1     M         2.070   2.100   2.208   2.357   2.400   2.568   2.341   2.388   2.579
2     S        -0.422  -0.448  -0.471  -0.485  -0.519  -0.566  -0.448  -0.482  -0.498
3     F        -1.523  -1.504  -1.456  -1.458  -1.388  -1.348  -1.145  -1.121  -1.047
4     V        -0.596  -0.630  -0.582  -0.924  -1.004  -0.942  -0.680  -0.708  -0.637
5     S         1.166   1.195   1.099   1.123   1.166   1.037   1.179   1.225   1.025
6     K         0.164   0.060   0.087   0.192   0.051   0.081  -0.002  -0.161  -0.132
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     L        -1.060  -1.066  -1.041  -1.267  -1.261  -1.250  -0.913  -0.914  -0.862
10    L         0.330   0.245   0.194   0.106  -0.053  -0.122   0.249   0.115   0.033
11    Y         1.166   1.047   1.061   1.372   1.201   1.228   1.179   0.960   0.954
12    T        -1.060  -1.049  -1.024  -0.959  -0.968  -0.908  -0.913  -0.898  -0.846
13    V        -0.422  -0.464  -0.476  -0.460  -0.537  -0.593  -0.448  -0.501  -0.503
14    S         0.042   0.100   0.073  -0.077   0.033  -0.018  -0.215  -0.125  -0.164
15    A        -1.523  -1.504  -1.456  -1.341  -1.314  -1.229  -1.145  -1.121  -1.047
16    L         1.166   1.211   1.099   0.917   0.973   0.792   1.179   1.252   1.026
17    V         0.042   0.112   0.072  -0.203  -0.122  -0.151  -0.215  -0.114  -0.168
18    L         0.330   0.398   0.249   0.106   0.196  -0.031   0.249   0.352   0.119
19    F        -1.060  -1.062  -1.027  -1.204  -1.207  -1.151  -0.913  -0.910  -0.849
20    H         2.070   2.100   2.208   2.290   2.333   2.500   2.341   2.388   2.579
21    S         0.680   0.701   0.792   0.390   0.420   0.558   0.249   0.280   0.406
22    G         0.330   0.257   0.204   0.578   0.487   0.421   0.249   0.133   0.049
23    F         0.042   0.100   0.073   0.058   0.152   0.111  -0.215  -0.125  -0.164
24    S         2.070   2.100   2.208   1.944   1.991   2.145   2.341   2.388   2.579
25    S         1.166   1.047   1.061   1.116   0.951   0.969   1.179   0.960   0.954
26    Y         0.042  -0.025   0.042   0.103   0.015   0.120  -0.215  -0.297  -0.210
27    E         2.070   2.100   2.208   2.050   2.091   2.254   2.341   2.388   2.579
28    F         1.166   1.047   1.061   1.350   1.186   1.215   1.179   0.960   0.954
29    H         1.166   1.047   1.061   1.458   1.284   1.310   1.179   0.960   0.954
30    H        -0.422  -0.464  -0.478  -0.118  -0.187  -0.207  -0.448  -0.502  -0.507
31    L         0.164   0.263   0.155  -0.183  -0.041  -0.221  -0.002   0.149  -0.027
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    L        -1.060  -1.074  -1.024  -1.155  -1.183  -1.080  -0.913  -0.921  -0.846
38    K         0.330   0.232   0.198   0.335   0.228   0.118   0.249   0.097   0.039
39    L        -0.422  -0.326  -0.463  -0.267  -0.110  -0.358  -0.448  -0.321  -0.488
40    N        -0.422  -0.454  -0.487  -0.234  -0.315  -0.380  -0.448  -0.490  -0.518
41    S        -0.602  -0.611  -0.564  -0.826  -0.828  -0.764  -0.671  -0.680  -0.611
42    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    Q        -1.523  -1.504  -1.456  -1.107  -1.081  -0.988  -1.145  -1.121  -1.047
47    G        -1.523  -1.504  -1.456  -1.083  -1.067  -0.964  -1.145  -1.121  -1.047
48    A        -0.596  -0.551  -0.559  -0.561  -0.492  -0.503  -0.680  -0.626  -0.611
49    I        -1.060  -1.056  -1.051  -0.881  -0.881  -0.872  -0.913  -0.904  -0.872
50    S        -1.060  -1.002  -1.021  -1.055  -0.980  -0.983  -0.913  -0.845  -0.842
51    K        -1.523  -1.504  -1.456  -1.479  -1.458  -1.370  -1.145  -1.121  -1.047
52    L         1.166   1.195   1.099   0.991   1.025   0.906   1.179   1.225   1.025
53    P         2.070   2.100   2.208   2.250   2.292   2.458   2.341   2.388   2.579
54    K        -1.523  -1.504  -1.456  -1.382  -1.351  -1.270  -1.145  -1.121  -1.047
55    D         1.166   1.226   1.106   1.343   1.434   1.251   1.179   1.278   1.039
