1     M         1.511   1.511   1.511   1.668   1.668   1.668   1.511   1.511   1.511
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     D        -0.657  -0.657  -0.657  -0.309  -0.309  -0.309  -0.657  -0.657  -0.657
6     A        -0.657  -0.657  -0.657  -0.585  -0.585  -0.585  -0.657  -0.657  -0.657
7     T         1.511   1.511   1.511   1.549   1.549   1.549   1.511   1.511   1.511
8     Q        -0.657  -0.657  -0.657  -0.275  -0.275  -0.275  -0.657  -0.657  -0.657
9     P         1.511   1.511   1.511   1.762   1.762   1.762   1.511   1.511   1.511
10    Q        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
11    Y        -0.657  -0.657  -0.657  -0.480  -0.480  -0.480  -0.657  -0.657  -0.657
12    E        -0.657  -0.657  -0.657  -0.342  -0.342  -0.342  -0.657  -0.657  -0.657
13    L        -0.657  -0.657  -0.657  -1.157  -1.157  -1.157  -0.657  -0.657  -0.657
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    S        -0.657  -0.657  -0.657  -0.462  -0.462  -0.462  -0.657  -0.657  -0.657
16    V        -0.657  -0.657  -0.657  -1.137  -1.137  -1.137  -0.657  -0.657  -0.657
17    V        -0.657  -0.657  -0.657  -0.900  -0.900  -0.900  -0.657  -0.657  -0.657
18    T        -0.657  -0.657  -0.657  -0.675  -0.675  -0.675  -0.657  -0.657  -0.657
19    Q        -0.657  -0.657  -0.657  -0.326  -0.326  -0.326  -0.657  -0.657  -0.657
20    C        -0.657  -0.657  -0.657  -0.712  -0.712  -0.712  -0.657  -0.657  -0.657
21    L         1.511   1.511   1.511   0.943   0.943   0.943   1.511   1.511   1.511
22    K        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
23    S        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
24    A        -0.657  -0.657  -0.657  -0.585  -0.585  -0.585  -0.657  -0.657  -0.657
25    I         1.511   1.511   1.511   1.253   1.253   1.253   1.511   1.511   1.511
26    D        -0.657  -0.657  -0.657  -0.242  -0.242  -0.242  -0.657  -0.657  -0.657
27    V        -0.657  -0.657  -0.657  -0.749  -0.749  -0.749  -0.657  -0.657  -0.657
28    I        -0.657  -0.657  -0.657  -1.157  -1.157  -1.157  -0.657  -0.657  -0.657
29    Q         1.511   1.511   1.511   1.549   1.549   1.549   1.511   1.511   1.511
30    W        -0.657  -0.657  -0.657  -0.462  -0.462  -0.462  -0.657  -0.657  -0.657
31    L         1.511   1.511   1.511   0.943   0.943   0.943   1.511   1.511   1.511
32    I         1.511   1.511   1.511   1.253   1.253   1.253   1.511   1.511   1.511
33    P         1.511   1.511   1.511   1.762   1.762   1.762   1.511   1.511   1.511
34    T        -0.657  -0.657  -0.657  -0.675  -0.675  -0.675  -0.657  -0.657  -0.657
35    I         1.511   1.511   1.511   1.253   1.253   1.253   1.511   1.511   1.511
36    T        -0.657  -0.657  -0.657  -0.675  -0.675  -0.675  -0.657  -0.657  -0.657
37    K        -0.657  -0.657  -0.657  -0.359  -0.359  -0.359  -0.657  -0.657  -0.657
38    F         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
39    S         1.511   1.511   1.511   1.573   1.573   1.573   1.511   1.511   1.511
40    Q        -0.657  -0.657  -0.657  -0.428  -0.428  -0.428  -0.657  -0.657  -0.657
41    S        -0.657  -0.657  -0.657  -0.393  -0.393  -0.393  -0.657  -0.657  -0.657
42    H        -0.657  -0.657  -0.657  -0.342  -0.342  -0.342  -0.657  -0.657  -0.657
43    P         1.511   1.511   1.511   1.762   1.762   1.762   1.511   1.511   1.511
44    L        -0.657  -0.657  -0.657  -0.919  -0.919  -0.919  -0.657  -0.657  -0.657
45    V        -0.657  -0.657  -0.657  -0.585  -0.585  -0.585  -0.657  -0.657  -0.657
46    F         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
47    Q        -0.657  -0.657  -0.657  -0.694  -0.694  -0.694  -0.657  -0.657  -0.657
48    L        -0.657  -0.657  -0.657  -1.137  -1.137  -1.137  -0.657  -0.657  -0.657
