1     M         1.677   1.723   1.825   1.905   1.967   2.131   1.857   1.925   2.103
2     S        -1.643  -1.478  -1.547  -1.407  -1.134  -1.268  -1.259  -1.097  -1.111
3     Q        -1.288  -1.314  -1.213  -1.414  -1.438  -1.294  -1.112  -1.124  -0.988
4     S        -1.288  -1.192  -1.195  -1.283  -1.121  -1.139  -1.112  -1.006  -0.971
5     R        -1.726  -1.689  -1.591  -1.574  -1.495  -1.368  -1.324  -1.277  -1.145
6     W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     I        -0.854  -0.869  -0.783  -0.894  -0.946  -0.805  -0.891  -0.903  -0.782
9     V        -0.128  -0.058  -0.141  -0.067   0.063  -0.102  -0.280  -0.178  -0.309
10    L         0.360   0.395   0.504   0.059   0.103   0.275  -0.051  -0.002   0.154
11    I        -0.683  -0.574  -0.704  -0.696  -0.547  -0.723  -0.688  -0.546  -0.691
12    F        -0.244  -0.215  -0.213  -0.284  -0.265  -0.220  -0.476  -0.452  -0.423
13    A        -1.125  -1.172  -1.158  -1.004  -1.102  -1.053  -0.947  -0.991  -0.936
14    L         0.164   0.247  -0.018   0.215   0.342  -0.046   0.143   0.263  -0.126
15    F        -0.231  -0.145  -0.172  -0.290  -0.162  -0.176  -0.480  -0.370  -0.368
16    I        -0.749  -0.687  -0.705  -0.839  -0.736  -0.759  -0.791  -0.707  -0.699
17    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    T        -1.125  -1.092  -1.147  -1.033  -1.005  -1.075  -0.947  -0.909  -0.925
21    G        -1.267  -1.199  -1.198  -1.288  -1.189  -1.180  -1.103  -1.029  -0.976
22    V         0.541   0.626   0.594   0.406   0.533   0.462   0.299   0.443   0.337
23    N        -0.749  -0.720  -0.746  -0.805  -0.822  -0.801  -0.791  -0.764  -0.747
24    A        -0.849  -0.817  -0.775  -0.922  -0.855  -0.810  -0.900  -0.851  -0.776
25    F         1.677   1.723   1.825   1.713   1.780   1.938   1.857   1.925   2.103
26    F         0.399   0.396   0.504   0.182   0.148   0.315   0.025  -0.001   0.155
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    N        -0.244  -0.300  -0.201  -0.392  -0.470  -0.331  -0.476  -0.541  -0.406
29    F         0.898   0.924   0.753   1.002   1.044   0.791   0.922   0.959   0.641
30    G        -0.749  -0.681  -0.751  -0.810  -0.733  -0.808  -0.791  -0.727  -0.753
31    H        -0.849  -0.836  -0.771  -0.862  -0.846  -0.766  -0.900  -0.877  -0.772
32    -         0.399   0.507   0.565   0.056   0.235   0.314   0.025   0.219   0.279
33    -        -0.854  -0.745  -0.762  -0.790  -0.595  -0.676  -0.891  -0.757  -0.758
34    -        -0.298  -0.252  -0.208  -0.451  -0.379  -0.335  -0.529  -0.465  -0.407
35    -        -0.956  -0.918  -0.818  -1.095  -1.055  -0.887  -1.006  -0.954  -0.820
36    -         0.609   0.587   0.612   0.505   0.452   0.472   0.426   0.371   0.372
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -0.854  -0.837  -0.760  -0.895  -0.863  -0.751  -0.891  -0.865  -0.756
39    H        -1.267  -1.234  -1.194  -1.192  -1.143  -1.049  -1.103  -1.060  -0.973
40    Q         0.898   0.818   0.736   0.789   0.677   0.548   0.922   0.784   0.610
41    Q         0.898   0.818   0.736   0.799   0.696   0.568   0.922   0.784   0.610
42    Q        -0.515  -0.639  -0.684  -0.509  -0.686  -0.732  -0.480  -0.633  -0.667
43    Q         0.164   0.152  -0.045   0.135   0.119  -0.150   0.143   0.120  -0.166
44    Q         0.164   0.149  -0.041   0.128   0.098  -0.157   0.143   0.116  -0.160
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    Q         0.164   0.152  -0.045   0.173   0.161  -0.084   0.143   0.120  -0.166
48    Q        -0.138  -0.146  -0.156  -0.271  -0.266  -0.256  -0.324  -0.311  -0.336
49    Q        -0.138  -0.146  -0.156  -0.383  -0.368  -0.400  -0.324  -0.311  -0.336
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    Q        -0.749  -0.756  -0.726  -0.974  -0.995  -0.926  -0.791  -0.790  -0.726
67    S        -0.231  -0.289  -0.201  -0.265  -0.340  -0.192  -0.480  -0.533  -0.409
68    Y         1.677   1.723   1.825   1.807   1.869   2.033   1.857   1.925   2.103
