1     M         0.644   0.651   0.697   0.806   0.816   0.852   0.658   0.672   0.727
2     S        -0.364  -0.722  -0.941  -0.152  -0.641  -1.129  -0.295  -0.790  -1.114
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     G        -1.957  -2.140  -1.929  -2.171  -2.431  -2.018  -1.906  -2.112  -1.771
6     N        -3.172  -3.181  -2.631  -3.168  -3.235  -2.441  -2.812  -2.793  -2.096
7     G        -0.886  -0.806  -0.936  -1.308  -1.204  -1.405  -1.010  -0.912  -1.106
8     A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
9     Q        -2.063  -2.143  -1.930  -1.742  -1.851  -1.564  -2.083  -2.123  -1.772
10    G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
11    T        -1.808  -2.018  -1.929  -1.318  -1.701  -1.757  -1.726  -1.964  -1.770
12    K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
13    F        -2.063  -2.224  -1.933  -1.503  -1.761  -1.449  -2.083  -2.229  -1.775
14    R        -0.886  -1.042  -0.962  -0.858  -1.148  -1.089  -1.010  -1.271  -1.147
15    I        -1.195  -0.963  -0.947  -1.109  -0.780  -0.816  -1.487  -1.148  -1.123
16    S        -1.195  -1.232  -0.968  -1.142  -1.220  -0.831  -1.487  -1.579  -1.156
17    L        -0.364  -0.268  -0.922  -0.087   0.010  -0.851  -0.295  -0.183  -1.084
18    G        -0.886  -0.765  -0.942  -1.308  -1.139  -1.417  -1.010  -0.851  -1.115
19    L         0.644   0.651   0.697   0.696   0.710   0.767   0.658   0.672   0.727
20    P         0.644   0.651   0.697   0.757   0.762   0.815   0.658   0.672   0.727
21    V        -0.886  -0.643  -0.932  -0.990  -0.686  -0.987  -1.010  -0.677  -1.101
22    G        -0.886  -0.806  -0.936  -1.067  -0.979  -1.005  -1.010  -0.912  -1.106
23    A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
24    I        -0.886  -0.793  -0.950  -0.733  -0.630  -1.019  -1.010  -0.893  -1.129
25    M        -0.364  -0.314  -0.929  -0.028   0.018  -0.975  -0.295  -0.240  -1.095
26    N         0.644   0.651   0.697   0.757   0.774   0.815   0.658   0.672   0.727
27    C         0.644   0.651   0.697   1.041   1.047   1.034   0.658   0.672   0.727
28    A        -0.364  -0.314  -0.929  -0.470  -0.399  -1.016  -0.295  -0.240  -1.095
29    D         0.644   0.651   0.697   0.891   0.903   0.918   0.658   0.672   0.727
30    N         0.644   0.651   0.697   0.757   0.774   0.815   0.658   0.672   0.727
31    S         0.644   0.651   0.697   0.696   0.722   0.767   0.658   0.672   0.727
32    G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
33    A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
34    R        -0.886  -0.806  -0.936  -0.858  -0.759  -1.033  -1.010  -0.912  -1.106
35    N         0.644   0.651   0.697   0.757   0.774   0.815   0.658   0.672   0.727
36    L         0.644   0.651   0.697   0.696   0.710   0.767   0.658   0.672   0.727
37    Y         0.644   0.651   0.697   1.005   1.011   1.006   0.658   0.672   0.727
38    I        -0.886  -0.765  -0.942  -0.733  -0.585  -0.998  -1.010  -0.851  -1.115
39    I        -3.143  -2.889  -2.621  -3.028  -2.734  -2.285  -2.798  -2.564  -2.089
40    A        -1.341  -1.270  -0.965  -1.865  -1.716  -1.198  -1.726  -1.642  -1.152
41    V         0.644   0.651   0.697   0.392   0.417   0.532   0.658   0.672   0.727
42    K        -0.886  -0.806  -0.936  -0.849  -0.763  -0.877  -1.010  -0.912  -1.106
43    G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
44    S        -3.587  -3.554  -3.163  -2.785  -2.781  -2.217  -2.918  -2.866  -2.282
45    G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
46    S        -1.195  -0.963  -0.947  -1.648  -1.292  -1.207  -1.487  -1.148  -1.123
47    R         0.644   0.651   0.697   0.658   0.681   0.738   0.658   0.672   0.727
