1     M         0.755   0.765   0.805   0.994   0.998   1.034   0.793   0.808   0.859
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    D        -1.909  -1.981  -1.776  -1.791  -1.867  -1.610  -1.851  -1.893  -1.581
32    I        -1.312  -1.224  -1.219  -1.693  -1.575  -1.499  -1.490  -1.394  -1.284
33    F        -1.523  -1.761  -1.766  -1.350  -1.730  -1.868  -1.370  -1.633  -1.571
34    G        -1.451  -1.413  -1.239  -1.641  -1.580  -1.294  -1.610  -1.569  -1.307
35    W        -0.044  -0.139  -0.423   0.310   0.189  -0.307  -0.048  -0.186  -0.657
36    F        -0.044  -0.139  -0.423   0.045  -0.088  -0.691  -0.048  -0.186  -0.657
37    R        -1.541  -1.422  -1.237  -1.473  -1.281  -1.033  -1.730  -1.582  -1.304
38    D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
39    V        -1.312  -1.359  -1.226  -1.428  -1.487  -1.271  -1.490  -1.526  -1.293
40    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
41    A        -0.716  -0.677  -0.490  -0.987  -0.907  -0.606  -1.130  -1.069  -0.771
42    S        -0.806  -0.986  -1.201  -0.473  -0.709  -1.049  -0.769  -1.000  -1.259
43    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
44    G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
45    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
46    W        -0.806  -0.986  -1.201  -0.482  -0.761  -1.299  -0.769  -1.000  -1.259
47    N         0.755   0.765   0.805   0.901   0.911   0.956   0.793   0.808   0.859
48    K         0.755   0.765   0.805   0.834   0.841   0.900   0.793   0.808   0.859
49    H        -0.044  -0.147  -0.422   0.336   0.198  -0.280  -0.048  -0.197  -0.655
50    G        -0.716  -0.683  -0.492  -1.132  -1.072  -0.734  -1.130  -1.081  -0.775
51    K         0.755   0.765   0.805   0.834   0.841   0.900   0.793   0.808   0.859
52    L        -0.044  -0.142  -0.423  -0.393  -0.503  -0.785  -0.048  -0.190  -0.657
53    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
54    F         0.755   0.765   0.805   0.822   0.843   0.890   0.793   0.808   0.859
55    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
56    G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
57    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
58    D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
59    N         0.755   0.765   0.805   0.901   0.911   0.956   0.793   0.808   0.859
60    A         0.755   0.765   0.805   0.730   0.747   0.814   0.793   0.808   0.859
61    G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
62    K         0.755   0.765   0.805   0.834   0.841   0.900   0.793   0.808   0.859
63    T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
64    T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
65    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
66    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
67    H         0.755   0.765   0.805   1.029   1.035   1.062   0.793   0.808   0.859
68    M         0.755   0.765   0.805   0.994   0.998   1.034   0.793   0.808   0.859
69    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
70    K         0.755   0.765   0.805   0.834   0.841   0.900   0.793   0.808   0.859
71    N         0.755   0.765   0.805   0.901   0.911   0.956   0.793   0.808   0.859
72    D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
73    R         0.755   0.765   0.805   0.889   0.899   0.946   0.793   0.808   0.859
74    L        -0.806  -0.990  -1.200  -1.092  -1.323  -1.490  -0.769  -1.006  -1.258
75    A         0.755   0.765   0.805   0.730   0.747   0.814   0.793   0.808   0.859
76    T        -1.155  -1.305  -1.232  -1.087  -1.337  -1.232  -1.250  -1.446  -1.299
77    L        -0.806  -0.992  -1.200  -1.071  -1.298  -1.439  -0.769  -1.009  -1.258
78    Q        -0.044  -0.147  -0.422   0.282   0.147  -0.320  -0.048  -0.197  -0.655
