1     M         1.736   1.747   1.821   1.967   1.983   2.098   1.900   1.918   2.037
2     S         0.646   0.605   0.634   0.425   0.351   0.372   0.384   0.294   0.293
3     -        -1.195  -1.151  -1.019  -1.231  -1.177  -0.986  -1.071  -1.022  -0.871
4     S        -0.590  -0.635  -0.575  -0.684  -0.744  -0.656  -0.677  -0.723  -0.637
5     Q         0.285   0.206   0.077   0.278   0.187  -0.032   0.232   0.112  -0.099
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     K        -0.366  -0.486  -0.521  -0.359  -0.530  -0.575  -0.374  -0.527  -0.569
9     I         0.646   0.582   0.632   0.558   0.447   0.498   0.384   0.249   0.290
10    D         0.989   0.917   0.807   1.169   1.079   0.910   0.990   0.866   0.634
11    L         0.989   0.917   0.807   0.903   0.803   0.651   0.990   0.866   0.634
12    T        -0.366  -0.366  -0.476  -0.170  -0.186  -0.388  -0.374  -0.380  -0.515
13    K        -0.590  -0.425  -0.527  -0.810  -0.541  -0.721  -0.677  -0.487  -0.585
14    L         1.736   1.747   1.821   1.574   1.585   1.719   1.900   1.918   2.037
15    N        -0.590  -0.531  -0.523  -0.633  -0.533  -0.522  -0.677  -0.589  -0.574
16    P         0.285   0.147   0.046   0.609   0.388   0.173   0.232   0.026  -0.145
17    E         0.492   0.499   0.598   0.134   0.145   0.284   0.081   0.083   0.220
18    Q         1.736   1.747   1.821   1.603   1.645   1.747   1.900   1.918   2.037
19    L         0.989   0.973   0.819   0.903   0.879   0.669   0.990   0.961   0.655
20    N        -1.087  -1.011  -0.976  -1.030  -0.940  -0.886  -0.981  -0.908  -0.834
21    A        -0.229  -0.149  -0.095  -0.459  -0.340  -0.265  -0.526  -0.413  -0.355
22    V         0.646   0.641   0.665   0.659   0.644   0.681   0.384   0.363   0.356
23    K        -0.005  -0.068  -0.038  -0.108  -0.178  -0.133  -0.223  -0.309  -0.277
24    Q         0.492   0.499   0.598   0.036   0.059   0.193   0.081   0.082   0.220
25    Q         0.646   0.641   0.665   0.377   0.384   0.374   0.384   0.363   0.356
26    F        -0.590  -0.491  -0.526  -0.653  -0.532  -0.531  -0.677  -0.560  -0.585
27    D         0.989   0.973   0.819   1.150   1.135   0.892   0.990   0.961   0.655
28    Q         0.096   0.050   0.004  -0.068  -0.124  -0.235  -0.073  -0.139  -0.221
29    E         1.736   1.747   1.821   1.666   1.680   1.808   1.900   1.918   2.037
30    L        -0.235  -0.231  -0.112  -0.512  -0.497  -0.320  -0.538  -0.531  -0.378
31    Q        -0.551  -0.492  -0.532  -0.682  -0.565  -0.592  -0.654  -0.570  -0.589
32    H         0.396   0.233   0.119   0.905   0.700   0.529   0.391   0.150  -0.036
33    F         0.531   0.505   0.600   0.460   0.360   0.493   0.159   0.094   0.225
34    T         0.096   0.012   0.012   0.166   0.055   0.005  -0.073  -0.182  -0.209
35    Q        -0.220  -0.392  -0.471  -0.159  -0.395  -0.546  -0.189  -0.409  -0.509
36    S         1.736   1.747   1.821   1.636   1.668   1.779   1.900   1.918   2.037
37    L         0.096  -0.037  -0.014   0.078  -0.087  -0.026  -0.073  -0.262  -0.245
38    Q        -0.220  -0.186  -0.413  -0.045  -0.004  -0.271  -0.189  -0.157  -0.437
39    A         0.096  -0.037  -0.014  -0.016  -0.240  -0.250  -0.073  -0.262  -0.245
40    L         1.736   1.747   1.821   1.589   1.608   1.734   1.900   1.918   2.037
41    T        -1.736  -1.720  -1.601  -1.493  -1.495  -1.344  -1.234  -1.211  -1.071
