1     M         0.961   0.963   0.999   1.229   1.227   1.256   0.987   0.989   1.048
2     -         0.961   0.963   0.999   0.846   0.849   0.931   0.987   0.989   1.048
3     A         0.062   0.054  -0.375   0.128   0.120  -0.435   0.120   0.111  -0.530
4     S        -0.795  -0.872  -1.249  -0.508  -0.601  -1.183  -0.623  -0.711  -1.165
5     L        -1.110  -1.304  -1.290  -0.899  -1.174  -1.229  -0.994  -1.230  -1.213
6     P         0.961   0.963   0.999   1.136   1.133   1.177   0.987   0.989   1.048
7     H         0.961   0.963   0.999   1.044   1.051   1.099   0.987   0.989   1.048
8     P         0.961   0.963   0.999   1.146   1.142   1.186   0.987   0.989   1.048
9     K        -0.381  -0.424  -0.402  -0.768  -0.818  -0.737  -0.499  -0.565  -0.572
10    I         0.961   0.963   0.999   1.065   1.066   1.117   0.987   0.989   1.048
11    V         0.062   0.015  -0.367   0.143   0.091  -0.419   0.120   0.060  -0.517
12    K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
13    K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
14    H        -1.188  -1.227  -1.268  -0.934  -1.005  -1.074  -1.118  -1.168  -1.188
15    T         0.062  -0.010  -0.378   0.331   0.244  -0.384   0.120   0.027  -0.534
16    K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
17    K        -1.188  -1.278  -1.280  -1.421  -1.528  -1.481  -1.118  -1.220  -1.201
18    F         0.961   0.963   0.999   1.200   1.199   1.232   0.987   0.989   1.048
19    K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
20    R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
21    H         0.961   0.963   0.999   1.100   1.111   1.147   0.987   0.989   1.048
22    H        -0.618  -0.643  -0.460  -0.466  -0.500  -0.269  -0.870  -0.913  -0.666
23    S         0.961   0.963   0.999   0.945   0.953   1.015   0.987   0.989   1.048
24    D         0.961   0.963   0.999   1.217   1.219   1.246   0.987   0.989   1.048
25    R         0.062   0.025  -0.366   0.044  -0.002  -0.520   0.120   0.073  -0.515
26    Y        -0.618  -0.643  -0.460  -0.400  -0.453  -0.237  -0.870  -0.913  -0.666
27    H        -1.520  -1.536  -1.300  -1.475  -1.520  -1.216  -1.489  -1.504  -1.225
28    R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
29    V         0.961   0.963   0.999   0.859   0.864   0.942   0.987   0.989   1.048
30    A        -1.622  -1.570  -1.313  -1.750  -1.666  -1.320  -1.613  -1.551  -1.239
31    E         0.961   0.963   0.999   1.141   1.140   1.182   0.987   0.989   1.048
32    N        -0.618  -0.643  -0.460  -0.694  -0.749  -0.503  -0.870  -0.913  -0.666
33    W         0.961   0.963   0.999   1.326   1.326   1.339   0.987   0.989   1.048
34    R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
35    K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
36    Q        -0.618  -0.643  -0.460  -0.375  -0.434  -0.227  -0.870  -0.913  -0.666
37    K        -0.381  -0.424  -0.402  -0.865  -0.929  -0.876  -0.499  -0.565  -0.572
38    G         0.961   0.963   0.999   1.017   1.018   1.076   0.987   0.989   1.048
39    I         0.961   0.963   0.999   1.065   1.066   1.117   0.987   0.989   1.048
40    D         0.961   0.963   0.999   1.217   1.219   1.246   0.987   0.989   1.048
41    S         0.961   0.963   0.999   0.945   0.953   1.015   0.987   0.989   1.048
42    V        -0.618  -0.559  -0.441  -0.485  -0.376  -0.306  -0.870  -0.777  -0.636
43    V         0.961   0.963   0.999   0.859   0.864   0.942   0.987   0.989   1.048
44    R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
45    R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
46    R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
