1     M         0.615   0.636   0.656   0.941   0.942   0.936   0.638   0.665   0.693
2     G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
3     R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
4     M         0.615   0.636   0.656   0.941   0.942   0.936   0.638   0.665   0.693
5     H         0.615   0.636   0.656   0.885   0.897   0.892   0.638   0.665   0.693
6     S         0.615   0.636   0.656   0.391   0.449   0.508   0.638   0.665   0.693
7     A        -1.947  -1.501  -1.732  -2.396  -1.709  -1.991  -2.081  -1.503  -1.693
8     G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
9     K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
10    G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
11    I        -0.864  -0.667  -0.849  -0.887  -0.616  -0.837  -1.079  -0.780  -1.087
12    S        -0.376  -0.672  -0.836  -0.462  -0.851  -1.128  -0.364  -0.788  -1.066
13    S        -0.864  -0.894  -0.860  -1.158  -1.216  -1.172  -1.079  -1.135  -1.107
14    S         0.615   0.636   0.656   0.391   0.449   0.508   0.638   0.665   0.693
15    A         0.615   0.636   0.656   0.464   0.518   0.564   0.638   0.665   0.693
16    I        -1.753  -1.597  -1.742  -1.878  -1.724  -1.923  -1.795  -1.626  -1.705
17    P         0.615   0.636   0.656   0.724   0.736   0.767   0.638   0.665   0.693
18    Y         0.615   0.636   0.656   0.794   0.824   0.821   0.638   0.665   0.693
19    S        -0.376  -0.672  -0.836  -0.441  -0.814  -1.059  -0.364  -0.788  -1.066
20    R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
21    N        -0.376  -0.672  -0.836  -0.028  -0.458  -0.864  -0.364  -0.788  -1.066
22    A        -0.864  -1.030  -0.867  -1.000  -1.275  -0.991  -1.079  -1.360  -1.119
23    P         0.615   0.636   0.656   0.724   0.736   0.767   0.638   0.665   0.693
24    A        -1.125  -1.022  -0.866  -1.597  -1.431  -1.179  -1.509  -1.346  -1.117
25    W         0.615   0.636   0.656   0.981   0.984   0.966   0.638   0.665   0.693
26    F        -1.320  -1.724  -1.742  -0.641  -1.234  -1.393  -1.222  -1.706  -1.704
27    K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
28    L        -2.575  -2.512  -2.379  -2.511  -2.486  -2.205  -2.367  -2.265  -2.015
29    S        -1.947  -1.995  -1.748  -2.025  -1.981  -1.609  -2.081  -2.046  -1.711
30    S        -3.314  -3.056  -2.876  -3.135  -2.859  -2.476  -2.797  -2.514  -2.202
31    E        -1.947  -1.666  -1.740  -1.692  -1.361  -1.411  -2.081  -1.729  -1.703
32    S        -3.314  -3.005  -2.873  -3.075  -2.684  -2.446  -2.797  -2.440  -2.200
33    V         0.615   0.636   0.656   0.607   0.643   0.676   0.638   0.665   0.693
34    I        -0.864  -0.531  -0.826  -0.933  -0.441  -0.944  -1.079  -0.579  -1.051
35    E        -0.376  -0.545  -0.829  -0.007  -0.224  -0.681  -0.364  -0.600  -1.056
36    Q         0.615   0.636   0.656   0.925   0.926   0.923   0.638   0.665   0.693
37    I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
38    V        -2.208  -2.357  -2.378  -1.898  -2.162  -2.131  -1.938  -2.094  -2.014
39    K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
40    Y        -1.320  -1.724  -1.742  -0.831  -1.397  -1.525  -1.222  -1.706  -1.704
41    A        -0.376  -0.672  -0.836  -0.399  -0.802  -1.114  -0.364  -0.788  -1.066
42    R        -0.864  -1.030  -0.867  -1.091  -1.450  -1.174  -1.079  -1.360  -1.119
43    K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
44    G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
45    L        -1.320  -1.724  -1.742  -1.204  -1.728  -1.727  -1.222  -1.706  -1.704
46    T        -0.376  -0.672  -0.836  -0.039  -0.485  -0.872  -0.364  -0.788  -1.066
47    P         0.615   0.636   0.656   0.724   0.736   0.767   0.638   0.665   0.693
48    S         0.615   0.636   0.656   0.391   0.449   0.508   0.638   0.665   0.693
49    Q         0.615   0.636   0.656   0.925   0.926   0.923   0.638   0.665   0.693
50    I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
