1     M         1.281   1.292   1.361   1.439   1.455   1.557   1.396   1.412   1.518
2     T        -0.337  -0.322  -0.352  -0.358  -0.349  -0.415  -0.541  -0.526  -0.557
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    P        -0.337  -0.355  -0.357  -0.536  -0.558  -0.546  -0.541  -0.566  -0.563
11    K        -0.881  -0.941  -0.847  -0.956  -1.018  -0.868  -0.956  -1.005  -0.875
12    I        -0.067   0.089  -0.255   0.007   0.215  -0.280  -0.126   0.094  -0.408
13    S         0.587   0.536   0.394   0.557   0.505   0.291   0.566   0.483   0.201
14    V         1.281   1.292   1.361   1.261   1.283   1.388   1.396   1.412   1.518
15    A         0.268   0.200   0.260   0.217   0.084   0.164   0.013  -0.122  -0.058
16    F         1.281   1.292   1.361   1.213   1.239   1.343   1.396   1.412   1.518
17    I         0.587   0.579   0.403   0.626   0.622   0.347   0.566   0.553   0.217
18    C         1.281   1.292   1.361   1.435   1.456   1.553   1.396   1.412   1.518
19    L         1.281   1.292   1.361   1.321   1.338   1.445   1.396   1.412   1.518
20    G         1.281   1.292   1.361   1.209   1.219   1.339   1.396   1.412   1.518
21    N         1.281   1.292   1.361   1.321   1.343   1.445   1.396   1.412   1.518
22    F         0.587   0.579   0.403   0.607   0.601   0.323   0.566   0.553   0.217
23    C         1.281   1.292   1.361   1.435   1.456   1.553   1.396   1.412   1.518
24    R         1.281   1.292   1.361   1.360   1.376   1.481   1.396   1.412   1.518
25    S         1.281   1.292   1.361   1.173   1.202   1.305   1.396   1.412   1.518
26    P         0.587   0.484   0.388   0.769   0.635   0.475   0.566   0.395   0.189
27    M         1.281   1.292   1.361   1.441   1.475   1.559   1.396   1.412   1.518
28    A         1.281   1.292   1.361   1.303   1.308   1.428   1.396   1.412   1.518
29    E         1.281   1.292   1.361   1.234   1.237   1.362   1.396   1.412   1.518
30    A         0.643   0.545   0.435   0.735   0.589   0.427   0.655   0.497   0.276
31    I         0.161   0.192   0.263  -0.056   0.038   0.094  -0.193  -0.137  -0.051
32    F         1.281   1.292   1.361   1.215   1.235   1.344   1.396   1.412   1.518
33    K        -0.243  -0.344  -0.351  -0.342  -0.485  -0.473  -0.404  -0.538  -0.553
34    H        -0.536  -0.661  -0.788  -0.273  -0.469  -0.712  -0.510  -0.662  -0.805
35    E        -1.652  -1.610  -1.514  -1.492  -1.421  -1.296  -1.358  -1.313  -1.167
36    V         0.329   0.262   0.277   0.266   0.177   0.148   0.125  -0.003  -0.024
37    E        -0.368  -0.322  -0.339  -0.608  -0.570  -0.517  -0.616  -0.559  -0.544
38    K        -0.844  -0.820  -0.822  -1.011  -0.985  -0.942  -0.934  -0.894  -0.851
39    A        -1.652  -1.610  -1.514  -1.484  -1.412  -1.291  -1.358  -1.313  -1.167
40    N        -0.243  -0.290  -0.305  -0.315  -0.390  -0.411  -0.404  -0.452  -0.486
41    L        -0.368  -0.385  -0.356  -0.432  -0.460  -0.416  -0.616  -0.630  -0.566
42    E        -1.248  -1.252  -1.200  -1.296  -1.321  -1.219  -1.146  -1.137  -1.037
43    N        -1.945  -1.916  -1.779  -1.825  -1.817  -1.597  -1.464  -1.429  -1.255
44    R        -1.065  -0.971  -1.144  -0.826  -0.690  -0.986  -0.934  -0.827  -0.981
45    F         0.643   0.545   0.435   0.653   0.532   0.361   0.655   0.497   0.276
46    N        -1.248  -1.267  -1.206  -1.347  -1.385  -1.276  -1.146  -1.157  -1.044
47    K        -0.955  -0.926  -0.851  -1.096  -1.048  -0.918  -1.040  -0.994  -0.881
