1     M         1.586   1.607   1.734   1.765   1.790   1.990   1.730   1.762   1.977
2     V        -1.033  -1.110  -1.029  -0.966  -1.059  -0.925  -0.971  -1.032  -0.912
3     V         0.008  -0.065  -0.061  -0.110  -0.218  -0.249  -0.183  -0.291  -0.297
4     K         0.297   0.193   0.052   0.256   0.118  -0.091   0.267   0.115  -0.112
5     A        -0.295  -0.325  -0.485  -0.147  -0.196  -0.463  -0.296  -0.338  -0.531
6     I         0.008  -0.028  -0.052  -0.124  -0.171  -0.232  -0.183  -0.229  -0.282
7     A        -1.033  -0.983  -0.989  -0.875  -0.781  -0.785  -0.971  -0.903  -0.873
8     R        -0.311  -0.226  -0.139  -0.589  -0.459  -0.331  -0.633  -0.526  -0.407
9     N        -0.843  -0.795  -0.667  -1.056  -0.974  -0.788  -0.971  -0.913  -0.750
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    S         0.926   0.871   0.773   0.885   0.810   0.677   0.942   0.850   0.640
12    I         0.297   0.193   0.049   0.325   0.183  -0.043   0.267   0.115  -0.117
13    G        -1.033  -1.081  -0.992  -1.079  -1.157  -1.044  -0.971  -1.003  -0.879
14    R         0.297   0.193   0.052   0.357   0.220  -0.043   0.267   0.115  -0.112
15    N         1.586   1.607   1.734   1.501   1.538   1.728   1.730   1.762   1.977
16    G         1.586   1.607   1.734   1.510   1.539   1.737   1.730   1.762   1.977
17    V         0.008  -0.037  -0.054  -0.120  -0.179  -0.244  -0.183  -0.247  -0.280
18    G         1.586   1.607   1.734   1.510   1.539   1.737   1.730   1.762   1.977
19    A         0.297   0.193   0.052   0.404   0.255   0.003   0.267   0.115  -0.112
20    F         0.926   0.928   0.790   1.138   1.139   0.976   0.942   0.942   0.672
21    V         0.926   0.884   0.781   0.964   0.929   0.789   0.942   0.871   0.654
22    F        -0.843  -0.722  -0.901  -0.695  -0.533  -0.790  -0.746  -0.614  -0.780
23    P         0.600   0.549   0.594   0.616   0.515   0.572   0.379   0.270   0.288
24    C         1.586   1.607   1.734   1.770   1.797   1.995   1.730   1.762   1.977
25    R        -0.236  -0.210  -0.130  -0.512  -0.467  -0.359  -0.521  -0.486  -0.389
26    K         0.600   0.577   0.596   0.346   0.303   0.296   0.379   0.325   0.290
27    I         0.008  -0.015  -0.048  -0.142  -0.166  -0.253  -0.183  -0.209  -0.275
28    T        -0.843  -0.851  -0.926  -0.533  -0.550  -0.696  -0.746  -0.754  -0.806
29    L        -0.729  -0.754  -0.647  -0.867  -0.884  -0.740  -0.859  -0.876  -0.730
30    Q        -0.295  -0.433  -0.525  -0.033  -0.238  -0.418  -0.296  -0.469  -0.580
31    F         0.926   1.062   0.805   1.194   1.351   1.043   0.942   1.148   0.701
32    C         0.926   0.884   0.783   1.167   1.110   0.945   0.942   0.871   0.658
33    N         0.926   0.884   0.783   0.937   0.898   0.765   0.942   0.871   0.658
34    W         0.926   0.928   0.790   1.221   1.228   1.045   0.942   0.942   0.672
35    G         0.926   0.884   0.783   0.926   0.875   0.733   0.942   0.871   0.658
36    G         1.586   1.607   1.734   1.510   1.539   1.737   1.730   1.762   1.977
