1     M         1.429   1.429   1.429   1.901   1.901   1.901   1.429   1.429   1.429
2     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
7     K        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
8     Q        -0.696  -0.696  -0.696  -0.656  -0.656  -0.656  -0.696  -0.696  -0.696
9     W         1.429   1.429   1.429   2.037   2.037   2.037   1.429   1.429   1.429
10    E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
11    R         1.429   1.429   1.429   1.602   1.602   1.602   1.429   1.429   1.429
12    I        -0.696  -0.696  -0.696  -0.479  -0.479  -0.479  -0.696  -0.696  -0.696
13    Q        -0.696  -0.696  -0.696  -0.351  -0.351  -0.351  -0.696  -0.696  -0.696
14    Q        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
15    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
16    E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
17    K        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
18    E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
19    H         1.429   1.429   1.429   1.862   1.862   1.862   1.429   1.429   1.429
20    V         1.429   1.429   1.429   1.723   1.723   1.723   1.429   1.429   1.429
21    E        -0.696  -0.696  -0.696  -0.886  -0.886  -0.886  -0.696  -0.696  -0.696
22    V        -0.696  -0.696  -0.696  -1.046  -1.046  -1.046  -0.696  -0.696  -0.696
23    Y         1.429   1.429   1.429   1.901   1.901   1.901   1.429   1.429   1.429
24    R        -0.696  -0.696  -0.696  -0.523  -0.523  -0.523  -0.696  -0.696  -0.696
25    E        -0.696  -0.696  -0.696  -1.014  -1.014  -1.014  -0.696  -0.696  -0.696
26    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
27    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
28    I        -0.696  -0.696  -0.696  -0.567  -0.567  -0.567  -0.696  -0.696  -0.696
29    T        -0.696  -0.696  -0.696  -0.436  -0.436  -0.436  -0.696  -0.696  -0.696
30    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
31    D         1.429   1.429   1.429   1.703   1.703   1.703   1.429   1.429   1.429
32    R        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
33    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
34    Y        -0.696  -0.696  -0.696  -0.212  -0.212  -0.212  -0.696  -0.696  -0.696
35    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
36    I        -0.696  -0.696  -0.696  -0.917  -0.917  -0.917  -0.696  -0.696  -0.696
37    R         1.429   1.429   1.429   1.602   1.602   1.602   1.429   1.429   1.429
38    K        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
39    H        -0.696  -0.696  -0.696  -0.309  -0.309  -0.309  -0.696  -0.696  -0.696
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    N         1.429   1.429   1.429   1.763   1.763   1.763   1.429   1.429   1.429
42    H         1.429   1.429   1.429   1.862   1.862   1.862   1.429   1.429   1.429
43    A        -0.696  -0.696  -0.696  -0.494  -0.494  -0.494  -0.696  -0.696  -0.696
44    V         1.429   1.429   1.429   1.723   1.723   1.723   1.429   1.429   1.429
45    I         1.429   1.429   1.429   1.663   1.663   1.663   1.429   1.429   1.429
46    L        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
47    S        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
48    H        -0.696  -0.696  -0.696  -0.351  -0.351  -0.351  -0.696  -0.696  -0.696
49    T        -0.696  -0.696  -0.696  -0.870  -0.870  -0.870  -0.696  -0.696  -0.696
50    Q         1.429   1.429   1.429   1.540   1.540   1.540   1.429   1.429   1.429
51    Q        -0.696  -0.696  -0.696  -1.014  -1.014  -1.014  -0.696  -0.696  -0.696
52    R        -0.696  -0.696  -0.696  -0.494  -0.494  -0.494  -0.696  -0.696  -0.696
53    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
54    L        -0.696  -0.696  -0.696  -0.902  -0.902  -0.902  -0.696  -0.696  -0.696
55    E        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
56    I        -0.696  -0.696  -0.696  -0.479  -0.479  -0.479  -0.696  -0.696  -0.696
57    R         1.429   1.429   1.429   1.602   1.602   1.602   1.429   1.429   1.429
58    H        -0.696  -0.696  -0.696  -0.422  -0.422  -0.422  -0.696  -0.696  -0.696
59    Q         1.429   1.429   1.429   1.540   1.540   1.540   1.429   1.429   1.429
60    L        -0.696  -0.696  -0.696  -0.902  -0.902  -0.902  -0.696  -0.696  -0.696
61    Q         1.429   1.429   1.429   1.540   1.540   1.540   1.429   1.429   1.429
62    I        -0.696  -0.696  -0.696  -0.267  -0.267  -0.267  -0.696  -0.696  -0.696
63    N        -0.696  -0.696  -0.696  -0.281  -0.281  -0.281  -0.696  -0.696  -0.696
64    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
