1     M         0.994   0.994   0.994   1.357   1.358   1.357   0.994   0.994   0.994
2     K        -0.994  -0.994  -0.994  -1.056  -1.039  -1.056  -0.994  -0.994  -0.994
3     S         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
4     S        -0.994  -0.994  -0.994  -1.216  -1.265  -1.216  -0.994  -0.994  -0.994
5     I         0.994   0.994   0.994   0.982   0.998   0.982   0.994   0.994   0.994
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     P        -0.994  -0.994  -0.994  -0.852  -0.824  -0.852  -0.994  -0.994  -0.994
10    I        -0.994  -0.994  -0.994  -1.004  -1.011  -1.004  -0.994  -0.994  -0.994
11    T         0.994   0.994   0.994   0.982   0.998   0.982   0.994   0.994   0.994
12    E        -0.994  -0.994  -0.994  -0.978  -1.011  -0.978  -0.994  -0.994  -0.994
13    V        -0.994  -0.994  -0.994  -1.056  -1.011  -1.056  -0.994  -0.994  -0.994
14    L        -0.994  -0.994  -0.994  -1.108  -1.094  -1.108  -0.994  -0.994  -0.994
15    P        -0.994  -0.994  -0.994  -0.609  -0.570  -0.609  -0.994  -0.994  -0.994
16    R        -0.994  -0.994  -0.994  -0.777  -0.798  -0.777  -0.994  -0.994  -0.994
17    A        -0.994  -0.994  -0.994  -0.978  -0.984  -0.978  -0.994  -0.994  -0.994
18    V        -0.994  -0.994  -0.994  -1.056  -1.011  -1.056  -0.994  -0.994  -0.994
19    G         0.994   0.994   0.994   0.840   0.886   0.840   0.994   0.994   0.994
20    S        -0.994  -0.994  -0.994  -1.004  -1.011  -1.004  -0.994  -0.994  -0.994
21    L         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
22    T         0.994   0.994   0.994   0.982   0.998   0.982   0.994   0.994   0.994
23    F         0.994   0.994   0.994   1.121   1.108   1.121   0.994   0.994   0.994
24    D         0.994   0.994   0.994   1.017   0.998   1.017   0.994   0.994   0.994
25    E         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
26    N        -0.994  -0.994  -0.994  -1.082  -1.094  -1.082  -0.994  -0.994  -0.994
27    Y        -0.994  -0.994  -0.994  -0.705  -0.721  -0.705  -0.994  -0.994  -0.994
28    N        -0.994  -0.994  -0.994  -0.705  -0.695  -0.705  -0.994  -0.994  -0.994
29    L         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
30    L        -0.994  -0.994  -0.994  -1.004  -1.011  -1.004  -0.994  -0.994  -0.994
31    D         0.994   0.994   0.994   1.017   0.998   1.017   0.994   0.994   0.994
32    T         0.994   0.994   0.994   0.982   0.998   0.982   0.994   0.994   0.994
33    S         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
34    G         0.994   0.994   0.994   0.840   0.886   0.840   0.994   0.994   0.994
35    V        -0.994  -0.994  -0.994  -1.056  -0.984  -1.056  -0.994  -0.994  -0.994
36    A        -0.994  -0.994  -0.994  -1.082  -1.066  -1.082  -0.994  -0.994  -0.994
37    K        -0.994  -0.994  -0.994  -1.216  -1.265  -1.216  -0.994  -0.994  -0.994
38    V        -0.994  -0.994  -0.994  -1.270  -1.236  -1.270  -0.994  -0.994  -0.994
39    I         0.994   0.994   0.994   0.982   0.998   0.982   0.994   0.994   0.994
40    E        -0.994  -0.994  -0.994  -0.877  -0.877  -0.877  -0.994  -0.994  -0.994
41    K         0.994   0.994   0.994   0.694   0.655   0.694   0.994   0.994   0.994
42    S         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
43    P        -0.994  -0.994  -0.994  -0.753  -0.721  -0.753  -0.994  -0.994  -0.994
44    I        -0.994  -0.994  -0.994  -1.056  -0.984  -1.056  -0.994  -0.994  -0.994
45    A         0.994   0.994   0.994   1.017   0.998   1.017   0.994   0.994   0.994
46    E        -0.994  -0.994  -0.994  -0.978  -1.011  -0.978  -0.994  -0.994  -0.994
47    I        -0.994  -0.994  -0.994  -0.978  -0.984  -0.978  -0.994  -0.994  -0.994
48    I        -0.994  -0.994  -0.994  -1.056  -0.984  -1.056  -0.994  -0.994  -0.994