37    S         1.586   1.607   1.734   1.468   1.490   1.696   1.730   1.762   1.977
38    S         1.586   1.607   1.734   1.468   1.490   1.696   1.730   1.762   1.977
39    E        -2.058  -1.999  -1.879  -1.793  -1.730  -1.542  -1.421  -1.368  -1.214
40    G         0.926   0.928   0.789   0.941   0.948   0.775   0.942   0.942   0.671
41    M         0.008   0.040  -0.040   0.116   0.172  -0.010  -0.183  -0.131  -0.263
42    R         0.297   0.204   0.056   0.349   0.227  -0.051   0.267   0.131  -0.106
43    K        -1.451  -1.381  -1.330  -1.280  -1.175  -1.123  -1.196  -1.132  -1.026
44    F         0.008  -0.047  -0.053   0.104   0.024   0.008  -0.183  -0.260  -0.278
45    L         0.926   0.884   0.783   0.947   0.902   0.735   0.942   0.871   0.658
46    T        -0.079  -0.062  -0.091   0.019   0.047  -0.059  -0.287  -0.267  -0.331
47    S        -0.295  -0.400  -0.504  -0.281  -0.436  -0.618  -0.296  -0.427  -0.554
48    K        -1.451  -1.397  -1.345  -1.594  -1.508  -1.434  -1.196  -1.143  -1.037
49    R        -1.336  -1.428  -1.351  -1.373  -1.548  -1.495  -1.084  -1.156  -1.041
50    L         0.926   1.021   0.800   0.987   1.111   0.844   0.942   1.087   0.690
51    D        -1.451  -1.447  -1.361  -1.296  -1.290  -1.165  -1.196  -1.177  -1.049
52    K        -1.033  -0.933  -0.975  -1.160  -1.058  -1.047  -0.971  -0.876  -0.863
53    W        -1.451  -1.471  -1.348  -1.160  -1.195  -1.009  -1.196  -1.194  -1.039
54    G         0.926   1.062   0.805   1.004   1.174   0.832   0.942   1.148   0.701
55    Q        -1.033  -0.922  -0.975  -1.070  -0.951  -0.992  -0.971  -0.867  -0.864
56    E        -1.147  -1.138  -1.024  -1.239  -1.198  -1.039  -1.084  -1.058  -0.909
57    F        -1.451  -1.324  -1.344  -1.478  -1.348  -1.284  -1.196  -1.088  -1.036
58    P         0.297   0.243   0.071   0.478   0.396   0.140   0.267   0.188  -0.083
59    W        -1.754  -1.664  -1.613  -1.332  -1.230  -1.136  -1.309  -1.231  -1.126
60    I         0.926   0.884   0.781   0.897   0.843   0.690   0.942   0.871   0.654
61    Q        -0.311  -0.267  -0.147  -0.362  -0.299  -0.122  -0.633  -0.569  -0.414
62    F         1.586   1.607   1.734   1.699   1.722   1.925   1.730   1.762   1.977
63    E        -0.540  -0.610  -0.589  -0.491  -0.611  -0.594  -0.633  -0.719  -0.667
64    V        -0.122  -0.145  -0.088  -0.373  -0.385  -0.306  -0.408  -0.426  -0.341
65    M        -1.033  -0.999  -0.991  -1.002  -0.971  -0.939  -0.971  -0.938  -0.878
66    R        -1.147  -1.132  -1.023  -1.314  -1.282  -1.113  -1.084  -1.053  -0.908
67    K        -1.033  -1.077  -1.017  -1.106  -1.131  -1.025  -0.971  -1.004  -0.901
68    S        -1.336  -1.428  -1.351  -1.337  -1.489  -1.380  -1.084  -1.156  -1.041
69    G         0.926   0.884   0.783   0.926   0.875   0.733   0.942   0.871   0.658
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    H         1.586   1.607   1.734   1.704   1.731   1.929   1.730   1.762   1.977
72    P         1.586   1.607   1.734   1.641   1.658   1.868   1.730   1.762   1.977
73    L        -1.033  -1.044  -1.009  -1.151  -1.169  -1.119  -0.971  -0.976  -0.893
