1     M         1.011   1.034   1.091   1.171   1.189   1.274   1.045   1.079   1.166
2     V         1.011   1.034   1.091   0.900   0.946   1.054   1.045   1.079   1.166
3     R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
4     K        -2.035  -1.884  -1.627  -2.154  -1.934  -1.530  -1.878  -1.676  -1.354
5     L         0.142  -0.009  -0.188  -0.019  -0.173  -0.371   0.156  -0.063  -0.373
6     K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
7     H         1.011   1.034   1.091   1.111   1.147   1.225   1.045   1.079   1.166
8     H         0.142  -0.004  -0.182   0.386   0.200  -0.093   0.156  -0.056  -0.364
9     E         1.011   1.034   1.091   1.098   1.128   1.215   1.045   1.079   1.166
10    Q        -0.686  -0.650  -0.990  -0.390  -0.353  -0.920  -0.607  -0.585  -0.983
11    K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
12    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
13    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
14    K        -0.286  -0.377  -0.269  -0.656  -0.820  -0.643  -0.480  -0.647  -0.509
15    K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
16    V         0.142  -0.004  -0.182   0.171  -0.004  -0.278   0.156  -0.056  -0.364
17    D         1.011   1.034   1.091   0.897   0.949   1.051   1.045   1.079   1.166
18    F         1.011   1.034   1.091   1.239   1.258   1.329   1.045   1.079   1.166
19    L        -1.465  -1.537  -1.604  -1.493  -1.625  -1.639  -1.243  -1.329  -1.331
20    E        -1.485  -1.158  -1.048  -1.653  -1.111  -0.995  -1.624  -1.210  -1.052
21    W        -0.286  -0.377  -0.269   0.010  -0.189  -0.105  -0.480  -0.647  -0.509
22    K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    Q        -1.465  -1.750  -1.628  -1.091  -1.544  -1.443  -1.243  -1.532  -1.354
25    D         1.011   1.034   1.091   0.897   0.949   1.051   1.045   1.079   1.166
26    Q        -0.515  -0.474  -0.266  -0.602  -0.558  -0.252  -0.861  -0.813  -0.504
27    G        -1.065  -1.120  -1.043  -0.855  -0.981  -0.970  -1.115  -1.158  -1.049
28    H         1.011   1.034   1.091   1.111   1.147   1.225   1.045   1.079   1.166
29    R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
30    D         0.142  -0.009  -0.188   0.164  -0.014  -0.281   0.156  -0.063  -0.373
31    T        -1.465  -1.750  -1.628  -1.125  -1.565  -1.450  -1.243  -1.532  -1.354
32    Q        -0.686  -0.904  -1.017  -0.372  -0.690  -0.923  -0.607  -0.878  -1.015
33    V         1.011   1.034   1.091   0.910   0.960   1.062   1.045   1.079   1.166
34    M         0.142  -0.004  -0.182   0.445   0.241  -0.049   0.156  -0.056  -0.364
35    R         0.142  -0.009  -0.188   0.144  -0.027  -0.262   0.156  -0.063  -0.373
36    T        -0.286  -0.377  -0.269  -0.341  -0.549  -0.429  -0.480  -0.647  -0.509
37    Y         0.142  -0.009  -0.188   0.436   0.251  -0.042   0.156  -0.063  -0.373
38    H         0.142  -0.004  -0.182   0.388   0.201  -0.088   0.156  -0.056  -0.364
39    I         0.142  -0.009  -0.188   0.256   0.047  -0.330   0.156  -0.063  -0.373
40    Q         0.142   0.053  -0.180   0.372   0.263  -0.109   0.156   0.027  -0.361
41    N        -1.065  -1.224  -1.059  -1.046  -1.397  -1.205  -1.115  -1.302  -1.068
42    R         0.142  -0.004  -0.182   0.145  -0.019  -0.252   0.156  -0.056  -0.364
43    E         0.142  -0.009  -0.188   0.336   0.123  -0.213   0.156  -0.063  -0.373
44    D         0.142   0.053  -0.180   0.164   0.069  -0.270   0.156   0.027  -0.361
45    Y         1.011   1.034   1.091   1.150   1.189   1.257   1.045   1.079   1.166
46    H        -0.686  -0.908  -1.016  -0.337  -0.643  -0.855  -0.607  -0.883  -1.014
47    K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
48    Y         1.011   1.034   1.091   1.150   1.189   1.257   1.045   1.079   1.166
