1     M         1.985   2.008   2.083   2.055   2.091   2.220   2.230   2.268   2.387
2     T        -0.637  -0.650  -0.651  -0.989  -1.041  -1.021  -0.641  -0.659  -0.631
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     L         0.830   0.759   0.777   0.690   0.581   0.590   0.678   0.537   0.527
5     N        -0.092  -0.128  -0.085  -0.134  -0.169  -0.133  -0.299  -0.336  -0.282
6     N        -0.230  -0.210  -0.141  -0.151  -0.109  -0.027  -0.472  -0.447  -0.358
7     V         0.350   0.245   0.082   0.546   0.416   0.173   0.372   0.220  -0.031
8     A         0.204   0.275   0.102   0.534   0.642   0.354   0.161   0.265  -0.000
9     R         1.985   2.008   2.083   2.217   2.257   2.382   2.230   2.268   2.387
10    P        -0.790  -0.752  -0.707  -0.886  -0.877  -0.781  -0.810  -0.767  -0.690
11    D         1.985   2.008   2.083   2.121   2.160   2.285   2.230   2.268   2.387
12    L         1.985   2.008   2.083   1.868   1.908   2.032   2.230   2.268   2.387
13    C        -0.077  -0.123  -0.067   0.075   0.040   0.118  -0.303  -0.348  -0.267
14    V         0.023  -0.004  -0.032   0.017  -0.020  -0.088  -0.134  -0.175  -0.213
15    S        -0.384  -0.347  -0.564  -0.323  -0.276  -0.609  -0.303  -0.255  -0.518
16    Y         1.985   2.008   2.083   2.204   2.245   2.369   2.230   2.268   2.387
17    K        -0.384  -0.495  -0.588  -0.051  -0.190  -0.344  -0.303  -0.439  -0.547
18    K         0.023  -0.019  -0.022   0.374   0.342   0.319  -0.134  -0.179  -0.191
19    I        -1.043  -1.076  -1.118  -0.890  -0.953  -1.057  -0.810  -0.841  -0.859
20    A        -0.637  -0.636  -0.647  -0.789  -0.815  -0.799  -0.641  -0.643  -0.628
21    P         0.023   0.039  -0.008  -0.252  -0.223  -0.270  -0.134  -0.103  -0.170
22    P         0.583   0.606   0.679   0.326   0.370   0.463   0.203   0.238   0.333
23    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    S         0.830   0.759   0.777   0.591   0.473   0.499   0.678   0.537   0.527
28    A        -1.219  -1.220  -1.145  -1.263  -1.258  -1.162  -0.988  -0.985  -0.885
29    T        -1.197  -1.221  -1.152  -1.100  -1.180  -1.074  -0.979  -0.991  -0.893
30    P        -1.197  -1.155  -1.130  -1.211  -1.157  -1.092  -0.979  -0.936  -0.876
31    S        -0.230  -0.219  -0.151  -0.352  -0.332  -0.201  -0.472  -0.457  -0.372
32    I        -1.197  -1.198  -1.144  -1.374  -1.365  -1.273  -0.979  -0.974  -0.888
33    S        -0.077  -0.015  -0.047  -0.235  -0.131  -0.156  -0.303  -0.228  -0.242
34    G         0.757   0.709   0.719   0.773   0.660   0.625   0.541   0.440   0.413
35    V        -1.197  -1.218  -1.135  -0.937  -0.966  -0.846  -0.979  -0.989  -0.880
36    V        -0.230  -0.233  -0.149  -0.359  -0.371  -0.254  -0.472  -0.478  -0.368
37    N        -0.790  -0.777  -0.709  -1.022  -1.010  -0.913  -0.810  -0.788  -0.691
38    Q         0.350   0.245   0.082   0.609   0.453   0.176   0.372   0.220  -0.031
39    S         0.757   0.737   0.727   0.467   0.425   0.404   0.541   0.495   0.429
40    M         0.583   0.606   0.679   0.326   0.360   0.474   0.203   0.238   0.333
41    P         1.985   2.008   2.083   1.840   1.875   2.004   2.230   2.268   2.387
42    M         1.985   2.008   2.083   2.055   2.091   2.220   2.230   2.268   2.387
43    A         1.985   2.008   2.083   1.715   1.748   1.879   2.230   2.268   2.387
44    A         1.985   2.008   2.083   1.715   1.748   1.879   2.230   2.268   2.387
45    I         0.583   0.593   0.676   0.512   0.528   0.651   0.203   0.213   0.326
46    F         1.985   2.008   2.083   2.101   2.139   2.266   2.230   2.268   2.387
47    L         0.583   0.606   0.679   0.365   0.401   0.501   0.203   0.238   0.332
48    R         0.583   0.614   0.679   0.596   0.657   0.733   0.203   0.254   0.332
