1     M         0.918   0.967   0.998   1.087   1.158   1.190   0.976   1.040   1.092
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     S        -0.162  -0.260  -0.151  -0.294  -0.463  -0.272  -0.442  -0.628  -0.470
5     K         0.178  -0.054  -0.080   0.148  -0.145  -0.187   0.125  -0.255  -0.337
6     V        -0.162  -0.042  -0.108  -0.179   0.011  -0.139  -0.442  -0.234  -0.389
7     P         0.918   0.967   0.998   0.835   0.898   0.967   0.976   1.040   1.092
8     R         0.918   0.967   0.998   1.035   1.105   1.143   0.976   1.040   1.092
9     N        -0.162   0.012  -0.099  -0.281   0.023  -0.221  -0.442  -0.142  -0.373
10    F         0.918   0.967   0.998   1.108   1.195   1.208   0.976   1.040   1.092
11    R        -0.315  -0.187  -0.129  -0.619  -0.401  -0.311  -0.726  -0.492  -0.427
12    L         0.918   0.967   0.998   0.741   0.817   0.883   0.976   1.040   1.092
13    L         0.918   0.967   0.998   0.741   0.817   0.883   0.976   1.040   1.092
14    E         0.178  -0.054  -0.080   0.110  -0.218  -0.237   0.125  -0.255  -0.337
15    E         0.918   0.967   0.998   0.769   0.846   0.908   0.976   1.040   1.092
16    L         0.918   0.967   0.998   0.741   0.817   0.883   0.976   1.040   1.092
17    E         0.918   0.967   0.998   0.769   0.846   0.908   0.976   1.040   1.092
18    K         0.918   0.967   0.998   0.797   0.894   0.932   0.976   1.040   1.092
19    G         0.918   0.967   0.998   0.896   0.949   1.020   0.976   1.040   1.092
20    E         0.918   0.967   0.998   0.769   0.846   0.908   0.976   1.040   1.092
21    K         0.918   0.967   0.998   0.797   0.894   0.932   0.976   1.040   1.092
22    G         0.918   0.967   0.998   0.896   0.949   1.020   0.976   1.040   1.092
23    F        -0.520  -0.634  -0.763  -0.544  -0.718  -0.826  -0.584  -0.755  -0.911
24    G         0.918   0.967   0.998   0.896   0.949   1.020   0.976   1.040   1.092
25    P        -0.895  -0.859  -0.797  -1.071  -0.999  -0.910  -1.152  -1.056  -0.958
26    E        -0.520  -0.766  -0.780  -0.608  -1.007  -1.027  -0.584  -0.913  -0.934
27    S         0.178  -0.054  -0.080   0.197  -0.115  -0.168   0.125  -0.255  -0.337
28    C        -0.162  -0.042  -0.108  -0.071   0.128  -0.051  -0.442  -0.234  -0.389
29    S         0.918   0.967   0.998   0.857   0.953   0.986   0.976   1.040   1.092
30    Y         0.918   0.967   0.998   1.061   1.129   1.167   0.976   1.040   1.092
31    G         0.918   0.967   0.998   0.896   0.949   1.020   0.976   1.040   1.092
32    L         0.918   0.967   0.998   0.741   0.817   0.883   0.976   1.040   1.092
33    A        -1.388  -1.365  -1.283  -1.463  -1.479  -1.339  -1.435  -1.373  -1.236
34    D        -0.315  -0.257  -0.150  -0.493  -0.399  -0.239  -0.726  -0.621  -0.467
35    S        -1.523  -1.532  -1.297  -1.530  -1.585  -1.211  -1.577  -1.528  -1.250
36    D         0.178  -0.054  -0.080   0.297  -0.080  -0.181   0.125  -0.255  -0.337
37    D         0.918   0.967   0.998   1.008   1.084   1.120   0.976   1.040   1.092