56    I         1.166   1.211   1.099   1.055   1.110   0.954   1.179   1.252   1.026
57    M        -1.060  -1.066  -1.041  -0.937  -0.932  -0.886  -0.913  -0.914  -0.862
58    Y        -1.060  -1.049  -1.024  -1.245  -1.275  -1.179  -0.913  -0.898  -0.846
59    E         2.070   2.100   2.208   2.050   2.091   2.254   2.341   2.388   2.579
60    T        -0.596  -0.570  -0.553  -0.565  -0.535  -0.496  -0.680  -0.644  -0.606
61    Y        -0.596  -0.556  -0.556  -0.957  -0.913  -0.875  -0.680  -0.631  -0.609
62    A        -1.060  -1.066  -1.041  -0.881  -0.919  -0.895  -0.913  -0.914  -0.862
63    G         0.680   0.701   0.792   0.536   0.560   0.703   0.249   0.280   0.406
64    L         0.042  -0.023   0.064  -0.390  -0.479  -0.355  -0.215  -0.293  -0.184
65    I         0.042   0.054   0.062  -0.401  -0.426  -0.394  -0.215  -0.210  -0.188
66    L        -1.060  -1.062  -1.025  -1.229  -1.244  -1.163  -0.913  -0.910  -0.847
67    F         0.330   0.232   0.198   0.374   0.191   0.103   0.249   0.097   0.039
68    V         0.042   0.105   0.083  -0.126  -0.036  -0.061  -0.215  -0.124  -0.154
69    L         0.793   0.832   0.878   0.284   0.337   0.384   0.482   0.548   0.587
70    A         1.166   1.240   1.104   1.318   1.422   1.237   1.179   1.302   1.035
71    V        -0.596  -0.630  -0.582  -0.800  -0.895  -0.783  -0.680  -0.708  -0.637
72    F         0.042  -0.025   0.042  -0.114  -0.224  -0.126  -0.215  -0.297  -0.210
73    T        -0.596  -0.557  -0.549  -0.943  -0.919  -0.861  -0.680  -0.632  -0.602
74    S         1.166   1.047   1.061   1.106   0.943   0.952   1.179   0.960   0.954
75    F        -1.060  -1.078  -1.047  -0.894  -0.932  -0.872  -0.913  -0.925  -0.868
76    E        -0.422  -0.483  -0.483  -0.318  -0.408  -0.403  -0.448  -0.525  -0.512
77    K        -0.596  -0.620  -0.578  -0.577  -0.569  -0.533  -0.680  -0.699  -0.633
78    L         0.330   0.384   0.218   0.200   0.270   0.051   0.249   0.331   0.070
79    Q        -0.596  -0.630  -0.582  -0.393  -0.426  -0.363  -0.680  -0.708  -0.637
80    Y        -0.422  -0.474  -0.511  -0.207  -0.273  -0.353  -0.448  -0.514  -0.547
81    L         0.330   0.265   0.201   0.116  -0.015  -0.097   0.249   0.144   0.044
82    P         0.042  -0.012   0.053  -0.053  -0.112  -0.011  -0.215  -0.275  -0.194
83    I         0.330   0.265   0.201   0.238   0.153   0.037   0.249   0.144   0.044
84    E        -0.422  -0.345  -0.450  -0.128  -0.023  -0.175  -0.448  -0.345  -0.472
85    S        -0.596  -0.618  -0.578  -0.591  -0.619  -0.574  -0.680  -0.697  -0.633
86    N        -1.060  -1.066  -1.041  -0.868  -0.835  -0.813  -0.913  -0.914  -0.862
87    D        -0.602  -0.623  -0.579  -0.603  -0.649  -0.566  -0.671  -0.695  -0.629
88    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    K        -0.422  -0.366  -0.469  -0.510  -0.383  -0.616  -0.448  -0.371  -0.495
92    I         1.166   1.236   1.105   1.085   1.171   1.009   1.179   1.294   1.037
93    I        -1.060  -1.068  -1.041  -1.260  -1.263  -1.234  -0.913  -0.916  -0.862
94    S        -1.523  -1.504  -1.456  -1.263  -1.216  -1.148  -1.145  -1.121  -1.047
95    Q        -1.060  -1.056  -1.051  -0.754  -0.776  -0.725  -0.913  -0.904  -0.872
96    G        -0.596  -0.560  -0.553  -0.617  -0.539  -0.560  -0.680  -0.635  -0.607
97    N        -0.596  -0.538  -0.557  -0.639  -0.538  -0.551  -0.680  -0.613  -0.609
98    Y         2.070   2.100   2.208   2.169   2.208   2.375   2.341   2.388   2.579
99    L         2.070   2.100   2.208   1.790   1.833   1.986   2.341   2.388   2.579
100   K         0.164   0.168   0.127   0.050   0.060  -0.033  -0.002   0.004  -0.071
101   E        -1.060  -1.002  -1.021  -0.935  -0.836  -0.863  -0.913  -0.845  -0.842
102   I         1.166   1.047   1.061   1.063   0.889   0.909   1.179   0.960   0.954
103   A        -0.422  -0.438  -0.493  -0.357  -0.381  -0.470  -0.448  -0.471  -0.526
104   L         0.793   0.832   0.878   0.509   0.556   0.633   0.482   0.548   0.587
