1     M         1.375   1.389   1.416   1.653   1.656   1.705   1.466   1.484   1.524
2     T        -0.037  -0.007   0.029  -0.020   0.021   0.083  -0.313  -0.262  -0.220
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
6     K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
7     D        -0.619  -0.740  -0.760  -0.581  -0.760  -0.770  -0.609  -0.757  -0.779
8     K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
9     K        -1.420  -1.446  -1.368  -1.494  -1.501  -1.310  -1.202  -1.215  -1.111
10    A        -0.930  -0.887  -0.799  -0.928  -0.833  -0.733  -1.004  -0.941  -0.827
11    K        -0.930  -0.887  -0.799  -1.113  -1.111  -0.908  -1.004  -0.941  -0.827
12    G         0.039  -0.009   0.052   0.011  -0.063   0.031  -0.181  -0.266  -0.181
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    P         1.375   1.389   1.416   1.584   1.598   1.640   1.466   1.484   1.524
30    K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
31    M        -2.001  -1.944  -1.829  -1.671  -1.614  -1.435  -1.498  -1.432  -1.297
32    S        -1.420  -1.259  -1.350  -0.992  -0.775  -0.919  -1.202  -1.020  -1.094
33    T        -0.838  -0.761  -0.777  -0.783  -0.685  -0.676  -0.905  -0.803  -0.801
34    I        -0.838  -0.761  -0.777  -0.773  -0.672  -0.687  -0.905  -0.803  -0.801
35    T        -0.838  -0.735  -0.775  -0.822  -0.684  -0.727  -0.905  -0.780  -0.800
36    T        -0.037  -0.055   0.019  -0.087  -0.127  -0.006  -0.313  -0.345  -0.239
37    K        -0.037  -0.055   0.019  -0.521  -0.510  -0.373  -0.313  -0.345  -0.239
38    S         0.325   0.459   0.176   0.465   0.641   0.198   0.280   0.480   0.029
39    G        -0.037  -0.055   0.019   0.084   0.024   0.135  -0.313  -0.345  -0.239
40    E         1.375   1.389   1.416   1.228   1.253   1.304   1.466   1.484   1.524
41    S         0.325   0.402   0.163   0.500   0.592   0.231   0.280   0.396   0.007
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    L        -1.420  -1.446  -1.368  -1.183  -1.213  -1.102  -1.202  -1.215  -1.111
58    K         0.325   0.222   0.141   0.070  -0.052  -0.140   0.280   0.118  -0.029
59    V        -0.037  -0.055   0.019  -0.284  -0.344  -0.232  -0.313  -0.345  -0.239
60    F         1.375   1.389   1.416   1.485   1.502   1.546   1.466   1.484   1.524
61    E         0.325   0.272   0.145   0.188   0.111  -0.107   0.280   0.197  -0.022
62    D         0.325   0.272   0.145   0.244   0.167  -0.072   0.280   0.197  -0.022
63    L         0.325   0.222   0.141   0.451   0.296   0.149   0.280   0.118  -0.029
64    H        -1.420  -1.446  -1.365  -1.322  -1.394  -1.297  -1.202  -1.215  -1.108
65    D        -0.619  -0.740  -0.760  -0.490  -0.639  -0.632  -0.609  -0.757  -0.779
66    F         1.375   1.389   1.416   1.485   1.502   1.546   1.466   1.484   1.524
67    E         1.375   1.389   1.416   1.228   1.253   1.304   1.466   1.484   1.524
68    T        -0.838  -0.735  -0.775  -0.751  -0.634  -0.635  -0.905  -0.780  -0.800
69    Y        -0.037  -0.036   0.021  -0.031  -0.037   0.057  -0.313  -0.312  -0.235
70    L        -0.619  -0.606  -0.697  -0.410  -0.398  -0.566  -0.609  -0.589  -0.701
71    K        -0.037  -0.055   0.019  -0.400  -0.374  -0.233  -0.313  -0.345  -0.239
72    G        -0.838  -0.761  -0.776  -0.817  -0.736  -0.700  -0.905  -0.803  -0.801
73    E         1.375   1.389   1.416   1.228   1.253   1.304   1.466   1.484   1.524
74    T         1.375   1.389   1.416   1.470   1.487   1.532   1.466   1.484   1.524
