1     M         1.031   1.045   1.109   1.380   1.366   1.445   1.058   1.080   1.177
2     A        -1.163  -1.300  -1.191  -1.238  -1.474  -1.306  -1.135  -1.306  -1.134
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
5     F        -0.260  -0.288  -0.296  -0.110  -0.163  -0.231  -0.369  -0.424  -0.477
6     L        -0.260  -0.154  -0.292  -0.100   0.019  -0.217  -0.369  -0.223  -0.471
7     K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
8     A        -2.163  -2.151  -1.796  -2.009  -1.958  -1.524  -1.898  -1.845  -1.428
9     G         0.181  -0.025  -0.262   0.454   0.192  -0.179   0.243  -0.037  -0.422
10    K         0.181  -0.025  -0.262  -0.248  -0.457  -0.740   0.243  -0.037  -0.422
11    V         1.031   1.045   1.109   0.804   0.842   0.965   1.058   1.080   1.177
12    A         0.181  -0.025  -0.262   0.332   0.126  -0.174   0.243  -0.037  -0.422
13    V        -1.554  -1.300  -1.168  -1.673  -1.239  -1.123  -1.593  -1.280  -1.107
14    V         0.181   0.130  -0.244   0.138   0.103  -0.377   0.243   0.174  -0.394
15    V        -0.520  -0.559  -0.350  -0.847  -0.910  -0.578  -0.777  -0.860  -0.566
16    R         1.031   1.045   1.109   1.088   1.078   1.202   1.058   1.080   1.177
17    G         1.031   1.045   1.109   1.125   1.128   1.233   1.058   1.080   1.177
18    R         1.031   1.045   1.109   1.088   1.078   1.202   1.058   1.080   1.177
19    Y        -0.520  -0.483  -0.346  -0.387  -0.366  -0.249  -0.777  -0.735  -0.559
20    A         1.031   1.045   1.109   0.964   1.000   1.098   1.058   1.080   1.177
21    G         1.031   1.045   1.109   1.125   1.128   1.233   1.058   1.080   1.177
22    K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
23    K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
24    V         1.031   1.045   1.109   0.804   0.842   0.965   1.058   1.080   1.177
25    V         1.031   1.045   1.109   0.804   0.842   0.965   1.058   1.080   1.177
26    I         1.031   1.045   1.109   1.225   1.221   1.316   1.058   1.080   1.177
27    V        -1.394  -1.471  -1.196  -1.510  -1.604  -1.188  -1.389  -1.489  -1.140
28    K        -0.520  -0.559  -0.350  -1.062  -1.030  -0.655  -0.777  -0.860  -0.566
29    P        -1.037  -1.088  -1.166  -0.726  -0.834  -1.001  -0.981  -1.055  -1.108
30    H        -1.037  -1.174  -1.177  -0.708  -0.972  -1.081  -0.981  -1.163  -1.119
31    D         1.031   1.045   1.109   1.370   1.363   1.436   1.058   1.080   1.177
32    E        -1.037  -1.228  -1.171  -0.692  -0.928  -0.880  -0.981  -1.200  -1.112
33    G         1.031   1.045   1.109   1.125   1.128   1.233   1.058   1.080   1.177
34    S        -0.643  -0.553  -0.347  -0.729  -0.617  -0.328  -0.981  -0.850  -0.561
35    K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
36    S        -1.252  -1.317  -1.165  -1.158  -1.232  -1.080  -1.287  -1.321  -1.107
37    H         1.031   1.045   1.109   1.272   1.283   1.355   1.058   1.080   1.177
38    P         1.031   1.045   1.109   1.189   1.191   1.285   1.058   1.080   1.177
39    F         0.181  -0.025  -0.262   0.453   0.213  -0.144   0.243  -0.037  -0.422
40    G        -1.394  -1.227  -1.183  -1.288  -1.055  -1.092  -1.389  -1.194  -1.125
41    H         1.031   1.045   1.109   1.272   1.283   1.355   1.058   1.080   1.177
42    A         1.031   1.045   1.109   0.964   1.000   1.098   1.058   1.080   1.177
43    L        -1.554  -1.506  -1.188  -1.590  -1.556  -1.139  -1.593  -1.532  -1.131
44    V         1.031   1.045   1.109   0.804   0.842   0.965   1.058   1.080   1.177
45    A         0.181   0.284  -0.243   0.245   0.386  -0.423   0.243   0.370  -0.392
46    G         1.031   1.045   1.109   1.125   1.128   1.233   1.058   1.080   1.177
47    I        -0.520  -0.523  -0.348  -0.593  -0.657  -0.472  -0.777  -0.801  -0.562
48    E         1.031   1.045   1.109   1.099   1.118   1.210   1.058   1.080   1.177
