1     M         1.432   1.432   1.432   1.738   1.738   1.738   1.432   1.432   1.432
2     S        -0.693  -0.693  -0.693  -0.641  -0.641  -0.641  -0.693  -0.693  -0.693
3     N        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
4     K        -0.693  -0.693  -0.693  -0.673  -0.673  -0.673  -0.693  -0.693  -0.693
5     A        -0.693  -0.693  -0.693  -0.437  -0.437  -0.437  -0.693  -0.693  -0.693
6     S        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
7     D        -0.693  -0.693  -0.693  -0.923  -0.923  -0.923  -0.693  -0.693  -0.693
8     Q        -0.693  -0.693  -0.693  -0.285  -0.285  -0.285  -0.693  -0.693  -0.693
9     S        -0.693  -0.693  -0.693  -0.641  -0.641  -0.641  -0.693  -0.693  -0.693
10    A        -0.693  -0.693  -0.693  -0.285  -0.285  -0.285  -0.693  -0.693  -0.693
11    R        -0.693  -0.693  -0.693  -0.421  -0.421  -0.421  -0.693  -0.693  -0.693
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    T        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
14    A        -0.693  -0.693  -0.693  -0.437  -0.437  -0.437  -0.693  -0.693  -0.693
15    S        -0.693  -0.693  -0.693  -1.135  -1.135  -1.135  -0.693  -0.693  -0.693
16    I        -0.693  -0.693  -0.693  -0.545  -0.545  -0.545  -0.693  -0.693  -0.693
17    L         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
18    K        -0.693  -0.693  -0.693  -1.135  -1.135  -1.135  -0.693  -0.693  -0.693
19    T        -0.693  -0.693  -0.693  -0.530  -0.530  -0.530  -0.693  -0.693  -0.693
20    D        -0.693  -0.693  -0.693  -0.805  -0.805  -0.805  -0.693  -0.693  -0.693
21    I        -0.693  -0.693  -0.693  -0.657  -0.657  -0.657  -0.693  -0.693  -0.693
22    T        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
23    R        -0.693  -0.693  -0.693  -0.788  -0.788  -0.788  -0.693  -0.693  -0.693
24    E        -0.693  -0.693  -0.693  -0.625  -0.625  -0.625  -0.693  -0.693  -0.693
25    N         1.432   1.432   1.432   1.172   1.172   1.172   1.432   1.432   1.432
26    T         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
27    I        -0.693  -0.693  -0.693  -0.467  -0.467  -0.467  -0.693  -0.693  -0.693
28    T        -0.693  -0.693  -0.693  -0.530  -0.530  -0.530  -0.693  -0.693  -0.693
29    R        -0.693  -0.693  -0.693  -0.330  -0.330  -0.330  -0.693  -0.693  -0.693
30    S        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
31    S        -0.693  -0.693  -0.693  -0.805  -0.805  -0.805  -0.693  -0.693  -0.693
32    S        -0.693  -0.693  -0.693  -0.657  -0.657  -0.657  -0.693  -0.693  -0.693
33    S        -0.693  -0.693  -0.693  -0.657  -0.657  -0.657  -0.693  -0.693  -0.693
34    N        -0.693  -0.693  -0.693  -0.657  -0.657  -0.657  -0.693  -0.693  -0.693
35    N        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
36    D         1.432   1.432   1.432   1.439   1.439   1.439   1.432   1.432   1.432
37    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    G         1.432   1.432   1.432   1.633   1.633   1.633   1.432   1.432   1.432
55    E        -0.693  -0.693  -0.693  -0.738  -0.738  -0.738  -0.693  -0.693  -0.693
56    D         1.432   1.432   1.432   1.439   1.439   1.439   1.432   1.432   1.432
57    A         1.432   1.432   1.432   1.590   1.590   1.590   1.432   1.432   1.432
58    N        -0.693  -0.693  -0.693  -0.673  -0.673  -0.673  -0.693  -0.693  -0.693
59    K        -0.693  -0.693  -0.693  -0.673  -0.673  -0.673  -0.693  -0.693  -0.693
60    E        -0.693  -0.693  -0.693  -0.625  -0.625  -0.625  -0.693  -0.693  -0.693
61    N        -0.693  -0.693  -0.693  -0.805  -0.805  -0.805  -0.693  -0.693  -0.693
62    I        -0.693  -0.693  -0.693  -0.545  -0.545  -0.545  -0.693  -0.693  -0.693
63    P        -0.693  -0.693  -0.693  -0.609  -0.609  -0.609  -0.693  -0.693  -0.693
64    N        -0.693  -0.693  -0.693  -1.010  -1.010  -1.010  -0.693  -0.693  -0.693
65    L         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
