1     M         0.911   0.930   0.972   1.264   1.275   1.298   0.937   0.963   1.017
2     V        -1.590  -1.488  -1.386  -1.892  -1.666  -1.510  -1.602  -1.440  -1.277
3     A        -1.590  -1.488  -1.386  -1.782  -1.637  -1.470  -1.602  -1.440  -1.277
4     E        -2.377  -2.226  -2.033  -2.298  -2.004  -1.774  -2.064  -1.872  -1.596
5     V        -0.203  -0.389  -0.484  -0.304  -0.534  -0.666  -0.217  -0.491  -0.646
6     Q        -0.203  -0.389  -0.484   0.121  -0.165  -0.384  -0.217  -0.491  -0.646
7     K        -1.590  -1.279  -1.369  -1.483  -1.074  -1.121  -1.602  -1.196  -1.258
8     Q        -0.203  -0.321  -0.483  -0.016  -0.167  -0.402  -0.217  -0.391  -0.645
9     A         0.911   0.930   0.972   0.736   0.778   0.858   0.937   0.963   1.017
10    P         0.911   0.930   0.972   0.928   0.960   1.018   0.937   0.963   1.017
11    P        -1.590  -1.599  -1.412  -1.556  -1.590  -1.298  -1.602  -1.581  -1.306
12    F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
13    K         0.911   0.930   0.972   0.799   0.835   0.911   0.937   0.963   1.017
14    K        -0.203  -0.389  -0.484  -0.198  -0.466  -0.618  -0.217  -0.491  -0.646
15    T         0.911   0.930   0.972   0.973   1.004   1.055   0.937   0.963   1.017
16    A         0.911   0.930   0.972   0.736   0.778   0.858   0.937   0.963   1.017
17    V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
18    V        -0.203  -0.112  -0.465  -0.306  -0.158  -0.642  -0.217  -0.094  -0.616
19    D        -1.234  -1.313  -1.392  -0.984  -1.128  -1.240  -1.141  -1.240  -1.283
20    G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
21    I        -1.234  -1.471  -1.404  -1.295  -1.646  -1.528  -1.141  -1.419  -1.297
22    F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
23    E         0.911   0.930   0.972   0.805   0.861   0.915   0.937   0.963   1.017
24    E        -0.203  -0.047  -0.463  -0.177   0.042  -0.545  -0.217  -0.008  -0.612
25    I        -0.663  -0.707  -0.541  -0.971  -1.022  -0.728  -0.910  -0.993  -0.737
26    S        -1.590  -1.488  -1.386  -1.567  -1.421  -1.292  -1.602  -1.440  -1.277
27    L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
28    E        -1.234  -1.313  -1.392  -1.170  -1.310  -1.436  -1.141  -1.240  -1.283
29    K        -1.234  -1.471  -1.404  -0.847  -1.255  -1.231  -1.141  -1.419  -1.297
30    Y        -0.203  -0.112  -0.465   0.135   0.243  -0.325  -0.217  -0.094  -0.616
31    K         0.911   0.930   0.972   0.799   0.835   0.911   0.937   0.963   1.017
32    G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
33    K         0.911   0.930   0.972   0.799   0.835   0.911   0.937   0.963   1.017
34    Y        -0.203  -0.321  -0.483   0.246   0.079  -0.211  -0.217  -0.391  -0.645
35    V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
36    V        -1.590  -1.629  -1.412  -1.880  -1.930  -1.566  -1.602  -1.611  -1.306
37    L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
38    A        -0.203  -0.389  -0.484  -0.260  -0.523  -0.665  -0.217  -0.491  -0.646
39    F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
40    V        -2.162  -2.209  -2.044  -1.886  -2.009  -1.784  -1.833  -1.861  -1.606
41    P         0.911   0.930   0.972   0.928   0.960   1.018   0.937   0.963   1.017
42    L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
43    A        -0.203  -0.389  -0.484  -0.245  -0.499  -0.630  -0.217  -0.491  -0.646
44    F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
45    S        -0.203  -0.321  -0.483  -0.009  -0.174  -0.452  -0.217  -0.391  -0.645
46    F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
47    V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
48    C         0.911   0.930   0.972   1.232   1.245   1.272   0.937   0.963   1.017
49    P         0.911   0.930   0.972   0.928   0.960   1.018   0.937   0.963   1.017
50    T        -0.663  -0.347  -0.467  -0.701  -0.210  -0.423  -0.910  -0.428  -0.619
51    E         0.911   0.930   0.972   0.805   0.861   0.915   0.937   0.963   1.017
