1     M         1.253   1.255   1.260   1.486   1.490   1.498   1.296   1.297   1.304
2     M        -1.616  -1.605  -1.588  -1.424  -1.434  -1.385  -1.328  -1.314  -1.289
3     K        -1.616  -1.605  -1.588  -1.323  -1.333  -1.284  -1.328  -1.314  -1.289
4     G         1.253   1.255   1.260   1.217   1.216   1.232   1.296   1.297   1.304
5     S        -0.557  -0.556  -0.537  -1.164  -1.164  -1.127  -0.672  -0.669  -0.641
6     R         1.253   1.255   1.260   1.507   1.515   1.519   1.296   1.297   1.304
7     R         1.253   1.255   1.260   1.415   1.415   1.428   1.296   1.297   1.304
8     T        -1.616  -1.605  -1.588  -1.470  -1.446  -1.431  -1.328  -1.314  -1.289
9     G        -1.616  -1.605  -1.588  -1.436  -1.411  -1.396  -1.328  -1.314  -1.289
10    N        -0.410  -0.475  -0.473  -0.123  -0.231  -0.238  -0.454  -0.547  -0.546
11    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    T        -1.616  -1.605  -1.588  -1.589  -1.527  -1.548  -1.328  -1.314  -1.289
15    T        -0.410  -0.475  -0.473  -0.422  -0.488  -0.491  -0.454  -0.547  -0.546
16    L         1.253   1.255   1.260   1.198   1.198   1.213   1.296   1.297   1.304
17    N        -0.410  -0.475  -0.473  -0.220  -0.335  -0.354  -0.454  -0.547  -0.546
18    T        -0.410  -0.475  -0.473  -0.553  -0.641  -0.647  -0.454  -0.547  -0.546
19    P         1.253   1.255   1.260   1.362   1.363   1.375   1.296   1.297   1.304
20    V         1.253   1.255   1.260   1.253   1.255   1.268   1.296   1.297   1.304
21    V         1.253   1.255   1.260   1.253   1.255   1.268   1.296   1.297   1.304
22    I        -0.410  -0.367  -0.482  -0.261  -0.205  -0.364  -0.454  -0.391  -0.558
23    H        -0.410  -0.475  -0.473  -0.012  -0.131  -0.134  -0.454  -0.547  -0.546
24    A        -1.616  -1.605  -1.588  -1.565  -1.520  -1.524  -1.328  -1.314  -1.289
25    T        -1.616  -1.605  -1.588  -1.447  -1.411  -1.408  -1.328  -1.314  -1.289
26    Q        -0.410  -0.367  -0.482  -0.320  -0.270  -0.426  -0.454  -0.391  -0.558
27    L        -1.616  -1.605  -1.588  -1.589  -1.561  -1.548  -1.328  -1.314  -1.289
28    P         1.253   1.255   1.260   1.362   1.363   1.375   1.296   1.297   1.304
29    Q        -0.410  -0.367  -0.482  -0.345  -0.272  -0.491  -0.454  -0.391  -0.558
30    H        -0.410  -0.367  -0.482   0.149   0.207   0.047  -0.454  -0.391  -0.558
31    V        -0.410  -0.367  -0.482  -0.354  -0.295  -0.477  -0.454  -0.391  -0.558
32    S         1.253   1.255   1.260   1.049   1.065   1.065   1.296   1.297   1.304
33    T        -1.616  -1.605  -1.588  -1.436  -1.400  -1.396  -1.328  -1.314  -1.289
34    D        -0.410  -0.475  -0.473  -0.237  -0.343  -0.344  -0.454  -0.547  -0.546
35    E         1.253   1.255   1.260   1.272   1.276   1.286   1.296   1.297   1.304
36    V        -0.410  -0.475  -0.473  -0.220  -0.315  -0.303  -0.454  -0.547  -0.546
37    L         1.253   1.255   1.260   1.198   1.198   1.213   1.296   1.297   1.304
