1     M         1.359   1.373   1.403   1.604   1.636   1.675   1.461   1.477   1.518
2     I        -0.759  -0.652  -0.756  -0.642  -0.479  -0.633  -0.795  -0.649  -0.769
3     A         0.214   0.296   0.136   0.090   0.236  -0.049   0.108   0.240  -0.023
4     T         0.214   0.220   0.116   0.253   0.259   0.074   0.108   0.120  -0.057
5     P        -1.465  -1.442  -1.407  -1.501  -1.445  -1.398  -1.246  -1.212  -1.149
6     I        -1.465  -1.442  -1.407  -1.487  -1.439  -1.385  -1.246  -1.212  -1.149
7     R        -1.465  -1.442  -1.407  -1.416  -1.383  -1.314  -1.246  -1.212  -1.149
8     L         1.359   1.373   1.403   1.377   1.403   1.451   1.461   1.477   1.518
9     A         0.214   0.105   0.104   0.178   0.018   0.018   0.108  -0.069  -0.076
10    K         1.359   1.373   1.403   1.264   1.292   1.338   1.461   1.477   1.518
11    S         0.062   0.069   0.043  -0.161  -0.148  -0.202  -0.143  -0.131  -0.181
12    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    Y         1.359   1.373   1.403   1.556   1.588   1.628   1.461   1.477   1.518
15    E        -0.759  -0.820  -0.788  -0.750  -0.844  -0.798  -0.795  -0.864  -0.810
16    P         1.359   1.373   1.403   1.212   1.226   1.288   1.461   1.477   1.518
17    M         0.214   0.220   0.116   0.406   0.422   0.219   0.108   0.120  -0.057
18    I         1.359   1.373   1.403   1.458   1.495   1.530   1.461   1.477   1.518
19    K         1.359   1.373   1.403   1.295   1.333   1.370   1.461   1.477   1.518
20    F         1.359   1.373   1.403   1.492   1.516   1.564   1.461   1.477   1.518
21    V         0.214   0.105   0.104   0.178   0.011   0.001   0.108  -0.069  -0.076
22    G         1.359   1.373   1.403   1.366   1.388   1.439   1.461   1.477   1.518
23    T        -0.759  -0.820  -0.788  -0.769  -0.889  -0.832  -0.795  -0.864  -0.810
24    R        -0.759  -0.707  -0.770  -0.805  -0.723  -0.843  -0.795  -0.720  -0.787
25    H         0.214   0.105   0.104   0.359   0.163   0.145   0.108  -0.069  -0.076
26    P         0.214   0.105   0.104   0.086  -0.092  -0.074   0.108  -0.069  -0.076
27    L        -1.465  -1.442  -1.407  -1.409  -1.361  -1.307  -1.246  -1.212  -1.149
28    V         0.214   0.296   0.136   0.178   0.317   0.056   0.108   0.240  -0.023
29    K         0.214   0.220   0.116   0.167   0.191   0.020   0.108   0.120  -0.057
30    H         0.214   0.105   0.104   0.395   0.218   0.197   0.108  -0.069  -0.076
31    A        -1.465  -1.442  -1.407  -1.416  -1.346  -1.314  -1.246  -1.212  -1.149
32    T        -0.759  -0.820  -0.788  -0.681  -0.762  -0.725  -0.795  -0.864  -0.810
33    E        -1.465  -1.442  -1.407  -1.327  -1.292  -1.226  -1.246  -1.212  -1.149
34    V        -1.465  -1.442  -1.407  -1.501  -1.471  -1.398  -1.246  -1.212  -1.149
35    V        -1.465  -1.442  -1.407  -1.428  -1.375  -1.327  -1.246  -1.212  -1.149
36    V        -1.465  -1.442  -1.407  -1.589  -1.577  -1.486  -1.246  -1.212  -1.149
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    H         1.359   1.373   1.403   1.570   1.604   1.642   1.461   1.477   1.518
39    P         1.359   1.373   1.403   1.212   1.226   1.288   1.461   1.477   1.518
40    C         0.214   0.105   0.104   0.505   0.324   0.307   0.108  -0.069  -0.076
41    A        -0.759  -0.777  -0.780  -0.815  -0.870  -0.868  -0.795  -0.814  -0.799
42    T        -0.759  -0.777  -0.780  -0.871  -0.930  -0.907  -0.795  -0.814  -0.799
43    N        -0.759  -0.820  -0.788  -0.618  -0.715  -0.647  -0.795  -0.864  -0.810
44    G         0.214   0.220   0.116   0.174   0.180  -0.001   0.108   0.120  -0.057