52    I         0.911   0.930   0.972   0.951   0.969   1.037   0.937   0.963   1.017
53    V        -0.663  -0.707  -0.541  -0.841  -0.998  -0.735  -0.910  -0.993  -0.737
54    A         0.911   0.930   0.972   0.736   0.778   0.858   0.937   0.963   1.017
55    F        -0.663  -0.707  -0.541  -0.579  -0.730  -0.491  -0.910  -0.993  -0.737
56    S         0.911   0.930   0.972   0.940   0.970   1.028   0.937   0.963   1.017
57    D        -0.663  -0.645  -0.538  -0.860  -0.833  -0.665  -0.910  -0.891  -0.732
58    A         0.911   0.930   0.972   0.736   0.778   0.858   0.937   0.963   1.017
59    A        -0.663  -0.707  -0.541  -1.073  -1.157  -0.867  -0.910  -0.993  -0.737
60    K        -0.663  -0.669  -0.540  -0.860  -0.883  -0.664  -0.910  -0.931  -0.735
61    K        -0.203  -0.112  -0.465  -0.144  -0.024  -0.468  -0.217  -0.094  -0.616
62    F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
63    E        -1.234  -1.259  -1.386  -1.253  -1.299  -1.500  -1.141  -1.169  -1.277
64    D        -0.203  -0.321  -0.483  -0.177  -0.320  -0.579  -0.217  -0.391  -0.645
65    Q        -1.590  -1.599  -1.412  -1.519  -1.481  -1.184  -1.602  -1.581  -1.306
66    G        -1.590  -1.629  -1.412  -1.566  -1.640  -1.283  -1.602  -1.611  -1.306
67    A        -0.203  -0.047  -0.463  -0.236  -0.031  -0.576  -0.217  -0.008  -0.612
68    Q        -0.663  -0.526  -0.520  -0.626  -0.401  -0.484  -0.910  -0.701  -0.703
69    V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
70    L        -0.203  -0.389  -0.484  -0.235  -0.493  -0.616  -0.217  -0.491  -0.646
71    F        -0.203  -0.389  -0.484  -0.119  -0.407  -0.596  -0.217  -0.491  -0.646
72    A        -0.203  -0.389  -0.484  -0.236  -0.481  -0.609  -0.217  -0.491  -0.646
73    S         0.911   0.930   0.972   0.940   0.970   1.028   0.937   0.963   1.017
74    T         0.911   0.930   0.972   0.973   1.004   1.055   0.937   0.963   1.017
75    D         0.911   0.930   0.972   0.928   0.947   1.018   0.937   0.963   1.017
76    S         0.911   0.930   0.972   0.940   0.970   1.028   0.937   0.963   1.017
77    E         0.911   0.930   0.972   0.805   0.861   0.915   0.937   0.963   1.017
78    Y         0.911   0.930   0.972   1.125   1.147   1.183   0.937   0.963   1.017
79    S        -0.663  -0.347  -0.467  -0.716  -0.233  -0.434  -0.910  -0.428  -0.619
80    L        -1.590  -1.488  -1.386  -1.486  -1.345  -1.139  -1.602  -1.440  -1.277
81    L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
82    A         0.911   0.930   0.972   0.736   0.778   0.858   0.937   0.963   1.017
83    W        -0.203  -0.389  -0.484   0.203  -0.083  -0.311  -0.217  -0.491  -0.646
84    T        -0.203  -0.389  -0.484  -0.006  -0.273  -0.449  -0.217  -0.491  -0.646
85    N         0.911   0.930   0.972   1.071   1.083   1.138   0.937   0.963   1.017
86    L        -1.234  -1.471  -1.404  -1.288  -1.623  -1.514  -1.141  -1.419  -1.297
87    P        -0.663  -0.707  -0.541  -0.923  -0.994  -0.705  -0.910  -0.993  -0.737
88    R         0.911   0.930   0.972   1.104   1.120   1.165   0.937   0.963   1.017
89    K         0.911   0.930   0.972   0.799   0.835   0.911   0.937   0.963   1.017
90    D        -0.203  -0.389  -0.484  -0.079  -0.361  -0.547  -0.217  -0.491  -0.646
91    G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
92    G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
93    L        -0.663  -0.347  -0.467  -0.907  -0.432  -0.589  -0.910  -0.428  -0.619
94    G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
95    P        -1.590  -1.488  -1.386  -1.658  -1.479  -1.351  -1.602  -1.440  -1.277
96    V        -0.663  -0.653  -0.539  -0.971  -0.945  -0.736  -0.910  -0.906  -0.733
97    K        -1.590  -1.441  -1.385  -1.481  -1.260  -1.224  -1.602  -1.383  -1.276
98    V        -2.377  -2.190  -2.036  -2.388  -2.134  -1.939  -2.064  -1.842  -1.599
99    P         0.911   0.930   0.972   0.928   0.960   1.018   0.937   0.963   1.017
100   L        -0.663  -0.347  -0.467  -1.038  -0.502  -0.713  -0.910  -0.428  -0.619