75    E        -0.037  -0.055   0.019  -0.175  -0.167  -0.035  -0.313  -0.345  -0.239
76    D         1.375   1.389   1.416   1.303   1.333   1.374   1.466   1.484   1.524
77    Q        -0.838  -0.761  -0.776  -0.862  -0.725  -0.720  -0.905  -0.803  -0.801
78    E        -0.037  -0.055   0.019  -0.436  -0.466  -0.341  -0.313  -0.345  -0.239
79    F         1.375   1.389   1.416   1.485   1.502   1.546   1.466   1.484   1.524
80    D         1.375   1.389   1.416   1.303   1.333   1.374   1.466   1.484   1.524
81    H        -0.037  -0.055   0.019  -0.097  -0.109   0.002  -0.313  -0.345  -0.239
82    V        -1.420  -1.420  -1.361  -1.152  -1.144  -1.057  -1.202  -1.192  -1.104
83    H         1.375   1.389   1.416   1.405   1.440   1.471   1.466   1.484   1.524
84    C        -0.619  -0.740  -0.760  -0.129  -0.318  -0.364  -0.609  -0.757  -0.779
85    Q        -1.420  -1.335  -1.324  -1.328  -1.165  -1.193  -1.202  -1.104  -1.069
86    L         1.375   1.389   1.416   1.456   1.477   1.519   1.466   1.484   1.524
87    K        -1.420  -1.420  -1.361  -1.662  -1.637  -1.503  -1.202  -1.192  -1.104
88    Y         1.375   1.389   1.416   1.619   1.634   1.673   1.466   1.484   1.524
89    Y         1.375   1.389   1.416   1.619   1.634   1.673   1.466   1.484   1.524
90    P         1.375   1.389   1.416   1.584   1.598   1.640   1.466   1.484   1.524
91    P         1.375   1.389   1.416   1.584   1.598   1.640   1.466   1.484   1.524
92    F         1.375   1.389   1.416   1.485   1.502   1.546   1.466   1.484   1.524
93    V         0.325   0.222   0.141   0.466   0.322   0.182   0.280   0.118  -0.029
94    L        -0.619  -0.740  -0.760  -0.421  -0.611  -0.634  -0.609  -0.757  -0.779
95    H        -0.037  -0.055   0.019  -0.444  -0.514  -0.411  -0.313  -0.345  -0.239
96    D        -0.619  -0.606  -0.697  -0.738  -0.717  -0.860  -0.609  -0.589  -0.701
97    A        -1.420  -1.446  -1.365  -1.075  -1.133  -0.990  -1.202  -1.215  -1.108
98    H         0.325   0.272   0.145   0.461   0.403   0.214   0.280   0.197  -0.022
99    D        -1.420  -1.446  -1.368  -1.376  -1.374  -1.275  -1.202  -1.215  -1.111
100   D        -0.037  -0.055   0.019  -0.216  -0.233  -0.106  -0.313  -0.345  -0.239
101   P        -0.619  -0.740  -0.760  -0.308  -0.505  -0.551  -0.609  -0.757  -0.779
102   E         0.325   0.222   0.141   0.188   0.030  -0.115   0.280   0.118  -0.029
103   K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
104   I         1.375   1.389   1.416   1.541   1.558   1.600   1.466   1.484   1.524
105   K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
106   E        -0.838  -0.761  -0.776  -0.960  -0.797  -0.875  -0.905  -0.803  -0.801
107   T         0.325   0.402   0.163   0.479   0.578   0.222   0.280   0.396   0.007
108   A        -0.838  -0.735  -0.775  -0.555  -0.428  -0.473  -0.905  -0.780  -0.800
109   N         1.375   1.389   1.416   1.563   1.572   1.620   1.466   1.484   1.524
110   S        -0.037  -0.055   0.019  -0.352  -0.459  -0.334  -0.313  -0.345  -0.239
111   H        -0.619  -0.740  -0.760  -0.637  -0.854  -0.934  -0.609  -0.757  -0.779
112   S         0.325   0.459   0.176   0.528   0.687   0.297   0.280   0.480   0.029
113   K         0.325   0.222   0.141   0.070  -0.052  -0.140   0.280   0.118  -0.029
114   K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
115   F         1.375   1.389   1.416   1.485   1.502   1.546   1.466   1.484   1.524
116   V        -0.619  -0.740  -0.760  -0.563  -0.782  -0.849  -0.609  -0.757  -0.779
