1     M         1.155   1.167   1.240   1.335   1.352   1.448   1.225   1.245   1.354
2     T        -1.456  -1.448  -1.279  -1.328  -1.315  -1.045  -1.382  -1.364  -1.136
3     Q        -0.853  -0.855  -0.756  -0.659  -0.702  -0.552  -0.992  -1.005  -0.856
4     L        -0.929  -0.881  -0.747  -1.334  -1.242  -1.026  -1.092  -1.031  -0.844
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    K        -0.691  -0.669  -0.699  -0.705  -0.663  -0.691  -0.802  -0.755  -0.784
14    Y        -0.785  -0.815  -0.739  -0.771  -0.813  -0.696  -0.947  -0.972  -0.838
15    L        -0.383  -0.494  -0.669  -0.470  -0.611  -0.806  -0.368  -0.516  -0.743
16    L         0.363   0.434   0.117   0.186   0.278  -0.125   0.356   0.458  -0.057
17    L         0.363   0.293   0.105   0.218   0.140  -0.069   0.356   0.250  -0.079
18    V        -1.312  -1.209  -1.250  -1.367  -1.213  -1.320  -1.237  -1.147  -1.110
19    S         0.363   0.293   0.105   0.479   0.385   0.116   0.356   0.250  -0.079
20    R         1.155   1.167   1.240   1.217   1.235   1.339   1.225   1.245   1.354
21    Q         0.363   0.293   0.105   0.648   0.557   0.257   0.356   0.250  -0.079
22    G         0.363   0.293   0.105   0.628   0.533   0.210   0.356   0.250  -0.079
23    K         0.363   0.293   0.105   0.399   0.310   0.046   0.356   0.250  -0.079
24    I        -0.929  -0.915  -0.765  -1.121  -1.109  -0.876  -1.092  -1.076  -0.867
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    R         1.155   1.167   1.240   1.217   1.235   1.339   1.225   1.245   1.354
27    L         1.155   1.167   1.240   0.877   0.898   1.024   1.225   1.245   1.354
28    K        -1.312  -1.314  -1.264  -1.330  -1.346  -1.287  -1.237  -1.245  -1.123
29    K         0.363   0.348   0.106   0.383   0.366   0.013   0.356   0.333  -0.077
30    W         1.155   1.167   1.240   1.474   1.488   1.577   1.225   1.245   1.354
31    Y        -0.001  -0.077  -0.010   0.032  -0.107  -0.022  -0.223  -0.363  -0.282
32    T        -1.312  -1.331  -1.259  -1.046  -1.083  -0.976  -1.237  -1.258  -1.119
33    A        -0.691  -0.634  -0.718  -0.471  -0.397  -0.510  -0.802  -0.731  -0.810
34    M        -1.312  -1.239  -1.244  -1.570  -1.444  -1.369  -1.237  -1.148  -1.101
35    S         0.363   0.348   0.106   0.455   0.432   0.062   0.356   0.333  -0.077
36    A        -1.839  -1.794  -1.682  -1.608  -1.565  -1.366  -1.526  -1.483  -1.303
37    G         0.363   0.414   0.115   0.405   0.468   0.076   0.356   0.430  -0.061
38    E        -0.383  -0.468  -0.659  -0.315  -0.433  -0.719  -0.368  -0.480  -0.730
39    K         0.363   0.263   0.097   0.383   0.251  -0.002   0.356   0.203  -0.093
40    A        -0.691  -0.625  -0.696  -0.595  -0.480  -0.576  -0.802  -0.701  -0.779
41    K         1.155   1.167   1.240   1.086   1.102   1.217   1.225   1.245   1.354
42    I         1.155   1.167   1.240   1.013   1.038   1.151   1.225   1.245   1.354
43    V        -1.312  -1.251  -1.239  -1.493  -1.424  -1.375  -1.237  -1.182  -1.100
44    K        -0.164  -0.147  -0.025  -0.405  -0.378  -0.195  -0.513  -0.489  -0.309
45    D        -0.164  -0.121  -0.020  -0.458  -0.375  -0.231  -0.513  -0.443  -0.301
46    L        -0.164  -0.166  -0.029  -0.638  -0.625  -0.380  -0.513  -0.525  -0.317
47    T        -0.164  -0.164  -0.029  -0.294  -0.316  -0.104  -0.513  -0.521  -0.318
48    P        -1.312  -1.384  -1.266  -1.012  -1.117  -0.955  -1.237  -1.298  -1.124