47    F         0.961   0.963   0.999   1.200   1.199   1.232   0.987   0.989   1.048
48    R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
49    G         0.961   0.963   0.999   1.017   1.018   1.076   0.987   0.989   1.048
50    N        -0.618  -0.559  -0.441  -0.604  -0.502  -0.382  -0.870  -0.777  -0.636
51    I         0.961   0.963   0.999   1.065   1.066   1.117   0.987   0.989   1.048
52    S        -0.795  -0.868  -1.245  -0.507  -0.601  -1.174  -0.623  -0.707  -1.161
53    Q        -1.622  -1.570  -1.313  -1.229  -1.167  -0.880  -1.613  -1.551  -1.239
54    P         0.961   0.963   0.999   1.153   1.154   1.192   0.987   0.989   1.048
55    K        -1.520  -1.444  -1.296  -1.815  -1.707  -1.425  -1.489  -1.395  -1.220
56    I         0.961   0.963   0.999   1.065   1.066   1.117   0.987   0.989   1.048
57    G         0.961   0.963   0.999   1.017   1.018   1.076   0.987   0.989   1.048
58    Y         0.961   0.963   0.999   1.234   1.237   1.261   0.987   0.989   1.048
59    G         0.961   0.963   0.999   1.017   1.018   1.076   0.987   0.989   1.048
60    S        -0.381  -0.424  -0.402  -0.352  -0.414  -0.417  -0.499  -0.565  -0.572
61    N         0.062  -0.010  -0.378   0.299   0.211  -0.388   0.120   0.027  -0.534
62    K         0.062   0.142  -0.367  -0.245  -0.139  -0.817   0.120   0.222  -0.517
63    K         0.062  -0.010  -0.378  -0.235  -0.311  -0.804   0.120   0.027  -0.534
64    T         0.961   0.963   0.999   1.088   1.095   1.137   0.987   0.989   1.048
65    K        -0.618  -0.611  -0.454  -1.268  -1.254  -0.959  -0.870  -0.861  -0.657
66    F        -1.520  -1.536  -1.300  -1.152  -1.180  -0.935  -1.489  -1.504  -1.225
67    L        -1.520  -1.516  -1.290  -1.135  -1.131  -0.917  -1.489  -1.481  -1.214
68    S        -1.934  -1.864  -1.890  -1.435  -1.318  -1.478  -1.613  -1.524  -1.501
69    P         0.961   0.963   0.999   1.153   1.154   1.192   0.987   0.989   1.048
70    S        -1.934  -1.959  -1.891  -1.643  -1.683  -1.603  -1.613  -1.637  -1.501
71    G         0.961   0.963   0.999   1.017   1.018   1.076   0.987   0.989   1.048
72    H        -1.934  -1.959  -1.891  -1.544  -1.589  -1.556  -1.613  -1.637  -1.501
73    K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
74    T        -1.364  -1.285  -1.287  -1.496  -1.395  -1.316  -1.365  -1.278  -1.212
75    F        -1.188  -1.139  -1.267  -0.809  -0.732  -0.982  -1.118  -1.049  -1.187
76    L         0.961   0.963   0.999   0.981   0.989   1.046   0.987   0.989   1.048
77    V         0.961   0.963   0.999   0.859   0.864   0.942   0.987   0.989   1.048
78    A        -2.191  -2.135  -1.905  -2.470  -2.388  -2.083  -1.861  -1.807  -1.515
79    N         0.961   0.963   0.999   1.047   1.051   1.102   0.987   0.989   1.048
80    V        -1.188  -1.151  -1.266  -1.113  -1.037  -1.211  -1.118  -1.052  -1.187
81    K        -1.188  -1.278  -1.280  -1.446  -1.551  -1.441  -1.118  -1.220  -1.201
82    D        -0.795  -0.862  -1.248  -0.201  -0.285  -0.903  -0.623  -0.700  -1.164
83    L        -0.618  -0.643  -0.460  -0.797  -0.855  -0.596  -0.870  -0.913  -0.666
84    E        -1.188  -1.151  -1.272  -0.761  -0.713  -0.928  -1.118  -1.066  -1.193
85    T        -2.191  -2.113  -1.914  -2.001  -1.882  -1.624  -1.861  -1.773  -1.522
86    L         0.961   0.963   0.999   0.981   0.989   1.046   0.987   0.989   1.048
87    T        -0.381  -0.273  -0.405  -0.303  -0.146  -0.378  -0.499  -0.339  -0.578
88    M        -0.381  -0.338  -0.427  -0.100  -0.040  -0.288  -0.499  -0.435  -0.613
89    H         0.961   0.963   0.999   1.100   1.111   1.147   0.987   0.989   1.048
90    T        -1.188  -1.155  -1.259  -0.899  -0.875  -1.074  -1.118  -1.097  -1.178