117   R         1.375   1.389   1.416   1.660   1.666   1.712   1.466   1.484   1.524
118   H        -0.619  -0.740  -0.760  -0.549  -0.731  -0.795  -0.609  -0.757  -0.779
119   L         1.375   1.389   1.416   1.456   1.477   1.519   1.466   1.484   1.524
120   H        -0.037  -0.055   0.019  -0.057  -0.063   0.050  -0.313  -0.345  -0.239
121   Q        -0.037  -0.055   0.019   0.022  -0.044   0.056  -0.313  -0.345  -0.239
122   H         1.375   1.389   1.416   1.405   1.440   1.471   1.466   1.484   1.524
123   V        -0.037   0.045   0.069  -0.079   0.071   0.089  -0.313  -0.173  -0.151
124   E        -0.037  -0.055   0.019  -0.204  -0.201  -0.069  -0.313  -0.345  -0.239
125   K         1.375   1.389   1.416   1.014   1.052   1.102   1.466   1.484   1.524
126   H         1.375   1.389   1.416   1.405   1.440   1.471   1.466   1.484   1.524
127   L         1.375   1.389   1.416   1.456   1.477   1.519   1.466   1.484   1.524
128   L        -0.619  -0.740  -0.760  -0.399  -0.578  -0.600  -0.609  -0.757  -0.779
129   K         0.325   0.222   0.141   0.049  -0.077  -0.176   0.280   0.118  -0.029
130   D         0.325   0.222   0.141   0.244   0.083  -0.081   0.280   0.118  -0.029
131   I        -0.619  -0.740  -0.760  -0.347  -0.539  -0.580  -0.609  -0.757  -0.779
132   K         1.375   1.389   1.416   0.963   0.975   1.053   1.466   1.484   1.524
133   T         0.325   0.402   0.165   0.231   0.343  -0.002   0.280   0.397   0.011
134   A        -0.838  -0.761  -0.777  -0.944  -0.900  -0.833  -0.905  -0.803  -0.801
135   I        -0.838  -0.735  -0.775  -0.631  -0.472  -0.551  -0.905  -0.780  -0.800
136   N        -2.001  -1.944  -1.829  -1.842  -1.726  -1.596  -1.498  -1.432  -1.297
137   K        -0.838  -0.761  -0.777  -1.010  -0.811  -0.867  -0.905  -0.803  -0.801
138   P        -0.619  -0.740  -0.760  -0.310  -0.510  -0.554  -0.609  -0.757  -0.779
139   E        -0.619  -0.645  -0.706  -0.750  -0.786  -0.892  -0.609  -0.641  -0.713
140   L         0.325   0.222   0.141   0.501   0.354   0.236   0.280   0.118  -0.029
141   K        -0.619  -0.740  -0.760  -0.928  -1.094  -1.087  -0.609  -0.757  -0.779
142   F         1.375   1.389   1.416   1.485   1.502   1.546   1.466   1.484   1.524
143   H        -0.838  -0.761  -0.777  -0.893  -0.718  -0.844  -0.905  -0.803  -0.801
144   D        -0.037  -0.055   0.019  -0.539  -0.604  -0.490  -0.313  -0.345  -0.239
145   K        -0.619  -0.740  -0.760  -0.762  -0.885  -0.837  -0.609  -0.757  -0.779
146   K        -2.001  -1.944  -1.829  -1.899  -1.802  -1.650  -1.498  -1.432  -1.297
147   K        -0.037  -0.055   0.019  -0.534  -0.517  -0.389  -0.313  -0.345  -0.239
148   Q        -1.420  -1.335  -1.324  -1.450  -1.324  -1.294  -1.202  -1.104  -1.069
149   E         1.375   1.389   1.416   1.228   1.253   1.304   1.466   1.484   1.524
150   S        -0.037   0.023   0.053  -0.108  -0.019   0.031  -0.313  -0.210  -0.179
151   F        -0.619  -0.740  -0.760  -0.468  -0.666  -0.726  -0.609  -0.757  -0.779
152   D        -1.420  -1.446  -1.365  -1.497  -1.514  -1.387  -1.202  -1.215  -1.108
153   R        -1.420  -1.446  -1.365  -1.343  -1.399  -1.268  -1.202  -1.215  -1.108
154   I        -0.619  -0.740  -0.760  -0.410  -0.613  -0.678  -0.609  -0.757  -0.779
155   V        -0.619  -0.740  -0.760  -0.626  -0.855  -0.949  -0.609  -0.757  -0.779
156   W         1.375   1.389   1.416   1.736   1.746   1.783   1.466   1.484   1.524
157   N        -0.619  -0.453  -0.682  -0.892  -0.641  -0.945  -0.609  -0.390  -0.682
