1     M         0.812   0.821   0.868   1.106   1.105   1.140   0.843   0.856   0.919
2     A        -0.063  -0.149  -0.361   0.121  -0.016  -0.408  -0.095  -0.226  -0.581
3     H         0.812   0.821   0.868   0.881   0.894   0.955   0.843   0.856   0.919
4     E         0.812   0.821   0.868   1.002   1.006   1.054   0.843   0.856   0.919
5     N        -0.464  -0.448  -0.413  -0.615  -0.602  -0.587  -0.720  -0.703  -0.670
6     V        -0.063  -0.216  -0.361   0.256   0.028  -0.255  -0.095  -0.327  -0.581
7     W         0.812   0.821   0.868   1.106   1.105   1.140   0.843   0.856   0.919
8     F        -0.887  -0.877  -1.130  -0.717  -0.712  -1.079  -0.876  -0.872  -1.166
9     S         0.812   0.821   0.868   0.694   0.730   0.802   0.843   0.856   0.919
10    H        -0.063  -0.149  -0.361   0.011  -0.125  -0.580  -0.095  -0.226  -0.581
11    P         0.812   0.821   0.868   1.106   1.105   1.140   0.843   0.856   0.919
12    R         0.812   0.821   0.868   0.384   0.422   0.549   0.843   0.856   0.919
13    R        -2.494  -2.374  -2.136  -2.548  -2.331  -2.003  -2.126  -1.999  -1.661
14    Y        -0.645  -0.532  -0.412  -0.818  -0.609  -0.442  -1.032  -0.847  -0.669
15    G         0.812   0.821   0.868   0.662   0.683   0.776   0.843   0.856   0.919
16    K         0.812   0.821   0.868   0.773   0.782   0.866   0.843   0.856   0.919
17    G         0.812   0.821   0.868   0.662   0.683   0.776   0.843   0.856   0.919
18    S        -0.063  -0.216  -0.361  -0.133  -0.337  -0.606  -0.095  -0.327  -0.581
19    R         0.812   0.821   0.868   0.384   0.422   0.549   0.843   0.856   0.919
20    Q        -0.887  -1.092  -1.147  -0.603  -0.940  -1.130  -0.876  -1.142  -1.188
21    C         0.812   0.821   0.868   0.912   0.931   0.980   0.843   0.856   0.919
22    R        -0.063  -0.063  -0.353  -0.395  -0.371  -0.699  -0.095  -0.098  -0.568
23    V        -1.490  -1.409  -1.186  -1.505  -1.403  -1.077  -1.657  -1.550  -1.234
24    C        -1.227  -1.177  -1.166  -1.132  -1.077  -1.065  -1.345  -1.305  -1.212
25    S        -1.912  -1.965  -1.716  -2.079  -2.116  -1.669  -1.813  -1.832  -1.497
26    S        -1.649  -1.804  -1.705  -1.730  -1.976  -1.864  -1.501  -1.663  -1.487
27    H        -1.649  -1.804  -1.705  -1.546  -1.811  -1.756  -1.501  -1.663  -1.487
28    T        -2.335  -2.285  -2.129  -2.161  -2.136  -1.791  -1.970  -1.918  -1.657
29    G        -0.063  -0.216  -0.361  -0.117  -0.318  -0.507  -0.095  -0.327  -0.581
30    L        -0.063  -0.216  -0.361   0.209   0.000  -0.241  -0.095  -0.327  -0.581
31    I         0.812   0.821   0.868   0.881   0.884   0.955   0.843   0.856   0.919
32    R         0.812   0.821   0.868   0.384   0.422   0.549   0.843   0.856   0.919
33    K         0.812   0.821   0.868   0.773   0.782   0.866   0.843   0.856   0.919
34    Y         0.812   0.821   0.868   0.957   0.963   1.017   0.843   0.856   0.919
35    G        -0.063   0.037  -0.342  -0.096   0.035  -0.428  -0.095   0.043  -0.550
36    L         0.812   0.821   0.868   0.972   0.980   1.030   0.843   0.856   0.919
37    N        -0.063   0.094  -0.337   0.091   0.271  -0.284  -0.095   0.121  -0.541
38    I        -0.464  -0.462  -0.415  -0.481  -0.495  -0.427  -0.720  -0.726  -0.673
39    C        -0.887  -0.800  -1.127  -0.650  -0.533  -1.043  -0.876  -0.769  -1.163
40    R         0.812   0.821   0.868   0.384   0.422   0.549   0.843   0.856   0.919
41    Q         0.812   0.821   0.868   1.017   1.024   1.067   0.843   0.856   0.919
42    C        -0.645  -0.603  -0.428  -0.941  -0.876  -0.594  -1.032  -0.972  -0.696
43    F         0.812   0.821   0.868   0.835   0.856   0.917   0.843   0.856   0.919
44    R         0.812   0.821   0.868   0.384   0.422   0.549   0.843   0.856   0.919
45    E         0.812   0.821   0.868   1.002   1.006   1.054   0.843   0.856   0.919
46    K        -0.887  -0.799  -1.119  -0.868  -0.742  -1.283  -0.876  -0.768  -1.153
47    A         0.812   0.821   0.868   0.942   0.939   1.005   0.843   0.856   0.919
48    N        -1.227  -1.137  -1.154  -1.263  -1.155  -1.167  -1.345  -1.245  -1.197
49    D         0.812   0.821   0.868   1.062   1.069   1.103   0.843   0.856   0.919
50    I         0.812   0.821   0.868   0.881   0.884   0.955   0.843   0.856   0.919
51    G         0.812   0.821   0.868   0.662   0.683   0.776   0.843   0.856   0.919
52    F         0.812   0.821   0.868   0.835   0.856   0.917   0.843   0.856   0.919
53    N        -1.912  -1.819  -1.707  -1.694  -1.560  -1.350  -1.813  -1.709  -1.489
54    K         0.812   0.821   0.868   0.773   0.782   0.866   0.843   0.856   0.919
55    F        -1.330  -1.315  -1.165  -1.398  -1.358  -1.113  -1.501  -1.453  -1.211
56    R         0.812   0.821   0.868   0.384   0.422   0.549   0.843   0.856   0.919
* 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/P41057
Output conservation file - output/P41057
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
