1     M         1.717   1.730   1.835   1.934   1.950   2.114   1.946   1.965   2.150
2     P        -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     L        -0.030   0.008  -0.018  -0.121  -0.083  -0.063  -0.310  -0.268  -0.271
5     F        -0.963  -0.951  -0.931  -0.821  -0.802  -0.757  -0.904  -0.889  -0.827
6     L         1.717   1.730   1.835   1.711   1.722   1.894   1.946   1.965   2.150
7     V        -1.702  -1.719  -1.604  -1.480  -1.504  -1.336  -1.260  -1.266  -1.119
8     L        -0.459  -0.401  -0.473  -0.402  -0.312  -0.408  -0.548  -0.464  -0.539
9     K        -0.770  -0.797  -0.876  -0.651  -0.697  -0.801  -0.666  -0.697  -0.763
10    A         1.041   1.044   0.882   1.178   1.185   0.971   1.115   1.117   0.803
11    T        -0.030   0.002  -0.018  -0.430  -0.382  -0.385  -0.310  -0.274  -0.272
12    L         1.717   1.730   1.835   1.711   1.722   1.894   1.946   1.965   2.150
13    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    E        -1.274  -1.234  -1.278  -1.373  -1.305  -1.346  -1.023  -0.981  -0.983
15    N         0.531   0.530   0.625   0.426   0.416   0.550   0.165   0.156   0.280
16    V         0.709   0.729   0.717   0.688   0.723   0.675   0.521   0.555   0.474
17    T        -0.209  -0.236  -0.412   0.004  -0.031  -0.295  -0.191  -0.227  -0.455
18    K        -1.391  -1.375  -1.309  -1.276  -1.257  -1.195  -1.141  -1.123  -1.011
19    V         0.102   0.102   0.013   0.101   0.085  -0.038  -0.073  -0.085  -0.214
20    S        -2.013  -1.998  -1.854  -1.720  -1.696  -1.498  -1.379  -1.361  -1.196
21    I         1.041   0.995   0.874   1.303   1.247   1.076   1.115   1.036   0.787
22    E        -1.418  -1.391  -1.303  -1.477  -1.437  -1.329  -1.156  -1.126  -1.004
23    N         0.982   0.943   0.843   1.014   0.967   0.826   1.015   0.947   0.726
24    T         0.909   0.908   0.801   0.931   0.932   0.737   0.891   0.886   0.643
25    N        -0.512  -0.492  -0.523  -0.661  -0.629  -0.650  -0.587  -0.562  -0.597
26    E        -0.459  -0.430  -0.484  -0.612  -0.572  -0.612  -0.548  -0.510  -0.555
27    S        -0.963  -0.954  -0.952  -0.988  -0.999  -0.968  -0.904  -0.884  -0.847
28    R        -0.209  -0.303  -0.427   0.145   0.011  -0.202  -0.191  -0.314  -0.474
29    A        -0.224  -0.209  -0.105  -0.320  -0.296  -0.135  -0.548  -0.526  -0.387
30    E         0.398   0.389   0.154   0.299   0.292   0.028   0.402   0.387   0.016
31    F         0.709   0.675   0.677   0.821   0.760   0.716   0.521   0.451   0.391
32    A        -0.148  -0.185  -0.093  -0.317  -0.386  -0.270  -0.429  -0.487  -0.369
33    F         1.717   1.730   1.835   1.731   1.750   1.914   1.946   1.965   2.150
34    D        -0.459  -0.405  -0.487  -0.387  -0.335  -0.389  -0.548  -0.494  -0.559
35    L        -0.148  -0.158  -0.070  -0.250  -0.272  -0.155  -0.429  -0.445  -0.334
36    Q        -0.459  -0.430  -0.484  -0.382  -0.328  -0.450  -0.548  -0.508  -0.556
37    C         1.717   1.730   1.835   1.838   1.852   2.019   1.946   1.965   2.150
38    T         0.398   0.332   0.156   0.547   0.459   0.192   0.402   0.305   0.019
39    S        -0.209  -0.219  -0.398  -0.092  -0.107  -0.340  -0.191  -0.206  -0.437
40    C         1.717   1.730   1.835   1.838   1.852   2.019   1.946   1.965   2.150
41    R         1.041   1.031   0.881   1.284   1.280   1.096   1.115   1.096   0.801
42    E         0.398   0.496   0.172   0.263   0.388  -0.015   0.402   0.547   0.044
43    L        -1.274  -1.296  -1.279  -1.140  -1.169  -1.202  -1.023  -1.040  -0.983
