1     M         0.961   0.968   1.028   1.368   1.356   1.397   1.007   1.016   1.109
2     K         0.224   0.094  -0.153  -0.181  -0.304  -0.669   0.251   0.064  -0.360
3     V        -0.831  -0.928  -0.955  -0.480  -0.606  -0.648  -0.881  -0.992  -1.023
4     E         0.224   0.094  -0.153   0.572   0.419   0.091   0.251   0.064  -0.360
5     V        -1.728  -1.644  -1.494  -1.301  -1.191  -1.000  -1.637  -1.518  -1.315
6     D        -0.158  -0.173  -0.164   0.290   0.255   0.213  -0.315  -0.351  -0.378
7     S         0.224   0.094  -0.153   0.362   0.232  -0.093   0.251   0.064  -0.360
8     F         0.961   0.968   1.028   1.222   1.225   1.276   1.007   1.016   1.109
9     S         0.961   0.968   1.028   0.920   0.944   1.026   1.007   1.016   1.109
10    G         0.961   0.968   1.028   1.115   1.113   1.187   1.007   1.016   1.109
11    A        -2.133  -2.095  -1.917  -1.969  -1.834  -1.490  -1.825  -1.746  -1.492
12    K         0.224   0.094  -0.153  -0.181  -0.304  -0.669   0.251   0.064  -0.360
13    I        -0.158  -0.173  -0.164   0.130   0.081   0.030  -0.315  -0.351  -0.378
14    Y         0.961   0.968   1.028   1.338   1.325   1.372   1.007   1.016   1.109
15    P         0.961   0.968   1.028   1.292   1.281   1.334   1.007   1.016   1.109
16    G         0.961   0.968   1.028   1.115   1.113   1.187   1.007   1.016   1.109
17    R        -0.831  -0.947  -0.943  -1.100  -1.322  -1.431  -0.881  -1.019  -1.006
18    G         0.961   0.968   1.028   1.115   1.113   1.187   1.007   1.016   1.109
19    T        -0.831  -0.947  -0.943  -0.574  -0.814  -1.011  -0.881  -1.019  -1.006
20    L         0.961   0.968   1.028   1.183   1.185   1.243   1.007   1.016   1.109
21    F         0.224   0.094  -0.153   0.674   0.524   0.165   0.251   0.064  -0.360
22    V         0.961   0.968   1.028   1.067   1.071   1.147   1.007   1.016   1.109
23    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
24    G         0.961   0.968   1.028   1.115   1.113   1.187   1.007   1.016   1.109
25    D         0.961   0.968   1.028   1.272   1.276   1.318   1.007   1.016   1.109
26    S        -0.158  -0.173  -0.164  -0.076  -0.093  -0.083  -0.315  -0.351  -0.378
27    K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
28    I        -0.158  -0.173  -0.164   0.130   0.081   0.030  -0.315  -0.351  -0.378
29    F         0.961   0.968   1.028   1.222   1.225   1.276   1.007   1.016   1.109
30    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
31    F         0.961   0.968   1.028   1.222   1.225   1.276   1.007   1.016   1.109
32    Q        -0.831  -0.939  -0.937  -0.391  -0.536  -0.562  -0.881  -1.009  -0.999
33    N        -0.490  -0.410  -0.244  -0.456  -0.336  -0.142  -0.881  -0.754  -0.519
34    S        -0.831  -0.947  -0.943  -0.883  -1.054  -1.089  -0.881  -1.019  -1.006
35    K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
36    S         0.224   0.105  -0.149   0.362   0.244  -0.087   0.251   0.079  -0.353
37    A        -0.383  -0.400  -0.242  -0.690  -0.701  -0.427  -0.693  -0.736  -0.515
38    S         0.961   0.968   1.028   0.920   0.944   1.026   1.007   1.016   1.109
39    L         0.961   0.968   1.028   1.183   1.185   1.243   1.007   1.016   1.109
