1     M         0.897   0.904   0.954   1.287   1.279   1.307   0.935   0.946   1.021
2     A         0.145  -0.020  -0.273  -0.010  -0.193  -0.508   0.180  -0.052  -0.480
3     N         0.897   0.904   0.954   1.154   1.155   1.198   0.935   0.946   1.021
4     L         0.897   0.904   0.954   0.891   0.893   0.979   0.935   0.946   1.021
5     R         0.145   0.080  -0.266  -0.204  -0.279  -0.783   0.180   0.091  -0.468
6     T         0.897   0.904   0.954   1.185   1.184   1.223   0.935   0.946   1.021
7     Q         0.145   0.080  -0.266   0.588   0.506  -0.023   0.180   0.091  -0.468
8     K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
9     R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
10    L         0.897   0.904   0.954   0.891   0.893   0.979   0.935   0.946   1.021
11    A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
12    A         0.145  -0.020  -0.273  -0.002  -0.181  -0.481   0.180  -0.052  -0.480
13    S         0.897   0.904   0.954   1.144   1.148   1.189   0.935   0.946   1.021
14    V         0.897   0.904   0.954   1.085   1.088   1.140   0.935   0.946   1.021
15    V        -1.848  -1.649  -1.639  -1.798  -1.510  -1.545  -1.709  -1.499  -1.419
16    G        -0.245  -0.235  -0.284  -0.113  -0.107  -0.305  -0.387  -0.377  -0.499
17    V        -0.933  -0.808  -1.050  -0.600  -0.439  -0.885  -0.954  -0.821  -1.081
18    G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
19    K         0.145  -0.020  -0.273   0.084  -0.101  -0.402   0.180  -0.052  -0.480
20    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
21    K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
22    V        -0.584  -0.568  -0.354  -0.584  -0.563  -0.259  -0.954  -0.936  -0.619
23    W         0.897   0.904   0.954   1.337   1.332   1.349   0.935   0.946   1.021
24    L        -0.475  -0.430  -0.342  -0.505  -0.444  -0.294  -0.765  -0.696  -0.598
25    D         0.897   0.904   0.954   1.253   1.250   1.280   0.935   0.946   1.021
26    P         0.897   0.904   0.954   1.317   1.311   1.332   0.935   0.946   1.021
27    N        -0.577  -0.552  -1.036  -0.046  -0.023  -0.706  -0.482  -0.458  -1.064
28    E         0.897   0.904   0.954   1.005   1.005   1.074   0.935   0.946   1.021
29    T        -2.180  -2.279  -2.071  -1.727  -1.879  -1.755  -1.804  -1.884  -1.594
30    S        -1.123  -1.026  -1.081  -0.926  -0.792  -0.967  -1.237  -1.135  -1.122
31    E         0.145   0.080  -0.266   0.411   0.334  -0.132   0.180   0.091  -0.468
32    I         0.897   0.904   0.954   1.151   1.149   1.195   0.935   0.946   1.021
33    A        -0.584  -0.569  -0.354  -0.966  -0.898  -0.537  -0.954  -0.936  -0.619
34    Q        -0.475  -0.358  -0.313  -0.314  -0.129  -0.126  -0.765  -0.575  -0.548
35    A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
36    N         0.897   0.904   0.954   1.154   1.155   1.198   0.935   0.946   1.021
37    S         0.897   0.904   0.954   1.144   1.148   1.189   0.935   0.946   1.021
38    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
39    N        -1.123  -0.970  -1.068  -0.814  -0.590  -0.746  -1.237  -1.037  -1.105
40    A        -1.580  -1.740  -1.643  -1.560  -1.714  -1.448  -1.426  -1.583  -1.421
41    I        -0.245  -0.278  -0.330   0.018  -0.042  -0.208  -0.387  -0.445  -0.577
42    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
43    K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
44    L         0.897   0.904   0.954   0.891   0.893   0.979   0.935   0.946   1.021
45    V        -0.933  -0.865  -1.050  -0.557  -0.464  -0.736  -0.954  -0.862  -1.081
46    K        -1.265  -1.426  -1.611  -1.309  -1.544  -1.939  -1.048  -1.233  -1.391
47    N        -0.584  -0.568  -0.352  -0.466  -0.440  -0.151  -0.954  -0.935  -0.614
48    G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
