1     M         1.555   1.563   1.623   1.762   1.774   1.866   1.699   1.710   1.807
2     T        -0.703  -0.739  -0.703  -0.682  -0.731  -0.685  -0.736  -0.765  -0.710
3     -        -0.897  -0.877  -0.787  -1.065  -1.046  -0.902  -0.932  -0.908  -0.796
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    G        -1.205  -1.164  -1.138  -1.152  -1.077  -1.063  -1.030  -0.987  -0.937
17    Y         0.829   0.740   0.630   1.003   0.882   0.717   0.840   0.692   0.478
18    P         1.555   1.563   1.623   1.630   1.638   1.737   1.699   1.710   1.807
19    D        -0.703  -0.667  -0.710  -0.871  -0.830  -0.871  -0.736  -0.701  -0.719
20    V        -0.221  -0.269  -0.227  -0.274  -0.333  -0.239  -0.449  -0.497  -0.433
21    A         0.347   0.363   0.435   0.138   0.153   0.274  -0.020   0.007   0.104
22    A         0.497   0.510   0.498   0.389   0.401   0.380   0.267   0.287   0.229
23    F         0.829   0.809   0.640   1.009   0.980   0.756   0.840   0.805   0.495
24    D         1.555   1.563   1.623   1.470   1.482   1.580   1.699   1.710   1.807
25    L         1.555   1.563   1.623   1.415   1.433   1.526   1.699   1.710   1.807
26    D         1.555   1.563   1.623   1.470   1.482   1.580   1.699   1.710   1.807
27    Y         1.555   1.563   1.623   1.650   1.662   1.757   1.699   1.710   1.807
28    T         1.555   1.563   1.623   1.606   1.622   1.713   1.699   1.710   1.807
29    I        -0.135  -0.095  -0.183  -0.359  -0.304  -0.430  -0.306  -0.255  -0.368
30    W         1.555   1.563   1.623   1.746   1.758   1.851   1.699   1.710   1.807
31    P         1.555   1.563   1.623   1.630   1.638   1.737   1.699   1.710   1.807
32    C         0.829   0.740   0.630   1.090   0.960   0.763   0.840   0.692   0.478
33    Y        -0.135  -0.120  -0.178   0.023   0.052  -0.048  -0.306  -0.275  -0.358
34    C         0.829   0.740   0.630   1.114   0.988   0.809   0.840   0.692   0.478
35    D         1.555   1.563   1.623   1.470   1.482   1.580   1.699   1.710   1.807
36    T         0.829   0.870   0.653   0.952   1.009   0.698   0.840   0.901   0.519
37    H         1.555   1.563   1.623   1.714   1.733   1.820   1.699   1.710   1.807
38    L        -0.353  -0.351  -0.279  -0.649  -0.655  -0.552  -0.592  -0.589  -0.495
39    H        -1.054  -1.036  -1.081  -0.781  -0.765  -0.815  -0.879  -0.860  -0.883
40    G        -1.536  -1.504  -1.459  -1.237  -1.199  -1.130  -1.165  -1.135  -1.060
41    P         1.555   1.563   1.623   1.630   1.638   1.737   1.699   1.710   1.807
42    F        -0.221  -0.214  -0.214  -0.417  -0.405  -0.389  -0.449  -0.438  -0.417
43    K         0.829   0.809   0.640   0.789   0.774   0.528   0.840   0.805   0.495
44    P         0.147   0.185  -0.073   0.343   0.392   0.013   0.124   0.177  -0.201
45    V        -0.485  -0.574  -0.659  -0.398  -0.537  -0.670  -0.449  -0.557  -0.652
46    K        -0.836  -0.811  -0.757  -0.998  -0.961  -0.883  -0.879  -0.852  -0.767
47    S        -0.703  -0.640  -0.697  -0.645  -0.541  -0.649  -0.736  -0.662  -0.704
48    S        -1.054  -0.992  -1.073  -1.008  -0.923  -1.043  -0.879  -0.812  -0.875
