1     M         1.169   1.170   1.186   1.462   1.467   1.485   1.213   1.215   1.233
2     P         1.169   1.170   1.186   1.388   1.388   1.412   1.213   1.215   1.233
3     Q         1.169   1.170   1.186   1.534   1.539   1.557   1.213   1.215   1.233
4     L         1.169   1.170   1.186   0.542   0.549   0.574   1.213   1.215   1.233
5     V         1.169   1.170   1.186   1.276   1.269   1.301   1.213   1.215   1.233
6     P         1.169   1.170   1.186   1.388   1.388   1.412   1.213   1.215   1.233
7     F         1.169   1.170   1.186   1.200   1.210   1.226   1.213   1.215   1.233
8     Y         1.169   1.170   1.186   1.388   1.389   1.412   1.213   1.215   1.233
9     F        -0.228  -0.247  -0.281  -0.009  -0.023  -0.057  -0.361  -0.389  -0.440
10    M        -0.228  -0.235  -0.278  -0.043  -0.056  -0.165  -0.361  -0.371  -0.435
11    N         1.169   1.170   1.186   1.534   1.532   1.557   1.213   1.215   1.233
12    Q        -1.242  -1.239  -1.208  -1.501  -1.527  -1.448  -1.147  -1.142  -1.089
13    L         1.169   1.170   1.186   0.542   0.549   0.574   1.213   1.215   1.233
14    T        -0.228  -0.235  -0.278   0.075   0.059  -0.031  -0.361  -0.371  -0.435
15    Y        -1.242  -1.239  -1.208  -0.931  -0.921  -0.884  -1.147  -1.142  -1.089
16    G         1.169   1.170   1.186   1.606   1.606   1.628   1.213   1.215   1.233
17    F        -0.228  -0.247  -0.281  -0.289  -0.319  -0.402  -0.361  -0.389  -0.440
18    L        -0.228  -0.247  -0.281  -0.675  -0.691  -0.685  -0.361  -0.389  -0.440
19    L        -1.242  -1.239  -1.208  -1.501  -1.467  -1.448  -1.147  -1.142  -1.089
20    M        -1.242  -1.239  -1.208  -1.022  -1.021  -0.974  -1.147  -1.142  -1.089
21    I        -1.242  -1.239  -1.208  -1.068  -1.059  -1.020  -1.147  -1.142  -1.089
22    T        -1.242  -1.239  -1.208  -1.068  -1.086  -1.020  -1.147  -1.142  -1.089
23    L         1.169   1.170   1.186   0.542   0.549   0.574   1.213   1.215   1.233
24    L         1.169   1.170   1.186   0.542   0.549   0.574   1.213   1.215   1.233
25    I        -0.228  -0.195  -0.268  -0.112  -0.053  -0.208  -0.361  -0.309  -0.419
26    L        -0.228  -0.235  -0.278  -0.931  -0.940  -0.995  -0.361  -0.371  -0.435
27    F        -0.228  -0.195  -0.268  -0.164  -0.106  -0.245  -0.361  -0.309  -0.419
28    S        -0.228  -0.247  -0.281  -0.009  -0.040  -0.078  -0.361  -0.389  -0.440
29    Q        -1.242  -1.239  -1.208  -0.801  -0.803  -0.755  -1.147  -1.142  -1.089
30    F        -1.242  -1.239  -1.208  -1.188  -1.182  -1.138  -1.147  -1.142  -1.089
31    F        -1.242  -1.239  -1.208  -1.263  -1.263  -1.212  -1.147  -1.142  -1.089
32    L         1.169   1.170   1.186   0.542   0.549   0.574   1.213   1.215   1.233
33    P         1.169   1.170   1.186   1.388   1.388   1.412   1.213   1.215   1.233
34    M        -1.242  -1.239  -1.208  -0.716  -0.711  -0.671  -1.147  -1.142  -1.089
35    I        -1.242  -1.239  -1.208  -1.140  -1.135  -1.090  -1.147  -1.142  -1.089
36    L        -0.228  -0.235  -0.278  -0.675  -0.677  -0.685  -0.361  -0.371  -0.435
37    R        -0.228  -0.235  -0.278   0.221   0.209   0.156  -0.361  -0.371  -0.435
38    L         1.169   1.170   1.186   0.542   0.549   0.574   1.213   1.215   1.233
39    Y        -1.242  -1.239  -1.208  -1.529  -1.538  -1.476  -1.147  -1.142  -1.089
40    V        -0.228  -0.235  -0.278  -0.217  -0.242  -0.328  -0.361  -0.371  -0.435
41    S        -0.228  -0.247  -0.281  -0.009  -0.040  -0.078  -0.361  -0.389  -0.440
42    R         1.169   1.170   1.186   1.462   1.460   1.485   1.213   1.215   1.233
43    L        -1.242  -1.239  -1.208  -1.366  -1.329  -1.314  -1.147  -1.142  -1.089
44    F        -0.228  -0.195  -0.268  -0.345  -0.293  -0.415  -0.361  -0.309  -0.419
45    I         1.169   1.170   1.186   1.083   1.078   1.110   1.213   1.215   1.233
46    S        -0.228  -0.247  -0.281  -0.129  -0.166  -0.225  -0.361  -0.389  -0.440
47    K        -1.242  -1.239  -1.208  -0.737  -0.743  -0.692  -1.147  -1.142  -1.089
48    L        -0.228  -0.247  -0.281  -0.822  -0.844  -0.864  -0.361  -0.389  -0.440
* 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/P00856
Output conservation file - output/P00856
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
