1     M         0.644   0.674   0.713   0.923   0.917   0.936   0.656   0.693   0.745
2     T        -0.927  -1.112  -0.885  -0.861  -1.291  -1.020  -1.112  -1.411  -1.088
3     R         0.644   0.674   0.713   0.498   0.547   0.646   0.656   0.693   0.745
4     S        -2.053  -1.811  -1.797  -1.795  -1.489  -1.553  -2.077  -1.753  -1.674
5     S         0.644   0.674   0.713   0.665   0.698   0.760   0.656   0.693   0.745
6     V         0.644   0.674   0.713   0.361   0.431   0.553   0.656   0.693   0.745
7     L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
8     A        -0.134  -0.316  -0.843   0.111  -0.035  -0.767  -0.040  -0.253  -1.021
9     D         0.644   0.674   0.713   0.784   0.803   0.841   0.656   0.693   0.745
10    A        -0.596  -0.892  -0.859  -0.363  -0.723  -0.714  -0.630  -1.062  -1.046
11    L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
12    N        -0.895  -0.885  -1.781  -0.464  -0.441  -1.640  -0.684  -0.649  -1.656
13    A        -2.356  -2.212  -1.806  -2.457  -2.202  -1.664  -2.506  -2.196  -1.684
14    I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
15    N        -1.764  -1.958  -1.810  -1.520  -1.904  -1.736  -1.702  -1.908  -1.688
16    N         0.644   0.674   0.713   0.688   0.725   0.776   0.656   0.693   0.745
17    A         0.644   0.674   0.713   0.670   0.732   0.763   0.656   0.693   0.745
18    E         0.644   0.674   0.713   0.752   0.780   0.819   0.656   0.693   0.745
19    K        -0.596  -0.892  -0.859  -0.651  -1.072  -1.058  -0.630  -1.062  -1.046
20    T        -2.053  -2.193  -1.812  -1.857  -2.165  -1.696  -2.077  -2.174  -1.691
21    G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
22    K        -0.596  -0.892  -0.859  -0.651  -1.072  -1.058  -0.630  -1.062  -1.046
23    R         0.644   0.674   0.713   0.498   0.547   0.646   0.656   0.693   0.745
24    Q         0.644   0.674   0.713   0.806   0.813   0.856   0.656   0.693   0.745
25    V         0.644   0.674   0.713   0.361   0.431   0.553   0.656   0.693   0.745
26    L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
27    I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
28    R         0.644   0.674   0.713   0.498   0.547   0.646   0.656   0.693   0.745
29    P         0.644   0.674   0.713   0.940   0.934   0.948   0.656   0.693   0.745
30    S        -0.134  -0.168  -0.837   0.091   0.068  -0.840  -0.040  -0.072  -1.012
31    S         0.644   0.674   0.713   0.665   0.698   0.760   0.656   0.693   0.745
32    K         0.644   0.674   0.713   0.475   0.549   0.630   0.656   0.693   0.745
33    V         0.644   0.674   0.713   0.361   0.431   0.553   0.656   0.693   0.745
34    I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
35    I        -0.927  -1.004  -0.884  -1.295  -1.424  -1.242  -1.112  -1.237  -1.086
36    K         0.644   0.674   0.713   0.475   0.549   0.630   0.656   0.693   0.745
37    F         0.644   0.674   0.713   0.806   0.821   0.856   0.656   0.693   0.745
38    L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
39    Q        -1.452  -1.151  -0.883  -1.624  -1.149  -0.798  -1.970  -1.474  -1.085
40    V         0.644   0.674   0.713   0.361   0.431   0.553   0.656   0.693   0.745
41    M         0.644   0.674   0.713   0.923   0.917   0.936   0.656   0.693   0.745
42    Q         0.644   0.674   0.713   0.806   0.813   0.856   0.656   0.693   0.745
43    K        -1.339  -0.854  -1.773  -1.208  -0.583  -1.731  -1.220  -0.614  -1.647
44    H         0.644   0.674   0.713   0.874   0.885   0.902   0.656   0.693   0.745
