1     M         1.444   1.444   1.464   1.584   1.585   1.614   1.516   1.517   1.539
2     G        -1.456  -1.455  -1.411  -1.387  -1.386  -1.312  -1.235  -1.234  -1.164
3     S        -0.236  -0.228  -0.287  -0.334  -0.323  -0.405  -0.318  -0.306  -0.391
4     F         1.444   1.444   1.464   1.523   1.524   1.554   1.516   1.517   1.539
5     W        -0.236  -0.228  -0.287   0.135   0.149   0.038  -0.318  -0.306  -0.391
6     D         1.444   1.444   1.464   1.421   1.420   1.453   1.516   1.517   1.539
7     A        -0.236  -0.228  -0.273  -0.393  -0.376  -0.457  -0.318  -0.306  -0.371
8     F         1.444   1.444   1.464   1.523   1.524   1.554   1.516   1.517   1.539
9     A        -0.236  -0.228  -0.287  -0.393  -0.376  -0.481  -0.318  -0.306  -0.391
10    V         1.444   1.444   1.464   1.462   1.461   1.494   1.516   1.517   1.539
11    Y         1.444   1.444   1.464   1.604   1.604   1.633   1.516   1.517   1.539
12    D        -0.236  -0.250  -0.293  -0.315  -0.337  -0.402  -0.318  -0.339  -0.401
13    K        -0.236  -0.228  -0.273  -0.334  -0.321  -0.385  -0.318  -0.306  -0.371
14    K        -0.236  -0.250  -0.293  -0.373  -0.396  -0.473  -0.318  -0.339  -0.401
15    K         1.444   1.444   1.464   1.296   1.297   1.330   1.516   1.517   1.539
16    H         1.444   1.444   1.464   1.644   1.644   1.673   1.516   1.517   1.539
17    A         1.444   1.444   1.464   1.317   1.321   1.351   1.516   1.517   1.539
18    D        -1.456  -1.455  -1.411  -1.374  -1.372  -1.299  -1.235  -1.234  -1.164
19    P        -1.456  -1.455  -1.411  -1.374  -1.367  -1.299  -1.235  -1.234  -1.164
20    S        -0.236  -0.250  -0.293  -0.295  -0.321  -0.401  -0.318  -0.339  -0.401
21    V        -0.236  -0.228  -0.287  -0.153  -0.142  -0.230  -0.318  -0.306  -0.391
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    Y        -0.236  -0.250  -0.293   0.047   0.026  -0.045  -0.318  -0.339  -0.401
25    G         1.444   1.444   1.464   1.400   1.401   1.433   1.516   1.517   1.539
26    G         1.444   1.444   1.464   1.400   1.401   1.433   1.516   1.517   1.539
27    N        -1.456  -1.455  -1.411  -1.361  -1.362  -1.287  -1.235  -1.234  -1.164
28    H        -0.386  -0.385  -0.350  -0.260  -0.259  -0.203  -0.547  -0.546  -0.489
29    N        -0.236  -0.250  -0.293  -0.393  -0.417  -0.486  -0.318  -0.339  -0.401
30    N        -1.456  -1.455  -1.411  -1.260  -1.262  -1.187  -1.235  -1.234  -1.164
31    T        -0.236  -0.250  -0.293  -0.248  -0.266  -0.321  -0.318  -0.339  -0.401
32    G        -1.456  -1.455  -1.411  -1.199  -1.198  -1.127  -1.235  -1.234  -1.164
33    D        -0.236  -0.250  -0.293  -0.257  -0.280  -0.349  -0.318  -0.339  -0.401
34    S        -1.456  -1.455  -1.411  -1.532  -1.529  -1.455  -1.235  -1.234  -1.164
35    K        -1.456  -1.455  -1.411  -1.273  -1.275  -1.200  -1.235  -1.234  -1.164
36    T        -0.236  -0.228  -0.273  -0.052  -0.038  -0.112  -0.318  -0.306  -0.371
37    Q        -1.456  -1.455  -1.411  -1.248  -1.243  -1.175  -1.235  -1.234  -1.164
38    V        -0.236  -0.250  -0.293  -0.052  -0.076  -0.154  -0.318  -0.339  -0.401
39    M        -0.236  -0.228  -0.273  -0.034  -0.020  -0.095  -0.318  -0.306  -0.371
40    F        -0.236  -0.228  -0.273  -0.079  -0.067  -0.136  -0.318  -0.306  -0.371