69    E        -0.138  -0.249  -0.196  -0.119  -0.341  -0.252  -0.324  -0.476  -0.401
70    D        -1.643  -1.663  -1.578  -1.650  -1.702  -1.567  -1.259  -1.259  -1.136
71    Q        -1.643  -1.580  -1.551  -1.463  -1.347  -1.323  -1.259  -1.193  -1.115
72    V        -1.125  -1.221  -1.178  -0.940  -1.075  -1.022  -0.947  -1.037  -0.955
73    L         0.164  -0.040  -0.093   0.152  -0.161  -0.288   0.143  -0.150  -0.238
74    N        -0.231  -0.283  -0.194  -0.354  -0.399  -0.268  -0.480  -0.522  -0.399
75    N        -0.231  -0.286  -0.192  -0.366  -0.434  -0.295  -0.480  -0.528  -0.397
76    P        -1.125  -1.090  -1.146  -1.060  -1.005  -1.108  -0.947  -0.907  -0.924
77    C         1.677   1.723   1.825   1.672   1.739   1.898   1.857   1.925   2.103
78    D        -0.683  -0.588  -0.699  -0.689  -0.536  -0.734  -0.688  -0.563  -0.685
79    G         0.029   0.127  -0.103   0.110   0.254  -0.090  -0.051   0.090  -0.253
80    Y         0.898   0.818   0.736   1.125   1.021   0.914   0.922   0.784   0.610
81    L         0.898   0.818   0.736   0.896   0.804   0.663   0.922   0.784   0.610
82    C         1.677   1.723   1.825   1.656   1.717   1.881   1.857   1.925   2.103
83    P         0.898   1.013   0.776   0.952   1.110   0.780   0.922   1.101   0.684
84    D         0.898   0.924   0.753   0.920   0.962   0.679   0.922   0.959   0.641
85    T         1.677   1.723   1.825   1.819   1.882   2.045   1.857   1.925   2.103
86    L         0.164   0.319  -0.037   0.191   0.415  -0.118   0.143   0.366  -0.154
87    T        -1.643  -1.599  -1.551  -1.421  -1.377  -1.291  -1.259  -1.209  -1.114
88    C         1.677   1.723   1.825   1.656   1.717   1.881   1.857   1.925   2.103
89    V         1.677   1.723   1.825   1.713   1.793   1.938   1.857   1.925   2.103
90    A        -1.643  -1.646  -1.566  -1.391  -1.384  -1.252  -1.259  -1.248  -1.126
91    Q        -1.267  -1.244  -1.199  -1.303  -1.264  -1.165  -1.103  -1.069  -0.978
92    Q        -0.515  -0.348  -0.625  -0.414  -0.169  -0.592  -0.480  -0.266  -0.596
93    K        -0.515  -0.694  -0.712  -0.395  -0.662  -0.698  -0.480  -0.694  -0.700
94    D        -0.749  -0.847  -0.764  -0.709  -0.821  -0.680  -0.791  -0.877  -0.763
95    C         1.677   1.723   1.825   1.656   1.717   1.881   1.857   1.925   2.103
96    P         0.898   0.924   0.753   0.944   0.986   0.727   0.922   0.959   0.641
97    C         1.677   1.723   1.825   1.656   1.717   1.881   1.857   1.925   2.103
98    P         0.898   0.818   0.736   0.920   0.807   0.650   0.922   0.784   0.610
99    F        -0.138  -0.173  -0.164  -0.085  -0.105  -0.091  -0.324  -0.349  -0.348
100   P         1.677   1.723   1.825   1.662   1.732   1.887   1.857   1.925   2.103
101   K        -1.267  -1.333  -1.223  -1.310  -1.415  -1.245  -1.103  -1.141  -0.998
102   S         0.898   0.782   0.722   1.020   0.867   0.791   0.922   0.722   0.584
103   Q         0.541   0.455   0.532   0.312   0.162   0.291   0.299   0.118   0.211
104   L        -0.138  -0.243  -0.181  -0.261  -0.406  -0.328  -0.324  -0.459  -0.380
105   K         0.541   0.649   0.614   0.447   0.614   0.548   0.299   0.485   0.376
106   C         0.898   0.782   0.722   0.938   0.768   0.669   0.922   0.722   0.584
107   V        -1.267  -1.270  -1.200  -1.104  -1.096  -0.970  -1.103  -1.090  -0.978
108   L         0.898   0.818   0.736   0.912   0.821   0.695   0.922   0.784   0.610
109   P         0.898   0.782   0.722   0.944   0.782   0.675   0.922   0.722   0.584
110   D        -0.749  -0.756  -0.726  -0.764  -0.760  -0.714  -0.791  -0.790  -0.726
111   N         0.164   0.190  -0.042   0.247   0.261  -0.070   0.143   0.170  -0.162
112   K        -0.891  -0.809  -0.783  -1.051  -0.971  -0.902  -0.947  -0.860  -0.786
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   F        -0.749  -0.777  -0.730  -0.641  -0.656  -0.601  -0.791  -0.800  -0.727
