1     M         1.729   1.773   1.876   2.017   2.076   2.234   1.882   1.945   2.112
2     A        -0.415  -0.361  -0.468  -0.529  -0.480  -0.606  -0.506  -0.450  -0.547
3     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     F         1.063   0.948   0.869   1.257   1.131   1.022   1.086   0.886   0.701
5     F         0.138   0.009   0.021   0.246   0.070   0.067  -0.051  -0.232  -0.237
6     V         0.735   0.736   0.728   0.731   0.710   0.647   0.517   0.500   0.423
7     R        -1.218  -1.156  -1.205  -0.993  -0.916  -0.964  -0.961  -0.892  -0.897
8     L         1.729   1.773   1.876   1.439   1.505   1.655   1.882   1.945   2.112
9     W         1.729   1.773   1.876   1.946   2.004   2.163   1.882   1.945   2.112
10    E         1.063   1.169   0.927   1.140   1.265   0.983   1.086   1.246   0.811
11    S         1.729   1.773   1.876   1.618   1.679   1.835   1.882   1.945   2.112
12    V         0.560   0.653   0.692   0.345   0.512   0.534   0.176   0.339   0.350
13    F         1.729   1.773   1.876   1.808   1.875   2.024   1.882   1.945   2.112
14    E         0.138   0.259   0.118   0.072   0.249   0.064  -0.051   0.132  -0.082
15    P         1.729   1.773   1.876   1.941   1.998   2.158   1.882   1.945   2.112
16    G         1.729   1.773   1.876   1.957   2.011   2.174   1.882   1.945   2.112
17    T         0.429   0.219   0.112   0.542   0.257   0.112   0.404   0.094  -0.086
18    S         0.560   0.641   0.711   0.215   0.354   0.438   0.176   0.316   0.388
19    P         1.729   1.773   1.876   1.941   1.998   2.158   1.882   1.945   2.112
20    Q        -0.605  -0.643  -0.539  -0.597  -0.667  -0.530  -0.734  -0.755  -0.624
21    L         1.729   1.773   1.876   1.439   1.505   1.655   1.882   1.945   2.112
22    I        -0.168  -0.332  -0.456  -0.120  -0.389  -0.644  -0.165  -0.375  -0.521
23    I         0.007   0.077   0.029  -0.195  -0.081  -0.161  -0.279  -0.201  -0.231
24    A         1.063   0.948   0.869   1.072   0.891   0.761   1.086   0.886   0.701
25    T         1.063   0.948   0.869   1.070   0.901   0.771   1.086   0.886   0.701
26    H         1.063   0.982   0.880   1.416   1.313   1.162   1.086   0.944   0.723
27    V        -0.605  -0.497  -0.478  -0.663  -0.472  -0.439  -0.734  -0.593  -0.553
28    S         0.429   0.219   0.112   0.417   0.102  -0.098   0.404   0.094  -0.086
29    F         1.063   0.948   0.869   1.260   1.132   1.027   1.086   0.886   0.701
30    V        -0.605  -0.610  -0.523  -0.701  -0.680  -0.549  -0.734  -0.714  -0.606
31    A         0.007   0.112   0.045  -0.320  -0.166  -0.218  -0.279  -0.135  -0.207
32    L         1.729   1.773   1.876   1.439   1.505   1.655   1.882   1.945   2.112
33    L        -0.490  -0.599  -0.510  -0.753  -0.834  -0.701  -0.620  -0.711  -0.593
34    L        -0.912  -0.893  -0.881  -1.022  -0.987  -0.950  -0.847  -0.815  -0.766
35    T         0.007   0.058   0.036  -0.203  -0.126  -0.126  -0.279  -0.227  -0.221
36    L         1.063   0.948   0.869   0.855   0.716   0.588   1.086   0.886   0.701
37    I        -0.168  -0.165  -0.390  -0.296  -0.298  -0.613  -0.165  -0.162  -0.439
38    W        -1.333  -1.353  -1.255  -1.023  -1.007  -0.887  -1.075  -1.071  -0.941
39    L         1.063   1.135   0.906   0.881   0.980   0.700   1.086   1.194   0.771
40    I         0.429   0.219   0.112   0.511   0.239   0.021   0.404   0.094  -0.086
41    Y        -0.415  -0.490  -0.489  -0.096  -0.226  -0.252  -0.506  -0.590  -0.570
