1     M         1.637   1.677   1.781   1.920   1.965   2.127   1.789   1.845   2.011
2     S         0.247   0.138   0.042   0.404   0.237   0.032   0.165   0.001  -0.163
3     -        -1.087  -1.107  -0.993  -0.826  -0.854  -0.701  -1.024  -1.029  -0.879
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    -         0.123   0.107   0.052  -0.108  -0.119  -0.223  -0.020  -0.046  -0.149
33    E        -0.783  -0.881  -0.911  -1.044  -1.187  -1.298  -0.698  -0.796  -0.799
34    L         0.979   1.102   0.850   0.907   1.056   0.747   0.998   1.183   0.731
35    G        -0.480  -0.354  -0.461  -0.246  -0.064  -0.204  -0.585  -0.407  -0.524
36    A        -1.388  -1.373  -1.292  -1.323  -1.306  -1.192  -1.150  -1.115  -0.990
37    K        -0.064  -0.108  -0.035  -0.574  -0.653  -0.561  -0.359  -0.406  -0.298
38    Y         0.655   0.672   0.660   0.923   0.939   0.898   0.432   0.447   0.360
39    Q        -0.480  -0.450  -0.519  -0.612  -0.589  -0.690  -0.585  -0.557  -0.601
40    Q        -0.971  -0.845  -0.912  -0.897  -0.704  -0.831  -0.924  -0.793  -0.808
41    L        -0.237  -0.313  -0.456  -0.130  -0.207  -0.380  -0.246  -0.341  -0.516
42    Q         0.979   0.961   0.835   0.936   0.910   0.761   0.998   0.960   0.703
43    N        -1.388  -1.438  -1.296  -1.145  -1.236  -1.054  -1.150  -1.165  -0.993
44    E        -0.237  -0.313  -0.456  -0.395  -0.489  -0.711  -0.246  -0.341  -0.516
45    L         0.353   0.257   0.108   0.389   0.277   0.097   0.319   0.178  -0.062
46    E        -0.669  -0.704  -0.590  -1.010  -0.987  -0.820  -0.811  -0.835  -0.680
47    E        -0.237  -0.386  -0.464  -0.447  -0.651  -0.821  -0.246  -0.433  -0.525
48    F        -0.783  -0.805  -0.886  -0.540  -0.550  -0.591  -0.698  -0.718  -0.774
49    I        -0.064   0.002  -0.012  -0.041   0.063   0.078  -0.359  -0.257  -0.264
50    V        -1.085  -1.089  -0.967  -1.240  -1.263  -1.089  -1.037  -1.015  -0.859
51    A         0.066  -0.036  -0.019   0.236   0.085   0.111  -0.133  -0.281  -0.267
52    R         0.979   0.931   0.830   1.198   1.135   0.957   0.998   0.911   0.693
53    Q        -0.237  -0.347  -0.454  -0.209  -0.376  -0.538  -0.246  -0.384  -0.512
54    K         0.353   0.303   0.111   0.325   0.239  -0.036   0.319   0.243  -0.057
55    L         1.637   1.677   1.781   1.471   1.519   1.683   1.789   1.845   2.011
56    E         1.637   1.677   1.781   1.312   1.377   1.526   1.789   1.845   2.011
57    T         0.655   0.638   0.645   0.713   0.677   0.657   0.432   0.381   0.331
58    Q         1.637   1.677   1.781   1.493   1.531   1.705   1.789   1.845   2.011
59    L         0.066   0.012  -0.004  -0.030  -0.100  -0.125  -0.133  -0.215  -0.243
60    Q         1.637   1.677   1.781   1.493   1.531   1.705   1.789   1.845   2.011
61    E         1.637   1.677   1.781   1.312   1.377   1.526   1.789   1.845   2.011
62    N         0.979   0.915   0.825   1.207   1.129   0.998   0.998   0.883   0.684
63    K        -0.480  -0.582  -0.539  -0.649  -0.812  -0.733  -0.585  -0.701  -0.626
64    I         0.353   0.260   0.105   0.565   0.436   0.219   0.319   0.182  -0.067
65    V         1.637   1.677   1.781   1.719   1.762   1.929   1.789   1.845   2.011
66    N        -1.388  -1.378  -1.284  -1.547  -1.602  -1.475  -1.150  -1.120  -0.984
67    E        -0.669  -0.625  -0.553  -0.764  -0.622  -0.578  -0.811  -0.737  -0.639
