1     M         1.228   1.228   1.228   1.465   1.465   1.465   1.228   1.228   1.228
2     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     T        -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     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    E        -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    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    A        -0.807  -0.807  -0.807  -0.925  -0.925  -0.925  -0.807  -0.807  -0.807
26    T        -0.807  -0.807  -0.807  -0.522  -0.522  -0.522  -0.807  -0.807  -0.807
27    L        -0.807  -0.807  -0.807  -1.121  -1.121  -1.121  -0.807  -0.807  -0.807
28    P        -0.807  -0.807  -0.807  -0.737  -0.737  -0.737  -0.807  -0.807  -0.807
29    A        -0.807  -0.807  -0.807  -0.756  -0.756  -0.756  -0.807  -0.807  -0.807
30    D         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
31    D        -0.807  -0.807  -0.807  -0.737  -0.737  -0.737  -0.807  -0.807  -0.807
32    R        -0.807  -0.807  -0.807  -1.022  -1.022  -1.022  -0.807  -0.807  -0.807
33    S         1.228   1.228   1.228   0.930   0.930   0.930   1.228   1.228   1.228
34    K        -0.807  -0.807  -0.807  -0.811  -0.811  -0.811  -0.807  -0.807  -0.807
35    K        -0.807  -0.807  -0.807  -0.719  -0.719  -0.719  -0.807  -0.807  -0.807
36    I        -0.807  -0.807  -0.807  -0.887  -0.887  -0.887  -0.807  -0.807  -0.807
37    P        -0.807  -0.807  -0.807  -0.737  -0.737  -0.737  -0.807  -0.807  -0.807
38    I        -0.807  -0.807  -0.807  -0.664  -0.664  -0.664  -0.807  -0.807  -0.807
39    S        -0.807  -0.807  -0.807  -1.061  -1.061  -1.061  -0.807  -0.807  -0.807
40    L        -0.807  -0.807  -0.807  -1.121  -1.121  -1.121  -0.807  -0.807  -0.807
41    V        -0.807  -0.807  -0.807  -0.756  -0.756  -0.756  -0.807  -0.807  -0.807
42    V        -0.807  -0.807  -0.807  -0.887  -0.887  -0.887  -0.807  -0.807  -0.807
43    G         1.228   1.228   1.228   1.367   1.367   1.367   1.228   1.228   1.228
44    F        -0.807  -0.807  -0.807  -0.593  -0.593  -0.593  -0.807  -0.807  -0.807
45    K         1.228   1.228   1.228   1.267   1.267   1.267   1.228   1.228   1.228
46    Q        -0.807  -0.807  -0.807  -0.756  -0.756  -0.756  -0.807  -0.807  -0.807
47    E        -0.807  -0.807  -0.807  -0.611  -0.611  -0.611  -0.807  -0.807  -0.807
48    A        -0.807  -0.807  -0.807  -0.756  -0.756  -0.756  -0.807  -0.807  -0.807
49    S         1.228   1.228   1.228   0.930   0.930   0.930   1.228   1.228   1.228
50    L         1.228   1.228   1.228   0.849   0.849   0.849   1.228   1.228   1.228
51    N         1.228   1.228   1.228   1.416   1.416   1.416   1.228   1.228   1.228
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    S        -0.807  -0.807  -0.807  -0.983  -0.983  -0.983  -0.807  -0.807  -0.807
62    S         1.228   1.228   1.228   0.930   0.930   0.930   1.228   1.228   1.228
63    S         1.228   1.228   1.228   0.930   0.930   0.930   1.228   1.228   1.228
64    S        -0.807  -0.807  -0.807  -0.963  -0.963  -0.963  -0.807  -0.807  -0.807
65    L         1.228   1.228   1.228   0.849   0.849   0.849   1.228   1.228   1.228
66    S        -0.807  -0.807  -0.807  -0.925  -0.925  -0.925  -0.807  -0.807  -0.807
67    C         1.228   1.228   1.228   1.465   1.465   1.465   1.228   1.228   1.228