45    G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
46    Y         0.644   0.674   0.713   0.896   0.911   0.917   0.656   0.693   0.745
47    I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
48    G        -1.339  -1.646  -1.799  -1.166  -1.541  -1.703  -1.220  -1.592  -1.676
49    E         0.644   0.674   0.713   0.752   0.780   0.819   0.656   0.693   0.745
50    F         0.644   0.674   0.713   0.806   0.821   0.856   0.656   0.693   0.745
51    E        -0.927  -1.079  -0.885  -0.779  -1.054  -0.827  -1.112  -1.358  -1.087
52    Y        -0.927  -1.112  -0.885  -0.646  -1.024  -0.771  -1.112  -1.411  -1.088
53    I        -0.927  -0.946  -0.882  -1.295  -1.320  -1.238  -1.112  -1.146  -1.082
54    D         0.644   0.674   0.713   0.784   0.803   0.841   0.656   0.693   0.745
55    D         0.644   0.674   0.713   0.784   0.803   0.841   0.656   0.693   0.745
56    H         0.644   0.674   0.713   0.874   0.885   0.902   0.656   0.693   0.745
57    R         0.644   0.674   0.713   0.498   0.547   0.646   0.656   0.693   0.745
58    S         0.644   0.674   0.713   0.665   0.698   0.760   0.656   0.693   0.745
59    G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
60    K         0.644   0.674   0.713   0.475   0.549   0.630   0.656   0.693   0.745
61    I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
62    V         0.644   0.674   0.713   0.361   0.431   0.553   0.656   0.693   0.745
63    V        -0.596  -0.892  -0.859  -0.792  -1.229  -1.191  -0.630  -1.062  -1.046
64    Q        -0.134  -0.168  -0.837   0.238   0.188  -0.727  -0.040  -0.072  -1.012
65    L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
66    N         0.644   0.674   0.713   0.688   0.725   0.776   0.656   0.693   0.745
67    G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
68    R         0.644   0.674   0.713   0.498   0.547   0.646   0.656   0.693   0.745
69    L        -1.339  -1.767  -1.805  -1.206  -1.791  -1.777  -1.220  -1.710  -1.683
70    N         0.644   0.674   0.713   0.688   0.725   0.776   0.656   0.693   0.745
71    K         0.644   0.674   0.713   0.475   0.549   0.630   0.656   0.693   0.745
72    C         0.644   0.674   0.713   1.055   1.021   1.026   0.656   0.693   0.745
73    G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
74    V         0.644   0.674   0.713   0.361   0.431   0.553   0.656   0.693   0.745
75    I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
76    S        -0.596  -0.171  -0.835  -0.410   0.074  -0.783  -0.630  -0.075  -1.008
77    P         0.644   0.674   0.713   0.940   0.934   0.948   0.656   0.693   0.745
78    R         0.644   0.674   0.713   0.498   0.547   0.646   0.656   0.693   0.745
79    F        -0.134  -0.316  -0.843   0.249   0.056  -0.682  -0.040  -0.253  -1.021
80    N         0.644   0.674   0.713   0.688   0.725   0.776   0.656   0.693   0.745
81    V         0.644   0.674   0.713   0.361   0.431   0.553   0.656   0.693   0.745
82    K        -0.134  -0.316  -0.843  -0.113  -0.266  -1.030  -0.040  -0.253  -1.021
83    I        -2.053  -1.822  -1.808  -2.371  -2.108  -2.017  -2.077  -1.843  -1.686
84    G        -3.987  -3.462  -2.995  -3.939  -3.214  -2.574  -3.363  -2.732  -2.185
85    D        -0.134  -0.316  -0.843   0.216   0.020  -0.750  -0.040  -0.253  -1.021
86    I        -2.970  -2.576  -2.472  -3.163  -2.511  -2.362  -2.774  -2.193  -1.996
87    E         0.644   0.674   0.713   0.752   0.780   0.819   0.656   0.693   0.745
88    K        -1.165  -0.636  -0.850  -1.522  -0.680  -1.042  -1.488  -0.685  -1.032
