1     M         1.096   1.102   1.181   1.419   1.426   1.524   1.175   1.191   1.317
2     S        -0.033  -0.125  -0.086  -0.089  -0.267  -0.246  -0.210  -0.377  -0.352
3     T        -0.232  -0.211  -0.093  -0.303  -0.271  -0.122  -0.556  -0.531  -0.365
4     L        -1.686  -1.816  -1.771  -1.678  -1.893  -1.813  -1.364  -1.497  -1.382
5     L        -0.380  -0.472  -0.756  -0.440  -0.565  -1.004  -0.325  -0.449  -0.823
6     K        -0.033  -0.053  -0.075  -0.155  -0.190  -0.198  -0.210  -0.254  -0.332
7     S         0.340   0.306   0.020   0.488   0.448   0.058   0.367   0.318  -0.163
8     A        -0.033  -0.080  -0.080  -0.190  -0.281  -0.339  -0.210  -0.300  -0.340
9     K         0.340   0.388   0.038   0.328   0.388  -0.044   0.367   0.435  -0.131
10    S         1.096   1.102   1.181   1.114   1.119   1.250   1.175   1.191   1.317
11    I        -0.295  -0.265  -0.105  -0.710  -0.673  -0.398  -0.672  -0.630  -0.386
12    V        -1.686  -1.705  -1.770  -1.593  -1.627  -1.738  -1.364  -1.389  -1.381
13    P         1.096   1.102   1.181   1.187   1.198   1.315   1.175   1.191   1.317
14    L         1.096   1.102   1.181   0.882   0.898   1.041   1.175   1.191   1.317
15    M        -0.991  -0.864  -0.791  -1.046  -0.891  -0.736  -1.133  -0.974  -0.868
16    D         1.096   1.102   1.181   1.226   1.246   1.351   1.175   1.191   1.317
17    R         1.096   1.102   1.181   1.317   1.317   1.433   1.175   1.191   1.317
18    V        -0.033  -0.112  -0.087  -0.221  -0.351  -0.325  -0.210  -0.355  -0.354
19    L         1.096   1.102   1.181   0.882   0.898   1.041   1.175   1.191   1.317
20    V         1.096   1.102   1.181   0.951   0.973   1.103   1.175   1.191   1.317
21    Q         1.096   1.102   1.181   1.297   1.319   1.415   1.175   1.191   1.317
22    R         1.096   1.102   1.181   1.317   1.317   1.433   1.175   1.191   1.317
23    I        -0.711  -0.728  -0.782  -0.788  -0.813  -0.966  -0.787  -0.804  -0.858
24    K         1.096   1.102   1.181   0.951   0.963   1.103   1.175   1.191   1.317
25    A        -0.033   0.009  -0.019  -0.113  -0.052  -0.107  -0.210  -0.148  -0.232
26    Q        -1.424  -1.392  -1.359  -1.383  -1.354  -1.220  -1.364  -1.336  -1.210
27    A        -0.991  -1.005  -0.857  -1.106  -1.131  -0.900  -1.133  -1.161  -0.955
28    K         0.340   0.306   0.020   0.328   0.293  -0.071   0.367   0.318  -0.163
29    T         1.096   1.102   1.181   1.246   1.264   1.368   1.175   1.191   1.317
30    A         0.340   0.360   0.035   0.389   0.414  -0.045   0.367   0.395  -0.137
31    S         0.340   0.360   0.035   0.482   0.503   0.067   0.367   0.395  -0.137
32    G         1.096   1.102   1.181   1.067   1.072   1.207   1.175   1.191   1.317
33    L        -0.232  -0.118  -0.055  -0.536  -0.310  -0.253  -0.556  -0.365  -0.295
34    Y        -0.232  -0.240  -0.105  -0.042  -0.074   0.105  -0.556  -0.585  -0.387
35    L        -0.232  -0.211  -0.093  -0.622  -0.591  -0.386  -0.556  -0.531  -0.365
36    P         1.096   1.102   1.181   1.187   1.198   1.315   1.175   1.191   1.317