49    T        -0.584  -0.568  -0.352  -0.667  -0.680  -0.357  -0.954  -0.935  -0.614
50    I        -0.245  -0.235  -0.284   0.018   0.023  -0.124  -0.387  -0.377  -0.499
51    V        -0.475  -0.512  -0.349  -0.394  -0.466  -0.252  -0.765  -0.837  -0.609
52    K        -0.475  -0.482  -0.346  -1.088  -1.112  -0.900  -0.765  -0.785  -0.604
53    K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
54    A        -0.245  -0.120  -0.284   0.055   0.254  -0.192  -0.387  -0.199  -0.499
55    V        -1.722  -1.599  -1.630  -1.387  -1.247  -1.250  -1.615  -1.508  -1.410
56    T        -2.180  -2.118  -2.052  -1.931  -1.852  -1.975  -1.804  -1.747  -1.579
57    V        -1.183  -1.074  -1.090  -0.911  -0.759  -0.760  -1.332  -1.212  -1.132
58    H         0.897   0.904   0.954   1.195   1.192   1.232   0.935   0.946   1.021
59    S         0.897   0.904   0.954   1.144   1.148   1.189   0.935   0.946   1.021
60    K         0.145   0.208  -0.259  -0.204  -0.117  -0.770   0.180   0.261  -0.456
61    S        -0.933  -0.888  -1.053  -0.557  -0.499  -0.869  -0.954  -0.906  -1.085
62    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
63    T        -1.390  -1.370  -1.099  -1.469  -1.465  -1.083  -1.520  -1.497  -1.143
64    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
65    A        -1.248  -1.257  -1.093  -1.691  -1.691  -1.397  -1.332  -1.347  -1.136
66    H        -1.848  -1.691  -1.628  -1.592  -1.409  -1.238  -1.709  -1.550  -1.407
67    A        -2.180  -2.195  -2.063  -2.201  -2.177  -1.989  -1.804  -1.817  -1.588
68    Q        -1.848  -1.806  -1.637  -1.893  -1.858  -1.573  -1.709  -1.673  -1.416
69    S        -0.584  -0.568  -0.352  -0.877  -0.900  -0.557  -0.954  -0.935  -0.614
70    K         0.145  -0.020  -0.273  -0.010  -0.237  -0.717   0.180  -0.052  -0.480
71    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
72    E        -2.386  -2.355  -2.071  -2.425  -2.365  -1.873  -1.993  -1.951  -1.594
73    G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
74    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
75    H         0.897   0.904   0.954   1.195   1.192   1.232   0.935   0.946   1.021
76    S        -1.580  -1.604  -1.622  -1.112  -1.193  -1.323  -1.426  -1.443  -1.402
77    G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
78    Y        -0.245  -0.371  -0.338   0.204   0.011  -0.014  -0.387  -0.598  -0.591
79    G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
80    K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
81    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
82    K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
83    G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
84    T         0.897   0.904   0.954   1.185   1.184   1.223   0.935   0.946   1.021
85    R        -1.183  -1.096  -1.090  -1.854  -1.690  -1.688  -1.332  -1.228  -1.132
86    E        -1.123  -1.173  -1.091  -0.919  -0.975  -0.833  -1.237  -1.292  -1.134
87    A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
88    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
89    L        -0.475  -0.358  -0.313  -0.326  -0.118  -0.167  -0.765  -0.575  -0.548
90    P         0.145   0.189  -0.256   0.707   0.746   0.069   0.180   0.237  -0.452
91    S        -0.933  -1.005  -1.081  -0.668  -0.815  -1.060  -0.954  -1.079  -1.121
92    Q        -0.577  -0.570  -1.043  -0.082  -0.079  -0.886  -0.482  -0.475  -1.073
93    V         0.897   0.904   0.954   1.085   1.088   1.140   0.935   0.946   1.021
94    V        -0.584  -0.569  -0.354  -0.749  -0.744  -0.415  -0.954  -0.937  -0.619
95    W         0.897   0.904   0.954   1.337   1.332   1.349   0.935   0.946   1.021
96    I        -0.475  -0.358  -0.313  -0.214  -0.029  -0.053  -0.765  -0.575  -0.548
