1     M         1.486   1.519   1.624   1.782   1.817   1.977   1.609   1.656   1.834
2     L        -0.842  -0.930  -0.892  -0.665  -0.829  -0.812  -0.830  -0.924  -0.843
3     R         0.075  -0.012  -0.235   0.465   0.355  -0.000   0.099  -0.019  -0.341
4     S        -1.381  -1.415  -1.327  -1.318  -1.331  -1.197  -1.178  -1.195  -1.052
5     I        -1.507  -1.456  -1.340  -1.452  -1.385  -1.191  -1.294  -1.240  -1.067
6     I        -1.509  -1.430  -1.346  -1.406  -1.251  -1.202  -1.281  -1.200  -1.068
7     G        -1.065  -1.065  -0.935  -1.176  -1.213  -1.020  -1.075  -1.063  -0.885
8     K        -0.348  -0.246  -0.343  -0.260  -0.125  -0.244  -0.515  -0.377  -0.501
9     S        -1.509  -1.498  -1.372  -1.584  -1.554  -1.376  -1.281  -1.264  -1.091
10    A        -0.898  -0.896  -0.876  -1.029  -1.000  -0.977  -0.869  -0.871  -0.819
11    S        -1.952  -1.894  -1.718  -1.999  -1.907  -1.669  -1.488  -1.429  -1.218
12    R        -1.065  -1.054  -0.931  -0.918  -0.909  -0.718  -1.075  -1.056  -0.881
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    S        -0.179  -0.314  -0.335  -0.335  -0.579  -0.691  -0.249  -0.444  -0.483
18    L        -1.345  -1.198  -1.296  -1.372  -1.137  -1.323  -1.121  -0.962  -1.023
19    N        -0.584  -0.470  -0.376  -0.445  -0.265  -0.150  -0.818  -0.661  -0.541
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    F        -0.538  -0.439  -0.395  -0.661  -0.488  -0.410  -0.770  -0.642  -0.568
22    V        -1.345  -1.427  -1.327  -1.272  -1.385  -1.232  -1.121  -1.197  -1.052
23    A        -0.964  -1.050  -0.934  -1.268  -1.355  -1.160  -0.970  -1.044  -0.885
24    K        -0.441  -0.510  -0.361  -0.356  -0.440  -0.221  -0.666  -0.730  -0.530
25    R         1.486   1.519   1.624   1.667   1.707   1.866   1.609   1.656   1.834
26    S        -1.488  -1.368  -1.334  -1.139  -0.981  -0.921  -1.273  -1.153  -1.061
27    Y         1.486   1.519   1.624   1.753   1.788   1.950   1.609   1.656   1.834
28    A         1.486   1.519   1.624   1.200   1.257   1.416   1.609   1.656   1.834
29    E        -0.964  -1.009  -0.909  -0.844  -0.907  -0.738  -0.970  -1.005  -0.858
30    A         0.338   0.416   0.424  -0.045   0.086   0.072   0.092   0.218   0.183
31    A         0.338   0.258   0.345  -0.091  -0.250  -0.136   0.092  -0.073   0.030
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    A        -1.602  -1.538  -1.378  -1.774  -1.655  -1.452  -1.364  -1.296  -1.096
34    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    S        -1.488  -1.456  -1.338  -1.519  -1.458  -1.245  -1.273  -1.235  -1.063
36    S        -0.964  -0.948  -0.910  -0.847  -0.847  -0.798  -0.970  -0.948  -0.860
37    G        -0.584  -0.567  -0.418  -0.895  -0.845  -0.617  -0.818  -0.797  -0.598
38    L         0.699   0.670   0.505   0.627   0.598   0.373   0.699   0.648   0.334
39    K         0.075  -0.129  -0.260   0.327   0.035  -0.178   0.099  -0.183  -0.377
40    L         0.763   0.704   0.535   0.759   0.708   0.524   0.796   0.702   0.389
41    Q        -0.842  -0.776  -0.851  -0.787  -0.678  -0.746  -0.830  -0.731  -0.795
42    F        -0.923  -1.022  -0.906  -0.794  -0.883  -0.700  -0.946  -1.023  -0.858
43    A         0.075  -0.012  -0.235  -0.083  -0.192  -0.571   0.099  -0.019  -0.341
44    L         0.763   0.704   0.535   0.719   0.658   0.429   0.796   0.702   0.389
45    P         0.763   0.704   0.535   0.997   0.915   0.633   0.796   0.702   0.389
46    H         0.075  -0.129  -0.260   0.604   0.346   0.146   0.099  -0.183  -0.377
