1     M         0.845   0.851   0.888   1.220   1.211   1.218   0.874   0.883   0.935
2     G         0.845   0.851   0.888   0.859   0.873   0.919   0.874   0.883   0.935
3     I        -1.145  -1.090  -1.191  -1.053  -0.920  -1.268  -1.163  -1.073  -1.193
4     D         0.845   0.851   0.888   1.089   1.091   1.110   0.874   0.883   0.935
5     H        -0.261  -0.519  -0.443   0.077  -0.346  -0.322  -0.353  -0.772  -0.686
6     T        -1.837  -1.970  -1.787  -1.569  -1.757  -1.547  -1.643  -1.760  -1.515
7     S        -1.837  -1.970  -1.787  -1.597  -1.813  -1.638  -1.643  -1.760  -1.515
8     K        -0.398  -0.392  -0.407  -0.724  -0.720  -0.784  -0.564  -0.565  -0.625
9     Q        -1.309  -1.348  -1.224  -1.019  -1.090  -1.011  -1.403  -1.427  -1.233
10    H         0.845   0.851   0.888   1.109   1.107   1.126   0.874   0.883   0.935
11    K        -2.458  -2.402  -2.208  -2.210  -2.082  -1.781  -2.002  -1.934  -1.673
12    R        -0.398  -0.457  -0.441  -0.804  -0.901  -0.879  -0.564  -0.669  -0.682
13    S        -1.145  -1.229  -1.208  -1.041  -1.153  -1.137  -1.163  -1.259  -1.213
14    G        -1.309  -1.292  -1.200  -1.308  -1.227  -1.126  -1.403  -1.343  -1.205
15    H        -1.145  -1.229  -1.208  -0.688  -0.800  -0.828  -1.163  -1.259  -1.213
16    R         0.845   0.851   0.888   0.530   0.555   0.647   0.874   0.883   0.935
17    T        -1.837  -1.801  -1.773  -1.621  -1.625  -1.573  -1.643  -1.613  -1.502
18    A        -0.398  -0.392  -0.407  -0.647  -0.630  -0.698  -0.564  -0.565  -0.625
19    P         0.845   0.851   0.888   1.015   1.022   1.048   0.874   0.883   0.935
20    K        -0.398  -0.392  -0.407  -0.672  -0.664  -0.708  -0.564  -0.565  -0.625
21    S         0.845   0.851   0.888   0.916   0.927   0.966   0.874   0.883   0.935
22    D        -0.618  -0.615  -0.452  -0.472  -0.488  -0.285  -0.924  -0.935  -0.701
23    N         0.845   0.851   0.888   1.070   1.067   1.094   0.874   0.883   0.935
24    V         0.845   0.851   0.888   0.819   0.821   0.886   0.874   0.883   0.935
25    Y         0.845   0.851   0.888   1.189   1.183   1.193   0.874   0.883   0.935
26    L         0.845   0.851   0.888   0.728   0.739   0.811   0.874   0.883   0.935
27    K        -0.781  -0.763  -1.174  -0.685  -0.682  -1.139  -0.684  -0.679  -1.173
28    L         0.074   0.136  -0.367   0.150   0.192  -0.347   0.116   0.195  -0.559
29    L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
30    V         0.845   0.851   0.888   0.813   0.805   0.881   0.874   0.883   0.935
31    K         0.074   0.136  -0.367  -0.011   0.109  -0.693   0.116   0.195  -0.559
32    L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
33    Y         0.845   0.851   0.888   1.194   1.217   1.197   0.874   0.883   0.935
34    T        -1.969  -1.652  -1.763  -2.180  -1.736  -1.849  -1.777  -1.443  -1.493
35    F         0.845   0.851   0.888   0.994   0.976   1.031   0.874   0.883   0.935
36    L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
37    A         0.845   0.851   0.888   0.675   0.657   0.767   0.874   0.883   0.935
38    R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
39    R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
40    T         0.845   0.851   0.888   0.901   0.906   0.954   0.874   0.883   0.935
41    D         0.845   0.851   0.888   1.090   1.125   1.110   0.874   0.883   0.935
42    A        -0.674  -0.627  -0.444  -1.005  -0.866  -0.599  -1.020  -0.955  -0.688
43    P        -1.695  -1.877  -1.783  -1.530  -1.873  -1.880  -1.493  -1.669  -1.512
44    F         0.845   0.851   0.888   0.994   0.976   1.031   0.874   0.883   0.935
45    N         0.845   0.851   0.888   1.072   1.088   1.096   0.874   0.883   0.935
46    K         0.845   0.851   0.888   0.660   0.712   0.754   0.874   0.883   0.935
47    V        -1.031  -1.121  -1.202  -1.057  -1.240  -1.443  -1.020  -1.129  -1.207
