1     M         1.179   1.181   1.196   1.400   1.406   1.423   1.224   1.226   1.243
2     N        -1.236  -1.231  -1.204  -0.905  -0.899  -0.854  -1.141  -1.134  -1.086
3     Y        -0.344  -0.343  -0.318  -0.140  -0.141  -0.098  -0.550  -0.546  -0.504
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     L        -1.236  -1.231  -1.204  -1.276  -1.276  -1.220  -1.141  -1.134  -1.086
6     E         1.179   1.181   1.196   0.962   0.970   0.990   1.224   1.226   1.243
7     T        -1.236  -1.231  -1.204  -0.917  -0.910  -0.866  -1.141  -1.134  -1.086
8     Q        -0.220  -0.207  -0.265  -0.143  -0.125  -0.206  -0.353  -0.332  -0.420
9     L        -0.220  -0.251  -0.278  -0.454  -0.511  -0.546  -0.353  -0.401  -0.440
10    N        -0.220  -0.251  -0.278   0.004  -0.044  -0.090  -0.353  -0.401  -0.440
11    K        -1.236  -1.231  -1.204  -1.495  -1.489  -1.438  -1.141  -1.134  -1.086
12    K        -0.220  -0.251  -0.278  -0.684  -0.740  -0.787  -0.353  -0.401  -0.440
13    Q        -0.220  -0.251  -0.278  -0.403  -0.472  -0.550  -0.353  -0.401  -0.440
14    K        -1.236  -1.231  -1.204  -1.370  -1.347  -1.313  -1.141  -1.134  -1.086
15    Q        -1.236  -1.231  -1.204  -0.928  -0.915  -0.877  -1.141  -1.134  -1.086
16    I        -0.220  -0.192  -0.262  -0.454  -0.413  -0.521  -0.353  -0.310  -0.416
17    Q        -1.236  -1.231  -1.204  -1.036  -1.029  -0.983  -1.141  -1.134  -1.086
18    E        -0.220  -0.207  -0.265  -0.403  -0.383  -0.455  -0.353  -0.332  -0.420
19    Y        -0.220  -0.192  -0.262  -0.344  -0.307  -0.391  -0.353  -0.310  -0.416
20    E        -1.236  -1.231  -1.204  -1.643  -1.619  -1.584  -1.141  -1.134  -1.086
21    S        -1.236  -1.231  -1.204  -1.134  -1.151  -1.081  -1.141  -1.134  -1.086
22    M        -1.236  -1.231  -1.204  -1.011  -1.015  -0.959  -1.141  -1.134  -1.086
23    N        -1.236  -1.231  -1.204  -0.905  -0.897  -0.854  -1.141  -1.134  -1.086
24    G        -1.236  -1.231  -1.204  -1.329  -1.346  -1.273  -1.141  -1.134  -1.086
25    N        -1.236  -1.231  -1.204  -1.172  -1.156  -1.118  -1.141  -1.134  -1.086
26    L         1.179   1.181   1.196   1.005   1.008   1.033   1.224   1.226   1.243
27    I        -1.236  -1.231  -1.204  -1.356  -1.341  -1.300  -1.141  -1.134  -1.086
28    K        -0.220  -0.251  -0.278  -0.706  -0.760  -0.814  -0.353  -0.401  -0.440
29    M        -0.220  -0.192  -0.262  -0.484  -0.445  -0.522  -0.353  -0.310  -0.416
30    F         1.179   1.181   1.196   1.479   1.482   1.501   1.224   1.226   1.243
31    E        -1.236  -1.231  -1.204  -1.425  -1.416  -1.368  -1.141  -1.134  -1.086
32    Q        -0.220  -0.207  -0.265  -0.133  -0.115  -0.195  -0.353  -0.332  -0.420
33    L         1.179   1.181   1.196   1.005   1.008   1.033   1.224   1.226   1.243
34    S        -1.236  -1.231  -1.204  -0.882  -0.877  -0.831  -1.141  -1.134  -1.086
35    K        -0.220  -0.207  -0.265  -0.423  -0.406  -0.453  -0.353  -0.332  -0.420
36    E        -0.220  -0.251  -0.278  -0.383  -0.424  -0.446  -0.353  -0.401  -0.440
37    K        -1.236  -1.231  -1.204  -1.510  -1.483  -1.452  -1.141  -1.134  -1.086
38    K        -1.236  -1.231  -1.204  -1.147  -1.126  -1.093  -1.141  -1.134  -1.086
39    N        -1.236  -1.231  -1.204  -1.159  -1.161  -1.106  -1.141  -1.134  -1.086
40    D        -1.236  -1.231  -1.204  -0.940  -0.931  -0.889  -1.141  -1.134  -1.086
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    E         1.179   1.181   1.196   0.962   0.970   0.990   1.224   1.226   1.243
50    T        -0.220  -0.251  -0.278   0.048  -0.003  -0.052  -0.353  -0.401  -0.440
51    P         1.179   1.181   1.196   1.557   1.562   1.578   1.224   1.226   1.243
52    K        -1.236  -1.231  -1.204  -1.510  -1.479  -1.452  -1.141  -1.134  -1.086
53    K         1.179   1.181   1.196   0.852   0.860   0.881   1.224   1.226   1.243
54    I         1.179   1.181   1.196   1.175   1.174   1.201   1.224   1.226   1.243
55    S        -1.236  -1.231  -1.204  -1.048  -1.055  -0.995  -1.141  -1.134  -1.086