40    F         0.961   0.968   1.028   1.222   1.225   1.276   1.007   1.016   1.109
41    K        -1.808  -1.573  -1.506  -1.752  -1.434  -1.268  -1.731  -1.486  -1.327
42    Q         0.961   0.968   1.028   1.190   1.199   1.250   1.007   1.016   1.109
43    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
44    K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
45    N         0.961   0.968   1.028   1.299   1.283   1.340   1.007   1.016   1.109
46    P         0.961   0.968   1.028   1.292   1.281   1.334   1.007   1.016   1.109
47    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
48    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
49    I        -0.831  -0.663  -0.908  -0.387  -0.235  -0.568  -0.881  -0.714  -0.962
50    A        -0.490  -0.417  -0.243  -0.965  -0.837  -0.547  -0.881  -0.766  -0.516
51    W         0.961   0.968   1.028   1.380   1.369   1.407   1.007   1.016   1.109
52    T         0.961   0.968   1.028   1.241   1.238   1.292   1.007   1.016   1.109
53    V         0.961   0.968   1.028   1.067   1.071   1.147   1.007   1.016   1.109
54    L         0.961   0.968   1.028   1.183   1.185   1.243   1.007   1.016   1.109
55    F         0.224   0.320  -0.133   0.774   0.852   0.239   0.251   0.375  -0.325
56    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
57    K         0.224   0.320  -0.133   0.088   0.210  -0.504   0.251   0.375  -0.325
58    H        -1.728  -1.758  -1.505  -1.181  -1.294  -1.096  -1.637  -1.637  -1.326
59    H         0.961   0.968   1.028   1.322   1.316   1.359   1.007   1.016   1.109
60    K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
61    K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
62    G         0.961   0.968   1.028   1.115   1.113   1.187   1.007   1.016   1.109
63    I         0.961   0.968   1.028   1.202   1.200   1.259   1.007   1.016   1.109
64    T        -0.490  -0.404  -0.240  -0.554  -0.432  -0.201  -0.881  -0.743  -0.511
65    E         0.961   0.968   1.028   1.119   1.119   1.191   1.007   1.016   1.109
66    E         0.961   0.968   1.028   1.119   1.119   1.191   1.007   1.016   1.109
67    V        -1.466  -1.266  -1.466  -1.081  -0.849  -1.222  -1.353  -1.156  -1.286
68    A         0.224   0.105  -0.149   0.078  -0.053  -0.403   0.251   0.079  -0.353
69    K         0.224   0.365  -0.127  -0.181   0.027  -0.625   0.251   0.432  -0.316
70    K         0.224   0.345  -0.129  -0.181   0.005  -0.628   0.251   0.407  -0.319
71    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
72    S        -0.490  -0.433  -0.247  -0.503  -0.441  -0.200  -0.881  -0.796  -0.524
73    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
74    K        -0.383  -0.400  -0.242  -1.101  -1.108  -0.813  -0.693  -0.736  -0.515
75    T        -0.158  -0.148  -0.216   0.129   0.120  -0.107  -0.315  -0.309  -0.469
76    V         0.961   0.968   1.028   1.067   1.071   1.147   1.007   1.016   1.109
77    K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
78    A        -1.018  -0.871  -0.951  -1.011  -0.847  -0.786  -1.165  -0.994  -1.019
79    Q         0.224   0.105  -0.149   0.609   0.466   0.046   0.251   0.079  -0.353
80    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