74    L        -0.122  -0.036  -0.069  -0.373  -0.262  -0.293  -0.408  -0.316  -0.321
75    R        -0.843  -0.838  -0.938  -0.749  -0.723  -0.934  -0.746  -0.738  -0.819
76    A        -0.311  -0.286  -0.153  -0.529  -0.495  -0.297  -0.633  -0.599  -0.425
77    E        -1.033  -0.933  -0.983  -0.759  -0.629  -0.665  -0.971  -0.869  -0.870
78    Y         0.926   0.871   0.773   1.194   1.121   0.991   0.942   0.850   0.640
79    T        -0.729  -0.683  -0.620  -0.883  -0.814  -0.737  -0.859  -0.790  -0.701
80    N         0.926   0.884   0.781   0.937   0.897   0.762   0.942   0.871   0.654
81    G         0.297   0.283   0.063   0.358   0.345   0.024   0.267   0.246  -0.097
82    R        -0.295  -0.365  -0.511  -0.157  -0.242  -0.486  -0.296  -0.384  -0.563
83    E        -0.236  -0.221  -0.151  -0.310  -0.285  -0.209  -0.521  -0.502  -0.419
84    K         0.926   0.928   0.790   0.813   0.818   0.620   0.942   0.942   0.672
85    V        -1.033  -1.065  -1.002  -0.954  -0.976  -0.871  -0.971  -0.991  -0.888
86    I         0.600   0.601   0.636   0.414   0.410   0.431   0.379   0.370   0.372
87    C         0.297   0.283   0.063   0.597   0.578   0.229   0.267   0.246  -0.097
88    V        -0.540  -0.621  -0.594  -0.558  -0.654  -0.598  -0.633  -0.721  -0.669
89    R        -0.122  -0.114  -0.080  -0.399  -0.382  -0.336  -0.408  -0.396  -0.335
90    N         0.926   0.884   0.781   0.890   0.842   0.663   0.942   0.871   0.654
91    L        -1.033  -1.019  -0.993  -0.981  -0.969  -0.928  -0.971  -0.957  -0.880
92    N        -1.336  -1.428  -1.351  -1.280  -1.422  -1.320  -1.084  -1.156  -1.041
93    I        -0.729  -0.738  -0.644  -0.847  -0.853  -0.686  -0.859  -0.863  -0.729
94    D        -1.033  -1.094  -1.014  -0.991  -1.114  -1.033  -0.971  -1.019  -0.899
95    N        -0.614  -0.646  -0.597  -0.694  -0.701  -0.636  -0.746  -0.758  -0.675
96    V         0.427   0.544   0.610   0.093   0.309   0.380   0.042   0.260   0.318
97    E        -1.336  -1.428  -1.351  -1.172  -1.333  -1.265  -1.084  -1.156  -1.041
98    N        -0.540  -0.632  -0.588  -0.688  -0.833  -0.784  -0.633  -0.738  -0.667
99    K         0.926   0.928   0.789   0.848   0.852   0.691   0.942   0.942   0.671
100   L        -0.729  -0.745  -0.633  -0.883  -0.887  -0.732  -0.859  -0.864  -0.718
101   K        -1.033  -1.072  -1.018  -1.120  -1.155  -1.065  -0.971  -1.000  -0.903
102   L         0.008  -0.047  -0.053   0.004  -0.061  -0.066  -0.183  -0.260  -0.278
103   L        -0.843  -0.838  -0.942  -0.630  -0.605  -0.754  -0.746  -0.738  -0.823
104   K        -0.311  -0.288  -0.151  -0.736  -0.690  -0.492  -0.633  -0.600  -0.421
105   D         0.008  -0.047  -0.053   0.140   0.055   0.012  -0.183  -0.260  -0.278
106   S        -0.540  -0.456  -0.535  -0.603  -0.504  -0.577  -0.633  -0.537  -0.602
107   D         0.427   0.440   0.543   0.185   0.202   0.361   0.042   0.055   0.181
108   G         1.586   1.607   1.734   1.510   1.539   1.737   1.730   1.762   1.977
109   D        -1.033  -1.021  -1.001  -0.960  -0.964  -0.909  -0.971  -0.957  -0.885