158   Y        -0.037  -0.055   0.019   0.006  -0.054   0.059  -0.313  -0.345  -0.239
159   G        -1.420  -1.446  -1.368  -1.334  -1.465  -1.362  -1.202  -1.215  -1.111
160   E        -0.037   0.045   0.069  -0.414  -0.244  -0.225  -0.313  -0.173  -0.151
161   E        -0.619  -0.645  -0.706  -0.701  -0.741  -0.825  -0.609  -0.641  -0.713
162   T         0.325   0.222   0.141   0.479   0.315   0.186   0.280   0.118  -0.029
163   E        -0.838  -0.761  -0.777  -1.050  -0.924  -0.891  -0.905  -0.803  -0.801
164   L        -0.838  -0.761  -0.776  -0.785  -0.680  -0.702  -0.905  -0.803  -0.801
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   N        -1.420  -1.446  -1.365  -1.214  -1.247  -1.119  -1.202  -1.215  -1.108
175   A        -0.619  -0.500  -0.688  -0.495  -0.333  -0.560  -0.609  -0.451  -0.689
176   K        -0.037   0.023   0.053  -0.212  -0.077  -0.075  -0.313  -0.210  -0.179
177   K        -0.838  -0.761  -0.777  -1.280  -1.077  -1.143  -0.905  -0.803  -0.801
178   F        -0.037  -0.055   0.019   0.036   0.014   0.135  -0.313  -0.345  -0.239
179   K        -0.838  -0.781  -0.751  -1.104  -1.033  -0.980  -0.905  -0.831  -0.774
180   V        -0.838  -0.761  -0.776  -0.807  -0.696  -0.718  -0.905  -0.803  -0.801
181   S        -1.420  -1.367  -1.324  -1.195  -1.133  -1.095  -1.202  -1.135  -1.069
182   V        -0.838  -0.761  -0.777  -0.840  -0.718  -0.731  -0.905  -0.803  -0.801
183   E        -0.838  -0.837  -0.754  -1.072  -1.083  -0.955  -0.905  -0.886  -0.775
184   V         1.375   1.389   1.416   1.449   1.477   1.512   1.466   1.484   1.524
185   V        -1.420  -1.367  -1.324  -1.358  -1.277  -1.235  -1.202  -1.135  -1.069
186   C         1.375   1.389   1.416   1.708   1.720   1.758   1.466   1.484   1.524
187   K        -1.420  -1.367  -1.324  -1.398  -1.297  -1.291  -1.202  -1.135  -1.069
188   H        -0.037   0.045   0.069  -0.085   0.067   0.084  -0.313  -0.173  -0.151
189   D        -0.037  -0.055   0.019  -0.414  -0.460  -0.339  -0.313  -0.345  -0.239
190   G        -1.420  -1.359  -1.328  -1.183  -1.109  -1.061  -1.202  -1.131  -1.073
191   A         0.325   0.222   0.141   0.683   0.525   0.381   0.280   0.118  -0.029
192   M        -0.619  -0.645  -0.706  -0.278  -0.351  -0.457  -0.609  -0.641  -0.713
193   V         1.375   1.389   1.416   1.449   1.477   1.512   1.466   1.484   1.524
194   D         0.325   0.222   0.141   0.244   0.083  -0.081   0.280   0.118  -0.029
195   V         1.375   1.389   1.416   1.449   1.477   1.512   1.466   1.484   1.524
196   D         0.325   0.272   0.145   0.244   0.167  -0.072   0.280   0.197  -0.022
197   Y         1.375   1.389   1.416   1.619   1.634   1.673   1.466   1.484   1.524
198   K        -0.619  -0.645  -0.706  -0.841  -0.855  -0.907  -0.609  -0.641  -0.713
199   T        -0.619  -0.740  -0.760  -0.395  -0.581  -0.604  -0.609  -0.757  -0.779
200   E        -0.619  -0.500  -0.688  -0.612  -0.404  -0.819  -0.609  -0.451  -0.689
201   P         1.375   1.389   1.416   1.584   1.598   1.640   1.466   1.484   1.524
202   L        -0.619  -0.740  -0.760  -0.399  -0.582  -0.600  -0.609  -0.757  -0.779
203   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
206   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
207   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
208   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P40188
Output conservation file - output/P40188
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