49    N         1.985   2.008   2.083   2.127   2.174   2.292   2.230   2.268   2.387
50    K         1.143   1.056   0.937   1.337   1.249   1.096   1.217   1.071   0.833
51    F        -0.637  -0.641  -0.660  -0.474  -0.464  -0.504  -0.641  -0.641  -0.639
52    I        -0.077  -0.077  -0.068  -0.129  -0.108  -0.090  -0.303  -0.297  -0.269
53    A        -0.077  -0.123  -0.078  -0.486  -0.534  -0.436  -0.303  -0.348  -0.281
54    W         1.985   2.008   2.083   2.274   2.314   2.439   2.230   2.268   2.387
55    F        -0.637  -0.641  -0.660  -0.605  -0.631  -0.705  -0.641  -0.641  -0.639
56    S         0.583   0.626   0.686  -0.001   0.068   0.153   0.203   0.278   0.346
57    L         0.757   0.709   0.715   0.575   0.493   0.479   0.541   0.440   0.404
58    I        -0.637  -0.690  -0.670  -0.436  -0.508  -0.509  -0.641  -0.689  -0.648
59    Q        -0.790  -0.808  -0.707  -0.762  -0.770  -0.628  -0.810  -0.816  -0.689
60    S        -0.230  -0.193  -0.124  -0.697  -0.650  -0.534  -0.472  -0.420  -0.333
61    V         0.023   0.029  -0.027   0.143   0.170   0.107  -0.134  -0.119  -0.202
62    H        -0.077  -0.079  -0.069   0.149   0.151   0.167  -0.303  -0.300  -0.270
63    Y        -0.384  -0.399  -0.547  -0.398  -0.430  -0.642  -0.303  -0.319  -0.497
64    Y         0.023  -0.062  -0.055   0.347   0.236   0.239  -0.134  -0.248  -0.247
65    L         1.143   1.132   0.940   1.150   1.145   0.892   1.217   1.198   0.838
66    N         0.350   0.246   0.083   0.712   0.584   0.339   0.372   0.221  -0.029
67    T        -0.637  -0.584  -0.637  -0.423  -0.345  -0.435  -0.641  -0.575  -0.610
68    D        -0.637  -0.690  -0.670  -0.640  -0.727  -0.691  -0.641  -0.689  -0.648
69    E        -0.637  -0.628  -0.652  -0.400  -0.371  -0.458  -0.641  -0.616  -0.627
70    D        -0.637  -0.585  -0.618  -0.290  -0.202  -0.240  -0.641  -0.569  -0.588
71    I        -0.092  -0.090  -0.089  -0.088  -0.091  -0.085  -0.299  -0.303  -0.293
72    I        -0.861  -0.846  -0.746  -0.901  -0.876  -0.740  -0.873  -0.853  -0.727
73    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    K        -0.750  -0.700  -0.681  -0.652  -0.577  -0.565  -0.749  -0.688  -0.656
80    A        -0.750  -0.765  -0.720  -0.589  -0.618  -0.580  -0.749  -0.763  -0.700
81    P        -1.197  -1.183  -1.144  -1.358  -1.328  -1.276  -0.979  -0.962  -0.888
82    S        -0.637  -0.638  -0.659  -0.611  -0.618  -0.592  -0.641  -0.639  -0.638
83    P        -1.604  -1.568  -1.514  -1.516  -1.466  -1.392  -1.148  -1.110  -1.028
84    M        -2.010  -1.987  -1.887  -1.775  -1.784  -1.616  -1.317  -1.292  -1.172
85    D        -0.637  -0.584  -0.637  -0.649  -0.593  -0.631  -0.641  -0.575  -0.610
86    Q         0.350   0.246   0.083   0.679   0.541   0.302   0.372   0.221  -0.029
87    P         1.143   1.133   0.937   1.070   1.057   0.760   1.217   1.198   0.832
88    P         0.350   0.245   0.082   0.377   0.235  -0.019   0.372   0.220  -0.031
89    A        -1.197  -1.222  -1.136  -0.966  -0.969  -0.873  -0.979  -0.992  -0.881
90    I        -1.197  -1.222  -1.143  -1.038  -1.056  -0.940  -0.979  -0.993  -0.887
91    K         0.757   0.709   0.719   0.647   0.550   0.508   0.541   0.440   0.413
92    L        -0.077  -0.043  -0.050  -0.102  -0.049  -0.063  -0.303  -0.260  -0.245
93    F        -1.197  -1.131  -1.136  -1.068  -0.957  -0.986  -0.979  -0.915  -0.881
94    M         0.023   0.068  -0.006   0.148   0.224   0.108  -0.134  -0.055  -0.167
95    S         0.583   0.619   0.686   0.007   0.064   0.159   0.203   0.264   0.345
96    L         0.350   0.401   0.115   0.444   0.515   0.127   0.372   0.444   0.018
97    I        -0.637  -0.683  -0.633  -0.521  -0.573  -0.516  -0.641  -0.679  -0.612
