1     M         1.977   1.986   2.071   2.031   2.045   2.183   2.184   2.193   2.336
2     I        -0.659  -0.749  -0.751  -0.699  -0.839  -0.851  -0.580  -0.684  -0.674
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    -        -1.437  -1.411  -1.328  -1.344  -1.295  -1.188  -1.133  -1.106  -0.998
14    -        -0.849  -0.896  -0.837  -0.772  -0.804  -0.699  -0.801  -0.852  -0.769
15    -        -0.849  -0.896  -0.837  -1.055  -1.122  -1.039  -0.801  -0.852  -0.769
16    -        -0.849  -0.806  -0.799  -0.811  -0.762  -0.722  -0.801  -0.755  -0.728
17    -        -0.261  -0.291  -0.207  -0.332  -0.353  -0.226  -0.470  -0.501  -0.387
18    -        -0.849  -0.806  -0.799  -0.933  -0.887  -0.869  -0.801  -0.755  -0.728
19    -        -0.039   0.002  -0.087   0.097   0.147   0.014  -0.138  -0.084  -0.214
20    -        -0.261  -0.291  -0.207  -0.452  -0.498  -0.371  -0.470  -0.501  -0.387
21    -        -0.039  -0.055  -0.117  -0.017  -0.041  -0.122  -0.138  -0.163  -0.257
22    -         0.784   0.834   0.758   0.815   0.903   0.740   0.629   0.712   0.543
23    -        -0.228  -0.277  -0.226  -0.402  -0.476  -0.388  -0.408  -0.476  -0.411
24    E        -1.437  -1.410  -1.328  -1.331  -1.276  -1.175  -1.133  -1.106  -0.998
25    E        -0.261  -0.233  -0.201  -0.443  -0.377  -0.323  -0.470  -0.429  -0.380
26    K         0.550   0.525   0.612   0.161   0.116   0.243   0.194   0.141   0.262
27    K        -1.437  -1.410  -1.328  -1.315  -1.299  -1.159  -1.133  -1.106  -0.998
28    E        -0.039  -0.071  -0.127  -0.056  -0.119  -0.257  -0.138  -0.185  -0.271
29    L        -0.039  -0.142  -0.134   0.082  -0.109  -0.143  -0.138  -0.286  -0.281
30    K        -0.659  -0.671  -0.711  -0.595  -0.621  -0.675  -0.580  -0.597  -0.629
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    K        -1.334  -1.272  -1.271  -1.150  -1.084  -1.049  -1.041  -0.979  -0.948
33    R         1.977   1.986   2.071   2.044   2.055   2.196   2.184   2.193   2.336
34    R         1.977   1.986   2.071   2.044   2.055   2.196   2.184   2.193   2.336
35    V         0.137   0.051  -0.036   0.237   0.130   0.021   0.111  -0.011  -0.142
36    L        -1.334  -1.262  -1.284  -1.142  -1.054  -1.040  -1.041  -0.969  -0.959
37    Q         1.977   1.986   2.071   2.063   2.072   2.215   2.184   2.193   2.336
38    M         1.021   0.967   0.867   1.155   1.082   0.925   1.032   0.939   0.743
39    A        -0.844  -0.819  -0.788  -0.934  -0.925  -0.854  -0.811  -0.782  -0.722
40    R         0.507   0.517   0.608   0.193   0.204   0.343   0.111   0.125   0.254
41    F         1.977   1.986   2.071   1.973   1.986   2.125   2.184   2.193   2.336
42    Y        -0.659  -0.662  -0.709  -0.375  -0.371  -0.435  -0.580  -0.585  -0.626
43    G         1.021   1.094   0.881   1.133   1.239   0.931   1.032   1.144   0.770
44    A         0.137   0.238   0.006   0.090   0.228  -0.098   0.111   0.252  -0.081
45    A        -0.168  -0.109  -0.154  -0.447  -0.363  -0.441  -0.350  -0.277  -0.322
46    A         0.137   0.056  -0.046   0.005  -0.125  -0.311   0.111  -0.004  -0.156
47    F        -1.334  -1.265  -1.269  -1.301  -1.212  -1.203  -1.041  -0.972  -0.947
48    T         1.977   1.986   2.071   1.861   1.868   2.014   2.184   2.193   2.336
