1     M         0.965   0.972   1.032   1.374   1.360   1.400   1.008   1.017   1.110
2     K         0.229   0.101  -0.146  -0.182  -0.302  -0.666   0.255   0.070  -0.353
3     V        -0.826  -0.921  -0.947  -0.469  -0.595  -0.640  -0.876  -0.986  -1.016
4     E         0.229   0.101  -0.146   0.576   0.425   0.095   0.255   0.070  -0.353
5     I        -1.801  -1.760  -1.500  -1.393  -1.332  -1.004  -1.724  -1.638  -1.320
6     D        -0.153  -0.166  -0.157   0.293   0.261   0.217  -0.311  -0.342  -0.371
7     S         0.229   0.101  -0.146   0.361   0.233  -0.093   0.255   0.070  -0.353
8     F         0.965   0.972   1.032   1.223   1.226   1.275   1.008   1.017   1.110
9     S         0.965   0.972   1.032   0.921   0.944   1.025   1.008   1.017   1.110
10    G         0.965   0.972   1.032   1.124   1.121   1.193   1.008   1.017   1.110
11    A        -2.126  -2.088  -1.908  -1.974  -1.838  -1.490  -1.818  -1.740  -1.484
12    K         0.229   0.101  -0.146  -0.182  -0.302  -0.666   0.255   0.070  -0.353
13    I        -0.153  -0.166  -0.157   0.133   0.088   0.036  -0.311  -0.342  -0.371
14    Y         0.965   0.972   1.032   1.343   1.329   1.375   1.008   1.017   1.110
15    P         0.965   0.972   1.032   1.297   1.285   1.337   1.008   1.017   1.110
16    G         0.965   0.972   1.032   1.124   1.121   1.193   1.008   1.017   1.110
17    R        -0.826  -0.938  -0.935  -1.096  -1.310  -1.424  -0.876  -1.009  -0.998
18    G         0.965   0.972   1.032   1.124   1.121   1.193   1.008   1.017   1.110
19    T        -0.826  -0.938  -0.935  -0.575  -0.808  -1.008  -0.876  -1.009  -0.998
20    L         0.965   0.972   1.032   1.188   1.188   1.246   1.008   1.017   1.110
21    F         0.229   0.101  -0.146   0.674   0.526   0.167   0.255   0.070  -0.353
22    V         0.965   0.972   1.032   1.084   1.085   1.160   1.008   1.017   1.110
23    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
24    G         0.965   0.972   1.032   1.124   1.121   1.193   1.008   1.017   1.110
25    D         0.965   0.972   1.032   1.278   1.280   1.320   1.008   1.017   1.110
26    S        -0.153  -0.166  -0.157  -0.078  -0.090  -0.082  -0.311  -0.342  -0.371
27    K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
28    I        -0.153  -0.166  -0.157   0.133   0.088   0.036  -0.311  -0.342  -0.371
29    F         0.965   0.972   1.032   1.223   1.226   1.275   1.008   1.017   1.110
30    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
31    F         0.965   0.972   1.032   1.223   1.226   1.275   1.008   1.017   1.110
32    Q        -0.826  -0.932  -0.929  -0.385  -0.527  -0.553  -0.876  -1.002  -0.991
33    N        -0.485  -0.405  -0.238  -0.456  -0.334  -0.140  -0.876  -0.749  -0.513
34    S        -0.826  -0.938  -0.935  -0.887  -1.049  -1.087  -0.876  -1.009  -0.998
35    K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
36    S         0.229   0.108  -0.142   0.361   0.241  -0.087   0.255   0.081  -0.346
37    A        -0.378  -0.393  -0.236  -0.688  -0.697  -0.423  -0.688  -0.729  -0.509
38    S         0.965   0.972   1.032   0.921   0.944   1.025   1.008   1.017   1.110
39    L         0.965   0.972   1.032   1.188   1.188   1.246   1.008   1.017   1.110