56    S        -1.236  -1.231  -1.204  -1.159  -1.155  -1.106  -1.141  -1.134  -1.086
57    T        -0.220  -0.192  -0.262  -0.464  -0.425  -0.498  -0.353  -0.310  -0.416
58    Y        -0.220  -0.192  -0.262   0.119   0.163   0.040  -0.353  -0.310  -0.416
59    I         1.179   1.181   1.196   1.175   1.174   1.201   1.224   1.226   1.243
60    K        -0.220  -0.207  -0.265  -0.505  -0.485  -0.549  -0.353  -0.332  -0.420
61    E        -1.236  -1.231  -1.204  -1.210  -1.190  -1.156  -1.141  -1.134  -1.086
62    L         1.179   1.181   1.196   1.005   1.008   1.033   1.224   1.226   1.243
63    K         1.179   1.181   1.196   0.852   0.860   0.881   1.224   1.226   1.243
64    E        -1.236  -1.231  -1.204  -1.383  -1.354  -1.327  -1.141  -1.134  -1.086
65    Y         1.179   1.181   1.196   1.400   1.406   1.423   1.224   1.226   1.243
66    N         1.179   1.181   1.196   1.380   1.387   1.403   1.224   1.226   1.243
67    E         1.179   1.181   1.196   0.962   0.970   0.990   1.224   1.226   1.243
68    L         1.179   1.181   1.196   1.005   1.008   1.033   1.224   1.226   1.243
69    R         1.179   1.181   1.196   1.420   1.424   1.442   1.224   1.226   1.243
70    D         1.179   1.181   1.196   1.319   1.325   1.343   1.224   1.226   1.243
71    A        -1.236  -1.231  -1.204  -0.905  -0.902  -0.854  -1.141  -1.134  -1.086
72    G         1.179   1.181   1.196   1.420   1.423   1.442   1.224   1.226   1.243
73    L         1.179   1.181   1.196   1.005   1.008   1.033   1.224   1.226   1.243
74    R        -0.220  -0.251  -0.278  -0.209  -0.280  -0.368  -0.353  -0.401  -0.440
75    L         1.179   1.181   1.196   1.005   1.008   1.033   1.224   1.226   1.243
76    A        -0.220  -0.207  -0.265  -0.023  -0.007  -0.097  -0.353  -0.332  -0.420
77    Q         1.179   1.181   1.196   1.217   1.220   1.242   1.224   1.226   1.243
78    I        -1.236  -1.231  -1.204  -0.940  -0.925  -0.889  -1.141  -1.134  -1.086
79    I        -0.220  -0.192  -0.262  -0.087  -0.044  -0.178  -0.353  -0.310  -0.416
80    A         1.179   1.181   1.196   1.360   1.362   1.383   1.224   1.226   1.243
81    D         1.179   1.181   1.196   1.319   1.325   1.343   1.224   1.226   1.243
82    E         1.179   1.181   1.196   0.962   0.970   0.990   1.224   1.226   1.243
83    K         1.179   1.181   1.196   0.852   0.860   0.881   1.224   1.226   1.243
84    Q        -0.220  -0.251  -0.278  -0.161  -0.209  -0.247  -0.353  -0.401  -0.440
85    C        -0.220  -0.251  -0.278   0.154   0.097   0.044  -0.353  -0.401  -0.440
86    K        -0.220  -0.251  -0.278  -0.484  -0.523  -0.538  -0.353  -0.401  -0.440
87    I        -0.220  -0.207  -0.265  -0.190  -0.175  -0.252  -0.353  -0.332  -0.420
88    K        -0.220  -0.251  -0.278  -0.474  -0.511  -0.525  -0.353  -0.401  -0.440
89    D        -0.220  -0.251  -0.278  -0.143  -0.199  -0.254  -0.353  -0.401  -0.440
90    V        -0.220  -0.251  -0.278  -0.087  -0.153  -0.209  -0.353  -0.401  -0.440
91    F         1.179   1.181   1.196   1.479   1.482   1.501   1.224   1.226   1.243
92    E         1.179   1.181   1.196   0.962   0.970   0.990   1.224   1.226   1.243
93    E         1.179   1.181   1.196   0.962   0.970   0.990   1.224   1.226   1.243
94    I         1.179   1.181   1.196   1.175   1.174   1.201   1.224   1.226   1.243
95    G         1.179   1.181   1.196   1.420   1.423   1.442   1.224   1.226   1.243
96    Y        -0.220  -0.251  -0.278  -0.087  -0.148  -0.209  -0.353  -0.401  -0.440
97    S        -0.220  -0.207  -0.265  -0.180  -0.155  -0.295  -0.353  -0.332  -0.420
98    M         1.179   1.181   1.196   1.400   1.406   1.423   1.224   1.226   1.243
99    K         1.179   1.181   1.196   0.852   0.860   0.881   1.224   1.226   1.243
100   D         1.179   1.181   1.196   1.319   1.325   1.343   1.224   1.226   1.243
101   -        -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/P89114
Output conservation file - output/P89114
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
