1     M         0.988   1.004   1.035   1.162   1.180   1.219   1.037   1.064   1.112
2     S        -1.211  -1.323  -1.202  -1.327  -1.450  -1.257  -1.237  -1.342  -1.168
3     S        -2.532  -2.530  -2.280  -2.685  -2.671  -2.218  -1.954  -1.952  -1.659
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     N        -1.750  -1.662  -1.789  -1.407  -1.286  -1.524  -1.476  -1.385  -1.458
6     L         0.988   1.004   1.035   0.906   0.944   0.992   1.037   1.064   1.112
7     T        -0.281  -0.168  -0.321  -0.198  -0.047  -0.346  -0.399  -0.239  -0.501
8     E         0.138  -0.099  -0.320  -0.054  -0.390  -0.741   0.199  -0.135  -0.498
9     E        -1.044  -0.964  -1.165  -1.211  -1.121  -1.387  -0.997  -0.897  -1.123
10    Q         0.988   1.004   1.035   1.211   1.236   1.263   1.037   1.064   1.112
11    I        -0.281  -0.262  -0.349  -0.153  -0.140  -0.311  -0.399  -0.382  -0.547
12    A         0.138   0.180  -0.296   0.258   0.318  -0.413   0.199   0.252  -0.460
13    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
14    F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
15    K        -0.281  -0.410  -0.383  -0.127  -0.335  -0.318  -0.399  -0.619  -0.603
16    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
17    A         0.988   1.004   1.035   0.984   1.016   1.061   1.037   1.064   1.112
18    F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
19    A        -0.505  -0.418  -0.347  -0.772  -0.617  -0.532  -0.758  -0.632  -0.543
20    L         0.988   1.004   1.035   0.906   0.944   0.992   1.037   1.064   1.112
21    F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
22    D         0.988   1.004   1.035   0.822   0.839   0.917   1.037   1.064   1.112
23    K         0.138  -0.099  -0.320   0.413   0.126  -0.221   0.199  -0.135  -0.498
24    D         0.138   0.129  -0.297   0.129   0.110  -0.444   0.199   0.184  -0.462
25    N        -1.750  -1.805  -1.792  -1.405  -1.490  -1.527  -1.476  -1.537  -1.461
26    N        -1.044  -0.901  -1.171  -1.096  -0.915  -1.297  -0.997  -0.826  -1.130
27    G         0.988   1.004   1.035   1.096   1.114   1.161   1.037   1.064   1.112
28    S        -1.845  -1.919  -1.811  -1.697  -1.775  -1.570  -1.596  -1.660  -1.477
29    I         0.988   1.004   1.035   1.096   1.121   1.161   1.037   1.064   1.112
30    S        -0.505  -0.418  -0.347  -0.616  -0.480  -0.399  -0.758  -0.632  -0.543
31    S        -1.211  -1.168  -1.204  -1.220  -1.208  -1.236  -1.237  -1.209  -1.171
32    S        -1.211  -1.319  -1.208  -1.218  -1.325  -1.173  -1.237  -1.335  -1.174
33    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
34    L         0.988   1.004   1.035   0.906   0.944   0.992   1.037   1.064   1.112
35    A        -0.505  -0.418  -0.347  -0.602  -0.464  -0.384  -0.758  -0.632  -0.543
36    T         0.138  -0.099  -0.320   0.434   0.107  -0.237   0.199  -0.135  -0.498
37    V         0.988   1.004   1.035   1.142   1.155   1.201   1.037   1.064   1.112
38    M         0.988   1.004   1.035   1.162   1.180   1.219   1.037   1.064   1.112
39    R         0.988   1.004   1.035   1.236   1.246   1.285   1.037   1.064   1.112
40    S         0.988   1.004   1.035   0.906   0.949   0.992   1.037   1.064   1.112
41    L         0.988   1.004   1.035   0.906   0.944   0.992   1.037   1.064   1.112
42    G         0.988   1.004   1.035   1.096   1.114   1.161   1.037   1.064   1.112
43    L        -0.505  -0.418  -0.347  -0.540  -0.384  -0.333  -0.758  -0.632  -0.543
44    S        -0.576  -0.541  -0.392  -0.784  -0.745  -0.513  -0.878  -0.839  -0.618
45    P         0.988   1.004   1.035   1.378   1.400   1.411   1.037   1.064   1.112
46    S         0.138  -0.099  -0.320   0.212  -0.077  -0.416   0.199  -0.135  -0.498
47    E         0.138  -0.099  -0.320  -0.029  -0.345  -0.661   0.199  -0.135  -0.498
48    A        -0.576  -0.541  -0.392  -0.899  -0.837  -0.607  -0.878  -0.839  -0.618
49    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
50    V        -0.505  -0.418  -0.347  -0.686  -0.556  -0.451  -0.758  -0.632  -0.543
51    N        -1.993  -1.940  -1.803  -1.743  -1.714  -1.512  -1.715  -1.686  -1.472
