1     M         1.231   1.231   1.248   1.457   1.456   1.478   1.283   1.284   1.302
2     F        -0.322  -0.337  -0.370  -0.404  -0.430  -0.455  -0.420  -0.443  -0.490
3     G        -0.460  -0.460  -0.425  -0.438  -0.445  -0.377  -0.633  -0.633  -0.575
4     K        -0.322  -0.300  -0.367  -0.564  -0.505  -0.637  -0.420  -0.387  -0.486
5     V        -0.322  -0.300  -0.367  -0.141  -0.109  -0.212  -0.420  -0.387  -0.486
6     F        -1.449  -1.448  -1.404  -1.390  -1.398  -1.310  -1.272  -1.271  -1.200
7     V        -0.322  -0.300  -0.367  -0.191  -0.158  -0.271  -0.420  -0.387  -0.486
8     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    S        -0.322  -0.327  -0.376  -0.528  -0.526  -0.635  -0.420  -0.428  -0.498
29    S        -0.322  -0.300  -0.367  -0.546  -0.520  -0.611  -0.420  -0.387  -0.486
30    S        -1.449  -1.448  -1.404  -1.401  -1.410  -1.321  -1.272  -1.271  -1.200
31    L        -1.449  -1.448  -1.404  -1.555  -1.557  -1.471  -1.272  -1.271  -1.200
32    S         1.231   1.231   1.248   1.045   1.038   1.075   1.283   1.284   1.302
33    F        -1.449  -1.448  -1.404  -1.579  -1.568  -1.495  -1.272  -1.271  -1.200
34    D        -0.322  -0.327  -0.376  -0.421  -0.417  -0.504  -0.420  -0.428  -0.498
35    K        -1.449  -1.448  -1.404  -1.367  -1.360  -1.287  -1.272  -1.271  -1.200
36    E        -1.449  -1.448  -1.404  -1.378  -1.381  -1.298  -1.272  -1.271  -1.200
37    A        -0.322  -0.327  -0.376  -0.439  -0.453  -0.494  -0.420  -0.428  -0.498
38    C        -0.460  -0.460  -0.425  -0.496  -0.499  -0.434  -0.633  -0.633  -0.575
39    F         1.231   1.231   1.248   1.083   1.081   1.112   1.283   1.284   1.302
40    P        -0.322  -0.327  -0.376  -0.317  -0.311  -0.378  -0.420  -0.428  -0.498
41    F         1.231   1.231   1.248   1.084   1.081   1.112   1.283   1.284   1.302
42    K        -0.322  -0.337  -0.370  -0.564  -0.568  -0.642  -0.420  -0.443  -0.490
43    K        -0.322  -0.327  -0.376  -0.519  -0.506  -0.624  -0.420  -0.428  -0.498
44    W         1.231   1.231   1.248   1.547   1.548   1.566   1.283   1.284   1.302
45    H        -0.322  -0.300  -0.367  -0.100  -0.070  -0.172  -0.420  -0.387  -0.486
46    E         1.231   1.231   1.248   1.366   1.367   1.389   1.283   1.284   1.302
47    L         1.231   1.231   1.248   1.255   1.252   1.280   1.283   1.284   1.302
48    N        -1.449  -1.448  -1.404  -1.322  -1.328  -1.243  -1.272  -1.271  -1.200
49    M        -1.449  -1.448  -1.404  -1.200  -1.205  -1.124  -1.272  -1.271  -1.200
50    S        -0.322  -0.327  -0.376  -0.249  -0.263  -0.377  -0.420  -0.428  -0.498
51    Q        -0.322  -0.327  -0.376  -0.158  -0.167  -0.240  -0.420  -0.428  -0.498
52    K        -0.322  -0.337  -0.370  -0.430  -0.440  -0.482  -0.420  -0.443  -0.490
53    Q        -0.322  -0.337  -0.370  -0.100  -0.130  -0.181  -0.420  -0.443  -0.490
54    E        -0.322  -0.327  -0.376  -0.466  -0.459  -0.531  -0.420  -0.428  -0.498
55    F         1.231   1.231   1.248   1.084   1.081   1.112   1.283   1.284   1.302
56    I        -0.322  -0.300  -0.367  -0.216  -0.185  -0.287  -0.420  -0.387  -0.486
57    Q        -1.449  -1.448  -1.404  -1.115  -1.118  -1.040  -1.272  -1.271  -1.200
58    R        -1.449  -1.448  -1.404  -1.603  -1.589  -1.519  -1.272  -1.271  -1.200
59    F         1.231   1.231   1.248   1.084   1.081   1.112   1.283   1.284   1.302