66    E        -0.693  -0.693  -0.693  -0.545  -0.545  -0.545  -0.693  -0.693  -0.693
67    E        -0.693  -0.693  -0.693  -0.406  -0.406  -0.406  -0.693  -0.693  -0.693
68    E        -0.693  -0.693  -0.693  -0.738  -0.738  -0.738  -0.693  -0.693  -0.693
69    I        -0.693  -0.693  -0.693  -0.330  -0.330  -0.330  -0.693  -0.693  -0.693
70    A         1.432   1.432   1.432   1.590   1.590   1.590   1.432   1.432   1.432
71    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    R        -0.693  -0.693  -0.693  -0.673  -0.673  -0.673  -0.693  -0.693  -0.693
74    I         1.432   1.432   1.432   1.633   1.633   1.633   1.432   1.432   1.432
75    F         1.432   1.432   1.432   1.633   1.633   1.633   1.432   1.432   1.432
76    R        -0.693  -0.693  -0.693  -0.673  -0.673  -0.673  -0.693  -0.693  -0.693
77    K        -0.693  -0.693  -0.693  -0.771  -0.771  -0.771  -0.693  -0.693  -0.693
78    K        -0.693  -0.693  -0.693  -1.135  -1.135  -1.135  -0.693  -0.693  -0.693
79    S         1.432   1.432   1.432   1.172   1.172   1.172   1.432   1.432   1.432
80    T        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
81    S        -0.693  -0.693  -0.693  -1.135  -1.135  -1.135  -0.693  -0.693  -0.693
82    N        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
83    L        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
84    K        -0.693  -0.693  -0.693  -0.771  -0.771  -0.771  -0.693  -0.693  -0.693
85    S        -0.693  -0.693  -0.693  -1.135  -1.135  -1.135  -0.693  -0.693  -0.693
86    S         1.432   1.432   1.432   1.172   1.172   1.172   1.432   1.432   1.432
87    H        -0.693  -0.693  -0.693  -0.577  -0.577  -0.577  -0.693  -0.693  -0.693
88    T         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
89    T        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
90    S        -0.693  -0.693  -0.693  -0.657  -0.657  -0.657  -0.693  -0.693  -0.693
91    N        -0.693  -0.693  -0.693  -0.545  -0.545  -0.545  -0.693  -0.693  -0.693
92    L        -0.693  -0.693  -0.693  -0.530  -0.530  -0.530  -0.693  -0.693  -0.693
93    V        -0.693  -0.693  -0.693  -0.315  -0.315  -0.315  -0.693  -0.693  -0.693
94    K         1.432   1.432   1.432   1.010   1.010   1.010   1.432   1.432   1.432
95    K         1.432   1.432   1.432   1.010   1.010   1.010   1.432   1.432   1.432
96    T         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
97    M        -0.693  -0.693  -0.693  -0.689  -0.689  -0.689  -0.693  -0.693  -0.693
98    F        -0.693  -0.693  -0.693  -0.330  -0.330  -0.330  -0.693  -0.693  -0.693
99    K        -0.693  -0.693  -0.693  -0.771  -0.771  -0.771  -0.693  -0.693  -0.693
100   R        -0.693  -0.693  -0.693  -0.345  -0.345  -0.345  -0.693  -0.693  -0.693
101   D        -0.693  -0.693  -0.693  -0.498  -0.498  -0.498  -0.693  -0.693  -0.693
102   L        -0.693  -0.693  -0.693  -0.545  -0.545  -0.545  -0.693  -0.693  -0.693
103   L        -0.693  -0.693  -0.693  -0.889  -0.889  -0.889  -0.693  -0.693  -0.693
104   K        -0.693  -0.693  -0.693  -0.771  -0.771  -0.771  -0.693  -0.693  -0.693
105   Q        -0.693  -0.693  -0.693  -0.545  -0.545  -0.545  -0.693  -0.693  -0.693
106   D        -0.693  -0.693  -0.693  -0.805  -0.805  -0.805  -0.693  -0.693  -0.693
107   P        -0.693  -0.693  -0.693  -0.182  -0.182  -0.182  -0.693  -0.693  -0.693
108   K        -0.693  -0.693  -0.693  -0.689  -0.689  -0.689  -0.693  -0.693  -0.693
109   R         1.432   1.432   1.432   1.612   1.612   1.612   1.432   1.432   1.432
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   K        -0.693  -0.693  -0.693  -0.923  -0.923  -0.923  -0.693  -0.693  -0.693
115   L         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
116   Q        -0.693  -0.693  -0.693  -0.657  -0.657  -0.657  -0.693  -0.693  -0.693
117   L         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
118   Q        -0.693  -0.693  -0.693  -0.345  -0.345  -0.345  -0.693  -0.693  -0.693