48    I         1.281   1.292   1.361   1.253   1.290   1.381   1.396   1.412   1.518
49    D         0.643   0.730   0.456   0.670   0.745   0.408   0.655   0.785   0.315
50    S         1.281   1.292   1.361   1.176   1.225   1.307   1.396   1.412   1.518
51    F        -0.368  -0.338  -0.362  -0.421  -0.343  -0.363  -0.616  -0.587  -0.573
52    G         1.281   1.292   1.361   1.207   1.209   1.337   1.396   1.412   1.518
53    T         1.281   1.292   1.361   1.367   1.390   1.488   1.396   1.412   1.518
54    S        -0.551  -0.495  -0.397  -0.855  -0.772  -0.615  -0.828  -0.753  -0.615
55    N        -0.243  -0.295  -0.330  -0.304  -0.414  -0.431  -0.404  -0.488  -0.524
56    Y        -0.243  -0.260  -0.329  -0.096  -0.136  -0.233  -0.404  -0.421  -0.523
57    H         1.281   1.292   1.361   1.397   1.404   1.517   1.396   1.412   1.518
58    V         0.161   0.183   0.249  -0.056   0.020   0.066  -0.193  -0.154  -0.079
59    G         1.281   1.292   1.361   1.207   1.209   1.337   1.396   1.412   1.518
60    E        -0.243  -0.248  -0.330  -0.305  -0.335  -0.446  -0.404  -0.406  -0.524
61    S        -1.541  -1.574  -1.519  -1.362  -1.400  -1.305  -1.252  -1.273  -1.169
62    P         1.281   1.292   1.361   1.385   1.421   1.506   1.396   1.412   1.518
63    D         1.281   1.292   1.361   1.234   1.220   1.362   1.396   1.412   1.518
64    H        -1.065  -1.172  -1.194  -0.918  -1.053  -1.078  -0.934  -1.041  -1.029
65    R         1.281   1.292   1.361   1.348   1.371   1.471   1.396   1.412   1.518
66    T         0.108   0.137   0.247  -0.150  -0.059   0.092  -0.299  -0.246  -0.083
67    V        -1.359  -1.367  -1.232  -1.342  -1.291  -1.136  -1.252  -1.241  -1.066
68    S        -0.551  -0.506  -0.410  -0.914  -0.828  -0.693  -0.828  -0.764  -0.631
69    I        -0.243  -0.265  -0.332  -0.178  -0.199  -0.345  -0.404  -0.439  -0.526
70    C         0.329   0.269   0.295   0.437   0.381   0.334   0.125   0.010   0.012
71    K        -0.844  -0.900  -0.827  -0.906  -0.976  -0.849  -0.934  -0.973  -0.856
72    Q        -1.065  -1.107  -1.164  -1.020  -1.092  -1.169  -0.934  -0.977  -1.001
73    H         0.161   0.177   0.242   0.088   0.109   0.184  -0.193  -0.167  -0.094
74    G         0.329   0.335   0.291   0.210   0.206   0.128   0.125   0.132   0.004
75    V         0.329   0.269   0.295   0.250   0.182   0.158   0.125   0.010   0.012
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    K        -0.536  -0.637  -0.758  -0.275  -0.424  -0.651  -0.510  -0.634  -0.770
78    I        -0.844  -0.895  -0.822  -0.869  -0.893  -0.795  -0.934  -0.969  -0.852
79    N        -1.359  -1.350  -1.232  -1.517  -1.492  -1.321  -1.252  -1.230  -1.066
80    H         1.281   1.292   1.361   1.397   1.404   1.517   1.396   1.412   1.518
81    K        -1.945  -1.909  -1.780  -1.768  -1.725  -1.554  -1.464  -1.425  -1.256
82    G         0.329   0.315   0.278   0.269   0.222   0.129   0.125   0.095  -0.022
83    K        -0.368  -0.372  -0.364  -0.402  -0.418  -0.407  -0.616  -0.621  -0.576
84    Q        -0.243  -0.318  -0.352  -0.216  -0.370  -0.433  -0.404  -0.517  -0.554
85    I        -0.243  -0.344  -0.351  -0.263  -0.381  -0.437  -0.404  -0.538  -0.553
86    K        -1.359  -1.289  -1.224  -1.443  -1.329  -1.213  -1.252  -1.184  -1.060
87    T        -1.248  -1.272  -1.211  -1.241  -1.256  -1.171  -1.146  -1.161  -1.048
88    K        -0.368  -0.278  -0.335  -0.637  -0.486  -0.533  -0.616  -0.498  -0.536