49    T        -1.312  -1.249  -1.250  -1.492  -1.400  -1.362  -1.237  -1.165  -1.108
50    I        -0.164  -0.166  -0.029  -0.524  -0.522  -0.290  -0.513  -0.525  -0.317
51    L         0.363   0.263   0.097   0.138   0.002  -0.270   0.356   0.203  -0.093
52    A        -0.785  -0.831  -0.733  -0.819  -0.874  -0.703  -0.947  -0.987  -0.831
53    R         1.155   1.167   1.240   1.217   1.235   1.339   1.225   1.245   1.354
54    K        -0.164  -0.135  -0.019  -0.432  -0.385  -0.200  -0.513  -0.467  -0.300
55    P        -1.312  -1.317  -1.255  -0.999  -0.993  -0.944  -1.237  -1.227  -1.112
56    K         0.363   0.293   0.105   0.383   0.292   0.011   0.356   0.250  -0.079
57    M         1.155   1.167   1.240   1.335   1.352   1.448   1.225   1.245   1.354
58    C         1.155   1.167   1.240   1.417   1.428   1.524   1.225   1.245   1.354
59    N         1.155   1.167   1.240   1.305   1.319   1.421   1.225   1.245   1.354
60    I        -0.929  -0.902  -0.760  -1.166  -1.111  -0.880  -1.092  -1.063  -0.862
61    I        -0.383  -0.436  -0.656  -0.564  -0.636  -0.976  -0.368  -0.444  -0.725
62    E         1.155   1.167   1.240   1.075   1.092   1.208   1.225   1.245   1.354
63    Y         1.155   1.167   1.240   1.251   1.267   1.371   1.225   1.245   1.354
64    N        -1.074  -1.003  -1.225  -0.915  -0.820  -1.110  -0.947  -0.867  -1.081
65    D         0.363   0.263   0.097   0.480   0.354   0.113   0.356   0.203  -0.093
66    H        -1.694  -1.686  -1.679  -1.435  -1.425  -1.566  -1.382  -1.379  -1.300
67    K         1.155   1.167   1.240   1.086   1.102   1.217   1.225   1.245   1.354
68    V        -0.164  -0.136  -0.021  -0.524  -0.477  -0.287  -0.513  -0.470  -0.302
69    V         0.363   0.434   0.117   0.431   0.520   0.026   0.356   0.458  -0.057
70    Y         0.363   0.436   0.118   0.559   0.650   0.201   0.356   0.462  -0.056
71    K        -0.001   0.018   0.017  -0.074  -0.045  -0.100  -0.223  -0.197  -0.234
72    R         0.363   0.348   0.106   0.493   0.474   0.076   0.356   0.333  -0.077
73    Y         1.155   1.167   1.240   1.251   1.267   1.371   1.225   1.245   1.354
74    A         1.155   1.167   1.240   1.256   1.264   1.375   1.225   1.245   1.354
75    S         1.155   1.167   1.240   1.167   1.178   1.292   1.225   1.245   1.354
76    L         1.155   1.167   1.240   0.877   0.898   1.024   1.225   1.245   1.354
77    Y        -0.164  -0.136  -0.021  -0.251  -0.209  -0.038  -0.513  -0.470  -0.302
78    F         1.155   1.167   1.240   1.281   1.292   1.398   1.225   1.245   1.354
79    I        -0.001  -0.019  -0.001  -0.238  -0.268  -0.256  -0.223  -0.260  -0.267
80    V        -1.456  -1.401  -1.276  -1.381  -1.295  -1.132  -1.382  -1.328  -1.135
81    G         1.155   1.167   1.240   1.340   1.357   1.452   1.225   1.245   1.354
82    M        -1.074  -1.048  -1.200  -0.957  -0.913  -1.088  -0.947  -0.921  -1.055
83    T        -1.839  -1.832  -1.685  -1.724  -1.732  -1.502  -1.526  -1.515  -1.305
84    P        -1.694  -1.699  -1.677  -1.530  -1.544  -1.536  -1.382  -1.387  -1.298
85    D        -0.691  -0.668  -0.695  -0.677  -0.635  -0.692  -0.802  -0.754  -0.782
86    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    D         1.155   1.167   1.240   1.162   1.180   1.288   1.225   1.245   1.354
88    N         1.155   1.167   1.240   1.305   1.319   1.421   1.225   1.245   1.354