98    G        -0.230  -0.218  -0.147  -0.471  -0.471  -0.400  -0.472  -0.457  -0.366
99    L        -0.077  -0.034  -0.048  -0.219  -0.161  -0.151  -0.303  -0.250  -0.243
100   C        -1.197  -1.241  -1.133  -0.922  -1.002  -0.836  -0.979  -1.008  -0.878
101   V        -0.077  -0.077  -0.073  -0.148  -0.144  -0.116  -0.303  -0.297  -0.274
102   C         0.350   0.246   0.083   0.849   0.713   0.460   0.372   0.221  -0.029
103   Y         1.985   2.008   2.083   2.204   2.245   2.369   2.230   2.268   2.387
104   M         0.023   0.042  -0.035   0.074   0.062  -0.031  -0.134  -0.133  -0.219
105   N        -0.637  -0.690  -0.670  -0.365  -0.443  -0.420  -0.641  -0.689  -0.648
106   L         1.143   1.223   0.970   1.135   1.244   0.911   1.217   1.343   0.894
107   V        -0.637  -0.584  -0.629  -0.514  -0.436  -0.511  -0.641  -0.576  -0.600
108   F         1.143   1.056   0.937   1.352   1.239   1.054   1.217   1.071   0.833
109   P         1.985   2.008   2.083   1.840   1.875   2.004   2.230   2.268   2.387
110   Q        -1.694  -1.674  -1.573  -1.374  -1.360  -1.215  -1.218  -1.195  -1.073
111   Q        -0.745  -0.694  -0.679  -0.751  -0.673  -0.677  -0.758  -0.703  -0.660
112   I        -1.219  -1.205  -1.162  -0.754  -0.733  -0.684  -0.988  -0.969  -0.901
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   A         0.830   0.823   0.793   0.587   0.547   0.505   0.678   0.656   0.558
126   Q         0.350   0.360   0.118   0.372   0.381   0.029   0.372   0.387   0.022
127   P         0.583   0.619   0.690   0.086   0.147   0.249   0.203   0.263   0.355
128   S        -0.790  -0.784  -0.702  -1.214  -1.210  -1.101  -0.810  -0.796  -0.687
129   S        -0.637  -0.571  -0.642  -0.579  -0.502  -0.534  -0.641  -0.580  -0.622
130   S        -0.230  -0.218  -0.147  -0.505  -0.489  -0.374  -0.472  -0.457  -0.366
131   G        -1.604  -1.618  -1.526  -1.186  -1.207  -1.105  -1.148  -1.153  -1.038
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   S        -1.043  -1.076  -1.118  -1.127  -1.173  -1.256  -0.810  -0.841  -0.859
135   K        -0.384  -0.422  -0.564  -0.094  -0.144  -0.372  -0.303  -0.353  -0.518
136   G        -1.219  -1.184  -1.137  -1.379  -1.344  -1.263  -0.988  -0.952  -0.877
137   N         0.204   0.168   0.034   0.061   0.020  -0.162   0.161   0.109  -0.101
138   T         0.562   0.582   0.669   0.156   0.181   0.324   0.161   0.190   0.313
139   E        -0.271  -0.250  -0.157  -0.380  -0.328  -0.199  -0.528  -0.500  -0.379
140   T         1.985   2.008   2.083   1.999   2.026   2.164   2.230   2.268   2.387
141   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   T        -0.861  -0.832  -0.746  -1.168  -1.093  -1.008  -0.873  -0.838  -0.727
145   T        -0.150  -0.138  -0.106  -0.626  -0.595  -0.570  -0.356  -0.346  -0.306
146   T        -0.150  -0.193  -0.130  -0.626  -0.688  -0.602  -0.356  -0.422  -0.340
147   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   E        -0.566  -0.538  -0.614  -0.651  -0.637  -0.720  -0.528  -0.495  -0.578
150   T        -1.219  -1.206  -1.154  -1.443  -1.442  -1.363  -0.988  -0.970  -0.893
151   E        -0.566  -0.538  -0.614  -0.583  -0.572  -0.636  -0.528  -0.495  -0.578
152   T         0.204   0.200   0.068   0.351   0.334   0.149   0.161   0.152  -0.051
153   A        -1.219  -1.199  -1.162  -0.978  -0.955  -0.931  -0.988  -0.964  -0.901
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -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   K        -1.197  -1.178  -1.149  -1.308  -1.288  -1.292  -0.979  -0.956  -0.891
167   Q        -0.637  -0.538  -0.614  -0.690  -0.567  -0.628  -0.641  -0.521  -0.589
* 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/Q12160
Output conservation file - output/Q12160
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
