1     M         1.450   1.469   1.490   1.611   1.637   1.670   1.537   1.561   1.589
2     S         0.308   0.399   0.235   0.263   0.404   0.140   0.194   0.336   0.066
3     D        -1.364  -1.337  -1.298  -1.222  -1.176  -1.116  -1.149  -1.110  -1.052
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     I        -0.661  -0.663  -0.671  -0.738  -0.739  -0.732  -0.702  -0.700  -0.699
9     L         1.450   1.469   1.490   1.300   1.338   1.365   1.537   1.561   1.589
10    D         1.450   1.469   1.490   1.414   1.438   1.477   1.537   1.561   1.589
11    E         0.308   0.222   0.195   0.255   0.132   0.069   0.194   0.052  -0.002
12    I        -0.661  -0.615  -0.651  -0.562  -0.500  -0.544  -0.702  -0.637  -0.674
13    V         0.308   0.222   0.195   0.218   0.099   0.061   0.194   0.052  -0.002
14    I        -0.661  -0.718  -0.693  -0.722  -0.802  -0.738  -0.702  -0.767  -0.727
15    E         1.450   1.469   1.490   1.464   1.471   1.526   1.537   1.561   1.589
16    D         1.450   1.469   1.490   1.414   1.438   1.477   1.537   1.561   1.589
17    V         0.043   0.073   0.104   0.008   0.050   0.116  -0.254  -0.203  -0.157
18    V        -0.661  -0.663  -0.671  -0.593  -0.584  -0.609  -0.702  -0.700  -0.699
19    A         0.308   0.222   0.195   0.492   0.345   0.295   0.194   0.052  -0.002
20    N        -0.661  -0.718  -0.693  -0.361  -0.460  -0.419  -0.702  -0.767  -0.727
21    C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
22    P         1.450   1.469   1.490   1.587   1.618   1.646   1.537   1.561   1.589
23    Q        -0.661  -0.615  -0.651  -0.635  -0.561  -0.607  -0.702  -0.637  -0.674
24    E         0.308   0.222   0.195   0.255   0.132   0.069   0.194   0.052  -0.002
25    F         1.450   1.469   1.490   1.575   1.615   1.634   1.537   1.561   1.589
26    L         1.450   1.469   1.490   1.300   1.338   1.365   1.537   1.561   1.589
27    Q        -1.364  -1.337  -1.298  -1.337  -1.280  -1.229  -1.149  -1.110  -1.052
28    Y         0.043   0.073   0.104   0.111   0.179   0.218  -0.254  -0.203  -0.157
29    H         1.450   1.469   1.490   1.683   1.717   1.741   1.537   1.561   1.589
30    K         0.043   0.073   0.104  -0.340  -0.286  -0.239  -0.254  -0.203  -0.157
31    C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
32    I        -0.661  -0.718  -0.693  -0.588  -0.703  -0.674  -0.702  -0.767  -0.727
33    R        -0.780  -0.748  -0.720  -0.691  -0.633  -0.593  -0.851  -0.802  -0.759
34    D        -0.780  -0.748  -0.720  -1.102  -1.035  -0.998  -0.851  -0.802  -0.759
35    N        -0.661  -0.718  -0.693  -0.490  -0.586  -0.546  -0.702  -0.767  -0.727
36    E        -1.364  -1.337  -1.298  -1.372  -1.312  -1.264  -1.149  -1.110  -1.052
37    E        -0.661  -0.718  -0.693  -0.516  -0.625  -0.577  -0.702  -0.767  -0.727
38    N         0.308   0.222   0.195   0.299   0.158   0.121   0.194   0.052  -0.002
39    P        -0.661  -0.615  -0.652  -0.485  -0.409  -0.473  -0.702  -0.637  -0.676
40    G        -0.661  -0.718  -0.693  -0.500  -0.587  -0.540  -0.702  -0.767  -0.727
41    K        -0.661  -0.545  -0.655  -0.955  -0.752  -0.945  -0.702  -0.546  -0.679
42    C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
43    K        -0.661  -0.663  -0.669  -0.609  -0.636  -0.640  -0.702  -0.700  -0.697
44    D        -1.364  -1.337  -1.298  -1.489  -1.428  -1.378  -1.149  -1.110  -1.052
45    G        -0.661  -0.663  -0.671  -0.651  -0.652  -0.668  -0.702  -0.700  -0.699
46    R         0.308   0.222   0.195   0.307   0.202   0.146   0.194   0.052  -0.002
47    M        -1.364  -1.337  -1.298  -1.043  -1.027  -0.940  -1.149  -1.110  -1.052
48    I        -1.364  -1.337  -1.298  -1.401  -1.377  -1.292  -1.149  -1.110  -1.052
49    L         1.450   1.469   1.490   1.300   1.338   1.365   1.537   1.561   1.589
50    S        -0.661  -0.545  -0.655  -0.625  -0.446  -0.604  -0.702  -0.546  -0.679
51    T        -0.661  -0.545  -0.655  -0.567  -0.362  -0.573  -0.702  -0.546  -0.679
52    C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
53    I         0.308   0.300   0.217   0.422   0.391   0.284   0.194   0.179   0.035
54    R         0.308   0.222   0.195   0.185   0.053   0.033   0.194   0.052  -0.002
55    E        -0.661  -0.663  -0.669  -0.614  -0.627  -0.656  -0.702  -0.700  -0.697
56    K        -0.661  -0.663  -0.669  -0.822  -0.848  -0.850  -0.702  -0.700  -0.697