49    N        -0.284  -0.333  -0.263  -0.344  -0.448  -0.355  -0.494  -0.566  -0.474
50    G         1.555   1.563   1.623   1.576   1.594   1.684   1.699   1.710   1.807
51    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    L         0.560   0.603   0.513   0.430   0.492   0.360   0.383   0.455   0.258
54    T        -0.703  -0.752  -0.712  -0.657  -0.733  -0.664  -0.736  -0.783  -0.720
55    I        -0.221  -0.185  -0.209  -0.514  -0.472  -0.477  -0.449  -0.406  -0.411
56    I        -0.135  -0.153  -0.193  -0.243  -0.286  -0.338  -0.306  -0.336  -0.385
57    C         0.829   0.878   0.653   0.847   0.906   0.627   0.840   0.913   0.519
58    R         0.147   0.043  -0.091   0.306   0.157  -0.082   0.124  -0.025  -0.227
59    D        -0.703  -0.672  -0.716  -0.600  -0.552  -0.633  -0.736  -0.699  -0.723
60    G         0.829   0.875   0.648   0.927   0.991   0.647   0.840   0.909   0.509
61    Y        -0.703  -0.715  -0.710  -0.560  -0.580  -0.559  -0.736  -0.741  -0.718
62    E        -0.703  -0.697  -0.714  -0.668  -0.660  -0.708  -0.736  -0.719  -0.719
63    L        -0.135  -0.199  -0.185  -0.359  -0.452  -0.432  -0.306  -0.385  -0.369
64    T        -0.703  -0.714  -0.702  -0.665  -0.656  -0.654  -0.736  -0.740  -0.706
65    I        -0.221  -0.187  -0.203  -0.417  -0.375  -0.373  -0.449  -0.411  -0.405
66    Y         0.829   0.870   0.653   1.003   1.054   0.754   0.840   0.901   0.519
67    K        -0.485  -0.529  -0.643  -0.449  -0.507  -0.675  -0.449  -0.504  -0.633
68    D         0.829   0.809   0.640   0.812   0.785   0.540   0.840   0.805   0.495
69    I         0.347   0.368   0.430   0.083   0.114   0.208  -0.020   0.017   0.095
70    P        -0.135  -0.173  -0.188  -0.124  -0.171  -0.210  -0.306  -0.343  -0.372
71    R        -1.054  -1.061  -1.118  -0.832  -0.844  -0.949  -0.879  -0.885  -0.918
72    I         1.555   1.563   1.623   1.565   1.575   1.673   1.699   1.710   1.807
73    L        -0.135  -0.099  -0.174  -0.316  -0.266  -0.363  -0.306  -0.259  -0.358
74    G        -1.886  -1.867  -1.760  -1.517  -1.475  -1.345  -1.308  -1.289  -1.168
75    D        -0.221  -0.214  -0.223  -0.392  -0.377  -0.353  -0.449  -0.438  -0.427
76    L         1.555   1.563   1.623   1.415   1.433   1.526   1.699   1.710   1.807
77    K        -0.135  -0.136  -0.197  -0.295  -0.298  -0.386  -0.306  -0.322  -0.389
78    D        -1.186  -1.206  -1.142  -1.156  -1.171  -1.064  -1.022  -1.034  -0.942
79    N        -0.836  -0.825  -0.756  -0.709  -0.684  -0.603  -0.879  -0.863  -0.767
80    G        -0.836  -0.858  -0.763  -0.952  -0.979  -0.842  -0.879  -0.891  -0.773
81    V         1.555   1.563   1.623   1.511   1.518   1.621   1.699   1.710   1.807
82    K         0.497   0.471   0.465   0.292   0.257   0.225   0.267   0.215   0.165
83    L         0.347   0.368   0.430  -0.009   0.026   0.122  -0.020   0.017   0.095
84    M        -0.703  -0.733  -0.716  -0.702  -0.749  -0.691  -0.736  -0.767  -0.724
85    T        -1.186  -1.181  -1.138  -1.079  -1.086  -1.014  -1.022  -1.014  -0.939
86    A         1.555   1.563   1.623   1.670   1.680   1.777   1.699   1.710   1.807
87    S         1.555   1.563   1.623   1.593   1.612   1.701   1.699   1.710   1.807