91    K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
92    T        -1.188  -1.197  -1.270  -0.953  -0.949  -1.172  -1.118  -1.111  -1.191
93    Y        -0.381  -0.419  -0.448  -0.027  -0.087  -0.217  -0.499  -0.557  -0.647
94    A         0.961   0.963   0.999   0.841   0.844   0.926   0.987   0.989   1.048
95    A         0.961   0.963   0.999   0.841   0.844   0.926   0.987   0.989   1.048
96    E         0.961   0.963   0.999   1.141   1.140   1.182   0.987   0.989   1.048
97    I         0.961   0.963   0.999   1.065   1.066   1.117   0.987   0.989   1.048
98    A         0.062   0.142  -0.367   0.107   0.199  -0.485   0.120   0.222  -0.517
99    H        -1.188  -1.242  -1.282  -0.912  -0.986  -1.131  -1.118  -1.177  -1.206
100   N         0.062   0.054  -0.375   0.313   0.306  -0.340   0.120   0.111  -0.530
101   I         0.062   0.133  -0.369   0.143   0.223  -0.423   0.120   0.210  -0.521
102   S         0.961   0.963   0.999   0.945   0.953   1.015   0.987   0.989   1.048
103   A        -0.693  -0.676  -0.463  -1.002  -0.974  -0.640  -0.994  -0.967  -0.671
104   K        -0.618  -0.559  -0.441  -1.172  -1.051  -0.892  -0.870  -0.777  -0.636
105   N        -0.693  -0.666  -0.459  -1.160  -1.141  -0.789  -0.994  -0.951  -0.664
106   R         0.961   0.963   0.999   0.773   0.772   0.868   0.987   0.989   1.048
107   V        -0.795  -0.862  -1.248  -0.573  -0.655  -1.190  -0.623  -0.700  -1.164
108   V        -1.934  -1.823  -1.891  -1.582  -1.470  -1.634  -1.613  -1.517  -1.503
109   I         0.062   0.171  -0.366   0.336   0.457  -0.294   0.120   0.257  -0.515
110   L        -0.693  -0.675  -0.463  -0.962  -0.934  -0.608  -0.994  -0.966  -0.672
111   A        -0.618  -0.643  -0.460  -0.769  -0.808  -0.521  -0.870  -0.913  -0.666
112   R        -1.364  -1.338  -1.288  -1.819  -1.773  -1.545  -1.365  -1.325  -1.213
113   A         0.961   0.963   0.999   0.841   0.844   0.926   0.987   0.989   1.048
114   K        -0.381  -0.424  -0.402  -0.865  -0.929  -0.876  -0.499  -0.565  -0.572
115   A        -0.618  -0.591  -0.456  -1.107  -1.053  -0.883  -0.870  -0.828  -0.660
116   L         0.062   0.061  -0.375   0.262   0.266  -0.347   0.120   0.120  -0.530
117   G         0.961   0.963   0.999   1.017   1.018   1.076   0.987   0.989   1.048
118   I        -0.381  -0.339  -0.424  -0.428  -0.369  -0.507  -0.499  -0.436  -0.609
119   K         0.961   0.963   0.999   0.517   0.533   0.651   0.987   0.989   1.048
120   V         0.961   0.963   0.999   0.859   0.864   0.942   0.987   0.989   1.048
121   T         0.961   0.963   0.999   1.088   1.095   1.137   0.987   0.989   1.048
122   N         0.961   0.963   0.999   1.047   1.051   1.102   0.987   0.989   1.048
123   P        -0.693  -0.676  -0.463  -0.847  -0.826  -0.509  -0.994  -0.967  -0.672
124   K        -1.188  -1.278  -1.280  -1.480  -1.595  -1.551  -1.118  -1.220  -1.201
125   G        -0.618  -0.629  -0.461  -0.774  -0.811  -0.586  -0.870  -0.890  -0.668
126   R        -0.618  -0.631  -0.459  -1.172  -1.215  -0.943  -0.870  -0.892  -0.665
127   L        -0.618  -0.611  -0.454  -0.797  -0.789  -0.583  -0.870  -0.861  -0.657
128   A        -2.191  -2.191  -1.913  -2.262  -2.274  -1.837  -1.861  -1.851  -1.521
129   L        -0.381  -0.424  -0.402  -0.350  -0.416  -0.437  -0.499  -0.565  -0.572
130   E        -0.618  -0.643  -0.460  -0.432  -0.477  -0.244  -0.870  -0.913  -0.666
131   A        -0.381  -0.424  -0.402  -0.420  -0.485  -0.450  -0.499  -0.565  -0.572
* 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/P38061
Output conservation file - output/P38061
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