89    H         0.161   0.215   0.278  -0.010   0.044   0.171  -0.193  -0.093  -0.022
90    F         1.281   1.292   1.361   1.215   1.235   1.344   1.396   1.412   1.518
91    D        -0.772  -0.771  -0.810  -0.868  -0.915  -0.898  -0.828  -0.836  -0.838
92    E        -1.248  -1.261  -1.211  -1.287  -1.337  -1.225  -1.146  -1.149  -1.048
93    Y         0.643   0.646   0.449   0.669   0.676   0.418   0.655   0.658   0.302
94    D         1.281   1.292   1.361   1.234   1.220   1.362   1.396   1.412   1.518
95    Y         1.281   1.292   1.361   1.363   1.361   1.485   1.396   1.412   1.518
96    I         0.329   0.383   0.336   0.240   0.355   0.228   0.125   0.220   0.090
97    I         0.161   0.139   0.236  -0.090  -0.130   0.003  -0.193  -0.242  -0.104
98    G        -0.551  -0.515  -0.415  -0.651  -0.594  -0.470  -0.828  -0.773  -0.638
99    M         1.281   1.292   1.361   1.441   1.475   1.559   1.396   1.412   1.518
100   D         1.281   1.292   1.361   1.234   1.220   1.362   1.396   1.412   1.518
101   E        -1.065  -1.137  -1.187  -0.906  -1.019  -1.097  -0.934  -1.007  -1.023
102   S         0.643   0.545   0.435   0.621   0.526   0.341   0.655   0.497   0.276
103   N         1.281   1.292   1.361   1.314   1.344   1.438   1.396   1.412   1.518
104   I        -0.536  -0.445  -0.709  -0.319  -0.178  -0.587  -0.510  -0.395  -0.711
105   N        -1.248  -1.154  -1.177  -1.191  -1.048  -1.107  -1.146  -1.045  -1.018
106   N        -0.243  -0.203  -0.312  -0.255  -0.215  -0.396  -0.404  -0.367  -0.500
107   L         0.329   0.307   0.292   0.298   0.279   0.194   0.125   0.081   0.006
108   K        -1.652  -1.609  -1.525  -1.574  -1.499  -1.374  -1.358  -1.312  -1.175
109   K        -0.536  -0.470  -0.719  -0.316  -0.225  -0.620  -0.510  -0.425  -0.723
110   I        -0.844  -0.808  -0.813  -0.838  -0.750  -0.751  -0.934  -0.885  -0.842
111   Q         0.161   0.162   0.248  -0.111  -0.119   0.031  -0.193  -0.197  -0.081
112   P         0.643   0.545   0.435   0.840   0.734   0.552   0.655   0.497   0.276
113   E        -0.844  -0.842  -0.820  -0.925  -0.914  -0.858  -0.934  -0.919  -0.850
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   G        -0.955  -0.971  -0.855  -1.107  -1.143  -0.937  -1.040  -1.039  -0.885
116   S         0.036   0.016  -0.218   0.074   0.064  -0.281   0.019  -0.016  -0.354
117   K         0.329   0.368   0.308   0.154   0.208   0.115   0.125   0.191   0.037
118   A         0.643   0.683   0.453   0.757   0.797   0.505   0.655   0.715   0.309
119   K        -0.955  -0.874  -0.845  -1.083  -0.971  -0.902  -1.040  -0.943  -0.874
120   V         0.036   0.186  -0.197   0.163   0.392  -0.172   0.019   0.228  -0.322
121   C        -1.652  -1.574  -1.517  -1.487  -1.321  -1.303  -1.358  -1.284  -1.169
122   L         1.281   1.292   1.361   1.318   1.352   1.442   1.396   1.412   1.518
123   F         0.643   0.616   0.427   0.653   0.627   0.348   0.655   0.611   0.262
124   G         1.281   1.292   1.361   1.207   1.209   1.337   1.396   1.412   1.518
125   D        -1.541  -1.447  -1.486  -1.407  -1.301  -1.349  -1.252  -1.156  -1.143
126   W        -0.243  -0.318  -0.352   0.019  -0.118  -0.175  -0.404  -0.517  -0.554
127   N        -1.248  -1.306  -1.219  -1.243  -1.318  -1.210  -1.146  -1.184  -1.054
128   T        -1.065  -1.137  -1.187  -0.846  -0.978  -1.109  -0.934  -1.007  -1.023
