1     M         1.089   1.116   1.169   1.319   1.357   1.414   1.153   1.190   1.265
2     P         1.089   1.116   1.169   1.092   1.122   1.210   1.153   1.190   1.265
3     A         1.089   1.116   1.169   1.104   1.133   1.220   1.153   1.190   1.265
4     Y        -0.232  -0.122  -0.518  -0.072   0.078  -0.609  -0.241  -0.092  -0.633
5     H        -0.099  -0.088   0.018  -0.133  -0.129  -0.011  -0.456  -0.445  -0.295
6     S         1.089   1.116   1.169   1.077   1.121   1.196   1.153   1.190   1.265
7     T        -0.232  -0.454  -0.553   0.002  -0.307  -0.498  -0.241  -0.538  -0.681
8     F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
9     P        -0.528  -0.524  -0.576  -0.893  -0.862  -0.932  -0.671  -0.637  -0.714
10    V        -1.594  -1.467  -1.461  -1.515  -1.371  -1.297  -1.422  -1.297  -1.204
11    D        -0.660  -0.720  -0.617  -0.831  -0.931  -0.801  -0.885  -0.929  -0.774
12    P        -1.400  -1.417  -1.461  -1.191  -1.235  -1.283  -1.207  -1.215  -1.201
13    N        -1.142  -1.025  -1.096  -0.986  -0.794  -0.998  -1.136  -0.987  -1.043
14    T        -1.594  -1.612  -1.489  -1.522  -1.572  -1.398  -1.422  -1.423  -1.227
15    D        -1.400  -1.556  -1.473  -1.150  -1.378  -1.259  -1.207  -1.351  -1.212
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    R         0.412   0.296   0.152   0.497   0.328   0.092   0.402   0.221  -0.050
23    M        -1.711  -1.629  -1.490  -1.763  -1.666  -1.436  -1.529  -1.439  -1.228
24    V        -0.528  -0.675  -0.610  -0.378  -0.616  -0.556  -0.671  -0.859  -0.763
25    G         1.089   1.116   1.169   1.222   1.249   1.326   1.153   1.190   1.265
26    N         1.089   1.116   1.169   1.062   1.111   1.183   1.153   1.190   1.265
27    F        -0.778  -0.756  -0.645  -1.138  -1.090  -0.955  -0.992  -0.957  -0.805
28    A        -0.839  -0.873  -1.050  -0.670  -0.745  -1.006  -0.778  -0.816  -0.992
29    L        -0.232  -0.328  -0.540  -0.382  -0.494  -0.750  -0.241  -0.371  -0.663
30    L         0.412   0.304   0.148   0.163   0.023  -0.213   0.402   0.234  -0.058
31    P         1.089   1.116   1.169   1.092   1.122   1.210   1.153   1.190   1.265
32    L        -0.528  -0.468  -0.589  -0.873  -0.771  -0.929  -0.671  -0.574  -0.733
33    N        -1.283  -1.325  -1.127  -1.307  -1.358  -1.062  -1.314  -1.332  -1.075
34    T         1.089   1.116   1.169   1.189   1.228   1.296   1.153   1.190   1.265
35    K        -0.232  -0.210  -0.530  -0.073  -0.035  -0.567  -0.241  -0.207  -0.650
36    F        -0.232  -0.256  -0.532  -0.143  -0.179  -0.579  -0.241  -0.280  -0.653
37    R         1.089   1.116   1.169   1.107   1.137   1.223   1.153   1.190   1.265
38    G         1.089   1.116   1.169   1.222   1.249   1.326   1.153   1.190   1.265
39    P         1.089   1.116   1.169   1.092   1.122   1.210   1.153   1.190   1.265
40    A        -0.778  -0.767  -0.653  -0.958  -0.953  -0.786  -0.992  -0.974  -0.815
41    Y         1.089   1.116   1.169   1.200   1.234   1.306   1.153   1.190   1.265
42    P        -0.528  -0.434  -0.571  -0.519  -0.381  -0.593  -0.671  -0.523  -0.708
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    S        -1.283  -1.285  -1.121  -1.434  -1.451  -1.172  -1.314  -1.301  -1.070
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    N        -0.839  -0.968  -1.057  -0.692  -0.888  -1.014  -0.778  -0.931  -1.001
61    S        -0.839  -0.848  -1.048  -0.672  -0.696  -0.980  -0.778  -0.788  -0.990
62    D        -0.232  -0.454  -0.553  -0.067  -0.371  -0.551  -0.241  -0.538  -0.681
63    Y         0.412   0.296   0.152   0.621   0.473   0.251   0.402   0.221  -0.050
