1     M         1.866   1.871   1.917   2.115   2.115   2.194   2.030   2.037   2.103
2     K        -0.514  -0.539  -0.542  -0.475  -0.512  -0.505  -0.546  -0.577  -0.572
3     A        -1.308  -1.305  -1.268  -1.346  -1.358  -1.281  -1.061  -1.056  -0.998
4     S        -0.649  -0.644  -0.607  -0.755  -0.747  -0.688  -0.718  -0.710  -0.653
5     Y        -0.649  -0.644  -0.607  -0.367  -0.361  -0.299  -0.718  -0.710  -0.653
6     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     V        -0.649  -0.644  -0.607  -1.008  -0.961  -0.943  -0.718  -0.710  -0.653
8     L        -0.514  -0.517  -0.538  -0.721  -0.735  -0.741  -0.546  -0.549  -0.565
9     I         0.578   0.558   0.491   0.456   0.416   0.285   0.484   0.450   0.329
10    F        -0.514  -0.505  -0.533  -0.294  -0.281  -0.316  -0.546  -0.533  -0.559
11    I        -1.308  -1.305  -1.268  -1.243  -1.229  -1.178  -1.061  -1.056  -0.998
12    S        -1.308  -1.305  -1.268  -1.010  -1.000  -0.944  -1.061  -1.056  -0.998
13    I         0.578   0.617   0.507   0.304   0.352   0.189   0.484   0.547   0.356
14    F        -0.514  -0.502  -0.522  -0.673  -0.670  -0.668  -0.546  -0.530  -0.545
15    S         0.578   0.593   0.502   0.505   0.515   0.379   0.484   0.508   0.347
16    M        -1.308  -1.305  -1.268  -0.875  -0.891  -0.809  -1.061  -1.056  -0.998
17    A        -0.514  -0.505  -0.533  -0.659  -0.655  -0.665  -0.546  -0.533  -0.559
18    Q        -0.649  -0.643  -0.607  -0.411  -0.384  -0.343  -0.718  -0.709  -0.653
19    A         0.409   0.376   0.390   0.490   0.450   0.460   0.198   0.141   0.153
20    S        -0.649  -0.643  -0.607  -0.834  -0.838  -0.767  -0.718  -0.709  -0.653
21    S        -0.649  -0.643  -0.607  -0.923  -0.940  -0.857  -0.718  -0.709  -0.653
22    L         0.409   0.450   0.409   0.447   0.534   0.417   0.198   0.269   0.187
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    S        -0.514  -0.520  -0.525  -0.424  -0.435  -0.423  -0.546  -0.552  -0.549
27    S         0.578   0.558   0.491   0.495   0.444   0.348   0.484   0.450   0.329
28    Y         0.578   0.562   0.490   0.659   0.619   0.483   0.484   0.457   0.328
29    I         0.578   0.562   0.490   0.631   0.607   0.515   0.484   0.457   0.328
30    V        -0.514  -0.520  -0.525  -0.693  -0.691  -0.728  -0.546  -0.552  -0.549
31    T        -1.308  -1.305  -1.268  -1.390  -1.416  -1.326  -1.061  -1.056  -0.998
32    F        -0.514  -0.539  -0.542  -0.443  -0.505  -0.507  -0.546  -0.577  -0.572
33    P        -0.514  -0.520  -0.525  -0.368  -0.386  -0.401  -0.546  -0.552  -0.549
34    K        -0.514  -0.482  -0.520  -0.612  -0.554  -0.627  -0.546  -0.503  -0.543
35    T        -0.514  -0.505  -0.533  -0.533  -0.543  -0.555  -0.546  -0.533  -0.559
36    D        -0.514  -0.502  -0.522  -0.546  -0.545  -0.553  -0.546  -0.530  -0.545
37    N        -1.308  -1.305  -1.268  -0.875  -0.861  -0.809  -1.061  -1.056  -0.998
38    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    A         1.866   1.871   1.917   1.947   1.946   2.026   2.030   2.037   2.103
40    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    Q        -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    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    I        -1.308  -1.305  -1.268  -1.251  -1.237  -1.186  -1.061  -1.056  -0.998
46    I        -1.308  -1.305  -1.268  -1.010  -0.998  -0.944  -1.061  -1.056  -0.998
47    E        -0.514  -0.539  -0.542  -0.500  -0.522  -0.538  -0.546  -0.577  -0.572
48    D         0.578   0.593   0.502   0.525   0.543   0.395   0.484   0.508   0.347
49    V        -0.514  -0.517  -0.538  -0.645  -0.644  -0.698  -0.546  -0.549  -0.565
50    K        -0.514  -0.517  -0.538  -0.714  -0.714  -0.771  -0.546  -0.549  -0.565
51    K        -1.308  -1.305  -1.268  -1.144  -1.129  -1.079  -1.061  -1.056  -0.998
52    Y        -1.308  -1.305  -1.268  -1.144  -1.146  -1.079  -1.061  -1.056  -0.998
53    V         0.279   0.282   0.324   0.094   0.112   0.165  -0.031  -0.026   0.036
54    V        -1.308  -1.305  -1.268  -1.251  -1.224  -1.186  -1.061  -1.056  -0.998
55    D        -0.514  -0.505  -0.533  -0.619  -0.600  -0.656  -0.546  -0.533  -0.559
56    I         0.279   0.282   0.324  -0.165  -0.169  -0.097  -0.031  -0.026   0.036
57    G         0.578   0.562   0.490   0.688   0.665   0.535   0.484   0.457   0.328
58    G         0.578   0.593   0.502   0.692   0.726   0.562   0.484   0.508   0.347
59    K         0.578   0.562   0.490   0.588   0.560   0.463   0.484   0.457   0.328