47    E         0.407   0.501   0.420   0.367   0.503   0.331   0.215   0.367   0.175
48    T         0.075  -0.012  -0.235   0.331   0.212  -0.218   0.099  -0.019  -0.341
49    L         0.217   0.193   0.331  -0.061  -0.096   0.127  -0.133  -0.196   0.003
50    Y         0.407   0.525   0.436   0.680   0.844   0.686   0.215   0.408   0.205
51    S        -0.923  -0.989  -0.886  -0.897  -0.966  -0.822  -0.946  -0.990  -0.839
52    G        -1.714  -1.768  -1.693  -1.356  -1.469  -1.380  -1.294  -1.334  -1.200
53    S        -1.714  -1.752  -1.674  -1.578  -1.686  -1.534  -1.294  -1.323  -1.185
54    E        -0.241  -0.275  -0.340  -0.189  -0.245  -0.289  -0.365  -0.415  -0.499
55    V         1.486   1.519   1.624   1.331   1.373   1.542   1.609   1.656   1.834
56    T        -0.842  -0.730  -0.872  -0.714  -0.559  -0.819  -0.830  -0.707  -0.822
57    Q         1.486   1.519   1.624   1.511   1.549   1.716   1.609   1.656   1.834
58    V         1.486   1.519   1.624   1.331   1.373   1.542   1.609   1.656   1.834
59    N         0.763   0.624   0.506   1.051   0.881   0.711   0.796   0.574   0.335
60    L         0.217   0.193   0.331  -0.061  -0.096   0.127  -0.133  -0.196   0.003
61    P         1.486   1.519   1.624   1.636   1.674   1.837   1.609   1.656   1.834
62    A         0.217   0.253   0.359  -0.298  -0.237  -0.084  -0.133  -0.082   0.058
63    K        -1.381  -1.434  -1.334  -1.247  -1.359  -1.199  -1.178  -1.217  -1.061
64    S        -0.842  -0.945  -0.886  -0.823  -0.960  -0.888  -0.830  -0.924  -0.832
65    G         1.486   1.519   1.624   1.566   1.606   1.769   1.609   1.656   1.834
66    R        -1.381  -1.172  -1.299  -1.188  -0.936  -1.075  -1.178  -0.964  -1.026
67    I        -0.591  -0.585  -0.424  -0.668  -0.643  -0.388  -0.830  -0.819  -0.606
68    G         1.486   1.519   1.624   1.566   1.606   1.769   1.609   1.656   1.834
69    V         0.407   0.461   0.387   0.409   0.481   0.284   0.215   0.298   0.111
70    L         1.486   1.519   1.624   1.322   1.374   1.534   1.609   1.656   1.834
71    A         0.763   0.624   0.506   0.590   0.428   0.259   0.796   0.574   0.335
72    N         0.763   0.624   0.506   1.051   0.881   0.711   0.796   0.574   0.335
73    H         1.486   1.519   1.624   1.770   1.811   1.966   1.609   1.656   1.834
74    V         0.407   0.508   0.450   0.248   0.389   0.303   0.215   0.378   0.231
75    P         1.486   1.519   1.624   1.636   1.674   1.837   1.609   1.656   1.834
76    T        -0.842  -0.911  -0.897  -0.556  -0.626  -0.639  -0.830  -0.888  -0.845
77    V         0.217   0.193   0.331  -0.054  -0.097   0.133  -0.133  -0.196   0.003
78    E         0.407   0.305   0.366   0.298   0.108   0.192   0.215   0.016   0.071
79    Q         0.763   0.624   0.506   0.944   0.782   0.649   0.796   0.574   0.335
80    L         1.486   1.519   1.624   1.322   1.374   1.534   1.609   1.656   1.834
81    L        -1.381  -1.172  -1.299  -1.144  -0.841  -1.068  -1.178  -0.964  -1.026
82    P         1.486   1.519   1.624   1.636   1.674   1.837   1.609   1.656   1.834
83    G         1.486   1.519   1.624   1.566   1.606   1.769   1.609   1.656   1.834
84    V         0.217   0.269   0.347  -0.195  -0.107  -0.020  -0.133  -0.051   0.034
85    V        -0.241  -0.293  -0.318  -0.404  -0.449  -0.509  -0.365  -0.415  -0.460
86    E         0.763   0.624   0.506   0.769   0.574   0.376   0.796   0.574   0.335
87    V         0.407   0.508   0.450   0.248   0.389   0.303   0.215   0.378   0.231
