1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    M         1.552   1.591   1.704   1.938   1.994   2.167   1.695   1.755   1.944
43    S         1.552   1.591   1.704   1.495   1.525   1.735   1.695   1.755   1.944
44    D         0.791   0.718   0.557   0.918   0.810   0.614   0.843   0.725   0.429
45    A        -0.615  -0.743  -0.886  -0.429  -0.571  -0.749  -0.497  -0.668  -0.795
46    G         0.417   0.333   0.388   0.264   0.115   0.138   0.234   0.064   0.113
47    R         1.552   1.591   1.704   1.931   1.987   2.160   1.695   1.755   1.944
48    K         1.552   1.591   1.704   1.290   1.341   1.536   1.695   1.755   1.944
49    G        -0.615  -0.824  -0.899  -0.188  -0.554  -0.713  -0.497  -0.760  -0.809
50    F        -0.266  -0.064  -0.283   0.186   0.474   0.148  -0.375  -0.074  -0.380
51    G        -0.547  -0.550  -0.450  -0.784  -0.819  -0.659  -0.740  -0.758  -0.614
52    E        -0.547  -0.452  -0.364  -0.763  -0.669  -0.525  -0.740  -0.631  -0.505
53    K         0.791   0.558   0.556   0.645   0.337   0.357   0.843   0.463   0.427
54    A        -1.597  -1.564  -1.428  -1.277  -1.259  -1.097  -1.349  -1.299  -1.114
55    S        -0.415  -0.475  -0.357  -0.513  -0.667  -0.454  -0.618  -0.649  -0.494
56    E         1.552   1.591   1.704   1.425   1.509   1.668   1.695   1.755   1.944
57    A        -0.897  -0.990  -0.951  -1.112  -1.323  -1.261  -0.862  -0.966  -0.875
58    L        -1.115  -1.167  -1.004  -0.704  -0.744  -0.546  -1.105  -1.135  -0.929
59    K         0.417   0.531   0.427   0.300   0.489   0.229   0.234   0.418   0.187
60    P         1.552   1.591   1.704   1.912   1.969   2.142   1.695   1.755   1.944
61    D         0.417   0.653   0.546   0.309   0.665   0.494   0.234   0.621   0.407
62    S         0.791   0.819   0.560   0.865   0.884   0.591   0.843   0.882   0.433
63    Q        -0.266  -0.286  -0.275  -0.198  -0.200  -0.229  -0.375  -0.380  -0.368
64    K         1.552   1.591   1.704   1.290   1.341   1.536   1.695   1.755   1.944
65    S         0.791   0.897   0.577   0.821   0.934   0.515   0.843   0.997   0.463
66    Y         0.417   0.531   0.427   0.493   0.658   0.512   0.234   0.418   0.187
67    A        -0.615  -0.546  -0.864  -0.082  -0.004  -0.482  -0.497  -0.418  -0.770
68    E         0.417   0.340   0.398   0.218   0.084   0.150   0.234   0.077   0.133
69    Q         0.791   0.890   0.579   0.645   0.764   0.392   0.843   0.986   0.468
70    G        -0.615  -0.875  -0.922  -0.425  -0.808  -0.883  -0.497  -0.813  -0.836
71    K         0.791   0.718   0.557   0.612   0.504   0.279   0.843   0.725   0.429
72    E         1.552   1.591   1.704   1.425   1.509   1.668   1.695   1.755   1.944
73    Y        -2.296  -2.248  -2.137  -1.885  -1.970  -1.690  -1.593  -1.537  -1.371
74    I        -0.266  -0.407  -0.374  -0.091  -0.273  -0.258  -0.375  -0.578  -0.519
75    T         1.552   1.591   1.704   1.597   1.658   1.835   1.695   1.755   1.944
76    D        -0.266  -0.286  -0.275  -0.312  -0.350  -0.331  -0.375  -0.380  -0.368
77    K        -1.947  -1.744  -1.799  -1.928  -1.617  -1.717  -1.471  -1.280  -1.254
78    A        -1.597  -1.437  -1.432  -1.324  -1.039  -1.102  -1.349  -1.185  -1.116
