1     M         1.058   1.066   1.121   1.421   1.426   1.461   1.092   1.104   1.186
2     K         1.058   1.066   1.121   1.244   1.248   1.304   1.092   1.104   1.186
3     Y         1.058   1.066   1.121   1.428   1.433   1.467   1.092   1.104   1.186
4     L         1.058   1.066   1.121   1.031   1.038   1.116   1.092   1.104   1.186
5     A         1.058   1.066   1.121   0.463   0.477   0.612   1.092   1.104   1.186
6     A         1.058   1.066   1.121   0.463   0.477   0.612   1.092   1.104   1.186
7     Y         1.058   1.066   1.121   1.428   1.433   1.467   1.092   1.104   1.186
8     L         1.058   1.066   1.121   1.031   1.038   1.116   1.092   1.104   1.186
9     L         1.058   1.066   1.121   1.031   1.038   1.116   1.092   1.104   1.186
10    L         1.058   1.066   1.121   1.031   1.038   1.116   1.092   1.104   1.186
11    N        -1.190  -1.172  -1.086  -0.513  -0.482  -0.441  -1.242  -1.213  -1.058
12    A        -1.190  -1.172  -1.086  -1.210  -1.237  -1.005  -1.242  -1.213  -1.058
13    A        -0.471  -0.411  -0.273  -1.030  -0.954  -0.713  -0.775  -0.680  -0.492
14    G         1.058   1.066   1.121   1.024   1.036   1.109   1.092   1.104   1.186
15    N        -0.471  -0.411  -0.273  -0.120  -0.024   0.086  -0.775  -0.680  -0.492
16    -        -2.544  -2.478  -2.151  -1.722  -1.693  -1.323  -1.958  -1.905  -1.542
17    T        -0.281  -0.349  -0.266  -0.119  -0.203  -0.097  -0.464  -0.578  -0.482
18    P         1.058   1.066   1.121   1.361   1.368   1.408   1.092   1.104   1.186
19    D         0.140   0.055  -0.195   0.322   0.225  -0.099   0.158   0.040  -0.365
20    A         0.140   0.076  -0.194  -0.262  -0.330  -0.641   0.158   0.070  -0.363
21    T        -1.524  -1.641  -1.656  -1.090  -1.223  -1.352  -1.242  -1.363  -1.334
22    K        -0.725  -0.860  -1.039  -0.089  -0.236  -0.498  -0.620  -0.785  -1.001
23    I         0.140   0.076  -0.194   0.642   0.576   0.168   0.158   0.070  -0.363
24    K        -0.471  -0.478  -0.288  -0.667  -0.644  -0.382  -0.775  -0.792  -0.518
25    A        -1.081  -1.130  -1.081  -1.116  -1.250  -1.170  -1.086  -1.156  -1.052
26    I         0.140   0.055  -0.195   0.585   0.493   0.141   0.158   0.040  -0.365
27    L         0.140   0.142  -0.187   0.369   0.373  -0.019   0.158   0.161  -0.352
28    E        -0.471  -0.478  -0.288  -0.768  -0.812  -0.541  -0.775  -0.792  -0.518
29    S        -0.471  -0.411  -0.273  -0.338  -0.275  -0.101  -0.775  -0.680  -0.492
30    V         1.058   1.066   1.121   1.251   1.253   1.310   1.092   1.104   1.186
31    G         0.140   0.133  -0.189   0.307   0.304  -0.165   0.158   0.149  -0.355
32    I         1.058   1.066   1.121   1.320   1.330   1.371   1.092   1.104   1.186
33    E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
34    I        -1.800  -1.743  -1.667  -1.518  -1.377  -1.379  -1.553  -1.493  -1.344
35    E         0.140   0.142  -0.187   0.029   0.035  -0.323   0.158   0.161  -0.352
36    D        -1.800  -1.850  -1.672  -1.810  -1.896  -1.755  -1.553  -1.597  -1.350
37    E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
38    K        -0.471  -0.478  -0.288  -0.035  -0.065   0.122  -0.775  -0.792  -0.518
39    V        -0.281  -0.223  -0.260   0.085   0.159   0.049  -0.464  -0.376  -0.472
40    S        -1.190  -1.166  -1.085  -1.484  -1.413  -1.423  -1.242  -1.207  -1.057
41    S        -1.800  -1.697  -1.651  -1.565  -1.412  -1.292  -1.553  -1.450  -1.331
42    V         0.140   0.055  -0.195   0.357   0.266  -0.060   0.158   0.040  -0.365
43    L        -0.471  -0.411  -0.273  -0.358  -0.283  -0.120  -0.775  -0.680  -0.492
44    S        -1.800  -1.697  -1.651  -1.427  -1.326  -1.308  -1.553  -1.450  -1.331
45    A        -1.081  -1.130  -1.081  -1.427  -1.544  -1.410  -1.086  -1.156  -1.052
46    L         0.140   0.133  -0.189   0.357   0.350  -0.051   0.158   0.149  -0.355
47    E        -1.081  -0.933  -1.069  -0.956  -0.802  -0.861  -1.086  -0.911  -1.037
48    G         1.058   1.066   1.121   1.024   1.036   1.109   1.092   1.104   1.186
49    K         1.058   1.066   1.121   1.244   1.248   1.304   1.092   1.104   1.186
50    S        -1.357  -1.281  -1.096  -1.003  -0.916  -0.688  -1.397  -1.307  -1.069
51    V        -1.190  -1.172  -1.086  -0.821  -0.797  -0.862  -1.242  -1.213  -1.058
52    D        -0.471  -0.469  -0.288  -0.578  -0.595  -0.392  -0.775  -0.778  -0.519
53    E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
54    L         1.058   1.066   1.121   1.031   1.038   1.116   1.092   1.104   1.186
55    I         0.140   0.142  -0.187   0.642   0.647   0.178   0.158   0.161  -0.352