42    M        -0.986  -1.059  -0.969  -0.672  -0.822  -0.692  -0.886  -0.945  -0.828
43    A         1.736   1.747   1.821   1.700   1.720   1.841   1.900   1.918   2.037
44    K        -0.039   0.079  -0.007  -0.327  -0.166  -0.223  -0.306  -0.168  -0.243
45    G        -1.301  -1.282  -1.267  -1.107  -1.098  -1.061  -1.002  -0.987  -0.933
46    K         1.049   1.053   0.873   0.989   1.006   0.798   1.087   1.090   0.756
47    F         0.711   0.726   0.710   0.830   0.850   0.771   0.507   0.524   0.445
48    T        -0.473  -0.510  -0.483  -0.531  -0.568  -0.522  -0.538  -0.558  -0.528
49    E         0.711   0.653   0.664   0.621   0.519   0.531   0.507   0.387   0.354
50    C         1.736   1.747   1.821   2.035   2.052   2.163   1.900   1.918   2.037
51    I         0.096  -0.037  -0.014   0.037  -0.175  -0.197  -0.073  -0.262  -0.245
52    D        -1.420  -1.404  -1.305  -1.231  -1.225  -1.081  -1.118  -1.087  -0.965
53    D        -0.551  -0.556  -0.540  -0.560  -0.554  -0.531  -0.654  -0.636  -0.599
54    I         0.531   0.625   0.658   0.354   0.520   0.551   0.159   0.334   0.342
55    K        -0.986  -1.054  -0.969  -0.966  -1.012  -0.885  -0.886  -0.941  -0.829
56    T        -0.986  -1.009  -0.956  -0.769  -0.802  -0.742  -0.886  -0.904  -0.816
57    V        -0.789  -0.839  -0.916  -0.523  -0.617  -0.732  -0.654  -0.706  -0.773
58    S         0.096   0.066   0.023  -0.017  -0.055  -0.133  -0.073  -0.113  -0.187
59    Q        -0.726  -0.702  -0.591  -0.882  -0.830  -0.692  -0.829  -0.794  -0.656
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    A        -0.106   0.007  -0.037  -0.334  -0.176  -0.226  -0.370  -0.227  -0.280
62    G        -0.527  -0.361  -0.499  -0.408  -0.195  -0.365  -0.576  -0.378  -0.543
63    N        -0.551  -0.616  -0.534  -0.614  -0.708  -0.588  -0.654  -0.706  -0.596
64    E        -0.986  -0.788  -0.921  -0.943  -0.629  -0.874  -0.886  -0.685  -0.785
65    G        -1.420  -1.393  -1.287  -1.234  -1.204  -1.075  -1.118  -1.085  -0.953
66    Q        -0.986  -1.035  -0.974  -1.109  -1.167  -1.083  -0.886  -0.926  -0.833
67    K        -0.986  -0.764  -0.906  -0.876  -0.604  -0.758  -0.886  -0.675  -0.771
68    L         0.096   0.084   0.018  -0.030  -0.037  -0.145  -0.073  -0.083  -0.201
69    L         1.049   0.923   0.852   1.030   0.880   0.808   1.087   0.876   0.717
70    V         1.736   1.747   1.821   1.746   1.757   1.885   1.900   1.918   2.037
71    P         1.736   1.747   1.821   1.979   1.999   2.110   1.900   1.918   2.037
72    A         0.396   0.604   0.197   0.423   0.675   0.163   0.391   0.680   0.081
73    S         0.473   0.502   0.604   0.216   0.280   0.434   0.043   0.089   0.233
74    A        -0.220  -0.035  -0.366  -0.086   0.153  -0.287  -0.189   0.035  -0.379
75    S         1.736   1.747   1.821   1.636   1.668   1.779   1.900   1.918   2.037
76    L         1.736   1.747   1.821   1.589   1.608   1.734   1.900   1.918   2.037
77    Y         1.736   1.747   1.821   1.915   1.932   2.048   1.900   1.918   2.037
78    I        -0.039   0.018   0.003  -0.161  -0.059  -0.093  -0.306  -0.210  -0.229
79    P         0.396   0.481   0.173   0.752   0.860   0.382   0.391   0.502   0.045
80    G         1.736   1.747   1.821   1.858   1.865   1.993   1.900   1.918   2.037
81    K        -0.220  -0.238  -0.410  -0.200  -0.212  -0.474  -0.189  -0.226  -0.434
82    I        -0.473  -0.566  -0.539  -0.422  -0.558  -0.525  -0.538  -0.648  -0.599
