1     M         1.394   1.394   1.394   1.650   1.650   1.650   1.394   1.394   1.394
2     S         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
3     P        -0.714  -0.714  -0.714  -0.599  -0.599  -0.599  -0.714  -0.714  -0.714
4     T         1.394   1.394   1.394   1.266   1.266   1.266   1.394   1.394   1.394
5     G        -0.714  -0.714  -0.714  -0.587  -0.587  -0.587  -0.714  -0.714  -0.714
6     N        -0.714  -0.714  -0.714  -0.538  -0.538  -0.538  -0.714  -0.714  -0.714
7     Y        -0.714  -0.714  -0.714  -0.478  -0.478  -0.478  -0.714  -0.714  -0.714
8     L        -0.714  -0.714  -0.714  -1.036  -1.036  -1.036  -0.714  -0.714  -0.714
9     N         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
10    A         1.394   1.394   1.394   1.020   1.020   1.020   1.394   1.394   1.394
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    I         1.394   1.394   1.394   1.435   1.435   1.435   1.394   1.394   1.394
16    T        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
17    N        -0.714  -0.714  -0.714  -0.526  -0.526  -0.526  -0.714  -0.714  -0.714
18    R         1.394   1.394   1.394   1.552   1.552   1.552   1.394   1.394   1.394
19    R         1.394   1.394   1.394   1.552   1.552   1.552   1.394   1.394   1.394
20    T         1.394   1.394   1.394   1.266   1.266   1.266   1.394   1.394   1.394
21    I        -0.714  -0.714  -0.714  -0.431  -0.431  -0.431  -0.714  -0.714  -0.714
22    Y         1.394   1.394   1.394   1.601   1.601   1.601   1.394   1.394   1.394
23    N        -0.714  -0.714  -0.714  -0.538  -0.538  -0.538  -0.714  -0.714  -0.714
24    L         1.394   1.394   1.394   1.196   1.196   1.196   1.394   1.394   1.394
25    K        -0.714  -0.714  -0.714  -0.636  -0.636  -0.636  -0.714  -0.714  -0.714
26    P        -0.714  -0.714  -0.714  -0.587  -0.587  -0.587  -0.714  -0.714  -0.714
27    E        -0.714  -0.714  -0.714  -0.599  -0.599  -0.599  -0.714  -0.714  -0.714
28    L         1.394   1.394   1.394   1.196   1.196   1.196   1.394   1.394   1.394
29    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    Q        -0.714  -0.714  -0.714  -0.587  -0.587  -0.587  -0.714  -0.714  -0.714
31    G        -0.714  -0.714  -0.714  -0.648  -0.648  -0.648  -0.714  -0.714  -0.714
32    V        -0.714  -0.714  -0.714  -0.890  -0.890  -0.890  -0.714  -0.714  -0.714
33    G        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
34    L        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
35    D        -0.714  -0.714  -0.714  -0.599  -0.599  -0.599  -0.714  -0.714  -0.714
36    D        -0.714  -0.714  -0.714  -0.443  -0.443  -0.443  -0.714  -0.714  -0.714
37    V        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
38    K        -0.714  -0.714  -0.714  -0.574  -0.574  -0.574  -0.714  -0.714  -0.714
39    R        -0.714  -0.714  -0.714  -0.538  -0.538  -0.538  -0.714  -0.714  -0.714
40    T        -0.714  -0.714  -0.714  -0.673  -0.673  -0.673  -0.714  -0.714  -0.714
41    V         1.394   1.394   1.394   1.214   1.214   1.214   1.394   1.394   1.394
42    H        -0.714  -0.714  -0.714  -0.454  -0.454  -0.454  -0.714  -0.714  -0.714
43    V        -0.714  -0.714  -0.714  -0.786  -0.786  -0.786  -0.714  -0.714  -0.714
44    I        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
45    L         1.394   1.394   1.394   1.196   1.196   1.196   1.394   1.394   1.394
46    K        -0.714  -0.714  -0.714  -0.574  -0.574  -0.574  -0.714  -0.714  -0.714
47    N        -0.714  -0.714  -0.714  -0.407  -0.407  -0.407  -0.714  -0.714  -0.714
48    T        -0.714  -0.714  -0.714  -0.838  -0.838  -0.838  -0.714  -0.714  -0.714
49    P         1.394   1.394   1.394   1.435   1.435   1.435   1.394   1.394   1.394
50    T        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
51    A        -0.714  -0.714  -0.714  -0.903  -0.903  -0.903  -0.714  -0.714  -0.714
52    F         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
53    N         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
