1     M         1.532   1.551   1.688   1.694   1.712   1.937   1.644   1.670   1.881
2     L        -0.271  -0.214  -0.332  -0.331  -0.277  -0.369  -0.403  -0.378  -0.484
3     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L        -0.419  -0.459  -0.365  -0.688  -0.713  -0.544  -0.643  -0.678  -0.529
5     R         0.777   0.692   0.554   0.902   0.790   0.623   0.801   0.665   0.394
6     Q        -1.175  -1.135  -0.959  -1.277  -1.231  -0.975  -1.186  -1.127  -0.895
7     S        -0.982  -1.038  -0.918  -1.083  -1.135  -0.953  -1.004  -1.036  -0.855
8     I        -1.113  -1.035  -0.931  -1.182  -1.075  -0.907  -1.125  -1.017  -0.868
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    R         0.059   0.058  -0.223   0.207   0.187  -0.230   0.079   0.070  -0.320
14    F        -1.113  -1.068  -0.953  -1.063  -1.032  -0.881  -1.125  -1.078  -0.891
15    F        -0.271  -0.227  -0.292  -0.268  -0.207  -0.297  -0.403  -0.321  -0.420
16    K        -0.271  -0.121  -0.289  -0.327  -0.101  -0.400  -0.403  -0.195  -0.421
17    P        -0.382  -0.445  -0.370  -0.415  -0.512  -0.400  -0.557  -0.646  -0.534
18    A        -0.419  -0.460  -0.369  -0.520  -0.568  -0.417  -0.643  -0.679  -0.534
19    T        -0.618  -0.704  -0.851  -0.469  -0.587  -0.830  -0.523  -0.630  -0.773
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    R         0.777   0.705   0.559   0.863   0.755   0.538   0.801   0.685   0.403
30    T        -2.285  -2.199  -2.042  -2.240  -2.134  -1.924  -1.606  -1.527  -1.306
31    L        -0.419  -0.450  -0.354  -0.544  -0.535  -0.365  -0.643  -0.671  -0.517
32    C        -1.460  -1.310  -1.360  -1.345  -1.204  -1.166  -1.245  -1.110  -1.062
33    S         0.207   0.221   0.356  -0.093  -0.074   0.116  -0.162  -0.153   0.024
34    S        -0.550  -0.579  -0.424  -0.794  -0.870  -0.649  -0.764  -0.807  -0.600
35    R        -0.897  -0.934  -0.916  -0.902  -1.000  -0.964  -0.884  -0.936  -0.852
36    Y        -0.897  -0.853  -0.885  -0.840  -0.811  -0.807  -0.884  -0.853  -0.821
37    L        -0.271  -0.276  -0.342  -0.457  -0.491  -0.580  -0.403  -0.442  -0.497
38    L        -1.807  -1.756  -1.702  -1.652  -1.581  -1.483  -1.366  -1.314  -1.183
39    Q        -1.113  -1.018  -0.933  -0.995  -0.856  -0.740  -1.125  -1.019  -0.868
40    Q        -1.591  -1.587  -1.383  -1.532  -1.531  -1.235  -1.366  -1.334  -1.081
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    K        -1.113  -1.087  -0.952  -1.102  -1.058  -0.846  -1.125  -1.089  -0.890
46    P        -1.131  -1.113  -0.952  -1.253  -1.196  -0.975  -1.138  -1.105  -0.886
47    V        -0.419  -0.446  -0.367  -0.649  -0.682  -0.548  -0.643  -0.665  -0.532
48    V        -0.618  -0.545  -0.801  -0.506  -0.410  -0.821  -0.523  -0.445  -0.716
49    K         0.777   0.714   0.564   0.878   0.803   0.561   0.801   0.699   0.411
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    T        -0.897  -1.004  -0.916  -0.910  -1.056  -0.932  -0.884  -0.992  -0.852
52    A         0.777   0.714   0.564   0.835   0.748   0.561   0.801   0.699   0.411
53    Q        -1.113  -1.115  -0.952  -1.136  -1.135  -0.935  -1.125  -1.109  -0.889
54    N        -1.807  -1.673  -1.687  -1.565  -1.409  -1.426  -1.366  -1.246  -1.171
55    L         1.532   1.551   1.688   1.377   1.415   1.634   1.644   1.670   1.881
56    A         0.207   0.200   0.353  -0.093  -0.133   0.110  -0.162  -0.192   0.018
