1     M         0.736   0.750   0.778   1.005   1.012   1.026   0.769   0.788   0.828
2     A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
3     R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
4     R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
5     P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
6     A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
7     R        -0.045  -0.162  -0.525  -0.217  -0.361  -0.913  -0.009  -0.169  -0.749
8     C         0.736   0.750   0.778   0.987   0.994   1.011   0.769   0.788   0.828
9     Y         0.736   0.750   0.778   0.859   0.876   0.905   0.769   0.788   0.828
10    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
11    Y         0.736   0.750   0.778   0.859   0.876   0.905   0.769   0.788   0.828
12    Q        -0.803  -0.731  -0.581  -0.786  -0.671  -0.474  -1.177  -1.064  -0.844
13    K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
14    N         0.736   0.750   0.778   0.856   0.869   0.902   0.769   0.788   0.828
15    K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
16    P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
17    Y        -0.045  -0.162  -0.525   0.221   0.083  -0.476  -0.009  -0.169  -0.749
18    P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
19    K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
20    S         0.736   0.750   0.778   0.797   0.818   0.853   0.769   0.788   0.828
21    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
22    Y        -0.045  -0.264  -0.531   0.221  -0.050  -0.487  -0.009  -0.316  -0.759
23    N         0.736   0.750   0.778   0.856   0.869   0.902   0.769   0.788   0.828
24    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
25    A        -0.045  -0.264  -0.531  -0.085  -0.362  -0.760  -0.009  -0.316  -0.759
26    V         0.736   0.750   0.778   0.775   0.797   0.835   0.769   0.788   0.828
27    P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
28    D         0.736   0.750   0.778   0.847   0.869   0.894   0.769   0.788   0.828
29    S        -1.493  -1.476  -1.372  -1.534  -1.517  -1.405  -1.566  -1.559  -1.400
30    K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
31    I         0.736   0.750   0.778   0.766   0.780   0.827   0.769   0.788   0.828
32    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
33    I         0.736   0.750   0.778   0.766   0.780   0.827   0.769   0.788   0.828
34    Y        -0.690  -0.727  -0.583  -0.702  -0.784  -0.579  -0.982  -1.056  -0.848
35    D         0.736   0.750   0.778   0.847   0.869   0.894   0.769   0.788   0.828
36    L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
37    G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
38    K        -0.690  -0.517  -0.551  -1.220  -0.907  -0.964  -0.982  -0.706  -0.794
39    K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
40    K        -0.803  -0.751  -0.580  -1.430  -1.345  -1.017  -1.177  -1.097  -0.842
41    A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
42    T        -1.165  -1.254  -1.343  -0.825  -0.946  -1.124  -1.177  -1.271  -1.364
43    V         0.736   0.750   0.778   0.775   0.797   0.835   0.769   0.788   0.828
44    D         0.736   0.750   0.778   0.847   0.869   0.894   0.769   0.788   0.828
45    E        -0.450  -0.623  -0.582  -0.355  -0.641  -0.615  -0.593  -0.880  -0.846
46    F         0.736   0.750   0.778   0.871   0.884   0.915   0.769   0.788   0.828
47    P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
48    L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
49    C         0.736   0.750   0.778   0.987   0.994   1.011   0.769   0.788   0.828
50    V        -0.690  -0.517  -0.551  -0.831  -0.542  -0.634  -0.982  -0.706  -0.794
51    H         0.736   0.750   0.778   0.990   1.001   1.013   0.769   0.788   0.828
52    L        -0.045  -0.264  -0.531   0.061  -0.192  -0.553  -0.009  -0.316  -0.759
53    V         0.736   0.750   0.778   0.775   0.797   0.835   0.769   0.788   0.828
54    S         0.736   0.750   0.778   0.797   0.818   0.853   0.769   0.788   0.828
55    N         0.736   0.750   0.778   0.856   0.869   0.902   0.769   0.788   0.828
56    E         0.736   0.750   0.778   0.822   0.836   0.874   0.769   0.788   0.828
57    L        -1.363  -1.452  -1.371  -1.478  -1.596  -1.508  -1.469  -1.555  -1.399
58    E         0.736   0.750   0.778   0.822   0.836   0.874   0.769   0.788   0.828