45    M        -0.759  -0.777  -0.780  -0.740  -0.806  -0.763  -0.795  -0.814  -0.799
46    L        -0.759  -0.707  -0.770  -0.710  -0.632  -0.714  -0.795  -0.720  -0.787
47    P         1.359   1.373   1.403   1.212   1.226   1.288   1.461   1.477   1.518
48    G         0.214   0.105   0.104   0.159  -0.044  -0.044   0.108  -0.069  -0.076
49    S        -0.759  -0.707  -0.770  -0.935  -0.857  -0.947  -0.795  -0.720  -0.787
50    K        -0.879  -0.872  -0.824  -1.214  -1.201  -1.114  -0.945  -0.927  -0.853
51    E         0.062   0.040   0.035  -0.016  -0.059  -0.074  -0.143  -0.179  -0.196
52    C         0.062   0.107   0.052   0.270   0.354   0.241  -0.143  -0.066  -0.166
53    I        -0.879  -0.872  -0.824  -1.078  -1.070  -0.980  -0.945  -0.927  -0.853
54    P        -0.879  -0.872  -0.824  -0.842  -0.833  -0.746  -0.945  -0.927  -0.853
55    V         1.359   1.373   1.403   1.279   1.300   1.353   1.461   1.477   1.518
56    S        -0.879  -0.872  -0.824  -1.097  -1.081  -0.998  -0.945  -0.927  -0.853
57    K        -0.879  -0.872  -0.824  -0.922  -0.914  -0.825  -0.945  -0.927  -0.853
58    F         0.214   0.220   0.116   0.319   0.334   0.147   0.108   0.120  -0.057
59    M        -0.759  -0.820  -0.788  -0.599  -0.707  -0.670  -0.795  -0.864  -0.810
60    E        -0.759  -0.777  -0.780  -0.882  -0.909  -0.910  -0.795  -0.814  -0.799
61    N        -0.759  -0.820  -0.788  -0.810  -0.919  -0.877  -0.795  -0.864  -0.810
62    Y        -0.759  -0.820  -0.788  -0.460  -0.560  -0.494  -0.795  -0.864  -0.810
63    K        -1.465  -1.442  -1.407  -1.422  -1.364  -1.320  -1.246  -1.212  -1.149
64    P         1.359   1.373   1.403   1.212   1.226   1.288   1.461   1.477   1.518
65    F         0.214   0.105   0.104   0.334   0.150   0.147   0.108  -0.069  -0.076
66    R        -1.465  -1.442  -1.407  -1.266  -1.248  -1.166  -1.246  -1.212  -1.149
67    V         1.359   1.373   1.403   1.279   1.300   1.353   1.461   1.477   1.518
68    V         1.359   1.373   1.403   1.279   1.300   1.353   1.461   1.477   1.518
69    P         1.359   1.373   1.403   1.249   1.273   1.323   1.461   1.477   1.518
70    I         0.062   0.069   0.043   0.156   0.174   0.110  -0.143  -0.131  -0.181
71    K         0.062   0.040   0.035  -0.182  -0.224  -0.240  -0.143  -0.179  -0.196
72    H         0.062   0.069   0.043   0.110   0.127   0.084  -0.143  -0.131  -0.181
73    S         1.359   1.373   1.403   1.294   1.315   1.368   1.461   1.477   1.518
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    A         0.062   0.040   0.035  -0.175  -0.213  -0.236  -0.143  -0.179  -0.196
76    N         0.062   0.040   0.035  -0.009  -0.053  -0.079  -0.143  -0.179  -0.196
77    A         0.062   0.107   0.052  -0.161  -0.079  -0.185  -0.143  -0.066  -0.166
78    G         0.062   0.069   0.043  -0.112  -0.105  -0.147  -0.143  -0.131  -0.181
79    L        -0.879  -0.872  -0.824  -0.931  -0.921  -0.834  -0.945  -0.927  -0.853
80    S        -0.759  -0.652  -0.756  -0.950  -0.751  -0.947  -0.795  -0.649  -0.769
81    S         0.214   0.296   0.136   0.174   0.303   0.038   0.108   0.240  -0.023
82    S         1.359   1.373   1.403   1.260   1.274   1.335   1.461   1.477   1.518
83    K         0.214   0.296   0.136   0.082   0.206  -0.046   0.108   0.240  -0.023
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    T         0.062   0.069   0.043  -0.084  -0.067  -0.105  -0.143  -0.131  -0.181
93    S         0.062   0.069   0.043   0.097   0.112   0.039  -0.143  -0.131  -0.181
94    V         0.062   0.107   0.052   0.004   0.068   0.009  -0.143  -0.066  -0.166