79    D         1.552   1.591   1.704   1.563   1.597   1.802   1.695   1.755   1.944
80    K         0.791   0.819   0.560   0.601   0.638   0.258   0.843   0.882   0.433
81    V        -1.115  -0.925  -0.947  -1.000  -0.659  -0.679  -1.105  -0.873  -0.868
82    A         0.417   0.653   0.546   0.252   0.623   0.448   0.234   0.621   0.407
83    G         0.067  -0.233  -0.288   0.220  -0.196  -0.280   0.112  -0.309  -0.387
84    K        -0.547  -0.482  -0.391  -1.060  -1.003  -0.838  -0.740  -0.679  -0.541
85    V        -1.115  -1.023  -0.951  -0.885  -0.745  -0.658  -1.105  -1.001  -0.875
86    Q        -1.465  -1.530  -1.430  -1.197  -1.292  -1.149  -1.227  -1.262  -1.113
87    P         0.067  -0.063  -0.244   0.565   0.334   0.043   0.112  -0.095  -0.324
88    E        -0.415  -0.326  -0.368  -0.648  -0.535  -0.524  -0.618  -0.518  -0.512
89    D        -1.115  -1.026  -0.955  -1.227  -1.128  -1.020  -1.105  -0.986  -0.880
90    N        -0.415  -0.516  -0.391  -0.286  -0.423  -0.243  -0.618  -0.710  -0.542
91    K         1.552   1.591   1.704   1.290   1.341   1.536   1.695   1.755   1.944
92    G         0.216   0.324   0.374  -0.099   0.070   0.136  -0.131   0.048   0.085
93    V        -1.115  -1.025  -1.006  -0.843  -0.781  -0.703  -1.105  -1.012  -0.931
94    F        -1.465  -1.454  -1.420  -1.390  -1.428  -1.330  -1.227  -1.211  -1.107
95    Q         1.552   1.591   1.704   1.711   1.780   1.946   1.695   1.755   1.944
96    G        -0.897  -1.048  -0.965  -0.966  -1.244  -1.180  -0.862  -1.008  -0.887
97    V        -0.615  -0.727  -0.871  -0.217  -0.410  -0.548  -0.497  -0.651  -0.777
98    H        -0.897  -0.809  -0.916  -0.593  -0.400  -0.674  -0.862  -0.729  -0.829
99    D         1.552   1.591   1.704   1.563   1.597   1.802   1.695   1.755   1.944
100   S        -0.415  -0.274  -0.376  -0.739  -0.661  -0.640  -0.618  -0.476  -0.528
101   A        -0.415  -0.391  -0.381  -0.546  -0.451  -0.406  -0.618  -0.552  -0.525
102   E         0.417   0.423   0.393   0.454   0.464   0.318   0.234   0.228   0.123
103   K        -1.597  -1.552  -1.433  -1.698  -1.580  -1.439  -1.349  -1.289  -1.117
104   G         0.067  -0.233  -0.288   0.247  -0.128  -0.219   0.112  -0.309  -0.387
105   K        -1.947  -1.941  -1.813  -2.007  -1.948  -1.745  -1.471  -1.443  -1.264
106   D         0.067  -0.006  -0.266   0.201   0.067  -0.348   0.112   0.010  -0.355
107   N        -0.476  -0.449  -0.392  -0.507  -0.521  -0.431  -0.691  -0.630  -0.542
108   A         1.552   1.591   1.704   1.410   1.492   1.653   1.695   1.755   1.944
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   E         0.642   0.639   0.483   0.633   0.643   0.427   0.613   0.598   0.292
121   G        -0.490  -0.472  -0.423  -0.895  -0.931  -0.869  -0.686  -0.673  -0.583
122   Q        -1.426  -1.388  -1.423  -1.339  -1.282  -1.300  -1.168  -1.119  -1.107
123   G        -0.476  -0.435  -0.396  -0.774  -0.680  -0.597  -0.691  -0.623  -0.546
124   E        -0.476  -0.436  -0.409  -1.010  -0.911  -0.889  -0.691  -0.624  -0.564
125   S         0.173   0.265   0.367  -0.107   0.039   0.197  -0.213  -0.063   0.071
126   L        -0.378  -0.388  -0.397   0.019  -0.017   0.009  -0.531  -0.565  -0.549