49    N         1.011   1.034   1.091   1.129   1.168   1.239   1.045   1.079   1.166
50    R        -1.236  -1.198  -1.045  -1.642  -1.547  -1.278  -1.370  -1.280  -1.052
51    I         0.142  -0.004  -0.182   0.323   0.148  -0.135   0.156  -0.056  -0.364
52    C         1.011   1.034   1.091   1.319   1.343   1.394   1.045   1.079   1.166
53    G         1.011   1.034   1.091   1.210   1.234   1.305   1.045   1.079   1.166
54    D        -1.787  -1.732  -1.622  -1.879  -1.890  -1.632  -1.624  -1.566  -1.350
55    I        -1.465  -1.492  -1.599  -1.191  -1.285  -1.515  -1.243  -1.277  -1.327
56    R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
57    R        -1.485  -1.158  -1.048  -1.887  -1.269  -1.179  -1.624  -1.210  -1.052
58    L         0.142   0.358  -0.158  -0.049   0.232  -0.407   0.156   0.437  -0.324
59    A         1.011   1.034   1.091   1.159   1.185   1.264   1.045   1.079   1.166
60    N        -0.686  -0.631  -0.992  -0.329  -0.291  -0.801  -0.607  -0.564  -0.985
61    K        -0.515  -0.464  -0.278  -1.070  -0.984  -0.655  -0.861  -0.796  -0.526
62    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
63    S         1.011   1.034   1.091   1.124   1.149   1.236   1.045   1.079   1.166
64    L         0.142  -0.009  -0.188  -0.040  -0.202  -0.429   0.156  -0.063  -0.373
65    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
66    P        -1.236  -1.195  -1.045  -1.176  -1.118  -0.936  -1.370  -1.276  -1.053
67    P         1.011   1.034   1.091   1.214   1.241   1.309   1.045   1.079   1.166
68    T        -1.065  -0.977  -1.043  -1.011  -1.017  -1.039  -1.115  -1.069  -1.049
69    D         0.142  -0.004  -0.182   0.168   0.002  -0.261   0.156  -0.056  -0.364
70    P         0.142  -0.004  -0.182   0.479   0.279  -0.041   0.156  -0.056  -0.364
71    F        -1.065  -0.979  -1.043  -0.833  -0.869  -0.919  -1.115  -1.071  -1.049
72    R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
73    R        -1.236  -1.195  -1.045  -1.479  -1.416  -1.233  -1.370  -1.276  -1.053
74    K         0.142   0.053  -0.180   0.006  -0.073  -0.384   0.156   0.027  -0.361
75    H        -0.686  -0.583  -0.983  -0.334  -0.227  -0.795  -0.607  -0.497  -0.973
76    E         1.011   1.034   1.091   1.098   1.128   1.215   1.045   1.079   1.166
77    Q        -1.465  -1.750  -1.628  -1.112  -1.583  -1.487  -1.243  -1.532  -1.354
78    L         0.142   0.358  -0.158  -0.030   0.242  -0.358   0.156   0.437  -0.324
79    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
80    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
81    D        -0.588  -0.467  -0.274  -0.906  -0.725  -0.415  -0.988  -0.802  -0.519
82    K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
83    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
84    Y         0.142   0.053  -0.180   0.436   0.331  -0.031   0.156   0.027  -0.361
85    A        -2.986  -2.579  -2.433  -2.628  -2.175  -1.917  -2.259  -1.898  -1.644
86    M         1.011   1.034   1.091   1.171   1.189   1.274   1.045   1.079   1.166
87    G         1.011   1.034   1.091   1.210   1.234   1.305   1.045   1.079   1.166
88    V        -0.515  -0.259  -0.227  -0.766  -0.309  -0.323  -0.861  -0.452  -0.439
89    L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
90    T        -1.787  -1.487  -1.584  -1.475  -1.086  -1.236  -1.624  -1.276  -1.313
91    T        -0.286  -0.377  -0.269  -0.257  -0.435  -0.290  -0.480  -0.647  -0.509
92    K         0.142  -0.009  -0.188   0.010  -0.149  -0.384   0.156  -0.063  -0.373
93    S         0.142  -0.009  -0.188   0.385   0.176  -0.131   0.156  -0.063  -0.373
94    K         0.142  -0.009  -0.188  -0.001  -0.166  -0.414   0.156  -0.063  -0.373
95    I        -1.465  -1.750  -1.628  -1.204  -1.693  -1.596  -1.243  -1.532  -1.354