38    I         0.918   0.967   0.998   0.955   1.025   1.073   0.976   1.040   1.092
39    T         0.178  -0.054  -0.080   0.185  -0.173  -0.280   0.125  -0.255  -0.337
40    M         0.238   0.213  -0.014   0.453   0.431   0.011   0.216   0.179  -0.218
41    T         0.238   0.213  -0.014   0.281   0.227  -0.106   0.216   0.179  -0.218
42    K        -2.211  -2.202  -1.975  -1.966  -1.920  -1.593  -1.847  -1.777  -1.516
43    W         0.918   0.967   0.998   1.156   1.196   1.251   0.976   1.040   1.092
44    N         0.238   0.016  -0.033   0.340  -0.025  -0.083   0.216  -0.135  -0.252
45    G         0.238   0.213  -0.014   0.311   0.342  -0.033   0.216   0.179  -0.218
46    T         0.918   0.967   0.998   0.898   0.937   1.022   0.976   1.040   1.092
47    I         0.918   0.967   0.998   0.951   0.989   1.069   0.976   1.040   1.092
48    L         0.238   0.016  -0.033   0.170  -0.059  -0.155   0.216  -0.135  -0.252
49    G         0.918   0.967   0.998   0.898   1.025   1.022   0.976   1.040   1.092
50    P         0.918   0.967   0.998   0.813   0.799   0.947   0.976   1.040   1.092
51    P         0.238   0.213  -0.014   0.227   0.118  -0.103   0.216   0.179  -0.218
52    H         0.918   0.967   0.998   1.114   1.130   1.213   0.976   1.040   1.092
53    S         0.238   0.016  -0.033   0.252  -0.013  -0.157   0.216  -0.135  -0.252
54    N        -1.020  -1.032  -1.234  -0.801  -0.870  -1.126  -0.979  -0.962  -1.183
55    H         0.918   0.967   0.998   1.114   1.130   1.213   0.976   1.040   1.092
56    E         0.918   0.967   0.998   0.788   0.948   0.925   0.976   1.040   1.092
57    N         0.918   0.967   0.998   0.951   0.988   1.069   0.976   1.040   1.092
58    R         0.918   0.967   0.998   1.033   1.092   1.142   0.976   1.040   1.092
59    I         0.918   0.967   0.998   0.951   0.989   1.069   0.976   1.040   1.092
60    Y         0.918   0.967   0.998   1.062   1.112   1.167   0.976   1.040   1.092
61    S         0.238   0.016  -0.033   0.236  -0.035  -0.198   0.216  -0.135  -0.252
62    L        -0.097   0.100  -0.060  -0.319   0.025  -0.250  -0.327   0.002  -0.301
63    S        -1.898  -1.703  -1.657  -2.137  -1.821  -1.761  -1.739  -1.524  -1.400
64    I        -0.410  -0.628  -0.753  -0.258  -0.591  -0.809  -0.436  -0.727  -0.897
65    D        -1.585  -1.424  -1.604  -1.467  -1.195  -1.454  -1.413  -1.208  -1.352
66    C         0.918   0.967   0.998   1.137   1.211   1.234   0.976   1.040   1.092
67    G        -0.276  -0.216  -0.133  -0.481  -0.329  -0.255  -0.653  -0.546  -0.435
68    P        -1.272  -1.223  -1.266  -1.302  -1.301  -1.247  -1.304  -1.251  -1.220
69    N        -1.349  -1.223  -1.262  -1.465  -1.256  -1.301  -1.413  -1.236  -1.216
70    Y         0.918   0.967   0.998   1.062   1.112   1.167   0.976   1.040   1.092
71    P         0.918   0.967   0.998   0.813   0.799   0.947   0.976   1.040   1.092
72    D        -0.410  -0.579  -0.725  -0.234  -0.461  -0.798  -0.436  -0.668  -0.860
73    S        -1.780  -1.700  -1.644  -1.869  -1.639  -1.596  -1.630  -1.499  -1.388