48    L         0.644   0.651   0.697   0.696   0.710   0.767   0.658   0.672   0.727
49    N         0.644   0.651   0.697   0.757   0.774   0.815   0.658   0.672   0.727
50    R         0.644   0.651   0.697   0.658   0.681   0.738   0.658   0.672   0.727
51    L         0.644   0.651   0.697   0.696   0.710   0.767   0.658   0.672   0.727
52    P         0.644   0.651   0.697   0.757   0.762   0.815   0.658   0.672   0.727
53    A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
54    A        -0.364  -0.722  -0.941  -0.572  -1.054  -1.414  -0.295  -0.790  -1.114
55    S        -1.808  -1.860  -1.928  -1.731  -1.942  -2.142  -1.726  -1.849  -1.770
56    L        -3.143  -3.149  -2.628  -3.146  -3.224  -2.437  -2.798  -2.766  -2.094
57    G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
58    D         0.644   0.651   0.697   0.891   0.903   0.918   0.658   0.672   0.727
59    M         0.644   0.651   0.697   0.806   0.816   0.852   0.658   0.672   0.727
60    V         0.644   0.651   0.697   0.392   0.417   0.532   0.658   0.672   0.727
61    M        -0.886  -0.806  -0.936  -0.663  -0.578  -0.853  -1.010  -0.912  -1.106
62    A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
63    T         0.644   0.651   0.697   0.963   0.971   0.974   0.658   0.672   0.727
64    V         0.644   0.651   0.697   0.392   0.417   0.532   0.658   0.672   0.727
65    K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
66    K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
67    G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
68    K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
69    P         0.644   0.651   0.697   0.757   0.762   0.815   0.658   0.672   0.727
70    E        -0.886  -0.806  -0.936  -0.464  -0.389  -0.669  -1.010  -0.912  -1.106
71    L         0.644   0.651   0.697   0.696   0.710   0.767   0.658   0.672   0.727
72    R         0.644   0.651   0.697   0.658   0.681   0.738   0.658   0.672   0.727
73    K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
74    K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
75    V        -1.195  -1.107  -0.961  -1.485  -1.379  -1.086  -1.487  -1.376  -1.146
76    M        -0.364  -0.722  -0.941   0.067  -0.351  -0.647  -0.295  -0.790  -1.114
77    P         0.644   0.651   0.697   0.757   0.762   0.815   0.658   0.672   0.727
78    A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
79    I        -0.364  -0.722  -0.941  -0.015  -0.521  -0.995  -0.295  -0.790  -1.114
80    V        -0.364  -0.722  -0.941  -0.389  -0.824  -1.067  -0.295  -0.790  -1.114
81    V        -0.364  -0.277  -0.928  -0.389  -0.293  -1.051  -0.295  -0.195  -1.094
82    R         0.644   0.651   0.697   0.658   0.681   0.738   0.658   0.672   0.727
83    Q         0.644   0.651   0.697   1.082   1.085   1.065   0.658   0.672   0.727
84    A        -2.230  -2.046  -1.925  -2.271  -2.008  -1.966  -2.202  -1.998  -1.767
85    K        -0.364  -0.314  -0.929  -0.288  -0.236  -1.049  -0.295  -0.240  -1.095
86    S        -2.144  -1.925  -1.928  -2.364  -2.062  -1.927  -2.202  -1.981  -1.770
87    W         0.644   0.651   0.697   1.058   1.059   1.047   0.658   0.672   0.727
88    R        -0.364  -0.722  -0.941  -0.161  -0.634  -1.044  -0.295  -0.790  -1.114
89    R         0.644   0.651   0.697   0.658   0.681   0.738   0.658   0.672   0.727
90    R        -1.808  -1.961  -1.927  -1.661  -1.831  -1.727  -1.726  -1.894  -1.768
91    D         0.644   0.651   0.697   0.891   0.903   0.918   0.658   0.672   0.727
92    G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
93    V         0.644   0.651   0.697   0.392   0.417   0.532   0.658   0.672   0.727
94    F        -1.195  -1.191  -0.966  -0.832  -0.879  -0.620  -1.487  -1.512  -1.154
