1     M         0.924   0.933   0.966   1.342   1.345   1.346   0.952   0.965   1.019
2     A         0.145   0.027  -0.383   0.280   0.151  -0.483   0.225   0.074  -0.552
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     Q         0.145   0.052  -0.384   0.442   0.343  -0.292   0.225   0.106  -0.553
5     R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
6     V         0.924   0.933   0.966   0.863   0.895   0.955   0.952   0.965   1.019
7     T         0.924   0.933   0.966   0.985   1.000   1.054   0.952   0.965   1.019
8     F        -0.539  -0.398  -0.425  -0.237  -0.053  -0.143  -0.745  -0.533  -0.620
9     R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
10    R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
11    R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
12    N        -0.275  -0.372  -0.404   0.032  -0.147  -0.257  -0.341  -0.492  -0.585
13    P        -0.996  -1.183  -1.250  -0.609  -0.916  -1.085  -0.906  -1.129  -1.193
14    Y         0.924   0.933   0.966   1.206   1.211   1.235   0.952   0.965   1.019
15    N         0.924   0.933   0.966   1.164   1.165   1.200   0.952   0.965   1.019
16    T         0.924   0.933   0.966   0.985   1.000   1.054   0.952   0.965   1.019
17    R        -1.684  -1.535  -1.841  -1.800  -1.581  -2.008  -1.391  -1.221  -1.487
18    S         0.924   0.933   0.966   1.083   1.105   1.135   0.952   0.965   1.019
19    N         0.924   0.933   0.966   1.164   1.165   1.200   0.952   0.965   1.019
20    K        -0.275  -0.379  -0.440  -0.756  -0.898  -1.003  -0.341  -0.504  -0.644
21    I        -1.227  -1.355  -1.276  -1.080  -1.317  -1.212  -1.229  -1.371  -1.224
22    K        -0.539  -0.606  -0.456  -1.205  -1.322  -1.029  -0.745  -0.863  -0.671
23    V        -0.688  -0.680  -0.458  -0.904  -0.894  -0.532  -0.987  -0.987  -0.675
24    V        -0.539  -0.613  -0.455  -0.659  -0.793  -0.541  -0.745  -0.874  -0.669
25    K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
26    T         0.924   0.933   0.966   0.985   1.000   1.054   0.952   0.965   1.019
27    P         0.924   0.933   0.966   1.153   1.153   1.192   0.952   0.965   1.019
28    G         0.924   0.933   0.966   0.990   1.000   1.059   0.952   0.965   1.019
29    G        -0.275  -0.372  -0.404  -0.109  -0.267  -0.329  -0.341  -0.492  -0.585
30    I        -2.680  -2.533  -2.335  -2.625  -2.305  -2.072  -2.118  -1.958  -1.689
31    L        -0.275  -0.372  -0.404  -0.076  -0.258  -0.332  -0.341  -0.492  -0.585
32    R        -0.539  -0.338  -0.407  -0.921  -0.610  -0.697  -0.745  -0.441  -0.590
33    A        -1.874  -1.904  -1.870  -1.616  -1.652  -1.586  -1.633  -1.657  -1.513
34    Q        -0.688  -0.680  -0.458  -0.756  -0.785  -0.437  -0.987  -0.987  -0.675
35    H         0.924   0.933   0.966   1.311   1.319   1.321   0.952   0.965   1.019
36    V        -0.688  -0.680  -0.458  -0.904  -0.894  -0.532  -0.987  -0.987  -0.675
37    K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
38    K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
39    L        -0.996  -1.075  -1.257  -0.752  -0.902  -1.288  -0.906  -0.990  -1.202
40    A        -0.539  -0.606  -0.456  -0.646  -0.781  -0.554  -0.745  -0.863  -0.671
41    T        -1.227  -1.154  -1.244  -1.086  -0.951  -1.108  -1.229  -1.090  -1.186
42    R        -0.996  -1.162  -1.254  -1.048  -1.301  -1.366  -0.906  -1.108  -1.197
43    P         0.145   0.282  -0.372   0.526   0.660  -0.280   0.225   0.388  -0.534
