1     M         1.135   1.157   1.224   1.631   1.648   1.707   1.187   1.219   1.322
2     A        -0.437  -0.657  -0.755  -0.302  -0.592  -0.726  -0.396  -0.682  -0.811
3     G        -0.566  -0.846  -0.800  -0.126  -0.682  -0.753  -0.563  -0.928  -0.868
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     V        -0.437  -0.347  -0.714  -0.070   0.005  -0.589  -0.396  -0.305  -0.758
7     K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
8     A        -0.279  -0.170  -0.063  -0.559  -0.376  -0.200  -0.640  -0.471  -0.332
9     Y        -1.548  -1.534  -1.339  -1.062  -1.041  -0.785  -1.493  -1.405  -1.158
10    E         0.330   0.180   0.046   0.567   0.357   0.069   0.334   0.106  -0.143
11    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
12    R        -0.437  -0.657  -0.755  -0.290  -0.555  -0.616  -0.396  -0.682  -0.811
13    T        -1.159  -1.414  -1.342  -0.940  -1.461  -1.454  -1.005  -1.273  -1.160
14    K        -0.437  -0.622  -0.745  -0.760  -0.945  -1.038  -0.396  -0.634  -0.799
15    S         0.330   0.180   0.046   0.761   0.544   0.328   0.334   0.106  -0.143
16    K         0.330   0.222   0.048  -0.095  -0.175  -0.415   0.334   0.171  -0.138
17    E        -0.789  -0.826  -0.787  -0.587  -0.660  -0.632  -0.884  -0.915  -0.857
18    Q        -0.789  -0.914  -0.805  -0.703  -0.876  -0.693  -0.884  -1.039  -0.877
19    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
20    A        -0.789  -0.844  -0.784  -0.724  -0.816  -0.790  -0.884  -0.931  -0.852
21    S        -2.568  -2.286  -2.105  -2.474  -2.173  -1.799  -1.980  -1.697  -1.451
22    Q         0.330   0.240   0.049   0.396   0.283  -0.171   0.334   0.198  -0.136
23    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
24    V        -1.159  -1.212  -1.311  -0.746  -0.836  -1.094  -1.005  -1.072  -1.129
25    D        -0.437  -0.041  -0.682  -0.041   0.425  -0.380  -0.396   0.093  -0.717
26    L         0.330   0.240   0.049   0.295   0.189  -0.019   0.334   0.198  -0.136
27    K         0.330   0.222   0.048  -0.121  -0.220  -0.485   0.334   0.171  -0.138
28    K        -1.177  -1.034  -0.822  -1.803  -1.418  -1.096  -1.371  -1.172  -0.897
29    E         0.330   0.481   0.071   0.635   0.823   0.281   0.334   0.539  -0.100
30    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
31    A         0.330   0.180   0.046   0.417   0.258   0.081   0.334   0.106  -0.143
32    E        -2.058  -1.955  -1.769  -1.702  -1.592  -1.325  -1.736  -1.593  -1.340
33    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
34    K        -0.947  -0.706  -0.775  -1.721  -1.234  -1.234  -1.127  -0.836  -0.841
35    V         0.330   0.180   0.046   0.685   0.498   0.236   0.334   0.106  -0.143
36    Q         1.135   1.157   1.224   1.203   1.275   1.350   1.187   1.219   1.322
37    K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
38    L        -0.067  -0.164  -0.065  -0.279  -0.445  -0.234  -0.275  -0.460  -0.336
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    S        -0.279  -0.164  -0.060  -0.305  -0.125  -0.015  -0.640  -0.460  -0.328
43    R        -1.457  -1.405  -1.340  -1.504  -1.341  -1.304  -1.371  -1.305  -1.160
44    P        -1.159  -1.414  -1.342  -0.520  -0.933  -0.871  -1.005  -1.273  -1.160
45    S        -0.279  -0.232  -0.061  -0.585  -0.710  -0.420  -0.640  -0.582  -0.329