38    Q        -0.410  -0.475  -0.473  -0.295  -0.414  -0.414  -0.454  -0.547  -0.546
39    F         1.253   1.255   1.260   1.451   1.456   1.463   1.296   1.297   1.304
40    L         1.253   1.255   1.260   1.198   1.198   1.213   1.296   1.297   1.304
41    E        -1.616  -1.605  -1.588  -1.413  -1.383  -1.374  -1.328  -1.314  -1.289
42    S        -0.410  -0.475  -0.473  -0.509  -0.600  -0.599  -0.454  -0.547  -0.546
43    F         1.253   1.255   1.260   1.451   1.456   1.463   1.296   1.297   1.304
44    I        -0.410  -0.475  -0.473  -0.196  -0.306  -0.308  -0.454  -0.547  -0.546
45    D        -1.616  -1.605  -1.588  -1.367  -1.346  -1.329  -1.328  -1.314  -1.289
46    E        -0.410  -0.475  -0.473  -0.270  -0.376  -0.367  -0.454  -0.547  -0.546
47    K         1.253   1.255   1.260   1.272   1.273   1.286   1.296   1.297   1.304
48    E         1.253   1.255   1.260   1.272   1.276   1.286   1.296   1.297   1.304
49    N        -1.616  -1.605  -1.588  -1.345  -1.315  -1.307  -1.328  -1.314  -1.289
50    I        -1.616  -1.605  -1.588  -1.390  -1.386  -1.351  -1.328  -1.314  -1.289
51    I        -1.616  -1.605  -1.588  -1.390  -1.394  -1.351  -1.328  -1.314  -1.289
52    D        -0.410  -0.367  -0.482  -0.320  -0.265  -0.426  -0.454  -0.391  -0.558
53    S        -0.557  -0.556  -0.537  -0.872  -0.871  -0.837  -0.672  -0.669  -0.641
54    T         1.253   1.255   1.260   0.945   0.951   0.962   1.296   1.297   1.304
55    T        -0.557  -0.556  -0.537  -0.758  -0.757  -0.725  -0.672  -0.669  -0.641
56    M        -0.557  -0.556  -0.537  -0.436  -0.434  -0.406  -0.672  -0.669  -0.641
57    N        -0.557  -0.556  -0.537  -0.758  -0.757  -0.725  -0.672  -0.669  -0.641
58    T        -0.557  -0.556  -0.537  -1.164  -1.164  -1.127  -0.672  -0.669  -0.641
59    I        -0.557  -0.556  -0.537  -0.392  -0.390  -0.363  -0.672  -0.669  -0.641
60    S        -0.557  -0.556  -0.537  -1.006  -1.006  -0.971  -0.672  -0.669  -0.641
61    G        -0.557  -0.556  -0.537  -0.855  -0.854  -0.821  -0.672  -0.669  -0.641
62    N        -0.557  -0.556  -0.537  -0.648  -0.646  -0.616  -0.672  -0.669  -0.641
63    A        -0.557  -0.556  -0.537  -0.888  -0.887  -0.854  -0.672  -0.669  -0.641
64    A        -0.557  -0.556  -0.537  -0.540  -0.539  -0.509  -0.672  -0.669  -0.641
65    D        -0.557  -0.556  -0.537  -0.451  -0.449  -0.421  -0.672  -0.669  -0.641
66    A         1.253   1.255   1.260   1.138   1.146   1.154   1.296   1.297   1.304
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    D        -0.557  -0.556  -0.537  -0.726  -0.725  -0.693  -0.672  -0.669  -0.641
69    A        -0.557  -0.556  -0.537  -1.006  -1.006  -0.971  -0.672  -0.669  -0.641
70    A        -0.557  -0.556  -0.537  -0.601  -0.600  -0.570  -0.672  -0.669  -0.641
71    A        -0.557  -0.556  -0.537  -0.601  -0.600  -0.570  -0.672  -0.669  -0.641
72    V        -0.557  -0.556  -0.537  -0.407  -0.405  -0.377  -0.672  -0.669  -0.641