44    K        -0.275  -0.372  -0.404  -0.756  -0.885  -0.938  -0.341  -0.492  -0.585
45    C         0.924   0.933   0.966   1.227   1.238   1.252   0.952   0.965   1.019
46    G         0.924   0.933   0.966   0.990   1.000   1.059   0.952   0.965   1.019
47    D         0.145   0.027  -0.383   0.702   0.561  -0.089   0.225   0.074  -0.552
48    C        -0.539  -0.565  -0.456  -0.349  -0.430  -0.353  -0.745  -0.796  -0.670
49    G         0.924   0.933   0.966   0.990   1.000   1.059   0.952   0.965   1.019
50    S        -2.348  -2.116  -1.870  -2.143  -1.899  -1.518  -2.037  -1.818  -1.513
51    A        -1.227  -1.311  -1.272  -1.200  -1.336  -1.349  -1.229  -1.317  -1.219
52    L         0.924   0.933   0.966   1.051   1.044   1.108   0.952   0.965   1.019
53    Q        -1.352  -1.351  -1.286  -1.147  -1.171  -1.143  -1.310  -1.309  -1.234
54    G         0.924   0.933   0.966   0.990   1.000   1.059   0.952   0.965   1.019
55    I        -0.275  -0.297  -0.446  -0.113  -0.174  -0.500  -0.341  -0.379  -0.654
56    S        -1.335  -1.233  -1.266  -1.162  -1.041  -1.072  -1.391  -1.276  -1.213
57    T        -0.539  -0.606  -0.456  -0.606  -0.757  -0.551  -0.745  -0.863  -0.671
58    L         0.924   0.933   0.966   1.051   1.044   1.108   0.952   0.965   1.019
59    R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
60    P         0.924   0.933   0.966   1.153   1.153   1.192   0.952   0.965   1.019
61    R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
62    Q        -0.688  -0.558  -0.445  -0.686  -0.468  -0.360  -0.987  -0.785  -0.653
63    Y        -0.996  -1.183  -1.250  -0.438  -0.710  -0.862  -0.906  -1.129  -1.193
64    A         0.924   0.933   0.966   0.908   0.934   0.991   0.952   0.965   1.019
65    T        -2.141  -2.079  -1.864  -2.078  -2.073  -1.696  -1.876  -1.808  -1.508
66    V        -1.227  -1.214  -1.269  -1.201  -1.236  -1.201  -1.229  -1.247  -1.216
67    S         0.924   0.933   0.966   1.083   1.105   1.135   0.952   0.965   1.019
68    K        -1.352  -1.443  -1.275  -1.718  -1.812  -1.528  -1.310  -1.421  -1.222
69    T        -1.352  -1.496  -1.282  -1.123  -1.363  -1.055  -1.310  -1.486  -1.230
70    H        -1.874  -2.009  -1.854  -1.619  -1.888  -1.735  -1.633  -1.731  -1.499
71    K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
72    T         0.145   0.040  -0.373   0.316   0.183  -0.563   0.225   0.091  -0.536
73    V         0.924   0.933   0.966   0.863   0.895   0.955   0.952   0.965   1.019
74    S        -0.539  -0.398  -0.425  -0.480  -0.264  -0.363  -0.745  -0.533  -0.620
75    R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
76    A         0.145   0.218  -0.376   0.280   0.372  -0.471   0.225   0.313  -0.541
77    Y         0.924   0.933   0.966   1.206   1.211   1.235   0.952   0.965   1.019
78    G         0.924   0.933   0.966   0.990   1.000   1.059   0.952   0.965   1.019
79    G         0.924   0.933   0.966   0.990   1.000   1.059   0.952   0.965   1.019
80    S        -0.275  -0.372  -0.404  -0.003  -0.144  -0.236  -0.341  -0.492  -0.585
81    R        -1.227  -1.231  -1.270  -1.469  -1.516  -1.552  -1.229  -1.264  -1.217
82    C        -0.539  -0.565  -0.456  -0.311  -0.383  -0.301  -0.745  -0.796  -0.670
83    A         0.145   0.052  -0.384   0.294   0.196  -0.431   0.225   0.106  -0.553
84    N         0.924   0.933   0.966   1.164   1.165   1.200   0.952   0.965   1.019