57    E         0.059   0.112  -0.221   0.210   0.272  -0.171   0.079   0.133  -0.317
58    V         0.059  -0.089  -0.259   0.176  -0.023  -0.290   0.079  -0.126  -0.371
59    N        -0.635  -0.603  -0.427  -0.768  -0.737  -0.486  -0.884  -0.839  -0.603
60    G         0.059  -0.089  -0.259  -0.018  -0.217  -0.501   0.079  -0.126  -0.371
61    P        -0.271  -0.264  -0.313  -0.324  -0.294  -0.419  -0.403  -0.378  -0.457
62    E        -0.982  -0.968  -0.902  -1.093  -1.069  -0.962  -1.004  -0.973  -0.839
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    T        -0.550  -0.496  -0.395  -0.765  -0.687  -0.557  -0.764  -0.701  -0.562
65    L         1.532   1.551   1.688   1.377   1.415   1.634   1.644   1.670   1.881
66    I         0.059   0.132  -0.209   0.359   0.455  -0.052   0.079   0.162  -0.300
67    G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
68    P         0.777   0.705   0.559   0.849   0.759   0.525   0.801   0.685   0.403
69    G         0.777   0.705   0.559   0.654   0.566   0.352   0.801   0.685   0.403
70    A         0.406   0.439   0.417   0.207   0.246   0.141   0.199   0.244   0.141
71    K        -0.271  -0.397  -0.357  -0.300  -0.517  -0.484  -0.403  -0.578  -0.517
72    E        -0.550  -0.581  -0.426  -0.763  -0.830  -0.605  -0.764  -0.809  -0.603
73    G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
74    T         0.207   0.256   0.372  -0.103  -0.013   0.137  -0.162  -0.086   0.056
75    V         0.207   0.288   0.385  -0.002   0.133   0.268  -0.162  -0.026   0.079
76    P         1.532   1.551   1.688   1.524   1.552   1.775   1.644   1.670   1.881
77    T         0.777   0.798   0.580   0.812   0.850   0.533   0.801   0.826   0.440
78    D         0.406   0.546   0.468   0.326   0.544   0.384   0.199   0.428   0.236
79    L         0.777   0.842   0.582   0.736   0.828   0.505   0.801   0.891   0.444
80    D         0.406   0.554   0.480   0.293   0.519   0.382   0.199   0.442   0.258
81    Q         1.532   1.551   1.688   1.699   1.722   1.942   1.644   1.670   1.881
82    E         0.406   0.454   0.424   0.262   0.324   0.241   0.199   0.271   0.154
83    T         1.532   1.551   1.688   1.482   1.518   1.734   1.644   1.670   1.881
84    G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
85    L         1.532   1.551   1.688   1.377   1.415   1.634   1.644   1.670   1.881
86    A        -0.419  -0.369  -0.348  -0.613  -0.566  -0.462  -0.643  -0.592  -0.510
87    R         1.532   1.551   1.688   1.538   1.552   1.788   1.644   1.670   1.881
88    L         0.059  -0.015  -0.230   0.119   0.041  -0.231   0.079  -0.027  -0.330
89    E         1.532   1.551   1.688   1.496   1.518   1.748   1.644   1.670   1.881
90    L         0.777   0.714   0.564   0.731   0.667   0.466   0.801   0.699   0.411
91    L         1.532   1.551   1.688   1.377   1.415   1.634   1.644   1.670   1.881
92    G         0.777   0.692   0.554   0.654   0.549   0.343   0.801   0.665   0.394
93    K         0.777   0.692   0.554   0.879   0.773   0.546   0.801   0.665   0.394
94    L        -0.419  -0.369  -0.350  -0.607  -0.519  -0.447  -0.643  -0.591  -0.513
95    E         0.059  -0.097  -0.260   0.169  -0.051  -0.320   0.079  -0.137  -0.372
96    G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
97    I        -0.271  -0.347  -0.337  -0.181  -0.306  -0.346  -0.403  -0.501  -0.490