79    P         0.755   0.765   0.805   0.932   0.938   0.982   0.793   0.808   0.859
80    T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
81    W        -1.312  -1.321  -1.226  -1.728  -1.740  -1.485  -1.490  -1.469  -1.291
82    H         0.755   0.765   0.805   1.029   1.035   1.062   0.793   0.808   0.859
83    P         0.755   0.765   0.805   0.932   0.938   0.982   0.793   0.808   0.859
84    T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
85    S         0.755   0.765   0.805   0.881   0.893   0.940   0.793   0.808   0.859
86    E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
87    E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
88    L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
89    A        -0.438  -0.535  -0.480  -0.520  -0.681  -0.602  -0.649  -0.820  -0.755
90    I        -0.044  -0.139  -0.423   0.163   0.032  -0.450  -0.048  -0.186  -0.657
91    G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
92    N        -0.438  -0.298  -0.442  -0.356  -0.140  -0.418  -0.649  -0.428  -0.690
93    I        -1.312  -1.321  -1.226  -1.347  -1.322  -1.115  -1.490  -1.469  -1.291
94    K        -0.649  -0.604  -0.483  -0.784  -0.714  -0.534  -1.009  -0.939  -0.759
95    F         0.755   0.765   0.805   0.822   0.843   0.890   0.793   0.808   0.859
96    T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
97    T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
98    F         0.755   0.765   0.805   0.822   0.843   0.890   0.793   0.808   0.859
99    D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
100   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
101   G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
102   G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
103   H         0.755   0.765   0.805   1.029   1.035   1.062   0.793   0.808   0.859
104   I        -1.819  -1.720  -1.761  -1.685  -1.547  -1.748  -1.730  -1.623  -1.568
105   Q         0.755   0.765   0.805   0.975   0.982   1.017   0.793   0.808   0.859
106   A         0.755   0.765   0.805   0.730   0.747   0.814   0.793   0.808   0.859
107   R         0.755   0.765   0.805   0.889   0.899   0.946   0.793   0.808   0.859
108   R         0.755   0.765   0.805   0.889   0.899   0.946   0.793   0.808   0.859
109   L        -0.044  -0.147  -0.422  -0.429  -0.555  -0.891  -0.048  -0.197  -0.655
110   W         0.755   0.765   0.805   1.006   1.018   1.043   0.793   0.808   0.859
111   K        -0.044  -0.142  -0.423   0.140   0.012  -0.429  -0.048  -0.190  -0.657
112   D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
113   Y         0.755   0.765   0.805   1.029   1.031   1.062   0.793   0.808   0.859
114   F         0.755   0.765   0.805   0.822   0.843   0.890   0.793   0.808   0.859
115   P         0.755   0.765   0.805   0.932   0.938   0.982   0.793   0.808   0.859
116   E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
117   V         0.755   0.765   0.805   0.770   0.779   0.847   0.793   0.808   0.859
118   N         0.755   0.765   0.805   0.901   0.911   0.956   0.793   0.808   0.859
119   G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
120   I         0.755   0.765   0.805   0.873   0.880   0.933   0.793   0.808   0.859
121   V         0.755   0.765   0.805   0.770   0.779   0.847   0.793   0.808   0.859
122   F        -0.044  -0.142  -0.423   0.149   0.038  -0.378  -0.048  -0.190  -0.657
123   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
124   V         0.755   0.765   0.805   0.770   0.779   0.847   0.793   0.808   0.859
125   D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
126   A        -0.806  -0.816  -1.186  -0.603  -0.609  -1.083  -0.769  -0.790  -1.241
127   A        -0.806  -0.986  -1.201  -0.611  -0.837  -1.119  -0.769  -1.000  -1.259