57    V         1.450   1.469   1.490   1.611   1.629   1.670   1.537   1.561   1.589
58    P         1.450   1.469   1.490   1.587   1.618   1.646   1.537   1.561   1.589
59    S        -0.661  -0.615  -0.652  -0.625  -0.544  -0.601  -0.702  -0.637  -0.676
60    V         0.308   0.222   0.195   0.480   0.356   0.302   0.194   0.052  -0.002
61    K        -1.364  -1.337  -1.298  -1.430  -1.400  -1.320  -1.149  -1.110  -1.052
62    S         0.308   0.222   0.195   0.113  -0.031  -0.071   0.194   0.052  -0.002
63    I         1.450   1.469   1.490   1.514   1.525   1.574   1.537   1.561   1.589
64    M        -0.661  -0.718  -0.693  -0.738  -0.795  -0.786  -0.702  -0.767  -0.727
65    S        -1.364  -1.337  -1.298  -1.365  -1.346  -1.257  -1.149  -1.110  -1.052
66    E        -0.661  -0.615  -0.652  -0.625  -0.585  -0.608  -0.702  -0.637  -0.676
67    C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
68    S        -0.661  -0.615  -0.651  -0.684  -0.613  -0.663  -0.702  -0.637  -0.674
69    E        -0.661  -0.718  -0.693  -0.593  -0.707  -0.668  -0.702  -0.767  -0.727
70    P        -0.661  -0.718  -0.693  -0.689  -0.749  -0.687  -0.702  -0.767  -0.727
71    M         0.043   0.059   0.097  -0.143  -0.104  -0.043  -0.254  -0.228  -0.169
72    K         0.043   0.073   0.104  -0.340  -0.286  -0.239  -0.254  -0.203  -0.157
73    K         0.308   0.222   0.195   0.299   0.147   0.076   0.194   0.052  -0.002
74    Y         1.450   1.469   1.490   1.694   1.722   1.752   1.537   1.561   1.589
75    D         0.308   0.222   0.195   0.311   0.145   0.113   0.194   0.052  -0.002
76    Q        -0.661  -0.718  -0.693  -0.641  -0.729  -0.703  -0.702  -0.767  -0.727
77    C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
78    I         0.308   0.222   0.195   0.185   0.055   0.013   0.194   0.052  -0.002
79    R         0.043   0.073   0.104  -0.161  -0.089  -0.032  -0.254  -0.203  -0.157
80    D        -0.661  -0.718  -0.693  -0.546  -0.659  -0.623  -0.702  -0.767  -0.727
81    N         1.450   1.469   1.490   1.526   1.546   1.587   1.537   1.561   1.589
82    M        -1.364  -1.337  -1.298  -1.330  -1.252  -1.222  -1.149  -1.110  -1.052
83    G        -0.661  -0.718  -0.693  -0.635  -0.713  -0.669  -0.702  -0.767  -0.727
84    T        -1.364  -1.337  -1.298  -1.255  -1.196  -1.148  -1.149  -1.110  -1.052
85    R        -0.661  -0.545  -0.655  -0.495  -0.304  -0.493  -0.702  -0.546  -0.679
86    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    E        -0.661  -0.718  -0.693  -0.867  -0.967  -0.903  -0.702  -0.767  -0.727
90    N        -1.364  -1.337  -1.298  -1.430  -1.378  -1.320  -1.149  -1.110  -1.052
91    C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
92    L        -0.661  -0.718  -0.693  -0.733  -0.826  -0.788  -0.702  -0.767  -0.727
93    G        -1.364  -1.337  -1.298  -1.209  -1.149  -1.103  -1.149  -1.110  -1.052
94    F        -1.364  -1.337  -1.298  -1.401  -1.351  -1.292  -1.149  -1.110  -1.052
95    L         1.450   1.469   1.490   1.300   1.338   1.365   1.537   1.561   1.589
96    Q         1.450   1.469   1.490   1.389   1.443   1.452   1.537   1.561   1.589
97    D        -1.364  -1.337  -1.298  -1.323  -1.284  -1.216  -1.149  -1.110  -1.052
98    L         0.308   0.300   0.217   0.218   0.216   0.094   0.194   0.179   0.035
99    R         1.450   1.469   1.490   1.623   1.641   1.682   1.537   1.561   1.589
100   K        -0.661  -0.545  -0.655  -0.839  -0.675  -0.817  -0.702  -0.546  -0.679
101   C         1.450   1.469   1.490   1.402   1.431   1.465   1.537   1.561   1.589
102   A         0.308   0.300   0.217   0.347   0.342   0.186   0.194   0.179   0.035
103   E        -0.661  -0.718  -0.693  -0.557  -0.658  -0.624  -0.702  -0.767  -0.727
104   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   K        -0.661  -0.718  -0.693  -0.630  -0.759  -0.714  -0.702  -0.767  -0.727
110   N        -1.364  -1.337  -1.298  -1.209  -1.161  -1.103  -1.149  -1.110  -1.052
111   I         0.308   0.399   0.235   0.323   0.455   0.184   0.194   0.336   0.066
112   K         0.308   0.222   0.195   0.214   0.051  -0.004   0.194   0.052  -0.002
113   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   D         0.308   0.222   0.195   0.113  -0.034  -0.071   0.194   0.052  -0.002
* 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/Q04341
Output conservation file - output/Q04341
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