97    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
98    R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
99    L        -0.584  -0.568  -0.352  -0.710  -0.663  -0.333  -0.954  -0.935  -0.614
100   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
101   V         0.897   0.904   0.954   1.085   1.088   1.140   0.935   0.946   1.021
102   L         0.145   0.080  -0.266   0.284   0.206  -0.257   0.180   0.091  -0.468
103   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
104   R         0.145   0.218  -0.259  -0.204  -0.105  -0.770   0.180   0.274  -0.456
105   L         0.897   0.904   0.954   0.891   0.893   0.979   0.935   0.946   1.021
106   L         0.897   0.904   0.954   0.891   0.893   0.979   0.935   0.946   1.021
107   A        -1.580  -1.740  -1.643  -1.876  -2.068  -1.815  -1.426  -1.583  -1.421
108   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
109   Y         0.897   0.904   0.954   1.270   1.269   1.293   0.935   0.946   1.021
110   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
111   D        -1.123  -1.241  -1.100  -0.924  -1.131  -1.046  -1.237  -1.359  -1.144
112   A        -1.123  -1.188  -1.100  -1.313  -1.343  -1.097  -1.237  -1.314  -1.144
113   G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
114   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
115   I         0.897   0.904   0.954   1.151   1.149   1.195   0.935   0.946   1.021
116   D         0.897   0.904   0.954   1.253   1.250   1.280   0.935   0.946   1.021
117   K         0.145   0.242  -0.257  -0.010   0.121  -0.681   0.180   0.306  -0.454
118   H         0.897   0.904   0.954   1.195   1.192   1.232   0.935   0.946   1.021
119   L         0.897   0.904   0.954   0.891   0.893   0.979   0.935   0.946   1.021
120   Y         0.897   0.904   0.954   1.270   1.269   1.293   0.935   0.946   1.021
121   H         0.897   0.904   0.954   1.195   1.192   1.232   0.935   0.946   1.021
122   V        -2.512  -2.408  -2.075  -2.104  -1.982  -1.545  -2.087  -1.996  -1.597
123   L         0.897   0.904   0.954   0.891   0.893   0.979   0.935   0.946   1.021
124   Y         0.897   0.904   0.954   1.270   1.269   1.293   0.935   0.946   1.021
125   K        -0.933  -1.064  -1.074  -1.058  -1.207  -1.163  -0.954  -1.106  -1.110
126   E        -1.848  -1.802  -1.647  -1.787  -1.757  -1.589  -1.709  -1.676  -1.426
127   S         0.145   0.208  -0.259  -0.002   0.084  -0.462   0.180   0.261  -0.456
128   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
129   G         0.897   0.904   0.954   1.127   1.126   1.175   0.935   0.946   1.021
130   N         0.897   0.904   0.954   1.154   1.155   1.198   0.935   0.946   1.021
131   A        -0.475  -0.380  -0.324  -0.542  -0.346  -0.396  -0.765  -0.612  -0.567
132   F         0.897   0.904   0.954   1.350   1.343   1.360   0.935   0.946   1.021
133   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
134   H         0.897   0.904   0.954   1.195   1.192   1.232   0.935   0.946   1.021
135   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
136   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
137   A        -0.245  -0.172  -0.299  -0.495  -0.378  -0.515  -0.387  -0.278  -0.524
138   L         0.145   0.080  -0.266   0.276   0.197  -0.284   0.180   0.091  -0.468
139   V        -0.245  -0.235  -0.284  -0.027  -0.018  -0.144  -0.387  -0.377  -0.499
140   E         0.897   0.904   0.954   1.005   1.005   1.074   0.935   0.946   1.021
141   H         0.897   0.904   0.954   1.195   1.192   1.232   0.935   0.946   1.021
142   I         0.145   0.080  -0.266   0.535   0.452  -0.092   0.180   0.091  -0.468
143   I        -0.933  -1.064  -1.074  -0.513  -0.681  -0.744  -0.954  -1.106  -1.110
144   Q        -1.722  -1.709  -1.643  -1.892  -1.958  -1.934  -1.615  -1.601  -1.422