60    V        -0.322  -0.337  -0.370  -0.133  -0.159  -0.207  -0.420  -0.443  -0.490
61    K        -0.322  -0.327  -0.376  -0.326  -0.329  -0.446  -0.420  -0.428  -0.498
62    N         1.231   1.231   1.248   1.236   1.234   1.262   1.283   1.284   1.302
63    Y         1.231   1.231   1.248   1.366   1.366   1.389   1.283   1.284   1.302
64    R        -0.322  -0.300  -0.367  -0.519  -0.457  -0.607  -0.420  -0.387  -0.486
65    H        -0.322  -0.327  -0.376  -0.439  -0.435  -0.499  -0.420  -0.428  -0.498
66    Q        -0.322  -0.337  -0.370  -0.216  -0.240  -0.320  -0.420  -0.443  -0.490
67    Y         1.231   1.231   1.248   1.366   1.366   1.389   1.283   1.284   1.302
68    P         1.231   1.231   1.248   1.493   1.493   1.514   1.283   1.284   1.302
69    S        -0.322  -0.327  -0.376  -0.404  -0.420  -0.520  -0.420  -0.428  -0.498
70    S         1.231   1.231   1.248   1.045   1.038   1.075   1.283   1.284   1.302
71    K         1.231   1.231   1.248   1.064   1.081   1.094   1.283   1.284   1.302
72    T         1.231   1.231   1.248   1.439   1.442   1.461   1.283   1.284   1.302
73    N         1.231   1.231   1.248   1.236   1.234   1.262   1.283   1.284   1.302
74    V        -0.322  -0.337  -0.370  -0.224  -0.256  -0.316  -0.420  -0.443  -0.490
75    S         1.231   1.231   1.248   1.045   1.038   1.075   1.283   1.284   1.302
76    L        -0.322  -0.337  -0.370  -0.421  -0.455  -0.520  -0.420  -0.443  -0.490
77    K        -0.322  -0.327  -0.376  -0.519  -0.506  -0.624  -0.420  -0.428  -0.498
78    G         1.231   1.231   1.248   1.292   1.291   1.317   1.283   1.284   1.302
79    L         1.231   1.231   1.248   1.255   1.252   1.280   1.283   1.284   1.302
80    S        -1.449  -1.448  -1.404  -1.310  -1.317  -1.232  -1.272  -1.271  -1.200
81    I        -1.449  -1.448  -1.404  -1.378  -1.379  -1.298  -1.272  -1.271  -1.200
82    G        -0.322  -0.327  -0.376  -0.309  -0.322  -0.399  -0.420  -0.428  -0.498
83    M        -0.322  -0.337  -0.370  -0.125  -0.154  -0.215  -0.420  -0.443  -0.490
84    D        -0.322  -0.300  -0.367  -0.275  -0.243  -0.344  -0.420  -0.387  -0.486
85    E        -1.449  -1.448  -1.404  -1.310  -1.294  -1.232  -1.272  -1.271  -1.200
86    H        -0.322  -0.327  -0.376  -0.166  -0.177  -0.250  -0.420  -0.428  -0.498
87    N        -0.322  -0.337  -0.370  -0.448  -0.473  -0.547  -0.420  -0.443  -0.490
88    D         1.231   1.231   1.248   1.273   1.271   1.298   1.283   1.284   1.302
89    S        -0.322  -0.300  -0.367  -0.439  -0.416  -0.484  -0.420  -0.387  -0.486
90    P         1.231   1.231   1.248   1.493   1.493   1.514   1.283   1.284   1.302
91    S         1.231   1.231   1.248   1.045   1.038   1.075   1.283   1.284   1.302
92    V         1.231   1.231   1.248   1.384   1.382   1.407   1.283   1.284   1.302
93    F         1.231   1.231   1.248   1.084   1.081   1.112   1.283   1.284   1.302
94    G         1.231   1.231   1.248   1.292   1.291   1.317   1.283   1.284   1.302
95    I         1.231   1.231   1.248   1.329   1.328   1.353   1.283   1.284   1.302
96    F         1.231   1.231   1.248   1.084   1.081   1.112   1.283   1.284   1.302
97    Y         1.231   1.231   1.248   1.366   1.366   1.389   1.283   1.284   1.302
98    N         1.231   1.231   1.248   1.236   1.234   1.262   1.283   1.284   1.302
99    D        -0.322  -0.337  -0.370  -0.421  -0.458  -0.524  -0.420  -0.443  -0.490