41    S        -0.236  -0.250  -0.293  -0.393  -0.413  -0.492  -0.318  -0.339  -0.401
42    K        -0.236  -0.228  -0.287  -0.334  -0.321  -0.405  -0.318  -0.306  -0.391
43    E         1.444   1.444   1.464   1.296   1.296   1.330   1.516   1.517   1.539
44    Y        -0.236  -0.228  -0.273   0.029   0.041  -0.026  -0.318  -0.306  -0.371
45    R         1.444   1.444   1.464   1.442   1.443   1.474   1.516   1.517   1.539
46    Q        -0.386  -0.385  -0.350  -0.347  -0.346  -0.288  -0.547  -0.546  -0.489
47    P         1.444   1.444   1.464   1.547   1.548   1.578   1.516   1.517   1.539
48    R        -0.386  -0.385  -0.350  -0.639  -0.638  -0.576  -0.547  -0.546  -0.489
49    T         1.444   1.444   1.464   1.599   1.599   1.629   1.516   1.517   1.539
50    H        -0.386  -0.385  -0.350  -0.291  -0.289  -0.232  -0.547  -0.546  -0.489
51    Q        -0.386  -0.385  -0.350  -0.423  -0.422  -0.363  -0.547  -0.546  -0.489
52    Q        -0.386  -0.385  -0.350  -0.423  -0.422  -0.363  -0.547  -0.546  -0.489
53    E        -0.386  -0.385  -0.350  -0.660  -0.658  -0.596  -0.547  -0.546  -0.489
54    N        -0.386  -0.385  -0.350  -0.619  -0.618  -0.556  -0.547  -0.546  -0.489
55    L        -0.386  -0.385  -0.350  -0.500  -0.499  -0.439  -0.547  -0.546  -0.489
56    Q        -0.386  -0.385  -0.350  -0.442  -0.441  -0.382  -0.547  -0.546  -0.489
57    S        -0.386  -0.385  -0.350  -0.763  -0.761  -0.697  -0.547  -0.546  -0.489
58    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    S        -0.386  -0.385  -0.350  -0.763  -0.761  -0.697  -0.547  -0.546  -0.489
66    Q        -0.386  -0.385  -0.350  -0.442  -0.441  -0.382  -0.547  -0.546  -0.489
67    D        -0.386  -0.385  -0.350  -0.385  -0.383  -0.325  -0.547  -0.546  -0.489
68    S        -0.386  -0.385  -0.350  -0.763  -0.761  -0.697  -0.547  -0.546  -0.489
69    S        -0.236  -0.250  -0.293  -0.393  -0.413  -0.492  -0.318  -0.339  -0.401
70    D         1.444   1.444   1.464   1.421   1.420   1.453   1.516   1.517   1.539
71    V        -0.236  -0.228  -0.273  -0.061  -0.051  -0.103  -0.318  -0.306  -0.371
72    E        -0.236  -0.250  -0.293  -0.412  -0.435  -0.510  -0.318  -0.339  -0.401
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    D        -1.456  -1.455  -1.411  -1.505  -1.502  -1.428  -1.235  -1.234  -1.164
84    V        -1.456  -1.455  -1.411  -1.336  -1.333  -1.262  -1.235  -1.234  -1.164
85    K        -1.456  -1.455  -1.411  -1.600  -1.596  -1.522  -1.235  -1.234  -1.164
86    E        -0.236  -0.250  -0.293  -0.295  -0.321  -0.401  -0.318  -0.339  -0.401
87    G        -0.236  -0.228  -0.287  -0.315  -0.301  -0.408  -0.318  -0.306  -0.391
88    R        -1.456  -1.455  -1.411  -1.336  -1.334  -1.262  -1.235  -1.234  -1.164
89    L        -0.236  -0.228  -0.287  -0.107  -0.094  -0.194  -0.318  -0.306  -0.391
90    P        -1.456  -1.455  -1.411  -1.452  -1.446  -1.376  -1.235  -1.234  -1.164
91    A        -0.236  -0.228  -0.287  -0.393  -0.376  -0.481  -0.318  -0.306  -0.391
92    E        -1.456  -1.455  -1.411  -1.614  -1.612  -1.536  -1.235  -1.234  -1.164
93    V        -0.236  -0.228  -0.273  -0.061  -0.051  -0.103  -0.318  -0.306  -0.371
94    E        -0.236  -0.228  -0.287  -0.412  -0.399  -0.499  -0.318  -0.306  -0.391