48    V        -0.674  -0.635  -0.453  -0.783  -0.739  -0.476  -1.020  -0.970  -0.703
49    L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
50    K        -0.326  -0.349  -0.435  -0.589  -0.598  -0.840  -0.452  -0.497  -0.671
51    A        -1.841  -1.760  -1.777  -1.941  -1.865  -1.865  -1.682  -1.606  -1.507
52    L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
53    F         0.845   0.851   0.888   0.994   0.976   1.031   0.874   0.883   0.935
54    L        -1.031  -1.185  -1.208  -0.865  -1.037  -0.985  -1.020  -1.200  -1.214
55    S         0.845   0.851   0.888   0.922   0.984   0.972   0.874   0.883   0.935
56    K         0.074  -0.094  -0.384  -0.011  -0.193  -0.729   0.116  -0.116  -0.587
57    I        -1.031  -1.121  -1.202  -0.720  -0.844  -1.068  -1.020  -1.129  -1.207
58    N         0.845   0.851   0.888   1.072   1.088   1.096   0.874   0.883   0.935
59    R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
60    P         0.845   0.851   0.888   1.012   1.025   1.046   0.874   0.883   0.935
61    P         0.845   0.851   0.888   1.012   1.025   1.046   0.874   0.883   0.935
62    V        -1.031  -1.185  -1.208  -0.825  -0.998  -0.987  -1.020  -1.200  -1.214
63    S         0.845   0.851   0.888   0.922   0.984   0.972   0.874   0.883   0.935
64    V        -1.288  -1.262  -1.207  -1.252  -1.141  -1.087  -1.398  -1.331  -1.214
65    S         0.074  -0.014  -0.385   0.295   0.245  -0.387   0.116  -0.005  -0.588
66    R        -0.562  -0.580  -0.451  -1.097  -1.124  -0.891  -0.830  -0.874  -0.699
67    I         0.845   0.851   0.888   1.037   1.059   1.067   0.874   0.883   0.935
68    A        -1.355  -1.313  -1.221  -1.521  -1.504  -1.318  -1.398  -1.365  -1.229
69    R        -1.226  -1.292  -1.222  -1.597  -1.693  -1.402  -1.304  -1.375  -1.232
70    A        -1.355  -1.434  -1.228  -1.493  -1.626  -1.260  -1.398  -1.503  -1.238
71    L        -0.326  -0.348  -0.406  -0.411  -0.476  -0.544  -0.452  -0.495  -0.624
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    K         0.845   0.851   0.888   0.669   0.721   0.762   0.874   0.883   0.935
75    Q        -1.145  -1.301  -1.225  -0.786  -1.003  -1.045  -1.163  -1.354  -1.235
76    E        -1.500  -1.412  -1.212  -1.700  -1.573  -1.284  -1.588  -1.475  -1.220
77    G        -1.031  -0.924  -1.189  -0.844  -0.720  -1.047  -1.020  -0.923  -1.192
78    A        -1.695  -1.800  -1.778  -1.586  -1.728  -1.646  -1.493  -1.616  -1.508
79    A        -1.695  -1.665  -1.770  -1.509  -1.489  -1.499  -1.493  -1.493  -1.501
80    N        -3.331  -3.245  -2.863  -2.556  -2.451  -2.050  -2.345  -2.257  -1.865
81    K         0.845   0.851   0.888   0.660   0.712   0.754   0.874   0.883   0.935
82    T         0.074  -0.014  -0.385   0.295   0.198  -0.326   0.116  -0.005  -0.588
83    V        -1.500  -1.396  -1.215  -1.525  -1.388  -1.128  -1.588  -1.456  -1.223
84    V         0.845   0.851   0.888   0.813   0.805   0.881   0.874   0.883   0.935
85    V         0.074   0.052  -0.372   0.208   0.174  -0.371   0.116   0.085  -0.567
86    V         0.845   0.851   0.888   0.813   0.805   0.881   0.874   0.883   0.935
87    G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
88    T         0.845   0.851   0.888   0.901   0.906   0.954   0.874   0.883   0.935
89    V         0.845   0.851   0.888   0.813   0.805   0.881   0.874   0.883   0.935
90    T         0.845   0.851   0.888   0.901   0.906   0.954   0.874   0.883   0.935
91    D         0.845   0.851   0.888   1.090   1.125   1.110   0.874   0.883   0.935
92    D         0.845   0.851   0.888   1.090   1.125   1.110   0.874   0.883   0.935
93    A        -1.969  -1.932  -1.774  -1.652  -1.566  -1.435  -1.777  -1.723  -1.504
94    R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
95    I        -1.031  -0.892  -1.175  -0.903  -0.723  -1.007  -1.020  -0.830  -1.175