49    R         1.031   1.045   1.109   1.088   1.078   1.202   1.058   1.080   1.177
50    Y         0.181   0.242  -0.246   0.605   0.653  -0.105   0.243   0.318  -0.396
51    P         1.031   1.045   1.109   1.189   1.191   1.285   1.058   1.080   1.177
52    S        -0.260  -0.282  -0.331  -0.110  -0.176  -0.299  -0.369  -0.415  -0.535
53    K         0.181   0.132  -0.253  -0.212  -0.217  -0.612   0.243   0.177  -0.409
54    V         0.181  -0.025  -0.262   0.138  -0.083  -0.402   0.243  -0.037  -0.422
55    T         0.181   0.132  -0.253   0.433   0.352  -0.181   0.243   0.177  -0.409
56    K        -0.635  -0.876  -1.135  -0.949  -1.213  -1.537  -0.471  -0.764  -1.068
57    K        -2.680  -2.585  -2.266  -2.689  -2.484  -1.948  -2.102  -2.001  -1.606
58    H        -1.769  -1.303  -1.733  -1.063  -0.516  -1.137  -1.491  -0.993  -1.370
59    G        -1.037  -1.197  -1.165  -0.677  -0.899  -0.885  -0.981  -1.159  -1.106
60    A         0.181  -0.025  -0.262   0.201  -0.070  -0.611   0.243  -0.037  -0.422
61    K         0.181  -0.025  -0.262  -0.246  -0.453  -0.732   0.243  -0.037  -0.422
62    K        -0.520  -0.559  -0.350  -1.195  -1.209  -0.819  -0.777  -0.860  -0.566
63    V        -1.930  -1.932  -1.786  -1.820  -1.745  -1.519  -1.694  -1.676  -1.420
64    A        -0.635  -0.778  -1.123  -0.392  -0.563  -1.086  -0.471  -0.655  -1.054
65    K         0.181   0.130  -0.244  -0.248  -0.264  -0.716   0.243   0.174  -0.394
66    R         1.031   1.045   1.109   1.088   1.078   1.202   1.058   1.080   1.177
67    T        -0.520  -0.559  -0.350  -0.532  -0.647  -0.339  -0.777  -0.860  -0.566
68    K        -0.260  -0.288  -0.296  -0.811  -0.821  -0.784  -0.369  -0.424  -0.477
69    I        -0.520  -0.254  -0.280  -0.787  -0.388  -0.428  -0.777  -0.372  -0.452
70    K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
71    P         1.031   1.045   1.109   1.189   1.191   1.285   1.058   1.080   1.177
72    F         1.031   1.045   1.109   1.109   1.126   1.219   1.058   1.080   1.177
73    I        -0.260  -0.154  -0.292  -0.112   0.026  -0.325  -0.369  -0.223  -0.471
74    K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
75    V        -1.037  -0.767  -1.131  -1.106  -0.754  -1.255  -0.981  -0.679  -1.065
76    V        -0.643  -0.575  -0.351  -0.956  -0.847  -0.502  -0.981  -0.887  -0.568
77    N         1.031   1.045   1.109   1.314   1.310   1.389   1.058   1.080   1.177
78    Y         1.031   1.045   1.109   1.303   1.296   1.381   1.058   1.080   1.177
79    N         1.031   1.045   1.109   1.314   1.310   1.389   1.058   1.080   1.177
80    H         1.031   1.045   1.109   1.272   1.283   1.355   1.058   1.080   1.177
81    L         0.181   0.132  -0.253   0.474   0.401  -0.092   0.243   0.177  -0.409
82    L        -0.520  -0.254  -0.280  -0.313   0.085  -0.054  -0.777  -0.372  -0.452
83    P         1.031   1.045   1.109   1.189   1.191   1.285   1.058   1.080   1.177
84    T         1.031   1.045   1.109   1.104   1.096   1.215   1.058   1.080   1.177
85    R         1.031   1.045   1.109   1.088   1.078   1.202   1.058   1.080   1.177
86    Y         1.031   1.045   1.109   1.303   1.296   1.381   1.058   1.080   1.177
87    T        -1.394  -1.324  -1.174  -1.308  -1.253  -1.093  -1.389  -1.311  -1.114
88    L         1.031   1.045   1.109   1.120   1.117   1.228   1.058   1.080   1.177
89    D        -0.520  -0.559  -0.350  -0.331  -0.466  -0.224  -0.777  -0.860  -0.566
90    V        -0.643  -0.574  -0.340  -1.027  -0.873  -0.518  -0.981  -0.885  -0.549
91    E        -1.037  -1.103  -1.157  -0.712  -0.805  -0.922  -0.981  -1.064  -1.094
92    A        -2.071  -2.030  -1.788  -1.747  -1.682  -1.447  -1.796  -1.731  -1.421
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    F        -0.643  -0.574  -0.340  -0.782  -0.691  -0.355  -0.981  -0.885  -0.549