96    S         1.011   1.034   1.091   1.124   1.149   1.236   1.045   1.079   1.166
97    D        -1.465  -1.537  -1.604  -1.235  -1.364  -1.414  -1.243  -1.329  -1.331
98    L        -0.686  -0.904  -1.017  -0.802  -1.086  -1.242  -0.607  -0.878  -1.015
99    E         1.011   1.034   1.091   1.098   1.128   1.215   1.045   1.079   1.166
100   N        -0.686  -0.956  -1.021  -0.330  -0.709  -0.876  -0.607  -0.943  -1.020
101   K         0.142  -0.004  -0.182   0.006  -0.149  -0.387   0.156  -0.056  -0.364
102   V        -0.686  -0.908  -1.016  -0.540  -0.831  -0.994  -0.607  -0.883  -1.014
103   T        -0.686  -0.908  -1.016  -0.385  -0.689  -0.880  -0.607  -0.883  -1.014
104   V         1.011   1.034   1.091   0.910   0.960   1.062   1.045   1.079   1.166
105   S         1.011   1.034   1.091   1.124   1.149   1.236   1.045   1.079   1.166
106   A         0.142   0.348  -0.158   0.428   0.656  -0.030   0.156   0.424  -0.324
107   I        -1.387  -1.160  -1.042  -1.522  -1.148  -1.029  -1.497  -1.211  -1.047
108   C        -0.286  -0.401  -0.274   0.000  -0.244  -0.121  -0.480  -0.687  -0.518
109   R         0.142  -0.009  -0.188   0.076  -0.125  -0.454   0.156  -0.063  -0.373
110   R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
111   R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
112   L        -0.286  -0.023  -0.188  -0.638  -0.233  -0.454  -0.480  -0.085  -0.374
113   P         0.142   0.348  -0.158   0.495   0.720   0.041   0.156   0.424  -0.324
114   V         1.011   1.034   1.091   0.910   0.960   1.062   1.045   1.079   1.166
115   I        -0.588  -0.473  -0.274  -0.935  -0.735  -0.425  -0.988  -0.812  -0.519
116   M         1.011   1.034   1.091   1.171   1.189   1.274   1.045   1.079   1.166
117   H        -1.236  -1.224  -1.047  -1.074  -1.051  -0.825  -1.370  -1.304  -1.054
118   R        -0.286  -0.379  -0.272  -0.575  -0.777  -0.636  -0.480  -0.651  -0.515
119   L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
120   K        -0.515  -0.464  -0.278  -1.070  -0.984  -0.655  -0.861  -0.796  -0.526
121   M         1.011   1.034   1.091   1.171   1.189   1.274   1.045   1.079   1.166
122   A        -0.686  -0.908  -1.016  -0.299  -0.624  -0.843  -0.607  -0.883  -1.014
123   E        -0.515  -0.465  -0.278  -0.619  -0.572  -0.294  -0.861  -0.798  -0.525
124   T        -0.686  -0.908  -1.016  -0.483  -0.833  -1.116  -0.607  -0.883  -1.014
125   I        -1.485  -1.308  -1.066  -1.886  -1.632  -1.281  -1.624  -1.388  -1.074
126   Q        -2.035  -1.907  -1.630  -2.112  -1.911  -1.569  -1.878  -1.697  -1.357
127   D        -1.065  -1.195  -1.056  -1.070  -1.252  -1.013  -1.115  -1.276  -1.064
128   A        -0.286  -0.254  -0.258  -0.135  -0.115  -0.165  -0.480  -0.445  -0.491
129   V        -0.515  -0.474  -0.266  -0.807  -0.734  -0.396  -0.861  -0.813  -0.504
130   K        -2.186  -2.045  -2.051  -2.113  -1.964  -1.901  -1.751  -1.610  -1.513
131   F        -1.065  -1.195  -1.056  -0.819  -1.109  -0.978  -1.115  -1.276  -1.064
132   I         0.142   0.356  -0.159   0.286   0.553  -0.192   0.156   0.435  -0.326
133   E         1.011   1.034   1.091   1.098   1.128   1.215   1.045   1.079   1.166
134   Q         1.011   1.034   1.091   1.103   1.140   1.218   1.045   1.079   1.166
135   G         1.011   1.034   1.091   1.210   1.234   1.305   1.045   1.079   1.166
136   H         1.011   1.034   1.091   1.111   1.147   1.225   1.045   1.079   1.166
137   V         1.011   1.034   1.091   0.910   0.960   1.062   1.045   1.079   1.166
138   R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
139   V         1.011   1.034   1.091   0.910   0.960   1.062   1.045   1.079   1.166
140   G         1.011   1.034   1.091   1.210   1.234   1.305   1.045   1.079   1.166
141   P         0.142  -0.004  -0.182   0.453   0.244  -0.112   0.156  -0.056  -0.364