105   N        -0.422  -0.474  -0.511  -0.203  -0.280  -0.348  -0.448  -0.514  -0.547
106   K         0.330   0.232   0.198   0.398   0.299   0.212   0.249   0.097   0.039
107   A         0.330   0.265   0.201   0.511   0.402   0.296   0.249   0.144   0.044
108   T        -1.060  -1.066  -1.041  -0.932  -0.948  -0.867  -0.913  -0.914  -0.862
109   N        -1.060  -1.078  -1.047  -0.854  -0.904  -0.833  -0.913  -0.925  -0.868
110   V        -1.060  -1.002  -1.021  -1.149  -1.059  -1.105  -0.913  -0.845  -0.842
111   D        -0.422  -0.474  -0.511  -0.282  -0.379  -0.458  -0.448  -0.514  -0.547
112   N        -0.596  -0.630  -0.582  -0.634  -0.679  -0.613  -0.680  -0.708  -0.637
113   L        -0.596  -0.630  -0.582  -0.868  -0.863  -0.822  -0.680  -0.708  -0.637
114   I         0.042  -0.016   0.064  -0.195  -0.274  -0.150  -0.215  -0.281  -0.182
115   G         0.330   0.245   0.194   0.564   0.455   0.384   0.249   0.115   0.033
116   S        -1.060  -1.056  -1.051  -1.152  -1.138  -1.121  -0.913  -0.904  -0.872
117   N        -0.596  -0.564  -0.560  -0.512  -0.457  -0.454  -0.680  -0.638  -0.613
118   P         0.330   0.384   0.218   0.612   0.693   0.446   0.249   0.331   0.070
119   N        -0.133  -0.113  -0.035  -0.180  -0.154  -0.032  -0.448  -0.419  -0.316
120   G         0.042  -0.025   0.042  -0.008  -0.099   0.001  -0.215  -0.297  -0.210
121   E         1.166   1.047   1.061   1.222   1.052   1.074   1.179   0.960   0.954
122   I        -0.596  -0.620  -0.578  -0.811  -0.887  -0.807  -0.680  -0.699  -0.633
123   I        -1.060  -1.049  -1.024  -1.029  -1.014  -0.990  -0.913  -0.898  -0.846
124   F         0.042   0.112   0.072  -0.116  -0.017  -0.062  -0.215  -0.114  -0.168
125   T         0.042   0.100   0.073   0.085   0.165   0.114  -0.215  -0.125  -0.164
126   P         0.330   0.384   0.218   0.601   0.675   0.430   0.249   0.331   0.070
127   S         1.166   1.226   1.106   1.118   1.205   1.039   1.179   1.278   1.039
128   F         2.070   2.100   2.208   2.161   2.202   2.368   2.341   2.388   2.579
129   V         0.793   0.832   0.878   0.568   0.626   0.671   0.482   0.548   0.587
130   D         2.070   2.100   2.208   2.203   2.251   2.410   2.341   2.388   2.579
131   V         1.166   1.240   1.104   1.055   1.149   0.962   1.179   1.302   1.035
132   H        -0.596  -0.636  -0.564  -0.474  -0.494  -0.407  -0.680  -0.715  -0.617
133   M        -1.060  -1.056  -1.051  -0.675  -0.680  -0.647  -0.913  -0.904  -0.872
134   K         1.166   1.047   1.061   1.202   1.084   1.064   1.179   0.960   0.954
135   R         2.070   2.100   2.208   2.277   2.306   2.486   2.341   2.388   2.579
136   K         1.166   1.236   1.105   1.157   1.299   1.062   1.179   1.294   1.037
137   I        -0.422  -0.326  -0.463  -0.478  -0.329  -0.575  -0.448  -0.321  -0.488
138   C        -0.596  -0.538  -0.557  -0.424  -0.357  -0.341  -0.680  -0.613  -0.609
139   R        -1.523  -1.504  -1.456  -1.257  -1.217  -1.142  -1.145  -1.121  -1.047
140   E         0.042   0.100   0.079  -0.065   0.034  -0.010  -0.215  -0.132  -0.154
141   W         1.166   1.211   1.099   1.550   1.607   1.462   1.179   1.252   1.026
142   A         0.330   0.269   0.194   0.116  -0.013  -0.108   0.249   0.150   0.033
143   S        -1.060  -1.072  -1.026  -0.948  -0.960  -0.904  -0.913  -0.920  -0.848
144   N        -0.596  -0.553  -0.564  -0.587  -0.493  -0.513  -0.680  -0.628  -0.617
145   T        -0.710  -0.685  -0.627  -0.881  -0.857  -0.756  -0.797  -0.763  -0.684
146   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   E        -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     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   K        -0.602  -0.566  -0.557  -0.792  -0.717  -0.739  -0.671  -0.624  -0.603
* 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/P40540
Output conservation file - output/P40540
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
