1     M         1.647   1.647   1.647   2.110   2.110   2.110   1.647   1.647   1.647
2     N        -0.603  -0.603  -0.603  -0.561  -0.561  -0.561  -0.603  -0.603  -0.603
3     S         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
4     E        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
5     Q        -0.603  -0.603  -0.603  -0.476  -0.476  -0.476  -0.603  -0.603  -0.603
6     L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
7     L        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
8     H        -0.603  -0.603  -0.603  -0.260  -0.260  -0.260  -0.603  -0.603  -0.603
9     N        -0.603  -0.603  -0.603  -0.260  -0.260  -0.260  -0.603  -0.603  -0.603
10    Y        -0.603  -0.603  -0.603  -0.008  -0.008  -0.008  -0.603  -0.603  -0.603
11    V        -0.603  -0.603  -0.603  -0.101  -0.101  -0.101  -0.603  -0.603  -0.603
12    S        -0.603  -0.603  -0.603  -0.561  -0.561  -0.561  -0.603  -0.603  -0.603
13    D        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
14    S        -0.603  -0.603  -0.603  -1.172  -1.172  -1.172  -0.603  -0.603  -0.603
15    L        -0.603  -0.603  -0.603  -0.847  -0.847  -0.847  -0.603  -0.603  -0.603
16    L        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
17    T        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
18    T        -0.603  -0.603  -0.603  -0.196  -0.196  -0.196  -0.603  -0.603  -0.603
19    L        -0.603  -0.603  -0.603  -0.684  -0.684  -0.684  -0.603  -0.603  -0.603
20    I        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
21    S         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
22    F        -0.603  -0.603  -0.603  -0.375  -0.375  -0.375  -0.603  -0.603  -0.603
23    Q        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
24    E        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
25    F         1.647   1.647   1.647   1.910   1.910   1.910   1.647   1.647   1.647
26    K         1.647   1.647   1.647   1.820   1.820   1.820   1.647   1.647   1.647
27    Q        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    Q         1.647   1.647   1.647   1.612   1.612   1.612   1.647   1.647   1.647
32    L        -0.603  -0.603  -0.603  -1.172  -1.172  -1.172  -0.603  -0.603  -0.603
33    Q        -0.603  -0.603  -0.603  -0.442  -0.442  -0.442  -0.603  -0.603  -0.603
34    S        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
35    Y        -0.603  -0.603  -0.603  -0.054  -0.054  -0.054  -0.603  -0.603  -0.603
36    T        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
37    S        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
38    D        -0.603  -0.603  -0.603  -0.148  -0.148  -0.148  -0.603  -0.603  -0.603
39    E        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
40    Q        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
41    Q        -0.603  -0.603  -0.603  -0.476  -0.476  -0.476  -0.603  -0.603  -0.603
42    L        -0.603  -0.603  -0.603  -0.684  -0.684  -0.684  -0.603  -0.603  -0.603
43    Q        -0.603  -0.603  -0.603  -0.409  -0.409  -0.409  -0.603  -0.603  -0.603
44    H        -0.603  -0.603  -0.603  -0.117  -0.117  -0.117  -0.603  -0.603  -0.603
45    W         1.647   1.647   1.647   2.153   2.153   2.153   1.647   1.647   1.647
46    Y         1.647   1.647   1.647   1.977   1.977   1.977   1.647   1.647   1.647
47    E        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
48    L        -0.603  -0.603  -0.603  -1.172  -1.172  -1.172  -0.603  -0.603  -0.603
49    L        -0.603  -0.603  -0.603  -0.702  -0.702  -0.702  -0.603  -0.603  -0.603
50    Q        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
51    A        -0.603  -0.603  -0.603  -0.309  -0.309  -0.309  -0.603  -0.603  -0.603
52    R        -0.603  -0.603  -0.603  -0.309  -0.309  -0.309  -0.603  -0.603  -0.603
53    D        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
54    A        -0.603  -0.603  -0.603  -0.442  -0.442  -0.442  -0.603  -0.603  -0.603
55    R        -0.603  -0.603  -0.603  -0.309  -0.309  -0.309  -0.603  -0.603  -0.603
56    V        -0.603  -0.603  -0.603  -0.164  -0.164  -0.164  -0.603  -0.603  -0.603
57    T        -0.603  -0.603  -0.603  -0.684  -0.684  -0.684  -0.603  -0.603  -0.603
58    S        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
59    E        -0.603  -0.603  -0.603  -1.172  -1.172  -1.172  -0.603  -0.603  -0.603
60    L        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
61    E        -0.603  -0.603  -0.603  -0.614  -0.614  -0.614  -0.603  -0.603  -0.603
62    A        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
63    R         1.647   1.647   1.647   1.797   1.797   1.797   1.647   1.647   1.647
64    I        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
65    K        -0.603  -0.603  -0.603  -0.309  -0.309  -0.309  -0.603  -0.603  -0.603
66    Q        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
67    F         1.647   1.647   1.647   1.910   1.910   1.910   1.647   1.647   1.647
68    F        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
69    I        -0.603  -0.603  -0.603  -0.442  -0.442  -0.442  -0.603  -0.603  -0.603
70    T        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
71    L        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
72    R         1.647   1.647   1.647   1.797   1.797   1.797   1.647   1.647   1.647
73    S        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
74    R         1.647   1.647   1.647   1.797   1.797   1.797   1.647   1.647   1.647
75    L        -0.603  -0.603  -0.603  -1.172  -1.172  -1.172  -0.603  -0.603  -0.603
76    L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
77    R        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
78    F        -0.603  -0.603  -0.603  -0.228  -0.228  -0.228  -0.603  -0.603  -0.603
79    L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
80    E         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
81    S        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
82    E         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