85    C        -0.539  -0.565  -0.456  -0.378  -0.460  -0.394  -0.745  -0.796  -0.670
86    V         0.924   0.933   0.966   0.863   0.895   0.955   0.952   0.965   1.019
87    K         0.145   0.052  -0.384  -0.185  -0.253  -0.901   0.225   0.106  -0.553
88    E        -0.688  -0.680  -0.458  -0.543  -0.535  -0.236  -0.987  -0.987  -0.675
89    R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
90    I        -0.275  -0.394  -0.444  -0.113  -0.332  -0.496  -0.341  -0.527  -0.651
91    V         0.924   0.933   0.966   0.863   0.895   0.955   0.952   0.965   1.019
92    R         0.924   0.933   0.966   0.675   0.684   0.801   0.952   0.965   1.019
93    A         0.924   0.933   0.966   0.908   0.934   0.991   0.952   0.965   1.019
94    F         0.924   0.933   0.966   1.322   1.326   1.329   0.952   0.965   1.019
95    L         0.924   0.933   0.966   1.051   1.044   1.108   0.952   0.965   1.019
96    I         0.924   0.933   0.966   1.061   1.061   1.117   0.952   0.965   1.019
97    E         0.924   0.933   0.966   1.131   1.150   1.174   0.952   0.965   1.019
98    E         0.924   0.933   0.966   1.131   1.150   1.174   0.952   0.965   1.019
99    Q         0.924   0.933   0.966   1.045   1.066   1.103   0.952   0.965   1.019
100   K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
101   I         0.924   0.933   0.966   1.061   1.061   1.117   0.952   0.965   1.019
102   V         0.924   0.933   0.966   0.863   0.895   0.955   0.952   0.965   1.019
103   K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
104   K        -2.141  -2.180  -1.871  -2.583  -2.593  -2.075  -1.876  -1.877  -1.514
105   V        -0.275  -0.372  -0.404  -0.406  -0.570  -0.732  -0.341  -0.492  -0.585
106   V        -0.996  -0.794  -1.230  -0.712  -0.462  -1.106  -0.906  -0.654  -1.169
107   K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
108   E        -0.996  -0.974  -1.238  -0.550  -0.587  -0.902  -0.906  -0.921  -1.178
109   Q        -1.328  -1.583  -1.844  -0.724  -1.043  -1.420  -0.987  -1.249  -1.489
110   T        -1.707  -1.514  -1.279  -1.722  -1.420  -1.126  -1.741  -1.508  -1.226
111   E        -1.365  -1.472  -1.280  -1.013  -1.204  -0.960  -1.356  -1.461  -1.227
112   A        -0.712  -0.545  -0.444  -1.343  -0.929  -0.861  -1.027  -0.764  -0.651
113   A        -0.712  -0.621  -0.455  -0.830  -0.668  -0.465  -1.027  -0.889  -0.669
114   K        -0.509  -0.284  -0.424  -1.090  -0.737  -0.848  -0.697  -0.361  -0.618
115   K         0.924   0.933   0.966   0.348   0.381   0.534   0.952   0.965   1.019
116   S        -1.498  -1.302  -1.283  -1.539  -1.265  -1.230  -1.517  -1.267  -1.231
117   E        -1.498  -1.335  -1.291  -1.425  -1.175  -1.170  -1.517  -1.312  -1.240
118   K         0.924   0.933   0.966   0.348   0.381   0.534   0.952   0.965   1.019
119   K         0.924   0.933   0.966   0.348   0.381   0.534   0.952   0.965   1.019
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   S        -0.600  -0.415  -0.420  -0.592  -0.293  -0.370  -0.843  -0.559  -0.612
125   K        -0.345  -0.491  -0.418  -0.788  -0.967  -0.803  -0.444  -0.678  -0.609
126   K         0.924   0.933   0.966   0.469   0.535   0.633   0.952   0.965   1.019
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -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/P40525
Output conservation file - output/P40525
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
