1     M         1.137   1.137   1.137   1.440   1.440   1.440   1.137   1.137   1.137
2     G        -0.871  -0.871  -0.871  -0.735  -0.735  -0.735  -0.871  -0.871  -0.871
3     K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    C        -0.871  -0.871  -0.871  -0.615  -0.615  -0.615  -0.871  -0.871  -0.871
18    S         1.137   1.137   1.137   0.935   0.935   0.935   1.137   1.137   1.137
19    M        -0.871  -0.871  -0.871  -0.459  -0.459  -0.459  -0.871  -0.871  -0.871
20    K        -0.871  -0.871  -0.871  -1.575  -1.575  -1.575  -0.871  -0.871  -0.871
21    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
22    K        -0.871  -0.871  -0.871  -1.575  -1.575  -1.575  -0.871  -0.871  -0.871
23    G        -0.871  -0.871  -0.871  -0.735  -0.735  -0.735  -0.871  -0.871  -0.871
24    V         1.137   1.137   1.137   1.386   1.386   1.386   1.137   1.137   1.137
25    G        -0.871  -0.871  -0.871  -0.289  -0.289  -0.289  -0.871  -0.871  -0.871
26    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
27    N        -0.871  -0.871  -0.871  -1.166  -1.166  -1.166  -0.871  -0.871  -0.871
28    V        -0.871  -0.871  -0.871  -0.595  -0.595  -0.595  -0.871  -0.871  -0.871
29    G         1.137   1.137   1.137   1.467   1.467   1.467   1.137   1.137   1.137
30    V         1.137   1.137   1.137   1.386   1.386   1.386   1.137   1.137   1.137
31    G        -0.871  -0.871  -0.871  -0.401  -0.401  -0.401  -0.871  -0.871  -0.871
32    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
33    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    I         1.137   1.137   1.137   1.331   1.331   1.331   1.137   1.137   1.137
41    S         1.137   1.137   1.137   0.935   0.935   0.935   1.137   1.137   1.137
42    T        -0.871  -0.871  -0.871  -0.595  -0.595  -0.595  -0.871  -0.871  -0.871
43    A        -0.871  -0.871  -0.871  -0.797  -0.797  -0.797  -0.871  -0.871  -0.871
44    E         1.137   1.137   1.137   1.108   1.108   1.108   1.137   1.137   1.137
45    R         1.137   1.137   1.137   1.359   1.359   1.359   1.137   1.137   1.137
46    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
47    R        -0.871  -0.871  -0.871  -1.212  -1.212  -1.212  -0.871  -0.871  -0.871
48    T        -0.871  -0.871  -0.871  -0.924  -0.924  -0.924  -0.871  -0.871  -0.871
49    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
50    L        -0.871  -0.871  -0.871  -0.675  -0.675  -0.675  -0.871  -0.871  -0.871
51    Q        -0.871  -0.871  -0.871  -0.634  -0.634  -0.634  -0.871  -0.871  -0.871
52    V        -0.871  -0.871  -0.871  -0.595  -0.595  -0.595  -0.871  -0.871  -0.871
53    E        -0.871  -0.871  -0.871  -0.675  -0.675  -0.675  -0.871  -0.871  -0.871
54    K        -0.871  -0.871  -0.871  -1.212  -1.212  -1.212  -0.871  -0.871  -0.871
55    L         1.137   1.137   1.137   1.165   1.165   1.165   1.137   1.137   1.137
56    N         1.137   1.137   1.137   1.413   1.413   1.413   1.137   1.137   1.137
57    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
58    S        -0.871  -0.871  -0.871  -0.776  -0.776  -0.776  -0.871  -0.871  -0.871
59    S        -0.871  -0.871  -0.871  -0.797  -0.797  -0.797  -0.871  -0.871  -0.871
60    E        -0.871  -0.871  -0.871  -0.654  -0.654  -0.654  -0.871  -0.871  -0.871
61    T        -0.871  -0.871  -0.871  -0.595  -0.595  -0.595  -0.871  -0.871  -0.871
62    M        -0.871  -0.871  -0.871  -0.439  -0.439  -0.439  -0.871  -0.871  -0.871
63    I        -0.871  -0.871  -0.871  -0.715  -0.715  -0.715  -0.871  -0.871  -0.871
64    P        -0.871  -0.871  -0.871  -0.497  -0.497  -0.497  -0.871  -0.871  -0.871
65    T        -0.871  -0.871  -0.871  -1.329  -1.329  -1.329  -0.871  -0.871  -0.871
66    L        -0.871  -0.871  -0.871  -0.675  -0.675  -0.675  -0.871  -0.871  -0.871
67    L        -0.871  -0.871  -0.871  -0.675  -0.675  -0.675  -0.871  -0.871  -0.871
68    R        -0.871  -0.871  -0.871  -0.497  -0.497  -0.497  -0.871  -0.871  -0.871
69    E         1.137   1.137   1.137   1.108   1.108   1.108   1.137   1.137   1.137
70    A        -0.871  -0.871  -0.871  -0.634  -0.634  -0.634  -0.871  -0.871  -0.871
71    S        -0.871  -0.871  -0.871  -0.776  -0.776  -0.776  -0.871  -0.871  -0.871
72    T        -0.871  -0.871  -0.871  -0.575  -0.575  -0.575  -0.871  -0.871  -0.871
73    Q        -0.871  -0.871  -0.871  -0.459  -0.459  -0.459  -0.871  -0.871  -0.871
74    E        -0.871  -0.871  -0.871  -1.425  -1.425  -1.425  -0.871  -0.871  -0.871
75    P        -0.871  -0.871  -0.871  -0.382  -0.382  -0.382  -0.871  -0.871  -0.871