73    A        -0.557  -0.556  -0.537  -1.006  -1.006  -0.971  -0.672  -0.669  -0.641
74    N        -0.557  -0.556  -0.537  -0.510  -0.509  -0.480  -0.672  -0.669  -0.641
75    T        -0.557  -0.556  -0.537  -0.726  -0.725  -0.693  -0.672  -0.669  -0.641
76    S        -0.557  -0.556  -0.537  -0.872  -0.871  -0.837  -0.672  -0.669  -0.641
77    L        -0.557  -0.556  -0.537  -0.320  -0.318  -0.291  -0.672  -0.669  -0.641
78    N        -0.557  -0.556  -0.537  -0.510  -0.509  -0.480  -0.672  -0.669  -0.641
79    I        -0.557  -0.556  -0.537  -0.407  -0.405  -0.377  -0.672  -0.669  -0.641
80    D         1.253   1.255   1.260   1.346   1.354   1.360   1.296   1.297   1.304
81    T         1.253   1.255   1.260   0.945   0.951   0.962   1.296   1.297   1.304
82    N        -0.557  -0.556  -0.537  -0.320  -0.318  -0.291  -0.672  -0.669  -0.641
83    L         1.253   1.255   1.260   1.305   1.313   1.319   1.296   1.297   1.304
84    S         1.253   1.255   1.260   0.789   0.795   0.808   1.296   1.297   1.304
85    S        -0.410  -0.475  -0.473  -0.535  -0.631  -0.631  -0.454  -0.547  -0.546
86    S        -0.410  -0.367  -0.482  -0.571  -0.492  -0.687  -0.454  -0.391  -0.558
87    I        -0.410  -0.367  -0.482  -0.311  -0.257  -0.411  -0.454  -0.391  -0.558
88    S        -0.410  -0.367  -0.482  -0.526  -0.442  -0.659  -0.454  -0.391  -0.558
89    Q        -0.410  -0.475  -0.473  -0.270  -0.393  -0.384  -0.454  -0.547  -0.546
90    L         1.253   1.255   1.260   1.198   1.198   1.213   1.296   1.297   1.304
91    K         1.253   1.255   1.260   1.272   1.273   1.286   1.296   1.297   1.304
92    R         1.253   1.255   1.260   1.415   1.415   1.428   1.296   1.297   1.304
93    I        -0.410  -0.367  -0.482  -0.196  -0.127  -0.323  -0.454  -0.391  -0.558
94    Q        -0.410  -0.367  -0.482  -0.237  -0.180  -0.358  -0.454  -0.391  -0.558
95    R         1.253   1.255   1.260   1.415   1.415   1.428   1.296   1.297   1.304
96    D         1.253   1.255   1.260   1.344   1.353   1.358   1.296   1.297   1.304
97    F         1.253   1.255   1.260   1.451   1.456   1.463   1.296   1.297   1.304
98    K         1.253   1.255   1.260   1.272   1.273   1.286   1.296   1.297   1.304
99    G         1.253   1.255   1.260   1.217   1.216   1.232   1.296   1.297   1.304
100   L         1.253   1.255   1.260   1.198   1.198   1.213   1.296   1.297   1.304
101   P         1.253   1.255   1.260   1.362   1.363   1.375   1.296   1.297   1.304
102   P         1.253   1.255   1.260   1.362   1.363   1.375   1.296   1.297   1.304
103   A        -0.410  -0.367  -0.482  -0.295  -0.229  -0.429  -0.454  -0.391  -0.558
104   Q        -1.616  -1.605  -1.588  -1.494  -1.498  -1.454  -1.328  -1.314  -1.289
105   D        -0.557  -0.556  -0.537  -0.292  -0.289  -0.263  -0.672  -0.669  -0.641
106   F        -0.557  -0.556  -0.537  -0.349  -0.347  -0.320  -0.672  -0.669  -0.641
