1     M         1.183   1.183   1.183   1.533   1.533   1.533   1.183   1.183   1.183
2     N        -0.840  -0.840  -0.840  -0.942  -0.929  -0.942  -0.840  -0.840  -0.840
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     V        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
5     T        -0.840  -0.840  -0.840  -0.794  -0.795  -0.794  -0.840  -0.840  -0.840
6     V        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
7     T         1.183   1.183   1.183   1.429   1.429   1.429   1.183   1.183   1.183
8     V         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
9     Y         1.183   1.183   1.183   1.464   1.464   1.464   1.183   1.183   1.183
10    D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
11    K        -0.840  -0.840  -0.840  -0.538  -0.539  -0.538  -0.840  -0.840  -0.840
12    N         1.183   1.183   1.183   1.199   1.216   1.199   1.183   1.183   1.183
13    V        -0.840  -0.840  -0.840  -0.729  -0.730  -0.729  -0.840  -0.840  -0.840
14    K        -0.840  -0.840  -0.840  -0.391  -0.391  -0.391  -0.840  -0.840  -0.840
15    Y        -0.840  -0.840  -0.840  -0.343  -0.343  -0.343  -0.840  -0.840  -0.840
16    R        -0.840  -0.840  -0.840  -0.874  -0.875  -0.874  -0.840  -0.840  -0.840
17    L        -0.840  -0.840  -0.840  -0.834  -0.835  -0.834  -0.840  -0.840  -0.840
18    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    E        -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    K         1.183   1.183   1.183   1.377   1.376   1.377   1.183   1.183   1.183
41    S        -0.840  -0.840  -0.840  -0.834  -0.835  -0.834  -0.840  -0.840  -0.840
42    T        -0.840  -0.840  -0.840  -0.768  -0.769  -0.768  -0.840  -0.840  -0.840
43    D        -0.840  -0.840  -0.840  -1.194  -1.197  -1.194  -0.840  -0.840  -0.840
44    G         1.183   1.183   1.183   1.412   1.412   1.412   1.183   1.183   1.183
45    S        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
46    D        -0.840  -0.840  -0.840  -0.887  -0.889  -0.887  -0.840  -0.840  -0.840
47    Y        -0.840  -0.840  -0.840  -0.538  -0.539  -0.538  -0.840  -0.840  -0.840
48    A         1.183   1.183   1.183   1.412   1.412   1.412   1.183   1.183   1.183
49    M         1.183   1.183   1.183   1.533   1.533   1.533   1.183   1.183   1.183
50    F         1.183   1.183   1.183   1.482   1.481   1.482   1.183   1.183   1.183
51    P         1.183   1.183   1.183   1.447   1.446   1.447   1.183   1.183   1.183
52    T         1.183   1.183   1.183   1.429   1.429   1.429   1.183   1.183   1.183
53    N         1.183   1.183   1.183   1.199   1.216   1.199   1.183   1.183   1.183
54    I         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
55    K         1.183   1.183   1.183   1.377   1.376   1.377   1.183   1.183   1.183
56    Y         1.183   1.183   1.183   1.464   1.464   1.464   1.183   1.183   1.183
57    I         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
58    F         1.183   1.183   1.183   1.482   1.481   1.482   1.183   1.183   1.183
59    E         1.183   1.183   1.183   1.053   1.051   1.053   1.183   1.183   1.183
60    D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
61    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    N        -0.840  -0.840  -0.840  -1.080  -1.068  -1.080  -0.840  -0.840  -0.840
63    D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
64    E        -0.840  -0.840  -0.840  -1.194  -1.197  -1.194  -0.840  -0.840  -0.840
65    L        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
66    V        -0.840  -0.840  -0.840  -0.626  -0.627  -0.626  -0.840  -0.840  -0.840
67    D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
68    S        -0.840  -0.840  -0.840  -0.914  -0.916  -0.914  -0.840  -0.840  -0.840
69    S        -0.840  -0.840  -0.840  -1.224  -1.226  -1.224  -0.840  -0.840  -0.840
70    D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
71    A        -0.840  -0.840  -0.840  -0.887  -0.889  -0.887  -0.840  -0.840  -0.840
72    A        -0.840  -0.840  -0.840  -0.626  -0.627  -0.626  -0.840  -0.840  -0.840
73    L        -0.840  -0.840  -0.840  -0.834  -0.835  -0.834  -0.840  -0.840  -0.840
74    T        -0.840  -0.840  -0.840  -0.563  -0.564  -0.563  -0.840  -0.840  -0.840
75    A        -0.840  -0.840  -0.840  -0.576  -0.576  -0.576  -0.840  -0.840  -0.840
76    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    D        -0.840  -0.840  -0.840  -0.969  -0.971  -0.969  -0.840  -0.840  -0.840
79    K        -0.840  -0.840  -0.840  -0.601  -0.602  -0.601  -0.840  -0.840  -0.840
80    V        -0.840  -0.840  -0.840  -0.601  -0.602  -0.601  -0.840  -0.840  -0.840
81    G        -0.840  -0.840  -0.840  -0.914  -0.916  -0.914  -0.840  -0.840  -0.840