40    F         0.965   0.972   1.032   1.223   1.226   1.275   1.008   1.017   1.110
41    K        -1.801  -1.566  -1.498  -1.755  -1.439  -1.266  -1.724  -1.479  -1.319
42    Q         0.965   0.972   1.032   1.195   1.203   1.253   1.008   1.017   1.110
43    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
44    K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
45    N         0.965   0.972   1.032   1.305   1.287   1.343   1.008   1.017   1.110
46    P         0.965   0.972   1.032   1.297   1.285   1.337   1.008   1.017   1.110
47    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
48    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
49    I        -0.826  -0.653  -0.900  -0.387  -0.228  -0.561  -0.876  -0.703  -0.954
50    A        -0.485  -0.411  -0.237  -0.967  -0.836  -0.546  -0.876  -0.760  -0.510
51    W         0.965   0.972   1.032   1.385   1.373   1.410   1.008   1.017   1.110
52    T         0.965   0.972   1.032   1.243   1.239   1.291   1.008   1.017   1.110
53    V         0.965   0.972   1.032   1.084   1.085   1.160   1.008   1.017   1.110
54    L         0.965   0.972   1.032   1.188   1.188   1.246   1.008   1.017   1.110
55    F         0.229   0.309  -0.127   0.778   0.840   0.241   0.255   0.359  -0.320
56    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
57    K         0.229   0.309  -0.127   0.095   0.199  -0.499   0.255   0.359  -0.320
58    H        -1.722  -1.751  -1.496  -1.181  -1.293  -1.093  -1.630  -1.629  -1.317
59    H         0.965   0.972   1.032   1.328   1.320   1.362   1.008   1.017   1.110
60    K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
61    K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
62    G         0.965   0.972   1.032   1.124   1.121   1.193   1.008   1.017   1.110
63    I         0.965   0.972   1.032   1.203   1.200   1.259   1.008   1.017   1.110
64    T        -0.485  -0.401  -0.234  -0.558  -0.436  -0.203  -0.876  -0.742  -0.505
65    E         0.965   0.972   1.032   1.124   1.122   1.193   1.008   1.017   1.110
66    E         0.965   0.972   1.032   1.124   1.122   1.193   1.008   1.017   1.110
67    V        -1.460  -1.256  -1.457  -1.070  -0.833  -1.212  -1.347  -1.146  -1.278
68    A         0.229   0.108  -0.142   0.080  -0.052  -0.399   0.255   0.081  -0.346
69    K         0.229   0.372  -0.121  -0.182   0.029  -0.622   0.255   0.439  -0.309
70    K         0.229   0.351  -0.123  -0.182   0.006  -0.625   0.255   0.412  -0.313
71    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
72    S        -0.485  -0.429  -0.241  -0.507  -0.445  -0.202  -0.876  -0.792  -0.519
73    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
74    K        -0.378  -0.393  -0.236  -1.102  -1.106  -0.810  -0.688  -0.729  -0.509
75    T        -0.153  -0.143  -0.210   0.127   0.119  -0.107  -0.311  -0.305  -0.463
76    V         0.965   0.972   1.032   1.084   1.085   1.160   1.008   1.017   1.110
77    K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
78    A        -1.012  -0.863  -0.943  -1.010  -0.842  -0.783  -1.159  -0.985  -1.012
79    Q         0.229   0.108  -0.142   0.615   0.470   0.056   0.255   0.081  -0.346
80    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
