1     M         1.410   1.447   1.525   1.607   1.655   1.778   1.530   1.581   1.713
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     E         0.744   0.767   0.547   0.632   0.663   0.268   0.762   0.794   0.398
4     N         0.744   0.759   0.547   0.473   0.516   0.191   0.762   0.782   0.398
5     P         1.410   1.447   1.525   1.694   1.746   1.863   1.530   1.581   1.713
6     H        -0.181  -0.103  -0.221   0.162   0.283   0.084  -0.335  -0.210  -0.388
7     E         1.410   1.447   1.525   1.297   1.342   1.479   1.530   1.581   1.713
8     Q        -0.924  -0.920  -0.820  -1.011  -0.984  -0.845  -0.993  -0.977  -0.839
9     V        -0.733  -0.838  -0.783  -0.602  -0.733  -0.639  -0.774  -0.882  -0.797
10    Q         0.744   0.776   0.553   0.929   0.976   0.681   0.762   0.807   0.409
11    A        -0.808  -0.686  -0.768  -1.155  -0.986  -1.019  -0.884  -0.755  -0.785
12    N        -0.808  -0.884  -0.803  -1.032  -1.067  -0.965  -0.884  -0.940  -0.820
13    I        -0.733  -0.735  -0.780  -0.827  -0.818  -0.878  -0.774  -0.765  -0.792
14    L         1.410   1.447   1.525   1.326   1.378   1.506   1.530   1.581   1.713
15    S        -0.181  -0.234  -0.270  -0.099  -0.219  -0.212  -0.335  -0.423  -0.465
16    R         1.410   1.447   1.525   1.642   1.689   1.812   1.530   1.581   1.713
17    I         1.410   1.447   1.525   1.509   1.555   1.684   1.530   1.581   1.713
18    I         1.410   1.447   1.525   1.509   1.555   1.684   1.530   1.581   1.713
19    G        -1.230  -1.140  -1.164  -1.091  -0.990  -1.024  -1.103  -0.997  -0.980
20    N         0.744   0.593   0.534   0.520   0.359   0.278   0.762   0.514   0.374
21    V         0.416   0.480   0.443   0.430   0.523   0.443   0.213   0.316   0.202
22    K         0.110   0.033  -0.158   0.103  -0.034  -0.297   0.104  -0.018  -0.293
23    R        -0.733  -0.629  -0.737  -0.658  -0.478  -0.737  -0.774  -0.635  -0.743
24    L         1.410   1.447   1.525   1.326   1.378   1.506   1.530   1.581   1.713
25    N         1.410   1.447   1.525   1.086   1.159   1.275   1.530   1.581   1.713
26    E        -0.181  -0.246  -0.244  -0.363  -0.461  -0.472  -0.335  -0.402  -0.422
27    S         0.744   0.759   0.547   0.877   0.872   0.602   0.762   0.782   0.398
28    V         0.241   0.236   0.339   0.073   0.039   0.195  -0.116  -0.142  -0.001
29    A        -0.733  -0.696  -0.760  -0.573  -0.546  -0.590  -0.774  -0.742  -0.774
30    I        -1.345  -1.311  -1.205  -1.135  -1.077  -0.935  -1.213  -1.160  -1.018
31    L        -0.427  -0.446  -0.345  -0.662  -0.701  -0.540  -0.664  -0.691  -0.562
32    N         1.410   1.447   1.525   1.086   1.159   1.275   1.530   1.581   1.713
33    Q        -0.808  -0.880  -0.804  -0.782  -0.895  -0.770  -0.884  -0.936  -0.821
34    E        -0.808  -0.884  -0.803  -0.992  -1.106  -0.934  -0.884  -0.940  -0.820
35    L         0.744   0.593   0.534   0.720   0.515   0.409   0.762   0.514   0.374
36    V        -0.733  -0.680  -0.778  -0.759  -0.719  -0.863  -0.774  -0.722  -0.793
37    T        -1.958  -1.838  -1.784  -1.969  -1.790  -1.719  -1.432  -1.321  -1.221
38    I         0.241   0.248   0.348   0.079   0.069   0.217  -0.116  -0.117   0.017
