1     M         0.985   0.986   1.003   1.045   1.054   1.072   1.019   1.020   1.041
2     F        -0.177  -0.158  -0.339  -0.033  -0.005  -0.324  -0.267  -0.238  -0.521
3     L        -1.285  -1.281  -1.205  -1.262  -1.263  -1.140  -1.268  -1.261  -1.151
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    Q        -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    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    M        -1.285  -1.281  -1.205  -1.302  -1.293  -1.178  -1.268  -1.261  -1.151
18    P        -0.447  -0.445  -0.390  -0.492  -0.491  -0.402  -0.696  -0.691  -0.602
19    R        -1.163  -1.116  -1.171  -1.262  -1.194  -1.250  -1.125  -1.066  -1.113
20    M        -1.879  -1.872  -1.783  -1.541  -1.537  -1.407  -1.553  -1.544  -1.425
21    F        -1.163  -1.175  -1.188  -1.161  -1.174  -1.174  -1.125  -1.137  -1.133
22    L        -0.177  -0.197  -0.321  -0.211  -0.240  -0.417  -0.267  -0.297  -0.491
23    H        -0.177  -0.215  -0.348   0.047  -0.004  -0.193  -0.267  -0.325  -0.535
24    M        -1.285  -1.281  -1.205  -1.182  -1.177  -1.063  -1.268  -1.261  -1.151
25    K        -1.285  -1.281  -1.205  -1.530  -1.531  -1.397  -1.268  -1.261  -1.151
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    P        -1.163  -1.198  -1.179  -1.383  -1.438  -1.403  -1.125  -1.164  -1.122
28    S        -0.447  -0.445  -0.390  -0.694  -0.688  -0.594  -0.696  -0.691  -0.602
29    P        -1.163  -1.153  -1.186  -0.941  -0.938  -0.973  -1.125  -1.112  -1.129
30    I        -1.879  -1.872  -1.783  -1.849  -1.826  -1.702  -1.553  -1.544  -1.425
31    T        -1.163  -1.153  -1.186  -1.062  -1.047  -1.109  -1.125  -1.112  -1.129
32    I        -1.163  -1.153  -1.186  -0.948  -0.925  -1.008  -1.125  -1.112  -1.129
33    T        -0.177  -0.215  -0.348  -0.238  -0.297  -0.489  -0.267  -0.325  -0.535
34    R        -1.163  -1.164  -1.180  -1.360  -1.354  -1.377  -1.125  -1.124  -1.123
35    A        -1.163  -1.175  -1.188  -0.988  -1.003  -1.039  -1.125  -1.137  -1.133
36    C        -1.163  -1.175  -1.188  -0.974  -0.989  -0.983  -1.125  -1.137  -1.133
37    T        -1.879  -1.872  -1.783  -1.739  -1.723  -1.597  -1.553  -1.544  -1.425
38    V        -1.163  -1.175  -1.188  -1.270  -1.292  -1.309  -1.125  -1.137  -1.133
39    P        -1.285  -1.278  -1.205  -1.511  -1.489  -1.379  -1.268  -1.257  -1.151
40    S        -0.330  -0.290  -0.352  -0.432  -0.366  -0.471  -0.505  -0.440  -0.541
41    L        -0.330  -0.365  -0.364  -0.473  -0.533  -0.535  -0.505  -0.560  -0.561
42    L        -0.330  -0.323  -0.363  -0.401  -0.386  -0.481  -0.505  -0.493  -0.559
43    S        -0.330  -0.323  -0.363  -0.432  -0.424  -0.504  -0.505  -0.493  -0.559
44    V        -0.330  -0.323  -0.363  -0.442  -0.432  -0.517  -0.505  -0.493  -0.559
45    A        -0.330  -0.365  -0.364  -0.167  -0.225  -0.241  -0.505  -0.560  -0.561
46    A        -0.330  -0.365  -0.364  -0.263  -0.328  -0.363  -0.505  -0.560  -0.561
47    P        -1.285  -1.278  -1.205  -1.248  -1.249  -1.126  -1.268  -1.257  -1.151
48    Q        -1.285  -1.278  -1.205  -1.274  -1.251  -1.152  -1.268  -1.257  -1.151
49    P         0.985   0.986   1.003   1.022   1.026   1.050   1.019   1.020   1.041
50    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    P        -0.447  -0.444  -0.386  -0.646  -0.640  -0.534  -0.696  -0.690  -0.596
58    L         0.985   0.986   1.003   0.882   0.885   0.916   1.019   1.020   1.041
59    V        -1.285  -1.279  -1.205  -1.443  -1.424  -1.313  -1.268  -1.258  -1.151
60    F        -0.330  -0.360  -0.364  -0.296  -0.350  -0.376  -0.505  -0.553  -0.561