54    S         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
55    Q         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
56    V        -0.714  -0.714  -0.714  -0.761  -0.761  -0.761  -0.714  -0.714  -0.714
57    N         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
58    R         1.394   1.394   1.394   1.552   1.552   1.552   1.394   1.394   1.394
59    A        -0.714  -0.714  -0.714  -1.023  -1.023  -1.023  -0.714  -0.714  -0.714
60    V         1.394   1.394   1.394   1.214   1.214   1.214   1.394   1.394   1.394
61    I        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
62    I        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
63    V        -0.714  -0.714  -0.714  -0.890  -0.890  -0.890  -0.714  -0.714  -0.714
64    G         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
65    D        -0.714  -0.714  -0.714  -0.825  -0.825  -0.825  -0.714  -0.714  -0.714
66    T        -0.714  -0.714  -0.714  -0.748  -0.748  -0.748  -0.714  -0.714  -0.714
67    H         1.394   1.394   1.394   1.617   1.617   1.617   1.394   1.394   1.394
68    K        -0.714  -0.714  -0.714  -0.660  -0.660  -0.660  -0.714  -0.714  -0.714
69    R        -0.714  -0.714  -0.714  -0.502  -0.502  -0.502  -0.714  -0.714  -0.714
70    I        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
71    W         1.394   1.394   1.394   1.634   1.634   1.634   1.394   1.394   1.394
72    D         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
73    A        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
74    V        -0.714  -0.714  -0.714  -0.838  -0.838  -0.838  -0.714  -0.714  -0.714
75    A        -0.714  -0.714  -0.714  -0.982  -0.982  -0.982  -0.714  -0.714  -0.714
76    S        -0.714  -0.714  -0.714  -0.673  -0.673  -0.673  -0.714  -0.714  -0.714
77    A        -0.714  -0.714  -0.714  -0.982  -0.982  -0.982  -0.714  -0.714  -0.714
78    M        -0.714  -0.714  -0.714  -0.562  -0.562  -0.562  -0.714  -0.714  -0.714
79    P        -0.714  -0.714  -0.714  -0.587  -0.587  -0.587  -0.714  -0.714  -0.714
80    T        -0.714  -0.714  -0.714  -0.982  -0.982  -0.982  -0.714  -0.714  -0.714
81    A        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
82    E        -0.714  -0.714  -0.714  -0.786  -0.786  -0.786  -0.714  -0.714  -0.714
83    A        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
84    K        -0.714  -0.714  -0.714  -0.660  -0.660  -0.660  -0.714  -0.714  -0.714
85    K        -0.714  -0.714  -0.714  -0.562  -0.562  -0.562  -0.714  -0.714  -0.714
86    R        -0.714  -0.714  -0.714  -0.514  -0.514  -0.514  -0.714  -0.714  -0.714
87    P        -0.714  -0.714  -0.714  -0.526  -0.526  -0.526  -0.714  -0.714  -0.714
88    E        -0.714  -0.714  -0.714  -0.929  -0.929  -0.929  -0.714  -0.714  -0.714
89    S         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
90    C        -0.714  -0.714  -0.714  -0.454  -0.454  -0.454  -0.714  -0.714  -0.714
91    R        -0.714  -0.714  -0.714  -0.761  -0.761  -0.761  -0.714  -0.714  -0.714
92    D        -0.714  -0.714  -0.714  -0.574  -0.574  -0.574  -0.714  -0.714  -0.714
93    E        -0.714  -0.714  -0.714  -0.660  -0.660  -0.660  -0.714  -0.714  -0.714
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   A         1.394   1.394   1.394   1.020   1.020   1.020   1.394   1.394   1.394
101   Y        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
102   G         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
103   S        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
104   V        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
105   I        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
106   F         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
107   F         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
108   T        -0.714  -0.714  -0.714  -0.748  -0.748  -0.748  -0.714  -0.714  -0.714
109   D         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