44    H         1.717   1.730   1.835   1.949   1.969   2.129   1.946   1.965   2.150
45    D         0.102   0.113   0.041  -0.000   0.021  -0.132  -0.073  -0.050  -0.176
46    S        -0.224  -0.226  -0.111  -0.494  -0.500  -0.315  -0.548  -0.548  -0.395
47    K        -0.770  -0.827  -0.873  -0.380  -0.461  -0.558  -0.666  -0.730  -0.760
48    V         0.531   0.543   0.622   0.373   0.394   0.493   0.165   0.183   0.273
49    I        -1.702  -1.697  -1.595  -1.479  -1.493  -1.331  -1.260  -1.250  -1.113
50    I         0.398   0.425   0.168   0.624   0.663   0.324   0.402   0.443   0.039
51    N         0.709   0.706   0.705   0.688   0.676   0.628   0.521   0.511   0.448
52    T        -0.459  -0.469  -0.493  -0.260  -0.277  -0.311  -0.548  -0.561  -0.572
53    F        -0.459  -0.495  -0.489  -0.326  -0.374  -0.357  -0.548  -0.582  -0.565
54    E         1.041   1.031   0.881   0.803   0.793   0.588   1.115   1.096   0.801
55    E        -0.770  -0.797  -0.876  -0.691  -0.747  -0.912  -0.666  -0.697  -0.763
56    Y        -0.209  -0.231  -0.403   0.218   0.188  -0.084  -0.191  -0.221  -0.444
57    A        -0.459  -0.531  -0.502  -0.778  -0.876  -0.830  -0.548  -0.626  -0.582
58    M         0.531   0.531   0.625   0.532   0.525   0.648   0.165   0.159   0.280
59    P        -0.535  -0.500  -0.520  -0.546  -0.485  -0.501  -0.666  -0.626  -0.608
60    A         1.041   0.995   0.874   1.191   1.135   0.968   1.115   1.036   0.787
61    S         1.717   1.730   1.835   1.607   1.619   1.790   1.946   1.965   2.150
62    K         0.531   0.518   0.619   0.420   0.391   0.521   0.165   0.132   0.266
63    G         1.717   1.730   1.835   1.779   1.797   1.961   1.946   1.965   2.150
64    T        -0.209  -0.244  -0.407  -0.342  -0.389  -0.616  -0.191  -0.237  -0.448
65    A         1.041   1.044   0.882   1.171   1.179   0.958   1.115   1.117   0.803
66    S         0.531   0.530   0.625   0.267   0.257   0.406   0.165   0.156   0.280
67    F         1.041   0.992   0.874   1.136   1.074   0.908   1.115   1.030   0.788
68    L        -0.209  -0.303  -0.427   0.006  -0.124  -0.329  -0.191  -0.314  -0.474
69    M        -0.224  -0.218  -0.106  -0.186  -0.168  -0.003  -0.548  -0.538  -0.388
70    K         0.102   0.108   0.058   0.116   0.140   0.057  -0.073  -0.048  -0.141
71    C         1.717   1.730   1.835   1.838   1.852   2.019   1.946   1.965   2.150
72    K         0.709   0.734   0.715   0.662   0.703   0.658   0.521   0.565   0.470
73    F        -0.148  -0.111  -0.056  -0.384  -0.305  -0.263  -0.429  -0.374  -0.312
74    C         1.717   1.730   1.835   1.838   1.852   2.019   1.946   1.965   2.150
75    S        -0.459  -0.526  -0.529  -0.430  -0.520  -0.533  -0.548  -0.620  -0.610
76    K        -1.080  -1.033  -0.978  -0.909  -0.859  -0.746  -1.023  -0.978  -0.874
77    E         1.041   0.992   0.874   0.813   0.755   0.599   1.115   1.030   0.788
78    L        -1.080  -1.092  -0.980  -0.902  -0.923  -0.749  -1.023  -1.024  -0.876
79    S         1.717   1.730   1.835   1.607   1.619   1.790   1.946   1.965   2.150
80    V        -0.459  -0.526  -0.529  -0.370  -0.459  -0.480  -0.548  -0.620  -0.610
81    N        -0.535  -0.568  -0.544  -0.598  -0.627  -0.582  -0.666  -0.692  -0.633
82    L         0.474   0.486   0.607   0.233   0.245   0.435   0.046   0.064   0.242
83    C        -1.274  -1.287  -1.260  -1.196  -1.231  -1.231  -1.023  -1.032  -0.967
84    A        -0.963  -1.007  -0.937  -0.793  -0.856  -0.774  -0.904  -0.942  -0.835