96    F        -1.226  -1.176  -1.200  -1.284  -1.231  -1.213  -1.304  -1.207  -1.205
97    E        -1.226  -1.188  -1.215  -0.973  -0.963  -0.961  -1.304  -1.283  -1.224
98    F        -1.226  -1.188  -1.215  -1.163  -1.195  -1.200  -1.304  -1.283  -1.224
99    P         0.845   0.851   0.888   1.012   1.025   1.046   0.874   0.883   0.935
100   K         0.845   0.851   0.888   0.660   0.712   0.754   0.874   0.883   0.935
101   T        -1.969  -1.957  -1.778  -1.999  -2.006  -1.773  -1.777  -1.744  -1.507
102   T        -0.562  -0.599  -0.451  -0.620  -0.668  -0.492  -0.830  -0.907  -0.699
103   V        -0.326  -0.260  -0.435  -0.292  -0.210  -0.462  -0.452  -0.359  -0.672
104   A         0.845   0.851   0.888   0.675   0.657   0.767   0.874   0.883   0.935
105   A         0.845   0.851   0.888   0.675   0.657   0.767   0.874   0.883   0.935
106   L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
107   R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
108   F         0.845   0.851   0.888   0.994   0.976   1.031   0.874   0.883   0.935
109   T         0.845   0.851   0.888   0.901   0.906   0.954   0.874   0.883   0.935
110   A        -1.031  -1.121  -1.202  -1.145  -1.291  -1.395  -1.020  -1.129  -1.207
111   G        -1.355  -1.434  -1.228  -1.320  -1.437  -1.175  -1.398  -1.503  -1.238
112   A         0.845   0.851   0.888   0.675   0.657   0.767   0.874   0.883   0.935
113   R        -0.562  -0.391  -0.417  -1.097  -0.790  -0.832  -0.830  -0.563  -0.641
114   A         0.074   0.208  -0.371   0.077   0.196  -0.448   0.116   0.283  -0.566
115   K        -1.031  -0.737  -1.176  -1.289  -0.877  -1.442  -1.020  -0.660  -1.176
116   I         0.845   0.851   0.888   1.037   1.059   1.067   0.874   0.883   0.935
117   V        -1.226  -1.298  -1.211  -1.333  -1.419  -1.204  -1.304  -1.359  -1.219
118   K         0.074  -0.094  -0.384   0.008  -0.169  -0.663   0.116  -0.116  -0.587
119   A         0.074   0.208  -0.371   0.075   0.192  -0.455   0.116   0.283  -0.566
120   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
121   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
122   E         0.074  -0.094  -0.384   0.497   0.317  -0.143   0.116  -0.116  -0.587
123   C        -1.355  -1.256  -1.200  -1.387  -1.306  -1.130  -1.398  -1.283  -1.205
124   I        -0.562  -0.580  -0.451  -0.581  -0.648  -0.512  -0.830  -0.874  -0.699
125   T         0.845   0.851   0.888   0.901   0.906   0.954   0.874   0.883   0.935
126   L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
127   D         0.845   0.851   0.888   1.090   1.125   1.110   0.874   0.883   0.935
128   Q         0.845   0.851   0.888   1.149   1.176   1.160   0.874   0.883   0.935
129   L         0.845   0.851   0.888   0.731   0.710   0.814   0.874   0.883   0.935
130   A         0.845   0.851   0.888   0.675   0.657   0.767   0.874   0.883   0.935
131   V        -0.674  -0.607  -0.448  -1.032  -0.956  -0.657  -1.020  -0.920  -0.693
132   R         0.074  -0.094  -0.384  -0.072  -0.262  -0.573   0.116  -0.116  -0.587
133   A         0.074  -0.094  -0.384   0.021  -0.214  -0.658   0.116  -0.116  -0.587
134   P         0.845   0.851   0.888   1.012   1.025   1.046   0.874   0.883   0.935
135   K        -0.674  -0.627  -0.444  -1.032  -0.895  -0.622  -1.020  -0.955  -0.688
136   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
137   Q        -1.695  -1.877  -1.783  -1.177  -1.428  -1.441  -1.493  -1.669  -1.512
138   N         0.845   0.851   0.888   1.072   1.088   1.096   0.874   0.883   0.935
139   T         0.845   0.851   0.888   0.901   0.906   0.954   0.874   0.883   0.935
140   L        -0.326  -0.348  -0.406  -0.436  -0.509  -0.586  -0.452  -0.495  -0.624
141   I        -1.288  -1.274  -1.207  -1.251  -1.220  -1.037  -1.398  -1.349  -1.214
142   L        -0.674  -0.583  -0.449  -1.032  -0.913  -0.660  -1.020  -0.880  -0.696