82    D        -0.840  -0.840  -0.840  -1.224  -1.226  -1.224  -0.840  -0.840  -0.840
83    E         1.183   1.183   1.183   1.053   1.051   1.053   1.183   1.183   1.183
84    L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
85    E         1.183   1.183   1.183   1.053   1.051   1.053   1.183   1.183   1.183
86    N         1.183   1.183   1.183   1.199   1.216   1.199   1.183   1.183   1.183
87    V         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
88    I         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
89    I         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
90    V         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
91    Q        -0.840  -0.840  -0.840  -0.834  -0.835  -0.834  -0.840  -0.840  -0.840
92    L        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
93    D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
94    E        -0.840  -0.840  -0.840  -0.781  -0.782  -0.781  -0.840  -0.840  -0.840
95    S        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
96    G         1.183   1.183   1.183   1.412   1.412   1.412   1.183   1.183   1.183
97    S        -0.840  -0.840  -0.840  -0.861  -0.862  -0.861  -0.840  -0.840  -0.840
98    L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
99    E         1.183   1.183   1.183   1.053   1.051   1.053   1.183   1.183   1.183
100   D        -0.840  -0.840  -0.840  -1.080  -1.068  -1.080  -0.840  -0.840  -0.840
101   I        -0.840  -0.840  -0.840  -0.729  -0.730  -0.729  -0.840  -0.840  -0.840
102   T        -0.840  -0.840  -0.840  -0.768  -0.769  -0.768  -0.840  -0.840  -0.840
103   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
104   I         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
105   S         1.183   1.183   1.183   1.016   1.014   1.016   1.183   1.183   1.183
106   D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
107   Q         1.183   1.183   1.183   1.342   1.341   1.342   1.183   1.183   1.183
108   Y         1.183   1.183   1.183   1.464   1.464   1.464   1.183   1.183   1.183
109   E         1.183   1.183   1.183   1.053   1.051   1.053   1.183   1.183   1.183
110   L        -0.840  -0.840  -0.840  -0.794  -0.795  -0.794  -0.840  -0.840  -0.840
111   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
112   S         1.183   1.183   1.183   1.016   1.014   1.016   1.183   1.183   1.183
113   H        -0.840  -0.840  -0.840  -0.343  -0.343  -0.343  -0.840  -0.840  -0.840
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   R         1.183   1.183   1.183   1.429   1.429   1.429   1.183   1.183   1.183
116   T        -0.840  -0.840  -0.840  -0.768  -0.769  -0.768  -0.840  -0.840  -0.840
117   N        -0.840  -0.840  -0.840  -0.664  -0.652  -0.664  -0.840  -0.840  -0.840
118   S        -0.840  -0.840  -0.840  -0.781  -0.782  -0.781  -0.840  -0.840  -0.840
119   L        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
120   S         1.183   1.183   1.183   1.016   1.014   1.016   1.183   1.183   1.183
121   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
122   E        -0.840  -0.840  -0.840  -0.781  -0.782  -0.781  -0.840  -0.840  -0.840
123   E        -0.840  -0.840  -0.840  -1.080  -1.082  -1.080  -0.840  -0.840  -0.840
124   N        -0.840  -0.840  -0.840  -0.729  -0.717  -0.729  -0.840  -0.840  -0.840
125   Q        -0.840  -0.840  -0.840  -0.563  -0.564  -0.563  -0.840  -0.840  -0.840
126   M        -0.840  -0.840  -0.840  -0.716  -0.717  -0.716  -0.840  -0.840  -0.840
127   R        -0.840  -0.840  -0.840  -0.874  -0.875  -0.874  -0.840  -0.840  -0.840
128   T        -0.840  -0.840  -0.840  -0.794  -0.795  -0.794  -0.840  -0.840  -0.840
129   L        -0.840  -0.840  -0.840  -0.716  -0.717  -0.716  -0.840  -0.840  -0.840
130   S        -0.840  -0.840  -0.840  -1.194  -1.197  -1.194  -0.840  -0.840  -0.840
131   S        -0.840  -0.840  -0.840  -0.794  -0.795  -0.794  -0.840  -0.840  -0.840
132   H        -0.840  -0.840  -0.840  -0.652  -0.652  -0.652  -0.840  -0.840  -0.840
133   G         1.183   1.183   1.183   1.412   1.412   1.412   1.183   1.183   1.183
134   D        -0.840  -0.840  -0.840  -1.080  -1.068  -1.080  -0.840  -0.840  -0.840
135   D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
136   K        -0.840  -0.840  -0.840  -0.538  -0.539  -0.538  -0.840  -0.840  -0.840
137   S        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
138   N        -0.840  -0.840  -0.840  -0.677  -0.665  -0.677  -0.840  -0.840  -0.840
139   D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
140   E        -0.840  -0.840  -0.840  -0.781  -0.782  -0.781  -0.840  -0.840  -0.840
141   E        -0.840  -0.840  -0.840  -0.781  -0.782  -0.781  -0.840  -0.840  -0.840
142   E        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
