1     M         1.107   1.110   1.138   1.521   1.521   1.535   1.170   1.172   1.208
2     H        -0.202  -0.162  -0.346   0.047   0.107  -0.190  -0.260  -0.200  -0.481
3     A        -0.202  -0.162  -0.346  -0.128  -0.058  -0.393  -0.260  -0.200  -0.481
4     R        -1.313  -1.284  -1.322  -0.940  -0.896  -0.930  -1.213  -1.176  -1.191
5     D         1.107   1.110   1.138   1.292   1.295   1.322   1.170   1.172   1.208
6     W         1.107   1.110   1.138   1.446   1.445   1.464   1.170   1.172   1.208
7     F        -0.202  -0.195  -0.351  -0.500  -0.497  -0.803  -0.260  -0.250  -0.488
8     L         1.107   1.110   1.138   0.678   0.673   0.749   1.170   1.172   1.208
9     V         1.107   1.110   1.138   1.253   1.251   1.285   1.170   1.172   1.208
10    F        -0.202  -0.195  -0.351  -0.500  -0.497  -0.803  -0.260  -0.250  -0.488
11    I        -0.506  -0.503  -0.424  -0.630  -0.629  -0.468  -0.737  -0.730  -0.604
12    A        -0.506  -0.503  -0.424  -0.747  -0.722  -0.575  -0.737  -0.730  -0.604
13    I        -0.506  -0.503  -0.424  -0.821  -0.816  -0.644  -0.737  -0.730  -0.604
14    F         1.107   1.110   1.138   0.993   0.989   1.043   1.170   1.172   1.208
15    I        -0.202  -0.204  -0.346  -0.641  -0.651  -0.799  -0.260  -0.262  -0.481
16    P         1.107   1.110   1.138   1.273   1.273   1.303   1.170   1.172   1.208
17    P         1.107   1.110   1.138   1.273   1.273   1.303   1.170   1.172   1.208
18    L        -0.202  -0.204  -0.346  -0.237  -0.247  -0.561  -0.260  -0.262  -0.481
19    A        -0.506  -0.503  -0.424  -0.574  -0.569  -0.415  -0.737  -0.730  -0.604
20    V         1.107   1.110   1.138   1.253   1.251   1.285   1.170   1.172   1.208
21    W        -1.313  -1.284  -1.322  -1.376  -1.312  -1.481  -1.213  -1.176  -1.191
22    L        -0.202  -0.204  -0.346  -0.297  -0.305  -0.613  -0.260  -0.262  -0.481
23    K         1.107   1.110   1.138   1.465   1.463   1.482   1.170   1.172   1.208
24    R         1.107   1.110   1.138   1.408   1.408   1.429   1.170   1.172   1.208
25    G         1.107   1.110   1.138   1.034   1.055   1.081   1.170   1.172   1.208
26    F        -0.202  -0.195  -0.351  -0.330  -0.326  -0.540  -0.260  -0.250  -0.488
27    F        -0.202  -0.195  -0.351  -0.317  -0.307  -0.520  -0.260  -0.250  -0.488
28    T        -0.506  -0.503  -0.424  -0.435  -0.411  -0.284  -0.737  -0.730  -0.604
29    K        -0.506  -0.503  -0.424  -0.435  -0.427  -0.284  -0.737  -0.730  -0.604
30    D         1.107   1.110   1.138   1.292   1.295   1.322   1.170   1.172   1.208
31    L        -0.202  -0.204  -0.346  -0.500  -0.512  -0.792  -0.260  -0.262  -0.481
32    L        -0.506  -0.503  -0.424  -0.851  -0.869  -0.678  -0.737  -0.730  -0.604
33    I        -0.202  -0.234  -0.348  -0.297  -0.366  -0.617  -0.260  -0.308  -0.483
34    N         1.107   1.110   1.138   1.427   1.429   1.447   1.170   1.172   1.208
35    F        -1.313  -1.335  -1.324  -1.359  -1.400  -1.361  -1.213  -1.236  -1.194
36    L         1.107   1.110   1.138   0.678   0.673   0.749   1.170   1.172   1.208
37    L         1.107   1.110   1.138   0.678   0.673   0.749   1.170   1.172   1.208
38    F        -0.506  -0.503  -0.424  -0.559  -0.569  -0.405  -0.737  -0.730  -0.604
39    L         1.107   1.110   1.138   0.678   0.673   0.749   1.170   1.172   1.208
40    L         1.107   1.110   1.138   0.678   0.673   0.749   1.170   1.172   1.208
41    G         1.107   1.110   1.138   1.034   1.055   1.081   1.170   1.172   1.208
