1     M         1.441   1.441   1.441   1.694   1.694   1.694   1.441   1.441   1.441
2     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S        -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        -0.689  -0.689  -0.689  -0.772  -0.772  -0.772  -0.689  -0.689  -0.689
6     Y         1.441   1.441   1.441   1.540   1.540   1.540   1.441   1.441   1.441
7     R        -0.689  -0.689  -0.689  -0.858  -0.858  -0.858  -0.689  -0.689  -0.689
8     D        -0.689  -0.689  -0.689  -0.875  -0.875  -0.875  -0.689  -0.689  -0.689
9     S         1.441   1.441   1.441   1.222   1.222   1.222   1.441   1.441   1.441
10    Y        -0.689  -0.689  -0.689  -0.444  -0.444  -0.444  -0.689  -0.689  -0.689
11    F         1.441   1.441   1.441   1.584   1.584   1.584   1.441   1.441   1.441
12    Q        -0.689  -0.689  -0.689  -0.721  -0.721  -0.721  -0.689  -0.689  -0.689
13    Y         1.441   1.441   1.441   1.540   1.540   1.540   1.441   1.441   1.441
14    R        -0.689  -0.689  -0.689  -0.540  -0.540  -0.540  -0.689  -0.689  -0.689
15    H         1.441   1.441   1.441   1.562   1.562   1.562   1.441   1.441   1.441
16    L         1.441   1.441   1.441   1.245   1.245   1.245   1.441   1.441   1.441
17    P        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
18    A        -0.689  -0.689  -0.689  -0.704  -0.704  -0.704  -0.689  -0.689  -0.689
19    P        -0.689  -0.689  -0.689  -0.671  -0.671  -0.671  -0.689  -0.689  -0.689
20    H         1.441   1.441   1.441   1.562   1.562   1.562   1.441   1.441   1.441
21    H        -0.689  -0.689  -0.689  -0.444  -0.444  -0.444  -0.689  -0.689  -0.689
22    I        -0.689  -0.689  -0.689  -0.365  -0.365  -0.365  -0.689  -0.689  -0.689
23    L         1.441   1.441   1.441   1.245   1.245   1.245   1.441   1.441   1.441
24    Y         1.441   1.441   1.441   1.540   1.540   1.540   1.441   1.441   1.441
25    A        -0.689  -0.689  -0.689  -0.841  -0.841  -0.841  -0.689  -0.689  -0.689
26    E         1.441   1.441   1.441   1.291   1.291   1.291   1.441   1.441   1.441
27    W         1.441   1.441   1.441   1.694   1.694   1.694   1.441   1.441   1.441
28    N         1.441   1.441   1.441   1.128   1.128   1.128   1.441   1.441   1.441
29    Q        -0.689  -0.689  -0.689  -0.381  -0.381  -0.381  -0.689  -0.689  -0.689
30    D         1.441   1.441   1.441   1.383   1.383   1.383   1.441   1.441   1.441
31    I        -0.689  -0.689  -0.689  -0.588  -0.588  -0.588  -0.689  -0.689  -0.689
32    L        -0.689  -0.689  -0.689  -0.638  -0.638  -0.638  -0.689  -0.689  -0.689
33    A        -0.689  -0.689  -0.689  -0.588  -0.588  -0.588  -0.689  -0.689  -0.689
34    L        -0.689  -0.689  -0.689  -0.981  -0.981  -0.981  -0.689  -0.689  -0.689
35    P         1.441   1.441   1.441   1.562   1.562   1.562   1.441   1.441   1.441
36    D        -0.689  -0.689  -0.689  -0.654  -0.654  -0.654  -0.689  -0.689  -0.689
37    E        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
38    V        -0.689  -0.689  -0.689  -0.491  -0.491  -0.491  -0.689  -0.689  -0.689
39    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    A         1.441   1.441   1.441   1.337   1.337   1.337   1.441   1.441   1.441
45    M        -0.689  -0.689  -0.689  -0.556  -0.556  -0.556  -0.689  -0.689  -0.689
46    K        -0.689  -0.689  -0.689  -0.491  -0.491  -0.491  -0.689  -0.689  -0.689
47    D        -0.689  -0.689  -0.689  -0.806  -0.806  -0.806  -0.689  -0.689  -0.689
48    N        -0.689  -0.689  -0.689  -0.858  -0.858  -0.858  -0.689  -0.689  -0.689
49    T        -0.689  -0.689  -0.689  -0.755  -0.755  -0.755  -0.689  -0.689  -0.689
50    R        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
51    T        -0.689  -0.689  -0.689  -0.621  -0.621  -0.621  -0.689  -0.689  -0.689
52    D        -0.689  -0.689  -0.689  -0.556  -0.556  -0.556  -0.689  -0.689  -0.689
53    A        -0.689  -0.689  -0.689  -0.841  -0.841  -0.841  -0.689  -0.689  -0.689
