1     M         0.583   0.600   0.621   1.104   1.090   1.024   0.585   0.608   0.644
2     S        -0.261  -0.405  -1.006   0.058  -0.069  -0.851  -0.150  -0.321  -1.201
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     G         0.583   0.600   0.621   0.303   0.347   0.442   0.585   0.608   0.644
5     G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
6     K         0.583   0.600   0.621   0.497   0.526   0.583   0.585   0.608   0.644
7     G        -1.555  -1.406  -1.029  -1.914  -1.631  -1.145  -1.972  -1.754  -1.239
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
10    K        -1.098  -1.262  -1.031  -1.169  -1.482  -1.254  -1.253  -1.524  -1.242
11    A        -1.876  -1.901  -1.995  -2.064  -2.180  -2.074  -1.805  -1.914  -1.870
12    G        -1.338  -1.433  -1.037  -1.842  -2.119  -1.498  -1.621  -1.798  -1.250
13    S        -1.555  -1.586  -1.983  -1.149  -1.315  -1.870  -1.376  -1.481  -1.857
14    A        -3.214  -3.228  -2.691  -3.271  -3.176  -2.586  -2.908  -2.829  -2.195
15    A        -2.479  -2.439  -2.004  -2.666  -2.611  -1.985  -2.479  -2.391  -1.880
16    K         0.583   0.600   0.621   0.497   0.526   0.583   0.585   0.608   0.644
17    A        -2.333  -2.860  -2.689  -2.133  -2.712  -2.374  -1.928  -2.450  -2.194
18    S        -1.098  -1.262  -1.031  -1.108  -1.461  -1.289  -1.253  -1.524  -1.242
19    Q        -2.089  -2.086  -1.994  -1.536  -1.490  -1.614  -2.112  -1.998  -1.869
20    S        -0.753  -0.513  -1.005  -0.442  -0.179  -0.850  -0.763  -0.456  -1.200
21    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
22    S         0.583   0.600   0.621   0.620   0.646   0.672   0.585   0.608   0.644
23    A        -0.261  -0.405  -1.006  -0.493  -0.610  -1.307  -0.150  -0.321  -1.201
24    K         0.583   0.600   0.621   0.497   0.526   0.583   0.585   0.608   0.644
25    A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
26    G        -0.261  -0.558  -1.009  -0.239  -0.503  -0.996  -0.150  -0.513  -1.207
27    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
28    T        -1.098  -1.262  -1.031  -0.799  -1.183  -1.101  -1.253  -1.524  -1.242
29    F         0.583   0.600   0.621   1.104   1.090   1.024   0.585   0.608   0.644
30    P         0.583   0.600   0.621   0.854   0.856   0.842   0.585   0.608   0.644
31    V         0.583   0.600   0.621   0.763   0.760   0.776   0.585   0.608   0.644
32    G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
33    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
34    V         0.583   0.600   0.621   0.763   0.760   0.776   0.585   0.608   0.644
35    H         0.583   0.600   0.621   0.962   0.952   0.921   0.585   0.608   0.644
36    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
37    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
38    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
39    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
40    R        -1.098  -0.786  -1.012  -1.081  -0.668  -1.075  -1.253  -0.818  -1.211
41    G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
42    N         0.583   0.600   0.621   0.731   0.746   0.753   0.585   0.608   0.644
43    Y         0.583   0.600   0.621   0.989   0.983   0.940   0.585   0.608   0.644
44    A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
45    Q         0.583   0.600   0.621   0.841   0.847   0.833   0.585   0.608   0.644
46    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
47    I        -1.490  -1.424  -1.037  -1.376  -1.332  -0.885  -1.866  -1.784  -1.252
48    G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
49    S        -1.338  -1.433  -1.037  -1.543  -1.872  -1.326  -1.621  -1.798  -1.250
50    G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
51    A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
52    P         0.583   0.600   0.621   0.854   0.856   0.842   0.585   0.608   0.644
53    V        -0.261  -0.558  -1.009   0.188  -0.136  -0.838  -0.150  -0.513  -1.207
54    Y         0.583   0.600   0.621   0.989   0.983   0.940   0.585   0.608   0.644
55    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
56    T        -1.338  -1.433  -1.037  -1.242  -1.628  -1.153  -1.621  -1.798  -1.250
57    A        -1.338  -1.050  -1.022  -1.823  -1.399  -1.324  -1.621  -1.198  -1.227
58    V         0.583   0.600   0.621   0.763   0.760   0.776   0.585   0.608   0.644
59    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
60    E         0.583   0.600   0.621   0.818   0.822   0.816   0.585   0.608   0.644
61    Y         0.583   0.600   0.621   0.989   0.983   0.940   0.585   0.608   0.644
62    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
63    A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
64    A        -0.261  -0.558  -1.009  -0.480  -0.757  -1.242  -0.150  -0.513  -1.207
65    E         0.583   0.600   0.621   0.818   0.822   0.816   0.585   0.608   0.644
66    I         0.583   0.600   0.621   0.777   0.789   0.786   0.585   0.608   0.644
67    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
68    E         0.583   0.600   0.621   0.818   0.822   0.816   0.585   0.608   0.644
69    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
70    A        -0.261  -0.558  -1.009  -0.493  -0.776  -1.311  -0.150  -0.513  -1.207