42    F         1.107   1.110   1.138   0.993   0.989   1.043   1.170   1.172   1.208
43    F        -0.202  -0.162  -0.346  -0.500  -0.435  -0.792  -0.260  -0.200  -0.481
44    P         1.107   1.110   1.138   1.273   1.273   1.303   1.170   1.172   1.208
45    G         1.107   1.110   1.138   1.034   1.055   1.081   1.170   1.172   1.208
46    L         1.107   1.110   1.138   0.678   0.673   0.749   1.170   1.172   1.208
47    I        -0.506  -0.503  -0.424  -1.054  -1.041  -0.858  -0.737  -0.730  -0.604
48    H         1.107   1.110   1.138   1.350   1.350   1.376   1.170   1.172   1.208
49    A        -1.313  -1.284  -1.322  -1.082  -1.030  -1.045  -1.213  -1.176  -1.191
50    L        -0.506  -0.503  -0.424  -1.006  -1.016  -0.821  -0.737  -0.730  -0.604
51    Y        -0.202  -0.234  -0.348   0.004  -0.042  -0.197  -0.260  -0.308  -0.483
52    V        -0.506  -0.503  -0.424  -0.630  -0.627  -0.467  -0.737  -0.730  -0.604
53    I         1.107   1.110   1.138   1.194   1.193   1.230   1.170   1.172   1.208
54    S        -0.202  -0.195  -0.351  -0.257  -0.232  -0.590  -0.260  -0.250  -0.488
55    C        -2.120  -2.116  -1.985  -1.675  -1.661  -1.440  -1.690  -1.682  -1.510
56    H        -0.506  -0.503  -0.424  -0.517  -0.508  -0.362  -0.737  -0.730  -0.604
57    P         1.107   1.110   1.138   1.273   1.273   1.303   1.170   1.172   1.208
58    Y         1.107   1.110   1.138   1.253   1.257   1.285   1.170   1.172   1.208
59    E        -1.313  -1.284  -1.322  -0.932  -0.880  -0.954  -1.213  -1.176  -1.191
60    E        -1.313  -1.309  -1.290  -0.994  -0.984  -0.964  -1.213  -1.206  -1.156
61    N        -2.120  -2.116  -1.985  -1.704  -1.685  -1.468  -1.690  -1.682  -1.510
62    E        -0.375  -0.469  -0.410  -0.279  -0.411  -0.289  -0.525  -0.674  -0.582
63    A         1.107   1.110   1.138   1.242   1.230   1.274   1.170   1.172   1.208
64    R        -1.450  -1.416  -1.337  -1.204  -1.142  -1.002  -1.372  -1.330  -1.208
65    Y        -0.375  -0.469  -0.410  -0.914  -1.059  -0.880  -0.525  -0.674  -0.582
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    S        -0.202  -0.204  -0.346  -0.277  -0.255  -0.478  -0.260  -0.262  -0.481
70    H        -0.202  -0.234  -0.348   0.047  -0.005  -0.193  -0.260  -0.308  -0.483
71    L        -1.313  -1.335  -1.324  -1.281  -1.326  -1.361  -1.213  -1.236  -1.194
72    S        -2.120  -2.116  -1.985  -2.102  -2.111  -1.837  -1.690  -1.682  -1.510
73    S        -0.506  -0.503  -0.424  -0.490  -0.476  -0.338  -0.737  -0.730  -0.604
74    S        -0.202  -0.234  -0.348  -0.027  -0.060  -0.231  -0.260  -0.308  -0.483
75    D        -1.313  -1.330  -1.294  -1.180  -1.203  -1.129  -1.213  -1.230  -1.160
76    D        -0.202  -0.234  -0.348   0.090   0.046  -0.093  -0.260  -0.308  -0.483
77    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    Y         1.107   1.110   1.138   1.253   1.257   1.285   1.170   1.172   1.208
79    G         1.107   1.110   1.138   1.034   1.055   1.081   1.170   1.172   1.208
80    S        -0.506  -0.503  -0.424  -0.602  -0.585  -0.441  -0.737  -0.730  -0.604
81    L        -1.313  -1.335  -1.324  -1.114  -1.151  -1.176  -1.213  -1.236  -1.194
82    A        -2.120  -2.116  -1.985  -1.824  -1.815  -1.579  -1.690  -1.682  -1.510
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -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/P56508
Output conservation file - output/P56508
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