81    P        -1.012  -0.941  -0.953  -1.127  -1.032  -0.890  -1.159  -1.089  -1.024
82    I         0.229   0.372  -0.121   0.622   0.761   0.098   0.255   0.439  -0.309
83    T         0.229   0.309  -0.127   0.524   0.600   0.056   0.255   0.359  -0.320
84    G         0.965   0.972   1.032   1.124   1.121   1.193   1.008   1.017   1.110
85    A         0.965   0.972   1.032   0.683   0.707   0.828   1.008   1.017   1.110
86    S        -0.153  -0.166  -0.157  -0.078  -0.090  -0.082  -0.311  -0.342  -0.371
87    L         0.965   0.972   1.032   1.188   1.188   1.246   1.008   1.017   1.110
88    D        -0.485  -0.430  -0.241  -0.378  -0.300  -0.057  -0.876  -0.794  -0.518
89    L        -0.485  -0.417  -0.231  -0.450  -0.377  -0.125  -0.876  -0.771  -0.500
90    I         0.965   0.972   1.032   1.203   1.200   1.259   1.008   1.017   1.110
91    K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
92    E         0.965   0.972   1.032   1.124   1.122   1.193   1.008   1.017   1.110
93    R        -0.378  -0.392  -0.237  -0.948  -1.021  -0.781  -0.688  -0.726  -0.511
94    R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
95    S        -0.378  -0.392  -0.237  -0.385  -0.396  -0.169  -0.688  -0.726  -0.511
96    L        -1.599  -1.636  -1.489  -1.166  -1.201  -1.078  -1.535  -1.514  -1.310
97    K        -0.485  -0.417  -0.231  -1.287  -1.094  -0.759  -0.876  -0.771  -0.500
98    P         0.965   0.972   1.032   1.297   1.285   1.337   1.008   1.017   1.110
99    E        -0.153   0.016  -0.164   0.011   0.242  -0.099  -0.311  -0.055  -0.383
100   V        -1.460  -1.510  -1.480  -1.030  -1.122  -1.140  -1.347  -1.366  -1.300
101   R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
102   K        -1.460  -1.623  -1.494  -1.841  -2.010  -1.680  -1.347  -1.498  -1.314
103   A         0.965   0.972   1.032   0.683   0.707   0.828   1.008   1.017   1.110
104   N        -1.785  -1.530  -1.870  -1.596  -1.265  -1.655  -1.441  -1.196  -1.454
105   R         0.965   0.972   1.032   0.757   0.769   0.889   1.008   1.017   1.110
106   E        -1.599  -1.564  -1.489  -1.344  -1.381  -1.212  -1.535  -1.472  -1.311
107   E        -2.574  -2.251  -2.244  -2.477  -2.170  -2.034  -2.006  -1.721  -1.595
108   K        -1.012  -1.078  -0.965  -1.600  -1.604  -1.268  -1.159  -1.218  -1.038
109   L        -1.460  -1.402  -1.472  -1.198  -1.120  -1.428  -1.347  -1.282  -1.295
110   K        -0.826  -0.780  -0.922  -1.299  -1.143  -1.323  -0.876  -0.792  -0.982
111   A        -1.722  -1.677  -1.494  -2.000  -1.836  -1.610  -1.630  -1.552  -1.314
112   N        -2.047  -2.104  -1.913  -1.594  -1.821  -1.583  -1.724  -1.749  -1.488
113   K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
114   E        -0.826  -0.938  -0.935  -0.493  -0.676  -0.780  -0.876  -1.009  -0.998
115   K        -0.826  -0.780  -0.922  -1.371  -1.239  -1.503  -0.876  -0.792  -0.982
116   K         0.229   0.206  -0.118  -0.182  -0.165  -0.616   0.255   0.220  -0.304
117   K        -1.460  -1.623  -1.494  -1.820  -1.974  -1.635  -1.347  -1.498  -1.314
118   A        -0.478  -0.706  -0.918  -0.560  -0.863  -1.230  -0.405  -0.696  -0.976
119   E        -2.249  -2.154  -1.911  -1.812  -1.718  -1.465  -1.912  -1.799  -1.487