128   D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
129   P        -1.523  -1.599  -1.750  -1.096  -1.211  -1.473  -1.370  -1.462  -1.556
130   E        -0.806  -0.821  -1.186  -0.621  -0.643  -1.190  -0.769  -0.796  -1.240
131   R         0.755   0.765   0.805   0.889   0.899   0.946   0.793   0.808   0.859
132   F        -0.438  -0.533  -0.478  -0.618  -0.830  -0.849  -0.649  -0.816  -0.751
133   D        -2.416  -2.434  -2.194  -2.287  -2.279  -1.915  -2.091  -2.082  -1.747
134   E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
135   A        -0.716  -0.683  -0.492  -0.987  -0.925  -0.613  -1.130  -1.081  -0.775
136   R        -0.649  -0.553  -0.469  -0.784  -0.623  -0.510  -1.009  -0.851  -0.736
137   V        -1.155  -1.007  -1.202  -1.200  -0.956  -1.251  -1.250  -1.040  -1.261
138   E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
139   L        -0.044  -0.139  -0.423  -0.413  -0.524  -0.843  -0.048  -0.186  -0.657
140   D        -0.438  -0.298  -0.442  -0.475  -0.248  -0.531  -0.649  -0.428  -0.690
141   A        -0.649  -0.606  -0.484  -0.879  -0.803  -0.607  -1.009  -0.942  -0.761
142   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
143   F        -0.649  -0.681  -0.492  -1.109  -1.257  -0.925  -1.009  -1.077  -0.775
144   N        -2.922  -2.797  -2.540  -2.636  -2.483  -2.096  -2.331  -2.220  -1.860
145   I        -0.438  -0.533  -0.478  -0.346  -0.509  -0.444  -0.649  -0.816  -0.751
146   A        -1.523  -1.294  -1.742  -1.309  -1.003  -1.666  -1.370  -1.115  -1.548
147   E        -0.044  -0.147  -0.422   0.089  -0.035  -0.437  -0.048  -0.197  -0.655
148   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
149   K        -1.909  -1.807  -1.764  -1.939  -1.807  -1.675  -1.851  -1.747  -1.571
150   D        -3.290  -3.253  -2.836  -2.847  -2.805  -2.239  -2.451  -2.407  -1.943
151   V         0.755   0.765   0.805   0.770   0.779   0.847   0.793   0.808   0.859
152   P         0.755   0.765   0.805   0.932   0.938   0.982   0.793   0.808   0.859
153   F         0.755   0.765   0.805   0.822   0.843   0.890   0.793   0.808   0.859
154   V        -1.312  -1.291  -1.226  -1.795  -1.803  -1.604  -1.490  -1.465  -1.293
155   I        -0.438  -0.478  -0.477  -0.417  -0.499  -0.560  -0.649  -0.721  -0.750
156   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
157   G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
158   N         0.755   0.765   0.805   0.901   0.911   0.956   0.793   0.808   0.859
159   K         0.755   0.765   0.805   0.834   0.841   0.900   0.793   0.808   0.859
160   I         0.755   0.765   0.805   0.873   0.880   0.933   0.793   0.808   0.859
161   D         0.755   0.765   0.805   0.814   0.829   0.884   0.793   0.808   0.859
162   A        -2.187  -2.238  -2.184  -1.888  -1.945  -1.850  -1.851  -1.900  -1.739
163   P        -0.806  -0.609  -1.172  -0.469  -0.225  -1.076  -0.769  -0.524  -1.223
164   N        -2.922  -2.927  -2.542  -2.635  -2.655  -2.137  -2.331  -2.311  -1.862
165   A         0.755   0.765   0.805   0.730   0.747   0.814   0.793   0.808   0.859
166   V        -0.044  -0.142  -0.423   0.075  -0.054  -0.482  -0.048  -0.190  -0.657
167   S        -0.438  -0.298  -0.442  -0.436  -0.207  -0.520  -0.649  -0.428  -0.690
168   E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
169   A        -2.555  -2.502  -2.200  -2.590  -2.542  -2.130  -2.211  -2.143  -1.751
170   E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
171   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
172   R        -0.716  -0.683  -0.492  -0.907  -0.859  -0.548  -1.130  -1.081  -0.775
173   S        -2.416  -2.446  -2.192  -2.216  -2.275  -1.893  -2.091  -2.106  -1.746
174   A        -0.044  -0.139  -0.423   0.037  -0.078  -0.505  -0.048  -0.186  -0.657
175   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
