1     M         0.586   0.590   0.606   0.956   0.957   0.921   0.592   0.598   0.621
2     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S        -1.616  -1.561  -1.251  -2.079  -1.986  -1.485  -1.926  -1.848  -1.403
4     S        -2.170  -2.051  -2.320  -2.124  -1.995  -2.395  -1.926  -1.798  -2.060
5     K         0.586   0.590   0.606   0.515   0.533   0.570   0.592   0.598   0.621
6     R         0.586   0.590   0.606   0.821   0.818   0.813   0.592   0.598   0.621
7     I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
8     A        -0.845  -0.884  -1.228  -0.507  -0.571  -1.202  -0.807  -0.862  -1.367
9     K        -0.845  -0.838  -1.226  -0.685  -0.675  -1.206  -0.807  -0.801  -1.364
10    E         0.586   0.590   0.606   0.866   0.872   0.850   0.592   0.598   0.621
11    L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
12    S        -1.616  -1.578  -1.254  -2.079  -2.036  -1.494  -1.926  -1.875  -1.407
13    D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
14    L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
15    G         0.586   0.590   0.606   0.683   0.689   0.704   0.592   0.598   0.621
16    R        -0.845  -0.838  -1.226  -0.443  -0.452  -1.156  -0.807  -0.801  -1.364
17    D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
18    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
19    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
20    A        -0.845  -0.884  -1.228  -0.890  -0.949  -1.457  -0.807  -0.862  -1.367
21    S         0.586   0.590   0.606   0.372   0.380   0.456   0.592   0.598   0.621
22    C         0.586   0.590   0.606   0.921   0.924   0.893   0.592   0.598   0.621
23    S         0.586   0.590   0.606   0.372   0.380   0.456   0.592   0.598   0.621
24    A         0.586   0.590   0.606   0.515   0.528   0.570   0.592   0.598   0.621
25    G         0.586   0.590   0.606   0.683   0.689   0.704   0.592   0.598   0.621
26    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
27    V        -0.845  -0.867  -1.227  -0.407  -0.449  -0.989  -0.807  -0.840  -1.366
28    G         0.586   0.590   0.606   0.683   0.689   0.704   0.592   0.598   0.621
29    D        -2.170  -2.325  -2.328  -1.864  -2.071  -2.005  -1.926  -2.109  -2.068
30    D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
31    L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
32    Y        -1.616  -1.561  -1.251  -1.621  -1.547  -1.124  -1.926  -1.848  -1.403
33    H         0.586   0.590   0.606   0.884   0.889   0.864   0.592   0.598   0.621
34    W         0.586   0.590   0.606   0.921   0.924   0.893   0.592   0.598   0.621
35    Q         0.586   0.590   0.606   0.930   0.935   0.900   0.592   0.598   0.621
36    A         0.586   0.590   0.606   0.515   0.528   0.570   0.592   0.598   0.621
37    S        -1.616  -1.561  -1.251  -2.001  -1.912  -1.421  -1.926  -1.848  -1.403
38    I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
39    M         0.586   0.590   0.606   0.956   0.957   0.921   0.592   0.598   0.621
40    G         0.586   0.590   0.606   0.683   0.689   0.704   0.592   0.598   0.621
41    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
42    S        -2.905  -2.812  -2.337  -3.387  -3.244  -2.525  -2.766  -2.665  -2.078
43    D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
44    S         0.586   0.590   0.606   0.372   0.380   0.456   0.592   0.598   0.621
45    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
46    Y         0.586   0.590   0.606   0.730   0.738   0.741   0.592   0.598   0.621
47    A        -2.170  -2.325  -2.328  -1.982  -2.240  -2.323  -1.926  -2.109  -2.068
48    G         0.586   0.590   0.606   0.683   0.689   0.704   0.592   0.598   0.621
49    G         0.586   0.590   0.606   0.683   0.689   0.704   0.592   0.598   0.621
50    V         0.586   0.590   0.606   0.775   0.775   0.777   0.592   0.598   0.621
51    F         0.586   0.590   0.606   0.785   0.787   0.784   0.592   0.598   0.621
