1     M         0.996   1.021   1.070   1.286   1.311   1.357   1.043   1.079   1.152
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     K        -0.208  -0.299  -0.168  -0.440  -0.601  -0.390  -0.444  -0.621  -0.447
4     Y        -0.564  -0.741  -0.829  -0.173  -0.431  -0.587  -0.568  -0.804  -0.903
5     I         0.996   1.021   1.070   0.775   0.800   0.930   1.043   1.079   1.152
6     Q        -0.564  -0.793  -0.845  -0.159  -0.458  -0.556  -0.568  -0.863  -0.923
7     T        -0.868  -1.044  -0.877  -0.779  -1.096  -0.887  -0.940  -1.173  -0.966
8     E        -0.350  -0.261  -0.162  -0.468  -0.323  -0.215  -0.692  -0.555  -0.437
9     Q        -0.770  -0.899  -0.869  -0.604  -0.856  -0.891  -0.878  -1.047  -0.957
10    Q        -2.537  -2.233  -2.123  -2.482  -1.965  -1.883  -1.993  -1.699  -1.517
11    I        -0.208  -0.007  -0.104  -0.307   0.017  -0.214  -0.444  -0.128  -0.334
12    E        -1.650  -1.578  -1.389  -1.472  -1.418  -1.174  -1.559  -1.479  -1.237
13    I        -0.419  -0.302  -0.159  -1.077  -0.860  -0.600  -0.816  -0.626  -0.431
14    P         0.996   1.021   1.070   1.245   1.276   1.323   1.043   1.079   1.152
15    E         0.370   0.291  -0.048   0.517   0.431  -0.098   0.423   0.316  -0.237
16    G         0.370   0.234  -0.068   0.513   0.354  -0.087   0.423   0.235  -0.272
17    V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
18    T        -0.237  -0.483  -0.796   0.057  -0.238  -0.751  -0.134  -0.440  -0.861
19    V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
20    S        -1.243  -1.065  -0.887  -1.245  -1.004  -0.761  -1.435  -1.211  -0.977
21    I         0.996   1.021   1.070   0.775   0.800   0.930   1.043   1.079   1.152
22    K        -0.564  -0.261  -0.784  -0.568  -0.157  -0.859  -0.568  -0.166  -0.845
23    S        -0.419  -0.348  -0.171  -0.498  -0.398  -0.138  -0.816  -0.710  -0.453
24    R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
25    I        -2.440  -2.387  -2.114  -2.598  -2.503  -2.013  -1.931  -1.828  -1.512
26    V        -0.350  -0.227  -0.151  -0.961  -0.738  -0.607  -0.692  -0.496  -0.417
27    K        -0.419  -0.320  -0.157  -0.765  -0.548  -0.312  -0.816  -0.660  -0.428
28    V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
29    V        -0.823  -0.988  -1.328  -0.478  -0.694  -1.328  -0.630  -0.821  -1.174
30    G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
31    P         0.996   1.021   1.070   1.245   1.276   1.323   1.043   1.079   1.152
32    R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
33    G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
34    T        -1.307  -1.254  -1.346  -1.309  -1.212  -1.411  -1.249  -1.161  -1.197
35    L         0.996   1.021   1.070   1.043   1.088   1.154   1.043   1.079   1.152
36    T        -1.243  -1.094  -0.892  -1.678  -1.446  -1.161  -1.435  -1.238  -0.983
37    K         0.022  -0.089  -0.095  -0.050  -0.183  -0.195  -0.072  -0.262  -0.318
38    N        -1.048  -0.863  -0.853  -1.039  -0.821  -0.793  -1.187  -0.972  -0.939
39    L         0.996   1.021   1.070   1.043   1.088   1.154   1.043   1.079   1.152
40    K        -0.868  -1.044  -0.877  -0.941  -1.209  -0.950  -0.940  -1.173  -0.966