49    L        -0.657  -0.657  -0.657  -1.157  -1.157  -1.157  -0.657  -0.657  -0.657
50    F        -0.657  -0.657  -0.657  -0.532  -0.532  -0.532  -0.657  -0.657  -0.657
51    I        -0.657  -0.657  -0.657  -1.157  -1.157  -1.157  -0.657  -0.657  -0.657
52    F        -0.657  -0.657  -0.657  -0.767  -0.767  -0.767  -0.657  -0.657  -0.657
53    F        -0.657  -0.657  -0.657  -0.767  -0.767  -0.767  -0.657  -0.657  -0.657
54    T        -0.657  -0.657  -0.657  -0.326  -0.326  -0.326  -0.657  -0.657  -0.657
55    F        -0.657  -0.657  -0.657  -0.997  -0.997  -0.997  -0.657  -0.657  -0.657
56    Y         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
57    V         1.511   1.511   1.511   1.278   1.278   1.278   1.511   1.511   1.511
58    F        -0.657  -0.657  -0.657  -0.749  -0.749  -0.749  -0.657  -0.657  -0.657
59    Y        -0.657  -0.657  -0.657  -0.326  -0.326  -0.326  -0.657  -0.657  -0.657
60    K        -0.657  -0.657  -0.657  -0.359  -0.359  -0.359  -0.657  -0.657  -0.657
61    L        -0.657  -0.657  -0.657  -0.712  -0.712  -0.712  -0.657  -0.657  -0.657
62    L        -0.657  -0.657  -0.657  -1.157  -1.157  -1.157  -0.657  -0.657  -0.657
63    M         1.511   1.511   1.511   1.668   1.668   1.668   1.511   1.511   1.511
64    N        -0.657  -0.657  -0.657  -0.393  -0.393  -0.393  -0.657  -0.657  -0.657
65    F        -0.657  -0.657  -0.657  -0.997  -0.997  -0.997  -0.657  -0.657  -0.657
66    I        -0.657  -0.657  -0.657  -0.767  -0.767  -0.767  -0.657  -0.657  -0.657
67    T        -0.657  -0.657  -0.657  -0.393  -0.393  -0.393  -0.657  -0.657  -0.657
68    L        -0.657  -0.657  -0.657  -0.824  -0.824  -0.824  -0.657  -0.657  -0.657
69    V         1.511   1.511   1.511   1.278   1.278   1.278   1.511   1.511   1.511
70    K        -0.657  -0.657  -0.657  -0.359  -0.359  -0.359  -0.657  -0.657  -0.657
71    R         1.511   1.511   1.511   1.644   1.644   1.644   1.511   1.511   1.511
72    F        -0.657  -0.657  -0.657  -0.997  -0.997  -0.997  -0.657  -0.657  -0.657
73    L        -0.657  -0.657  -0.657  -0.997  -0.997  -0.997  -0.657  -0.657  -0.657
74    Y         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
75    L         1.511   1.511   1.511   0.943   0.943   0.943   1.511   1.511   1.511
76    T        -0.657  -0.657  -0.657  -0.462  -0.462  -0.462  -0.657  -0.657  -0.657
77    L         1.511   1.511   1.511   0.943   0.943   0.943   1.511   1.511   1.511
78    V         1.511   1.511   1.511   1.278   1.278   1.278   1.511   1.511   1.511
79    V        -0.657  -0.657  -0.657  -1.137  -1.137  -1.137  -0.657  -0.657  -0.657
80    T        -0.657  -0.657  -0.657  -0.919  -0.919  -0.919  -0.657  -0.657  -0.657
81    C        -0.657  -0.657  -0.657  -0.480  -0.480  -0.480  -0.657  -0.657  -0.657
82    I        -0.657  -0.657  -0.657  -0.900  -0.900  -0.900  -0.657  -0.657  -0.657
83    G        -0.657  -0.657  -0.657  -0.144  -0.144  -0.144  -0.657  -0.657  -0.657
84    I        -0.657  -0.657  -0.657  -0.603  -0.603  -0.603  -0.657  -0.657  -0.657
85    Y         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
86    M         1.511   1.511   1.511   1.668   1.668   1.668   1.511   1.511   1.511
87    R         1.511   1.511   1.511   1.644   1.644   1.644   1.511   1.511   1.511
88    G         1.511   1.511   1.511   1.762   1.762   1.762   1.511   1.511   1.511
89    S        -0.657  -0.657  -0.657  -0.376  -0.376  -0.376  -0.657  -0.657  -0.657
90    Q        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
91    Q        -0.657  -0.657  -0.657  -0.919  -0.919  -0.919  -0.657  -0.657  -0.657
92    F         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
93    L        -0.657  -0.657  -0.657  -0.997  -0.997  -0.997  -0.657  -0.657  -0.657
94    T        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