81    P        -1.018  -0.936  -0.960  -1.131  -1.028  -0.896  -1.165  -1.086  -1.031
82    I         0.224   0.365  -0.127   0.621   0.757   0.092   0.251   0.432  -0.316
83    T         0.224   0.320  -0.133   0.508   0.601   0.045   0.251   0.375  -0.325
84    G         0.961   0.968   1.028   1.115   1.113   1.187   1.007   1.016   1.109
85    A         0.961   0.968   1.028   0.679   0.703   0.825   1.007   1.016   1.109
86    S        -0.158  -0.173  -0.164  -0.076  -0.093  -0.083  -0.315  -0.351  -0.378
87    L         0.961   0.968   1.028   1.183   1.185   1.243   1.007   1.016   1.109
88    D        -0.490  -0.435  -0.247  -0.380  -0.304  -0.061  -0.881  -0.799  -0.524
89    L        -0.490  -0.421  -0.236  -0.460  -0.387  -0.135  -0.881  -0.774  -0.504
90    I         0.961   0.968   1.028   1.202   1.200   1.259   1.007   1.016   1.109
91    K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
92    E         0.961   0.968   1.028   1.119   1.119   1.191   1.007   1.016   1.109
93    R        -0.383  -0.397  -0.243  -0.951  -1.026  -0.786  -0.693  -0.732  -0.517
94    R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
95    S        -0.383  -0.397  -0.243  -0.383  -0.397  -0.169  -0.693  -0.732  -0.517
96    L        -1.605  -1.640  -1.498  -1.167  -1.199  -1.081  -1.542  -1.518  -1.318
97    K        -0.490  -0.421  -0.236  -1.286  -1.095  -0.761  -0.881  -0.774  -0.504
98    P         0.961   0.968   1.028   1.292   1.281   1.334   1.007   1.016   1.109
99    E        -0.158   0.010  -0.170   0.010   0.238  -0.103  -0.315  -0.061  -0.390
100   V        -1.466  -1.518  -1.489  -1.041  -1.135  -1.150  -1.353  -1.374  -1.309
101   R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
102   K        -1.466  -1.631  -1.503  -1.835  -2.009  -1.679  -1.353  -1.507  -1.323
103   A         0.961   0.968   1.028   0.679   0.703   0.825   1.007   1.016   1.109
104   N        -1.791  -1.529  -1.880  -1.594  -1.258  -1.655  -1.448  -1.193  -1.462
105   R         0.961   0.968   1.028   0.748   0.761   0.882   1.007   1.016   1.109
106   E        -1.605  -1.562  -1.498  -1.344  -1.375  -1.215  -1.542  -1.473  -1.319
107   E        -2.581  -2.257  -2.254  -2.477  -2.168  -2.039  -2.014  -1.725  -1.604
108   K        -1.018  -1.084  -0.973  -1.595  -1.602  -1.268  -1.165  -1.223  -1.045
109   L        -1.466  -1.412  -1.482  -1.198  -1.127  -1.431  -1.353  -1.292  -1.303
110   K        -0.831  -0.786  -0.930  -1.294  -1.142  -1.325  -0.881  -0.798  -0.990
111   A        -1.728  -1.686  -1.502  -1.997  -1.840  -1.612  -1.637  -1.561  -1.322
112   N        -2.053  -2.104  -1.923  -1.595  -1.817  -1.587  -1.731  -1.751  -1.496
113   K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
114   E        -0.831  -0.947  -0.943  -0.495  -0.684  -0.785  -0.881  -1.019  -1.006
115   K        -0.831  -0.786  -0.930  -1.367  -1.238  -1.507  -0.881  -0.798  -0.990
116   K         0.224   0.199  -0.124  -0.181  -0.167  -0.619   0.251   0.213  -0.311
117   R        -2.053  -2.104  -1.923  -2.419  -2.410  -2.035  -1.731  -1.751  -1.496
118   A        -0.483  -0.712  -0.926  -0.561  -0.865  -1.233  -0.409  -0.701  -0.985
119   E        -2.256  -2.162  -1.921  -1.808  -1.717  -1.467  -1.920  -1.807  -1.496