61    N        -1.163  -1.164  -1.180  -0.915  -0.915  -0.939  -1.125  -1.124  -1.123
62    R         0.985   0.986   1.003   0.799   0.803   0.836   1.019   1.020   1.041
63    G         0.985   0.986   1.003   1.093   1.095   1.118   1.019   1.020   1.041
64    F         0.985   0.986   1.003   1.109   1.110   1.133   1.019   1.020   1.041
65    K         0.985   0.986   1.003   0.782   0.785   0.820   1.019   1.020   1.041
66    V         0.985   0.986   1.003   0.866   0.866   0.900   1.019   1.020   1.041
67    R         0.985   0.986   1.003   0.799   0.803   0.836   1.019   1.020   1.041
68    T         0.985   0.986   1.003   1.077   1.076   1.103   1.019   1.020   1.041
69    S         0.985   0.986   1.003   0.981   0.987   1.010   1.019   1.020   1.041
70    V        -0.177  -0.158  -0.339  -0.184  -0.161  -0.389  -0.267  -0.238  -0.521
71    K         0.985   0.986   1.003   0.782   0.785   0.820   1.019   1.020   1.041
72    K         0.985   0.986   1.003   0.782   0.785   0.820   1.019   1.020   1.041
73    F        -0.177  -0.123  -0.321  -0.013   0.067  -0.259  -0.267  -0.186  -0.492
74    C         0.985   0.986   1.003   1.156   1.158   1.179   1.019   1.020   1.041
75    S        -1.163  -1.164  -1.180  -1.197  -1.200  -1.241  -1.125  -1.124  -1.123
76    D         0.985   0.986   1.003   1.296   1.298   1.312   1.019   1.020   1.041
77    C         0.985   0.986   1.003   1.156   1.158   1.179   1.019   1.020   1.041
78    Y         0.985   0.986   1.003   1.172   1.174   1.194   1.019   1.020   1.041
79    L        -1.163  -1.153  -1.186  -1.035  -1.028  -1.076  -1.125  -1.112  -1.129
80    V         0.985   0.986   1.003   0.866   0.866   0.900   1.019   1.020   1.041
81    R         0.985   0.986   1.003   0.799   0.803   0.836   1.019   1.020   1.041
82    R         0.985   0.986   1.003   0.799   0.803   0.836   1.019   1.020   1.041
83    K         0.985   0.986   1.003   0.782   0.785   0.820   1.019   1.020   1.041
84    G         0.985   0.986   1.003   1.093   1.095   1.118   1.019   1.020   1.041
85    R         0.985   0.986   1.003   0.799   0.803   0.836   1.019   1.020   1.041
86    V         0.985   0.986   1.003   0.866   0.866   0.900   1.019   1.020   1.041
87    Y         0.985   0.986   1.003   1.172   1.174   1.194   1.019   1.020   1.041
88    I        -0.177  -0.215  -0.348  -0.184  -0.238  -0.400  -0.267  -0.325  -0.535
89    Y         0.985   0.986   1.003   1.172   1.174   1.194   1.019   1.020   1.041
90    C         0.985   0.986   1.003   1.156   1.158   1.179   1.019   1.020   1.041
91    K         0.985   0.986   1.003   0.782   0.785   0.820   1.019   1.020   1.041
92    S         0.985   0.986   1.003   0.981   0.987   1.010   1.019   1.020   1.041
93    N         0.985   0.986   1.003   1.093   1.097   1.118   1.019   1.020   1.041
94    K        -0.177  -0.197  -0.321  -0.314  -0.342  -0.511  -0.267  -0.297  -0.491
95    K         0.985   0.986   1.003   0.782   0.785   0.820   1.019   1.020   1.041
96    H         0.985   0.986   1.003   1.280   1.281   1.298   1.019   1.020   1.041
97    K         0.985   0.986   1.003   0.782   0.785   0.820   1.019   1.020   1.041
98    Q         0.985   0.986   1.003   1.172   1.173   1.194   1.019   1.020   1.041
99    R         0.985   0.986   1.003   0.799   0.803   0.836   1.019   1.020   1.041
100   Q         0.985   0.986   1.003   1.172   1.173   1.194   1.019   1.020   1.041
101   G         0.985   0.986   1.003   1.093   1.095   1.118   1.019   1.020   1.041
* 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/O14464
Output conservation file - output/O14464
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