89    E         1.155   1.167   1.240   1.075   1.092   1.208   1.225   1.245   1.354
90    L         1.155   1.167   1.240   0.877   0.898   1.024   1.225   1.245   1.354
91    L        -0.164  -0.136  -0.021  -0.711  -0.648  -0.470  -0.513  -0.470  -0.302
92    T        -1.074  -1.012  -1.218  -0.788  -0.726  -1.063  -0.947  -0.887  -1.074
93    L         1.155   1.167   1.240   0.877   0.898   1.024   1.225   1.245   1.354
94    E         1.155   1.167   1.240   1.075   1.092   1.208   1.225   1.245   1.354
95    I        -0.383  -0.417  -0.653  -0.452  -0.493  -0.911  -0.368  -0.419  -0.722
96    I         1.155   1.167   1.240   1.013   1.038   1.151   1.225   1.245   1.354
97    H         1.155   1.167   1.240   1.412   1.431   1.519   1.225   1.245   1.354
98    R         0.363   0.263   0.097   0.493   0.354   0.059   0.356   0.203  -0.093
99    F        -0.001  -0.001   0.002   0.049   0.038   0.006  -0.223  -0.230  -0.261
100   V         1.155   1.167   1.240   1.167   1.177   1.292   1.225   1.245   1.354
101   E         1.155   1.167   1.240   1.075   1.092   1.208   1.225   1.245   1.354
102   T        -0.785  -0.832  -0.741  -0.644  -0.692  -0.540  -0.947  -0.989  -0.840
103   M         0.363   0.263   0.097   0.578   0.429   0.082   0.356   0.203  -0.093
104   D         1.155   1.167   1.240   1.162   1.180   1.288   1.225   1.245   1.354
105   T        -0.691  -0.657  -0.713  -0.737  -0.680  -0.749  -0.802  -0.748  -0.802
106   Y        -0.383  -0.214  -0.644  -0.186   0.042  -0.640  -0.368  -0.150  -0.710
107   F        -0.164  -0.135  -0.019  -0.251  -0.207  -0.035  -0.513  -0.467  -0.300
108   G         0.363   0.436   0.118   0.614   0.711   0.202   0.356   0.462  -0.056
109   N         1.155   1.167   1.240   1.305   1.319   1.421   1.225   1.245   1.354
110   V         1.155   1.167   1.240   1.167   1.177   1.292   1.225   1.245   1.354
111   C         1.155   1.167   1.240   1.417   1.428   1.524   1.225   1.245   1.354
112   E         1.155   1.167   1.240   1.075   1.092   1.208   1.225   1.245   1.354
113   L         1.155   1.167   1.240   0.877   0.898   1.024   1.225   1.245   1.354
114   D         1.155   1.167   1.240   1.162   1.180   1.288   1.225   1.245   1.354
115   I         0.363   0.263   0.097   0.254   0.113  -0.204   0.356   0.203  -0.093
116   I         1.155   1.167   1.240   1.013   1.038   1.151   1.225   1.245   1.354
117   F         1.155   1.167   1.240   1.281   1.292   1.398   1.225   1.245   1.354
118   N        -0.691  -0.669  -0.699  -0.529  -0.487  -0.564  -0.802  -0.755  -0.784
119   F         1.155   1.167   1.240   1.281   1.292   1.398   1.225   1.245   1.354
120   S        -1.839  -1.855  -1.696  -1.700  -1.734  -1.463  -1.526  -1.533  -1.313
121   K         1.155   1.167   1.240   1.086   1.102   1.217   1.225   1.245   1.354
122   V         0.363   0.414   0.115   0.545   0.602   0.157   0.356   0.430  -0.061
123   Y         1.155   1.167   1.240   1.251   1.267   1.371   1.225   1.245   1.354
124   D        -1.456  -1.423  -1.284  -1.346  -1.303  -1.108  -1.382  -1.342  -1.141
125   I         0.363   0.263   0.097   0.303   0.174  -0.085   0.356   0.203  -0.093
126   L         0.363   0.263   0.097   0.196   0.075  -0.132   0.356   0.203  -0.093
127   N        -0.383  -0.436  -0.656  -0.236  -0.322  -0.656  -0.368  -0.444  -0.725