49    L         0.627   0.698   0.705   0.333   0.445   0.452   0.341   0.469   0.442
50    I        -0.353  -0.335  -0.240  -0.560  -0.548  -0.400  -0.580  -0.556  -0.430
51    T        -0.844  -0.831  -0.789  -1.031  -1.010  -0.946  -0.811  -0.795  -0.724
52    M        -0.844  -0.866  -0.811  -0.908  -0.917  -0.803  -0.811  -0.826  -0.743
53    R         1.021   0.967   0.867   1.155   1.075   0.916   1.032   0.939   0.743
54    L         1.021   1.094   0.881   0.899   0.993   0.717   1.032   1.144   0.770
55    I        -0.168  -0.211  -0.173  -0.408  -0.479  -0.400  -0.350  -0.407  -0.349
56    S        -0.844  -0.828  -0.813  -0.825  -0.827  -0.809  -0.811  -0.788  -0.745
57    R         0.627   0.684   0.667   0.531   0.634   0.565   0.341   0.442   0.370
58    A        -0.353  -0.343  -0.249  -0.678  -0.655  -0.526  -0.580  -0.566  -0.442
59    I        -0.168  -0.093  -0.136  -0.190  -0.065  -0.111  -0.350  -0.242  -0.290
60    K        -1.334  -1.301  -1.281  -1.341  -1.315  -1.260  -1.041  -1.007  -0.957
61    V        -0.168  -0.191  -0.150  -0.375  -0.398  -0.331  -0.350  -0.375  -0.318
62    R         1.977   1.986   2.071   2.044   2.055   2.196   2.184   2.193   2.336
63    K        -0.168  -0.149  -0.156  -0.223  -0.188  -0.182  -0.350  -0.311  -0.318
64    Y         1.977   1.986   2.071   2.158   2.175   2.310   2.184   2.193   2.336
65    V         0.627   0.644   0.658   0.601   0.627   0.640   0.341   0.367   0.353
66    P         1.977   1.986   2.071   2.132   2.145   2.285   2.184   2.193   2.336
67    S        -0.168  -0.183  -0.150  -0.424  -0.445  -0.406  -0.350  -0.364  -0.318
68    I        -0.844  -0.875  -0.808  -0.864  -0.884  -0.774  -0.811  -0.835  -0.740
69    F         1.977   1.986   2.071   1.973   1.986   2.125   2.184   2.193   2.336
70    Q         1.977   1.986   2.071   2.063   2.072   2.215   2.184   2.193   2.336
71    Q        -0.844  -0.866  -0.811  -0.932  -0.968  -0.890  -0.811  -0.826  -0.743
72    N         1.977   1.986   2.071   2.113   2.127   2.266   2.184   2.193   2.336
73    Y         0.137   0.051  -0.036   0.600   0.478   0.334   0.111  -0.011  -0.142
74    K        -0.659  -0.584  -0.732  -0.684  -0.559  -0.822  -0.580  -0.492  -0.652
75    L         0.137   0.051  -0.036   0.414   0.284   0.125   0.111  -0.011  -0.142
76    P         1.977   1.986   2.071   2.132   2.145   2.285   2.184   2.193   2.336
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    P        -0.844  -0.873  -0.812  -0.782  -0.805  -0.709  -0.811  -0.833  -0.745
79    F        -0.168  -0.149  -0.156  -0.130  -0.098  -0.124  -0.350  -0.311  -0.318
80    S        -0.168  -0.149  -0.156  -0.239  -0.206  -0.199  -0.350  -0.311  -0.318
81    Q        -1.334  -1.368  -1.311  -1.046  -1.100  -1.007  -1.041  -1.068  -0.983
82    R        -0.844  -0.866  -0.811  -0.869  -0.886  -0.785  -0.811  -0.826  -0.743
83    N        -1.334  -1.318  -1.263  -1.282  -1.249  -1.175  -1.041  -1.023  -0.941
84    E         0.627   0.698   0.705   0.578   0.697   0.694   0.341   0.469   0.442
85    A         1.021   1.065   0.868   0.947   0.999   0.759   1.032   1.098   0.746
86    M        -0.659  -0.700  -0.745  -0.562  -0.618  -0.653  -0.580  -0.629  -0.667
87    S        -1.334  -1.368  -1.311  -1.094  -1.167  -1.094  -1.041  -1.068  -0.983