71    G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
72    N         0.583   0.600   0.621   0.731   0.746   0.753   0.585   0.608   0.644
73    A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
74    A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
75    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
76    D         0.583   0.600   0.621   1.011   1.007   0.956   0.585   0.608   0.644
77    N         0.583   0.600   0.621   0.731   0.746   0.753   0.585   0.608   0.644
78    K         0.583   0.600   0.621   0.497   0.526   0.583   0.585   0.608   0.644
79    K         0.583   0.600   0.621   0.497   0.526   0.583   0.585   0.608   0.644
80    T        -1.565  -1.441  -1.037  -1.516  -1.342  -0.879  -1.989  -1.813  -1.252
81    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
82    I         0.583   0.600   0.621   0.777   0.789   0.786   0.585   0.608   0.644
83    I        -0.261  -0.558  -1.009   0.201  -0.111  -0.836  -0.150  -0.513  -1.207
84    P         0.583   0.600   0.621   0.854   0.856   0.842   0.585   0.608   0.644
85    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
86    H         0.583   0.600   0.621   0.962   0.952   0.921   0.585   0.608   0.644
87    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
88    Q         0.583   0.600   0.621   0.841   0.847   0.833   0.585   0.608   0.644
89    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
90    A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
91    I         0.583   0.600   0.621   0.777   0.789   0.786   0.585   0.608   0.644
92    R         0.583   0.600   0.621   0.610   0.629   0.666   0.585   0.608   0.644
93    N         0.583   0.600   0.621   0.731   0.746   0.753   0.585   0.608   0.644
94    D         0.583   0.600   0.621   1.011   1.007   0.956   0.585   0.608   0.644
95    D        -1.490  -1.177  -1.019  -1.209  -0.797  -0.718  -1.866  -1.391  -1.223
96    E         0.583   0.600   0.621   0.818   0.822   0.816   0.585   0.608   0.644
97    L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
98    N         0.583   0.600   0.621   0.731   0.746   0.753   0.585   0.608   0.644
99    K         0.583   0.600   0.621   0.497   0.526   0.583   0.585   0.608   0.644
100   L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
101   L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
102   G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
103   N        -2.567  -2.171  -1.992  -2.032  -1.515  -1.439  -2.602  -2.119  -1.867
104   V         0.583   0.600   0.621   0.763   0.760   0.776   0.585   0.608   0.644
105   T         0.583   0.600   0.621   0.931   0.936   0.898   0.585   0.608   0.644
106   I         0.583   0.600   0.621   0.777   0.789   0.786   0.585   0.608   0.644
107   A         0.583   0.600   0.621   0.097   0.143   0.293   0.585   0.608   0.644
108   Q         0.583   0.600   0.621   0.841   0.847   0.833   0.585   0.608   0.644
109   G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
110   G         0.583   0.600   0.621   0.315   0.355   0.451   0.585   0.608   0.644
111   V         0.583   0.600   0.621   0.763   0.760   0.776   0.585   0.608   0.644
112   L        -0.753  -0.951  -1.012  -0.949  -1.172  -1.217  -0.763  -1.052  -1.211
113   P         0.583   0.600   0.621   0.854   0.856   0.842   0.585   0.608   0.644
114   N         0.583   0.600   0.621   0.731   0.746   0.753   0.585   0.608   0.644
115   I         0.583   0.600   0.621   0.777   0.789   0.786   0.585   0.608   0.644
116   H        -0.753  -0.951  -1.012  -0.141  -0.441  -0.746  -0.763  -1.052  -1.211
117   Q        -0.753  -0.951  -1.012  -0.369  -0.700  -1.091  -0.763  -1.052  -1.211
118   N        -2.002  -2.007  -1.989  -1.406  -1.446  -1.608  -1.866  -1.893  -1.863
119   L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
120   L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
121   P         0.583   0.600   0.621   0.854   0.856   0.842   0.585   0.608   0.644
122   K        -1.555  -1.659  -1.987  -1.306  -1.391  -2.086  -1.376  -1.466  -1.861
123   K        -1.085  -1.399  -1.981  -0.628  -0.927  -1.644  -0.824  -1.168  -1.854
124   S        -1.555  -1.519  -1.984  -1.072  -0.997  -1.719  -1.376  -1.308  -1.858
125   A        -2.479  -2.225  -1.995  -2.950  -2.668  -2.225  -2.479  -2.235  -1.870
126   K        -0.261  -0.444  -1.002  -0.092  -0.267  -1.060  -0.150  -0.368  -1.196
127   T        -3.643  -3.326  -2.690  -3.648  -3.131  -2.406  -3.227  -2.903  -2.194
128   A        -1.167  -1.186  -1.033  -1.553  -1.611  -1.496  -1.357  -1.405  -1.245
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   K        -2.333  -1.893  -2.673  -1.824  -1.332  -2.497  -1.928  -1.463  -2.180
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   A        -0.753  -0.951  -1.012  -0.976  -1.198  -1.200  -0.763  -1.052  -1.211
133   S         0.583   0.600   0.621   0.620   0.646   0.672   0.585   0.608   0.644
134   Q         0.583   0.600   0.621   0.841   0.847   0.833   0.585   0.608   0.644
135   E         0.583   0.600   0.621   0.818   0.822   0.816   0.585   0.608   0.644
136   L         0.583   0.600   0.621   0.142   0.200   0.326   0.585   0.608   0.644
* 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/P04912
Output conservation file - output/P04912
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
