1     M         0.933   0.942   0.982   1.035   1.044   1.105   0.982   0.993   1.044
2     S         0.933   0.942   0.982   0.942   0.956   1.021   0.982   0.993   1.044
3     S        -1.166  -1.215  -1.261  -1.033  -1.114  -1.175  -1.138  -1.196  -1.208
4     S        -0.309  -0.422  -0.419  -0.353  -0.551  -0.588  -0.438  -0.617  -0.617
5     T        -1.494  -1.474  -1.295  -1.567  -1.529  -1.251  -1.542  -1.509  -1.247
6     P         0.933   0.942   0.982   1.096   1.104   1.160   0.982   0.993   1.044
7     F        -0.172  -0.214  -0.392   0.209   0.153  -0.136  -0.230  -0.290  -0.572
8     D         0.933   0.942   0.982   0.900   0.908   0.983   0.982   0.993   1.044
9     P         0.933   0.942   0.982   1.096   1.104   1.160   0.982   0.993   1.044
10    Y         0.933   0.942   0.982   1.196   1.205   1.251   0.982   0.993   1.044
11    A        -0.553  -0.532  -0.448  -1.074  -1.039  -0.866  -0.835  -0.798  -0.664
12    L        -1.166  -1.125  -1.251  -0.896  -0.843  -1.063  -1.138  -1.084  -1.197
13    S        -1.364  -1.261  -1.262  -1.393  -1.220  -1.246  -1.384  -1.250  -1.209
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    E        -2.129  -2.098  -1.891  -1.992  -1.934  -1.635  -1.857  -1.815  -1.534
23    H        -0.553  -0.503  -0.440  -0.447  -0.351  -0.291  -0.835  -0.750  -0.650
24    D        -2.010  -2.026  -1.879  -2.023  -2.055  -1.781  -1.744  -1.750  -1.523
25    E        -2.010  -1.929  -1.875  -1.908  -1.808  -1.652  -1.744  -1.653  -1.520
26    E        -1.397  -1.396  -1.281  -1.449  -1.458  -1.232  -1.441  -1.424  -1.233
27    R        -2.010  -1.957  -1.871  -1.811  -1.735  -1.603  -1.744  -1.681  -1.516
28    P        -2.622  -2.581  -2.354  -2.218  -2.160  -1.840  -2.047  -1.999  -1.706
29    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    Q        -1.397  -1.430  -1.282  -1.309  -1.360  -1.129  -1.441  -1.462  -1.233
33    S        -2.010  -1.985  -1.878  -1.790  -1.751  -1.580  -1.744  -1.711  -1.523
34    K        -0.172  -0.214  -0.392   0.000  -0.055  -0.363  -0.230  -0.290  -0.572
35    S        -2.010  -1.985  -1.878  -1.832  -1.826  -1.626  -1.744  -1.711  -1.523
36    R        -1.397  -1.430  -1.282  -1.505  -1.520  -1.295  -1.441  -1.462  -1.233
37    T         0.933   0.942   0.982   1.055   1.065   1.123   0.982   0.993   1.044
38    A         0.933   0.942   0.982   0.762   0.768   0.858   0.982   0.993   1.044
39    E        -1.166  -1.277  -1.264  -1.220  -1.379  -1.326  -1.138  -1.270  -1.212
40    L        -0.553  -0.576  -0.454  -0.932  -0.958  -0.709  -0.835  -0.873  -0.674
41    Q         0.933   0.942   0.982   1.025   1.027   1.096   0.982   0.993   1.044
42    A        -0.553  -0.563  -0.452  -0.820  -0.839  -0.622  -0.835  -0.851  -0.670
43    E        -0.172  -0.214  -0.392   0.023  -0.041  -0.307  -0.230  -0.290  -0.572
44    I         0.933   0.942   0.982   0.653   0.664   0.759   0.982   0.993   1.044
45    D         0.933   0.942   0.982   0.900   0.908   0.983   0.982   0.993   1.044
46    D         0.933   0.942   0.982   0.900   0.908   0.983   0.982   0.993   1.044
47    T         0.933   0.942   0.982   1.055   1.065   1.123   0.982   0.993   1.044
48    V         0.933   0.942   0.982   0.837   0.847   0.926   0.982   0.993   1.044
49    G         0.933   0.942   0.982   0.973   0.979   1.049   0.982   0.993   1.044