120   K        -1.466  -1.631  -1.503  -1.713  -1.875  -1.631  -1.353  -1.507  -1.323
121   A        -0.831  -0.939  -0.937  -0.971  -1.100  -1.047  -0.881  -1.009  -0.999
122   A        -0.831  -0.939  -0.937  -0.965  -1.117  -1.120  -0.881  -1.009  -0.999
123   R        -0.383  -0.400  -0.242  -0.951  -1.033  -0.782  -0.693  -0.736  -0.515
124   K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
125   A         0.224   0.365  -0.127   0.078   0.246  -0.368   0.251   0.432  -0.316
126   E        -0.831  -0.939  -0.937  -0.518  -0.701  -0.805  -0.881  -1.009  -0.999
127   K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
128   A         0.961   0.968   1.028   0.679   0.703   0.825   1.007   1.016   1.109
129   K         0.224   0.105  -0.149  -0.190  -0.301  -0.693   0.251   0.079  -0.353
130   S        -2.053  -1.961  -1.900  -1.630  -1.469  -1.422  -1.731  -1.611  -1.478
131   A        -0.158  -0.150  -0.220  -0.381  -0.365  -0.438  -0.315  -0.312  -0.477
132   G         0.224   0.320  -0.133   0.104   0.219  -0.298   0.251   0.375  -0.325
133   V        -1.605  -1.561  -1.493  -1.683  -1.584  -1.366  -1.542  -1.471  -1.314
134   Q        -1.808  -1.771  -1.503  -1.481  -1.432  -1.075  -1.731  -1.649  -1.323
135   G        -1.077  -1.091  -0.967  -1.327  -1.364  -1.237  -1.259  -1.231  -1.039
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   S        -1.466  -1.631  -1.503  -1.372  -1.639  -1.465  -1.353  -1.507  -1.323
138   K        -1.466  -1.454  -1.485  -1.729  -1.714  -1.659  -1.353  -1.344  -1.305
139   V        -0.158  -0.173  -0.164   0.034  -0.001  -0.021  -0.315  -0.351  -0.378
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   S        -0.158  -0.173  -0.164  -0.253  -0.285  -0.339  -0.315  -0.351  -0.378
142   K        -0.158  -0.173  -0.164  -0.567  -0.545  -0.475  -0.315  -0.351  -0.378
143   Q        -0.831  -0.939  -0.937  -0.600  -0.774  -0.855  -0.881  -1.009  -0.999
144   Q        -1.141  -1.200  -0.975  -0.761  -0.889  -0.626  -1.259  -1.335  -1.048
145   A         0.224   0.345  -0.129   0.078   0.225  -0.371   0.251   0.407  -0.319
146   K         0.961   0.968   1.028   0.448   0.506   0.634   1.007   1.016   1.109
147   G         0.961   0.968   1.028   1.115   1.109   1.187   1.007   1.016   1.109
148   A        -0.303  -0.323  -0.241  -0.646  -0.681  -0.544  -0.554  -0.602  -0.513
149   F        -0.721  -1.035  -0.970  -0.253  -0.742  -0.762  -0.710  -1.120  -1.040
150   Q        -0.721  -1.035  -0.970  -0.219  -0.655  -0.625  -0.710  -1.120  -1.040
151   K         0.961   0.968   1.028   0.420   0.483   0.610   1.007   1.016   1.109
152   V         0.961   0.968   1.028   1.089   1.094   1.166   1.007   1.016   1.109
153   A        -1.791  -1.696  -1.874  -1.628  -1.496  -1.712  -1.448  -1.353  -1.457
154   A         0.961   0.968   1.028   0.679   0.703   0.825   1.007   1.016   1.109
155   T        -0.831  -0.947  -0.943  -0.595  -0.836  -1.040  -0.881  -1.019  -1.006
156   S        -0.158  -0.173  -0.164  -0.234  -0.266  -0.311  -0.315  -0.351  -0.378
157   R         0.224   0.206  -0.123   0.202   0.187  -0.151   0.251   0.223  -0.309
* 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/P24000
Output conservation file - output/P24000
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