83    V        -0.986  -0.948  -0.944  -0.981  -0.953  -0.947  -0.886  -0.855  -0.807
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    D        -1.420  -1.346  -1.306  -1.204  -1.099  -1.070  -1.118  -1.042  -0.966
86    N        -1.301  -1.320  -1.280  -0.965  -1.010  -0.973  -1.002  -1.016  -0.944
87    K        -0.986  -1.053  -0.965  -0.984  -1.047  -0.903  -0.886  -0.941  -0.825
88    K        -0.220  -0.173  -0.397  -0.194  -0.124  -0.445  -0.189  -0.136  -0.418
89    F        -0.473  -0.522  -0.534  -0.176  -0.261  -0.316  -0.538  -0.588  -0.590
90    M        -0.039  -0.053  -0.033  -0.042  -0.080  -0.053  -0.306  -0.319  -0.280
91    V         1.736   1.747   1.821   1.746   1.757   1.885   1.900   1.918   2.037
92    D         1.736   1.747   1.821   1.825   1.848   1.961   1.900   1.918   2.037
93    I         0.531   0.530   0.608   0.355   0.353   0.453   0.159   0.145   0.240
94    G         1.736   1.747   1.821   1.858   1.865   1.993   1.900   1.918   2.037
95    T         1.736   1.747   1.821   1.825   1.845   1.961   1.900   1.918   2.037
96    G         1.736   1.747   1.821   1.858   1.865   1.993   1.900   1.918   2.037
97    Y         1.049   1.019   0.867   1.352   1.317   1.129   1.087   1.035   0.746
98    Y         1.049   1.053   0.873   1.352   1.358   1.136   1.087   1.090   0.756
99    V         1.736   1.747   1.821   1.746   1.757   1.885   1.900   1.918   2.037
100   E         0.396   0.513   0.180   0.514   0.649   0.233   0.391   0.550   0.055
101   K         1.736   1.747   1.821   1.550   1.577   1.696   1.900   1.918   2.037
102   S        -0.473  -0.452  -0.508  -0.488  -0.472  -0.539  -0.538  -0.536  -0.564
103   A         0.396   0.450   0.167   0.550   0.615   0.248   0.391   0.461   0.036
104   E        -0.473  -0.504  -0.530  -0.526  -0.590  -0.617  -0.538  -0.574  -0.590
105   A        -1.301  -1.228  -1.235  -1.195  -1.114  -1.133  -1.002  -0.939  -0.906
106   A         1.049   1.053   0.873   1.119   1.128   0.899   1.087   1.090   0.756
107   I        -0.158  -0.168  -0.093  -0.312  -0.321  -0.242  -0.422  -0.440  -0.351
108   A        -1.301  -1.262  -1.274  -1.243  -1.190  -1.275  -1.002  -0.963  -0.939
109   F        -0.789  -0.899  -0.919  -0.229  -0.382  -0.430  -0.654  -0.774  -0.776
110   Y         1.736   1.747   1.821   1.915   1.932   2.048   1.900   1.918   2.037
111   Q        -0.789  -0.839  -0.916  -0.726  -0.795  -0.947  -0.654  -0.706  -0.773
112   K        -0.789  -0.839  -0.916  -0.716  -0.781  -0.890  -0.654  -0.706  -0.773
113   K         1.736   1.747   1.821   1.550   1.577   1.696   1.900   1.918   2.037
114   V        -0.039  -0.045  -0.017  -0.069  -0.054   0.011  -0.306  -0.299  -0.259
115   D        -0.670  -0.719  -0.591  -0.735  -0.812  -0.642  -0.770  -0.809  -0.656
116   K        -0.220  -0.392  -0.471  -0.164  -0.394  -0.502  -0.189  -0.409  -0.509
117   L         1.736   1.747   1.821   1.589   1.608   1.734   1.900   1.918   2.037
118   N        -0.789  -0.920  -0.925  -0.476  -0.705  -0.720  -0.654  -0.796  -0.782
119   K        -1.301  -1.282  -1.281  -1.217  -1.206  -1.180  -1.002  -0.979  -0.945
120   E        -0.670  -0.687  -0.597  -0.729  -0.742  -0.614  -0.770  -0.780  -0.662
121   S        -0.473  -0.566  -0.539  -0.554  -0.698  -0.675  -0.538  -0.648  -0.599
122   V        -1.420  -1.403  -1.319  -1.511  -1.493  -1.385  -1.118  -1.092  -0.976