54    E        -0.689  -0.689  -0.689  -0.588  -0.588  -0.588  -0.689  -0.689  -0.689
55    E        -0.689  -0.689  -0.689  -0.755  -0.755  -0.755  -0.689  -0.689  -0.689
56    G        -0.689  -0.689  -0.689  -0.772  -0.772  -0.772  -0.689  -0.689  -0.689
57    R        -0.689  -0.689  -0.689  -0.704  -0.704  -0.704  -0.689  -0.689  -0.689
58    A        -0.689  -0.689  -0.689  -0.910  -0.910  -0.910  -0.689  -0.689  -0.689
59    P         1.441   1.441   1.441   1.562   1.562   1.562   1.441   1.441   1.441
60    Q        -0.689  -0.689  -0.689  -0.721  -0.721  -0.721  -0.689  -0.689  -0.689
61    D         1.441   1.441   1.441   1.383   1.383   1.383   1.441   1.441   1.441
62    G        -0.689  -0.689  -0.689  -0.755  -0.755  -0.755  -0.689  -0.689  -0.689
63    E        -0.689  -0.689  -0.689  -0.588  -0.588  -0.588  -0.689  -0.689  -0.689
64    R        -0.689  -0.689  -0.689  -0.508  -0.508  -0.508  -0.689  -0.689  -0.689
65    N        -0.689  -0.689  -0.689  -0.875  -0.875  -0.875  -0.689  -0.689  -0.689
66    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    N        -0.689  -0.689  -0.689  -0.875  -0.875  -0.875  -0.689  -0.689  -0.689
86    R        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
87    Y         1.441   1.441   1.441   1.540   1.540   1.540   1.441   1.441   1.441
88    W         1.441   1.441   1.441   1.694   1.694   1.694   1.441   1.441   1.441
89    N        -0.689  -0.689  -0.689  -0.875  -0.875  -0.875  -0.689  -0.689  -0.689
90    S        -0.689  -0.689  -0.689  -0.999  -0.999  -0.999  -0.689  -0.689  -0.689
91    F        -0.689  -0.689  -0.689  -0.428  -0.428  -0.428  -0.689  -0.689  -0.689
92    H        -0.689  -0.689  -0.689  -0.654  -0.654  -0.654  -0.689  -0.689  -0.689
93    D        -0.689  -0.689  -0.689  -0.755  -0.755  -0.755  -0.689  -0.689  -0.689
94    E         1.441   1.441   1.441   1.291   1.291   1.291   1.441   1.441   1.441
95    D        -0.689  -0.689  -0.689  -0.755  -0.755  -0.755  -0.689  -0.689  -0.689
96    D         1.441   1.441   1.441   1.383   1.383   1.383   1.441   1.441   1.441
97    W        -0.689  -0.689  -0.689  -0.350  -0.350  -0.350  -0.689  -0.689  -0.689
98    N        -0.689  -0.689  -0.689  -0.721  -0.721  -0.721  -0.689  -0.689  -0.689
99    L         1.441   1.441   1.441   1.245   1.245   1.245   1.441   1.441   1.441
100   F         1.441   1.441   1.441   1.584   1.584   1.584   1.441   1.441   1.441
101   N        -0.689  -0.689  -0.689  -0.704  -0.704  -0.704  -0.689  -0.689  -0.689
102   G        -0.689  -0.689  -0.689  -0.841  -0.841  -0.841  -0.689  -0.689  -0.689
103   M        -0.689  -0.689  -0.689  -0.491  -0.491  -0.491  -0.689  -0.689  -0.689
104   E        -0.689  -0.689  -0.689  -0.588  -0.588  -0.588  -0.689  -0.689  -0.689
105   L         1.441   1.441   1.441   1.245   1.245   1.245   1.441   1.441   1.441
106   E         1.441   1.441   1.441   1.291   1.291   1.291   1.441   1.441   1.441
107   S         1.441   1.441   1.441   1.222   1.222   1.222   1.441   1.441   1.441
108   N         1.441   1.441   1.441   1.128   1.128   1.128   1.441   1.441   1.441
109   G         1.441   1.441   1.441   1.428   1.428   1.428   1.441   1.441   1.441
110   V         1.441   1.441   1.441   1.606   1.606   1.606   1.441   1.441   1.441
111   V         1.441   1.441   1.441   1.606   1.606   1.606   1.441   1.441   1.441
112   T         1.441   1.441   1.441   1.428   1.428   1.428   1.441   1.441   1.441
113   F         1.441   1.441   1.441   1.584   1.584   1.584   1.441   1.441   1.441
114   A        -0.689  -0.689  -0.689  -0.688  -0.688  -0.688  -0.689  -0.689  -0.689
115   G        -0.689  -0.689  -0.689  -0.491  -0.491  -0.491  -0.689  -0.689  -0.689
116   Q        -0.689  -0.689  -0.689  -0.572  -0.572  -0.572  -0.689  -0.689  -0.689
117   A        -0.689  -0.689  -0.689  -0.910  -0.910  -0.910  -0.689  -0.689  -0.689
118   F        -0.689  -0.689  -0.689  -0.638  -0.638  -0.638  -0.689  -0.689  -0.689
119   D        -0.689  -0.689  -0.689  -0.806  -0.806  -0.806  -0.689  -0.689  -0.689