37    E         1.096   1.102   1.181   1.141   1.142   1.274   1.175   1.191   1.317
38    K         0.340   0.277   0.021   0.300   0.222  -0.144   0.367   0.275  -0.160
39    N        -0.033  -0.125  -0.086   0.100  -0.054  -0.077  -0.210  -0.377  -0.352
40    V        -0.033   0.009  -0.019  -0.161  -0.089  -0.129  -0.210  -0.148  -0.232
41    E         0.340   0.277   0.021   0.467   0.375  -0.046   0.367   0.275  -0.160
42    K         0.340   0.277   0.021   0.317   0.245  -0.098   0.367   0.275  -0.160
43    L         1.096   1.102   1.181   0.882   0.898   1.041   1.175   1.191   1.317
44    N         0.340   0.216   0.014   0.634   0.494   0.123   0.367   0.184  -0.173
45    Q        -0.232  -0.258  -0.107  -0.243  -0.319  -0.108  -0.556  -0.618  -0.390
46    A         0.340   0.216   0.014   0.383   0.220  -0.101   0.367   0.184  -0.173
47    E        -1.903  -1.893  -1.780  -1.653  -1.637  -1.483  -1.595  -1.589  -1.391
48    V         1.096   1.102   1.181   0.951   0.973   1.103   1.175   1.191   1.317
49    V        -1.076  -0.988  -0.835  -1.492  -1.347  -1.114  -1.249  -1.152  -0.928
50    A         0.340   0.216   0.014   0.389   0.230  -0.082   0.367   0.184  -0.173
51    V        -0.033   0.060  -0.057  -0.248  -0.095  -0.317  -0.210  -0.065  -0.300
52    G         1.096   1.102   1.181   1.067   1.072   1.207   1.175   1.191   1.317
53    P         0.340   0.216   0.014   0.514   0.346  -0.022   0.367   0.184  -0.173
54    G         1.096   1.102   1.181   1.067   1.072   1.207   1.175   1.191   1.317
55    F        -1.555  -1.588  -1.381  -1.440  -1.536  -1.264  -1.480  -1.505  -1.229
56    T        -1.059  -1.235  -1.341  -0.655  -0.904  -1.132  -0.902  -1.111  -1.189
57    D        -0.295  -0.260  -0.103  -0.340  -0.257  -0.052  -0.672  -0.620  -0.383
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    A        -2.034  -1.941  -1.795  -1.959  -1.841  -1.586  -1.710  -1.631  -1.402
60    N        -1.903  -1.979  -1.803  -1.579  -1.693  -1.515  -1.595  -1.654  -1.408
61    G         1.096   1.102   1.181   1.067   1.072   1.207   1.175   1.191   1.317
62    N        -1.903  -1.883  -1.791  -1.614  -1.630  -1.475  -1.595  -1.583  -1.399
63    K        -1.903  -1.979  -1.803  -2.030  -2.156  -1.845  -1.595  -1.654  -1.408
64    V        -1.424  -1.494  -1.361  -1.614  -1.721  -1.537  -1.364  -1.419  -1.212
65    V        -1.338  -1.252  -1.339  -1.124  -0.980  -1.155  -1.249  -1.152  -1.188
66    P        -1.059  -1.058  -1.312  -0.683  -0.682  -1.068  -0.902  -0.910  -1.158
67    Q        -0.711  -0.651  -0.767  -0.613  -0.525  -0.712  -0.787  -0.693  -0.838
68    V         1.096   1.102   1.181   0.951   0.973   1.103   1.175   1.191   1.317
69    K        -1.686  -1.670  -1.757  -1.509  -1.511  -1.585  -1.364  -1.363  -1.370
70    V        -0.859  -0.755  -0.812  -1.101  -0.962  -0.976  -1.018  -0.909  -0.902
71    G         1.096   1.102   1.181   1.067   1.072   1.207   1.175   1.191   1.317
72    D         1.096   1.102   1.181   1.226   1.246   1.351   1.175   1.191   1.317