51    G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
52    V         0.615   0.636   0.656   0.607   0.643   0.676   0.638   0.665   0.693
53    L        -1.947  -1.997  -1.748  -2.210  -2.196  -1.777  -2.081  -2.050  -1.712
54    L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
55    R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
56    D         0.615   0.636   0.656   0.834   0.842   0.852   0.638   0.665   0.693
57    A        -1.125  -1.065  -0.863  -1.597  -1.531  -1.176  -1.509  -1.419  -1.111
58    H         0.615   0.636   0.656   0.885   0.897   0.892   0.638   0.665   0.693
59    G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
60    V        -0.864  -1.030  -0.867  -0.933  -1.276  -1.031  -1.079  -1.360  -1.119
61    T        -2.687  -2.730  -2.386  -2.632  -2.702  -2.215  -2.510  -2.435  -2.021
62    Q         0.615   0.636   0.656   0.925   0.926   0.923   0.638   0.665   0.693
63    A        -1.125  -1.065  -0.863  -1.479  -1.376  -1.041  -1.509  -1.419  -1.111
64    R        -1.125  -1.027  -0.866  -1.621  -1.477  -1.176  -1.509  -1.353  -1.116
65    V        -0.376  -0.672  -0.836  -0.171  -0.527  -0.744  -0.364  -0.788  -1.066
66    I        -2.575  -2.307  -2.376  -2.440  -2.131  -2.115  -2.367  -2.058  -2.012
67    T         0.615   0.636   0.656   0.822   0.838   0.843   0.638   0.665   0.693
68    G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
69    N        -0.376  -0.672  -0.836   0.046  -0.328  -0.625  -0.364  -0.788  -1.066
70    K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
71    I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
72    M        -1.125  -1.027  -0.866  -1.337  -1.189  -0.897  -1.509  -1.353  -1.116
73    R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
74    I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
75    L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
76    K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
77    S        -0.376  -0.672  -0.836  -0.462  -0.851  -1.128  -0.364  -0.788  -1.066
78    N         0.615   0.636   0.656   0.834   0.867   0.852   0.638   0.665   0.693
79    G         0.615   0.636   0.656   0.678   0.702   0.731   0.638   0.665   0.693
80    L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
81    A         0.615   0.636   0.656   0.464   0.518   0.564   0.638   0.665   0.693
82    P         0.615   0.636   0.656   0.724   0.736   0.767   0.638   0.665   0.693
83    E        -0.376  -0.545  -0.829  -0.007  -0.224  -0.681  -0.364  -0.600  -1.056
84    I        -0.864  -1.030  -0.867  -1.061  -1.405  -1.143  -1.079  -1.360  -1.119
85    P         0.615   0.636   0.656   0.724   0.736   0.767   0.638   0.665   0.693
86    E         0.615   0.636   0.656   0.794   0.819   0.821   0.638   0.665   0.693
87    D         0.615   0.636   0.656   0.834   0.842   0.852   0.638   0.665   0.693
88    L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
89    Y         0.615   0.636   0.656   0.794   0.824   0.821   0.638   0.665   0.693
90    Y        -3.770  -3.592  -3.282  -2.906  -2.728  -2.381  -2.940  -2.720  -2.326
91    L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
92    I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
93    K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
94    K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
95    A         0.615   0.636   0.656   0.464   0.518   0.564   0.638   0.665   0.693
96    V         0.615   0.636   0.656   0.607   0.643   0.676   0.638   0.665   0.693
97    S        -0.376  -0.545  -0.829  -0.462  -0.663  -1.116  -0.364  -0.600  -1.056
98    V         0.615   0.636   0.656   0.607   0.643   0.676   0.638   0.665   0.693
99    R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
100   K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
101   H         0.615   0.636   0.656   0.885   0.897   0.892   0.638   0.665   0.693
102   L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
103   E        -0.376  -0.302  -0.822  -0.007   0.071  -0.670  -0.364  -0.265  -1.045