95    I        -1.456  -1.455  -1.411  -1.174  -1.168  -1.103  -1.235  -1.234  -1.164
96    -        -0.386  -0.385  -0.350  -0.497  -0.496  -0.436  -0.547  -0.546  -0.489
97    -        -0.386  -0.385  -0.350  -0.605  -0.604  -0.542  -0.547  -0.546  -0.489
98    -        -0.386  -0.385  -0.350  -0.433  -0.432  -0.373  -0.547  -0.546  -0.489
99    P         1.444   1.444   1.464   1.543   1.544   1.574   1.516   1.517   1.539
100   K        -1.456  -1.455  -1.411  -1.336  -1.338  -1.262  -1.235  -1.234  -1.164
101   N        -1.456  -1.455  -1.411  -1.248  -1.249  -1.175  -1.235  -1.234  -1.164
102   V         1.444   1.444   1.464   1.462   1.461   1.494   1.516   1.517   1.539
103   D         1.444   1.444   1.464   1.421   1.420   1.453   1.516   1.517   1.539
104   I        -0.236  -0.228  -0.273   0.056   0.069  -0.018  -0.318  -0.306  -0.371
105   S         1.444   1.444   1.464   1.296   1.295   1.330   1.516   1.517   1.539
106   N        -0.236  -0.228  -0.287  -0.373  -0.359  -0.462  -0.318  -0.306  -0.391
107   M        -0.236  -0.228  -0.287  -0.034  -0.020  -0.117  -0.318  -0.306  -0.391
108   S        -0.236  -0.250  -0.293  -0.163  -0.187  -0.278  -0.318  -0.339  -0.401
109   Q        -0.236  -0.228  -0.287  -0.089  -0.077  -0.177  -0.318  -0.306  -0.391
110   G        -1.456  -1.455  -1.411  -1.374  -1.373  -1.299  -1.235  -1.234  -1.164
111   E         1.444   1.444   1.464   1.296   1.296   1.330   1.516   1.517   1.539
112   F         1.444   1.444   1.464   1.523   1.524   1.554   1.516   1.517   1.539
113   L        -0.236  -0.250  -0.293  -0.295  -0.315  -0.368  -0.318  -0.339  -0.401
114   R        -0.236  -0.228  -0.287  -0.248  -0.233  -0.342  -0.318  -0.306  -0.391
115   L        -0.236  -0.228  -0.273  -0.061  -0.048  -0.119  -0.318  -0.306  -0.371
116   Y         1.444   1.444   1.464   1.604   1.604   1.633   1.516   1.517   1.539
117   E        -0.236  -0.250  -0.293  -0.373  -0.396  -0.473  -0.318  -0.339  -0.401
118   S        -0.236  -0.228  -0.287  -0.412  -0.400  -0.499  -0.318  -0.306  -0.391
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   L         1.444   1.444   1.464   1.543   1.544   1.574   1.516   1.517   1.539
125   R         1.444   1.444   1.464   1.462   1.462   1.494   1.516   1.517   1.539
126   R        -0.236  -0.250  -0.293  -0.334  -0.354  -0.415  -0.318  -0.339  -0.401
127   G         1.444   1.444   1.464   1.400   1.401   1.433   1.516   1.517   1.539
128   E         1.444   1.444   1.464   1.296   1.296   1.330   1.516   1.517   1.539
129   P         1.444   1.444   1.464   1.543   1.544   1.574   1.516   1.517   1.539
130   D        -0.236  -0.250  -0.293  -0.315  -0.337  -0.402  -0.318  -0.339  -0.401
131   N         1.444   1.444   1.464   1.338   1.339   1.372   1.516   1.517   1.539
132   K        -0.236  -0.228  -0.273  -0.334  -0.321  -0.385  -0.318  -0.306  -0.371
133   V         1.444   1.444   1.464   1.462   1.461   1.494   1.516   1.517   1.539
134   N         1.444   1.444   1.464   1.338   1.339   1.372   1.516   1.517   1.539
135   R        -0.236  -0.250  -0.293  -0.126  -0.147  -0.222  -0.318  -0.339  -0.401
* 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/Q04438
Output conservation file - output/Q04438
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