98    D         0.777   0.856   0.580   0.875   0.970   0.588   0.801   0.912   0.440
99    V         0.059  -0.097  -0.260   0.176  -0.033  -0.291   0.079  -0.137  -0.372
100   F         1.532   1.551   1.688   1.748   1.767   1.989   1.644   1.670   1.881
101   D         1.532   1.551   1.688   1.547   1.569   1.797   1.644   1.670   1.881
102   T        -0.419  -0.379  -0.329  -0.512  -0.393  -0.366  -0.643  -0.554  -0.475
103   K        -0.271  -0.299  -0.320  -0.335  -0.370  -0.475  -0.403  -0.430  -0.460
104   P         0.059   0.122  -0.216   0.262   0.345  -0.089   0.079   0.160  -0.310
105   L        -0.271  -0.299  -0.320  -0.461  -0.480  -0.547  -0.403  -0.430  -0.460
106   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   D        -0.271  -0.299  -0.320  -0.201  -0.230  -0.257  -0.403  -0.430  -0.460
110   S        -0.982  -0.980  -0.900  -1.010  -0.992  -0.824  -1.004  -0.981  -0.838
111   S         0.406   0.454   0.462   0.294   0.365   0.342   0.199   0.272   0.224
112   R        -0.271  -0.299  -0.320  -0.382  -0.423  -0.508  -0.403  -0.430  -0.460
113   K        -0.618  -0.613  -0.816  -0.394  -0.392  -0.706  -0.523  -0.520  -0.734
114   G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
115   T         0.777   0.798   0.580   0.812   0.850   0.533   0.801   0.826   0.440
116   M         0.059  -0.097  -0.260   0.340   0.109  -0.206   0.079  -0.137  -0.372
117   K        -1.591  -1.589  -1.383  -1.559  -1.558  -1.268  -1.366  -1.336  -1.082
118   D         0.406   0.412   0.418   0.409   0.413   0.412   0.199   0.198   0.141
119   P         1.532   1.551   1.688   1.524   1.552   1.775   1.644   1.670   1.881
120   I         0.406   0.454   0.462   0.517   0.586   0.574   0.199   0.272   0.224
121   I        -1.938  -1.912  -1.754  -1.749  -1.688  -1.466  -1.486  -1.445  -1.222
122   I         0.777   0.952   0.592   0.840   1.047   0.609   0.801   1.046   0.460
123   E        -1.460  -1.389  -1.367  -1.467  -1.356  -1.345  -1.245  -1.162  -1.066
124   S         0.207   0.224   0.366  -0.081  -0.062   0.141  -0.162  -0.147   0.043
125   Y         0.059  -0.089  -0.259   0.347   0.130  -0.207   0.079  -0.126  -0.371
126   D        -0.618  -0.624  -0.836  -0.404  -0.432  -0.752  -0.523  -0.533  -0.757
127   D        -0.897  -0.982  -0.919  -0.924  -1.034  -0.954  -0.884  -0.962  -0.852
128   Y         0.059  -0.078  -0.246   0.371   0.177  -0.131   0.079  -0.111  -0.353
129   R         0.777   0.714   0.564   0.894   0.808   0.620   0.801   0.699   0.411
130   Y         0.059  -0.097  -0.260   0.434   0.231  -0.019   0.079  -0.137  -0.372
131   V         0.059  -0.089  -0.259   0.176  -0.021  -0.290   0.079  -0.126  -0.371
132   G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
133   C         0.777   0.856   0.580   1.086   1.181   0.781   0.801   0.912   0.440
134   T        -0.618  -0.632  -0.846  -0.456  -0.471  -0.799  -0.523  -0.542  -0.768
135   G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
136   S        -0.897  -0.938  -0.915  -0.878  -0.932  -0.895  -0.884  -0.925  -0.850
137   P         0.777   0.798   0.580   0.827   0.858   0.510   0.801   0.826   0.440
138   A        -1.244  -1.315  -1.344  -1.125  -1.248  -1.331  -1.004  -1.074  -1.044
139   G        -0.271  -0.246  -0.330  -0.460  -0.437  -0.519  -0.403  -0.387  -0.481
140   S         0.406   0.454   0.462   0.311   0.380   0.364   0.199   0.272   0.224