76    A         1.137   1.137   1.137   1.386   1.386   1.386   1.137   1.137   1.137
77    K        -0.871  -0.871  -0.871  -1.425  -1.425  -1.425  -0.871  -0.871  -0.871
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    L        -0.871  -0.871  -0.871  -1.377  -1.377  -1.377  -0.871  -0.871  -0.871
81    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
82    A        -0.871  -0.871  -0.871  -0.497  -0.497  -0.497  -0.871  -0.871  -0.871
83    E        -0.871  -0.871  -0.871  -0.675  -0.675  -0.675  -0.871  -0.871  -0.871
84    T         1.137   1.137   1.137   1.221   1.221   1.221   1.137   1.137   1.137
85    T        -0.871  -0.871  -0.871  -0.595  -0.595  -0.595  -0.871  -0.871  -0.871
86    L         1.137   1.137   1.137   1.165   1.165   1.165   1.137   1.137   1.137
87    K        -0.871  -0.871  -0.871  -1.166  -1.166  -1.166  -0.871  -0.871  -0.871
88    A        -0.871  -0.871  -0.871  -0.439  -0.439  -0.439  -0.871  -0.871  -0.871
89    E        -0.871  -0.871  -0.871  -0.654  -0.654  -0.654  -0.871  -0.871  -0.871
90    E        -0.871  -0.871  -0.871  -0.497  -0.497  -0.497  -0.871  -0.871  -0.871
91    L         1.137   1.137   1.137   1.165   1.165   1.165   1.137   1.137   1.137
92    I        -0.871  -0.871  -0.871  -0.516  -0.516  -0.516  -0.871  -0.871  -0.871
93    K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
94    D         1.137   1.137   1.137   1.413   1.413   1.413   1.137   1.137   1.137
95    Q         1.137   1.137   1.137   1.386   1.386   1.386   1.137   1.137   1.137
96    E        -0.871  -0.871  -0.871  -1.425  -1.425  -1.425  -0.871  -0.871  -0.871
97    K        -0.871  -0.871  -0.871  -1.212  -1.212  -1.212  -0.871  -0.871  -0.871
98    D         1.137   1.137   1.137   1.413   1.413   1.413   1.137   1.137   1.137
99    S        -0.871  -0.871  -0.871  -1.575  -1.575  -1.575  -0.871  -0.871  -0.871
100   K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
101   V         1.137   1.137   1.137   1.386   1.386   1.386   1.137   1.137   1.137
102   R         1.137   1.137   1.137   1.359   1.359   1.359   1.137   1.137   1.137
103   E         1.137   1.137   1.137   1.108   1.108   1.108   1.137   1.137   1.137
104   Q        -0.871  -0.871  -0.871  -0.289  -0.289  -0.289  -0.871  -0.871  -0.871
105   I         1.137   1.137   1.137   1.331   1.331   1.331   1.137   1.137   1.137
106   R        -0.871  -0.871  -0.871  -0.695  -0.695  -0.695  -0.871  -0.871  -0.871
107   T        -0.871  -0.871  -0.871  -1.329  -1.329  -1.329  -0.871  -0.871  -0.871
108   E        -0.871  -0.871  -0.871  -0.715  -0.715  -0.715  -0.871  -0.871  -0.871
109   K        -0.871  -0.871  -0.871  -1.166  -1.166  -1.166  -0.871  -0.871  -0.871
110   S         1.137   1.137   1.137   0.935   0.935   0.935   1.137   1.137   1.137
111   K        -0.871  -0.871  -0.871  -1.425  -1.425  -1.425  -0.871  -0.871  -0.871
112   T         1.137   1.137   1.137   1.221   1.221   1.221   1.137   1.137   1.137
113   N         1.137   1.137   1.137   1.413   1.413   1.413   1.137   1.137   1.137
114   D        -0.871  -0.871  -0.871  -0.776  -0.776  -0.776  -0.871  -0.871  -0.871
115   S        -0.871  -0.871  -0.871  -0.776  -0.776  -0.776  -0.871  -0.871  -0.871
116   M         1.137   1.137   1.137   1.440   1.440   1.440   1.137   1.137   1.137
117   L         1.137   1.137   1.137   1.165   1.165   1.165   1.137   1.137   1.137
118   K         1.137   1.137   1.137   0.383   0.383   0.383   1.137   1.137   1.137
119   Q         1.137   1.137   1.137   1.386   1.386   1.386   1.137   1.137   1.137
120   I        -0.871  -0.871  -0.871  -0.675  -0.675  -0.675  -0.871  -0.871  -0.871
121   E         1.137   1.137   1.137   1.108   1.108   1.108   1.137   1.137   1.137
122   M        -0.871  -0.871  -0.871  -0.595  -0.595  -0.595  -0.871  -0.871  -0.871
123   I        -0.871  -0.871  -0.871  -0.478  -0.478  -0.478  -0.871  -0.871  -0.871
124   S         1.137   1.137   1.137   0.935   0.935   0.935   1.137   1.137   1.137
125   G         1.137   1.137   1.137   1.467   1.467   1.467   1.137   1.137   1.137
126   F         1.137   1.137   1.137   1.599   1.599   1.599   1.137   1.137   1.137
127   S         1.137   1.137   1.137   0.935   0.935   0.935   1.137   1.137   1.137
128   L         1.137   1.137   1.137   1.165   1.165   1.165   1.137   1.137   1.137
* 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/Q2V2Q1
Output conservation file - output/Q2V2Q1
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