120   H        -0.689  -0.689  -0.689  -0.654  -0.654  -0.654  -0.689  -0.689  -0.689
121   S        -0.689  -0.689  -0.689  -0.671  -0.671  -0.671  -0.689  -0.689  -0.689
122   L         1.441   1.441   1.441   1.245   1.245   1.245   1.441   1.441   1.441
123   N        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
124   G        -0.689  -0.689  -0.689  -0.772  -0.772  -0.772  -0.689  -0.689  -0.689
125   G        -0.689  -0.689  -0.689  -0.508  -0.508  -0.508  -0.689  -0.689  -0.689
126   T        -0.689  -0.689  -0.689  -0.841  -0.841  -0.841  -0.689  -0.689  -0.689
127   N        -0.689  -0.689  -0.689  -0.841  -0.841  -0.841  -0.689  -0.689  -0.689
128   S        -0.689  -0.689  -0.689  -0.841  -0.841  -0.841  -0.689  -0.689  -0.689
129   R        -0.689  -0.689  -0.689  -0.772  -0.772  -0.772  -0.689  -0.689  -0.689
130   N        -0.689  -0.689  -0.689  -0.946  -0.946  -0.946  -0.689  -0.689  -0.689
131   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   A        -0.689  -0.689  -0.689  -0.556  -0.556  -0.556  -0.689  -0.689  -0.689
134   N        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
135   E        -0.689  -0.689  -0.689  -0.946  -0.946  -0.946  -0.689  -0.689  -0.689
136   P        -0.689  -0.689  -0.689  -0.621  -0.621  -0.621  -0.689  -0.689  -0.689
137   R        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
138   K        -0.689  -0.689  -0.689  -0.638  -0.638  -0.638  -0.689  -0.689  -0.689
139   E        -0.689  -0.689  -0.689  -0.875  -0.875  -0.875  -0.689  -0.689  -0.689
140   T         1.441   1.441   1.441   1.428   1.428   1.428   1.441   1.441   1.441
141   I        -0.689  -0.689  -0.689  -0.621  -0.621  -0.621  -0.689  -0.689  -0.689
142   T         1.441   1.441   1.441   1.428   1.428   1.428   1.441   1.441   1.441
143   G         1.441   1.441   1.441   1.428   1.428   1.428   1.441   1.441   1.441
144   S         1.441   1.441   1.441   1.222   1.222   1.222   1.441   1.441   1.441
145   I         1.441   1.441   1.441   1.606   1.606   1.606   1.441   1.441   1.441
146   F         1.441   1.441   1.441   1.584   1.584   1.584   1.441   1.441   1.441
147   D        -0.689  -0.689  -0.689  -0.524  -0.524  -0.524  -0.689  -0.689  -0.689
148   R         1.441   1.441   1.441   1.405   1.405   1.405   1.441   1.441   1.441
149   R        -0.689  -0.689  -0.689  -0.671  -0.671  -0.671  -0.689  -0.689  -0.689
150   I        -0.689  -0.689  -0.689  -0.491  -0.491  -0.491  -0.689  -0.689  -0.689
151   T        -0.689  -0.689  -0.689  -0.638  -0.638  -0.638  -0.689  -0.689  -0.689
152   Q        -0.689  -0.689  -0.689  -0.381  -0.381  -0.381  -0.689  -0.689  -0.689
153   L        -0.689  -0.689  -0.689  -0.621  -0.621  -0.621  -0.689  -0.689  -0.689
154   A         1.441   1.441   1.441   1.337   1.337   1.337   1.441   1.441   1.441
155   Y        -0.689  -0.689  -0.689  -0.412  -0.412  -0.412  -0.689  -0.689  -0.689
156   A         1.441   1.441   1.441   1.337   1.337   1.337   1.441   1.441   1.441
157   R        -0.689  -0.689  -0.689  -0.508  -0.508  -0.508  -0.689  -0.689  -0.689
158   N        -0.689  -0.689  -0.689  -0.738  -0.738  -0.738  -0.689  -0.689  -0.689
159   N        -0.689  -0.689  -0.689  -0.858  -0.858  -0.858  -0.689  -0.689  -0.689
160   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   A        -0.689  -0.689  -0.689  -0.572  -0.572  -0.572  -0.689  -0.689  -0.689
166   L         1.441   1.441   1.441   1.245   1.245   1.245   1.441   1.441   1.441
167   P        -0.689  -0.689  -0.689  -0.524  -0.524  -0.524  -0.689  -0.689  -0.689
168   Q        -0.689  -0.689  -0.689  -0.508  -0.508  -0.508  -0.689  -0.689  -0.689
169   S        -0.689  -0.689  -0.689  -0.772  -0.772  -0.772  -0.689  -0.689  -0.689
170   R        -0.689  -0.689  -0.689  -0.772  -0.772  -0.772  -0.689  -0.689  -0.689
* 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/Q12379
Output conservation file - output/Q12379
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