117   V         0.541   0.494   0.536   0.480   0.402   0.429   0.299   0.193   0.220
118   C         1.677   1.723   1.825   1.656   1.717   1.881   1.857   1.925   2.103
119   I         0.898   0.782   0.722   1.054   0.907   0.792   0.922   0.722   0.584
120   S         1.677   1.723   1.825   1.700   1.763   1.926   1.857   1.925   2.103
121   K         1.677   1.723   1.825   1.656   1.722   1.881   1.857   1.925   2.103
122   P         0.898   0.782   0.722   0.944   0.783   0.675   0.922   0.722   0.584
123   A         0.541   0.455   0.532   0.385   0.188   0.308   0.299   0.118   0.211
124   T        -0.244  -0.303  -0.222  -0.301  -0.405  -0.292  -0.476  -0.537  -0.430
125   H        -0.244  -0.303  -0.222  -0.135  -0.247  -0.120  -0.476  -0.537  -0.430
126   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   K        -0.298  -0.339  -0.250  -0.409  -0.483  -0.340  -0.529  -0.587  -0.468
129   F        -0.854  -0.793  -0.789  -0.951  -0.844  -0.851  -0.891  -0.810  -0.788
130   R        -0.854  -0.835  -0.801  -0.859  -0.832  -0.784  -0.891  -0.862  -0.802
131   A        -0.327  -0.269  -0.228  -0.442  -0.346  -0.285  -0.586  -0.510  -0.442
132   I        -0.128  -0.086  -0.198  -0.115  -0.041  -0.275  -0.280  -0.217  -0.392
133   Y         0.898   0.782   0.722   1.098   0.935   0.834   0.922   0.722   0.584
134   D        -0.515  -0.502  -0.680  -0.426  -0.421  -0.700  -0.480  -0.467  -0.661
135   D         0.164  -0.040  -0.093   0.239  -0.074  -0.177   0.143  -0.150  -0.238
136   P         0.164  -0.040  -0.093   0.248  -0.057  -0.160   0.143  -0.150  -0.238
137   V        -0.749  -0.847  -0.764  -0.759  -0.878  -0.765  -0.791  -0.877  -0.763
138   K        -1.267  -1.149  -1.197  -1.198  -1.044  -1.101  -1.103  -0.979  -0.975
139   G        -0.749  -0.847  -0.764  -0.807  -0.959  -0.826  -0.791  -0.877  -0.763
140   P        -0.749  -0.847  -0.764  -0.650  -0.779  -0.646  -0.791  -0.877  -0.763
141   K         0.898   0.924   0.753   0.938   0.976   0.721   0.922   0.959   0.641
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   A         0.726   0.676   0.614   0.690   0.592   0.428   0.636   0.534   0.375
145   K        -0.244  -0.276  -0.215  -0.381  -0.437  -0.324  -0.476  -0.518  -0.425
146   N        -1.288  -1.282  -1.229  -1.194  -1.176  -1.078  -1.112  -1.097  -1.003
147   K        -0.244  -0.207  -0.201  -0.420  -0.352  -0.332  -0.476  -0.405  -0.400
148   G         0.468   0.550   0.562   0.280   0.411   0.401   0.161   0.301   0.272
149   F        -0.849  -0.861  -0.789  -0.823  -0.858  -0.716  -0.900  -0.901  -0.791
150   R         1.677   1.723   1.825   1.830   1.897   2.056   1.857   1.925   2.103
151   D         1.677   1.723   1.825   1.629   1.687   1.854   1.857   1.925   2.103
152   C         1.677   1.723   1.825   1.651   1.707   1.876   1.857   1.925   2.103
153   G         0.821   0.684   0.667   0.855   0.637   0.599   0.797   0.549   0.479
154   W         1.677   1.723   1.825   1.913   1.981   2.140   1.857   1.925   2.103
155   V         0.541   0.494   0.536   0.480   0.402   0.429   0.299   0.193   0.220
156   S        -1.643  -1.580  -1.551  -1.576  -1.450  -1.449  -1.259  -1.193  -1.115
157   D        -1.267  -1.304  -1.215  -1.297  -1.364  -1.252  -1.103  -1.119  -0.991
158   A         0.821   0.851   0.734   0.824   0.852   0.691   0.797   0.839   0.607
159   Y        -0.849  -0.902  -0.789  -0.674  -0.756  -0.588  -0.900  -0.938  -0.791
160   K        -0.244  -0.225  -0.184  -0.342  -0.315  -0.250  -0.476  -0.446  -0.383
161   N         0.821   0.923   0.751   0.828   0.968   0.721   0.797   0.959   0.638
162   H        -1.643  -1.644  -1.578  -1.400  -1.378  -1.258  -1.259  -1.246  -1.136
163   -        -0.244  -0.177  -0.174  -0.436  -0.324  -0.316  -0.476  -0.365  -0.362
* 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/Q08045
Output conservation file - output/Q08045
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
