1     M         1.731   1.794   1.906   1.903   1.985   2.169   1.929   2.029   2.228
2     S         0.592   0.653   0.662   0.429   0.503   0.505   0.331   0.424   0.378
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    N        -0.843  -0.751  -0.697  -0.823  -0.694  -0.609  -0.947  -0.835  -0.742
14    L         0.215   0.133   0.005   0.176   0.069  -0.127   0.172   0.034  -0.160
15    Y         0.950   0.800   0.793   1.161   0.963   0.947   0.971   0.699   0.639
16    K        -0.466  -0.289  -0.577  -0.241  -0.005  -0.384  -0.467  -0.232  -0.595
17    I         0.431   0.464   0.590   0.273   0.292   0.478   0.012   0.048   0.227
18    G        -0.466  -0.266  -0.534  -0.387  -0.120  -0.498  -0.467  -0.203  -0.542
19    T        -1.597  -1.574  -1.466  -1.392  -1.389  -1.191  -1.266  -1.230  -1.083
20    E         0.950   0.800   0.793   0.786   0.588   0.553   0.971   0.699   0.639
21    T         1.731   1.794   1.906   1.727   1.806   1.992   1.929   2.029   2.228
22    R        -0.700  -0.696  -0.645  -0.826  -0.783  -0.703  -0.787  -0.769  -0.681
23    N        -1.220  -1.252  -1.134  -1.232  -1.305  -1.163  -1.106  -1.114  -0.959
24    K        -1.597  -1.581  -1.489  -1.347  -1.363  -1.198  -1.266  -1.236  -1.101
25    I         0.431   0.493   0.608   0.010   0.113   0.271   0.012   0.107   0.266
26    K        -0.700  -0.712  -0.644  -0.737  -0.767  -0.667  -0.787  -0.785  -0.681
27    K         0.950   0.800   0.793   0.965   0.763   0.742   0.971   0.699   0.639
28    F         1.731   1.794   1.906   1.896   1.977   2.162   1.929   2.029   2.228
29    R         1.731   1.794   1.906   1.804   1.887   2.069   1.929   2.029   2.228
30    T        -0.843  -0.760  -0.697  -0.987  -0.908  -0.804  -0.947  -0.842  -0.742
31    S        -1.220  -1.203  -1.121  -1.035  -1.013  -0.864  -1.106  -1.075  -0.948
32    T        -0.089  -0.142  -0.078  -0.236  -0.336  -0.267  -0.308  -0.363  -0.291
33    A        -0.181  -0.250  -0.105  -0.368  -0.483  -0.258  -0.467  -0.534  -0.342
34    R         0.592   0.561   0.628   0.523   0.434   0.500   0.331   0.244   0.307
35    T        -0.784  -0.667  -0.650  -0.878  -0.736  -0.676  -0.884  -0.749  -0.692
36    D         0.215   0.025  -0.020   0.303   0.038  -0.011   0.172  -0.112  -0.198
37    S        -1.114  -1.046  -1.057  -1.164  -1.054  -1.073  -1.006  -0.918  -0.886
38    I        -0.578  -0.535  -0.621  -0.494  -0.443  -0.526  -0.640  -0.593  -0.661
39    K         0.017  -0.020  -0.026   0.170   0.153   0.096  -0.150  -0.180  -0.213
40    A         0.330   0.323   0.089   0.491   0.459   0.100   0.339   0.317  -0.032
41    L        -1.568  -1.553  -1.467  -1.446  -1.403  -1.258  -1.251  -1.222  -1.085
42    S        -0.578  -0.540  -0.605  -0.578  -0.489  -0.586  -0.640  -0.570  -0.634
43    I        -0.784  -0.807  -0.681  -0.893  -0.933  -0.774  -0.884  -0.888  -0.727
44    K        -0.578  -0.592  -0.595  -0.684  -0.692  -0.764  -0.640  -0.625  -0.621
45    I         1.014   0.889   0.840   1.049   0.891   0.817   1.073   0.857   0.730
46    E        -0.578  -0.528  -0.603  -0.648  -0.544  -0.632  -0.640  -0.562  -0.631