46    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
47    P        -1.159  -1.414  -1.342  -0.530  -0.941  -0.889  -1.005  -1.273  -1.160
48    K        -0.067   0.163   0.027  -0.737  -0.312  -0.523  -0.275   0.080  -0.174
49    I         1.135   1.157   1.224   1.390   1.420   1.505   1.187   1.219   1.322
50    K        -1.457  -1.296  -1.316  -1.145  -0.986  -1.044  -1.371  -1.186  -1.137
51    T        -0.067  -0.157  -0.064   0.101  -0.071   0.081  -0.275  -0.448  -0.335
52    V        -0.437  -0.673  -0.752  -0.082  -0.465  -0.693  -0.396  -0.701  -0.808
53    R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
54    K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
55    S        -1.087  -0.989  -0.829  -0.765  -0.679  -0.462  -1.249  -1.114  -0.904
56    I         1.135   1.157   1.224   1.390   1.420   1.505   1.187   1.219   1.322
57    A         1.135   1.157   1.224   1.091   1.157   1.256   1.187   1.219   1.322
58    C         0.330   0.574   0.079   0.380   0.661   0.124   0.334   0.657  -0.087
59    V         0.330   0.222   0.048   0.685   0.559   0.240   0.334   0.171  -0.138
60    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
61    T         1.135   1.157   1.224   1.313   1.338   1.441   1.187   1.219   1.322
62    V        -0.067  -0.045  -0.049   0.117   0.145   0.065  -0.275  -0.256  -0.308
63    I         0.330   0.240   0.049   0.628   0.481   0.097   0.334   0.198  -0.136
64    N         0.330   0.552   0.073   0.829   1.069   0.408   0.334   0.630  -0.096
65    E        -1.548  -1.391  -1.333  -1.762  -1.568  -1.427  -1.493  -1.301  -1.154
66    Q        -2.058  -2.038  -1.778  -1.840  -1.940  -1.581  -1.736  -1.643  -1.347
67    Q         0.330   0.222   0.048   0.520   0.419   0.150   0.334   0.171  -0.138
68    R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
69    E        -1.827  -1.729  -1.741  -1.534  -1.530  -1.542  -1.493  -1.388  -1.318
70    A        -1.087  -0.950  -0.813  -1.240  -1.062  -0.822  -1.249  -1.078  -0.886
71    V        -0.437  -0.673  -0.752  -0.118  -0.512  -0.779  -0.396  -0.701  -0.808
72    R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
73    Q        -1.687  -1.469  -1.318  -1.880  -1.512  -1.344  -1.614  -1.330  -1.136
74    L        -0.947  -0.825  -0.766  -1.007  -0.729  -0.721  -1.127  -0.911  -0.826
75    Y         1.135   1.157   1.224   1.527   1.551   1.620   1.187   1.219   1.322
76    K        -0.067   0.163   0.027  -0.718  -0.294  -0.499  -0.275   0.080  -0.174
77    G        -0.789  -0.905  -0.803  -0.278  -0.512  -0.369  -0.884  -1.031  -0.876
78    K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
79    K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
80    Y         0.330   0.240   0.049   0.840   0.714   0.395   0.334   0.198  -0.136
81    Q        -1.087  -1.032  -0.832  -1.302  -1.293  -0.947  -1.249  -1.169  -0.909
82    P         1.135   1.157   1.224   1.515   1.549   1.610   1.187   1.219   1.322
83    K        -0.067  -0.164  -0.065  -0.759  -0.930  -0.713  -0.275  -0.460  -0.336
84    D         1.135   1.157   1.224   1.564   1.577   1.651   1.187   1.219   1.322
85    L         0.330   0.525   0.073   0.312   0.535   0.053   0.334   0.596  -0.096
86    R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
87    A        -0.437  -0.622  -0.745  -0.297  -0.525  -0.702  -0.396  -0.634  -0.799