60    I         0.578   0.558   0.491   0.535   0.507   0.389   0.484   0.450   0.329
61    T         1.866   1.871   1.917   2.029   2.026   2.108   2.030   2.037   2.103
62    H         1.866   1.871   1.917   2.029   2.069   2.108   2.030   2.037   2.103
63    E         1.866   1.871   1.917   1.809   1.828   1.887   2.030   2.037   2.103
64    Y         1.866   1.871   1.917   2.015   2.013   2.094   2.030   2.037   2.103
65    S        -0.514  -0.539  -0.542  -0.533  -0.589  -0.569  -0.546  -0.577  -0.572
66    L         1.866   1.871   1.917   1.580   1.574   1.657   2.030   2.037   2.103
67    I         0.578   0.562   0.490   0.593   0.565   0.465   0.484   0.457   0.328
68    K         0.279   0.284   0.326   0.180   0.199   0.261  -0.031  -0.023   0.039
69    G         1.866   1.871   1.917   1.971   1.982   2.050   2.030   2.037   2.103
70    F         1.866   1.871   1.917   2.000   1.995   2.079   2.030   2.037   2.103
71    T        -0.514  -0.539  -0.542  -0.380  -0.437  -0.440  -0.546  -0.577  -0.572
72    V        -0.514  -0.505  -0.533  -0.756  -0.740  -0.774  -0.546  -0.533  -0.559
73    D         1.866   1.871   1.917   1.809   1.810   1.887   2.030   2.037   2.103
74    L        -0.514  -0.520  -0.525  -0.805  -0.814  -0.818  -0.546  -0.552  -0.549
75    P         1.866   1.871   1.917   2.087   2.085   2.166   2.030   2.037   2.103
76    D        -0.514  -0.505  -0.533  -0.559  -0.530  -0.589  -0.546  -0.533  -0.559
77    S        -0.514  -0.505  -0.533  -0.619  -0.599  -0.656  -0.546  -0.533  -0.559
78    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    L         0.409   0.376   0.390   0.060   0.008   0.038   0.198   0.141   0.153
85    K         0.409   0.376   0.390   0.299   0.262   0.251   0.198   0.141   0.153
86    E        -0.649  -0.644  -0.607  -0.779  -0.771  -0.712  -0.718  -0.710  -0.653
87    R        -0.514  -0.505  -0.533  -0.368  -0.337  -0.372  -0.546  -0.533  -0.559
88    L        -0.514  -0.539  -0.542  -0.714  -0.752  -0.739  -0.546  -0.577  -0.572
89    S        -0.514  -0.517  -0.538  -0.592  -0.612  -0.629  -0.546  -0.549  -0.565
90    Y        -1.308  -1.305  -1.268  -1.128  -1.125  -1.062  -1.061  -1.056  -0.998
91    I        -1.308  -1.305  -1.268  -1.209  -1.204  -1.144  -1.061  -1.056  -0.998
92    E         0.578   0.562   0.490   0.612   0.604   0.490   0.484   0.457   0.328
93    S        -0.514  -0.517  -0.538  -0.343  -0.350  -0.348  -0.546  -0.549  -0.565
94    E        -0.514  -0.502  -0.522  -0.507  -0.465  -0.514  -0.546  -0.530  -0.545
95    Y        -0.514  -0.539  -0.542  -0.228  -0.276  -0.263  -0.546  -0.577  -0.572
96    G         0.279   0.284   0.326   0.306   0.324   0.382  -0.031  -0.023   0.039
97    A        -1.308  -1.305  -1.268  -1.064  -1.044  -0.999  -1.061  -1.056  -0.998
98    K         0.578   0.562   0.490   0.569   0.545   0.438   0.484   0.457   0.328
99    C        -0.649  -0.644  -0.607  -0.659  -0.672  -0.592  -0.718  -0.710  -0.653
100   N        -1.308  -1.305  -1.268  -1.120  -1.102  -1.054  -1.061  -1.056  -0.998
101   L         0.279   0.284   0.326  -0.165  -0.158  -0.086  -0.031  -0.023   0.039
102   E         1.866   1.871   1.917   1.809   1.828   1.887   2.030   2.037   2.103
103   K         0.279   0.282   0.324  -0.005   0.009   0.065  -0.031  -0.026   0.036
104   D         1.866   1.871   1.917   1.809   1.810   1.887   2.030   2.037   2.103
105   S        -0.514  -0.482  -0.520  -0.246  -0.184  -0.262  -0.546  -0.503  -0.543
106   E         0.578   0.593   0.502   0.456   0.491   0.306   0.484   0.508   0.347
107   V         1.866   1.871   1.917   1.824   1.844   1.902   2.030   2.037   2.103
108   H         0.578   0.558   0.491   0.734   0.728   0.578   0.484   0.450   0.329
109   A         0.578   0.558   0.491   0.631   0.599   0.481   0.484   0.450   0.329
110   L        -0.514  -0.520  -0.525  -0.605  -0.619  -0.597  -0.546  -0.552  -0.549
111   N        -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   R        -0.649  -0.644  -0.607  -0.400  -0.400  -0.331  -0.718  -0.710  -0.653
115   D         0.409   0.423   0.399   0.227   0.242   0.206   0.198   0.221   0.169
116   H         1.866   1.871   1.917   2.036   2.036   2.115   2.030   2.037   2.103
117   L        -0.649  -0.644  -0.607  -0.943  -0.929  -0.877  -0.718  -0.710  -0.653
118   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   A        -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/P38841
Output conservation file - output/P38841
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