110   E         1.394   1.394   1.394   1.334   1.334   1.334   1.394   1.394   1.394
111   G        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
112   P        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
113   T        -0.714  -0.714  -0.714  -0.838  -0.838  -0.838  -0.714  -0.714  -0.714
114   E        -0.714  -0.714  -0.714  -0.660  -0.660  -0.660  -0.714  -0.714  -0.714
115   K        -0.714  -0.714  -0.714  -0.636  -0.636  -0.636  -0.714  -0.714  -0.714
116   L        -0.714  -0.714  -0.714  -0.562  -0.562  -0.562  -0.714  -0.714  -0.714
117   Q         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
118   R        -0.714  -0.714  -0.714  -0.538  -0.538  -0.538  -0.714  -0.714  -0.714
119   D        -0.714  -0.714  -0.714  -0.514  -0.514  -0.514  -0.714  -0.714  -0.714
120   F         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
121   P        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
122   A        -0.714  -0.714  -0.714  -1.023  -1.023  -1.023  -0.714  -0.714  -0.714
123   L        -0.714  -0.714  -0.714  -0.599  -0.599  -0.599  -0.714  -0.714  -0.714
124   A         1.394   1.394   1.394   1.020   1.020   1.020   1.394   1.394   1.394
125   A        -0.714  -0.714  -0.714  -0.825  -0.825  -0.825  -0.714  -0.714  -0.714
126   A        -0.714  -0.714  -0.714  -0.761  -0.761  -0.761  -0.714  -0.714  -0.714
127   F         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
128   P         1.394   1.394   1.394   1.435   1.435   1.435   1.394   1.394   1.394
129   T        -0.714  -0.714  -0.714  -0.838  -0.838  -0.838  -0.714  -0.714  -0.714
130   C        -0.714  -0.714  -0.714  -0.201  -0.201  -0.201  -0.714  -0.714  -0.714
131   A         1.394   1.394   1.394   1.020   1.020   1.020   1.394   1.394   1.394
132   A        -0.714  -0.714  -0.714  -1.023  -1.023  -1.023  -0.714  -0.714  -0.714
133   H        -0.714  -0.714  -0.714  -0.407  -0.407  -0.407  -0.714  -0.714  -0.714
134   T        -0.714  -0.714  -0.714  -0.723  -0.723  -0.723  -0.714  -0.714  -0.714
135   T        -0.714  -0.714  -0.714  -0.648  -0.648  -0.648  -0.714  -0.714  -0.714
136   G        -0.714  -0.714  -0.714  -0.903  -0.903  -0.903  -0.714  -0.714  -0.714
137   A        -0.714  -0.714  -0.714  -0.685  -0.685  -0.685  -0.714  -0.714  -0.714
138   V        -0.714  -0.714  -0.714  -0.890  -0.890  -0.890  -0.714  -0.714  -0.714
139   Q         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
140   I        -0.714  -0.714  -0.714  -0.419  -0.419  -0.419  -0.714  -0.714  -0.714
141   Q        -0.714  -0.714  -0.714  -0.660  -0.660  -0.660  -0.714  -0.714  -0.714
142   S        -0.714  -0.714  -0.714  -0.773  -0.773  -0.773  -0.714  -0.714  -0.714
143   W         1.394   1.394   1.394   1.634   1.634   1.634   1.394   1.394   1.394
144   T        -0.714  -0.714  -0.714  -0.838  -0.838  -0.838  -0.714  -0.714  -0.714
145   A         1.394   1.394   1.394   1.020   1.020   1.020   1.394   1.394   1.394
146   L         1.394   1.394   1.394   1.196   1.196   1.196   1.394   1.394   1.394
147   E         1.394   1.394   1.394   1.334   1.334   1.334   1.394   1.394   1.394
148   L        -0.714  -0.714  -0.714  -1.036  -1.036  -1.036  -0.714  -0.714  -0.714
149   L        -0.714  -0.714  -0.714  -0.799  -0.799  -0.799  -0.714  -0.714  -0.714
150   G         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
151   L         1.394   1.394   1.394   1.196   1.196   1.196   1.394   1.394   1.394
152   G         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
153   A         1.394   1.394   1.394   1.020   1.020   1.020   1.394   1.394   1.394
154   N         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
155   L         1.394   1.394   1.394   1.196   1.196   1.196   1.394   1.394   1.394
156   Q         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
157   H         1.394   1.394   1.394   1.617   1.617   1.617   1.394   1.394   1.394
158   Y         1.394   1.394   1.394   1.601   1.601   1.601   1.394   1.394   1.394
159   N         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