85    F        -0.459  -0.486  -0.507  -0.374  -0.412  -0.428  -0.548  -0.585  -0.585
86    E        -1.391  -1.377  -1.300  -1.424  -1.422  -1.248  -1.141  -1.123  -1.004
87    D        -0.770  -0.830  -0.886  -0.952  -1.047  -1.141  -0.666  -0.733  -0.773
88    E        -1.391  -1.397  -1.296  -1.343  -1.350  -1.219  -1.141  -1.140  -1.001
89    Y        -0.030   0.004  -0.005  -0.052  -0.015   0.012  -0.310  -0.276  -0.257
90    L        -1.702  -1.656  -1.583  -1.476  -1.393  -1.321  -1.260  -1.218  -1.104
91    T        -1.391  -1.378  -1.295  -1.170  -1.160  -1.027  -1.141  -1.125  -1.000
92    D        -1.080  -1.039  -0.971  -1.305  -1.244  -1.159  -1.023  -0.983  -0.868
93    Q        -0.652  -0.635  -0.568  -0.919  -0.871  -0.762  -0.785  -0.771  -0.662
94    S        -1.702  -1.675  -1.581  -1.786  -1.759  -1.591  -1.260  -1.233  -1.103
95    D        -1.418  -1.415  -1.322  -1.620  -1.607  -1.448  -1.156  -1.148  -1.020
96    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   D        -0.929  -0.921  -0.948  -0.933  -0.922  -1.012  -0.846  -0.835  -0.839
122   S        -1.063  -1.051  -0.961  -1.081  -1.060  -0.918  -1.001  -0.984  -0.857
123   F        -1.274  -1.285  -1.254  -0.982  -1.004  -0.962  -1.023  -1.030  -0.962
124   I        -1.702  -1.681  -1.594  -1.582  -1.559  -1.436  -1.260  -1.237  -1.112
125   P        -0.963  -0.999  -0.949  -0.768  -0.812  -0.721  -0.904  -0.932  -0.846
126   L         1.717   1.730   1.835   1.711   1.722   1.894   1.946   1.965   2.150
127   S        -0.459  -0.541  -0.509  -0.649  -0.752  -0.679  -0.548  -0.642  -0.590
128   L        -0.030   0.021  -0.008  -0.140  -0.071  -0.085  -0.310  -0.239  -0.255
129   D         1.041   0.992   0.874   1.026   0.958   0.755   1.115   1.030   0.788
130   C         0.709   0.775   0.743   0.771   0.874   0.801   0.521   0.642   0.527
131   R         1.717   1.730   1.835   1.845   1.868   2.026   1.946   1.965   2.150
132   G         1.717   1.730   1.835   1.779   1.797   1.961   1.946   1.965   2.150
133   C        -0.459  -0.374  -0.494  -0.319  -0.202  -0.380  -0.548  -0.444  -0.569
134   E         0.709   0.740   0.694   0.318   0.370   0.270   0.521   0.576   0.426
135   L        -0.535  -0.509  -0.515  -0.567  -0.531  -0.512  -0.666  -0.631  -0.600
136   I        -1.274  -1.275  -1.271  -1.102  -1.103  -1.138  -1.023  -1.020  -0.977
137   K         0.474   0.485   0.606  -0.041  -0.023   0.167   0.046   0.061   0.239
138   F         1.717   1.730   1.835   1.731   1.750   1.914   1.946   1.965   2.150
139   Y        -1.274  -1.278  -1.273  -0.978  -0.974  -0.985  -1.023  -1.022  -0.978
140   P         1.041   1.031   0.881   1.303   1.294   1.087   1.115   1.096   0.801
141   D        -0.963  -0.904  -0.920  -0.912  -0.819  -0.854  -0.904  -0.848  -0.819
142   T        -0.209  -0.233  -0.442   0.031  -0.001  -0.331  -0.191  -0.223  -0.493
143   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   T        -1.391  -1.347  -1.299  -1.491  -1.430  -1.343  -1.141  -1.101  -1.004
145   F         0.709   0.706   0.705   0.730   0.727   0.719   0.521   0.511   0.448
146   E        -1.391  -1.380  -1.297  -1.458  -1.433  -1.313  -1.141  -1.126  -1.001
147   V        -0.148  -0.152  -0.065  -0.196  -0.205  -0.085  -0.429  -0.436  -0.326
148   S        -1.274  -1.290  -1.262  -1.367  -1.394  -1.323  -1.023  -1.034  -0.968
149   L         0.531   0.530   0.625   0.370   0.360   0.490   0.165   0.157   0.279
150   S        -0.708  -0.699  -0.588  -0.801  -0.787  -0.613  -0.846  -0.831  -0.682