88    R         1.555   1.563   1.623   1.630   1.649   1.737   1.699   1.710   1.807
89    T         1.555   1.563   1.623   1.606   1.622   1.713   1.699   1.710   1.807
90    W        -0.221  -0.269  -0.227  -0.111  -0.167  -0.090  -0.449  -0.497  -0.433
91    A         0.347   0.368   0.430   0.228   0.264   0.350  -0.020   0.017   0.095
92    P         1.555   1.563   1.623   1.630   1.638   1.737   1.699   1.710   1.807
93    E        -1.054  -1.061  -1.118  -0.943  -0.968  -1.070  -0.879  -0.885  -0.918
94    I        -0.221  -0.269  -0.205  -0.381  -0.446  -0.333  -0.449  -0.497  -0.407
95    A         1.555   1.563   1.623   1.670   1.680   1.777   1.699   1.710   1.807
96    Q        -0.221  -0.227  -0.210  -0.307  -0.321  -0.285  -0.449  -0.449  -0.413
97    E        -0.135  -0.154  -0.197  -0.092  -0.119  -0.175  -0.306  -0.337  -0.389
98    I        -0.703  -0.760  -0.716  -0.774  -0.839  -0.748  -0.736  -0.789  -0.725
99    L         1.555   1.563   1.623   1.415   1.433   1.526   1.699   1.710   1.807
100   K        -0.135  -0.173  -0.188  -0.274  -0.302  -0.331  -0.306  -0.343  -0.372
101   I        -1.054  -0.978  -1.062  -0.997  -0.891  -0.996  -0.879  -0.796  -0.864
102   F        -0.485  -0.525  -0.653  -0.280  -0.338  -0.559  -0.449  -0.500  -0.645
103   K         0.497   0.543   0.513   0.335   0.417   0.359   0.267   0.349   0.257
104   V         0.497   0.473   0.468   0.379   0.325   0.289   0.267   0.219   0.170
105   K        -1.536  -1.522  -1.472  -1.404  -1.387  -1.288  -1.165  -1.149  -1.070
106   Y        -0.284  -0.333  -0.263  -0.276  -0.371  -0.253  -0.494  -0.566  -0.474
107   A        -0.897  -0.862  -0.787  -0.863  -0.848  -0.704  -0.932  -0.893  -0.796
108   G         1.555   1.563   1.623   1.576   1.594   1.684   1.699   1.710   1.807
109   V        -0.897  -0.862  -0.787  -1.139  -1.055  -0.974  -0.932  -0.893  -0.796
110   V        -1.186  -1.156  -1.129  -1.310  -1.273  -1.233  -1.022  -0.992  -0.931
111   T        -1.536  -1.518  -1.469  -1.493  -1.486  -1.401  -1.165  -1.147  -1.068
112   P         0.147   0.158  -0.069   0.338   0.349   0.011   0.124   0.138  -0.195
113   L        -0.703  -0.689  -0.727  -0.759  -0.745  -0.753  -0.736  -0.723  -0.736
114   A        -1.054  -1.020  -1.098  -0.886  -0.845  -0.961  -0.879  -0.841  -0.899
115   N        -0.703  -0.682  -0.700  -0.698  -0.657  -0.700  -0.736  -0.707  -0.707
116   L        -1.054  -1.075  -1.108  -0.845  -0.891  -0.960  -0.879  -0.900  -0.908
117   F         1.555   1.563   1.623   1.638   1.647   1.745   1.699   1.710   1.807
118   D        -0.135  -0.173  -0.188  -0.202  -0.247  -0.267  -0.306  -0.343  -0.372
119   E        -1.054  -1.096  -1.101  -0.888  -0.957  -0.981  -0.879  -0.921  -0.902
120   F        -0.135  -0.197  -0.184  -0.311  -0.401  -0.380  -0.306  -0.381  -0.368
121   Q        -0.703  -0.727  -0.712  -0.605  -0.656  -0.640  -0.736  -0.761  -0.720
122   W         0.829   0.740   0.630   1.103   0.983   0.817   0.840   0.692   0.478
123   G         0.829   0.740   0.630   0.973   0.862   0.707   0.840   0.692   0.478
124   E        -1.186  -1.206  -1.140  -1.035  -1.067  -0.974  -1.022  -1.033  -0.940