160   D        -0.714  -0.714  -0.714  -0.526  -0.526  -0.526  -0.714  -0.714  -0.714
161   Y        -0.714  -0.714  -0.714  -0.599  -0.599  -0.599  -0.714  -0.714  -0.714
162   V        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
163   K        -0.714  -0.714  -0.714  -0.562  -0.562  -0.562  -0.714  -0.714  -0.714
164   S        -0.714  -0.714  -0.714  -0.903  -0.903  -0.903  -0.714  -0.714  -0.714
165   A        -0.714  -0.714  -0.714  -0.890  -0.890  -0.890  -0.714  -0.714  -0.714
166   L        -0.714  -0.714  -0.714  -0.890  -0.890  -0.890  -0.714  -0.714  -0.714
167   P        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
168   Q        -0.714  -0.714  -0.714  -0.611  -0.611  -0.611  -0.714  -0.714  -0.714
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   D        -0.714  -0.714  -0.714  -0.574  -0.574  -0.574  -0.714  -0.714  -0.714
172   V        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
173   P         1.394   1.394   1.394   1.435   1.435   1.435   1.394   1.394   1.394
174   I        -0.714  -0.714  -0.714  -0.623  -0.623  -0.623  -0.714  -0.714  -0.714
175   A        -0.714  -0.714  -0.714  -0.903  -0.903  -0.903  -0.714  -0.714  -0.714
176   W         1.394   1.394   1.394   1.634   1.634   1.634   1.394   1.394   1.394
177   T        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
178   V        -0.714  -0.714  -0.714  -0.890  -0.890  -0.890  -0.714  -0.714  -0.714
179   Q        -0.714  -0.714  -0.714  -0.526  -0.526  -0.526  -0.714  -0.714  -0.714
180   S        -0.714  -0.714  -0.714  -0.903  -0.903  -0.903  -0.714  -0.714  -0.714
181   Q         1.394   1.394   1.394   1.452   1.452   1.452   1.394   1.394   1.394
182   L         1.394   1.394   1.394   1.196   1.196   1.196   1.394   1.394   1.394
183   V         1.394   1.394   1.394   1.214   1.214   1.214   1.394   1.394   1.394
184   F         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
185   G         1.394   1.394   1.394   1.368   1.368   1.368   1.394   1.394   1.394
186   V        -0.714  -0.714  -0.714  -0.761  -0.761  -0.761  -0.714  -0.714  -0.714
187   P        -0.714  -0.714  -0.714  -0.587  -0.587  -0.587  -0.714  -0.714  -0.714
188   T         1.394   1.394   1.394   1.266   1.266   1.266   1.394   1.394   1.394
189   A        -0.714  -0.714  -0.714  -0.903  -0.903  -0.903  -0.714  -0.714  -0.714
190   L        -0.714  -0.714  -0.714  -0.698  -0.698  -0.698  -0.714  -0.714  -0.714
191   P        -0.714  -0.714  -0.714  -0.851  -0.851  -0.851  -0.714  -0.714  -0.714
192   E        -0.714  -0.714  -0.714  -0.673  -0.673  -0.673  -0.714  -0.714  -0.714
193   E         1.394   1.394   1.394   1.334   1.334   1.334   1.394   1.394   1.394
194   K         1.394   1.394   1.394   1.385   1.385   1.385   1.394   1.394   1.394
195   T        -0.714  -0.714  -0.714  -0.982  -0.982  -0.982  -0.714  -0.714  -0.714
196   F         1.394   1.394   1.394   1.469   1.469   1.469   1.394   1.394   1.394
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   I        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
200   N        -0.714  -0.714  -0.714  -0.611  -0.611  -0.611  -0.714  -0.714  -0.714
201   N        -0.714  -0.714  -0.714  -0.611  -0.611  -0.611  -0.714  -0.714  -0.714
202   V        -0.714  -0.714  -0.714  -0.748  -0.748  -0.748  -0.714  -0.714  -0.714
203   I        -0.714  -0.714  -0.714  -0.526  -0.526  -0.526  -0.714  -0.714  -0.714
204   N        -0.714  -0.714  -0.714  -0.574  -0.574  -0.574  -0.714  -0.714  -0.714
205   V        -0.714  -0.714  -0.714  -0.761  -0.761  -0.761  -0.714  -0.714  -0.714
206   Y        -0.714  -0.714  -0.714  -0.407  -0.407  -0.407  -0.714  -0.714  -0.714
207   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
208   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
209   H        -0.714  -0.714  -0.714  -0.710  -0.710  -0.710  -0.714  -0.714  -0.714
* 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/P37261
Output conservation file - output/P37261
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