88    A         1.977   1.986   2.071   1.775   1.781   1.927   2.184   2.193   2.336
89    L         0.507   0.519   0.607   0.218   0.231   0.368   0.111   0.129   0.253
90    T        -0.659  -0.686  -0.735  -0.491  -0.524  -0.636  -0.580  -0.612  -0.655
91    Y        -0.844  -0.873  -0.812  -0.785  -0.817  -0.736  -0.811  -0.833  -0.745
92    A        -0.168  -0.218  -0.174  -0.320  -0.412  -0.365  -0.350  -0.414  -0.349
93    S         0.627   0.591   0.655   0.336   0.259   0.348   0.341   0.269   0.347
94    A        -0.844  -0.873  -0.812  -1.094  -1.123  -1.023  -0.811  -0.833  -0.745
95    A         0.137   0.069  -0.040   0.048  -0.050  -0.217   0.111   0.014  -0.147
96    S        -0.168  -0.149  -0.156  -0.236  -0.219  -0.229  -0.350  -0.311  -0.318
97    I        -0.844  -0.830  -0.801  -0.923  -0.910  -0.869  -0.811  -0.791  -0.733
98    G         0.507   0.519   0.607   0.193   0.231   0.352   0.111   0.129   0.253
99    T        -1.334  -1.368  -1.311  -1.114  -1.179  -1.119  -1.041  -1.068  -0.983
100   F         0.137   0.264  -0.024   0.232   0.417  -0.040   0.111   0.288  -0.125
101   S        -0.168  -0.123  -0.140  -0.447  -0.391  -0.391  -0.350  -0.299  -0.302
102   T         0.137   0.051  -0.036   0.341   0.217   0.072   0.111  -0.011  -0.142
103   L        -0.353  -0.343  -0.248  -0.601  -0.588  -0.439  -0.580  -0.566  -0.441
104   I        -0.844  -0.844  -0.788  -0.697  -0.699  -0.616  -0.811  -0.807  -0.722
105   F         1.021   0.967   0.867   1.101   1.026   0.876   1.032   0.939   0.743
106   G         1.977   1.986   2.071   2.005   2.027   2.157   2.184   2.193   2.336
107   F        -0.844  -0.813  -0.796  -0.920  -0.852  -0.840  -0.811  -0.776  -0.730
108   C         1.021   0.988   0.851   1.355   1.308   1.082   1.032   0.973   0.714
109   W         1.977   1.986   2.071   2.232   2.247   2.384   2.184   2.193   2.336
110   A        -0.168  -0.208  -0.175  -0.320  -0.411  -0.362  -0.350  -0.404  -0.349
111   L        -0.659  -0.605  -0.697  -0.544  -0.475  -0.563  -0.580  -0.516  -0.612
112   D         1.977   1.986   2.071   2.037   2.053   2.189   2.184   2.193   2.336
113   I         0.627   0.591   0.655   0.633   0.570   0.655   0.341   0.269   0.347
114   S         1.021   0.988   0.851   0.916   0.873   0.669   1.032   0.973   0.714
115   T        -0.353  -0.335  -0.240  -0.552  -0.546  -0.405  -0.580  -0.556  -0.430
116   A        -0.844  -0.769  -0.796  -1.051  -0.965  -0.959  -0.811  -0.736  -0.730
117   R        -0.659  -0.675  -0.708  -0.587  -0.621  -0.659  -0.580  -0.601  -0.624
118   E         0.137   0.056  -0.046   0.366   0.257   0.112   0.111  -0.004  -0.156
119   F         1.021   1.065   0.868   1.079   1.141   0.841   1.032   1.098   0.746
120   V        -0.659  -0.749  -0.751  -0.497  -0.635  -0.673  -0.580  -0.684  -0.674
121   F        -1.334  -1.368  -1.311  -0.901  -0.973  -0.910  -1.041  -1.068  -0.983
122   K         0.627   0.634   0.652   0.438   0.449   0.472   0.341   0.349   0.340
123   T         0.137   0.134  -0.021   0.280   0.277   0.006   0.111   0.104  -0.120
124   R         1.021   0.982   0.866   1.007   0.958   0.810   1.032   0.963   0.743
125   E        -0.353  -0.335  -0.240  -0.627  -0.592  -0.446  -0.580  -0.556  -0.430