47    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    K         1.731   1.794   1.906   1.678   1.778   1.944   1.929   2.029   2.228
49    P        -1.444  -1.484  -1.460  -1.062  -1.131  -1.089  -1.129  -1.158  -1.078
50    S         0.017  -0.141  -0.082  -0.073  -0.346  -0.259  -0.150  -0.382  -0.305
51    Y         0.017   0.036  -0.061   0.148   0.116   0.023  -0.150  -0.166  -0.275
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    E         0.330   0.288   0.093   0.266   0.235  -0.049   0.339   0.271  -0.026
55    I         1.731   1.794   1.906   1.668   1.759   1.934   1.929   2.029   2.228
56    I        -0.784  -0.807  -0.681  -0.908  -0.920  -0.739  -0.884  -0.888  -0.727
57    V        -1.568  -1.556  -1.460  -1.356  -1.355  -1.197  -1.251  -1.223  -1.080
58    D        -0.124  -0.139  -0.060  -0.482  -0.453  -0.360  -0.395  -0.378  -0.278
59    E         0.017  -0.020  -0.026  -0.134  -0.144  -0.193  -0.150  -0.180  -0.213
60    D         0.471   0.517   0.613   0.045   0.102   0.219   0.094   0.155   0.276
61    E        -0.700  -0.771  -0.678  -1.035  -1.128  -0.999  -0.787  -0.853  -0.722
62    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    D        -1.597  -1.592  -1.488  -1.462  -1.412  -1.285  -1.266  -1.245  -1.100
67    E        -1.238  -1.211  -1.108  -1.420  -1.361  -1.203  -1.129  -1.084  -0.938
68    I        -1.114  -1.166  -1.085  -1.012  -1.097  -0.961  -1.006  -1.043  -0.917
69    E        -1.444  -1.497  -1.439  -1.322  -1.403  -1.328  -1.129  -1.168  -1.061
70    D        -1.444  -1.220  -1.397  -1.194  -0.904  -1.115  -1.129  -0.894  -1.024
71    L        -0.124  -0.184  -0.090  -0.450  -0.524  -0.391  -0.395  -0.454  -0.323
72    S         0.330   0.505   0.101   0.239   0.481  -0.087   0.339   0.592  -0.013
73    E         0.660   0.796   0.715   0.330   0.550   0.376   0.461   0.692   0.485
74    L        -0.313  -0.401  -0.553  -0.268  -0.391  -0.613  -0.273  -0.387  -0.566
75    A        -0.784  -0.692  -0.670  -0.722  -0.621  -0.550  -0.884  -0.787  -0.716
76    E         0.660   0.597   0.637   0.330   0.208   0.230   0.461   0.316   0.327
77    I        -1.444  -1.383  -1.426  -1.494  -1.366  -1.470  -1.129  -1.060  -1.050
78    L         1.731   1.794   1.906   1.562   1.659   1.827   1.929   2.029   2.228
79    P         1.014   0.889   0.840   1.170   0.999   0.914   1.073   0.857   0.730
80    D         1.014   0.889   0.840   0.978   0.793   0.694   1.073   0.857   0.730
81    N         0.017  -0.018  -0.060   0.271   0.202   0.145  -0.150  -0.209  -0.273
82    S        -0.313  -0.460  -0.552  -0.110  -0.326  -0.413  -0.273  -0.467  -0.564
83    P         1.731   1.794   1.906   1.807   1.894   2.072   1.929   2.029   2.228
84    R         1.731   1.794   1.906   1.802   1.886   2.068   1.929   2.029   2.228
85    F         0.471   0.512   0.613   0.458   0.505   0.648   0.094   0.145   0.276
86    V         0.660   0.549   0.630   0.622   0.384   0.486   0.461   0.221   0.311
87    L         0.017   0.104  -0.020  -0.144  -0.029  -0.207  -0.150  -0.045  -0.210