95    K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
96    S        -1.252  -1.285  -1.185  -1.039  -1.129  -0.951  -1.287  -1.324  -1.129
97    V        -1.769  -1.881  -1.785  -1.711  -1.849  -1.718  -1.491  -1.602  -1.418
98    V        -0.260  -0.309  -0.330  -0.408  -0.466  -0.491  -0.369  -0.456  -0.533
99    S        -1.252  -1.256  -1.169  -1.082  -1.128  -1.012  -1.287  -1.282  -1.112
100   T        -2.071  -2.043  -1.796  -1.858  -1.883  -1.550  -1.796  -1.761  -1.429
101   E        -0.635  -0.701  -1.126  -0.218  -0.296  -0.893  -0.471  -0.551  -1.058
102   T         0.181   0.242  -0.246   0.405   0.454  -0.257   0.243   0.318  -0.396
103   F        -0.260  -0.154  -0.292  -0.140   0.001  -0.272  -0.369  -0.223  -0.471
104   E        -1.769  -1.884  -1.790  -1.681  -1.983  -1.915  -1.491  -1.616  -1.424
105   Q         0.181   0.377  -0.239   0.447   0.650  -0.103   0.243   0.482  -0.386
106   P         0.181  -0.025  -0.262   0.471   0.187  -0.287   0.243  -0.037  -0.422
107   S        -0.643  -0.571  -0.351  -0.729  -0.653  -0.338  -0.981  -0.880  -0.568
108   Q         0.181   0.132  -0.253   0.659   0.583  -0.033   0.243   0.177  -0.409
109   R         1.031   1.045   1.109   1.088   1.078   1.202   1.058   1.080   1.177
110   E        -0.260  -0.288  -0.296  -0.131  -0.185  -0.255  -0.369  -0.424  -0.477
111   E        -1.394  -1.471  -1.196  -1.245  -1.365  -1.022  -1.389  -1.489  -1.140
112   A         1.031   1.045   1.109   0.964   1.000   1.098   1.058   1.080   1.177
113   K         0.181   0.130  -0.244  -0.248  -0.264  -0.716   0.243   0.174  -0.394
114   K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
115   V        -0.643  -0.574  -0.340  -1.038  -0.891  -0.529  -0.981  -0.885  -0.549
116   V        -0.520  -0.371  -0.323  -0.787  -0.557  -0.483  -0.777  -0.554  -0.521
117   K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
118   K        -0.635  -0.699  -1.114  -0.849  -0.873  -1.248  -0.471  -0.549  -1.043
119   A        -1.037  -1.228  -1.171  -0.981  -1.259  -1.282  -0.981  -1.200  -1.112
120   F        -0.260  -0.324  -0.338  -0.140  -0.255  -0.354  -0.369  -0.481  -0.547
121   E         1.031   1.045   1.109   1.099   1.118   1.210   1.058   1.080   1.177
122   E         1.031   1.045   1.109   1.099   1.118   1.210   1.058   1.080   1.177
123   R        -0.643  -0.579  -0.352  -1.234  -1.149  -0.800  -0.981  -0.895  -0.569
124   H        -0.520  -0.559  -0.350  -0.329  -0.426  -0.171  -0.777  -0.860  -0.566
125   Q        -0.635  -0.876  -1.135  -0.104  -0.456  -1.096  -0.471  -0.764  -1.068
126   A        -1.252  -1.261  -1.168  -1.237  -1.243  -1.083  -1.287  -1.304  -1.110
127   G         1.031   1.045   1.109   1.125   1.128   1.233   1.058   1.080   1.177
128   K         1.031   1.045   1.109   0.439   0.501   0.661   1.058   1.080   1.177
129   N        -0.260  -0.288  -0.296   0.077  -0.002  -0.102  -0.369  -0.424  -0.477
130   Q        -2.163  -2.151  -1.796  -2.356  -2.379  -1.871  -1.898  -1.845  -1.428
131   W         1.031   1.045   1.109   1.441   1.434   1.496   1.058   1.080   1.177
132   F         1.031   1.045   1.109   1.109   1.126   1.219   1.058   1.080   1.177
133   F         1.031   1.045   1.109   1.109   1.126   1.219   1.058   1.080   1.177
134   S        -1.037  -0.755  -1.114  -0.731  -0.387  -0.856  -0.981  -0.625  -1.044
135   K        -0.520  -0.559  -0.350  -1.142  -1.132  -0.753  -0.777  -0.860  -0.566
136   L         1.031   1.045   1.109   1.120   1.117   1.228   1.058   1.080   1.177
137   R        -1.037  -0.805  -1.137  -0.717  -0.448  -0.872  -0.981  -0.690  -1.072
138   F         1.031   1.045   1.109   1.109   1.126   1.219   1.058   1.080   1.177
* 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/P0C2H7
Output conservation file - output/P0C2H7
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