65    E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
66    K        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
67    T        -0.696  -0.696  -0.696  -0.523  -0.523  -0.523  -0.696  -0.696  -0.696
68    A         1.429   1.429   1.429   1.763   1.763   1.763   1.429   1.429   1.429
69    L        -0.696  -0.696  -0.696  -1.014  -1.014  -1.014  -0.696  -0.696  -0.696
70    L        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
71    I        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
72    R         1.429   1.429   1.429   1.602   1.602   1.602   1.429   1.429   1.429
73    L        -0.696  -0.696  -0.696  -1.046  -1.046  -1.046  -0.696  -0.696  -0.696
74    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
75    E        -0.696  -0.696  -0.696  -1.014  -1.014  -1.014  -0.696  -0.696  -0.696
76    K        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
77    P        -0.696  -0.696  -0.696  -0.281  -0.281  -0.281  -0.696  -0.696  -0.696
78    D        -0.696  -0.696  -0.696  -0.422  -0.422  -0.422  -0.696  -0.696  -0.696
79    N        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    T        -0.696  -0.696  -0.696  -0.870  -0.870  -0.870  -0.696  -0.696  -0.696
90    N        -0.696  -0.696  -0.696  -0.422  -0.422  -0.422  -0.696  -0.696  -0.696
91    V        -0.696  -0.696  -0.696  -1.046  -1.046  -1.046  -0.696  -0.696  -0.696
92    L        -0.696  -0.696  -0.696  -1.046  -1.046  -1.046  -0.696  -0.696  -0.696
93    F        -0.696  -0.696  -0.696  -0.212  -0.212  -0.212  -0.696  -0.696  -0.696
94    T        -0.696  -0.696  -0.696  -0.870  -0.870  -0.870  -0.696  -0.696  -0.696
95    K        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
96    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
97    Q        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
98    N        -0.696  -0.696  -0.696  -0.494  -0.494  -0.494  -0.696  -0.696  -0.696
99    L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
100   L        -0.696  -0.696  -0.696  -0.902  -0.902  -0.902  -0.696  -0.696  -0.696
101   E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
102   E        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
103   S        -0.696  -0.696  -0.696  -0.422  -0.422  -0.422  -0.696  -0.696  -0.696
104   N        -0.696  -0.696  -0.696  -0.281  -0.281  -0.281  -0.696  -0.696  -0.696
105   S         1.429   1.429   1.429   1.602   1.602   1.602   1.429   1.429   1.429
106   L        -0.696  -0.696  -0.696  -1.046  -1.046  -1.046  -0.696  -0.696  -0.696
107   D        -0.696  -0.696  -0.696  -0.886  -0.886  -0.886  -0.696  -0.696  -0.696
108   Y        -0.696  -0.696  -0.696  -0.309  -0.309  -0.309  -0.696  -0.696  -0.696
109   E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
110   L        -0.696  -0.696  -0.696  -0.808  -0.808  -0.808  -0.696  -0.696  -0.696
111   L        -0.696  -0.696  -0.696  -0.902  -0.902  -0.902  -0.696  -0.696  -0.696
112   Q         1.429   1.429   1.429   1.540   1.540   1.540   1.429   1.429   1.429
113   S        -0.696  -0.696  -0.696  -0.567  -0.567  -0.567  -0.696  -0.696  -0.696
114   L        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
115   G        -0.696  -0.696  -0.696  -0.281  -0.281  -0.281  -0.696  -0.696  -0.696
116   A         1.429   1.429   1.429   1.763   1.763   1.763   1.429   1.429   1.429
117   Q        -0.696  -0.696  -0.696  -0.656  -0.656  -0.656  -0.696  -0.696  -0.696
118   S        -0.696  -0.696  -0.696  -1.145  -1.145  -1.145  -0.696  -0.696  -0.696
119   S        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
120   L        -0.696  -0.696  -0.696  -1.046  -1.046  -1.046  -0.696  -0.696  -0.696
121   H        -0.696  -0.696  -0.696  -0.422  -0.422  -0.422  -0.696  -0.696  -0.696
122   K        -0.696  -0.696  -0.696  -0.523  -0.523  -0.523  -0.696  -0.696  -0.696
123   Q        -0.696  -0.696  -0.696  -0.656  -0.656  -0.656  -0.696  -0.696  -0.696
124   L        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
125   I        -0.696  -0.696  -0.696  -0.281  -0.281  -0.281  -0.696  -0.696  -0.696
126   E        -0.696  -0.696  -0.696  -0.886  -0.886  -0.886  -0.696  -0.696  -0.696
127   S        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
128   R        -0.696  -0.696  -0.696  -0.656  -0.656  -0.656  -0.696  -0.696  -0.696
129   A        -0.696  -0.696  -0.696  -0.494  -0.494  -0.494  -0.696  -0.696  -0.696
130   E        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
131   R        -0.696  -0.696  -0.696  -0.323  -0.323  -0.323  -0.696  -0.696  -0.696
132   D        -0.696  -0.696  -0.696  -0.323  -0.323  -0.323  -0.696  -0.696  -0.696