59    Q         0.736   0.750   0.778   0.908   0.926   0.945   0.769   0.788   0.828
60    L        -0.450  -0.435  -0.530  -0.515  -0.491  -0.662  -0.593  -0.575  -0.759
61    S        -0.450  -0.435  -0.530  -0.342  -0.319  -0.483  -0.593  -0.575  -0.759
62    S         0.736   0.750   0.778   0.797   0.818   0.853   0.769   0.788   0.828
63    E         0.736   0.750   0.778   0.822   0.836   0.874   0.769   0.788   0.828
64    A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
65    L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
66    E         0.736   0.750   0.778   0.822   0.836   0.874   0.769   0.788   0.828
67    A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
68    A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
69    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
70    I         0.736   0.750   0.778   0.766   0.780   0.827   0.769   0.788   0.828
71    C        -0.045   0.084  -0.515   0.362   0.494  -0.323  -0.009   0.157  -0.733
72    A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
73    N         0.736   0.750   0.778   0.856   0.869   0.902   0.769   0.788   0.828
74    K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
75    Y         0.736   0.750   0.778   0.859   0.876   0.905   0.769   0.788   0.828
76    M        -2.200  -1.980  -1.935  -2.166  -1.902  -1.753  -2.053  -1.833  -1.681
77    T        -0.690  -0.727  -0.583  -0.637  -0.742  -0.558  -0.982  -1.056  -0.848
78    T        -0.045   0.092  -0.514  -0.074   0.096  -0.637  -0.009   0.166  -0.732
79    V        -1.985  -1.991  -1.926  -1.825  -1.816  -1.628  -1.858  -1.841  -1.673
80    S        -1.838  -1.891  -1.928  -1.632  -1.758  -1.790  -1.664  -1.716  -1.673
81    G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
82    R        -0.690  -0.727  -0.583  -1.220  -1.299  -1.023  -0.982  -1.056  -0.848
83    D        -0.450  -0.623  -0.582  -0.338  -0.625  -0.613  -0.593  -0.880  -0.846
84    A        -1.165  -1.344  -1.359  -1.089  -1.349  -1.458  -1.177  -1.378  -1.385
85    F         0.736   0.750   0.778   0.871   0.884   0.915   0.769   0.788   0.828
86    H         0.736   0.750   0.778   0.990   1.001   1.013   0.769   0.788   0.828
87    L        -0.045  -0.162  -0.525   0.061  -0.065  -0.544  -0.009  -0.169  -0.749
88    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
89    V        -0.450  -0.438  -0.564  -0.423  -0.406  -0.656  -0.593  -0.581  -0.816
90    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
91    V        -0.690  -0.700  -0.581  -0.915  -0.959  -0.796  -0.982  -1.010  -0.844
92    H         0.736   0.750   0.778   0.990   1.001   1.013   0.769   0.788   0.828
93    P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
94    F        -0.045  -0.264  -0.531   0.232  -0.043  -0.483  -0.009  -0.316  -0.759
95    H         0.736   0.750   0.778   0.990   1.001   1.013   0.769   0.788   0.828
96    V         0.736   0.750   0.778   0.775   0.797   0.835   0.769   0.788   0.828
97    L        -0.690  -0.727  -0.583  -0.909  -0.980  -0.747  -0.982  -1.056  -0.848
98    R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
99    I         0.736   0.750   0.778   0.766   0.780   0.827   0.769   0.788   0.828
100   N         0.736   0.750   0.778   0.856   0.869   0.902   0.769   0.788   0.828
101   K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
102   M        -0.045  -0.162  -0.525   0.355   0.203  -0.412  -0.009  -0.169  -0.749
103   L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
104   S         0.736   0.750   0.778   0.797   0.818   0.853   0.769   0.788   0.828
105   C         0.736   0.750   0.778   0.987   0.994   1.011   0.769   0.788   0.828
106   A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
107   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
108   A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
109   D         0.736   0.750   0.778   0.847   0.869   0.894   0.769   0.788   0.828
110   R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
111   L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
112   Q        -0.045  -0.162  -0.525   0.234   0.085  -0.569  -0.009  -0.169  -0.749
113   Q        -0.690  -0.727  -0.583  -0.610  -0.684  -0.489  -0.982  -1.056  -0.848
114   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
115   M         0.736   0.750   0.778   1.005   1.012   1.026   0.769   0.788   0.828