88    M        -1.174  -1.097  -1.288  -0.796  -0.703  -1.004  -0.946  -0.872  -1.015
89    E        -0.842  -0.867  -0.876  -0.830  -0.844  -0.835  -0.830  -0.843  -0.821
90    -        -0.538  -0.511  -0.393  -0.651  -0.624  -0.434  -0.770  -0.726  -0.565
91    G        -1.049  -1.036  -0.928  -1.077  -1.094  -0.948  -1.062  -1.047  -0.882
92    S        -0.384  -0.334  -0.352  -0.452  -0.392  -0.379  -0.598  -0.537  -0.519
93    N        -1.049  -1.003  -0.919  -1.077  -1.015  -0.856  -1.062  -1.010  -0.873
94    S        -0.923  -0.994  -0.884  -0.853  -0.913  -0.748  -0.946  -0.997  -0.837
95    K        -0.574  -0.585  -0.835  -0.272  -0.325  -0.696  -0.482  -0.505  -0.774
96    K        -0.384  -0.404  -0.353  -0.427  -0.459  -0.392  -0.598  -0.606  -0.519
97    F         0.407   0.561   0.446   0.680   0.895   0.703   0.215   0.469   0.224
98    F         1.486   1.519   1.624   1.661   1.706   1.860   1.609   1.656   1.834
99    I        -0.384  -0.394  -0.355  -0.575  -0.580  -0.513  -0.598  -0.609  -0.523
100   S         1.486   1.519   1.624   1.357   1.398   1.568   1.609   1.656   1.834
101   G         1.486   1.519   1.624   1.566   1.606   1.769   1.609   1.656   1.834
102   G         1.486   1.519   1.624   1.566   1.606   1.769   1.609   1.656   1.834
103   F         0.407   0.508   0.450   0.566   0.714   0.595   0.215   0.378   0.231
104   A         1.486   1.519   1.624   1.198   1.253   1.414   1.609   1.656   1.834
105   T        -0.842  -0.834  -0.882  -0.696  -0.745  -0.813  -0.830  -0.838  -0.833
106   V         0.763   0.624   0.506   0.718   0.538   0.366   0.796   0.574   0.335
107   Q         1.486   1.519   1.624   1.511   1.549   1.716   1.609   1.656   1.834
108   P         1.486   1.519   1.624   1.636   1.674   1.837   1.609   1.656   1.834
109   D        -0.384  -0.457  -0.365  -0.286  -0.398  -0.287  -0.598  -0.666  -0.534
110   S         0.217   0.230   0.336   0.004   0.015   0.192  -0.133  -0.126   0.013
111   Q        -1.049  -0.975  -0.923  -0.993  -0.941  -0.827  -1.062  -0.990  -0.876
112   L         1.486   1.519   1.624   1.322   1.374   1.534   1.609   1.656   1.834
113   C        -1.049  -0.876  -0.899  -1.000  -0.783  -0.817  -1.062  -0.873  -0.848
114   V         0.217   0.250   0.356   0.034   0.072   0.212  -0.133  -0.087   0.052
115   T        -0.509  -0.478  -0.385  -0.481  -0.425  -0.323  -0.714  -0.675  -0.554
116   A        -0.241  -0.339  -0.327  -0.574  -0.713  -0.733  -0.365  -0.484  -0.478
117   I        -0.384  -0.453  -0.357  -0.458  -0.533  -0.392  -0.598  -0.660  -0.524
118   E         1.486   1.519   1.624   1.405   1.441   1.614   1.609   1.656   1.834
119   A         0.763   0.757   0.524   0.592   0.601   0.292   0.796   0.783   0.368
120   F         0.407   0.327   0.359   0.621   0.492   0.523   0.215   0.057   0.058
121   P        -0.923  -0.953  -0.895  -0.819  -0.871  -0.817  -0.946  -0.956  -0.846
122   L        -0.574  -0.520  -0.811  -0.499  -0.441  -0.845  -0.482  -0.419  -0.746
123   E         0.407   0.472   0.390   0.356   0.438   0.326   0.215   0.318   0.117
124   S        -0.591  -0.505  -0.386  -0.696  -0.529  -0.367  -0.830  -0.716  -0.556
125   F         0.763   0.828   0.540   1.056   1.138   0.748   0.796   0.889   0.398
126   S         0.407   0.508   0.450   0.310   0.446   0.374   0.215   0.378   0.231
127   Q        -1.507  -1.511  -1.347  -1.614  -1.631  -1.414  -1.294  -1.280  -1.072
128   E        -0.842  -0.781  -0.875  -0.840  -0.807  -0.880  -0.830  -0.779  -0.827