125   R        -0.135  -0.120  -0.178  -0.098  -0.060  -0.148  -0.306  -0.275  -0.358
126   S         0.147   0.126  -0.086   0.310   0.285  -0.037   0.124   0.094  -0.220
127   K         1.555   1.563   1.623   1.436   1.459   1.547   1.699   1.710   1.807
128   I        -0.485  -0.498  -0.630  -0.318  -0.337  -0.536  -0.449  -0.468  -0.618
129   G        -0.836  -0.858  -0.763  -0.962  -0.984  -0.847  -0.879  -0.891  -0.773
130   H         1.555   1.563   1.623   1.714   1.733   1.820   1.699   1.710   1.807
131   L        -0.135  -0.134  -0.192  -0.195  -0.211  -0.304  -0.306  -0.319  -0.383
132   R        -0.703  -0.650  -0.703  -0.737  -0.660  -0.704  -0.736  -0.676  -0.709
133   D        -1.186  -1.206  -1.140  -1.286  -1.307  -1.193  -1.022  -1.033  -0.940
134   G         0.365   0.369   0.433   0.243   0.248   0.344   0.015   0.018   0.102
135   L        -0.801  -0.782  -0.769  -0.761  -0.740  -0.745  -0.827  -0.804  -0.777
136   K         1.555   1.563   1.623   1.460   1.478   1.570   1.699   1.710   1.807
137   D        -1.291  -1.280  -1.175  -1.372  -1.351  -1.202  -1.108  -1.093  -0.969
138   L        -0.135  -0.174  -0.190  -0.346  -0.411  -0.431  -0.306  -0.363  -0.380
139   Y        -1.054  -1.061  -1.118  -0.817  -0.820  -0.938  -0.879  -0.885  -0.918
140   N        -0.836  -0.825  -0.760  -0.776  -0.763  -0.681  -0.879  -0.863  -0.770
141   T        -1.186  -1.182  -1.124  -1.174  -1.170  -1.069  -1.022  -1.014  -0.928
142   S        -0.353  -0.356  -0.276  -0.545  -0.551  -0.439  -0.592  -0.596  -0.492
143   D        -1.186  -1.221  -1.125  -1.264  -1.303  -1.173  -1.022  -1.045  -0.928
144   L         0.147   0.065  -0.098   0.100  -0.017  -0.276   0.124   0.006  -0.237
145   K        -1.186  -1.154  -1.137  -1.280  -1.226  -1.180  -1.022  -0.989  -0.938
146   S        -1.886  -1.867  -1.760  -1.674  -1.625  -1.498  -1.308  -1.289  -1.168
147   K        -1.536  -1.544  -1.479  -1.419  -1.427  -1.355  -1.165  -1.167  -1.075
148   K        -0.703  -0.667  -0.710  -0.813  -0.760  -0.802  -0.736  -0.701  -0.719
149   I        -0.836  -0.831  -0.763  -0.798  -0.787  -0.687  -0.879  -0.867  -0.773
150   C        -0.221  -0.269  -0.227  -0.224  -0.297  -0.236  -0.449  -0.497  -0.433
151   L         0.497   0.455   0.463   0.285   0.215   0.222   0.267   0.184   0.161
152   F         1.555   1.563   1.623   1.638   1.647   1.745   1.699   1.710   1.807
153   D         1.555   1.563   1.623   1.470   1.482   1.580   1.699   1.710   1.807
154   D         1.555   1.563   1.623   1.470   1.482   1.580   1.699   1.710   1.807
155   E         1.555   1.563   1.623   1.569   1.586   1.677   1.699   1.710   1.807
156   S        -0.485  -0.423  -0.640  -0.311  -0.216  -0.557  -0.449  -0.372  -0.629
157   R         1.555   1.563   1.623   1.630   1.649   1.737   1.699   1.710   1.807
158   N         1.555   1.563   1.623   1.674   1.690   1.780   1.699   1.710   1.807
159   K         0.497   0.524   0.482   0.413   0.469   0.338   0.267   0.313   0.197
160   E         0.497   0.473   0.468   0.310   0.266   0.238   0.267   0.219   0.170
161   V         1.555   1.563   1.623   1.511   1.518   1.621   1.699   1.710   1.807