119   Q        -0.693  -0.693  -0.693  -0.771  -0.771  -0.771  -0.693  -0.693  -0.693
120   R        -0.693  -0.693  -0.693  -0.788  -0.788  -0.788  -0.693  -0.693  -0.693
121   F         1.432   1.432   1.432   1.633   1.633   1.633   1.432   1.432   1.432
122   A         1.432   1.432   1.432   1.590   1.590   1.590   1.432   1.432   1.432
123   S         1.432   1.432   1.432   1.172   1.172   1.172   1.432   1.432   1.432
124   P         1.432   1.432   1.432   1.696   1.696   1.696   1.432   1.432   1.432
125   T         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
126   D         1.432   1.432   1.432   1.439   1.439   1.439   1.432   1.432   1.432
127   R        -0.693  -0.693  -0.693  -0.271  -0.271  -0.271  -0.693  -0.693  -0.693
128   L         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
129   V        -0.693  -0.693  -0.693  -0.530  -0.530  -0.530  -0.693  -0.693  -0.693
130   S         1.432   1.432   1.432   1.172   1.172   1.172   1.432   1.432   1.432
131   P         1.432   1.432   1.432   1.696   1.696   1.696   1.432   1.432   1.432
132   C         1.432   1.432   1.432   1.780   1.780   1.780   1.432   1.432   1.432
133   S         1.432   1.432   1.432   1.172   1.172   1.172   1.432   1.432   1.432
134   L        -0.693  -0.693  -0.693  -1.010  -1.010  -1.010  -0.693  -0.693  -0.693
135   K         1.432   1.432   1.432   1.010   1.010   1.010   1.432   1.432   1.432
136   L         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
137   N        -0.693  -0.693  -0.693  -0.673  -0.673  -0.673  -0.693  -0.693  -0.693
138   E        -0.693  -0.693  -0.693  -0.545  -0.545  -0.545  -0.693  -0.693  -0.693
139   H         1.432   1.432   1.432   1.738   1.738   1.738   1.432   1.432   1.432
140   K         1.432   1.432   1.432   1.010   1.010   1.010   1.432   1.432   1.432
141   V        -0.693  -0.693  -0.693  -0.641  -0.641  -0.641  -0.693  -0.693  -0.693
142   K        -0.693  -0.693  -0.693  -1.135  -1.135  -1.135  -0.693  -0.693  -0.693
143   M        -0.693  -0.693  -0.693  -0.467  -0.467  -0.467  -0.693  -0.693  -0.693
144   F         1.432   1.432   1.432   1.633   1.633   1.633   1.432   1.432   1.432
145   G         1.432   1.432   1.432   1.633   1.633   1.633   1.432   1.432   1.432
146   K        -0.693  -0.693  -0.693  -1.010  -1.010  -1.010  -0.693  -0.693  -0.693
147   K         1.432   1.432   1.432   1.010   1.010   1.010   1.432   1.432   1.432
148   K        -0.693  -0.693  -0.693  -0.771  -0.771  -0.771  -0.693  -0.693  -0.693
149   K         1.432   1.432   1.432   1.010   1.010   1.010   1.432   1.432   1.432
150   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   P         1.432   1.432   1.432   1.696   1.696   1.696   1.432   1.432   1.432
153   M        -0.693  -0.693  -0.693  -0.467  -0.467  -0.467  -0.693  -0.693  -0.693
154   K         1.432   1.432   1.432   1.010   1.010   1.010   1.432   1.432   1.432
155   L         1.432   1.432   1.432   1.329   1.329   1.329   1.432   1.432   1.432
156   N        -0.693  -0.693  -0.693  -1.135  -1.135  -1.135  -0.693  -0.693  -0.693
157   F         1.432   1.432   1.432   1.633   1.633   1.633   1.432   1.432   1.432
158   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   E        -0.693  -0.693  -0.693  -0.625  -0.625  -0.625  -0.693  -0.693  -0.693
173   D         1.432   1.432   1.432   1.439   1.439   1.439   1.432   1.432   1.432
174   E        -0.693  -0.693  -0.693  -0.625  -0.625  -0.625  -0.693  -0.693  -0.693
175   E        -0.693  -0.693  -0.693  -0.406  -0.406  -0.406  -0.693  -0.693  -0.693
176   Y        -0.693  -0.693  -0.693  -0.561  -0.561  -0.561  -0.693  -0.693  -0.693
177   F        -0.693  -0.693  -0.693  -0.406  -0.406  -0.406  -0.693  -0.693  -0.693
178   Y        -0.693  -0.693  -0.693  -0.241  -0.241  -0.241  -0.693  -0.693  -0.693
* 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/P17123
Output conservation file - output/P17123
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