100   I         1.231   1.231   1.248   1.329   1.328   1.353   1.283   1.284   1.302
101   W         1.231   1.231   1.248   1.544   1.544   1.563   1.283   1.284   1.302
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   K         1.231   1.231   1.248   1.032   1.055   1.062   1.283   1.284   1.302
106   S        -0.460  -0.460  -0.425  -0.603  -0.606  -0.539  -0.633  -0.633  -0.575
107   F        -0.460  -0.460  -0.425  -0.712  -0.717  -0.646  -0.633  -0.633  -0.575
108   K         1.231   1.231   1.248   1.032   1.055   1.062   1.283   1.284   1.302
109   N        -0.460  -0.460  -0.425  -0.531  -0.534  -0.469  -0.633  -0.633  -0.575
110   E        -0.460  -0.460  -0.425  -0.712  -0.717  -0.646  -0.633  -0.633  -0.575
111   Q        -0.460  -0.460  -0.425  -0.461  -0.464  -0.400  -0.633  -0.633  -0.575
112   L        -0.460  -0.460  -0.425  -0.496  -0.499  -0.434  -0.633  -0.633  -0.575
113   G         1.231   1.231   1.248   1.306   1.305   1.330   1.283   1.284   1.302
114   T        -0.460  -0.460  -0.425  -0.496  -0.499  -0.434  -0.633  -0.633  -0.575
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -0.460  -0.460  -0.425  -0.304  -0.311  -0.246  -0.633  -0.633  -0.575
118   -         1.231   1.231   1.248   1.208   1.227   1.235   1.283   1.284   1.302
119   N        -0.322  -0.300  -0.367  -0.404  -0.361  -0.488  -0.420  -0.387  -0.486
120   N        -1.449  -1.448  -1.404  -1.459  -1.449  -1.378  -1.272  -1.271  -1.200
121   D        -0.322  -0.300  -0.367  -0.335  -0.302  -0.415  -0.420  -0.387  -0.486
122   N        -1.449  -1.448  -1.404  -1.344  -1.348  -1.265  -1.272  -1.271  -1.200
123   M        -1.449  -1.448  -1.404  -1.244  -1.247  -1.167  -1.272  -1.271  -1.200
124   K        -0.322  -0.337  -0.370  -0.564  -0.568  -0.642  -0.420  -0.443  -0.490
125   S        -0.322  -0.327  -0.376  -0.421  -0.438  -0.536  -0.420  -0.428  -0.498
126   G        -1.449  -1.448  -1.404  -1.355  -1.361  -1.276  -1.272  -1.271  -1.200
127   S        -0.322  -0.327  -0.376  -0.404  -0.420  -0.520  -0.420  -0.428  -0.498
128   R         1.231   1.231   1.248   1.160   1.178   1.188   1.283   1.284   1.302
129   F         1.231   1.231   1.248   1.084   1.081   1.112   1.283   1.284   1.302
130   S        -1.449  -1.448  -1.404  -1.413  -1.416  -1.332  -1.272  -1.271  -1.200
131   H         1.231   1.231   1.248   1.421   1.418   1.443   1.283   1.284   1.302
132   P        -1.449  -1.448  -1.404  -1.211  -1.215  -1.135  -1.272  -1.271  -1.200
133   S        -0.322  -0.300  -0.367  -0.448  -0.424  -0.494  -0.420  -0.387  -0.486
134   F         1.231   1.231   1.248   1.084   1.081   1.112   1.283   1.284   1.302
135   K        -1.449  -1.448  -1.404  -1.507  -1.495  -1.424  -1.272  -1.271  -1.200
136   Q        -1.449  -1.448  -1.404  -1.367  -1.363  -1.287  -1.272  -1.271  -1.200
137   L         1.231   1.231   1.248   1.255   1.252   1.280   1.283   1.284   1.302
138   L        -0.322  -0.337  -0.370  -0.283  -0.312  -0.354  -0.420  -0.443  -0.490
139   I        -0.322  -0.337  -0.370  -0.275  -0.305  -0.362  -0.420  -0.443  -0.490
140   Q        -1.449  -1.448  -1.404  -1.211  -1.213  -1.135  -1.272  -1.271  -1.200
141   K        -0.460  -0.460  -0.425  -0.739  -0.753  -0.673  -0.633  -0.633  -0.575
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q04814
Output conservation file - output/Q04814
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