68    Y         1.228   1.228   1.228   1.416   1.416   1.416   1.228   1.228   1.228
69    Y         1.228   1.228   1.228   1.416   1.416   1.416   1.228   1.228   1.228
70    Y         1.228   1.228   1.228   1.416   1.416   1.416   1.228   1.228   1.228
71    A        -0.807  -0.807  -0.807  -0.683  -0.683  -0.683  -0.807  -0.807  -0.807
72    I         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
73    P        -0.807  -0.807  -0.807  -0.522  -0.522  -0.522  -0.807  -0.807  -0.807
74    L        -0.807  -0.807  -0.807  -0.963  -0.963  -0.963  -0.807  -0.807  -0.807
75    M        -0.807  -0.807  -0.807  -0.575  -0.575  -0.575  -0.807  -0.807  -0.807
76    R        -0.807  -0.807  -0.807  -0.719  -0.719  -0.719  -0.807  -0.807  -0.807
77    D         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
78    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    N        -0.807  -0.807  -0.807  -0.701  -0.701  -0.701  -0.807  -0.807  -0.807
89    V         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
90    V        -0.807  -0.807  -0.807  -1.121  -1.121  -1.121  -0.807  -0.807  -0.807
91    G         1.228   1.228   1.228   1.367   1.367   1.367   1.228   1.228   1.228
92    I         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
93    P         1.228   1.228   1.228   1.367   1.367   1.367   1.228   1.228   1.228
94    L         1.228   1.228   1.228   0.849   0.849   0.849   1.228   1.228   1.228
95    L        -0.807  -0.807  -0.807  -1.022  -1.022  -1.022  -0.807  -0.807  -0.807
96    D         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
97    T         1.228   1.228   1.228   1.267   1.267   1.267   1.228   1.228   1.228
98    K        -0.807  -0.807  -0.807  -0.983  -0.983  -0.983  -0.807  -0.807  -0.807
99    D        -0.807  -0.807  -0.807  -1.061  -1.061  -1.061  -0.807  -0.807  -0.807
100   D         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
101   R        -0.807  -0.807  -0.807  -0.470  -0.470  -0.470  -0.807  -0.807  -0.807
102   I         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
103   R         1.228   1.228   1.228   1.292   1.292   1.292   1.228   1.228   1.228
104   D         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
105   M        -0.807  -0.807  -0.807  -0.887  -0.887  -0.887  -0.807  -0.807  -0.807
106   A         1.228   1.228   1.228   1.342   1.342   1.342   1.228   1.228   1.228
107   R         1.228   1.228   1.228   1.292   1.292   1.292   1.228   1.228   1.228
108   H        -0.807  -0.807  -0.807  -0.811  -0.811  -0.811  -0.807  -0.807  -0.807
109   M        -0.807  -0.807  -0.807  -0.453  -0.453  -0.453  -0.807  -0.807  -0.807
110   A         1.228   1.228   1.228   1.342   1.342   1.342   1.228   1.228   1.228
111   T         1.228   1.228   1.228   1.267   1.267   1.267   1.228   1.228   1.228
112   I        -0.807  -0.807  -0.807  -0.664  -0.664  -0.664  -0.807  -0.807  -0.807
113   I         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
114   S        -0.807  -0.807  -0.807  -0.983  -0.983  -0.983  -0.807  -0.807  -0.807
115   E        -0.807  -0.807  -0.807  -0.683  -0.683  -0.683  -0.807  -0.807  -0.807
116   R        -0.807  -0.807  -0.807  -0.719  -0.719  -0.719  -0.807  -0.807  -0.807
117   F        -0.807  -0.807  -0.807  -0.418  -0.418  -0.418  -0.807  -0.807  -0.807