120   K        -1.460  -1.623  -1.494  -1.718  -1.877  -1.630  -1.347  -1.498  -1.314
121   A        -0.826  -0.932  -0.929  -0.971  -1.097  -1.045  -0.876  -1.002  -0.991
122   A        -0.826  -0.932  -0.929  -0.963  -1.112  -1.114  -0.876  -1.002  -0.991
123   R        -0.378  -0.393  -0.236  -0.948  -1.026  -0.777  -0.688  -0.729  -0.509
124   K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
125   A         0.229   0.372  -0.121   0.080   0.252  -0.364   0.255   0.439  -0.309
126   E        -0.826  -0.932  -0.929  -0.517  -0.699  -0.801  -0.876  -1.002  -0.991
127   K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
128   A         0.965   0.972   1.032   0.683   0.707   0.828   1.008   1.017   1.110
129   K         0.229   0.108  -0.142  -0.192  -0.304  -0.691   0.255   0.081  -0.346
130   S        -2.047  -1.951  -1.890  -1.633  -1.466  -1.420  -1.724  -1.601  -1.469
131   A        -0.153  -0.145  -0.214  -0.376  -0.359  -0.428  -0.311  -0.309  -0.470
132   G         0.229   0.309  -0.127   0.108   0.207  -0.293   0.255   0.359  -0.320
133   T        -1.599  -1.563  -1.484  -1.647  -1.557  -1.297  -1.535  -1.471  -1.306
134   Q        -1.801  -1.764  -1.495  -1.480  -1.429  -1.070  -1.724  -1.642  -1.315
135   S        -1.599  -1.550  -1.486  -1.773  -1.742  -1.668  -1.535  -1.454  -1.308
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   S        -1.460  -1.623  -1.494  -1.374  -1.634  -1.461  -1.347  -1.498  -1.314
138   K        -1.460  -1.444  -1.477  -1.729  -1.707  -1.649  -1.347  -1.334  -1.297
139   F        -0.826  -0.766  -0.908  -0.474  -0.427  -0.599  -0.876  -0.817  -0.965
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   S        -0.153  -0.166  -0.157  -0.255  -0.281  -0.337  -0.311  -0.342  -0.371
142   K        -0.153  -0.166  -0.157  -0.571  -0.545  -0.476  -0.311  -0.342  -0.371
143   Q        -0.826  -0.932  -0.929  -0.599  -0.769  -0.851  -0.876  -1.002  -0.991
144   Q        -1.135  -1.192  -0.967  -0.758  -0.884  -0.620  -1.253  -1.327  -1.040
145   A         0.229   0.351  -0.123   0.080   0.230  -0.368   0.255   0.412  -0.313
146   K         0.965   0.972   1.032   0.447   0.505   0.633   1.008   1.017   1.110
147   G         0.965   0.972   1.032   1.125   1.117   1.194   1.008   1.017   1.110
148   A        -0.298  -0.318  -0.235  -0.647  -0.681  -0.544  -0.549  -0.597  -0.508
149   F        -0.716  -1.024  -0.962  -0.255  -0.736  -0.760  -0.705  -1.109  -1.032
150   Q        -0.716  -1.024  -0.962  -0.213  -0.641  -0.614  -0.705  -1.109  -1.032
151   K         0.965   0.972   1.032   0.418   0.481   0.608   1.008   1.017   1.110
152   V         0.965   0.972   1.032   1.110   1.111   1.181   1.008   1.017   1.110
153   A        -1.785  -1.686  -1.864  -1.626  -1.488  -1.704  -1.441  -1.345  -1.448
154   A         0.965   0.972   1.032   0.683   0.707   0.828   1.008   1.017   1.110
155   T        -0.826  -0.938  -0.935  -0.597  -0.831  -1.039  -0.876  -1.009  -0.998
156   S        -0.153  -0.166  -0.157  -0.235  -0.261  -0.308  -0.311  -0.342  -0.371
157   R         0.229   0.213  -0.117   0.209   0.197  -0.143   0.255   0.229  -0.302
* 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/P04449
Output conservation file - output/P04449
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