142   N        -1.065  -1.222  -1.056  -0.872  -1.137  -0.921  -1.115  -1.300  -1.064
143   L        -1.885  -1.903  -1.626  -2.161  -2.093  -1.670  -1.751  -1.694  -1.353
144   I        -0.286  -0.401  -0.274  -0.338  -0.576  -0.425  -0.480  -0.687  -0.518
145   N        -0.686  -0.626  -0.988  -0.428  -0.402  -0.932  -0.607  -0.558  -0.979
146   D         1.011   1.034   1.091   0.897   0.949   1.051   1.045   1.079   1.166
147   P         1.011   1.034   1.091   1.214   1.241   1.309   1.045   1.079   1.166
148   A         1.011   1.034   1.091   1.159   1.185   1.264   1.045   1.079   1.166
149   Y        -0.286  -0.401  -0.274  -0.134  -0.341  -0.181  -0.480  -0.687  -0.518
150   L         1.011   1.034   1.091   0.693   0.757   0.885   1.045   1.079   1.166
151   V         0.142   0.348  -0.158   0.169   0.425  -0.243   0.156   0.424  -0.324
152   T         1.011   1.034   1.091   1.060   1.097   1.183   1.045   1.079   1.166
153   R         1.011   1.034   1.091   0.861   0.911   1.022   1.045   1.079   1.166
154   N        -0.286  -0.377  -0.269  -0.191  -0.371  -0.246  -0.480  -0.647  -0.509
155   M        -0.588  -0.467  -0.274  -0.997  -0.771  -0.463  -0.988  -0.802  -0.519
156   E         1.011   1.034   1.091   1.098   1.128   1.215   1.045   1.079   1.166
157   D         1.011   1.034   1.091   0.897   0.949   1.051   1.045   1.079   1.166
158   Y        -0.515  -0.474  -0.266  -0.504  -0.458  -0.157  -0.861  -0.813  -0.504
159   V        -0.286  -0.023  -0.188  -0.541  -0.109  -0.436  -0.480  -0.085  -0.374
160   T         1.011   1.034   1.091   1.060   1.097   1.183   1.045   1.079   1.166
161   W         1.011   1.034   1.091   1.331   1.353   1.404   1.045   1.079   1.166
162   V        -1.236  -1.150  -1.023  -1.350  -1.149  -0.988  -1.370  -1.200  -1.024
163   D         0.142  -0.004  -0.182   0.136  -0.045  -0.348   0.156  -0.056  -0.364
164   N        -2.435  -2.437  -2.079  -2.111  -2.159  -1.698  -2.005  -1.931  -1.534
165   S         1.011   1.034   1.091   1.124   1.149   1.236   1.045   1.079   1.166
166   K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
167   I         1.011   1.034   1.091   1.046   1.093   1.173   1.045   1.079   1.166
168   K         1.011   1.034   1.091   0.739   0.803   0.922   1.045   1.079   1.166
169   K        -1.236  -1.224  -1.047  -1.655  -1.577  -1.262  -1.370  -1.304  -1.054
170   T        -1.236  -1.225  -1.045  -1.196  -1.154  -0.910  -1.370  -1.304  -1.052
171   L        -1.787  -1.726  -1.626  -1.833  -1.760  -1.646  -1.624  -1.562  -1.353
172   L        -0.686  -0.904  -1.017  -0.735  -0.995  -1.085  -0.607  -0.878  -1.015
173   R        -0.286  -0.012  -0.207  -0.656  -0.214  -0.532  -0.480  -0.068  -0.406
174   Y         1.011   1.034   1.091   1.150   1.189   1.257   1.045   1.079   1.166
175   R        -1.065  -0.920  -1.006  -1.261  -0.984  -1.151  -1.115  -0.899  -1.002
176   N        -0.286  -0.377  -0.269  -0.263  -0.465  -0.365  -0.480  -0.647  -0.509
177   Q        -1.787  -1.540  -1.596  -1.846  -1.511  -1.503  -1.624  -1.333  -1.324
178   I        -1.236  -0.987  -1.033  -1.539  -1.266  -1.254  -1.370  -1.081  -1.036
179   D         1.011   1.034   1.091   0.897   0.949   1.051   1.045   1.079   1.166
180   D         1.011   1.034   1.091   0.897   0.949   1.051   1.045   1.079   1.166
181   F        -0.286  -0.215  -0.251  -0.078  -0.001  -0.129  -0.480  -0.382  -0.480
182   D        -1.065  -1.148  -1.044  -1.088  -1.192  -1.030  -1.115  -1.196  -1.050
183   F        -1.465  -1.242  -1.579  -1.473  -1.210  -1.577  -1.243  -1.016  -1.308
184   S        -2.035  -1.907  -1.634  -2.026  -1.941  -1.505  -1.878  -1.698  -1.360
* 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/P32899
Output conservation file - output/P32899
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