127   A        -0.056  -0.172  -0.319  -0.007  -0.134  -0.368  -0.054  -0.226  -0.431
128   D         0.173   0.283   0.371  -0.173   0.037   0.149  -0.213  -0.029   0.079
129   Q         0.344   0.298   0.358   0.322   0.242   0.309   0.105  -0.000   0.055
130   A         0.724   0.715   0.515   0.689   0.704   0.390   0.741   0.722   0.351
131   R        -1.026  -1.098  -1.000  -0.846  -1.011  -0.886  -1.009  -1.069  -0.924
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   D         0.724   0.775   0.534   0.660   0.745   0.387   0.741   0.815   0.386
142   Y         1.552   1.591   1.704   1.883   1.941   2.113   1.695   1.755   1.944
143   M         0.344   0.398   0.409   0.435   0.530   0.538   0.105   0.184   0.153
144   G        -0.476  -0.405  -0.400  -0.769  -0.644  -0.623  -0.691  -0.594  -0.551
145   A        -1.577  -1.580  -1.459  -1.683  -1.667  -1.532  -1.327  -1.306  -1.138
146   A         1.552   1.591   1.704   1.432   1.509   1.674   1.695   1.755   1.944
147   K         1.552   1.591   1.704   1.301   1.356   1.547   1.695   1.755   1.944
148   S        -1.177  -1.082  -0.993  -1.358  -1.238  -1.060  -1.168  -1.056  -0.916
149   K        -1.026  -1.039  -0.984  -1.387  -1.386  -1.267  -1.009  -0.997  -0.905
150   L        -0.476  -0.456  -0.417  -0.235  -0.204  -0.183  -0.691  -0.656  -0.576
151   N        -0.476  -0.436  -0.409  -0.566  -0.461  -0.459  -0.691  -0.624  -0.564
152   D        -1.177  -1.082  -0.993  -1.379  -1.159  -1.048  -1.168  -1.056  -0.916
153   A         0.724   0.576   0.500   0.741   0.580   0.486   0.741   0.494   0.323
154   V        -0.378  -0.462  -0.403  -0.481  -0.552  -0.463  -0.531  -0.631  -0.553
155   E         0.724   0.576   0.500   0.642   0.441   0.286   0.741   0.494   0.323
156   Y         0.724   0.576   0.500   1.117   0.895   0.727   0.741   0.494   0.323
157   V        -0.378  -0.482  -0.410  -0.190  -0.303  -0.191  -0.531  -0.662  -0.565
158   S         1.552   1.591   1.704   1.522   1.569   1.762   1.695   1.755   1.944
159   G         0.344   0.397   0.403   0.051   0.127   0.074   0.105   0.181   0.141
160   R        -1.026  -0.993  -0.990  -0.910  -0.891  -0.815  -1.009  -0.973  -0.914
161   V         0.724   0.576   0.500   0.880   0.692   0.535   0.741   0.494   0.323
162   H        -1.026  -1.039  -0.984  -0.757  -0.780  -0.765  -1.009  -0.997  -0.905
163   G         0.724   0.576   0.500   0.725   0.507   0.372   0.741   0.494   0.323
164   E        -1.026  -1.002  -0.952  -1.271  -1.191  -1.156  -1.009  -0.959  -0.870
165   E        -1.026  -1.039  -0.984  -1.264  -1.281  -1.239  -1.009  -0.997  -0.905
166   D        -0.200  -0.319  -0.374  -0.256  -0.443  -0.548  -0.253  -0.429  -0.508
167   P         0.642   0.657   0.496   0.719   0.741   0.552   0.613   0.628   0.317
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   T         0.542   0.432   0.437   0.513   0.347   0.268   0.448   0.244   0.207
177   K         0.344   0.366   0.371  -0.030  -0.012  -0.007   0.105   0.125   0.080
178   K         0.791   0.558   0.556   0.666   0.374   0.409   0.843   0.463   0.427
* 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/P22943
Output conservation file - output/P22943
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