162   E         0.829   0.873   0.647   0.917   0.978   0.657   0.840   0.906   0.508
163   K        -0.353  -0.324  -0.252  -0.543  -0.480  -0.392  -0.592  -0.551  -0.459
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   Y        -0.836  -0.809  -0.762  -0.937  -0.915  -0.814  -0.879  -0.849  -0.772
166   G         0.497   0.543   0.513   0.476   0.553   0.486   0.267   0.349   0.257
167   V        -0.135  -0.120  -0.171  -0.146  -0.130  -0.192  -0.306  -0.275  -0.347
168   K        -1.054  -1.061  -1.118  -0.940  -0.946  -1.000  -0.879  -0.885  -0.918
169   F         0.829   0.809   0.640   0.993   0.963   0.726   0.840   0.805   0.495
170   V        -1.536  -1.545  -1.457  -1.374  -1.385  -1.256  -1.165  -1.168  -1.059
171   Y        -0.353  -0.348  -0.270  -0.458  -0.464  -0.356  -0.592  -0.585  -0.484
172   V         0.497   0.541   0.486   0.348   0.413   0.306   0.267   0.344   0.205
173   R        -0.311  -0.282  -0.255  -0.433  -0.385  -0.363  -0.547  -0.504  -0.465
174   D         0.829   0.870   0.653   0.830   0.882   0.595   0.840   0.901   0.519
175   P         0.329   0.338   0.419   0.130   0.145   0.268  -0.055  -0.043   0.073
176   E        -0.796  -0.789  -0.754  -0.871  -0.857  -0.809  -0.835  -0.823  -0.763
177   N        -1.205  -1.209  -1.139  -1.237  -1.241  -1.134  -1.030  -1.030  -0.938
178   G         1.555   1.563   1.623   1.602   1.617   1.709   1.699   1.710   1.807
179   P        -0.221  -0.214  -0.223  -0.437  -0.434  -0.434  -0.449  -0.438  -0.427
180   S        -0.353  -0.361  -0.276  -0.440  -0.449  -0.326  -0.592  -0.603  -0.492
181   W         0.347   0.351   0.423   0.304   0.307   0.408  -0.020  -0.017   0.081
182   K        -1.186  -1.182  -1.132  -1.144  -1.131  -1.037  -1.022  -1.015  -0.934
183   L        -1.536  -1.544  -1.476  -1.490  -1.489  -1.381  -1.165  -1.167  -1.074
184   Y         0.347   0.363   0.435   0.229   0.249   0.362  -0.020   0.007   0.104
185   Q        -0.836  -0.808  -0.757  -0.912  -0.882  -0.809  -0.879  -0.850  -0.767
186   D        -1.186  -1.171  -1.127  -1.098  -1.048  -1.011  -1.022  -1.003  -0.930
187   Y        -0.703  -0.688  -0.725  -0.614  -0.603  -0.650  -0.736  -0.722  -0.734
188   L         0.497   0.455   0.463   0.256   0.182   0.181   0.267   0.184   0.161
189   S        -1.536  -1.493  -1.457  -1.291  -1.223  -1.191  -1.165  -1.125  -1.059
190   G        -1.054  -1.075  -1.098  -0.895  -0.947  -0.989  -0.879  -0.900  -0.900
191   K        -1.054  -1.020  -1.098  -0.835  -0.781  -0.969  -0.879  -0.841  -0.899
192   V        -1.536  -1.530  -1.465  -1.430  -1.419  -1.360  -1.165  -1.156  -1.065
193   -        -0.796  -0.808  -0.742  -0.992  -1.010  -0.909  -0.835  -0.841  -0.751
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -0.284  -0.325  -0.267  -0.411  -0.503  -0.422  -0.494  -0.553  -0.479
198   -        -0.284  -0.325  -0.267  -0.304  -0.385  -0.305  -0.494  -0.553  -0.479
199   -        -0.284  -0.293  -0.248  -0.548  -0.548  -0.495  -0.494  -0.510  -0.453
* 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/P40081
Output conservation file - output/P40081
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