41    H         0.370   0.265  -0.050   0.740   0.617   0.115   0.423   0.280  -0.241
42    I         0.022  -0.089  -0.095  -0.220  -0.435  -0.457  -0.072  -0.262  -0.318
43    D        -0.237  -0.453  -0.811   0.091  -0.149  -0.684  -0.134  -0.403  -0.880
44    V         0.022  -0.089  -0.095  -0.317  -0.486  -0.501  -0.072  -0.262  -0.318
45    T        -1.127  -1.393  -1.381  -0.798  -1.184  -1.174  -1.002  -1.289  -1.228
46    F        -0.237  -0.430  -0.805   0.245   0.023  -0.518  -0.134  -0.373  -0.873
47    T        -2.168  -2.243  -2.134  -1.754  -1.948  -1.756  -1.683  -1.730  -1.523
48    K         0.370   0.234  -0.068   0.304   0.162  -0.358   0.423   0.235  -0.272
49    V        -0.868  -0.979  -0.871  -1.150  -1.303  -1.143  -0.940  -1.089  -0.959
50    N        -1.552  -1.614  -1.393  -1.456  -1.587  -1.303  -1.497  -1.517  -1.240
51    N        -1.127  -1.145  -1.344  -0.873  -0.901  -1.240  -1.002  -0.987  -1.190
52    Q        -1.935  -1.988  -1.802  -1.752  -1.827  -1.578  -1.641  -1.653  -1.411
53    L        -2.181  -2.120  -1.809  -1.948  -1.907  -1.536  -1.869  -1.762  -1.417
54    I         0.996   1.021   1.070   0.775   0.800   0.930   1.043   1.079   1.152
55    K         0.370   0.234  -0.068   0.339   0.212  -0.221   0.423   0.235  -0.272
56    V        -1.552  -1.581  -1.391  -1.807  -1.771  -1.478  -1.497  -1.481  -1.238
57    A        -1.127  -1.268  -1.372  -0.863  -1.142  -1.249  -1.002  -1.174  -1.218
58    V         0.022  -0.104  -0.151  -0.317  -0.511  -0.607  -0.072  -0.287  -0.418
59    H        -0.564  -0.741  -0.829  -0.065  -0.303  -0.450  -0.568  -0.804  -0.903
60    N        -0.770  -0.899  -0.869  -0.621  -0.805  -0.728  -0.878  -1.047  -0.957
61    G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
62    D        -1.127  -1.288  -1.374  -0.791  -1.043  -1.181  -1.002  -1.192  -1.220
63    R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
64    K         0.996   1.021   1.070   0.828   0.892   0.974   1.043   1.079   1.152
65    H         0.370   0.234  -0.068   0.742   0.580   0.089   0.423   0.235  -0.272
66    V         0.022  -0.089  -0.095  -0.264  -0.407  -0.399  -0.072  -0.262  -0.318
67    A         0.996   1.021   1.070   1.144   1.180   1.238   1.043   1.079   1.152
68    A         0.022  -0.089  -0.095   0.291   0.131   0.096  -0.072  -0.262  -0.318
69    L         0.022  -0.089  -0.095   0.077  -0.124  -0.194  -0.072  -0.262  -0.318
70    R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
71    T         0.370   0.291  -0.048   0.561   0.487   0.006   0.423   0.316  -0.237
72    V         0.370   0.265  -0.050   0.178   0.104  -0.274   0.423   0.280  -0.241
73    K        -0.564  -0.793  -0.845  -0.517  -0.799  -0.867  -0.568  -0.863  -0.923
74    S        -0.564  -0.634  -0.849  -0.287  -0.433  -0.720  -0.568  -0.695  -0.933
75    L        -0.208  -0.299  -0.168  -0.307  -0.547  -0.367  -0.444  -0.621  -0.447
76    V        -0.208  -0.007  -0.104  -0.616  -0.292  -0.476  -0.444  -0.128  -0.334
77    D        -1.761  -1.406  -1.376  -1.662  -1.196  -1.149  -1.683  -1.292  -1.224
78    N         0.996   1.021   1.070   1.003   1.028   1.121   1.043   1.079   1.152