49    R         0.994   0.994   0.994   1.257   1.252   1.257   0.994   0.994   0.994
50    K         0.994   0.994   0.994   0.694   0.655   0.694   0.994   0.994   0.994
51    S         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
52    N         0.994   0.994   0.994   1.155   1.180   1.155   0.994   0.994   0.994
53    A        -0.994  -0.994  -0.994  -0.952  -0.984  -0.952  -0.994  -0.994  -0.994
54    E         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
55    L         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
56    G         0.994   0.994   0.994   0.840   0.886   0.840   0.994   0.994   0.994
57    R        -0.994  -0.994  -0.994  -1.004  -1.039  -1.004  -0.994  -0.994  -0.994
58    L         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
59    G         0.994   0.994   0.994   0.840   0.886   0.840   0.994   0.994   0.994
60    Y         0.994   0.994   0.994   1.155   1.144   1.155   0.994   0.994   0.994
61    S        -0.994  -0.994  -0.994  -0.753  -0.772  -0.753  -0.994  -0.994  -0.994
62    V         0.994   0.994   0.994   0.911   0.998   0.911   0.994   0.994   0.994
63    Y         0.994   0.994   0.994   1.155   1.144   1.155   0.994   0.994   0.994
64    E         0.994   0.994   0.994   0.982   0.961   0.982   0.994   0.994   0.994
65    D         0.994   0.994   0.994   1.017   0.998   1.017   0.994   0.994   0.994
66    A        -0.994  -0.994  -0.994  -0.978  -1.011  -0.978  -0.994  -0.994  -0.994
67    Q        -0.994  -0.994  -0.994  -0.952  -0.984  -0.952  -0.994  -0.994  -0.994
68    Y        -0.994  -0.994  -0.994  -0.927  -0.877  -0.927  -0.994  -0.994  -0.994
69    I        -0.994  -0.994  -0.994  -1.056  -0.984  -1.056  -0.994  -0.994  -0.994
70    G         0.994   0.994   0.994   0.840   0.886   0.840   0.994   0.994   0.994
71    H         0.994   0.994   0.994   1.223   1.216   1.223   0.994   0.994   0.994
72    A         0.994   0.994   0.994   1.017   0.998   1.017   0.994   0.994   0.994
73    F         0.994   0.994   0.994   1.121   1.108   1.121   0.994   0.994   0.994
74    K         0.994   0.994   0.994   0.694   0.655   0.694   0.994   0.994   0.994
75    K        -0.994  -0.994  -0.994  -1.189  -1.236  -1.189  -0.994  -0.994  -0.994
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    A         0.994   0.994   0.994   1.017   0.998   1.017   0.994   0.994   0.994
78    G         0.994   0.994   0.994   0.840   0.886   0.840   0.994   0.994   0.994
79    H        -0.994  -0.994  -0.994  -1.030  -1.066  -1.030  -0.994  -0.994  -0.994
80    F        -0.994  -0.994  -0.994  -0.902  -0.903  -0.902  -0.994  -0.994  -0.994
81    I        -0.994  -0.994  -0.994  -1.004  -0.984  -1.004  -0.994  -0.994  -0.994
82    V         0.994   0.994   0.994   0.911   0.998   0.911   0.994   0.994   0.994
83    Y         0.994   0.994   0.994   1.155   1.144   1.155   0.994   0.994   0.994
84    F         0.994   0.994   0.994   1.121   1.108   1.121   0.994   0.994   0.994
85    T        -0.994  -0.994  -0.994  -0.827  -0.824  -0.827  -0.994  -0.994  -0.994
86    P        -0.994  -0.994  -0.994  -0.827  -0.798  -0.827  -0.994  -0.994  -0.994
87    K         0.994   0.994   0.994   0.694   0.655   0.694   0.994   0.994   0.994
88    N        -0.994  -0.994  -0.994  -1.082  -1.094  -1.082  -0.994  -0.994  -0.994
89    K        -0.994  -0.994  -0.994  -1.189  -1.236  -1.189  -0.994  -0.994  -0.994
90    N        -0.994  -0.994  -0.994  -0.877  -0.877  -0.877  -0.994  -0.994  -0.994
91    R        -0.994  -0.994  -0.994  -1.004  -1.039  -1.004  -0.994  -0.994  -0.994
92    E        -0.994  -0.994  -0.994  -1.216  -1.265  -1.216  -0.994  -0.994  -0.994
93    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q3E841
Output conservation file - output/Q3E841
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