133   E        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
134   L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
135   M        -0.696  -0.696  -0.696  -0.393  -0.393  -0.393  -0.696  -0.696  -0.696
136   S        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
137   K        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
138   L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
139   I        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
140   E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
141   L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
142   S        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
143   S        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
144   K        -0.696  -0.696  -0.696  -1.145  -1.145  -1.145  -0.696  -0.696  -0.696
145   F        -0.696  -0.696  -0.696  -0.116  -0.116  -0.116  -0.696  -0.696  -0.696
146   P        -0.696  -0.696  -0.696  -0.157  -0.157  -0.157  -0.696  -0.696  -0.696
147   K        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
148   P        -0.696  -0.696  -0.696  -0.407  -0.407  -0.407  -0.696  -0.696  -0.696
149   T        -0.696  -0.696  -0.696  -0.309  -0.309  -0.309  -0.696  -0.696  -0.696
150   I        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   P        -0.696  -0.696  -0.696  -0.253  -0.253  -0.253  -0.696  -0.696  -0.696
153   P         1.429   1.429   1.429   1.940   1.940   1.940   1.429   1.429   1.429
154   D        -0.696  -0.696  -0.696  -0.422  -0.422  -0.422  -0.696  -0.696  -0.696
155   D        -0.696  -0.696  -0.696  -0.537  -0.537  -0.537  -0.696  -0.696  -0.696
156   S        -0.696  -0.696  -0.696  -0.365  -0.365  -0.365  -0.696  -0.696  -0.696
157   D        -0.696  -0.696  -0.696  -0.422  -0.422  -0.422  -0.696  -0.696  -0.696
158   T        -0.696  -0.696  -0.696  -0.523  -0.523  -0.523  -0.696  -0.696  -0.696
159   A        -0.696  -0.696  -0.696  -0.407  -0.407  -0.407  -0.696  -0.696  -0.696
160   G        -0.696  -0.696  -0.696  -0.281  -0.281  -0.281  -0.696  -0.696  -0.696
161   K        -0.696  -0.696  -0.696  -0.965  -0.965  -0.965  -0.696  -0.696  -0.696
162   Q         1.429   1.429   1.429   1.540   1.540   1.540   1.429   1.429   1.429
163   V        -0.696  -0.696  -0.696  -0.870  -0.870  -0.870  -0.696  -0.696  -0.696
164   E        -0.696  -0.696  -0.696  -1.014  -1.014  -1.014  -0.696  -0.696  -0.696
165   V        -0.696  -0.696  -0.696  -1.046  -1.046  -1.046  -0.696  -0.696  -0.696
166   E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
167   K        -0.696  -0.696  -0.696  -0.611  -0.611  -0.611  -0.696  -0.696  -0.696
168   E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
169   N         1.429   1.429   1.429   1.763   1.763   1.763   1.429   1.429   1.429
170   E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
171   T         1.429   1.429   1.429   1.723   1.723   1.723   1.429   1.429   1.429
172   I        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
173   Q        -0.696  -0.696  -0.696  -0.656  -0.656  -0.656  -0.696  -0.696  -0.696
174   E         1.429   1.429   1.429   1.116   1.116   1.116   1.429   1.429   1.429
175   L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
176   M        -0.696  -0.696  -0.696  -0.902  -0.902  -0.902  -0.696  -0.696  -0.696
177   I        -0.696  -0.696  -0.696  -0.479  -0.479  -0.479  -0.696  -0.696  -0.696
178   A         1.429   1.429   1.429   1.763   1.763   1.763   1.429   1.429   1.429
179   L         1.429   1.429   1.429   0.870   0.870   0.870   1.429   1.429   1.429
180   Q         1.429   1.429   1.429   1.540   1.540   1.540   1.429   1.429   1.429
181   I        -0.696  -0.696  -0.696  -0.479  -0.479  -0.479  -0.696  -0.696  -0.696
182   H        -0.696  -0.696  -0.696  -0.212  -0.212  -0.212  -0.696  -0.696  -0.696
183   S         1.429   1.429   1.429   1.602   1.602   1.602   1.429   1.429   1.429
184   G         1.429   1.429   1.429   1.901   1.901   1.901   1.429   1.429   1.429
185   Y        -0.696  -0.696  -0.696  -0.393  -0.393  -0.393  -0.696  -0.696  -0.696
186   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   S        -0.696  -0.696  -0.696  -0.393  -0.393  -0.393  -0.696  -0.696  -0.696
190   Y        -0.696  -0.696  -0.696  -0.309  -0.309  -0.309  -0.696  -0.696  -0.696
191   T        -0.696  -0.696  -0.696  -0.436  -0.436  -0.436  -0.696  -0.696  -0.696
192   I        -0.696  -0.696  -0.696  -1.095  -1.095  -1.095  -0.696  -0.696  -0.696
* 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/Q12262
Output conservation file - output/Q12262
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