88    T        -0.313  -0.307  -0.533  -0.288  -0.282  -0.619  -0.273  -0.272  -0.540
89    A         0.660   0.792   0.739   0.540   0.726   0.637   0.461   0.684   0.533
90    Y         1.014   0.919   0.856   1.253   1.151   1.084   1.073   0.909   0.761
91    P         1.731   1.794   1.906   1.807   1.894   2.072   1.929   2.029   2.228
92    T        -1.238  -1.204  -1.100  -1.204  -1.188  -1.012  -1.129  -1.078  -0.931
93    T        -0.124  -0.184  -0.090  -0.299  -0.385  -0.254  -0.395  -0.454  -0.323
94    T        -1.114  -1.066  -1.060  -1.111  -1.040  -1.027  -1.006  -0.944  -0.892
95    K        -1.568  -1.466  -1.459  -1.475  -1.312  -1.317  -1.251  -1.152  -1.079
96    D         1.014   1.035   0.857   1.002   1.029   0.778   1.073   1.104   0.763
97    G         1.731   1.794   1.906   1.908   2.001   2.174   1.929   2.029   2.228
98    F         0.330   0.505   0.101   0.575   0.798   0.255   0.339   0.592  -0.013
99    K         0.411   0.461   0.590  -0.027   0.053   0.234  -0.028   0.040   0.228
100   Q        -0.329  -0.215  -0.137  -0.552  -0.382  -0.270  -0.640  -0.476  -0.379
101   T         0.330   0.212   0.074   0.490   0.317   0.109   0.339   0.165  -0.054
102   P         1.014   0.919   0.856   1.187   1.067   0.978   1.073   0.909   0.761
103   L         1.014   1.035   0.857   0.951   0.999   0.760   1.073   1.104   0.763
104   V        -0.313  -0.489  -0.549  -0.043  -0.303  -0.395  -0.273  -0.500  -0.560
105   L         0.411   0.489   0.598   0.143   0.310   0.447  -0.028   0.099   0.244
106   V        -0.124  -0.042  -0.072  -0.424  -0.320  -0.317  -0.395  -0.309  -0.302
107   Y         1.731   1.794   1.906   1.836   1.926   2.102   1.929   2.029   2.228
108   W         0.660   0.613   0.658   0.904   0.809   0.841   0.461   0.346   0.369
109   K        -0.784  -0.681  -0.658  -0.828  -0.630  -0.627  -0.884  -0.739  -0.701
110   P         1.731   1.794   1.906   1.807   1.894   2.072   1.929   2.029   2.228
111   M        -1.238  -1.130  -1.108  -1.116  -1.012  -0.905  -1.129  -1.016  -0.938
112   T         1.014   0.889   0.840   1.118   0.953   0.883   1.073   0.857   0.730
113   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   V        -0.784  -0.833  -0.697  -0.712  -0.804  -0.578  -0.884  -0.915  -0.744
115   S        -1.114  -1.217  -1.111  -0.928  -1.065  -0.880  -1.006  -1.078  -0.939
116   Q         0.330   0.185   0.042   0.676   0.492   0.260   0.339   0.124  -0.104
117   E         0.330   0.185   0.042   0.236   0.039  -0.189   0.339   0.124  -0.104
118   W        -1.114  -1.217  -1.111  -0.839  -1.011  -0.872  -1.006  -1.078  -0.939
119   K        -0.124  -0.206  -0.093  -0.268  -0.373  -0.210  -0.395  -0.483  -0.327
120   M         1.731   1.794   1.906   1.903   1.985   2.169   1.929   2.029   2.228
121   L         1.014   0.889   0.840   0.927   0.770   0.677   1.073   0.857   0.730
122   Y         1.731   1.794   1.906   1.836   1.926   2.102   1.929   2.029   2.228
123   A         1.731   1.794   1.906   1.772   1.852   2.038   1.929   2.029   2.228