151   S        -0.459  -0.439  -0.509  -0.751  -0.726  -0.789  -0.548  -0.527  -0.587
152   G        -0.652  -0.620  -0.571  -0.804  -0.758  -0.674  -0.785  -0.747  -0.661
153   K        -0.535  -0.510  -0.534  -0.529  -0.496  -0.502  -0.666  -0.637  -0.622
154   V         0.289   0.212   0.079   0.342   0.235  -0.033   0.240   0.123  -0.102
155   M        -0.963  -0.953  -0.951  -0.679  -0.652  -0.662  -0.904  -0.884  -0.847
156   S         0.102   0.072   0.017  -0.039  -0.079  -0.238  -0.073  -0.109  -0.208
157   C        -1.080  -1.067  -0.981  -1.043  -1.019  -0.899  -1.023  -1.004  -0.876
158   Q        -0.652  -0.668  -0.586  -0.833  -0.866  -0.740  -0.785  -0.801  -0.679
159   L        -0.770  -0.764  -0.861  -0.487  -0.479  -0.626  -0.666  -0.659  -0.747
160   E        -0.030  -0.068  -0.031  -0.400  -0.455  -0.389  -0.310  -0.354  -0.289
161   -         0.289   0.247   0.079   0.333   0.261  -0.060   0.240   0.177  -0.102
162   -        -0.512  -0.544  -0.552  -0.568  -0.618  -0.654  -0.587  -0.627  -0.632
163   D         0.709   0.712   0.683   0.318   0.325   0.250   0.521   0.523   0.402
164   N        -0.148  -0.173  -0.095  -0.235  -0.285  -0.193  -0.429  -0.468  -0.372
165   E         1.041   0.992   0.874   0.803   0.742   0.577   1.115   1.030   0.788
166   W         1.717   1.730   1.835   1.949   1.967   2.129   1.946   1.965   2.150
167   Y         0.709   0.729   0.708   0.821   0.853   0.778   0.521   0.556   0.456
168   D         1.717   1.730   1.835   1.663   1.682   1.847   1.946   1.965   2.150
169   Y         1.041   1.098   0.885   1.309   1.381   1.098   1.115   1.205   0.809
170   D         1.717   1.730   1.835   1.663   1.682   1.847   1.946   1.965   2.150
171   D         0.531   0.530   0.625   0.010   0.009   0.151   0.165   0.157   0.279
172   N        -0.030  -0.017  -0.023  -0.143  -0.129  -0.115  -0.310  -0.302  -0.280
173   L        -0.770  -0.791  -0.867  -0.507  -0.537  -0.664  -0.666  -0.689  -0.754
174   G        -0.224  -0.226  -0.111  -0.392  -0.409  -0.247  -0.548  -0.548  -0.395
175   E        -0.459  -0.425  -0.495  -0.778  -0.724  -0.820  -0.548  -0.496  -0.569
176   E         1.717   1.730   1.835   1.406   1.426   1.593   1.946   1.965   2.150
177   V         1.717   1.730   1.835   1.751   1.772   1.933   1.946   1.965   2.150
178   T         1.041   0.995   0.874   1.014   0.953   0.792   1.115   1.036   0.787
179   M         0.102   0.066   0.030   0.182   0.143   0.080  -0.073  -0.119  -0.193
180   T        -0.459  -0.356  -0.476  -0.409  -0.251  -0.438  -0.548  -0.414  -0.549
181   D         0.102   0.077   0.028  -0.067  -0.089  -0.227  -0.073  -0.100  -0.196
182   F        -0.963  -0.981  -0.957  -0.822  -0.853  -0.793  -0.904  -0.918  -0.852
183   S        -0.459  -0.480  -0.494  -0.565  -0.613  -0.661  -0.548  -0.572  -0.573
184   S         0.102   0.072   0.017   0.289   0.248   0.110  -0.073  -0.109  -0.208
185   S        -0.148  -0.185  -0.093  -0.655  -0.720  -0.577  -0.429  -0.487  -0.369
186   I         1.041   1.102   0.885   1.174   1.251   0.968   1.115   1.211   0.809
187   I        -1.391  -1.347  -1.299  -1.310  -1.253  -1.170  -1.141  -1.101  -1.004
188   K         0.474   0.488   0.609   0.282   0.303   0.482   0.046   0.069   0.246
189   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   K        -0.652  -0.639  -0.580  -0.793  -0.758  -0.675  -0.785  -0.762  -0.671
* 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/P25654
Output conservation file - output/P25654
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