42    A        -0.912  -0.924  -0.887  -1.134  -1.126  -1.048  -0.847  -0.852  -0.773
43    T         1.063   1.129   0.898   1.070   1.149   0.821   1.086   1.185   0.756
44    N        -1.218  -1.137  -1.186  -0.912  -0.786  -0.854  -0.961  -0.873  -0.880
45    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    N         0.007   0.110   0.060  -0.166  -0.032  -0.083  -0.279  -0.140  -0.184
47    I         1.729   1.773   1.876   1.688   1.768   1.905   1.882   1.945   2.112
48    H         1.729   1.773   1.876   1.990   2.050   2.207   1.882   1.945   2.112
49    F         0.429   0.348   0.132   0.669   0.580   0.250   0.404   0.277  -0.055
50    Y        -0.605  -0.645  -0.525  -0.647  -0.725  -0.558  -0.734  -0.758  -0.609
51    A        -1.027  -0.937  -0.925  -0.971  -0.862  -0.803  -0.961  -0.863  -0.808
52    L         1.729   1.773   1.876   1.439   1.505   1.655   1.882   1.945   2.112
53    F        -0.490  -0.503  -0.488  -0.795  -0.779  -0.782  -0.620  -0.617  -0.570
54    C        -0.912  -0.982  -0.920  -0.771  -0.887  -0.775  -0.847  -0.898  -0.802
55    I         0.735   0.635   0.677   0.518   0.302   0.270   0.517   0.303   0.319
56    S         0.429   0.402   0.170   0.537   0.496   0.176   0.404   0.357   0.002
57    L        -1.218  -1.241  -1.227  -1.303  -1.313  -1.277  -0.961  -0.975  -0.916
58    L        -0.415  -0.462  -0.489  -0.427  -0.457  -0.395  -0.506  -0.569  -0.570
59    L         1.729   1.773   1.876   1.439   1.505   1.655   1.882   1.945   2.112
60    W         0.735   0.851   0.785   0.956   1.122   1.019   0.517   0.714   0.537
61    I        -0.490  -0.500  -0.483  -0.534  -0.556  -0.541  -0.620  -0.618  -0.563
62    T         0.504   0.548   0.664   0.086   0.146   0.323   0.063   0.128   0.291
63    V         0.138   0.018   0.014   0.074  -0.157  -0.257  -0.051  -0.225  -0.246
64    I        -0.490  -0.478  -0.471  -0.611  -0.576  -0.541  -0.620  -0.594  -0.550
65    W         1.729   1.773   1.876   1.946   2.004   2.163   1.882   1.945   2.112
66    F         1.729   1.773   1.876   1.808   1.875   2.024   1.882   1.945   2.112
67    I         0.429   0.219   0.112   0.449   0.135  -0.120   0.404   0.094  -0.086
68    N        -0.912  -0.941  -0.898  -0.748  -0.830  -0.733  -0.847  -0.865  -0.782
69    E         1.729   1.773   1.876   1.700   1.752   1.916   1.882   1.945   2.112
70    L         1.063   1.129   0.898   0.859   0.953   0.641   1.086   1.185   0.756
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    S        -0.912  -0.877  -0.880  -0.780  -0.743  -0.741  -0.847  -0.799  -0.765
76    H        -1.333  -1.293  -1.242  -0.972  -0.907  -0.858  -1.075  -1.024  -0.930
77    V        -0.912  -0.889  -0.883  -0.792  -0.759  -0.717  -0.847  -0.805  -0.768
78    K         0.429   0.219   0.112   0.655   0.413   0.258   0.404   0.094  -0.086
79    L         0.429   0.219   0.112   0.264  -0.016  -0.202   0.404   0.094  -0.086
80    K        -0.415  -0.486  -0.485  -0.256  -0.337  -0.323  -0.506  -0.587  -0.565
81    D        -1.027  -1.077  -0.933  -1.043  -1.108  -0.891  -0.961  -0.979  -0.815
82    N         0.138   0.018   0.014   0.317   0.118   0.106  -0.051  -0.225  -0.246
83    D        -1.218  -1.153  -1.215  -1.147  -1.105  -1.175  -0.961  -0.892  -0.905
84    E        -0.721  -0.809  -0.865  -0.512  -0.637  -0.707  -0.620  -0.715  -0.744
85    L         0.429   0.219   0.112   0.298   0.027  -0.125   0.404   0.094  -0.086
86    D        -1.218  -1.157  -1.205  -0.993  -0.891  -0.936  -0.961  -0.892  -0.897