89    W         0.644   0.674   0.713   1.064   1.035   1.032   0.656   0.693   0.745
90    T        -1.867  -1.750  -1.797  -1.857  -1.859  -1.881  -1.970  -1.795  -1.674
91    A        -3.801  -3.507  -2.997  -3.500  -3.092  -2.497  -3.256  -2.755  -2.187
92    N        -1.339  -1.767  -1.805  -0.969  -1.552  -1.680  -1.220  -1.710  -1.683
93    L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
94    L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
95    P         0.644   0.674   0.713   0.940   0.934   0.948   0.656   0.693   0.745
96    A        -1.165  -1.154  -0.884  -1.272  -1.300  -0.923  -1.488  -1.479  -1.086
97    R         0.644   0.674   0.713   0.498   0.547   0.646   0.656   0.693   0.745
98    Q         0.644   0.674   0.713   0.806   0.813   0.856   0.656   0.693   0.745
99    F        -0.596  -0.892  -0.859  -0.342  -0.852  -0.923  -0.630  -1.062  -1.046
100   G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
101   Y        -0.596  -0.892  -0.859  -0.252  -0.765  -0.871  -0.630  -1.062  -1.046
102   V        -1.165  -1.154  -0.884  -1.693  -1.719  -1.243  -1.488  -1.479  -1.086
103   I        -0.596  -0.892  -0.859  -0.808  -1.225  -1.194  -0.630  -1.062  -1.046
104   L         0.644   0.674   0.713   0.494   0.565   0.643   0.656   0.693   0.745
105   T         0.644   0.674   0.713   0.779   0.823   0.838   0.656   0.693   0.745
106   T         0.644   0.674   0.713   0.779   0.823   0.838   0.656   0.693   0.745
107   S         0.644   0.674   0.713   0.665   0.698   0.760   0.656   0.693   0.745
108   A        -0.596  -0.892  -0.859  -0.456  -0.896  -0.946  -0.630  -1.062  -1.046
109   G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
110   I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
111   M         0.644   0.674   0.713   0.923   0.917   0.936   0.656   0.693   0.745
112   D        -0.596  -0.892  -0.859  -0.315  -0.775  -0.812  -0.630  -1.062  -1.046
113   H         0.644   0.674   0.713   0.874   0.885   0.902   0.656   0.693   0.745
114   E        -0.596  -0.892  -0.859  -0.343  -0.787  -0.821  -0.630  -1.062  -1.046
115   E         0.644   0.674   0.713   0.752   0.780   0.819   0.656   0.693   0.745
116   A         0.644   0.674   0.713   0.670   0.732   0.763   0.656   0.693   0.745
117   R        -0.596  -0.154  -0.833  -0.564  -0.051  -0.851  -0.630  -0.054  -1.006
118   R        -0.596  -0.892  -0.859  -0.599  -1.005  -0.971  -0.630  -1.062  -1.046
119   K        -0.596  -0.563  -0.859  -0.651  -0.578  -1.058  -0.630  -0.581  -1.046
120   H        -0.596  -0.892  -0.859  -0.207  -0.660  -0.714  -0.630  -1.062  -1.046
121   V        -0.596  -0.892  -0.859  -0.736  -1.117  -1.049  -0.630  -1.062  -1.046
122   S        -2.245  -2.166  -1.812  -2.300  -2.212  -1.751  -2.345  -2.142  -1.690
123   G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
124   K         0.644   0.674   0.713   0.475   0.549   0.630   0.656   0.693   0.745
125   I         0.644   0.674   0.713   0.342   0.438   0.540   0.656   0.693   0.745
126   L        -0.134  -0.316  -0.843  -0.106  -0.266  -1.082  -0.040  -0.253  -1.021
127   G         0.644   0.674   0.713   0.475   0.557   0.630   0.656   0.693   0.745
128   F         0.644   0.674   0.713   0.806   0.821   0.856   0.656   0.693   0.745
129   V        -1.327  -1.134  -0.868  -1.765  -1.346  -0.946  -1.756  -1.446  -1.060
130   Y         0.644   0.674   0.713   0.896   0.911   0.917   0.656   0.693   0.745
* 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/P0C0W1
Output conservation file - output/P0C0W1
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