73    Q        -1.076  -1.059  -0.857  -1.145  -1.127  -0.813  -1.249  -1.232  -0.954
74    V         1.096   1.102   1.181   0.951   0.973   1.103   1.175   1.191   1.317
75    L         1.096   1.102   1.181   0.882   0.898   1.041   1.175   1.191   1.317
76    I        -0.232  -0.233  -0.100  -0.536  -0.566  -0.367  -0.556  -0.572  -0.377
77    P         1.096   1.102   1.181   1.187   1.198   1.315   1.175   1.191   1.317
78    Q        -1.338  -1.414  -1.359  -1.090  -1.207  -1.185  -1.249  -1.324  -1.207
79    F        -0.033  -0.125  -0.086   0.272   0.123   0.137  -0.210  -0.377  -0.352
80    G         1.096   1.102   1.181   1.067   1.072   1.207   1.175   1.191   1.317
81    G         1.096   1.102   1.181   1.067   1.072   1.207   1.175   1.191   1.317
82    S        -0.033   0.009  -0.019  -0.010   0.052  -0.004  -0.210  -0.148  -0.232
83    T        -1.424  -1.470  -1.365  -1.234  -1.274  -1.137  -1.364  -1.395  -1.214
84    I        -0.859  -0.772  -0.806  -1.097  -0.983  -1.027  -1.018  -0.933  -0.894
85    K         1.096   1.102   1.181   0.951   0.963   1.103   1.175   1.191   1.317
86    L        -0.859  -0.803  -0.803  -1.238  -1.097  -1.075  -1.018  -0.926  -0.886
87    G         0.340   0.438   0.038   0.406   0.521  -0.045   0.367   0.505  -0.131
88    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    D        -0.295  -0.256  -0.102  -0.443  -0.389  -0.148  -0.672  -0.614  -0.380
90    D        -0.232  -0.136  -0.080  -0.336  -0.183  -0.111  -0.556  -0.398  -0.340
91    E         0.340   0.306   0.020   0.506   0.459   0.057   0.367   0.318  -0.163
92    V        -0.232  -0.118  -0.055  -0.254  -0.027   0.001  -0.556  -0.365  -0.295
93    I        -1.903  -1.874  -1.789  -1.993  -1.942  -1.795  -1.595  -1.563  -1.397
94    L         1.096   1.102   1.181   0.882   0.898   1.041   1.175   1.191   1.317
95    F        -0.232  -0.233  -0.100  -0.049  -0.062   0.113  -0.556  -0.572  -0.377
96    R        -0.033   0.009  -0.019   0.171   0.225   0.142  -0.210  -0.148  -0.232
97    D         1.096   1.102   1.181   1.226   1.246   1.351   1.175   1.191   1.317
98    A        -1.555  -1.566  -1.370  -1.619  -1.602  -1.284  -1.480  -1.481  -1.220
99    E         1.096   1.102   1.181   1.141   1.142   1.274   1.175   1.191   1.317
100   I         0.340   0.216   0.014   0.438   0.262  -0.105   0.367   0.184  -0.173
101   L         1.096   1.102   1.181   0.882   0.898   1.041   1.175   1.191   1.317
102   A         1.096   1.102   1.181   1.040   1.052   1.183   1.175   1.191   1.317
103   K         0.340   0.216   0.014   0.301   0.143  -0.154   0.367   0.184  -0.173
104   I         0.340   0.445   0.035   0.447   0.574  -0.038   0.367   0.514  -0.137
105   A        -2.034  -1.962  -1.786  -2.122  -2.021  -1.757  -1.710  -1.651  -1.396
106   K        -0.380  -0.178  -0.722  -0.161   0.082  -0.693  -0.325  -0.072  -0.777
107   D        -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/P38910
Output conservation file - output/P38910
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