176   G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
177   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
178   L        -1.819  -1.769  -1.761  -1.681  -1.527  -1.590  -1.730  -1.652  -1.567
179   N        -0.649  -0.681  -0.492  -0.681  -0.746  -0.456  -1.009  -1.077  -0.775
180   T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
181   T         0.755   0.765   0.805   0.850   0.865   0.913   0.793   0.808   0.859
182   G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
183   S        -1.155  -1.007  -1.202  -1.031  -0.805  -1.075  -1.250  -1.040  -1.261
184   Q        -2.048  -1.875  -1.767  -2.100  -1.848  -1.660  -1.971  -1.771  -1.572
185   R        -2.048  -2.039  -1.777  -2.021  -2.006  -1.638  -1.971  -1.943  -1.582
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.261  -1.345  -1.234  -1.237  -1.383  -1.236  -1.360  -1.471  -1.300
188   -        -0.673  -0.673  -0.491  -1.285  -1.253  -0.870  -1.053  -1.062  -0.774
189   I        -2.416  -2.501  -2.202  -2.341  -2.527  -2.152  -2.091  -2.138  -1.753
190   E        -0.806  -0.992  -1.200  -0.629  -0.885  -1.231  -0.769  -1.009  -1.258
191   G        -0.044  -0.147  -0.422  -0.006  -0.136  -0.531  -0.048  -0.197  -0.655
192   Q        -1.312  -1.232  -1.228  -1.238  -1.165  -1.115  -1.490  -1.413  -1.294
193   R         0.755   0.765   0.805   0.889   0.899   0.946   0.793   0.808   0.859
194   P         0.755   0.765   0.805   0.932   0.938   0.982   0.793   0.808   0.859
195   V        -0.438  -0.279  -0.431  -0.417  -0.170  -0.465  -0.649  -0.399  -0.670
196   E         0.755   0.765   0.805   0.770   0.784   0.847   0.793   0.808   0.859
197   V        -0.806  -0.889  -1.195  -0.702  -0.820  -1.409  -0.769  -0.878  -1.253
198   F         0.755   0.765   0.805   0.822   0.843   0.890   0.793   0.808   0.859
199   M         0.755   0.765   0.805   0.994   0.998   1.034   0.793   0.808   0.859
200   C        -0.438  -0.298  -0.442  -0.180   0.036  -0.310  -0.649  -0.428  -0.690
201   S         0.755   0.765   0.805   0.881   0.893   0.940   0.793   0.808   0.859
202   V        -0.044  -0.147  -0.422   0.075  -0.060  -0.481  -0.048  -0.197  -0.655
203   V         0.755   0.765   0.805   0.770   0.779   0.847   0.793   0.808   0.859
204   M        -0.044  -0.142  -0.423   0.219   0.065  -0.556  -0.048  -0.190  -0.657
205   R        -0.044  -0.025  -0.420   0.188   0.210  -0.406  -0.048  -0.023  -0.651
206   N        -2.048  -1.841  -1.768  -1.856  -1.553  -1.455  -1.971  -1.751  -1.574
207   G         0.755   0.765   0.805   0.685   0.697   0.776   0.793   0.808   0.859
208   Y         0.755   0.765   0.805   1.029   1.031   1.062   0.793   0.808   0.859
209   L        -1.155  -1.007  -1.202  -1.426  -1.138  -1.484  -1.250  -1.040  -1.261
210   E        -0.438  -0.431  -0.469  -0.503  -0.492  -0.591  -0.649  -0.643  -0.735
211   A        -0.649  -0.654  -0.489  -0.984  -1.007  -0.729  -1.009  -1.029  -0.771
212   F        -0.438  -0.535  -0.480  -0.434  -0.597  -0.546  -0.649  -0.820  -0.755
213   Q        -1.451  -1.400  -1.232  -1.452  -1.398  -1.139  -1.610  -1.554  -1.298
214   W         0.755   0.765   0.805   1.006   1.018   1.043   0.793   0.808   0.859
215   L         0.755   0.765   0.805   0.284   0.305   0.443   0.793   0.808   0.859
216   S        -0.044  -0.142  -0.423   0.165   0.035  -0.461  -0.048  -0.190  -0.657
217   Q        -0.044  -0.025  -0.420   0.264   0.284  -0.368  -0.048  -0.023  -0.651
218   Y         0.755   0.765   0.805   1.029   1.031   1.062   0.793   0.808   0.859
219   I        -0.649  -0.681  -0.492  -0.812  -0.907  -0.596  -1.009  -1.077  -0.775
* 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/P20606
Output conservation file - output/P20606
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