123   Q        -0.670  -0.717  -0.599  -0.871  -0.896  -0.731  -0.770  -0.807  -0.663
124   I         0.531   0.658   0.689   0.214   0.435   0.470   0.159   0.396   0.404
125   Q        -0.986  -1.072  -0.984  -1.100  -1.201  -1.076  -0.886  -0.955  -0.841
126   D        -0.670  -0.577  -0.562  -0.707  -0.610  -0.551  -0.770  -0.682  -0.625
127   I         0.396   0.233   0.119   0.566   0.354   0.156   0.391   0.150  -0.036
128   I        -0.473  -0.573  -0.539  -0.485  -0.637  -0.614  -0.538  -0.646  -0.596
129   K        -0.986  -1.072  -0.984  -1.095  -1.215  -1.082  -0.886  -0.955  -0.841
130   E        -0.551  -0.556  -0.540  -0.702  -0.683  -0.647  -0.654  -0.636  -0.599
131   K         1.736   1.747   1.821   1.550   1.577   1.696   1.900   1.918   2.037
132   T        -0.670  -0.695  -0.577  -0.650  -0.676  -0.519  -0.770  -0.781  -0.643
133   Q        -0.986  -1.072  -0.984  -1.090  -1.227  -1.090  -0.886  -0.955  -0.841
134   Y        -1.736  -1.582  -1.580  -1.512  -1.289  -1.326  -1.234  -1.107  -1.057
135   S        -0.039   0.013   0.005  -0.333  -0.207  -0.222  -0.306  -0.201  -0.216
136   L        -0.670  -0.717  -0.599  -0.708  -0.752  -0.566  -0.770  -0.807  -0.663
137   S        -0.986  -0.902  -0.916  -1.009  -0.872  -0.918  -0.886  -0.793  -0.780
138   I        -0.039   0.035  -0.013  -0.161  -0.066  -0.125  -0.306  -0.230  -0.257
139   E        -0.473  -0.582  -0.536  -0.463  -0.618  -0.559  -0.538  -0.655  -0.592
140   A        -0.986  -0.984  -0.950  -0.992  -1.031  -0.980  -0.886  -0.883  -0.810
141   Q        -0.235  -0.190  -0.094  -0.500  -0.384  -0.263  -0.538  -0.472  -0.353
142   I        -0.158  -0.118  -0.055  -0.301  -0.224  -0.132  -0.422  -0.378  -0.298
143   R         1.049   1.004   0.863   1.347   1.286   1.067   1.087   1.011   0.737
144   Q        -0.220  -0.103  -0.401  -0.084   0.083  -0.316  -0.189  -0.048  -0.422
145   A         0.531   0.658   0.689   0.151   0.378   0.411   0.159   0.396   0.404
146   A        -0.473  -0.561  -0.536  -0.397  -0.526  -0.470  -0.538  -0.636  -0.596
147   I        -0.789  -0.868  -0.909  -0.491  -0.616  -0.676  -0.654  -0.745  -0.766
148   R        -0.986  -0.780  -0.931  -0.949  -0.710  -0.864  -0.886  -0.698  -0.794
149   Q        -1.301  -1.327  -1.280  -1.010  -1.063  -0.944  -1.002  -1.023  -0.944
150   H        -0.986  -1.072  -0.984  -0.591  -0.732  -0.610  -0.886  -0.955  -0.841
151   E        -0.670  -0.665  -0.593  -0.947  -0.966  -0.859  -0.770  -0.763  -0.658
152   A        -0.951  -0.974  -0.946  -1.021  -1.088  -1.041  -0.829  -0.861  -0.803
153   M        -1.087  -1.084  -0.998  -1.027  -1.060  -0.933  -0.981  -0.967  -0.853
154   S        -1.107  -1.037  -0.978  -1.414  -1.337  -1.232  -0.989  -0.925  -0.833
155   K        -1.107  -1.091  -1.003  -1.106  -1.059  -0.991  -0.989  -0.973  -0.857
156   Q        -0.691  -0.603  -0.582  -0.891  -0.756  -0.733  -0.774  -0.677  -0.641
157   Q         0.005   0.010  -0.036  -0.232  -0.214  -0.332  -0.180  -0.186  -0.267
158   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   S        -1.195  -1.144  -1.019  -1.377  -1.304  -1.127  -1.071  -1.016  -0.871
167   T        -1.105  -1.115  -0.974  -1.283  -1.277  -1.083  -1.002  -0.992  -0.834
168   A        -0.986  -1.019  -0.941  -1.031  -1.091  -0.989  -0.886  -0.908  -0.804
* 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/Q04493
Output conservation file - output/Q04493
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
