1     M         1.008   1.017   1.057   1.356   1.344   1.372   1.028   1.045   1.110
2     S        -0.344  -0.447  -0.405  -0.232  -0.422  -0.479  -0.443  -0.615  -0.599
3     D        -0.344  -0.444  -0.384  -0.113  -0.290  -0.281  -0.443  -0.611  -0.565
4     A        -0.745  -0.647  -0.420  -1.020  -0.855  -0.527  -1.074  -0.936  -0.624
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     V         0.118   0.321  -0.320   0.252   0.490  -0.293   0.188   0.431  -0.464
9     T         1.008   1.017   1.057   1.134   1.135   1.196   1.028   1.045   1.110
10    I         0.118  -0.023  -0.337   0.532   0.343  -0.193   0.188   0.001  -0.490
11    R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
12    T         1.008   1.017   1.057   1.134   1.135   1.196   1.028   1.045   1.110
13    R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
14    K         1.008   1.017   1.057   0.570   0.613   0.747   1.028   1.045   1.110
15    V        -0.745  -0.620  -0.398  -0.945  -0.702  -0.406  -1.074  -0.892  -0.588
16    I        -0.344  -0.444  -0.384   0.023  -0.161  -0.128  -0.443  -0.611  -0.565
17    S        -1.699  -1.627  -1.278  -1.744  -1.738  -1.259  -1.704  -1.608  -1.195
18    N         1.008   1.017   1.057   1.216   1.237   1.261   1.028   1.045   1.110
19    P        -0.344  -0.444  -0.384  -0.110  -0.349  -0.390  -0.443  -0.611  -0.565
20    L         1.008   1.017   1.057   1.006   1.018   1.094   1.028   1.045   1.110
21    L         1.008   1.017   1.057   1.006   1.018   1.094   1.028   1.045   1.110
22    A        -1.531  -1.604  -1.281  -1.593  -1.737  -1.271  -1.494  -1.581  -1.199
23    R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
24    K        -0.616  -0.485  -0.405  -1.305  -1.083  -0.936  -0.863  -0.675  -0.599
25    Q         1.008   1.017   1.057   1.112   1.112   1.178   1.028   1.045   1.110
26    F        -0.616  -0.644  -0.421  -0.450  -0.528  -0.226  -0.863  -0.931  -0.625
27    V         1.008   1.017   1.057   0.933   0.983   1.036   1.028   1.045   1.110
28    V        -0.344  -0.098  -0.346  -0.308   0.028  -0.330  -0.443  -0.102  -0.505
29    D         1.008   1.017   1.057   1.167   1.191   1.222   1.028   1.045   1.110
30    V        -0.745  -0.620  -0.398  -0.888  -0.642  -0.349  -1.074  -0.892  -0.588
31    L         1.008   1.017   1.057   1.006   1.018   1.094   1.028   1.045   1.110
32    H         1.008   1.017   1.057   1.377   1.370   1.389   1.028   1.045   1.110
33    P         1.008   1.017   1.057   1.286   1.289   1.317   1.028   1.045   1.110
34    N        -1.158  -1.293  -1.251  -0.768  -1.028  -1.033  -1.074  -1.244  -1.165
35    R        -1.158  -1.293  -1.251  -1.412  -1.670  -1.541  -1.074  -1.244  -1.165
36    A        -0.344  -0.317  -0.403  -0.356  -0.303  -0.424  -0.443  -0.418  -0.596
37    N         1.008   1.017   1.057   1.216   1.237   1.261   1.028   1.045   1.110
38    V        -1.158  -1.327  -1.260  -0.977  -1.216  -1.128  -1.074  -1.283  -1.176
39    S         1.008   1.017   1.057   1.117   1.148   1.183   1.028   1.045   1.110
40    K         1.008   1.017   1.057   0.570   0.613   0.747   1.028   1.045   1.110
41    D        -0.344  -0.444  -0.384  -0.089  -0.258  -0.241  -0.443  -0.611  -0.565
42    E         0.118   0.008  -0.327   0.437   0.313  -0.195   0.188   0.042  -0.474
43    L         0.118   0.013  -0.330   0.325   0.196  -0.255   0.188   0.049  -0.479
44    R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
45    E         1.008   1.017   1.057   1.128   1.153   1.191   1.028   1.045   1.110
46    K         1.008   1.017   1.057   0.570   0.613   0.747   1.028   1.045   1.110
47    L         1.008   1.017   1.057   1.006   1.018   1.094   1.028   1.045   1.110
48    A        -0.737  -0.669  -1.192  -0.533  -0.451  -1.155  -0.548  -0.488  -1.097
