -0.651  -0.626  -0.626  -0.626  -0.651  -0.651  -0.651
90    K        -0.651  -0.651  -0.651  -0.566  -0.566  -0.566  -0.651  -0.651  -0.651
91    N         1.524   1.524   1.524   1.313   1.313   1.313   1.524   1.524   1.524
92    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    P         1.524   1.524   1.524   1.749   1.749   1.749   1.524   1.524   1.524
95    L        -0.651  -0.651  -0.651  -0.748  -0.748  -0.748  -0.651  -0.651  -0.651
96    D         1.524   1.524   1.524   1.199   1.199   1.199   1.524   1.524   1.524
97    Y        -0.651  -0.651  -0.651  -0.487  -0.487  -0.487  -0.651  -0.651  -0.651
98    D        -0.651  -0.651  -0.651  -0.961  -0.961  -0.961  -0.651  -0.651  -0.651
99    D        -0.651  -0.651  -0.651  -0.646  -0.646  -0.646  -0.651  -0.651  -0.651
100   I        -0.651  -0.651  -0.651  -0.626  -0.626  -0.626  -0.651  -0.651  -0.651
101   P        -0.651  -0.651  -0.651  -0.448  -0.448  -0.448  -0.651  -0.651  -0.651
102   G        -0.651  -0.651  -0.651  -0.769  -0.769  -0.769  -0.651  -0.651  -0.651
103   D         1.524   1.524   1.524   1.199   1.199   1.199   1.524   1.524   1.524
104   G        -0.651  -0.651  -0.651  -1.071  -1.071  -1.071  -0.651  -0.651  -0.651
105   A        -0.651  -0.651  -0.651  -0.769  -0.769  -0.769  -0.651  -0.651  -0.651
106   G        -0.651  -0.651  -0.651  -0.646  -0.646  -0.646  -0.651  -0.651  -0.651
107   T        -0.651  -0.651  -0.651  -0.707  -0.707  -0.707  -0.651  -0.651  -0.651
108   G        -0.651  -0.651  -0.651  -0.748  -0.748  -0.748  -0.651  -0.651  -0.651
109   S        -0.651  -0.651  -0.651  -0.626  -0.626  -0.626  -0.651  -0.651  -0.651
110   A        -0.651  -0.651  -0.651  -0.448  -0.448  -0.448  -0.651  -0.651  -0.651
111   F        -0.651  -0.651  -0.651  -0.333  -0.333  -0.333  -0.651  -0.651  -0.651
112   K        -0.651  -0.651  -0.651  -0.203  -0.203  -0.203  -0.651  -0.651  -0.651
113   S        -0.651  -0.651  -0.651  -0.982  -0.982  -0.982  -0.651  -0.651  -0.651
114   E         1.524   1.524   1.524   1.562   1.562   1.562   1.524   1.524   1.524
115   I        -0.651  -0.651  -0.651  -0.391  -0.391  -0.391  -0.651  -0.651  -0.651
116   Y         1.524   1.524   1.524   1.507   1.507   1.507   1.524   1.524   1.524
117   F         1.524   1.524   1.524   1.589   1.589   1.589   1.524   1.524   1.524
118   N         1.524   1.524   1.524   1.313   1.313   1.313   1.524   1.524   1.524
119   T         1.524   1.524   1.524   1.642   1.642   1.642   1.524   1.524   1.524
120   Y         1.524   1.524   1.524   1.507   1.507   1.507   1.524   1.524   1.524
121   G         1.524   1.524   1.524   1.171   1.171   1.171   1.524   1.524   1.524
122   G         1.524   1.524   1.524   1.171   1.171   1.171   1.524   1.524   1.524
123   I        -0.651  -0.651  -0.651  -0.315  -0.315  -0.315  -0.651  -0.651  -0.651
124   D         1.524   1.524   1.524   1.199   1.199   1.199   1.524   1.524   1.524
125   N        -0.651  -0.651  -0.651  -0.982  -0.982  -0.982  -0.651  -0.651  -0.651
126   Y        -0.651  -0.651  -0.651  -0.546  -0.546  -0.546  -0.651  -0.651  -0.651
127   C         1.524   1.524   1.524   1.801   1.801   1.801   1.524   1.524   1.524
128   N         1.524   1.524   1.524   1.313   1.313   1.313   1.524   1.524   1.524
129   D         1.524   1.524   1.524   1.199   1.199   1.199   1.524   1.524   1.524
130   E        -0.651  -0.651  -0.651  -0.487  -0.487  -0.487  -0.651  -0.651  -0.651
131   H        -0.651  -0.651  -0.651  -0.352  -0.352  -0.352  -0.651  -0.651  -0.651
132   I        -0.651  -0.651  -0.651  -0.258  -0.258  -0.258  -0.651  -0.651  -0.651
133   G        -0.651  -0.651  -0.651  -0.646  -0.646  -0.646  -0.651  -0.651  -0.651
134   A        -0.651  -0.651  -0.651  -0.546  -0.546  -0.546  -0.651  -0.651  -0.651
135   Q        -0.651  -0.651  -0.651  -0.410  -0.410  -0.410  -0.651  -0.651  -0.651
136   N        -0.651  -0.651  -0.651  -0.874  -0.874  -0.874  -0.651  -0.651  -0.651
137   T        -0.651  -0.651  -0.651  -0.707  -0.707  -0.707  -0.651  -0.651  -0.651
138   G        -0.651  -0.651  -0.651  -0.606  -0.606  -0.606  -0.651  -0.651  -0.651
139   D        -0.651  -0.651  -0.651  -0.961  -0.961  -0.961  -0.651  -0.651  -0.651
140   G         1.524   1.524   1.524   1.171   1.171   1.171   1.524   1.524   1.524
141   R        -0.651  -0.651  -0.651  -0.352  -0.352  -0.352  -0.651  -0.651  -0.651
* 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/P40102
Output conservation file - output/P40102
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