87    K        -1.218  -1.262  -1.248  -1.003  -1.072  -1.057  -0.961  -0.992  -0.933
88    D        -1.333  -1.282  -1.240  -1.256  -1.169  -1.099  -1.075  -1.018  -0.929
89    A        -1.010  -1.020  -0.925  -1.106  -1.148  -0.972  -0.940  -0.934  -0.806
90    N        -1.360  -1.261  -1.253  -1.433  -1.294  -1.289  -1.089  -0.989  -0.937
91    K        -1.010  -0.945  -0.923  -1.117  -1.012  -0.997  -0.940  -0.869  -0.805
92    K         0.196   0.204   0.128   0.238   0.244   0.104   0.063   0.064  -0.061
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    D        -0.467  -0.460  -0.468  -0.433  -0.435  -0.447  -0.544  -0.535  -0.536
100   D         0.196   0.387   0.162   0.372   0.667   0.272   0.063   0.343  -0.010
101   S        -0.621  -0.614  -0.524  -0.813  -0.786  -0.659  -0.746  -0.726  -0.605
102   A        -1.437  -1.387  -1.290  -1.464  -1.391  -1.251  -1.151  -1.093  -0.966
103   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   E        -0.058  -0.106   0.002  -0.203  -0.295  -0.124  -0.342  -0.402  -0.263
108   D        -1.029  -0.941  -0.915  -0.883  -0.754  -0.733  -0.948  -0.851  -0.794
109   S        -0.058   0.031   0.015  -0.477  -0.347  -0.400  -0.342  -0.233  -0.244
110   E        -1.029  -0.978  -0.919  -1.085  -1.013  -0.916  -0.948  -0.887  -0.798
111   D        -1.437  -1.387  -1.290  -1.310  -1.251  -1.096  -1.151  -1.093  -0.966
112   K        -0.467  -0.419  -0.449  -0.498  -0.435  -0.513  -0.544  -0.486  -0.512
113   Q        -1.029  -0.941  -0.915  -1.031  -0.938  -0.868  -0.948  -0.851  -0.794
114   E        -1.029  -1.010  -0.942  -1.091  -1.065  -0.976  -0.948  -0.922  -0.820
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   S         0.196   0.302   0.144   0.206   0.358   0.105   0.063   0.218  -0.037
145   G        -1.029  -0.974  -0.919  -1.088  -1.042  -0.919  -0.948  -0.883  -0.798
146   K        -0.467  -0.516  -0.481  -0.391  -0.432  -0.427  -0.544  -0.608  -0.551
147   S         0.196   0.345   0.169   0.177   0.373   0.153   0.063   0.281   0.001
148   T        -0.467  -0.557  -0.497  -0.706  -0.918  -0.853  -0.544  -0.652  -0.570
149   S        -0.213  -0.180  -0.061  -0.474  -0.424  -0.238  -0.544  -0.498  -0.345
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   T         0.196   0.195   0.131   0.236   0.211   0.152   0.063   0.050  -0.056
157   A        -0.621  -0.602  -0.524  -0.758  -0.703  -0.601  -0.746  -0.712  -0.605
158   R        -0.621  -0.610  -0.519  -0.623  -0.592  -0.453  -0.746  -0.723  -0.601
159   R        -1.029  -0.868  -0.914  -0.855  -0.643  -0.678  -0.948  -0.769  -0.793
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   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   A        -0.621  -0.610  -0.523  -0.749  -0.741  -0.591  -0.746  -0.720  -0.604
166   Q        -0.878  -0.891  -0.890  -0.579  -0.583  -0.559  -0.792  -0.801  -0.769
167   S        -1.010  -0.883  -0.907  -1.278  -1.080  -1.144  -0.940  -0.814  -0.791
168   R        -1.010  -1.061  -0.921  -0.905  -0.992  -0.795  -0.940  -0.966  -0.803
169   S        -0.912  -0.970  -0.914  -1.018  -1.117  -1.064  -0.847  -0.888  -0.796
170   R         0.007  -0.067   0.030   0.109   0.011   0.145  -0.279  -0.359  -0.230
171   K        -1.218  -1.263  -1.228  -0.925  -0.967  -0.926  -0.961  -0.993  -0.917
172   A        -1.218  -1.244  -1.215  -1.098  -1.185  -1.104  -0.961  -0.978  -0.905
* 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/Q03880
Output conservation file - output/Q03880
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