124   G         1.014   0.889   0.840   1.272   1.105   1.012   1.073   0.857   0.730
125   A         1.014   1.185   0.880   1.136   1.346   0.948   1.073   1.338   0.806
126   L        -0.329  -0.315  -0.181  -0.652  -0.624  -0.439  -0.640  -0.617  -0.440
127   E         1.014   0.889   0.840   0.870   0.723   0.643   1.073   0.857   0.730
128   M        -0.578  -0.538  -0.580  -0.510  -0.428  -0.447  -0.640  -0.572  -0.604
129   I        -0.908  -0.862  -0.721  -0.872  -0.805  -0.589  -1.006  -0.944  -0.768
130   R         1.014   0.889   0.840   1.200   1.045   0.985   1.073   0.857   0.730
131   E        -1.238  -1.204  -1.103  -1.243  -1.156  -1.021  -1.129  -1.078  -0.935
132   E        -0.659  -0.727  -0.664  -0.905  -0.952  -0.867  -0.762  -0.809  -0.708
133   C        -0.329  -0.315  -0.181  -0.341  -0.372  -0.168  -0.640  -0.617  -0.440
134   G        -0.313  -0.370  -0.548   0.051  -0.030  -0.340  -0.273  -0.351  -0.559
135   T         0.660   0.792   0.739   0.644   0.834   0.735   0.461   0.684   0.533
136   F        -1.444  -1.359  -1.410  -1.089  -0.982  -1.000  -1.129  -1.042  -1.035
137   K         1.731   1.794   1.906   1.678   1.778   1.944   1.929   2.029   2.228
138   L        -1.114  -1.137  -1.072  -1.103  -1.117  -1.002  -1.006  -1.017  -0.905
139   I         0.330   0.261   0.072   0.461   0.375   0.121   0.339   0.228  -0.057
140   E         0.330   0.424   0.103   0.219   0.359  -0.123   0.339   0.475  -0.010
141   V        -0.659  -0.658  -0.639  -0.744  -0.743  -0.718  -0.762  -0.745  -0.680
142   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   E        -0.313  -0.440  -0.536  -0.380  -0.568  -0.724  -0.273  -0.446  -0.544
147   D         0.330   0.424   0.103   0.342   0.467  -0.031   0.339   0.475  -0.010
148   D        -0.578  -0.637  -0.622  -0.813  -0.881  -0.866  -0.640  -0.684  -0.654
149   S         0.017   0.208  -0.008  -0.268   0.025  -0.321  -0.150   0.130  -0.185
150   D         0.660   0.613   0.658   0.428   0.307   0.327   0.461   0.346   0.369
151   V        -0.784  -0.756  -0.684  -0.790  -0.762  -0.691  -0.884  -0.838  -0.730
152   E         0.330   0.289   0.080   0.230   0.179  -0.140   0.339   0.265  -0.046
153   E        -0.578  -0.689  -0.619  -0.777  -0.892  -0.801  -0.640  -0.739  -0.650
154   L         0.330   0.185   0.042   0.266   0.055  -0.213   0.339   0.124  -0.104
155   R        -1.568  -1.414  -1.439  -1.521  -1.248  -1.340  -1.251  -1.098  -1.064
156   E        -1.114  -1.052  -1.057  -1.193  -1.116  -1.079  -1.006  -0.940  -0.891
157   Q        -0.908  -1.047  -1.051  -0.669  -0.933  -1.028  -0.762  -0.911  -0.877
158   L        -0.578  -0.709  -0.618  -0.777  -0.968  -0.863  -0.640  -0.765  -0.652
159   E        -0.078  -0.198  -0.126  -0.194  -0.336  -0.223  -0.263  -0.446  -0.359
160   N        -1.240  -1.211  -1.114  -1.127  -1.114  -0.949  -1.115  -1.077  -0.939
161   C        -1.898  -1.890  -1.766  -1.581  -1.556  -1.379  -1.373  -1.347  -1.187
* 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/Q12156
Output conservation file - output/Q12156
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