49    E        -1.924  -2.096  -1.891  -1.468  -1.787  -1.546  -1.599  -1.754  -1.486
50    V        -2.878  -2.649  -2.361  -2.460  -2.186  -1.875  -2.230  -2.012  -1.657
51    Y         1.008   1.017   1.057   1.270   1.284   1.304   1.028   1.045   1.110
52    K         0.118   0.040  -0.336  -0.115  -0.179  -0.582   0.188   0.084  -0.489
53    A        -1.383  -1.386  -1.252  -1.398  -1.388  -1.164  -1.389  -1.374  -1.169
54    E        -1.158  -1.341  -1.258  -0.794  -1.084  -1.015  -1.074  -1.293  -1.173
55    K        -0.737  -0.935  -1.228  -0.856  -1.092  -1.453  -0.548  -0.782  -1.139
56    D        -0.737  -0.935  -1.228  -0.218  -0.471  -0.968  -0.548  -0.782  -1.139
57    A        -0.737  -0.962  -1.211  -0.465  -0.706  -1.005  -0.548  -0.815  -1.118
58    V         1.008   1.017   1.057   0.933   0.983   1.036   1.028   1.045   1.110
59    S        -1.158  -1.341  -1.258  -0.809  -1.100  -1.012  -1.074  -1.293  -1.173
60    V        -0.344  -0.444  -0.384  -0.414  -0.574  -0.559  -0.443  -0.611  -0.565
61    F         1.008   1.017   1.057   1.156   1.181   1.213   1.028   1.045   1.110
62    G         1.008   1.017   1.057   0.995   1.011   1.085   1.028   1.045   1.110
63    F        -0.745  -0.620  -0.398  -0.863  -0.723  -0.396  -1.074  -0.892  -0.588
64    R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
65    T         1.008   1.017   1.057   1.134   1.135   1.196   1.028   1.045   1.110
66    Q        -0.344  -0.444  -0.384  -0.097  -0.279  -0.203  -0.443  -0.611  -0.565
67    F        -0.344  -0.288  -0.402  -0.085  -0.023  -0.251  -0.443  -0.375  -0.595
68    G         1.008   1.017   1.057   0.995   1.011   1.085   1.028   1.045   1.110
69    G         1.008   1.017   1.057   0.995   1.011   1.085   1.028   1.045   1.110
70    G         1.008   1.017   1.057   0.995   1.011   1.085   1.028   1.045   1.110
71    K        -0.344  -0.444  -0.384  -0.827  -1.009  -0.898  -0.443  -0.611  -0.565
72    S        -0.616  -0.641  -0.421  -0.586  -0.680  -0.374  -0.863  -0.925  -0.625
73    V         0.118   0.333  -0.323   0.414   0.629  -0.274   0.188   0.444  -0.468
74    G         1.008   1.017   1.057   0.995   1.011   1.085   1.028   1.045   1.110
75    F         1.008   1.017   1.057   1.156   1.181   1.213   1.028   1.045   1.110
76    G        -0.616  -0.644  -0.421  -0.819  -0.929  -0.598  -0.863  -0.931  -0.625
77    L         1.008   1.017   1.057   1.006   1.018   1.094   1.028   1.045   1.110
78    V        -0.745  -0.602  -0.410  -0.838  -0.602  -0.379  -1.074  -0.862  -0.608
79    Y         1.008   1.017   1.057   1.270   1.284   1.304   1.028   1.045   1.110
80    N        -1.699  -1.299  -1.241  -1.504  -0.957  -0.955  -1.704  -1.223  -1.153
81    S         0.118   0.008  -0.327   0.426   0.309  -0.203   0.188   0.042  -0.474
82    V        -1.158  -1.316  -1.251  -0.941  -1.155  -1.059  -1.074  -1.268  -1.167
83    A        -0.745  -0.620  -0.398  -1.013  -0.758  -0.455  -1.074  -0.892  -0.588
84    E        -2.092  -1.912  -1.859  -1.846  -1.687  -1.575  -1.809  -1.623  -1.459
85    A        -1.383  -1.399  -1.262  -1.296  -1.260  -1.079  -1.389  -1.392  -1.179
86    K         0.118   0.040  -0.336  -0.144  -0.218  -0.675   0.188   0.084  -0.489
87    K         0.118   0.303  -0.322  -0.184   0.050  -0.783   0.188   0.410  -0.466
88    F         1.008   1.017   1.057   1.156   1.181   1.213   1.028   1.045   1.110
89    E         1.008   1.017   1.057   1.128   1.153   1.191   1.028   1.045   1.110
90    P         1.008   1.017   1.057   1.286   1.289   1.317   1.028   1.045   1.110
91    T        -2.337  -1.940  -1.871  -2.028  -1.505  -1.462  -2.019  -1.638  -1.470
92    Y         1.008   1.017   1.057   1.270   1.284   1.304   1.028   1.045   1.110
93    R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
94    L         0.118   0.040  -0.336   0.308   0.204  -0.318   0.188   0.084  -0.489