52    F         0.586   0.590   0.606   0.785   0.787   0.784   0.592   0.598   0.621
53    L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
54    S        -0.845  -0.867  -1.227  -0.840  -0.875  -1.332  -0.807  -0.840  -1.366
55    I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
56    H        -0.845  -0.867  -1.227  -0.301  -0.338  -0.920  -0.807  -0.840  -1.366
57    F         0.586   0.590   0.606   0.785   0.787   0.784   0.592   0.598   0.621
58    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
59    T         0.586   0.590   0.606   0.618   0.618   0.652   0.592   0.598   0.621
60    D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
61    Y         0.586   0.590   0.606   0.730   0.738   0.741   0.592   0.598   0.621
62    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
63    F         0.586   0.590   0.606   0.785   0.787   0.784   0.592   0.598   0.621
64    K         0.586   0.590   0.606   0.515   0.533   0.570   0.592   0.598   0.621
65    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
66    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
67    K         0.586   0.590   0.606   0.515   0.533   0.570   0.592   0.598   0.621
68    V        -1.436  -1.222  -1.235  -1.413  -1.066  -1.219  -1.646  -1.334  -1.378
69    N        -3.639  -3.643  -3.107  -3.436  -3.454  -2.787  -3.045  -3.029  -2.416
70    F         0.586   0.590   0.606   0.785   0.787   0.784   0.592   0.598   0.621
71    T         0.586   0.590   0.606   0.618   0.618   0.652   0.592   0.598   0.621
72    T         0.586   0.590   0.606   0.618   0.618   0.652   0.592   0.598   0.621
73    K        -1.616  -1.561  -1.251  -1.747  -1.651  -1.218  -1.926  -1.848  -1.403
74    I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
75    Y         0.586   0.590   0.606   0.730   0.738   0.741   0.592   0.598   0.621
76    H         0.586   0.590   0.606   0.884   0.889   0.864   0.592   0.598   0.621
77    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
78    N         0.586   0.590   0.606   0.757   0.761   0.763   0.592   0.598   0.621
79    I        -0.845  -1.011  -1.233  -0.723  -0.936  -1.256  -0.807  -1.034  -1.374
80    N         0.586   0.590   0.606   0.757   0.761   0.763   0.592   0.598   0.621
81    S        -2.170  -2.161  -2.324  -2.045  -2.074  -2.257  -1.926  -1.931  -2.065
82    S        -0.845  -0.884  -1.228  -0.534  -0.601  -1.271  -0.807  -0.862  -1.367
83    G         0.586   0.590   0.606   0.683   0.689   0.704   0.592   0.598   0.621
84    N        -1.616  -1.561  -1.251  -1.896  -1.854  -1.354  -1.926  -1.848  -1.403
85    I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
86    C         0.586   0.590   0.606   0.921   0.924   0.893   0.592   0.598   0.621
87    L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
88    D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
89    I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
90    L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
91    K        -1.436  -1.430  -1.247  -1.498  -1.500  -1.230  -1.646  -1.644  -1.396
92    D        -0.845  -1.011  -1.233  -0.760  -0.973  -1.245  -0.807  -1.034  -1.374
93    Q        -0.845  -1.011  -1.233  -0.290  -0.521  -0.984  -0.807  -1.034  -1.374
94    W         0.586   0.590   0.606   0.921   0.924   0.893   0.592   0.598   0.621
95    S         0.586   0.590   0.606   0.372   0.380   0.456   0.592   0.598   0.621
96    P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
97    A         0.586   0.590   0.606   0.515   0.528   0.570   0.592   0.598   0.621
98    L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
99    T         0.586   0.590   0.606   0.618   0.618   0.652   0.592   0.598   0.621
100   L        -0.845  -0.884  -1.228  -0.804  -0.857  -1.453  -0.807  -0.862  -1.367
101   S         0.586   0.590   0.606   0.372   0.380   0.456   0.592   0.598   0.621