52    D         0.988   1.004   1.035   0.822   0.839   0.917   1.037   1.064   1.112
53    L        -0.505  -0.418  -0.347  -0.585  -0.435  -0.372  -0.758  -0.632  -0.543
54    M        -0.505  -0.418  -0.347  -0.509  -0.383  -0.297  -0.758  -0.632  -0.543
55    N         0.988   1.004   1.035   1.136   1.155   1.197   1.037   1.064   1.112
56    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
57    I        -0.505  -0.418  -0.347  -0.504  -0.379  -0.294  -0.758  -0.632  -0.543
58    D         0.988   1.004   1.035   0.822   0.839   0.917   1.037   1.064   1.112
59    V        -0.505  -0.533  -0.394  -0.562  -0.662  -0.456  -0.758  -0.825  -0.621
60    D        -0.281  -0.241  -0.357  -0.419  -0.381  -0.531  -0.399  -0.351  -0.559
61    G        -1.358  -1.269  -1.205  -1.325  -1.201  -1.155  -1.356  -1.262  -1.170
62    N        -0.505  -0.444  -0.374  -0.650  -0.561  -0.498  -0.758  -0.676  -0.588
63    H        -0.505  -0.418  -0.347  -0.395  -0.288  -0.189  -0.758  -0.632  -0.543
64    Q        -1.993  -1.844  -1.796  -1.819  -1.617  -1.590  -1.715  -1.574  -1.465
65    I         0.988   1.004   1.035   1.096   1.121   1.161   1.037   1.064   1.112
66    E        -0.505  -0.418  -0.347  -1.012  -0.866  -0.753  -0.758  -0.632  -0.543
67    F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
68    S        -1.845  -1.946  -1.812  -1.545  -1.683  -1.512  -1.596  -1.679  -1.478
69    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
70    F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
71    L         0.988   1.004   1.035   0.906   0.944   0.992   1.037   1.064   1.112
72    A        -0.505  -0.418  -0.347  -0.576  -0.450  -0.361  -0.758  -0.632  -0.543
73    L        -0.505  -0.418  -0.347  -0.585  -0.435  -0.372  -0.758  -0.632  -0.543
74    M         0.988   1.004   1.035   1.162   1.180   1.219   1.037   1.064   1.112
75    S        -0.505  -0.418  -0.347  -0.744  -0.586  -0.511  -0.758  -0.632  -0.543
76    R         0.988   1.004   1.035   1.236   1.246   1.285   1.037   1.064   1.112
77    Q        -0.505  -0.418  -0.347  -0.487  -0.353  -0.276  -0.758  -0.632  -0.543
78    L        -0.505  -0.418  -0.347  -0.585  -0.435  -0.372  -0.758  -0.632  -0.543
79    K         0.988   1.004   1.035   1.091   1.127   1.156   1.037   1.064   1.112
80    S        -1.044  -0.901  -1.171  -1.082  -0.890  -1.162  -0.997  -0.826  -1.130
81    N        -0.505  -0.418  -0.347  -0.496  -0.387  -0.286  -0.758  -0.632  -0.543
82    D         0.988   1.004   1.035   0.822   0.839   0.917   1.037   1.064   1.112
83    S         0.138  -0.099  -0.320   0.214  -0.071  -0.412   0.199  -0.135  -0.498
84    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
85    Q        -1.454  -1.360  -1.206  -1.670  -1.599  -1.355  -1.476  -1.380  -1.171
86    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
87    L        -1.211  -1.319  -1.208  -1.213  -1.332  -1.168  -1.237  -1.335  -1.174
88    L        -1.454  -1.360  -1.206  -1.506  -1.346  -1.141  -1.476  -1.380  -1.171
89    E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
90    A         0.988   1.004   1.035   0.984   1.016   1.061   1.037   1.064   1.112
91    F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
92    K         0.988   1.004   1.035   1.091   1.127   1.156   1.037   1.064   1.112
93    V         0.988   1.004   1.035   1.142   1.155   1.201   1.037   1.064   1.112
94    F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
95    D         0.988   1.004   1.035   0.822   0.839   0.917   1.037   1.064   1.112
96    K        -0.576  -0.541  -0.392  -0.579  -0.548  -0.329  -0.878  -0.839  -0.618
97    N        -0.505  -0.533  -0.394  -0.650  -0.775  -0.562  -0.758  -0.825  -0.621
98    G        -0.281  -0.262  -0.349  -0.154  -0.147  -0.313  -0.399  -0.382  -0.547
99    D        -0.505  -0.533  -0.394  -0.763  -0.822  -0.567  -0.758  -0.825  -0.621
100   G         0.988   1.004   1.035   1.096   1.114   1.161   1.037   1.064   1.112
101   L        -1.993  -2.047  -1.820  -1.836  -1.851  -1.505  -1.715  -1.758  -1.486
102   I         0.988   1.004   1.035   1.096   1.121   1.161   1.037   1.064   1.112
103   S         0.138  -0.099  -0.320   0.212  -0.077  -0.416   0.199  -0.135  -0.498