129   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   D         0.518   0.561   0.377   0.496   0.531   0.251   0.455   0.523   0.168
131   G        -1.945  -1.941  -1.790  -1.740  -1.697  -1.507  -1.464  -1.447  -1.263
132   T        -1.248  -1.258  -1.216  -1.371  -1.405  -1.307  -1.146  -1.149  -1.052
133   V        -0.243  -0.332  -0.333  -0.344  -0.468  -0.509  -0.404  -0.519  -0.528
134   Q        -1.652  -1.667  -1.528  -1.567  -1.576  -1.384  -1.358  -1.354  -1.177
135   T        -0.955  -0.908  -0.860  -1.071  -1.039  -0.950  -1.040  -0.994  -0.891
136   I         0.329   0.301   0.292   0.240   0.220   0.146   0.125   0.069   0.006
137   I         0.329   0.276   0.287   0.250   0.194   0.142   0.125   0.023  -0.005
138   E        -0.243  -0.270  -0.320  -0.269  -0.349  -0.388  -0.404  -0.447  -0.511
139   D         1.281   1.292   1.361   1.234   1.220   1.362   1.396   1.412   1.518
140   P         1.281   1.292   1.361   1.385   1.421   1.506   1.396   1.412   1.518
141   W         0.643   0.646   0.449   0.838   0.827   0.599   0.655   0.658   0.302
142   Y         1.281   1.292   1.361   1.363   1.361   1.485   1.396   1.412   1.518
143   G         1.281   1.292   1.361   1.207   1.209   1.337   1.396   1.412   1.518
144   D         0.643   0.646   0.449   0.643   0.628   0.371   0.655   0.658   0.302
145   I        -0.844  -0.794  -0.808  -1.024  -0.950  -0.951  -0.934  -0.876  -0.838
146   Q        -1.359  -1.311  -1.225  -1.444  -1.387  -1.225  -1.252  -1.197  -1.060
147   D         0.643   0.646   0.449   0.643   0.628   0.371   0.655   0.658   0.302
148   F         1.281   1.292   1.361   1.215   1.235   1.344   1.396   1.412   1.518
149   E         0.036  -0.010  -0.250   0.129   0.052  -0.287   0.019  -0.043  -0.400
150   Y        -1.065  -1.137  -1.187  -0.811  -0.969  -1.048  -0.934  -1.007  -1.023
151   N        -0.243  -0.312  -0.353  -0.179  -0.282  -0.343  -0.404  -0.511  -0.558
152   F         0.108   0.133   0.243  -0.125  -0.087   0.103  -0.299  -0.255  -0.091
153   K        -0.955  -0.947  -0.861  -1.127  -1.135  -0.970  -1.040  -1.023  -0.892
154   Q         1.281   1.292   1.361   1.367   1.381   1.488   1.396   1.412   1.518
155   I        -0.955  -0.972  -0.859  -1.032  -1.013  -0.878  -1.040  -1.041  -0.888
156   T        -1.065  -0.960  -1.125  -0.734  -0.569  -0.835  -0.934  -0.814  -0.962
157   Y        -0.844  -0.895  -0.830  -0.736  -0.826  -0.707  -0.934  -0.970  -0.859
158   F         1.281   1.292   1.361   1.215   1.235   1.344   1.396   1.412   1.518
159   S         0.643   0.683   0.453   0.631   0.715   0.389   0.655   0.715   0.309
160   K        -1.248  -1.207  -1.189  -1.287  -1.278  -1.194  -1.146  -1.105  -1.030
161   Q        -0.955  -0.964  -0.866  -1.007  -1.015  -0.864  -1.040  -1.040  -0.896
162   F         1.281   1.292   1.361   1.215   1.235   1.344   1.396   1.412   1.518
163   L         1.281   1.292   1.361   1.318   1.352   1.442   1.396   1.412   1.518
164   K         0.036   0.016  -0.218   0.009  -0.040  -0.367   0.019  -0.016  -0.354
165   K        -1.652  -1.646  -1.520  -1.532  -1.546  -1.373  -1.358  -1.339  -1.171
166   E        -0.536  -0.661  -0.788  -0.411  -0.589  -0.799  -0.510  -0.662  -0.805
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   L        -1.945  -1.914  -1.783  -1.865  -1.829  -1.664  -1.464  -1.428  -1.258
* 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/P40347
Output conservation file - output/P40347
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