64    D         1.089   1.116   1.169   1.118   1.161   1.233   1.153   1.190   1.265
65    I         1.089   1.116   1.169   1.148   1.185   1.260   1.153   1.190   1.265
66    I        -0.232  -0.263  -0.532  -0.085  -0.159  -0.596  -0.241  -0.288  -0.653
67    D         0.079   0.144   0.076   0.040   0.142  -0.002  -0.134  -0.029  -0.189
68    E         1.089   1.116   1.169   1.181   1.212   1.290   1.153   1.190   1.265
69    C        -0.778  -0.775  -0.654  -0.631  -0.639  -0.507  -0.992  -0.982  -0.816
70    L         0.412   0.296   0.152   0.179   0.033  -0.164   0.402   0.221  -0.050
71    D        -0.232  -0.454  -0.553  -0.072  -0.384  -0.562  -0.241  -0.538  -0.681
72    L         1.089   1.116   1.169   0.783   0.828   0.932   1.153   1.190   1.265
73    F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
74    R         1.089   1.116   1.169   1.107   1.137   1.223   1.153   1.190   1.265
75    A         1.089   1.116   1.169   1.104   1.133   1.220   1.153   1.190   1.265
76    N         1.089   1.116   1.169   1.062   1.111   1.183   1.153   1.190   1.265
77    S        -0.232  -0.454  -0.553  -0.072  -0.358  -0.503  -0.241  -0.538  -0.681
78    F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
79    F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
80    K         0.079  -0.033   0.039   0.044  -0.173  -0.086  -0.134  -0.342  -0.257
81    N         1.089   1.116   1.169   1.062   1.111   1.183   1.153   1.190   1.265
82    F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
83    E         1.089   1.116   1.169   1.181   1.212   1.290   1.153   1.190   1.265
84    I         1.089   1.116   1.169   1.148   1.185   1.260   1.153   1.190   1.265
85    K         0.412   0.304   0.148   0.564   0.430   0.185   0.402   0.234  -0.058
86    S        -0.528  -0.341  -0.564  -0.452  -0.170  -0.530  -0.671  -0.405  -0.697
87    P         0.079   0.139   0.067  -0.024   0.066  -0.094  -0.134  -0.037  -0.204
88    A         0.079   0.139   0.067  -0.008   0.080  -0.078  -0.134  -0.037  -0.204
89    D         1.089   1.116   1.169   1.118   1.161   1.233   1.153   1.190   1.265
90    R         1.089   1.116   1.169   1.107   1.137   1.223   1.153   1.190   1.265
91    V        -1.400  -1.333  -1.444  -1.504  -1.419  -1.494  -1.207  -1.133  -1.186
92    L         1.089   1.116   1.169   0.783   0.828   0.932   1.153   1.190   1.265
93    I         0.412   0.304   0.148   0.563   0.427   0.184   0.402   0.234  -0.058
94    Y         1.089   1.116   1.169   1.200   1.234   1.306   1.153   1.190   1.265
95    G         1.089   1.116   1.169   1.222   1.249   1.326   1.153   1.190   1.265
96    I         0.412   0.296   0.152   0.551   0.398   0.161   0.402   0.221  -0.050
97    L         0.412   0.304   0.148   0.217   0.095  -0.077   0.402   0.234  -0.058
98    F         0.079   0.064   0.049  -0.027  -0.052  -0.098  -0.134  -0.167  -0.237
99    I         0.079   0.158   0.074   0.098   0.217   0.062  -0.134  -0.005  -0.191
100   N        -0.156  -0.112   0.018  -0.497  -0.410  -0.208  -0.563  -0.490  -0.296
101   D        -0.528  -0.573  -0.601  -0.493  -0.575  -0.598  -0.671  -0.737  -0.751
102   C         1.089   1.116   1.169   1.376   1.411   1.465   1.153   1.190   1.265
103   L         1.089   1.116   1.169   0.783   0.828   0.932   1.153   1.190   1.265
104   A        -1.594  -1.421  -1.463  -1.501  -1.219  -1.329  -1.422  -1.229  -1.204
105   H        -1.283  -1.202  -1.118  -1.275  -1.197  -1.049  -1.314  -1.227  -1.067
106   L        -0.232  -0.454  -0.553  -0.391  -0.678  -0.786  -0.241  -0.538  -0.681