141   H         1.532   1.551   1.688   1.726   1.743   1.968   1.644   1.670   1.881
142   T        -1.113  -1.032  -0.928  -1.095  -0.925  -0.830  -1.125  -1.016  -0.862
143   I        -1.113  -1.040  -0.921  -1.244  -1.134  -0.978  -1.125  -1.023  -0.854
144   M        -1.113  -1.126  -0.960  -0.921  -0.935  -0.697  -1.125  -1.121  -0.896
145   W         1.532   1.551   1.688   1.806   1.829   2.045   1.644   1.670   1.881
146   L        -0.419  -0.453  -0.362  -0.563  -0.569  -0.395  -0.643  -0.672  -0.526
147   K        -0.271  -0.392  -0.357  -0.264  -0.452  -0.412  -0.403  -0.574  -0.516
148   P        -0.982  -1.017  -0.916  -1.073  -1.094  -0.939  -1.004  -1.011  -0.851
149   T        -0.897  -0.982  -0.919  -0.962  -1.073  -1.014  -0.884  -0.962  -0.852
150   V        -1.460  -1.477  -1.372  -1.479  -1.502  -1.350  -1.245  -1.244  -1.070
151   N        -1.113  -1.072  -0.941  -1.284  -1.239  -1.023  -1.125  -1.067  -0.877
152   E        -0.897  -0.732  -0.870  -0.807  -0.567  -0.782  -0.884  -0.687  -0.799
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   V         0.059  -0.015  -0.230   0.133   0.031  -0.334   0.079  -0.027  -0.330
155   A        -1.460  -1.498  -1.378  -1.607  -1.701  -1.512  -1.245  -1.265  -1.076
156   R         1.532   1.551   1.688   1.538   1.552   1.788   1.644   1.670   1.881
157   C         1.532   1.551   1.688   1.762   1.782   2.002   1.644   1.670   1.881
158   W        -0.271  -0.392  -0.357  -0.044  -0.265  -0.265  -0.403  -0.574  -0.516
159   E         0.406   0.454   0.462   0.342   0.411   0.415   0.199   0.272   0.224
160   C         0.777   0.856   0.580   1.086   1.183   0.781   0.801   0.912   0.440
161   G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
162   S        -1.460  -1.425  -1.358  -1.288  -1.246  -1.129  -1.245  -1.205  -1.060
163   V         1.532   1.551   1.688   1.487   1.516   1.739   1.644   1.670   1.881
164   Y         0.777   0.842   0.582   1.018   1.104   0.703   0.801   0.891   0.444
165   K         0.059  -0.003  -0.225   0.223   0.142  -0.214   0.079  -0.010  -0.323
166   L        -0.419  -0.446  -0.367  -0.709  -0.726  -0.569  -0.643  -0.665  -0.532
167   N        -0.897  -0.873  -0.868  -0.733  -0.676  -0.680  -0.884  -0.826  -0.794
168   P        -1.460  -1.418  -1.360  -1.201  -1.106  -1.050  -1.245  -1.180  -1.059
169   V        -0.419  -0.460  -0.369  -0.683  -0.719  -0.563  -0.643  -0.679  -0.534
170   G         1.532   1.551   1.688   1.324   1.356   1.583   1.644   1.670   1.881
171   V        -1.025  -1.105  -0.961  -1.145  -1.261  -1.059  -1.029  -1.096  -0.896
172   P         0.777   0.705   0.559   0.859   0.768   0.548   0.801   0.685   0.403
173   N        -1.113  -1.116  -0.952  -1.097  -1.102  -0.881  -1.125  -1.110  -0.888
174   D        -1.460  -1.440  -1.352  -1.368  -1.354  -1.190  -1.245  -1.211  -1.055
175   D        -1.938  -1.841  -1.729  -1.852  -1.746  -1.554  -1.486  -1.396  -1.205
176   H        -0.371  -0.297  -0.329  -0.278  -0.181  -0.286  -0.513  -0.424  -0.469
177   H         0.059  -0.089  -0.259   0.387   0.166  -0.144   0.079  -0.126  -0.371
178   H         1.532   1.551   1.688   1.726   1.743   1.968   1.644   1.670   1.881
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P04037
Output conservation file - output/P04037
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