68    E         1.637   1.677   1.781   1.312   1.377   1.526   1.789   1.845   2.011
69    F         0.979   0.931   0.830   1.275   1.206   1.032   0.998   0.911   0.693
70    D        -0.971  -0.871  -0.921  -0.940  -0.849  -0.893  -0.924  -0.829  -0.816
71    Q        -1.388  -1.296  -1.279  -1.461  -1.368  -1.321  -1.150  -1.062  -0.981
72    L         0.655   0.622   0.638   0.458   0.401   0.406   0.432   0.351   0.315
73    E        -0.480  -0.465  -0.508  -0.592  -0.554  -0.643  -0.585  -0.576  -0.587
74    E        -0.554  -0.616  -0.527  -0.674  -0.684  -0.567  -0.698  -0.739  -0.612
75    D         0.353   0.257   0.108   0.675   0.540   0.294   0.319   0.178  -0.062
76    T        -1.085  -1.093  -0.967  -0.962  -0.953  -0.795  -1.037  -1.019  -0.858
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    P        -1.690  -1.623  -1.561  -1.450  -1.375  -1.236  -1.263  -1.198  -1.079
94    V         0.427   0.480   0.594   0.260   0.332   0.508  -0.020   0.065   0.224
95    Y         0.979   0.961   0.835   1.360   1.338   1.183   0.998   0.960   0.703
96    K         1.637   1.677   1.781   1.482   1.514   1.694   1.789   1.845   2.011
97    L         0.979   0.931   0.830   0.873   0.808   0.644   0.998   0.911   0.693
98    T         0.066  -0.022  -0.022   0.167   0.017   0.008  -0.133  -0.273  -0.274
99    G         1.637   1.677   1.781   1.849   1.898   2.057   1.789   1.845   2.011
100   N         0.066   0.291   0.084   0.380   0.700   0.423  -0.133   0.208  -0.102
101   V         0.353   0.318   0.127   0.594   0.549   0.273   0.319   0.265  -0.034
102   L         1.637   1.677   1.781   1.471   1.519   1.683   1.789   1.845   2.011
103   L         0.066   0.050  -0.009  -0.018  -0.045  -0.084  -0.133  -0.172  -0.253
104   P         0.655   0.616   0.649   0.794   0.688   0.684   0.432   0.338   0.337
105   V         0.482   0.620   0.675   0.196   0.408   0.487   0.093   0.347   0.390
106   E        -0.178  -0.226  -0.115  -0.484  -0.497  -0.323  -0.472  -0.545  -0.399
107   Q        -0.971  -0.943  -0.915  -0.691  -0.606  -0.603  -0.924  -0.868  -0.807
108   S        -1.273  -1.207  -1.226  -0.805  -0.724  -0.750  -1.037  -0.964  -0.933
109   E         0.655   0.722   0.685   0.340   0.451   0.390   0.432   0.540   0.411
110   A         1.637   1.677   1.781   1.751   1.790   1.960   1.789   1.845   2.011
111   R        -0.237  -0.247  -0.419  -0.199  -0.226  -0.458  -0.246  -0.263  -0.469
112   T        -1.085  -1.036  -0.966  -0.993  -0.934  -0.796  -1.037  -0.979  -0.859
113   N         0.979   0.961   0.835   1.207   1.191   1.014   0.998   0.960   0.703
114   V         1.637   1.677   1.781   1.719   1.762   1.929   1.789   1.845   2.011
115   D        -1.085  -1.066  -0.971  -1.247  -1.228  -1.083  -1.037  -0.997  -0.862
116   K         0.353   0.260   0.105   0.387   0.266   0.078   0.319   0.182  -0.067
117   R         1.637   1.677   1.781   1.797   1.847   2.006   1.789   1.845   2.011
118   L         0.353   0.303   0.111   0.346   0.285   0.017   0.319   0.243  -0.057
119   E         0.979   0.931   0.830   0.763   0.729   0.597   0.998   0.911   0.693
120   F         1.637   1.677   1.781   1.874   1.918   2.082   1.789   1.845   2.011
121   I         1.637   1.677   1.781   1.682   1.716   1.892   1.789   1.845   2.011
122   E        -0.783  -0.795  -0.880  -0.777  -0.767  -0.835  -0.698  -0.709  -0.768