110   I        -1.033  -0.957  -0.970  -1.137  -1.018  -1.002  -0.971  -0.876  -0.854
111   L         0.008  -0.082  -0.075  -0.043  -0.180  -0.187  -0.183  -0.318  -0.316
112   R        -1.033  -1.031  -1.001  -0.953  -0.959  -0.901  -0.971  -0.965  -0.886
113   R        -0.843  -0.781  -0.917  -0.813  -0.731  -0.911  -0.746  -0.681  -0.797
114   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   K        -1.451  -1.424  -1.340  -1.323  -1.249  -1.122  -1.196  -1.160  -1.033
117   N        -0.122  -0.046  -0.085  -0.466  -0.385  -0.417  -0.408  -0.334  -0.340
118   D        -1.033  -1.070  -0.995  -0.861  -0.924  -0.832  -0.971  -0.986  -0.879
119   N        -0.311  -0.267  -0.147  -0.638  -0.554  -0.385  -0.633  -0.569  -0.414
120   V         1.586   1.607   1.734   1.528   1.570   1.755   1.730   1.762   1.977
121   E        -0.843  -0.838  -0.938  -0.595  -0.597  -0.763  -0.746  -0.738  -0.819
122   S         0.926   1.021   0.800   0.904   1.013   0.760   0.942   1.087   0.690
123   L        -0.311  -0.288  -0.163  -0.562  -0.514  -0.325  -0.633  -0.599  -0.437
124   N         1.586   1.607   1.734   1.501   1.538   1.728   1.730   1.762   1.977
125   S        -1.147  -1.025  -1.018  -1.027  -0.881  -0.841  -1.084  -0.977  -0.905
126   S         1.586   1.607   1.734   1.468   1.490   1.696   1.730   1.762   1.977
127   V         1.586   1.607   1.734   1.528   1.570   1.755   1.730   1.762   1.977
128   R         1.586   1.607   1.734   1.556   1.595   1.782   1.730   1.762   1.977
129   G         1.586   1.607   1.734   1.510   1.539   1.737   1.730   1.762   1.977
130   I         0.926   0.884   0.783   0.897   0.843   0.693   0.942   0.871   0.658
131   W         1.586   1.607   1.734   1.791   1.821   2.016   1.730   1.762   1.977
132   S         1.586   1.607   1.734   1.468   1.490   1.696   1.730   1.762   1.977
133   P         1.586   1.607   1.734   1.641   1.658   1.868   1.730   1.762   1.977
134   L        -0.540  -0.532  -0.578  -0.427  -0.426  -0.438  -0.633  -0.641  -0.653
135   H         0.297   0.243   0.069   0.540   0.463   0.193   0.267   0.188  -0.087
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -0.749  -0.655  -0.629  -0.739  -0.588  -0.591  -0.863  -0.747  -0.707
138   A        -0.783  -0.771  -0.651  -0.924  -0.905  -0.706  -0.916  -0.889  -0.734
139   A        -0.540  -0.605  -0.589  -0.582  -0.704  -0.700  -0.633  -0.708  -0.667
140   K        -1.754  -1.718  -1.623  -1.708  -1.634  -1.503  -1.309  -1.269  -1.133
141   R        -0.295  -0.295  -0.480  -0.211  -0.204  -0.527  -0.296  -0.302  -0.524
142   H         0.926   0.884   0.783   1.143   1.094   0.968   0.942   0.871   0.658
143   R        -0.295  -0.281  -0.474  -0.303  -0.288  -0.563  -0.296  -0.285  -0.517
144   I         0.427   0.478   0.567   0.093   0.186   0.296   0.042   0.131   0.232
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -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/Q06090
Output conservation file - output/Q06090
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