50    I        -0.172  -0.275  -0.397  -0.407  -0.561  -0.736  -0.230  -0.383  -0.580
51    M         0.933   0.942   0.982   1.035   1.044   1.105   0.982   0.993   1.044
52    R         0.933   0.942   0.982   0.847   0.888   0.935   0.982   0.993   1.044
53    D        -0.553  -0.534  -0.446  -0.614  -0.582  -0.462  -0.835  -0.801  -0.661
54    N         0.933   0.942   0.982   1.035   1.047   1.105   0.982   0.993   1.044
55    I         0.933   0.942   0.982   0.653   0.664   0.759   0.982   0.993   1.044
56    N        -0.172  -0.130  -0.381  -0.002   0.061  -0.348  -0.230  -0.166  -0.554
57    K         0.933   0.942   0.982   0.952   0.970   1.030   0.982   0.993   1.044
58    V         0.933   0.942   0.982   0.837   0.847   0.926   0.982   0.993   1.044
59    A        -0.553  -0.563  -0.452  -0.869  -0.885  -0.676  -0.835  -0.851  -0.670
60    E        -0.172  -0.275  -0.397   0.068  -0.085  -0.297  -0.230  -0.383  -0.580
61    R         0.933   0.942   0.982   0.847   0.888   0.935   0.982   0.993   1.044
62    G         0.933   0.942   0.982   0.973   0.979   1.049   0.982   0.993   1.044
63    E         0.933   0.942   0.982   1.086   1.094   1.151   0.982   0.993   1.044
64    R         0.933   0.942   0.982   0.847   0.888   0.935   0.982   0.993   1.044
65    L        -0.172  -0.275  -0.397  -0.112  -0.289  -0.549  -0.230  -0.383  -0.580
66    T        -0.172  -0.214  -0.392  -0.107  -0.164  -0.419  -0.230  -0.290  -0.572
67    S        -0.172  -0.275  -0.397  -0.137  -0.297  -0.539  -0.230  -0.383  -0.580
68    I        -0.553  -0.534  -0.446  -0.832  -0.802  -0.675  -0.835  -0.801  -0.661
69    E        -0.553  -0.534  -0.446  -0.563  -0.538  -0.396  -0.835  -0.801  -0.661
70    D        -1.166  -1.178  -1.247  -1.040  -1.060  -1.136  -1.138  -1.152  -1.193
71    K         0.933   0.942   0.982   0.952   0.970   1.030   0.982   0.993   1.044
72    A        -0.172  -0.214  -0.392  -0.025  -0.091  -0.436  -0.230  -0.290  -0.572
73    D         0.933   0.942   0.982   0.900   0.908   0.983   0.982   0.993   1.044
74    N        -0.172  -0.275  -0.397  -0.012  -0.166  -0.397  -0.230  -0.383  -0.580
75    L         0.933   0.942   0.982   0.994   0.996   1.068   0.982   0.993   1.044
76    A         0.933   0.942   0.982   0.762   0.768   0.858   0.982   0.993   1.044
77    V        -0.553  -0.553  -0.450  -0.973  -0.981  -0.804  -0.835  -0.834  -0.667
78    S         0.933   0.942   0.982   0.942   0.956   1.021   0.982   0.993   1.044
79    A         0.933   0.942   0.982   0.762   0.768   0.858   0.982   0.993   1.044
80    Q         0.933   0.942   0.982   1.025   1.027   1.096   0.982   0.993   1.044
81    G         0.933   0.942   0.982   0.973   0.979   1.049   0.982   0.993   1.044
82    F         0.933   0.942   0.982   1.166   1.180   1.224   0.982   0.993   1.044
83    K        -0.172  -0.214  -0.392  -0.184  -0.210  -0.512  -0.230  -0.290  -0.572
84    R         0.933   0.942   0.982   0.847   0.888   0.935   0.982   0.993   1.044
85    G         0.933   0.942   0.982   0.973   0.979   1.049   0.982   0.993   1.044
86    A         0.933   0.942   0.982   0.762   0.768   0.858   0.982   0.993   1.044
87    N         0.933   0.942   0.982   1.035   1.047   1.105   0.982   0.993   1.044
88    R        -0.172  -0.275  -0.397  -0.166  -0.283  -0.484  -0.230  -0.383  -0.580