104   A         0.138  -0.099  -0.320   0.292  -0.005  -0.348   0.199  -0.135  -0.498
105   A        -0.672  -0.905  -1.167  -0.448  -0.807  -1.233  -0.519  -0.817  -1.125
106   E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
107   L         0.988   1.004   1.035   0.906   0.944   0.992   1.037   1.064   1.112
108   K        -1.211  -1.319  -1.208  -0.991  -1.138  -0.996  -1.237  -1.335  -1.174
109   H         0.988   1.004   1.035   1.378   1.400   1.411   1.037   1.064   1.112
110   V         0.988   1.004   1.035   1.142   1.155   1.201   1.037   1.064   1.112
111   L        -0.281  -0.262  -0.349  -0.329  -0.301  -0.444  -0.399  -0.382  -0.547
112   T         0.988   1.004   1.035   1.126   1.130   1.188   1.037   1.064   1.112
113   S         0.988   1.004   1.035   0.906   0.949   0.992   1.037   1.064   1.112
114   I         0.138  -0.099  -0.320   0.371   0.049  -0.367   0.199  -0.135  -0.498
115   G         0.988   1.004   1.035   1.096   1.114   1.161   1.037   1.064   1.112
116   E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
117   K         0.138  -0.099  -0.320   0.413   0.126  -0.221   0.199  -0.135  -0.498
118   L         0.988   1.004   1.035   0.906   0.944   0.992   1.037   1.064   1.112
119   T        -0.505  -0.511  -0.391  -0.616  -0.673  -0.504  -0.758  -0.788  -0.616
120   D         0.138  -0.099  -0.320   0.141  -0.158  -0.442   0.199  -0.135  -0.498
121   A        -1.044  -1.118  -1.203  -1.130  -1.346  -1.523  -0.997  -1.128  -1.170
122   E        -0.281  -0.168  -0.321  -0.660  -0.497  -0.744  -0.399  -0.239  -0.501
123   V         0.988   1.004   1.035   1.142   1.155   1.201   1.037   1.064   1.112
124   D         0.138  -0.099  -0.320   0.106  -0.214  -0.552   0.199  -0.135  -0.498
125   D        -1.993  -1.967  -1.792  -2.159  -2.176  -1.838  -1.715  -1.698  -1.462
126   M         0.988   1.004   1.035   1.162   1.180   1.219   1.037   1.064   1.112
127   L        -0.505  -0.418  -0.347  -0.643  -0.490  -0.423  -0.758  -0.632  -0.543
128   R        -0.281  -0.241  -0.357  -0.035   0.002  -0.244  -0.399  -0.351  -0.559
129   E         0.988   1.004   1.035   0.687   0.708   0.797   1.037   1.064   1.112
130   V        -0.505  -0.418  -0.347  -0.618  -0.490  -0.392  -0.758  -0.632  -0.543
131   -         0.988   1.004   1.035   0.725   0.758   0.831   1.037   1.064   1.112
132   S        -2.384  -2.325  -2.264  -2.096  -2.050  -1.889  -1.835  -1.804  -1.648
133   D        -0.505  -0.444  -0.374  -0.763  -0.693  -0.555  -0.758  -0.676  -0.588
134   G        -0.281  -0.168  -0.321  -0.154  -0.007  -0.265  -0.399  -0.239  -0.501
135   S        -0.505  -0.418  -0.347  -0.891  -0.751  -0.639  -0.758  -0.632  -0.543
136   G         0.988   1.004   1.035   1.096   1.114   1.161   1.037   1.064   1.112
137   E        -1.044  -1.220  -1.202  -1.136  -1.379  -1.255  -0.997  -1.204  -1.167
138   I         0.988   1.004   1.035   1.096   1.121   1.161   1.037   1.064   1.112
139   N        -0.576  -0.541  -0.392  -0.845  -0.802  -0.552  -0.878  -0.839  -0.618
140   I        -0.505  -0.533  -0.394  -0.377  -0.424  -0.215  -0.758  -0.825  -0.621
141   Q        -1.750  -1.859  -1.799  -1.393  -1.642  -1.611  -1.476  -1.594  -1.467
142   Q        -0.505  -0.418  -0.347  -0.838  -0.732  -0.580  -0.758  -0.632  -0.543
143   F         0.988   1.004   1.035   1.106   1.129   1.170   1.037   1.064   1.112
144   A        -1.993  -2.047  -1.820  -1.872  -1.987  -1.664  -1.715  -1.758  -1.486
145   A        -1.845  -1.898  -1.806  -1.604  -1.660  -1.545  -1.596  -1.645  -1.473
146   L         0.138  -0.099  -0.320   0.214  -0.075  -0.409   0.199  -0.135  -0.498
147   L        -0.672  -0.860  -1.165  -0.467  -0.718  -1.131  -0.519  -0.767  -1.122
148   -        -2.019  -1.841  -1.801  -1.862  -1.621  -1.593  -1.720  -1.553  -1.469
149   S        -1.435  -1.258  -1.756  -1.137  -0.918  -1.581  -1.117  -0.940  -1.427
150   K         0.138   0.129  -0.297   0.366   0.366  -0.327   0.199   0.184  -0.462
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -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/P06787
Output conservation file - output/P06787
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