107   S        -0.557  -0.556  -0.537  -0.679  -0.678  -0.646  -0.672  -0.669  -0.641
108   A        -0.557  -0.556  -0.537  -0.617  -0.615  -0.585  -0.672  -0.669  -0.641
109   A        -0.557  -0.556  -0.537  -0.525  -0.524  -0.494  -0.672  -0.669  -0.641
110   P        -0.557  -0.556  -0.537  -0.774  -0.773  -0.741  -0.672  -0.669  -0.641
111   I        -0.557  -0.556  -0.537  -0.774  -0.773  -0.741  -0.672  -0.669  -0.641
112   Q        -0.557  -0.556  -0.537  -0.679  -0.678  -0.646  -0.672  -0.669  -0.641
113   V        -0.557  -0.556  -0.537  -0.872  -0.871  -0.837  -0.672  -0.669  -0.641
114   S         1.253   1.255   1.260   0.789   0.795   0.808   1.296   1.297   1.304
115   T         1.253   1.255   1.260   0.945   0.951   0.962   1.296   1.297   1.304
116   T        -0.557  -0.556  -0.537  -0.742  -0.741  -0.709  -0.672  -0.669  -0.641
117   E        -0.557  -0.556  -0.537  -0.392  -0.390  -0.363  -0.672  -0.669  -0.641
118   K        -0.557  -0.556  -0.537  -0.726  -0.725  -0.693  -0.672  -0.669  -0.641
119   K        -0.557  -0.556  -0.537  -0.466  -0.464  -0.435  -0.672  -0.669  -0.641
120   E         1.253   1.255   1.260   1.305   1.313   1.319   1.296   1.297   1.304
121   T        -0.557  -0.556  -0.537  -0.726  -0.725  -0.693  -0.672  -0.669  -0.641
122   S        -0.557  -0.556  -0.537  -1.164  -1.164  -1.127  -0.672  -0.669  -0.641
123   I        -0.557  -0.556  -0.537  -0.407  -0.405  -0.377  -0.672  -0.669  -0.641
124   G        -0.557  -0.556  -0.537  -0.601  -0.600  -0.570  -0.672  -0.669  -0.641
125   V        -0.557  -0.556  -0.537  -0.466  -0.464  -0.435  -0.672  -0.669  -0.641
126   S         1.253   1.255   1.260   0.789   0.795   0.808   1.296   1.297   1.304
127   A         1.253   1.255   1.260   1.138   1.146   1.154   1.296   1.297   1.304
128   T         1.253   1.255   1.260   0.945   0.951   0.962   1.296   1.297   1.304
129   G         1.253   1.255   1.260   1.326   1.333   1.339   1.296   1.297   1.304
130   G         1.253   1.255   1.260   1.326   1.333   1.339   1.296   1.297   1.304
131   K         1.253   1.255   1.260   1.346   1.354   1.360   1.296   1.297   1.304
132   K         1.253   1.255   1.260   1.346   1.354   1.360   1.296   1.297   1.304
133   T        -0.557  -0.556  -0.537  -0.663  -0.662  -0.631  -0.672  -0.669  -0.641
134   T        -0.557  -0.556  -0.537  -0.726  -0.725  -0.693  -0.672  -0.669  -0.641
135   F         1.253   1.255   1.260   1.507   1.515   1.519   1.296   1.297   1.304
136   A         1.253   1.255   1.260   1.138   1.146   1.154   1.296   1.297   1.304
137   D         1.253   1.255   1.260   1.346   1.354   1.360   1.296   1.297   1.304
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   E         1.253   1.255   1.260   1.272   1.276   1.286   1.296   1.297   1.304
* 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/P50106
Output conservation file - output/P50106
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