95    V         1.008   1.017   1.057   0.933   0.983   1.036   1.028   1.045   1.110
96    R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
97    Y        -0.616  -0.644  -0.421  -0.536  -0.673  -0.399  -0.863  -0.931  -0.625
98    G         1.008   1.017   1.057   0.995   1.011   1.085   1.028   1.045   1.110
99    L        -0.737  -0.935  -1.228  -0.341  -0.602  -0.971  -0.548  -0.782  -1.139
100   A         1.008   1.017   1.057   0.870   0.929   0.986   1.028   1.045   1.110
101   E        -0.737  -0.939  -1.226  -0.255  -0.518  -0.986  -0.548  -0.788  -1.136
102   K        -0.344  -0.444  -0.384  -0.648  -0.776  -0.600  -0.443  -0.611  -0.565
103   V        -0.616  -0.644  -0.421  -0.702  -0.739  -0.416  -0.863  -0.931  -0.625
104   E        -0.344  -0.444  -0.384  -0.155  -0.342  -0.314  -0.443  -0.611  -0.565
105   K         1.008   1.017   1.057   0.570   0.613   0.747   1.028   1.045   1.110
106   A        -0.344  -0.444  -0.384  -0.459  -0.604  -0.572  -0.443  -0.611  -0.565
107   S        -0.344  -0.444  -0.384  -0.232  -0.417  -0.431  -0.443  -0.611  -0.565
108   R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
109   Q         1.008   1.017   1.057   1.112   1.112   1.178   1.028   1.045   1.110
110   Q         1.008   1.017   1.057   1.112   1.112   1.178   1.028   1.045   1.110
111   R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
112   K         1.008   1.017   1.057   0.570   0.613   0.747   1.028   1.045   1.110
113   Q         1.008   1.017   1.057   1.112   1.112   1.178   1.028   1.045   1.110
114   K        -0.745  -0.513  -0.377  -1.532  -1.066  -0.853  -1.074  -0.718  -0.554
115   K         1.008   1.017   1.057   0.570   0.613   0.747   1.028   1.045   1.110
116   N         1.008   1.017   1.057   1.216   1.237   1.261   1.028   1.045   1.110
117   R         1.008   1.017   1.057   0.701   0.749   0.852   1.028   1.045   1.110
118   D        -1.383  -1.427  -1.257  -1.213  -1.315  -1.091  -1.389  -1.410  -1.173
119   K         1.008   1.017   1.057   0.570   0.613   0.747   1.028   1.045   1.110
120   K         0.118  -0.023  -0.337  -0.126  -0.272  -0.619   0.188   0.001  -0.490
121   I        -1.454  -1.384  -1.235  -1.382  -1.295  -1.111  -1.494  -1.352  -1.147
122   F        -0.344  -0.447  -0.405  -0.239  -0.458  -0.537  -0.443  -0.615  -0.599
123   G         1.008   1.017   1.057   0.995   1.011   1.085   1.028   1.045   1.110
124   T         1.008   1.017   1.057   1.134   1.135   1.196   1.028   1.045   1.110
125   G        -1.158  -1.060  -1.221  -0.982  -0.869  -1.163  -1.074  -0.931  -1.130
126   K        -1.383  -1.206  -1.228  -1.955  -1.615  -1.620  -1.389  -1.126  -1.139
127   R        -0.869  -0.840  -1.230  -0.937  -0.952  -1.496  -0.701  -0.693  -1.140
128   L        -1.289  -0.915  -1.225  -1.168  -0.682  -1.112  -1.233  -0.790  -1.134
129   A        -0.737  -0.700  -1.203  -0.543  -0.501  -1.196  -0.548  -0.526  -1.109
130   K         0.118   0.040  -0.336  -0.162  -0.234  -0.735   0.188   0.084  -0.489
131   K        -1.454  -1.427  -1.253  -2.076  -1.978  -1.625  -1.494  -1.412  -1.170
132   V        -0.616  -0.298  -0.392  -0.963  -0.402  -0.633  -0.863  -0.389  -0.579
133   A        -0.745  -0.620  -0.398  -1.384  -1.224  -0.833  -1.074  -0.892  -0.588
134   R        -1.924  -2.096  -1.891  -1.921  -2.153  -1.860  -1.599  -1.754  -1.486
135   R        -0.745  -0.620  -0.398  -1.532  -1.341  -0.924  -1.074  -0.892  -0.588
136   N        -1.531  -1.604  -1.281  -1.424  -1.708  -1.310  -1.494  -1.581  -1.199
137   A        -1.158  -1.341  -1.258  -1.061  -1.314  -1.189  -1.074  -1.293  -1.173
138   D        -0.737  -0.939  -1.226  -0.292  -0.586  -1.170  -0.548  -0.788  -1.136
* 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/P0CX31
Output conservation file - output/P0CX31
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