83    Q         1.647   1.647   1.647   1.612   1.612   1.612   1.647   1.647   1.647
84    L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
85    S         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
86    H        -0.603  -0.603  -0.603  -0.409  -0.409  -0.409  -0.603  -0.603  -0.603
87    S         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
88    L        -0.603  -0.603  -0.603  -0.702  -0.702  -0.702  -0.603  -0.603  -0.603
89    S        -0.603  -0.603  -0.603  -0.561  -0.561  -0.561  -0.603  -0.603  -0.603
90    L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
91    E         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
92    T        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
93    L        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
94    I         1.647   1.647   1.647   1.612   1.612   1.612   1.647   1.647   1.647
95    D        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
96    A        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
97    L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
98    Y         1.647   1.647   1.647   1.977   1.977   1.977   1.647   1.647   1.647
99    K         1.647   1.647   1.647   1.820   1.820   1.820   1.647   1.647   1.647
100   I        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
101   N         1.647   1.647   1.647   1.865   1.865   1.865   1.647   1.647   1.647
102   D        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
103   L        -0.603  -0.603  -0.603  -0.684  -0.684  -0.684  -0.603  -0.603  -0.603
104   L        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
105   Q        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
106   Q        -0.603  -0.603  -0.603  -0.228  -0.228  -0.228  -0.603  -0.603  -0.603
107   R        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
108   L        -0.603  -0.603  -0.603  -0.684  -0.684  -0.684  -0.603  -0.603  -0.603
109   Q        -0.603  -0.603  -0.603  -0.228  -0.228  -0.228  -0.603  -0.603  -0.603
110   I        -0.603  -0.603  -0.603  -0.409  -0.409  -0.409  -0.603  -0.603  -0.603
111   L        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
112   D        -0.603  -0.603  -0.603  -0.293  -0.293  -0.293  -0.603  -0.603  -0.603
113   D         1.647   1.647   1.647   1.774   1.774   1.774   1.647   1.647   1.647
114   A        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
115   I        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
116   Q        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
117   E        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
118   K         1.647   1.647   1.647   1.820   1.820   1.820   1.647   1.647   1.647
119   T        -0.603  -0.603  -0.603  -0.309  -0.309  -0.309  -0.603  -0.603  -0.603
120   S        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
121   E         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
122   L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
123   A         1.647   1.647   1.647   1.820   1.820   1.820   1.647   1.647   1.647
124   E        -0.603  -0.603  -0.603  -0.561  -0.561  -0.561  -0.603  -0.603  -0.603
125   F         1.647   1.647   1.647   1.910   1.910   1.910   1.647   1.647   1.647
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   E        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
128   N        -0.603  -0.603  -0.603  -0.085  -0.085  -0.085  -0.603  -0.603  -0.603
129   M        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
130   V        -0.603  -0.603  -0.603  -0.164  -0.164  -0.164  -0.603  -0.603  -0.603
131   R        -0.603  -0.603  -0.603  -0.309  -0.309  -0.309  -0.603  -0.603  -0.603
132   S         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
133   P        -0.603  -0.603  -0.603  -0.561  -0.561  -0.561  -0.603  -0.603  -0.603
134   S        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
135   A        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
136   G        -0.603  -0.603  -0.603  -0.375  -0.375  -0.375  -0.603  -0.603  -0.603
137   D         1.647   1.647   1.647   1.774   1.774   1.774   1.647   1.647   1.647
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   N        -0.603  -0.603  -0.603  -0.293  -0.293  -0.293  -0.603  -0.603  -0.603
143   A        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
144   I         1.647   1.647   1.647   1.612   1.612   1.612   1.647   1.647   1.647
145   P        -0.603  -0.603  -0.603  -0.023  -0.023  -0.023  -0.603  -0.603  -0.603
146   G        -0.603  -0.603  -0.603  -0.375  -0.375  -0.375  -0.603  -0.603  -0.603
147   L        -0.603  -0.603  -0.603  -1.172  -1.172  -1.172  -0.603  -0.603  -0.603
148   L        -0.603  -0.603  -0.603  -0.997  -0.997  -0.997  -0.603  -0.603  -0.603
149   Q        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
150   I        -0.603  -0.603  -0.603  -0.442  -0.442  -0.442  -0.603  -0.603  -0.603
151   I         1.647   1.647   1.647   1.612   1.612   1.612   1.647   1.647   1.647
152   Q        -0.603  -0.603  -0.603  -0.756  -0.756  -0.756  -0.603  -0.603  -0.603
153   S        -0.603  -0.603  -0.603  -0.596  -0.596  -0.596  -0.603  -0.603  -0.603
154   Y         1.647   1.647   1.647   1.977   1.977   1.977   1.647   1.647   1.647
155   I        -0.603  -0.603  -0.603  -0.459  -0.459  -0.459  -0.603  -0.603  -0.603
156   N        -0.603  -0.603  -0.603  -0.260  -0.260  -0.260  -0.603  -0.603  -0.603
157   L        -0.603  -0.603  -0.603  -0.828  -0.828  -0.828  -0.603  -0.603  -0.603
158   L         1.647   1.647   1.647   1.074   1.074   1.074   1.647   1.647   1.647
159   E        -0.603  -0.603  -0.603  -0.631  -0.631  -0.631  -0.603  -0.603  -0.603
160   E         1.647   1.647   1.647   1.397   1.397   1.397   1.647   1.647   1.647
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   N        -0.603  -0.603  -0.603  -0.561  -0.561  -0.561  -0.603  -0.603  -0.603
* 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/Q06162
Output conservation file - output/Q06162
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