123   T        -1.388  -1.267  -1.277  -1.289  -1.096  -1.137  -1.150  -1.041  -0.979
124   E         0.979   0.975   0.832   0.712   0.723   0.491   0.998   0.983   0.698
125   I         1.637   1.677   1.781   1.682   1.716   1.892   1.789   1.845   2.011
126   T        -0.971  -1.050  -0.942  -1.053  -1.168  -1.004  -0.924  -0.980  -0.835
127   R         0.353   0.257   0.108   0.678   0.559   0.328   0.319   0.178  -0.062
128   C        -0.669  -0.708  -0.591  -0.531  -0.641  -0.488  -0.811  -0.837  -0.682
129   E         1.637   1.677   1.781   1.312   1.377   1.526   1.789   1.845   2.011
130   K        -1.273  -1.216  -1.242  -1.018  -0.918  -1.007  -1.037  -0.975  -0.947
131   N        -0.971  -1.043  -0.965  -1.016  -1.182  -1.120  -0.924  -0.976  -0.856
132   I         0.353   0.272   0.107   0.564   0.452   0.220   0.319   0.200  -0.064
133   R        -0.480  -0.380  -0.451  -0.454  -0.312  -0.373  -0.585  -0.433  -0.511
134   D        -0.669  -0.682  -0.578  -0.752  -0.810  -0.649  -0.811  -0.810  -0.670
135   K        -1.273  -1.379  -1.296  -1.432  -1.618  -1.552  -1.037  -1.116  -0.992
136   Q         0.353   0.303   0.111   0.324   0.264  -0.049   0.319   0.243  -0.057
137   E        -0.669  -0.613  -0.557  -1.097  -0.965  -0.907  -0.811  -0.727  -0.643
138   E        -0.480  -0.561  -0.532  -0.883  -0.991  -0.970  -0.585  -0.670  -0.617
139   L        -0.554  -0.572  -0.529  -0.611  -0.567  -0.479  -0.698  -0.689  -0.612
140   E         0.353   0.219   0.104   0.208   0.063  -0.100   0.319   0.122  -0.069
141   K        -1.273  -1.200  -1.237  -1.050  -0.944  -0.954  -1.037  -0.959  -0.943
142   M        -1.388  -1.309  -1.271  -1.204  -1.138  -1.008  -1.150  -1.072  -0.975
143   R         0.655   0.593   0.629   0.700   0.560   0.549   0.432   0.294   0.297
144   S        -1.388  -1.413  -1.288  -1.182  -1.208  -1.067  -1.150  -1.147  -0.987
145   E        -0.554  -0.563  -0.515  -0.987  -0.957  -0.895  -0.698  -0.690  -0.601
146   L         0.655   0.616   0.649   0.445   0.371   0.404   0.432   0.338   0.337
147   I        -0.237  -0.252  -0.433   0.018  -0.027  -0.269  -0.246  -0.268  -0.486
148   K        -1.085  -1.027  -0.970  -1.195  -1.115  -0.996  -1.037  -0.971  -0.861
149   L        -0.971  -1.011  -0.935  -1.096  -1.133  -1.011  -0.924  -0.946  -0.829
150   N        -0.554  -0.517  -0.524  -0.542  -0.497  -0.464  -0.698  -0.652  -0.612
151   N        -1.068  -1.044  -0.958  -0.935  -0.907  -0.779  -1.016  -0.977  -0.849
152   T        -1.068  -1.074  -0.959  -1.121  -1.103  -0.953  -1.016  -1.002  -0.851
153   A        -0.128  -0.063  -0.050  -0.325  -0.245  -0.256  -0.421  -0.348  -0.313
154   A        -0.128  -0.141  -0.048  -0.417  -0.444  -0.308  -0.421  -0.429  -0.308
155   S        -1.087  -1.032  -0.963  -1.071  -0.983  -0.915  -1.024  -0.959  -0.851
156   T        -1.172  -1.131  -1.005  -1.123  -1.052  -0.882  -1.104  -1.052  -0.890
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   P        -0.938  -0.903  -0.901  -0.538  -0.478  -0.515  -0.868  -0.823  -0.790
167   G        -1.414  -1.335  -1.280  -1.277  -1.164  -1.066  -1.163  -1.078  -0.980
168   R        -0.971  -0.845  -0.909  -0.908  -0.733  -0.824  -0.924  -0.796  -0.805
* 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/P52553
Output conservation file - output/P52553
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