101   L        -0.203  -0.047  -0.463  -0.235  -0.038  -0.582  -0.217  -0.008  -0.612
102   A         0.911   0.930   0.972   0.736   0.778   0.858   0.937   0.963   1.017
103   D         0.911   0.930   0.972   0.928   0.947   1.018   0.937   0.963   1.017
104   K        -1.234  -1.471  -1.404  -0.990  -1.376  -1.321  -1.141  -1.419  -1.297
105   N        -0.203  -0.389  -0.484   0.089  -0.196  -0.383  -0.217  -0.491  -0.646
106   H         0.911   0.930   0.972   1.216   1.222   1.258   0.937   0.963   1.017
107   S        -1.234  -1.313  -1.392  -1.011  -1.170  -1.301  -1.141  -1.240  -1.283
108   L        -0.203  -0.389  -0.484  -0.291  -0.569  -0.746  -0.217  -0.491  -0.646
109   S        -0.203  -0.047  -0.463  -0.081   0.123  -0.527  -0.217  -0.008  -0.612
110   R        -0.663  -0.526  -0.520  -0.643  -0.434  -0.498  -0.910  -0.701  -0.703
111   D         0.911   0.930   0.972   0.928   0.947   1.018   0.937   0.963   1.017
112   Y         0.911   0.930   0.972   1.125   1.147   1.183   0.937   0.963   1.017
113   G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
114   V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
115   L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
116   I        -0.203  -0.047  -0.463  -0.069   0.121  -0.516  -0.217  -0.008  -0.612
117   E        -0.203  -0.112  -0.465  -0.177  -0.035  -0.549  -0.217  -0.094  -0.616
118   K        -1.590  -1.601  -1.409  -1.706  -1.718  -1.421  -1.602  -1.583  -1.304
119   E        -1.590  -1.450  -1.408  -1.780  -1.606  -1.476  -1.602  -1.443  -1.303
120   G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
121   I        -0.203  -0.321  -0.483  -0.304  -0.437  -0.664  -0.217  -0.391  -0.645
122   A         0.911   0.930   0.972   0.736   0.778   0.858   0.937   0.963   1.017
123   L        -0.203  -0.389  -0.484  -0.245  -0.507  -0.639  -0.217  -0.491  -0.646
124   R         0.911   0.930   0.972   1.104   1.120   1.165   0.937   0.963   1.017
125   G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
126   L        -0.663  -0.707  -0.541  -0.810  -0.970  -0.693  -0.910  -0.993  -0.737
127   F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
128   I        -0.663  -0.645  -0.538  -0.907  -0.895  -0.692  -0.910  -0.891  -0.732
129   I         0.911   0.930   0.972   0.951   0.969   1.037   0.937   0.963   1.017
130   D         0.911   0.930   0.972   0.928   0.947   1.018   0.937   0.963   1.017
131   P         0.911   0.930   0.972   0.928   0.960   1.018   0.937   0.963   1.017
132   K         0.911   0.930   0.972   0.799   0.835   0.911   0.937   0.963   1.017
133   G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
134   I        -0.203  -0.321  -0.483  -0.304  -0.437  -0.664  -0.217  -0.391  -0.645
135   I        -1.234  -1.259  -1.386  -1.242  -1.287  -1.486  -1.141  -1.169  -1.277
136   R         0.911   0.930   0.972   1.104   1.120   1.165   0.937   0.963   1.017
137   H        -0.203  -0.321  -0.483   0.191   0.032  -0.224  -0.217  -0.391  -0.645
138   I         0.911   0.930   0.972   0.951   0.969   1.037   0.937   0.963   1.017
139   T         0.911   0.930   0.972   0.973   1.004   1.055   0.937   0.963   1.017
140   I        -0.203  -0.047  -0.463  -0.082   0.115  -0.545  -0.217  -0.008  -0.612
141   N         0.911   0.930   0.972   1.071   1.083   1.138   0.937   0.963   1.017
142   D         0.911   0.930   0.972   0.928   0.947   1.018   0.937   0.963   1.017
143   L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
144   S        -0.203  -0.321  -0.483  -0.052  -0.216  -0.484  -0.217  -0.391  -0.645
145   V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
146   G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
147   R         0.911   0.930   0.972   1.104   1.120   1.165   0.937   0.963   1.017
148   N        -0.203  -0.321  -0.483  -0.015  -0.174  -0.416  -0.217  -0.391  -0.645
149   V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
150   N        -1.234  -1.471  -1.404  -1.086  -1.417  -1.300  -1.141  -1.419  -1.297