118   N         1.228   1.228   1.228   1.416   1.416   1.416   1.228   1.228   1.228
119   R        -0.807  -0.807  -0.807  -0.719  -0.719  -0.719  -0.807  -0.807  -0.807
120   P         1.228   1.228   1.228   1.367   1.367   1.367   1.228   1.228   1.228
121   C         1.228   1.228   1.228   1.465   1.465   1.465   1.228   1.228   1.228
122   Y         1.228   1.228   1.228   1.416   1.416   1.416   1.228   1.228   1.228
123   V         1.228   1.228   1.228   1.165   1.165   1.165   1.228   1.228   1.228
124   T         1.228   1.228   1.228   1.267   1.267   1.267   1.228   1.228   1.228
125   W        -0.807  -0.807  -0.807  -0.557  -0.557  -0.557  -0.807  -0.807  -0.807
126   S         1.228   1.228   1.228   0.930   0.930   0.930   1.228   1.228   1.228
127   S        -0.807  -0.807  -0.807  -0.983  -0.983  -0.983  -0.807  -0.807  -0.807
128   L        -0.807  -0.807  -0.807  -1.121  -1.121  -1.121  -0.807  -0.807  -0.807
129   P        -0.807  -0.807  -0.807  -0.593  -0.593  -0.593  -0.807  -0.807  -0.807
130   S        -0.807  -0.807  -0.807  -0.925  -0.925  -0.925  -0.807  -0.807  -0.807
131   E        -0.807  -0.807  -0.807  -0.575  -0.575  -0.575  -0.807  -0.807  -0.807
132   D        -0.807  -0.807  -0.807  -0.701  -0.701  -0.701  -0.807  -0.807  -0.807
133   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   L        -0.807  -0.807  -0.807  -0.811  -0.811  -0.811  -0.807  -0.807  -0.807
137   V        -0.807  -0.807  -0.807  -0.593  -0.593  -0.593  -0.807  -0.807  -0.807
138   A         1.228   1.228   1.228   1.342   1.342   1.342   1.228   1.228   1.228
139   N        -0.807  -0.807  -0.807  -0.868  -0.868  -0.868  -0.807  -0.807  -0.807
140   H        -0.807  -0.807  -0.807  -0.522  -0.522  -0.522  -0.807  -0.807  -0.807
141   L        -0.807  -0.807  -0.807  -1.121  -1.121  -1.121  -0.807  -0.807  -0.807
142   Y        -0.807  -0.807  -0.807  -0.557  -0.557  -0.557  -0.807  -0.807  -0.807
143   I        -0.807  -0.807  -0.807  -1.121  -1.121  -1.121  -0.807  -0.807  -0.807
144   L         1.228   1.228   1.228   0.849   0.849   0.849   1.228   1.228   1.228
145   K        -0.807  -0.807  -0.807  -0.683  -0.683  -0.683  -0.807  -0.807  -0.807
146   K        -0.807  -0.807  -0.807  -0.683  -0.683  -0.683  -0.807  -0.807  -0.807
147   C        -0.807  -0.807  -0.807  -0.664  -0.664  -0.664  -0.807  -0.807  -0.807
148   L        -0.807  -0.807  -0.807  -1.041  -1.041  -1.041  -0.807  -0.807  -0.807
149   D        -0.807  -0.807  -0.807  -0.756  -0.756  -0.756  -0.807  -0.807  -0.807
150   L        -0.807  -0.807  -0.807  -0.811  -0.811  -0.811  -0.807  -0.807  -0.807
151   L        -0.807  -0.807  -0.807  -1.121  -1.121  -1.121  -0.807  -0.807  -0.807
152   K        -0.807  -0.807  -0.807  -0.683  -0.683  -0.683  -0.807  -0.807  -0.807
153   T         1.228   1.228   1.228   1.267   1.267   1.267   1.228   1.228   1.228
154   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   L         1.228   1.228   1.228   0.849   0.849   0.849   1.228   1.228   1.228
156   G        -0.807  -0.807  -0.807  -0.737  -0.737  -0.737  -0.807  -0.807  -0.807
157   E        -0.807  -0.807  -0.807  -0.575  -0.575  -0.575  -0.807  -0.807  -0.807
* 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/Q12245
Output conservation file - output/Q12245
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