74    P         0.918   0.967   0.998   0.813   0.799   0.947   0.976   1.040   1.092
75    P         0.918   0.967   0.998   0.813   0.799   0.947   0.976   1.040   1.092
76    K        -1.467  -1.522  -1.292  -1.658  -1.739  -1.347  -1.522  -1.518  -1.245
77    V        -0.097  -0.160  -0.124  -0.072  -0.257  -0.178  -0.327  -0.442  -0.419
78    T        -1.272  -1.344  -1.268  -1.267  -1.389  -1.209  -1.304  -1.341  -1.221
79    F         0.918   0.967   0.998   1.109   1.204   1.209   0.976   1.040   1.092
80    I        -0.333  -0.275  -0.154  -0.531  -0.494  -0.243  -0.761  -0.655  -0.474
81    S         0.918   0.967   0.998   0.863   0.975   0.991   0.976   1.040   1.092
82    K        -0.410  -0.666  -0.730  -0.341  -0.652  -0.748  -0.436  -0.774  -0.866
83    I         0.918   0.967   0.998   0.951   0.989   1.069   0.976   1.040   1.092
84    N         0.918   0.967   0.998   0.951   0.988   1.069   0.976   1.040   1.092
85    L         0.238   0.258  -0.042   0.139   0.231  -0.250   0.216   0.248  -0.267
86    P         0.918   0.967   0.998   0.813   0.799   0.947   0.976   1.040   1.092
87    C        -0.097  -0.220  -0.133   0.021  -0.219  -0.141  -0.327  -0.553  -0.436
88    V         0.238   0.315  -0.011   0.420   0.478   0.035   0.216   0.331  -0.213
89    N        -0.841  -0.939  -0.792  -0.924  -1.049  -0.848  -1.087  -1.148  -0.953
90    P        -2.093  -1.862  -1.929  -1.912  -1.524  -1.787  -1.739  -1.483  -1.482
91    T        -1.325  -1.238  -1.266  -1.340  -1.227  -1.280  -1.341  -1.207  -1.218
92    T        -1.585  -1.641  -1.645  -1.399  -1.530  -1.488  -1.413  -1.445  -1.388
93    G         0.918   0.967   0.998   0.898   1.025   1.022   0.976   1.040   1.092
94    E        -1.780  -1.749  -1.653  -1.773  -1.687  -1.522  -1.630  -1.556  -1.396
95    V         0.918   0.967   0.998   1.024   1.053   1.133   0.976   1.040   1.092
96    -        -2.238  -2.150  -1.969  -2.103  -1.992  -1.728  -1.861  -1.738  -1.512
97    Q        -1.780  -1.504  -1.622  -1.817  -1.490  -1.516  -1.630  -1.302  -1.369
98    T        -2.093  -2.142  -1.965  -2.001  -2.046  -1.779  -1.739  -1.732  -1.509
99    D        -2.093  -2.061  -1.958  -1.995  -1.921  -1.781  -1.739  -1.671  -1.504
100   F        -1.020  -1.255  -1.263  -0.699  -1.068  -1.173  -0.979  -1.231  -1.214
101   H        -1.780  -1.759  -1.655  -1.625  -1.649  -1.493  -1.630  -1.560  -1.397
102   T        -0.959  -1.003  -0.828  -1.057  -1.179  -0.842  -1.196  -1.229  -0.996
103   L         0.918   0.967   0.998   0.743   0.879   0.884   0.976   1.040   1.092
104   R        -0.841  -0.823  -0.789  -0.994  -0.923  -0.832  -1.087  -1.034  -0.950
105   D        -1.467  -1.324  -1.280  -1.454  -1.256  -1.191  -1.522  -1.344  -1.234
106   W         0.918   0.967   0.998   1.156   1.196   1.251   0.976   1.040   1.092
107   K         0.238   0.016  -0.033   0.202  -0.082  -0.198   0.216  -0.135  -0.252
108   R         0.918   0.967   0.998   1.033   1.092   1.142   0.976   1.040   1.092