95    F         1.359   1.373   1.403   1.513   1.542   1.585   1.461   1.477   1.518
96    V        -0.879  -0.872  -0.824  -1.059  -1.055  -0.961  -0.945  -0.927  -0.853
97    N         0.062   0.107   0.052   0.123   0.201   0.114  -0.143  -0.066  -0.166
98    R         1.359   1.373   1.403   1.542   1.567   1.614   1.461   1.477   1.518
99    P         0.214   0.296   0.136   0.035   0.159  -0.091   0.108   0.240  -0.023
100   L         0.214   0.105   0.104   0.170  -0.029  -0.033   0.108  -0.069  -0.076
101   Q        -1.465  -1.442  -1.407  -1.340  -1.312  -1.239  -1.246  -1.212  -1.149
102   K        -1.465  -1.442  -1.407  -1.409  -1.317  -1.307  -1.246  -1.212  -1.149
103   D        -0.759  -0.820  -0.788  -0.585  -0.704  -0.650  -0.795  -0.864  -0.810
104   E         1.359   1.373   1.403   1.412   1.442   1.485   1.461   1.477   1.518
105   L        -0.759  -0.777  -0.780  -0.780  -0.796  -0.799  -0.795  -0.814  -0.799
106   A        -0.759  -0.707  -0.770  -0.919  -0.821  -0.936  -0.795  -0.720  -0.787
107   S         1.359   1.373   1.403   1.260   1.274   1.335   1.461   1.477   1.518
108   I         0.214   0.105   0.104   0.334   0.168   0.163   0.108  -0.069  -0.076
109   F        -1.465  -1.442  -1.407  -1.371  -1.352  -1.270  -1.246  -1.212  -1.149
110   E        -0.759  -0.707  -0.770  -0.552  -0.471  -0.542  -0.795  -0.720  -0.787
111   L         1.359   1.373   1.403   1.377   1.403   1.451   1.461   1.477   1.518
112   P         0.214   0.105   0.104   0.023  -0.178  -0.164   0.108  -0.069  -0.076
113   A        -1.465  -1.442  -1.407  -1.653  -1.612  -1.548  -1.246  -1.212  -1.149
114   R         1.359   1.373   1.403   1.480   1.491   1.553   1.461   1.477   1.518
115   F         1.359   1.373   1.403   1.492   1.516   1.564   1.461   1.477   1.518
116   R        -1.465  -1.442  -1.407  -1.195  -1.141  -1.095  -1.246  -1.212  -1.149
117   Y         0.214   0.220   0.116   0.410   0.431   0.239   0.108   0.120  -0.057
118   K        -0.053  -0.030   0.003  -0.229  -0.175  -0.120  -0.343  -0.302  -0.251
119   P         1.359   1.373   1.403   1.212   1.226   1.288   1.461   1.477   1.518
120   I        -0.759  -0.820  -0.788  -0.575  -0.660  -0.602  -0.795  -0.864  -0.810
121   N        -0.759  -0.777  -0.780  -0.628  -0.690  -0.682  -0.795  -0.814  -0.799
122   E         1.359   1.373   1.403   1.412   1.442   1.485   1.461   1.477   1.518
123   H        -1.465  -1.442  -1.407  -1.219  -1.173  -1.119  -1.246  -1.212  -1.149
124   E         1.359   1.373   1.403   1.412   1.442   1.485   1.461   1.477   1.518
125   L        -0.053  -0.030   0.003  -0.187  -0.129  -0.084  -0.343  -0.302  -0.251
126   E         0.214   0.105   0.104   0.275   0.106   0.101   0.108  -0.069  -0.076
127   S        -1.465  -1.442  -1.407  -1.487  -1.427  -1.385  -1.246  -1.212  -1.149
128   I         0.214   0.105   0.104   0.286   0.116   0.095   0.108  -0.069  -0.076
129   N         1.359   1.373   1.403   1.435   1.461   1.508   1.461   1.477   1.518
130   S        -0.053  -0.042  -0.002  -0.341  -0.338  -0.251  -0.343  -0.322  -0.259
131   G         1.359   1.373   1.403   1.366   1.388   1.439   1.461   1.477   1.518
132   G         1.359   1.373   1.403   1.366   1.388   1.439   1.461   1.477   1.518
133   A         1.359   1.373   1.403   1.310   1.345   1.384   1.461   1.477   1.518
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   W        -1.465  -1.442  -1.407  -1.080  -1.057  -0.982  -1.246  -1.212  -1.149
* 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/P19955
Output conservation file - output/P19955
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