95    V        -0.657  -0.657  -0.657  -0.462  -0.462  -0.462  -0.657  -0.657  -0.657
96    D         1.511   1.511   1.511   1.785   1.785   1.785   1.511   1.511   1.511
97    L        -0.657  -0.657  -0.657  -1.137  -1.137  -1.137  -0.657  -0.657  -0.657
98    L        -0.657  -0.657  -0.657  -0.749  -0.749  -0.749  -0.657  -0.657  -0.657
99    N        -0.657  -0.657  -0.657  -0.842  -0.842  -0.842  -0.657  -0.657  -0.657
100   F        -0.657  -0.657  -0.657  -0.749  -0.749  -0.749  -0.657  -0.657  -0.657
101   Y        -0.657  -0.657  -0.657  -0.462  -0.462  -0.462  -0.657  -0.657  -0.657
102   N         1.511   1.511   1.511   1.644   1.644   1.644   1.511   1.511   1.511
103   F        -0.657  -0.657  -0.657  -0.393  -0.393  -0.393  -0.657  -0.657  -0.657
104   V        -0.657  -0.657  -0.657  -0.900  -0.900  -0.900  -0.657  -0.657  -0.657
105   M        -0.657  -0.657  -0.657  -0.176  -0.176  -0.176  -0.657  -0.657  -0.657
106   S        -0.657  -0.657  -0.657  -0.292  -0.292  -0.292  -0.657  -0.657  -0.657
107   N         1.511   1.511   1.511   1.644   1.644   1.644   1.511   1.511   1.511
108   R         1.511   1.511   1.511   1.644   1.644   1.644   1.511   1.511   1.511
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   Y        -0.657  -0.657  -0.657  -0.550  -0.550  -0.550  -0.657  -0.657  -0.657
121   Y         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
122   A        -0.657  -0.657  -0.657  -0.242  -0.242  -0.242  -0.657  -0.657  -0.657
123   F        -0.657  -0.657  -0.657  -0.621  -0.621  -0.621  -0.657  -0.657  -0.657
124   K         1.511   1.511   1.511   1.621   1.621   1.621   1.511   1.511   1.511
125   I         1.511   1.511   1.511   1.253   1.253   1.253   1.511   1.511   1.511
126   Y        -0.657  -0.657  -0.657  -0.997  -0.997  -0.997  -0.657  -0.657  -0.657
127   T        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
128   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   E        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
135   R        -0.657  -0.657  -0.657  -0.342  -0.342  -0.342  -0.657  -0.657  -0.657
136   E        -0.657  -0.657  -0.657  -0.393  -0.393  -0.393  -0.657  -0.657  -0.657
137   I         1.511   1.511   1.511   1.253   1.253   1.253   1.511   1.511   1.511
138   N        -0.657  -0.657  -0.657  -0.621  -0.621  -0.621  -0.657  -0.657  -0.657
139   T        -0.657  -0.657  -0.657  -0.919  -0.919  -0.919  -0.657  -0.657  -0.657
140   V        -0.657  -0.657  -0.657  -0.749  -0.749  -0.749  -0.657  -0.657  -0.657
141   Y         1.511   1.511   1.511   1.452   1.452   1.452   1.511   1.511   1.511
142   H        -0.657  -0.657  -0.657  -0.342  -0.342  -0.342  -0.657  -0.657  -0.657
143   L         1.511   1.511   1.511   0.943   0.943   0.943   1.511   1.511   1.511
144   A        -0.657  -0.657  -0.657  -0.342  -0.342  -0.342  -0.657  -0.657  -0.657
145   Q        -0.657  -0.657  -0.657  -0.411  -0.411  -0.411  -0.657  -0.657  -0.657
146   M        -0.657  -0.657  -0.657  -0.393  -0.393  -0.393  -0.657  -0.657  -0.657
147   K        -0.657  -0.657  -0.657  -0.861  -0.861  -0.861  -0.657  -0.657  -0.657
148   M        -0.657  -0.657  -0.657  -0.326  -0.326  -0.326  -0.657  -0.657  -0.657
149   E         1.511   1.511   1.511   1.644   1.644   1.644   1.511   1.511   1.511
150   Q        -0.657  -0.657  -0.657  -0.393  -0.393  -0.393  -0.657  -0.657  -0.657
151   L        -0.657  -0.657  -0.657  -1.157  -1.157  -1.157  -0.657  -0.657  -0.657
152   L        -0.657  -0.657  -0.657  -0.919  -0.919  -0.919  -0.657  -0.657  -0.657
153   K         1.511   1.511   1.511   1.621   1.621   1.621   1.511   1.511   1.511
* 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/P40532
Output conservation file - output/P40532
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