89    V         0.933   0.942   0.982   0.837   0.847   0.926   0.982   0.993   1.044
90    R         0.933   0.942   0.982   0.847   0.888   0.935   0.982   0.993   1.044
91    K         0.933   0.942   0.982   0.952   0.970   1.030   0.982   0.993   1.044
92    A        -1.397  -1.336  -1.279  -1.592  -1.494  -1.377  -1.441  -1.368  -1.231
93    M         0.933   0.942   0.982   1.035   1.044   1.105   0.982   0.993   1.044
94    W         0.933   0.942   0.982   1.216   1.224   1.269   0.982   0.993   1.044
95    Y        -1.166  -1.125  -1.251  -0.719  -0.660  -0.883  -1.138  -1.084  -1.197
96    K         0.933   0.942   0.982   0.952   0.970   1.030   0.982   0.993   1.044
97    D         0.933   0.942   0.982   0.900   0.908   0.983   0.982   0.993   1.044
98    L        -1.397  -1.396  -1.281  -1.219  -1.220  -1.050  -1.441  -1.424  -1.233
99    K        -0.172  -0.130  -0.381  -0.107  -0.031  -0.458  -0.230  -0.166  -0.554
100   M         0.933   0.942   0.982   1.035   1.044   1.105   0.982   0.993   1.044
101   K        -0.553  -0.532  -0.448  -0.790  -0.723  -0.604  -0.835  -0.798  -0.664
102   M        -2.010  -1.985  -1.878  -1.965  -1.956  -1.810  -1.744  -1.711  -1.523
103   C         0.933   0.942   0.982   1.246   1.254   1.296   0.982   0.993   1.044
104   L        -0.172  -0.130  -0.381  -0.112  -0.056  -0.513  -0.230  -0.166  -0.554
105   A        -1.166  -1.125  -1.251  -1.440  -1.383  -1.560  -1.138  -1.084  -1.197
106   L        -2.010  -2.026  -1.879  -2.069  -2.102  -1.795  -1.744  -1.750  -1.523
107   V        -0.172  -0.214  -0.392  -0.089  -0.155  -0.467  -0.230  -0.290  -0.572
108   I        -0.172  -0.075  -0.380  -0.407  -0.270  -0.707  -0.230  -0.087  -0.552
109   I         0.933   0.942   0.982   0.653   0.664   0.759   0.982   0.993   1.044
110   I         0.933   0.942   0.982   0.653   0.664   0.759   0.982   0.993   1.044
111   L        -0.172  -0.080  -0.371  -0.068   0.055  -0.410  -0.230  -0.094  -0.538
112   L        -0.553  -0.482  -0.435  -0.832  -0.685  -0.643  -0.835  -0.715  -0.643
113   V        -0.172  -0.080  -0.371  -0.269  -0.132  -0.625  -0.230  -0.094  -0.538
114   V        -0.172  -0.275  -0.397  -0.269  -0.436  -0.679  -0.230  -0.383  -0.580
115   I         0.933   0.942   0.982   0.653   0.664   0.759   0.982   0.993   1.044
116   I        -0.553  -0.482  -0.435  -1.028  -0.904  -0.800  -0.835  -0.715  -0.643
117   V         0.933   0.942   0.982   0.837   0.847   0.926   0.982   0.993   1.044
118   P         0.933   0.942   0.982   1.096   1.104   1.160   0.982   0.993   1.044
119   I        -0.172  -0.275  -0.397  -0.427  -0.587  -0.775  -0.230  -0.383  -0.580
120   A        -0.172  -0.275  -0.397  -0.298  -0.458  -0.648  -0.230  -0.383  -0.580
121   V        -0.172  -0.130  -0.381  -0.169  -0.110  -0.453  -0.230  -0.166  -0.554
122   H        -1.166  -1.215  -1.261  -0.877  -0.973  -1.125  -1.138  -1.196  -1.208
123   F        -0.172  -0.275  -0.397   0.153   0.009  -0.220  -0.230  -0.383  -0.580
124   S        -0.309  -0.358  -0.419  -0.255  -0.325  -0.391  -0.438  -0.514  -0.617
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   R        -0.309  -0.247  -0.393  -0.377  -0.281  -0.510  -0.438  -0.341  -0.573
* 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/P31109
Output conservation file - output/P31109
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