104   R        -0.864  -0.646  -0.846  -1.091  -0.750  -1.124  -1.079  -0.749  -1.083
105   N         0.615   0.636   0.656   0.834   0.867   0.852   0.638   0.665   0.693
106   R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
107   K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
108   D         0.615   0.636   0.656   0.834   0.842   0.852   0.638   0.665   0.693
109   K        -0.376  -0.302  -0.822  -0.474  -0.380  -1.112  -0.364  -0.265  -1.045
110   D         0.615   0.636   0.656   0.834   0.842   0.852   0.638   0.665   0.693
111   A        -1.125  -0.815  -0.843  -1.623  -1.079  -1.142  -1.509  -1.008  -1.079
112   K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
113   F         0.615   0.636   0.656   0.975   0.979   0.962   0.638   0.665   0.693
114   R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
115   L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
116   I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
117   L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
118   I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
119   E         0.615   0.636   0.656   0.794   0.819   0.821   0.638   0.665   0.693
120   S         0.615   0.636   0.656   0.391   0.449   0.508   0.638   0.665   0.693
121   R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
122   I         0.615   0.636   0.656   0.506   0.555   0.597   0.638   0.665   0.693
123   H         0.615   0.636   0.656   0.885   0.897   0.892   0.638   0.665   0.693
124   R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
125   L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
126   A         0.615   0.636   0.656   0.464   0.518   0.564   0.638   0.665   0.693
127   R         0.615   0.636   0.656   0.488   0.539   0.583   0.638   0.665   0.693
128   Y         0.615   0.636   0.656   0.794   0.824   0.821   0.638   0.665   0.693
129   Y         0.615   0.636   0.656   0.794   0.824   0.821   0.638   0.665   0.693
130   R        -0.864  -0.894  -0.860  -1.091  -1.174  -1.156  -1.079  -1.135  -1.107
131   T        -1.320  -1.525  -1.734  -0.903  -1.282  -1.753  -1.222  -1.480  -1.694
132   V         0.615   0.636   0.656   0.607   0.643   0.676   0.638   0.665   0.693
133   A        -1.947  -1.642  -1.740  -2.152  -1.691  -1.821  -2.081  -1.711  -1.702
134   V        -0.376  -0.672  -0.836  -0.245  -0.659  -0.983  -0.364  -0.788  -1.066
135   L         0.615   0.636   0.656   0.416   0.466   0.527   0.638   0.665   0.693
136   P         0.615   0.636   0.656   0.724   0.736   0.767   0.638   0.665   0.693
137   P         0.615   0.636   0.656   0.724   0.736   0.767   0.638   0.665   0.693
138   N        -1.125  -1.065  -0.863  -1.042  -0.992  -0.719  -1.509  -1.419  -1.111
139   W         0.615   0.636   0.656   0.981   0.984   0.966   0.638   0.665   0.693
140   K         0.615   0.636   0.656   0.379   0.415   0.498   0.638   0.665   0.693
141   Y         0.615   0.636   0.656   0.794   0.824   0.821   0.638   0.665   0.693
142   E         0.615   0.636   0.656   0.794   0.819   0.821   0.638   0.665   0.693
143   S         0.615   0.636   0.656   0.391   0.449   0.508   0.638   0.665   0.693
144   A        -0.376  -0.545  -0.829  -0.399  -0.610  -1.101  -0.364  -0.600  -1.056
145   T         0.615   0.636   0.656   0.822   0.838   0.843   0.638   0.665   0.693
146   A         0.615   0.636   0.656   0.464   0.518   0.564   0.638   0.665   0.693
147   S         0.615   0.636   0.656   0.391   0.449   0.508   0.638   0.665   0.693
148   A        -0.864  -0.838  -0.861  -0.967  -0.927  -0.935  -1.079  -1.045  -1.107
149   L        -0.376  -0.545  -0.829  -0.431  -0.638  -1.080  -0.364  -0.600  -1.056
150   V         0.615   0.636   0.656   0.607   0.643   0.676   0.638   0.665   0.693
151   N        -1.753  -1.879  -1.747  -1.556  -1.831  -1.756  -1.795  -1.913  -1.710
* 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/P05756
Output conservation file - output/P05756
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