79    M        -0.350  -0.342  -0.173  -0.338  -0.330  -0.080  -0.692  -0.699  -0.456
80    I         0.996   1.021   1.070   0.775   0.800   0.930   1.043   1.079   1.152
81    T        -0.208  -0.299  -0.168  -0.310  -0.548  -0.369  -0.444  -0.621  -0.447
82    G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
83    V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
84    T         0.996   1.021   1.070   1.041   1.087   1.152   1.043   1.079   1.152
85    K        -0.564  -0.741  -0.829  -0.524  -0.741  -0.858  -0.568  -0.804  -0.903
86    G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
87    Y        -0.208  -0.299  -0.168  -0.024  -0.203  -0.046  -0.444  -0.621  -0.447
88    K         0.022  -0.089  -0.095  -0.092  -0.246  -0.272  -0.072  -0.262  -0.318
89    Y         0.996   1.021   1.070   1.191   1.228   1.278   1.043   1.079   1.152
90    K         0.996   1.021   1.070   0.828   0.892   0.974   1.043   1.079   1.152
91    M        -0.350  -0.096  -0.101  -0.248   0.169   0.084  -0.692  -0.273  -0.329
92    R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
93    Y        -0.564  -0.586  -0.820  -0.175  -0.266  -0.575  -0.568  -0.640  -0.892
94    V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
95    Y         0.996   1.021   1.070   1.191   1.228   1.278   1.043   1.079   1.152
96    A         0.996   1.021   1.070   1.144   1.180   1.238   1.043   1.079   1.152
97    H         0.996   1.021   1.070   1.230   1.263   1.310   1.043   1.079   1.152
98    F         0.996   1.021   1.070   1.183   1.219   1.271   1.043   1.079   1.152
99    P         0.996   1.021   1.070   1.245   1.276   1.323   1.043   1.079   1.152
100   I         0.996   1.021   1.070   0.775   0.800   0.930   1.043   1.079   1.152
101   N         0.996   1.021   1.070   1.003   1.028   1.121   1.043   1.079   1.152
102   V         0.022  -0.089  -0.095  -0.317  -0.486  -0.501  -0.072  -0.262  -0.318
103   N         0.996   1.021   1.070   1.003   1.028   1.121   1.043   1.079   1.152
104   I        -1.761  -1.545  -1.393  -2.097  -1.753  -1.544  -1.683  -1.457  -1.241
105   V        -1.404  -1.507  -1.387  -1.560  -1.716  -1.560  -1.311  -1.403  -1.235
106   E        -0.967  -0.903  -0.879  -0.974  -0.884  -0.943  -1.099  -0.990  -0.967
107   K        -0.564  -0.620  -0.824  -0.603  -0.693  -1.044  -0.568  -0.675  -0.897
108   D        -0.208  -0.299  -0.168  -0.222  -0.412  -0.236  -0.444  -0.621  -0.447
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
113   A        -1.717  -1.693  -1.409  -1.631  -1.593  -1.232  -1.651  -1.588  -1.255
114   K        -1.909  -1.966  -1.803  -1.749  -1.806  -1.521  -1.621  -1.656  -1.413
115   F        -1.552  -1.559  -1.399  -1.441  -1.558  -1.294  -1.497  -1.469  -1.246
116   I        -0.419  -0.239  -0.134  -1.095  -0.760  -0.575  -0.816  -0.515  -0.387
117   E         0.996   1.021   1.070   1.022   1.061   1.136   1.043   1.079   1.152
118   V         0.370   0.464  -0.052   0.250   0.351  -0.369   0.423   0.545  -0.244
119   R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
120   N         0.996   1.021   1.070   1.003   1.028   1.121   1.043   1.079   1.152
121   F         0.996   1.021   1.070   1.183   1.219   1.271   1.043   1.079   1.152