88    K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
89    K        -0.067  -0.157  -0.064  -0.676  -0.767  -0.570  -0.275  -0.448  -0.335
90    T         1.135   1.157   1.224   1.313   1.338   1.441   1.187   1.219   1.322
91    R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
92    A         1.135   1.157   1.224   1.091   1.157   1.256   1.187   1.219   1.322
93    L        -0.346  -0.157  -0.032  -0.685  -0.275  -0.090  -0.762  -0.448  -0.277
94    R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
95    R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
96    A        -1.457  -1.222  -1.331  -1.783  -1.480  -1.699  -1.371  -1.147  -1.151
97    L         1.135   1.157   1.224   0.977   1.016   1.161   1.187   1.219   1.322
98    T         0.330   0.180   0.046   0.617   0.404   0.199   0.334   0.106  -0.143
99    K        -0.067  -0.140  -0.063  -0.560  -0.589  -0.378  -0.275  -0.418  -0.332
100   F        -1.159  -1.414  -1.342  -0.582  -1.027  -1.010  -1.005  -1.273  -1.160
101   E        -0.437  -0.657  -0.755  -0.080  -0.381  -0.572  -0.396  -0.682  -0.811
102   A         0.330   0.222   0.048   0.361   0.244  -0.058   0.334   0.171  -0.138
103   S        -1.159  -0.960  -1.274  -0.823  -0.597  -1.230  -1.005  -0.787  -1.092
104   Q        -0.947  -0.907  -0.782  -1.248  -1.190  -0.994  -1.127  -1.034  -0.850
105   V        -1.457  -1.215  -1.325  -1.467  -1.286  -1.377  -1.371  -1.137  -1.146
106   T         0.330   0.180   0.046   0.552   0.303   0.028   0.334   0.106  -0.143
107   E        -1.159  -1.201  -1.304  -0.802  -0.948  -1.098  -1.005  -1.052  -1.123
108   K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
109   Q        -0.947  -0.942  -0.798  -1.167  -1.109  -0.892  -1.127  -1.071  -0.869
110   R        -1.457  -1.523  -1.342  -1.813  -1.953  -1.627  -1.371  -1.396  -1.162
111   K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
112   K        -0.789  -0.721  -0.750  -1.397  -1.242  -1.263  -0.884  -0.765  -0.805
113   Q        -1.827  -1.733  -1.749  -1.771  -1.635  -1.834  -1.493  -1.392  -1.323
114   I        -0.789  -0.914  -0.805  -0.620  -0.910  -0.775  -0.884  -1.039  -0.877
115   A        -0.789  -0.914  -0.805  -0.676  -0.779  -0.566  -0.884  -1.039  -0.877
116   F         1.135   1.157   1.224   1.527   1.549   1.620   1.187   1.219   1.322
117   P         1.135   1.157   1.224   1.515   1.549   1.610   1.187   1.219   1.322
118   Q        -0.067  -0.164  -0.065  -0.194  -0.424  -0.315  -0.275  -0.460  -0.336
119   R         1.135   1.157   1.224   1.038   1.088   1.211   1.187   1.219   1.322
120   K        -0.067  -0.026  -0.044  -0.737  -0.633  -0.646  -0.275  -0.224  -0.298
121   Y        -0.279  -0.184  -0.065  -0.071   0.050   0.196  -0.640  -0.496  -0.336
122   A         1.135   1.157   1.224   1.091   1.157   1.256   1.187   1.219   1.322
123   I        -0.789  -0.933  -0.804  -0.678  -1.011  -0.827  -0.884  -1.057  -0.876
124   K         1.135   1.157   1.224   0.641   0.740   0.880   1.187   1.219   1.322
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   A         1.135   1.157   1.224   1.091   1.157   1.256   1.187   1.219   1.322
* 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/P0CX84
Output conservation file - output/P0CX84
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