129   N        -0.842  -0.832  -0.880  -1.021  -1.017  -1.087  -0.830  -0.798  -0.826
130   I        -0.241  -0.355  -0.333  -0.377  -0.563  -0.550  -0.365  -0.507  -0.487
131   K        -0.384  -0.453  -0.357  -0.267  -0.344  -0.192  -0.598  -0.660  -0.524
132   N        -0.842  -0.912  -0.880  -0.865  -0.969  -0.933  -0.830  -0.890  -0.831
133   L         0.763   0.757   0.524   0.709   0.713   0.388   0.796   0.783   0.368
134   L        -0.384  -0.404  -0.353  -0.519  -0.528  -0.418  -0.598  -0.606  -0.519
135   A         0.763   0.624   0.506   0.568   0.394   0.200   0.796   0.574   0.335
136   E        -0.241  -0.293  -0.318  -0.196  -0.266  -0.285  -0.365  -0.415  -0.460
137   A         0.763   0.624   0.506   0.624   0.479   0.347   0.796   0.574   0.335
138   K        -0.241  -0.238  -0.336  -0.175  -0.198  -0.348  -0.365  -0.378  -0.493
139   K         0.763   0.624   0.506   0.897   0.693   0.457   0.796   0.574   0.335
140   N        -0.842  -0.911  -0.897  -0.531  -0.641  -0.642  -0.830  -0.888  -0.845
141   V        -0.923  -0.964  -0.900  -1.204  -1.210  -1.086  -0.946  -0.972  -0.852
142   S        -1.174  -1.277  -1.279  -1.000  -1.147  -1.147  -0.946  -1.051  -1.007
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   S         0.763   0.757   0.524   0.752   0.746   0.440   0.796   0.783   0.368
145   S        -0.842  -0.814  -0.856  -0.990  -0.945  -1.009  -0.830  -0.790  -0.803
146   D         0.763   0.757   0.524   1.051   1.038   0.670   0.796   0.783   0.368
147   A         0.075   0.146  -0.229   0.135   0.227  -0.353   0.099   0.192  -0.332
148   R        -1.839  -1.859  -1.681  -1.723  -1.762  -1.495  -1.410  -1.408  -1.192
149   E        -1.174  -1.001  -1.271  -1.073  -0.818  -1.231  -0.946  -0.759  -0.999
150   A         0.075   0.149  -0.225  -0.041   0.069  -0.463   0.099   0.197  -0.326
151   A         0.763   0.821   0.530   0.592   0.677   0.302   0.796   0.879   0.380
152   E         0.763   0.821   0.530   0.766   0.833   0.411   0.796   0.879   0.380
153   A         1.486   1.519   1.624   1.198   1.253   1.414   1.609   1.656   1.834
154   A        -1.381  -1.380  -1.320  -1.470  -1.475  -1.391  -1.178  -1.158  -1.046
155   I         0.407   0.327   0.359   0.409   0.235   0.220   0.215   0.057   0.058
156   Q        -0.384  -0.430  -0.356  -0.482  -0.514  -0.380  -0.598  -0.623  -0.518
157   V         0.407   0.379   0.367   0.157   0.102   0.021   0.215   0.152   0.073
158   E         0.763   0.624   0.506   0.769   0.574   0.376   0.796   0.574   0.335
159   V         1.486   1.519   1.624   1.331   1.373   1.542   1.609   1.656   1.834
160   L         1.486   1.519   1.624   1.322   1.374   1.534   1.609   1.656   1.834
161   E         0.763   0.828   0.540   0.817   0.889   0.551   0.796   0.889   0.398
162   N        -0.842  -0.800  -0.886  -1.037  -1.018  -1.044  -0.830  -0.807  -0.837
163   L         1.486   1.519   1.624   1.322   1.374   1.534   1.609   1.656   1.834
164   Q         0.075  -0.129  -0.260   0.213  -0.099  -0.381   0.099  -0.183  -0.377
165   S        -1.381  -1.355  -1.320  -1.290  -1.214  -1.143  -1.178  -1.154  -1.049
166   V        -0.591  -0.569  -0.416  -0.985  -0.940  -0.698  -0.830  -0.799  -0.595
167   L        -0.241  -0.190  -0.319  -0.452  -0.376  -0.584  -0.365  -0.303  -0.467
168   K         1.486   1.519   1.624   1.553   1.590   1.757   1.609   1.656   1.834
* 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/Q12165
Output conservation file - output/Q12165
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