128   E         1.155   1.167   1.240   1.075   1.092   1.208   1.225   1.245   1.354
129   M        -0.001   0.018   0.017  -0.300  -0.268  -0.243  -0.223  -0.197  -0.234
130   I        -0.691  -0.624  -0.717  -1.078  -0.979  -1.085  -0.802  -0.725  -0.808
131   M        -0.785  -0.728  -0.728  -1.034  -0.967  -0.959  -0.947  -0.886  -0.825
132   C        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   D        -0.001  -0.077  -0.010  -0.062  -0.199  -0.104  -0.223  -0.363  -0.282
134   G         1.155   1.167   1.240   1.340   1.357   1.452   1.225   1.245   1.354
135   S        -1.456  -1.391  -1.282  -1.518  -1.453  -1.248  -1.382  -1.318  -1.140
136   I        -0.164  -0.164  -0.029  -0.711  -0.724  -0.496  -0.513  -0.521  -0.318
137   A        -0.691  -0.657  -0.713  -0.568  -0.510  -0.659  -0.802  -0.748  -0.802
138   E         1.155   1.167   1.240   1.075   1.092   1.208   1.225   1.245   1.354
139   S         0.363   0.348   0.106   0.477   0.454   0.112   0.356   0.333  -0.077
140   S         1.155   1.167   1.240   1.167   1.178   1.292   1.225   1.245   1.354
141   R        -0.001   0.094   0.014  -0.149   0.002  -0.144  -0.223  -0.068  -0.239
142   K        -1.312  -1.334  -1.258  -1.322  -1.336  -1.213  -1.237  -1.246  -1.115
143   E        -0.001  -0.077  -0.010  -0.124  -0.250  -0.140  -0.223  -0.363  -0.282
144   V         1.155   1.167   1.240   1.167   1.177   1.292   1.225   1.245   1.354
145   L         0.363   0.348   0.106   0.138   0.124  -0.254   0.356   0.333  -0.077
146   H        -1.312  -1.367  -1.272  -1.141  -1.201  -1.113  -1.237  -1.277  -1.129
147   H        -1.839  -1.888  -1.700  -1.488  -1.547  -1.293  -1.526  -1.556  -1.317
148   V        -0.001  -0.001   0.002  -0.149  -0.160  -0.211  -0.223  -0.230  -0.261
149   T        -2.221  -2.234  -2.025  -2.050  -2.141  -1.800  -1.671  -1.676  -1.423
150   V        -0.929  -0.914  -0.763  -0.929  -0.917  -0.701  -1.092  -1.076  -0.866
151   M        -0.785  -0.832  -0.741  -0.632  -0.682  -0.544  -0.947  -0.989  -0.840
152   D         1.155   1.167   1.240   1.162   1.180   1.288   1.225   1.245   1.354
153   T        -1.312  -1.178  -1.237  -1.208  -1.000  -1.058  -1.237  -1.086  -1.094
154   M        -1.074  -1.135  -1.225  -1.221  -1.321  -1.430  -0.947  -1.020  -1.081
155   E         0.363   0.263   0.097   0.365   0.228  -0.032   0.356   0.203  -0.093
156   S        -1.413  -1.425  -1.286  -1.348  -1.398  -1.171  -1.337  -1.344  -1.143
157   N        -0.799  -0.841  -0.745  -0.671  -0.726  -0.598  -0.943  -0.981  -0.843
158   D         1.155   1.167   1.240   1.162   1.180   1.288   1.225   1.245   1.354
159   N        -2.221  -2.233  -2.039  -1.948  -1.955  -1.650  -1.671  -1.675  -1.432
160   L        -1.312  -1.367  -1.272  -1.469  -1.535  -1.346  -1.237  -1.277  -1.129
161   E        -1.312  -1.388  -1.257  -1.346  -1.436  -1.225  -1.237  -1.303  -1.116
162   R        -1.074  -1.012  -1.218  -0.852  -0.776  -1.106  -0.947  -0.887  -1.074
163   V        -1.312  -1.367  -1.272  -1.366  -1.419  -1.275  -1.237  -1.277  -1.129
164   L         0.363   0.293   0.105   0.165   0.076  -0.192   0.356   0.250  -0.079
165   S        -1.312  -1.367  -1.272  -1.259  -1.334  -1.199  -1.237  -1.277  -1.129
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -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/P35181
Output conservation file - output/P35181
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