56    T         0.140   0.055  -0.195  -0.186  -0.260  -0.444   0.158   0.040  -0.365
57    E        -0.471  -0.411  -0.273  -1.204  -1.059  -0.879  -0.775  -0.680  -0.492
58    G         1.058   1.066   1.121   1.024   1.036   1.109   1.092   1.104   1.186
59    N        -0.281  -0.310  -0.266   0.235   0.194   0.172  -0.464  -0.514  -0.482
60    E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
61    K         1.058   1.066   1.121   1.244   1.248   1.304   1.092   1.104   1.186
62    L         1.058   1.066   1.121   1.031   1.038   1.116   1.092   1.104   1.186
63    A        -0.281  -0.275  -0.269  -0.801  -0.789  -0.726  -0.464  -0.458  -0.486
64    A        -1.190  -1.222  -1.085  -0.948  -1.028  -0.985  -1.242  -1.262  -1.056
65    V         1.058   1.066   1.121   1.251   1.253   1.310   1.092   1.104   1.186
66    P         1.058   1.066   1.121   1.361   1.368   1.408   1.092   1.104   1.186
67    A        -1.081  -1.043  -1.068  -1.078  -1.118  -1.072  -1.086  -1.070  -1.037
68    A        -1.081  -1.154  -1.074  -1.157  -1.289  -1.289  -1.086  -1.172  -1.046
69    G         0.140   0.076  -0.194   0.307   0.238  -0.173   0.158   0.070  -0.363
70    P        -0.725  -0.860  -1.039  -0.889  -1.024  -1.140  -0.620  -0.785  -1.001
71    A         0.140   0.155  -0.189  -0.214  -0.190  -0.509   0.158   0.179  -0.355
72    S        -1.081  -1.073  -1.064  -1.352  -1.331  -1.174  -1.086  -1.075  -1.034
73    A         0.140   0.155  -0.189  -0.186  -0.161  -0.439   0.158   0.179  -0.355
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    G        -1.206  -1.267  -1.098  -1.596  -1.631  -1.331  -1.238  -1.305  -1.071
77    G        -1.081  -0.943  -1.057  -0.854  -0.659  -0.938  -1.086  -0.927  -1.025
78    A        -0.725  -0.608  -1.018  -0.889  -0.761  -1.126  -0.620  -0.482  -0.975
79    A         1.058   1.066   1.121   0.463   0.477   0.612   1.092   1.104   1.186
80    A         1.058   1.066   1.121   0.463   0.477   0.612   1.092   1.104   1.186
81    A        -1.081  -1.124  -1.070  -1.443  -1.481  -1.337  -1.086  -1.130  -1.041
82    S        -1.190  -1.166  -1.077  -1.231  -1.193  -1.187  -1.242  -1.212  -1.049
83    G        -1.524  -1.568  -1.640  -1.301  -1.377  -1.746  -1.242  -1.287  -1.319
84    D        -1.190  -1.209  -1.083  -1.346  -1.290  -1.133  -1.242  -1.249  -1.054
85    A        -0.725  -0.773  -1.030  -0.954  -1.013  -1.271  -0.620  -0.679  -0.989
86    A        -1.081  -1.120  -1.075  -0.820  -0.950  -0.999  -1.086  -1.146  -1.046
87    A         1.058   1.066   1.121   0.463   0.477   0.612   1.092   1.104   1.186
88    E         0.140   0.055  -0.195  -0.318  -0.420  -0.794   0.158   0.040  -0.365
89    E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
90    E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
91    K        -0.281  -0.321  -0.266  -0.691  -0.728  -0.568  -0.464  -0.531  -0.482
92    E        -1.723  -1.826  -1.673  -1.842  -1.952  -1.631  -1.449  -1.555  -1.350
93    E        -0.281  -0.150  -0.217  -0.454  -0.289  -0.343  -0.464  -0.262  -0.400
94    E        -0.281  -0.314  -0.268  -0.556  -0.605  -0.536  -0.464  -0.521  -0.485
95    A         0.140   0.055  -0.195  -0.103  -0.217  -0.690   0.158   0.040  -0.365
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    A        -1.357  -1.299  -1.086  -1.799  -1.680  -1.363  -1.397  -1.331  -1.057
100   E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
101   E         1.058   1.066   1.121   0.709   0.719   0.831   1.092   1.104   1.186
102   S         1.058   1.066   1.121   1.002   1.003   1.090   1.092   1.104   1.186
103   D         1.058   1.066   1.121   1.216   1.223   1.280   1.092   1.104   1.186
104   D        -1.190  -1.172  -1.086  -1.161  -1.077  -0.998  -1.242  -1.213  -1.058
105   D         1.058   1.066   1.121   1.216   1.223   1.280   1.092   1.104   1.186
106   M         1.058   1.066   1.121   1.421   1.426   1.461   1.092   1.104   1.186
107   G         1.058   1.066   1.121   1.024   1.036   1.109   1.092   1.104   1.186
108   F         0.140   0.133  -0.189   0.782   0.775   0.334   0.158   0.149  -0.355
109   G         1.058   1.066   1.121   1.024   1.036   1.109   1.092   1.104   1.186
110   L         1.058   1.066   1.121   1.031   1.038   1.116   1.092   1.104   1.186
111   F         1.058   1.066   1.121   1.435   1.439   1.473   1.092   1.104   1.186
112   D         1.058   1.066   1.121   1.216   1.223   1.280   1.092   1.104   1.186
* 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/P05319
Output conservation file - output/P05319
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