143   R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
144   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
145   P        -1.031  -1.121  -1.202  -0.801  -0.909  -1.142  -1.020  -1.129  -1.207
146   R        -0.562  -0.599  -0.451  -1.097  -1.159  -0.891  -0.830  -0.907  -0.699
147   N        -1.031  -0.939  -1.191  -0.639  -0.510  -0.986  -1.020  -0.938  -1.194
148   S        -0.674  -0.538  -0.430  -1.005  -0.788  -0.610  -1.020  -0.804  -0.664
149   R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
150   E         0.074  -0.014  -0.385   0.497   0.410  -0.144   0.116  -0.005  -0.588
151   A         0.845   0.851   0.888   0.675   0.657   0.767   0.874   0.883   0.935
152   V        -1.031  -0.939  -1.191  -0.860  -0.762  -1.119  -1.020  -0.938  -1.194
153   R         0.074  -0.094  -0.384  -0.130  -0.342  -0.773   0.116  -0.116  -0.587
154   H         0.845   0.851   0.888   1.118   1.182   1.134   0.874   0.883   0.935
155   F         0.845   0.851   0.888   0.994   0.976   1.031   0.874   0.883   0.935
156   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
157   M        -0.326  -0.186  -0.393  -0.066   0.096  -0.195  -0.452  -0.249  -0.601
158   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
159   P         0.845   0.851   0.888   1.012   1.025   1.046   0.874   0.883   0.935
160   H         0.845   0.851   0.888   1.118   1.182   1.134   0.874   0.883   0.935
161   K         0.845   0.851   0.888   0.660   0.712   0.754   0.874   0.883   0.935
162   G        -1.584  -1.472  -1.234  -1.462  -1.218  -0.987  -1.682  -1.550  -1.244
163   K         0.845   0.851   0.888   0.660   0.712   0.754   0.874   0.883   0.935
164   A         0.074  -0.094  -0.384   0.021  -0.214  -0.658   0.116  -0.116  -0.587
165   P         0.845   0.851   0.888   1.012   1.025   1.046   0.874   0.883   0.935
166   R        -0.562  -0.599  -0.451  -0.829  -0.837  -0.559  -0.830  -0.907  -0.699
167   I        -0.674  -0.627  -0.444  -0.783  -0.744  -0.474  -1.020  -0.955  -0.688
168   L        -2.522  -2.460  -2.211  -2.431  -2.447  -1.942  -2.061  -1.986  -1.675
169   S         0.845   0.851   0.888   0.922   0.984   0.972   0.874   0.883   0.935
170   T        -1.500  -1.391  -1.212  -1.649  -1.444  -1.200  -1.588  -1.448  -1.219
171   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
172   R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
173   K         0.845   0.851   0.888   0.660   0.712   0.754   0.874   0.883   0.935
174   F         0.845   0.851   0.888   0.994   0.976   1.031   0.874   0.883   0.935
175   E         0.845   0.851   0.888   1.090   1.101   1.110   0.874   0.883   0.935
176   R        -0.667  -0.767  -1.168  -0.749  -0.884  -1.416  -0.546  -0.681  -1.166
177   A         0.845   0.851   0.888   0.675   0.657   0.767   0.874   0.883   0.935
178   R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
179   G         0.845   0.851   0.888   0.857   0.865   0.918   0.874   0.883   0.935
180   R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
181   R         0.845   0.851   0.888   0.526   0.530   0.643   0.874   0.883   0.935
182   R        -0.326  -0.348  -0.406  -0.686  -0.719  -0.813  -0.452  -0.495  -0.624
183   S         0.845   0.851   0.888   0.922   0.984   0.972   0.874   0.883   0.935
184   K        -0.562  -0.536  -0.442  -1.097  -1.045  -0.877  -0.830  -0.801  -0.684
185   G        -0.562  -0.520  -0.448  -0.774  -0.723  -0.654  -0.830  -0.773  -0.695
186   F         0.845   0.851   0.888   0.994   0.976   1.031   0.874   0.883   0.935
187   K         0.845   0.851   0.888   0.660   0.712   0.754   0.874   0.883   0.935
188   V         0.845   0.851   0.888   0.813   0.805   0.881   0.874   0.883   0.935
* 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/P0CX50
Output conservation file - output/P0CX50
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