145   A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
146   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
147   A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
148   D        -0.475  -0.358  -0.313  -0.419  -0.246  -0.201  -0.765  -0.575  -0.548
149   A         0.145  -0.020  -0.273  -0.063  -0.270  -0.686   0.180  -0.052  -0.480
150   Q        -2.386  -2.441  -2.080  -2.067  -2.173  -1.742  -1.993  -2.015  -1.601
151   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
152   E        -0.245  -0.235  -0.284  -0.096  -0.088  -0.188  -0.387  -0.377  -0.499
153   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
154   A        -0.933  -0.888  -1.053  -1.146  -1.077  -1.216  -0.954  -0.906  -1.085
155   L        -0.475  -0.512  -0.349  -0.569  -0.632  -0.375  -0.765  -0.837  -0.609
156   N        -1.580  -1.417  -1.610  -1.487  -1.293  -1.408  -1.426  -1.267  -1.389
157   E        -0.245  -0.257  -0.322  -0.076  -0.098  -0.213  -0.387  -0.411  -0.563
158   E        -0.475  -0.417  -0.339  -0.447  -0.361  -0.268  -0.765  -0.674  -0.593
159   A        -0.933  -1.064  -1.074  -1.014  -1.140  -1.040  -0.954  -1.106  -1.110
160   E        -0.475  -0.512  -0.349  -0.419  -0.481  -0.246  -0.765  -0.837  -0.609
161   A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
162   R         0.145  -0.020  -0.273  -0.204  -0.417  -0.797   0.180  -0.052  -0.480
163   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
164   L        -2.386  -2.217  -2.071  -2.316  -2.132  -1.775  -1.993  -1.850  -1.594
165   K        -0.584  -0.535  -0.349  -1.407  -1.309  -0.932  -0.954  -0.878  -0.609
166   N        -0.933  -1.064  -1.074  -0.690  -0.862  -0.975  -0.954  -1.106  -1.110
167   R        -0.475  -0.512  -0.349  -1.196  -1.263  -0.932  -0.765  -0.837  -0.609
168   A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
169   A         0.897   0.904   0.954   0.606   0.627   0.744   0.935   0.946   1.021
170   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
171   D        -0.933  -0.872  -1.055  -0.641  -0.576  -0.787  -0.954  -0.889  -1.087
172   R         0.897   0.904   0.954   0.468   0.483   0.629   0.935   0.946   1.021
173   R         0.145  -0.020  -0.273  -0.204  -0.417  -0.797   0.180  -0.052  -0.480
174   A        -0.933  -1.011  -1.071  -1.083  -1.170  -1.203  -0.954  -1.034  -1.107
175   Q        -1.580  -1.740  -1.643  -1.327  -1.588  -1.629  -1.426  -1.583  -1.421
176   R        -0.245  -0.235  -0.284  -0.799  -0.775  -0.855  -0.387  -0.377  -0.499
177   V        -1.265  -1.402  -1.614  -0.734  -0.909  -1.271  -1.048  -1.209  -1.394
178   A        -0.933  -0.888  -1.053  -1.104  -1.035  -1.162  -0.954  -0.906  -1.085
179   E         0.145  -0.020  -0.273   0.331   0.100  -0.406   0.180  -0.052  -0.480
180   K         0.897   0.904   0.954   0.685   0.699   0.809   0.935   0.946   1.021
181   R         0.145   0.218  -0.259  -0.204  -0.105  -0.770   0.180   0.274  -0.456
182   D        -0.577  -0.677  -1.046  -0.183  -0.315  -0.790  -0.482  -0.617  -1.076
183   A        -0.475  -0.482  -0.346  -0.807  -0.799  -0.531  -0.765  -0.785  -0.604
184   L         0.145   0.151  -0.252   0.284   0.288  -0.237   0.180   0.187  -0.445
185   L        -1.580  -1.641  -1.628  -1.327  -1.447  -1.394  -1.426  -1.491  -1.407
186   K        -1.951  -1.993  -1.655  -2.216  -2.232  -1.703  -1.814  -1.837  -1.432
187   E        -0.315  -0.281  -0.291  -0.398  -0.342  -0.459  -0.499  -0.449  -0.510
188   D        -1.856  -1.810  -1.646  -1.876  -1.833  -1.496  -1.719  -1.671  -1.424
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   A        -1.929  -1.966  -1.648  -2.098  -2.111  -1.685  -1.804  -1.814  -1.426
* 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/P0CX82
Output conservation file - output/P0CX82
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