116   R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
117   G        -0.450  -0.435  -0.530  -0.405  -0.386  -0.526  -0.593  -0.575  -0.759
118   A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
119   W        -0.450  -0.435  -0.530  -0.105  -0.097  -0.333  -0.593  -0.575  -0.759
120   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
121   K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
122   P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
123   H        -1.363  -1.452  -1.371  -1.191  -1.352  -1.292  -1.469  -1.555  -1.399
124   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
125   L        -0.045  -0.264  -0.531   0.057  -0.198  -0.565  -0.009  -0.316  -0.759
126   A        -0.690  -0.727  -0.583  -1.010  -1.075  -0.816  -0.982  -1.056  -0.848
127   A         0.736   0.750   0.778   0.571   0.591   0.666   0.769   0.788   0.828
128   R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
129   V         0.736   0.750   0.778   0.775   0.797   0.835   0.769   0.788   0.828
130   D        -1.985  -1.760  -1.924  -1.833  -1.534  -1.770  -1.858  -1.632  -1.671
131   I         0.736   0.750   0.778   0.766   0.780   0.827   0.769   0.788   0.828
132   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
133   Q         0.736   0.750   0.778   0.908   0.926   0.945   0.769   0.788   0.828
134   I        -0.690  -0.670  -0.583  -0.831  -0.809  -0.692  -0.982  -0.959  -0.847
135   I        -0.803  -0.759  -0.586  -1.107  -1.040  -0.754  -1.177  -1.112  -0.852
136   F        -1.363  -1.320  -1.353  -1.139  -1.033  -1.160  -1.469  -1.363  -1.378
137   S         0.736   0.750   0.778   0.797   0.818   0.853   0.769   0.788   0.828
138   V        -1.165  -1.116  -1.344  -1.105  -0.990  -1.419  -1.177  -1.087  -1.367
139   R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
140   T         0.736   0.750   0.778   0.978   0.985   1.003   0.769   0.788   0.828
141   K        -0.045  -0.264  -0.531  -0.141  -0.423  -0.900  -0.009  -0.316  -0.759
142   D         0.736   0.750   0.778   0.847   0.869   0.894   0.769   0.788   0.828
143   S        -0.690  -0.626  -0.572  -0.766  -0.663  -0.609  -0.982  -0.885  -0.830
144   N        -0.450  -0.435  -0.530  -0.335  -0.320  -0.521  -0.593  -0.575  -0.759
145   K        -0.450  -0.435  -0.530  -0.732  -0.696  -0.899  -0.593  -0.575  -0.759
146   D        -0.803  -0.751  -0.580  -1.110  -1.064  -0.772  -1.177  -1.097  -0.842
147   V        -1.426  -1.495  -1.361  -1.345  -1.372  -1.196  -1.566  -1.588  -1.387
148   V        -0.690  -0.727  -0.583  -0.915  -1.020  -0.803  -0.982  -1.056  -0.848
149   V        -1.165  -1.198  -1.341  -1.063  -1.090  -1.365  -1.177  -1.188  -1.363
150   E         0.736   0.750   0.778   0.822   0.836   0.874   0.769   0.788   0.828
151   G        -0.690  -0.727  -0.583  -0.959  -1.067  -0.834  -0.982  -1.056  -0.848
152   L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
153   R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
154   R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
155   A        -1.363  -1.507  -1.369  -1.444  -1.589  -1.347  -1.469  -1.606  -1.397
156   R        -0.690  -0.727  -0.583  -1.044  -1.086  -0.805  -0.982  -1.056  -0.848
157   Y         0.736   0.750   0.778   0.859   0.876   0.905   0.769   0.788   0.828
158   K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
159   F         0.736   0.750   0.778   0.871   0.884   0.915   0.769   0.788   0.828
160   P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
161   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
162   Q        -0.045  -0.264  -0.531   0.221  -0.081  -0.628  -0.009  -0.316  -0.759
163   Q         0.736   0.750   0.778   0.908   0.926   0.945   0.769   0.788   0.828
164   K        -0.450  -0.435  -0.530  -0.732  -0.696  -0.899  -0.593  -0.575  -0.759
165   I         0.736   0.750   0.778   0.766   0.780   0.827   0.769   0.788   0.828
166   I         0.736   0.750   0.778   0.766   0.780   0.827   0.769   0.788   0.828
167   L        -1.838  -1.604  -1.906  -1.619  -1.339  -1.704  -1.664  -1.428  -1.653
168   S         0.736   0.750   0.778   0.797   0.818   0.853   0.769   0.788   0.828
169   K         0.736   0.750   0.778   0.549   0.586   0.647   0.769   0.788   0.828
170   K        -0.045  -0.264  -0.531  -0.091  -0.340  -0.716  -0.009  -0.316  -0.759