122   L         0.370   0.234  -0.068   0.533   0.372  -0.139   0.423   0.235  -0.272
123   G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
124   D        -0.419  -0.239  -0.134  -0.606  -0.301  -0.168  -0.816  -0.515  -0.387
125   K         0.022  -0.089  -0.095  -0.092  -0.246  -0.272  -0.072  -0.262  -0.318
126   K        -1.196  -1.141  -0.898  -1.590  -1.555  -1.136  -1.373  -1.298  -0.990
127   I        -0.564  -0.598  -0.821  -0.760  -0.812  -1.112  -0.568  -0.652  -0.893
128   R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
129   N        -2.376  -2.276  -2.125  -2.165  -2.134  -1.838  -1.869  -1.754  -1.518
130   V        -0.208  -0.242  -0.161  -0.693  -0.766  -0.624  -0.444  -0.521  -0.434
131   P        -0.887  -0.951  -0.865  -0.868  -1.007  -0.953  -1.064  -1.104  -0.953
132   V        -1.552  -1.635  -1.398  -1.754  -1.757  -1.338  -1.497  -1.541  -1.245
133   R        -1.909  -1.981  -1.803  -1.529  -1.640  -1.340  -1.621  -1.663  -1.413
134   D        -1.243  -1.143  -0.899  -1.243  -1.071  -0.762  -1.435  -1.301  -0.992
135   G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
136   V         0.370   0.297  -0.060   0.196   0.163  -0.221   0.423   0.324  -0.258
137   T        -1.243  -1.127  -0.892  -1.307  -1.144  -0.824  -1.435  -1.282  -0.984
138   I        -0.823  -0.746  -1.322  -0.781  -0.671  -1.333  -0.630  -0.546  -1.168
139   E        -0.868  -0.739  -0.820  -0.737  -0.599  -0.724  -0.940  -0.802  -0.892
140   F        -0.419  -0.326  -0.160  -0.654  -0.601  -0.306  -0.816  -0.670  -0.434
141   S         0.996   1.021   1.070   1.081   1.116   1.185   1.043   1.079   1.152
142   T        -1.307  -1.371  -1.382  -1.095  -1.216  -1.213  -1.249  -1.306  -1.231
143   N        -1.132  -0.970  -0.884  -1.140  -0.931  -0.794  -1.311  -1.121  -0.974
144   V        -0.208  -0.234  -0.162  -0.230  -0.322  -0.329  -0.444  -0.508  -0.437
145   K         0.996   1.021   1.070   0.828   0.892   0.974   1.043   1.079   1.152
146   D         0.996   1.021   1.070   1.049   1.102   1.159   1.043   1.079   1.152
147   E         0.996   1.021   1.070   1.022   1.061   1.136   1.043   1.079   1.152
148   I        -0.887  -0.763  -0.850  -1.158  -1.002  -1.086  -1.064  -0.900  -0.936
149   V        -0.770  -0.854  -0.855  -1.109  -1.218  -1.074  -0.878  -0.976  -0.941
150   L        -0.564  -0.583  -0.832  -0.447  -0.547  -1.011  -0.568  -0.636  -0.912
151   S        -0.564  -0.741  -0.829  -0.336  -0.623  -0.822  -0.568  -0.804  -0.903
152   G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
153   N         0.996   1.021   1.070   1.003   1.028   1.121   1.043   1.079   1.152
154   S         0.996   1.021   1.070   1.081   1.116   1.185   1.043   1.079   1.152
155   V        -0.924  -0.860  -0.844  -1.269  -1.043  -1.050  -1.126  -0.986  -0.925
156   E         0.996   1.021   1.070   1.022   1.061   1.136   1.043   1.079   1.152
157   D        -1.552  -1.453  -1.382  -1.421  -1.274  -1.184  -1.497  -1.338  -1.229
158   V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
159   S         0.996   1.021   1.070   1.081   1.116   1.185   1.043   1.079   1.152