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   -        -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   A        -1.585  -1.617  -1.625  -1.565  -1.659  -1.694  -1.413  -1.427  -1.370
124   Y        -0.410  -0.628  -0.753  -0.171  -0.542  -0.780  -0.436  -0.727  -0.897
125   T        -0.841  -0.733  -0.781  -1.056  -0.939  -0.926  -1.087  -0.951  -0.941
126   M         0.238   0.016  -0.033   0.453   0.126  -0.028   0.216  -0.135  -0.252
127   E         0.918   0.967   0.998   0.788   0.948   0.925   0.976   1.040   1.092
128   T         0.238   0.016  -0.033   0.311  -0.019  -0.064   0.216  -0.135  -0.252
129   L        -1.272  -1.257  -1.245  -1.189  -1.190  -1.179  -1.304  -1.249  -1.196
130   L         0.918   0.967   0.998   0.743   0.879   0.884   0.976   1.040   1.092
131   L         0.238   0.016  -0.033   0.139  -0.118  -0.236   0.216  -0.135  -0.252
132   D        -0.841  -0.950  -0.785  -1.026  -1.066  -0.870  -1.087  -1.164  -0.945
133   L         0.238   0.016  -0.033   0.139  -0.118  -0.236   0.216  -0.135  -0.252
134   R         0.238   0.213  -0.014   0.410   0.373  -0.009   0.216   0.179  -0.218
135   K         0.918   0.967   0.998   0.813   0.930   0.947   0.976   1.040   1.092
136   E        -1.272  -1.372  -1.276  -1.383  -1.412  -1.318  -1.304  -1.366  -1.228
137   M         0.918   0.967   0.998   1.086   1.158   1.188   0.976   1.040   1.092
138   A        -0.410  -0.628  -0.753  -0.168  -0.492  -0.781  -0.436  -0.727  -0.897
139   T        -1.388  -1.365  -1.281  -1.466  -1.407  -1.232  -1.435  -1.353  -1.233
140   P         0.178   0.073  -0.060   0.122  -0.101  -0.264   0.125  -0.042  -0.301
141   A        -1.272  -1.314  -1.254  -1.217  -1.297  -1.259  -1.304  -1.319  -1.207
142   N         0.238   0.016  -0.033   0.371   0.028  -0.002   0.216  -0.135  -0.252
143   K        -0.097  -0.105  -0.132  -0.248  -0.233  -0.305  -0.327  -0.344  -0.434
144   K         0.918   0.967   0.998   0.813   0.930   0.947   0.976   1.040   1.092
145   L         0.918   0.967   0.998   0.743   0.879   0.884   0.976   1.040   1.092
146   R        -2.093  -1.737  -1.925  -1.947  -1.556  -1.689  -1.739  -1.361  -1.480
147   Q         0.918   0.967   0.998   1.123   1.171   1.222   0.976   1.040   1.092
148   P         0.918   0.967   0.998   0.813   0.799   0.947   0.976   1.040   1.092
149   K        -2.093  -1.826  -1.941  -2.041  -1.732  -1.819  -1.739  -1.448  -1.491
150   E         0.918   0.967   0.998   0.788   0.948   0.925   0.976   1.040   1.092
151   G         0.918   0.967   0.998   0.898   1.025   1.022   0.976   1.040   1.092
152   E        -0.707  -0.492  -0.737  -0.839  -0.470  -0.906  -0.870  -0.555  -0.878
153   T         0.238   0.016  -0.033   0.274  -0.077  -0.160   0.216  -0.135  -0.252
154   F        -0.333  -0.268  -0.143  -0.391  -0.300  -0.102  -0.761  -0.643  -0.453
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     *
* 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/P53152
Output conservation file - output/P53152
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