171   W         0.736   0.750   0.778   1.074   1.081   1.083   0.769   0.788   0.828
172   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
173   F         0.736   0.750   0.778   0.871   0.884   0.915   0.769   0.788   0.828
174   T        -0.450  -0.435  -0.530  -0.217  -0.207  -0.433  -0.593  -0.575  -0.759
175   N        -2.200  -2.068  -1.932  -2.036  -1.867  -1.657  -2.053  -1.916  -1.678
176   L        -0.450  -0.435  -0.530  -0.489  -0.463  -0.619  -0.593  -0.575  -0.759
177   D        -2.200  -2.227  -1.938  -2.257  -2.328  -1.931  -2.053  -2.031  -1.683
178   R         0.736   0.750   0.778   0.463   0.483   0.576   0.769   0.788   0.828
179   P        -1.985  -1.780  -1.921  -1.845  -1.604  -1.763  -1.858  -1.674  -1.668
180   E         0.736   0.750   0.778   0.822   0.836   0.874   0.769   0.788   0.828
181   Y         0.736   0.750   0.778   0.859   0.876   0.905   0.769   0.788   0.828
182   L        -2.200  -2.136  -1.933  -2.219  -2.089  -1.759  -2.053  -1.954  -1.679
183   K        -2.200  -2.106  -1.942  -2.368  -2.116  -1.888  -2.053  -1.918  -1.686
184   K        -0.450  -0.437  -0.564  -0.732  -0.700  -0.973  -0.593  -0.578  -0.816
185   R        -0.690  -0.669  -0.581  -1.220  -1.186  -1.020  -0.982  -0.957  -0.845
186   E        -3.496  -3.356  -3.049  -2.978  -2.853  -2.404  -2.539  -2.411  -2.052
187   A        -1.640  -1.577  -1.366  -2.005  -1.913  -1.567  -1.761  -1.672  -1.393
188   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
189   E        -0.045  -0.264  -0.531   0.145  -0.151  -0.656  -0.009  -0.316  -0.759
190   V        -1.426  -1.495  -1.361  -1.533  -1.588  -1.397  -1.566  -1.588  -1.387
191   K        -1.363  -1.471  -1.366  -1.609  -1.720  -1.538  -1.469  -1.554  -1.394
192   D        -1.838  -2.061  -1.937  -1.535  -1.848  -1.714  -1.664  -1.867  -1.682
193   D         0.736   0.750   0.778   0.847   0.869   0.894   0.769   0.788   0.828
194   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
195   A        -0.450  -0.435  -0.530  -0.557  -0.535  -0.638  -0.593  -0.575  -0.759
196   F        -0.690  -0.517  -0.551  -0.702  -0.422  -0.523  -0.982  -0.706  -0.794
197   V        -0.450  -0.435  -0.530  -0.476  -0.455  -0.680  -0.593  -0.575  -0.759
198   K        -0.045  -0.264  -0.531  -0.084  -0.327  -0.692  -0.009  -0.316  -0.759
199   F         0.736   0.750   0.778   0.871   0.884   0.915   0.769   0.788   0.828
200   L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
201   S        -2.116  -2.204  -1.939  -1.922  -2.042  -1.681  -1.956  -2.007  -1.684
202   K        -0.796  -0.890  -1.334  -0.778  -0.882  -1.555  -0.690  -0.826  -1.353
203   K        -0.690  -0.727  -0.583  -1.179  -1.270  -1.017  -0.982  -1.056  -0.848
204   G         0.736   0.750   0.778   0.728   0.743   0.796   0.769   0.788   0.828
205   S        -1.510  -1.386  -1.909  -1.140  -0.986  -1.768  -1.274  -1.147  -1.656
206   L         0.736   0.750   0.778   0.680   0.703   0.756   0.769   0.788   0.828
207   E        -1.165  -1.254  -1.343  -0.982  -1.110  -1.319  -1.177  -1.271  -1.364
208   N        -2.183  -2.041  -2.359  -1.779  -1.668  -2.161  -1.761  -1.636  -1.839
209   N        -1.165  -1.254  -1.343  -1.028  -1.149  -1.355  -1.177  -1.271  -1.364
210   I        -1.838  -1.766  -1.921  -1.666  -1.541  -1.705  -1.664  -1.572  -1.667
211   R        -2.461  -2.553  -2.380  -2.525  -2.691  -2.361  -2.053  -2.113  -1.855
212   E        -2.116  -2.127  -1.938  -2.058  -2.112  -1.881  -1.956  -1.930  -1.683
213   F         0.736   0.750   0.778   0.871   0.884   0.915   0.769   0.788   0.828
214   P         0.736   0.750   0.778   0.850   0.861   0.897   0.769   0.788   0.828
215   E        -1.426  -1.284  -1.355  -1.409  -1.222  -1.248  -1.566  -1.407  -1.381
216   Y        -0.690  -0.727  -0.583  -0.837  -0.952  -0.748  -0.982  -1.056  -0.848
217   F        -2.116  -2.066  -1.930  -1.888  -1.804  -1.640  -1.956  -1.872  -1.675
218   A        -2.243  -2.156  -1.937  -2.274  -2.182  -1.811  -2.077  -1.970  -1.682
219   A        -2.676  -2.715  -2.386  -2.547  -2.530  -2.056  -2.248  -2.230  -1.859
220   Q        -2.676  -2.648  -2.380  -2.509  -2.474  -2.141  -2.248  -2.193  -1.855
221   A        -0.450  -0.438  -0.564  -0.620  -0.601  -0.791  -0.593  -0.581  -0.816
* 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/P41805
Output conservation file - output/P41805
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