160   Q         0.996   1.021   1.070   1.165   1.209   1.256   1.043   1.079   1.152
161   N        -0.770  -0.899  -0.869  -0.683  -0.900  -0.813  -0.878  -1.047  -0.957
162   A         0.370   0.297  -0.060   0.686   0.615   0.148   0.423   0.324  -0.258
163   A         0.996   1.021   1.070   1.144   1.180   1.238   1.043   1.079   1.152
164   D         0.022  -0.089  -0.095   0.131  -0.039  -0.098  -0.072  -0.262  -0.318
165   L        -0.564  -0.287  -0.788  -0.702  -0.332  -1.017  -0.568  -0.205  -0.851
166   Q         0.022  -0.089  -0.095   0.209   0.022  -0.080  -0.072  -0.262  -0.318
167   Q         0.996   1.021   1.070   1.165   1.209   1.256   1.043   1.079   1.152
168   I        -0.237  -0.263  -0.795  -0.236  -0.276  -1.028  -0.134  -0.169  -0.859
169   C         0.996   1.021   1.070   1.307   1.329   1.374   1.043   1.079   1.152
170   R         0.022  -0.089  -0.095   0.070  -0.119  -0.144  -0.072  -0.262  -0.318
171   V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
172   R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
173   N         0.996   1.021   1.070   1.003   1.028   1.121   1.043   1.079   1.152
174   K         0.996   1.021   1.070   0.828   0.892   0.974   1.043   1.079   1.152
175   D         0.996   1.021   1.070   1.049   1.102   1.159   1.043   1.079   1.152
176   I         0.996   1.021   1.070   0.775   0.800   0.930   1.043   1.079   1.152
177   R         0.996   1.021   1.070   0.987   1.020   1.107   1.043   1.079   1.152
178   K         0.996   1.021   1.070   0.828   0.892   0.974   1.043   1.079   1.152
179   F         0.996   1.021   1.070   1.183   1.219   1.271   1.043   1.079   1.152
180   L         0.996   1.021   1.070   1.043   1.088   1.154   1.043   1.079   1.152
181   D         0.996   1.021   1.070   1.049   1.102   1.159   1.043   1.079   1.152
182   G         0.996   1.021   1.070   1.000   1.036   1.118   1.043   1.079   1.152
183   I         0.996   1.021   1.070   0.775   0.800   0.930   1.043   1.079   1.152
184   Y         0.996   1.021   1.070   1.191   1.228   1.278   1.043   1.079   1.152
185   V         0.996   1.021   1.070   0.652   0.725   0.827   1.043   1.079   1.152
186   S         0.996   1.021   1.070   1.081   1.116   1.185   1.043   1.079   1.152
187   H        -0.208  -0.007  -0.104  -0.166   0.113  -0.038  -0.444  -0.128  -0.334
188   K        -0.350  -0.322  -0.171  -0.684  -0.643  -0.394  -0.692  -0.663  -0.452
189   G         0.370   0.297  -0.060   0.516   0.439  -0.059   0.423   0.324  -0.258
190   F        -2.020  -1.632  -1.769  -1.805  -1.306  -1.541  -1.745  -1.341  -1.385
191   I         0.370   0.297  -0.060   0.250   0.151  -0.385   0.423   0.324  -0.258
192   V        -1.307  -1.301  -1.367  -1.331  -1.367  -1.493  -1.249  -1.227  -1.218
193   E         0.996   1.021   1.070   1.022   1.061   1.136   1.043   1.079   1.152
194   D        -1.048  -1.076  -0.871  -1.033  -1.094  -0.821  -1.187  -1.215  -0.960
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   M        -2.310  -2.159  -2.120  -1.850  -1.669  -1.616  -1.806  -1.638  -1.514
* 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/P51401
Output conservation file - output/P51401
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