39    N         0.744   0.593   0.534   0.516   0.350   0.268   0.762   0.514   0.374
40    N        -1.958  -1.934  -1.795  -1.938  -1.907  -1.653  -1.432  -1.398  -1.228
41    R        -1.536  -1.482  -1.497  -1.275  -1.197  -1.300  -1.213  -1.146  -1.118
42    N         1.410   1.447   1.525   1.086   1.159   1.275   1.530   1.581   1.713
43    K        -0.502  -0.503  -0.360  -0.648  -0.678  -0.487  -0.774  -0.767  -0.583
44    N         0.110   0.193  -0.146  -0.072   0.057  -0.394   0.104   0.221  -0.275
45    L        -0.733  -0.708  -0.774  -0.761  -0.716  -0.814  -0.774  -0.727  -0.784
46    E         0.744   0.593   0.534   0.687   0.463   0.370   0.762   0.514   0.374
47    I        -0.924  -0.874  -0.812  -1.121  -1.059  -0.935  -0.993  -0.936  -0.831
48    M        -0.808  -0.780  -0.778  -0.791  -0.754  -0.759  -0.884  -0.834  -0.793
49    G        -0.427  -0.321  -0.289  -0.422  -0.299  -0.226  -0.664  -0.511  -0.483
50    A         0.110   0.033  -0.158   0.286   0.142  -0.154   0.104  -0.018  -0.293
51    I         0.241   0.256   0.352   0.175   0.182   0.314  -0.116  -0.102   0.025
52    C        -0.808  -0.884  -0.803  -0.326  -0.424  -0.316  -0.884  -0.940  -0.820
53    D        -1.039  -1.111  -1.144  -0.931  -1.056  -1.045  -0.884  -0.955  -0.958
54    N         1.410   1.447   1.525   1.086   1.159   1.275   1.530   1.581   1.713
55    Y         1.410   1.447   1.525   1.728   1.767   1.896   1.530   1.581   1.713
56    H        -1.651  -1.584  -1.517  -1.352  -1.284  -1.193  -1.323  -1.246  -1.135
57    S        -1.230  -1.243  -1.169  -1.087  -1.118  -1.031  -1.103  -1.102  -0.986
58    S         0.185   0.214   0.334  -0.374  -0.334  -0.133  -0.225  -0.184  -0.011
59    V         0.416   0.480   0.443   0.384   0.473   0.381   0.213   0.316   0.202
60    Q        -1.345  -1.319  -1.211  -1.366  -1.281  -1.154  -1.213  -1.168  -1.022
61    F         0.416   0.344   0.371   0.743   0.609   0.612   0.213   0.068   0.062
62    N        -0.733  -0.819  -0.783  -0.904  -0.961  -0.879  -0.774  -0.863  -0.797
63    L         1.410   1.447   1.525   1.326   1.378   1.506   1.530   1.581   1.713
64    E         0.110  -0.002  -0.173   0.120  -0.036  -0.284   0.104  -0.061  -0.314
65    A        -0.181  -0.239  -0.271  -0.119  -0.285  -0.356  -0.335  -0.435  -0.466
66    T         0.744   0.593   0.534   1.092   0.879   0.748   0.762   0.514   0.374
67    N        -1.039  -0.967  -1.121  -0.594  -0.468  -0.800  -0.884  -0.793  -0.935
68    N        -1.536  -1.565  -1.505  -1.691  -1.676  -1.579  -1.213  -1.227  -1.124
69    K        -0.181  -0.311  -0.273  -0.129  -0.321  -0.326  -0.335  -0.500  -0.465
70    K         0.744   0.806   0.555   0.975   1.064   0.683   0.762   0.853   0.412
71    P        -0.502  -0.428  -0.328  -0.569  -0.508  -0.330  -0.774  -0.674  -0.543
72    P         1.410   1.447   1.525   1.694   1.746   1.863   1.530   1.581   1.713
73    L        -0.733  -0.827  -0.783  -0.795  -0.896  -0.831  -0.774  -0.863  -0.797
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -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/P69851
Output conservation file - output/P69851
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