126   F        -0.659  -0.667  -0.706  -0.693  -0.709  -0.759  -0.580  -0.590  -0.622
127   M        -0.168  -0.197  -0.154  -0.260  -0.293  -0.247  -0.350  -0.381  -0.322
128   S         0.137   0.051  -0.036   0.325   0.214   0.063   0.111  -0.011  -0.142
129   L        -1.334  -1.368  -1.311  -1.268  -1.347  -1.282  -1.041  -1.068  -0.983
130   P        -1.824  -1.802  -1.713  -1.173  -1.151  -1.017  -1.271  -1.249  -1.137
131   Q        -0.844  -0.837  -0.802  -0.723  -0.700  -0.662  -0.811  -0.798  -0.734
132   A        -1.334  -1.301  -1.281  -1.279  -1.223  -1.231  -1.041  -1.007  -0.957
133   L        -0.844  -0.821  -0.793  -0.880  -0.863  -0.802  -0.811  -0.786  -0.727
134   E        -0.353  -0.335  -0.242  -0.483  -0.439  -0.303  -0.580  -0.555  -0.433
135   -        -0.261  -0.296  -0.194  -0.311  -0.335  -0.193  -0.470  -0.508  -0.374
136   -        -0.039  -0.138  -0.134  -0.135  -0.277  -0.263  -0.138  -0.281  -0.281
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   T        -0.849  -0.779  -0.806  -0.946  -0.822  -0.899  -0.801  -0.723  -0.735
140   D        -0.849  -0.795  -0.799  -0.648  -0.554  -0.593  -0.801  -0.743  -0.728
141   T        -1.334  -1.323  -1.274  -1.321  -1.297  -1.230  -1.041  -1.028  -0.951
142   S        -0.168  -0.198  -0.172  -0.065  -0.112  -0.092  -0.350  -0.387  -0.345
143   M         0.137   0.121  -0.027   0.262   0.239  -0.030   0.111   0.086  -0.128
144   D         1.021   0.988   0.851   1.165   1.122   0.911   1.032   0.973   0.714
145   E         0.627   0.594   0.638   0.621   0.568   0.634   0.341   0.273   0.314
146   E         1.021   1.065   0.868   1.161   1.219   0.961   1.032   1.098   0.746
147   T         0.627   0.698   0.705   0.336   0.462   0.448   0.341   0.469   0.442
148   S        -0.844  -0.828  -0.786  -0.843  -0.807  -0.758  -0.811  -0.792  -0.720
149   K        -0.659  -0.584  -0.732  -0.501  -0.399  -0.582  -0.580  -0.492  -0.652
150   L        -0.168  -0.136  -0.141  -0.325  -0.284  -0.261  -0.350  -0.311  -0.307
151   T        -0.659  -0.700  -0.745  -0.459  -0.531  -0.635  -0.580  -0.629  -0.667
152   K         0.137   0.051  -0.036   0.341   0.220   0.069   0.111  -0.011  -0.142
153   Q        -0.844  -0.837  -0.802  -0.885  -0.849  -0.804  -0.811  -0.798  -0.734
154   L         1.977   1.986   2.071   1.748   1.760   1.900   2.184   2.193   2.336
155   Q        -0.844  -0.866  -0.811  -0.684  -0.723  -0.649  -0.811  -0.826  -0.743
156   D        -0.168  -0.194  -0.171  -0.230  -0.270  -0.244  -0.350  -0.382  -0.344
157   L        -0.844  -0.828  -0.813  -0.944  -0.945  -0.907  -0.811  -0.788  -0.745
158   L         1.021   0.967   0.867   0.906   0.835   0.706   1.032   0.939   0.743
159   S         0.507   0.527   0.614   0.199   0.228   0.355   0.111   0.144   0.267
160   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   N        -0.844  -0.783  -0.794  -0.860  -0.755  -0.803  -0.811  -0.748  -0.728
177   N        -0.659  -0.588  -0.715  -0.562  -0.457  -0.637  -0.580  -0.497  -0.632
178   K         0.137   0.164  -0.019   0.227   0.264   0.030   0.111   0.146  -0.118
* 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/P87275
Output conservation file - output/P87275
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