143   E        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
144   L        -0.840  -0.840  -0.840  -1.194  -1.197  -1.194  -0.840  -0.840  -0.840
145   S        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
146   V        -0.840  -0.840  -0.840  -1.024  -1.026  -1.024  -0.840  -0.840  -0.840
147   D        -0.840  -0.840  -0.840  -1.024  -1.026  -1.024  -0.840  -0.840  -0.840
148   S         1.183   1.183   1.183   1.016   1.014   1.016   1.183   1.183   1.183
149   D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
150   R        -0.840  -0.840  -0.840  -0.489  -0.489  -0.489  -0.840  -0.840  -0.840
151   F        -0.840  -0.840  -0.840  -0.477  -0.477  -0.477  -0.840  -0.840  -0.840
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   R        -0.840  -0.840  -0.840  -0.768  -0.769  -0.768  -0.840  -0.840  -0.840
160   V        -0.840  -0.840  -0.840  -0.626  -0.627  -0.626  -0.840  -0.840  -0.840
161   D        -0.840  -0.840  -0.840  -0.887  -0.889  -0.887  -0.840  -0.840  -0.840
162   S        -0.840  -0.840  -0.840  -1.194  -1.197  -1.194  -0.840  -0.840  -0.840
163   D        -0.840  -0.840  -0.840  -1.224  -1.226  -1.224  -0.840  -0.840  -0.840
164   I         1.183   1.183   1.183   1.271   1.270   1.271   1.183   1.183   1.183
165   E         1.183   1.183   1.183   1.053   1.051   1.053   1.183   1.183   1.183
166   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
167   D        -0.840  -0.840  -0.840  -1.194  -1.197  -1.194  -0.840  -0.840  -0.840
168   V        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
169   I        -0.840  -0.840  -0.840  -0.729  -0.730  -0.729  -0.840  -0.840  -0.840
170   S         1.183   1.183   1.183   1.016   1.014   1.016   1.183   1.183   1.183
171   Q        -0.840  -0.840  -0.840  -0.834  -0.835  -0.834  -0.840  -0.840  -0.840
172   F         1.183   1.183   1.183   1.482   1.481   1.482   1.183   1.183   1.183
173   C        -0.840  -0.840  -0.840  -0.391  -0.391  -0.391  -0.840  -0.840  -0.840
174   D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
175   L        -0.840  -0.840  -0.840  -0.847  -0.849  -0.847  -0.840  -0.840  -0.840
176   S        -0.840  -0.840  -0.840  -0.794  -0.795  -0.794  -0.840  -0.840  -0.840
177   P        -0.840  -0.840  -0.840  -0.652  -0.640  -0.652  -0.840  -0.840  -0.840
178   F        -0.840  -0.840  -0.840  -0.834  -0.835  -0.834  -0.840  -0.840  -0.840
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
181   R        -0.840  -0.840  -0.840  -0.768  -0.769  -0.768  -0.840  -0.840  -0.840
182   D         1.183   1.183   1.183   0.865   0.863   0.865   1.183   1.183   1.183
183   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
184   S        -0.840  -0.840  -0.840  -0.834  -0.835  -0.834  -0.840  -0.840  -0.840
185   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
186   N        -0.840  -0.840  -0.840  -1.080  -1.068  -1.080  -0.840  -0.840  -0.840
187   D        -0.840  -0.840  -0.840  -1.194  -1.197  -1.194  -0.840  -0.840  -0.840
188   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
189   I        -0.840  -0.840  -0.840  -0.614  -0.614  -0.614  -0.840  -0.840  -0.840
190   K        -0.840  -0.840  -0.840  -0.538  -0.539  -0.538  -0.840  -0.840  -0.840
191   L        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
192   Y        -0.840  -0.840  -0.840  -0.440  -0.440  -0.440  -0.840  -0.840  -0.840
193   V        -0.840  -0.840  -0.840  -0.464  -0.465  -0.464  -0.840  -0.840  -0.840
194   T        -0.840  -0.840  -0.840  -0.614  -0.614  -0.614  -0.840  -0.840  -0.840
195   Q         1.183   1.183   1.183   1.342   1.341   1.342   1.183   1.183   1.183
196   N         1.183   1.183   1.183   1.199   1.216   1.199   1.183   1.183   1.183
197   E        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
198   Q         1.183   1.183   1.183   1.342   1.341   1.342   1.183   1.183   1.183
199   L         1.183   1.183   1.183   0.903   0.901   0.903   1.183   1.183   1.183
200   Q         1.183   1.183   1.183   1.342   1.341   1.342   1.183   1.183   1.183
201   M         1.183   1.183   1.183   1.533   1.533   1.533   1.183   1.183   1.183
202   L        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
203   S         1.183   1.183   1.183   1.016   1.014   1.016   1.183   1.183   1.183
204   N        -0.840  -0.840  -0.840  -1.080  -1.068  -1.080  -0.840  -0.840  -0.840
205   S        -0.840  -0.840  -0.840  -0.807  -0.809  -0.807  -0.840  -0.840  -0.840
206   V        -0.840  -0.840  -0.840  -0.996  -0.998  -0.996  -0.840  -0.840  -0.840
207   -        -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/Q12421
Output conservation file - output/Q12421
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