102   K         0.586   0.590   0.606   0.515   0.533   0.570   0.592   0.598   0.621
103   V         0.586   0.590   0.606   0.775   0.775   0.777   0.592   0.598   0.621
104   L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
105   L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
106   S         0.586   0.590   0.606   0.372   0.380   0.456   0.592   0.598   0.621
107   I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
108   C         0.586   0.590   0.606   0.921   0.924   0.893   0.592   0.598   0.621
109   S         0.586   0.590   0.606   0.372   0.380   0.456   0.592   0.598   0.621
110   L        -1.436  -1.495  -1.252  -1.563  -1.653  -1.239  -1.646  -1.745  -1.404
111   L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
112   T         0.586   0.590   0.606   0.618   0.618   0.652   0.592   0.598   0.621
113   D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
114   A        -1.616  -1.561  -1.251  -2.165  -2.102  -1.564  -1.926  -1.848  -1.403
115   N         0.586   0.590   0.606   0.757   0.761   0.763   0.592   0.598   0.621
116   P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
117   D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
118   D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
119   P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
120   L         0.586   0.590   0.606   0.372   0.381   0.456   0.592   0.598   0.621
121   V         0.586   0.590   0.606   0.775   0.775   0.777   0.592   0.598   0.621
122   P         0.586   0.590   0.606   0.255   0.268   0.363   0.592   0.598   0.621
123   E        -0.845  -1.011  -1.233  -0.415  -0.661  -1.182  -0.807  -1.034  -1.374
124   I         0.586   0.590   0.606   0.487   0.505   0.547   0.592   0.598   0.621
125   A        -0.845  -1.011  -1.233  -0.713  -0.936  -1.285  -0.807  -1.034  -1.374
126   Q        -0.845  -0.884  -1.228  -0.301  -0.358  -0.922  -0.807  -0.862  -1.367
127   I        -2.628  -2.710  -2.339  -2.623  -2.766  -2.271  -2.486  -2.562  -2.080
128   Y         0.586   0.590   0.606   0.730   0.738   0.741   0.592   0.598   0.621
129   K         0.586   0.590   0.606   0.515   0.533   0.570   0.592   0.598   0.621
130   T        -2.628  -2.592  -2.330  -2.322  -2.296  -1.955  -2.486  -2.418  -2.071
131   D         0.586   0.590   0.606   0.429   0.440   0.502   0.592   0.598   0.621
132   K        -0.845  -0.884  -1.228  -0.443  -0.513  -1.160  -0.807  -0.862  -1.367
133   A        -2.170  -1.949  -2.316  -2.008  -1.728  -2.351  -1.926  -1.684  -2.056
134   K        -1.616  -1.561  -1.251  -1.747  -1.651  -1.218  -1.926  -1.848  -1.403
135   Y         0.586   0.590   0.606   0.730   0.738   0.741   0.592   0.598   0.621
136   E        -0.845  -1.011  -1.233  -0.415  -0.661  -1.182  -0.807  -1.034  -1.374
137   A        -2.170  -2.011  -2.318  -2.043  -1.837  -2.420  -1.926  -1.751  -2.058
138   T        -0.845  -0.838  -1.226  -0.672  -0.681  -1.360  -0.807  -0.801  -1.364
139   A         0.586   0.590   0.606   0.515   0.528   0.570   0.592   0.598   0.621
140   K        -1.436  -1.430  -1.247  -1.498  -1.500  -1.230  -1.646  -1.644  -1.396
141   E         0.586   0.590   0.606   0.866   0.872   0.850   0.592   0.598   0.621
142   W         0.586   0.590   0.606   0.921   0.924   0.893   0.592   0.598   0.621
143   T         0.586   0.590   0.606   0.618   0.618   0.652   0.592   0.598   0.621
144   K        -1.436  -1.430  -1.247  -1.498  -1.500  -1.230  -1.646  -1.644  -1.396
145   K         0.586   0.590   0.606   0.515   0.533   0.570   0.592   0.598   0.621
146   Y         0.586   0.590   0.606   0.730   0.738   0.741   0.592   0.598   0.621
147   A         0.586   0.590   0.606   0.515   0.528   0.570   0.592   0.598   0.621
148   V        -1.436  -1.430  -1.247  -1.413  -1.433  -1.248  -1.646  -1.644  -1.396
* 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/P15732
Output conservation file - output/P15732
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