95    L         0.644   0.651   0.697   0.696   0.710   0.767   0.658   0.672   0.727
96    Y         0.644   0.651   0.697   1.005   1.011   1.006   0.658   0.672   0.727
97    F         0.644   0.651   0.697   1.041   1.039   1.034   0.658   0.672   0.727
98    E         0.644   0.651   0.697   0.957   0.958   0.969   0.658   0.672   0.727
99    D         0.644   0.651   0.697   0.891   0.903   0.918   0.658   0.672   0.727
100   N         0.644   0.651   0.697   0.757   0.774   0.815   0.658   0.672   0.727
101   A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
102   G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
103   V         0.644   0.651   0.697   0.392   0.417   0.532   0.658   0.672   0.727
104   I         0.644   0.651   0.697   0.819   0.821   0.862   0.658   0.672   0.727
105   A        -1.195  -0.963  -0.947  -1.743  -1.344  -1.347  -1.487  -1.148  -1.123
106   N         0.644   0.651   0.697   0.757   0.774   0.815   0.658   0.672   0.727
107   P         0.644   0.651   0.697   0.757   0.762   0.815   0.658   0.672   0.727
108   K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
109   G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
110   E         0.644   0.651   0.697   0.957   0.958   0.969   0.658   0.672   0.727
111   M         0.644   0.651   0.697   0.806   0.816   0.852   0.658   0.672   0.727
112   K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
113   G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
114   S         0.644   0.651   0.697   0.696   0.722   0.767   0.658   0.672   0.727
115   A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
116   I        -0.364  -0.200  -0.925  -0.015   0.151  -0.959  -0.295  -0.101  -1.090
117   T         0.644   0.651   0.697   0.963   0.971   0.974   0.658   0.672   0.727
118   G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
119   P         0.644   0.651   0.697   0.757   0.762   0.815   0.658   0.672   0.727
120   V         0.644   0.651   0.697   0.392   0.417   0.532   0.658   0.672   0.727
121   G        -1.341  -1.266  -0.968  -2.156  -2.055  -1.469  -1.726  -1.635  -1.156
122   K         0.644   0.651   0.697   0.514   0.530   0.626   0.658   0.672   0.727
123   E         0.644   0.651   0.697   0.957   0.958   0.969   0.658   0.672   0.727
124   C        -0.364  -0.722  -0.941   0.194  -0.318  -0.898  -0.295  -0.790  -1.114
125   A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
126   D        -0.364  -0.722  -0.941   0.126  -0.314  -0.688  -0.295  -0.790  -1.114
127   L         0.644   0.651   0.697   0.696   0.710   0.767   0.658   0.672   0.727
128   W         0.644   0.651   0.697   1.058   1.059   1.047   0.658   0.672   0.727
129   P         0.644   0.651   0.697   0.757   0.762   0.815   0.658   0.672   0.727
130   R         0.644   0.651   0.697   0.658   0.681   0.738   0.658   0.672   0.727
131   V        -0.886  -0.641  -0.936  -0.733  -0.402  -0.983  -1.010  -0.675  -1.106
132   A         0.644   0.651   0.697   0.281   0.320   0.446   0.658   0.672   0.727
133   S         0.644   0.651   0.697   0.696   0.722   0.767   0.658   0.672   0.727
134   N         0.644   0.651   0.697   0.757   0.774   0.815   0.658   0.672   0.727
135   S        -0.886  -0.806  -0.936  -0.885  -0.774  -1.116  -1.010  -0.912  -1.106
136   G         0.644   0.651   0.697   0.275   0.294   0.441   0.658   0.672   0.727
137   V        -0.886  -0.806  -0.936  -0.990  -0.893  -0.990  -1.010  -0.912  -1.106
138   V         0.644   0.651   0.697   0.392   0.417   0.532   0.658   0.672   0.727
139   V        -0.364  -0.722  -0.941  -0.391  -0.825  -1.073  -0.295  -0.790  -1.114
* 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/P0CX41
Output conservation file - output/P0CX41
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