151   E         0.911   0.930   0.972   0.805   0.861   0.915   0.937   0.963   1.017
152   A        -1.590  -1.479  -1.406  -1.650  -1.554  -1.384  -1.602  -1.464  -1.300
153   L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
154   R         0.911   0.930   0.972   1.104   1.120   1.165   0.937   0.963   1.017
155   L         0.911   0.930   0.972   0.742   0.777   0.863   0.937   0.963   1.017
156   V        -1.590  -1.474  -1.407  -1.865  -1.710  -1.537  -1.602  -1.457  -1.302
157   E        -0.663  -0.669  -0.540  -0.860  -0.875  -0.667  -0.910  -0.931  -0.735
158   G        -0.203  -0.321  -0.483  -0.260  -0.422  -0.663  -0.217  -0.391  -0.645
159   F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
160   Q         0.911   0.930   0.972   1.120   1.145   1.178   0.937   0.963   1.017
161   W        -0.203  -0.321  -0.483  -0.028  -0.179  -0.387  -0.217  -0.391  -0.645
162   T        -0.203  -0.389  -0.484  -0.060  -0.345  -0.573  -0.217  -0.491  -0.646
163   D        -0.203  -0.321  -0.483  -0.177  -0.320  -0.579  -0.217  -0.391  -0.645
164   K        -0.203  -0.389  -0.484  -0.208  -0.471  -0.642  -0.217  -0.491  -0.646
165   N        -1.590  -1.599  -1.412  -1.210  -1.239  -0.987  -1.602  -1.581  -1.306
166   G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
167   T        -0.203  -0.321  -0.483  -0.168  -0.304  -0.558  -0.217  -0.391  -0.645
168   V         0.911   0.930   0.972   0.673   0.735   0.805   0.937   0.963   1.017
169   L        -0.203  -0.321  -0.483   0.211   0.010  -0.349  -0.217  -0.391  -0.645
170   P         0.911   0.930   0.972   0.928   0.960   1.018   0.937   0.963   1.017
171   C        -0.203  -0.321  -0.483  -0.182  -0.314  -0.485  -0.217  -0.391  -0.645
172   N         0.911   0.930   0.972   1.071   1.083   1.138   0.937   0.963   1.017
173   W         0.911   0.930   0.972   1.195   1.215   1.241   0.937   0.963   1.017
174   T        -1.590  -1.556  -1.409  -1.214  -1.191  -1.025  -1.602  -1.526  -1.304
175   P        -0.663  -0.669  -0.540  -0.805  -0.855  -0.664  -0.910  -0.931  -0.735
176   G         0.911   0.930   0.972   0.856   0.876   0.958   0.937   0.963   1.017
177   A        -1.590  -1.441  -1.385  -1.609  -1.383  -1.336  -1.602  -1.383  -1.276
178   A        -1.590  -1.599  -1.412  -1.724  -1.736  -1.452  -1.602  -1.581  -1.306
179   T         0.911   0.930   0.972   0.973   1.004   1.055   0.937   0.963   1.017
180   I         0.911   0.930   0.972   0.951   0.969   1.037   0.937   0.963   1.017
181   K         0.911   0.930   0.972   0.788   0.817   0.901   0.937   0.963   1.017
182   P        -0.326  -0.338  -0.505  -0.267  -0.293  -0.621  -0.393  -0.415  -0.679
183   D        -1.590  -1.227  -1.370  -1.594  -1.051  -1.284  -1.602  -1.138  -1.259
184   V        -1.590  -1.628  -1.412  -1.695  -1.756  -1.429  -1.602  -1.610  -1.306
185   K        -2.377  -2.070  -2.028  -2.496  -2.016  -1.972  -2.064  -1.724  -1.592
186   D        -2.377  -2.190  -2.036  -2.259  -1.956  -1.746  -2.064  -1.842  -1.599
187   S        -1.234  -1.313  -1.392  -1.037  -1.178  -1.348  -1.141  -1.240  -1.283
188   K        -0.203  -0.389  -0.484  -0.208  -0.471  -0.642  -0.217  -0.491  -0.646
189   E        -0.203  -0.389  -0.484  -0.203  -0.454  -0.641  -0.217  -0.491  -0.646
190   Y         0.911   0.930   0.972   1.125   1.147   1.183   0.937   0.963   1.017
191   F         0.911   0.930   0.972   0.901   0.927   0.995   0.937   0.963   1.017
192   K        -2.949  -2.834  -2.542  -2.638  -2.564  -2.168  -2.294  -2.150  -1.790
193   N        -0.203  -0.321  -0.483  -0.154  -0.306  -0.516  -0.217  -0.391  -0.645
194   A        -0.753  -0.709  -0.537  -1.270  -1.189  -0.877  -1.057  -0.997  -0.730
195   N         0.911   0.930   0.972   1.074   1.083   1.140   0.937   0.963   1.017
196   N        -1.234  -1.471  -1.404  -1.019  -1.325  -1.173  -1.141  -1.419  -1.297
* 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/Q04120
Output conservation file - output/Q04120
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