107   K        -0.660  -0.643  -0.607  -0.799  -0.762  -0.690  -0.885  -0.852  -0.762
108   I        -1.694  -1.550  -1.492  -1.772  -1.567  -1.486  -1.509  -1.366  -1.229
109   T        -1.594  -1.677  -1.485  -1.463  -1.543  -1.297  -1.422  -1.466  -1.223
110   T        -0.839  -0.968  -1.057  -0.620  -0.851  -1.021  -0.778  -0.931  -1.001
111   S        -0.660  -0.730  -0.618  -0.850  -0.930  -0.741  -0.885  -0.947  -0.775
112   F        -2.022  -1.997  -1.797  -1.851  -1.791  -1.513  -1.636  -1.590  -1.337
113   N        -0.778  -0.801  -0.653  -0.981  -1.032  -0.799  -0.992  -1.022  -0.815
114   E         0.412   0.296   0.152   0.574   0.411   0.164   0.402   0.221  -0.050
115   A         1.089   1.116   1.169   1.104   1.133   1.220   1.153   1.190   1.265
116   V        -1.594  -1.548  -1.476  -1.420  -1.348  -1.275  -1.422  -1.352  -1.215
117   K         0.079   0.063   0.054   0.044   0.007  -0.054  -0.134  -0.170  -0.228
118   V        -2.022  -2.034  -1.809  -1.867  -1.879  -1.598  -1.636  -1.618  -1.345
119   L         0.412   0.304   0.148   0.199   0.073  -0.122   0.402   0.234  -0.058
120   T        -1.089  -0.938  -1.067  -1.050  -0.818  -0.986  -1.100  -0.903  -1.013
121   N        -0.232  -0.328  -0.540  -0.138  -0.266  -0.606  -0.241  -0.371  -0.663
122   V        -0.528  -0.474  -0.591  -0.843  -0.801  -0.865  -0.671  -0.626  -0.738
123   A        -0.528  -0.400  -0.574  -0.557  -0.382  -0.630  -0.671  -0.498  -0.713
124   L         0.079   0.104   0.060  -0.253  -0.211  -0.245  -0.134  -0.098  -0.217
125   D         0.079   0.030   0.046   0.040  -0.050  -0.055  -0.134  -0.228  -0.242
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   N        -1.089  -0.933  -1.057  -1.099  -0.842  -1.022  -1.100  -0.899  -1.003
128   F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
129   T        -1.089  -1.020  -1.076  -1.058  -0.978  -1.007  -1.100  -1.025  -1.025
130   L        -0.099  -0.089   0.019  -0.591  -0.572  -0.362  -0.456  -0.446  -0.293
131   P         1.089   1.116   1.169   1.092   1.122   1.210   1.153   1.190   1.265
132   G         1.089   1.116   1.169   1.222   1.249   1.326   1.153   1.190   1.265
133   T        -0.660  -0.683  -0.608  -0.768  -0.772  -0.675  -0.885  -0.872  -0.759
134   P        -1.594  -1.509  -1.475  -1.547  -1.462  -1.356  -1.422  -1.336  -1.216
135   G         1.089   1.116   1.169   1.222   1.249   1.326   1.153   1.190   1.265
136   F         0.412   0.304   0.148   0.476   0.352   0.139   0.402   0.234  -0.058
137   P         1.089   1.116   1.169   1.092   1.122   1.210   1.153   1.190   1.265
138   L         1.089   1.116   1.169   0.783   0.828   0.932   1.153   1.190   1.265
139   N         1.089   1.116   1.169   1.062   1.111   1.183   1.153   1.190   1.265
140   N        -1.400  -1.431  -1.455  -1.237  -1.291  -1.335  -1.207  -1.238  -1.196
141   V        -0.854  -0.821  -0.654  -1.105  -1.085  -0.795  -1.100  -1.045  -0.817
142   Y         1.089   1.116   1.169   1.200   1.234   1.306   1.153   1.190   1.265
143   Q        -1.711  -1.706  -1.496  -1.633  -1.626  -1.304  -1.529  -1.493  -1.233
144   V        -1.089  -0.930  -1.069  -1.068  -0.840  -1.028  -1.100  -0.898  -1.015
145   P         1.089   1.116   1.169   1.092   1.122   1.210   1.153   1.190   1.265
146   V        -1.711  -1.604  -1.492  -1.907  -1.799  -1.533  -1.529  -1.426  -1.230
147   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   D        -0.660  -0.708  -0.609  -0.847  -0.884  -0.750  -0.885  -0.910  -0.764
149   H        -1.400  -1.353  -1.138  -1.446  -1.411  -1.077  -1.422  -1.356  -1.086
150   N        -1.089  -1.088  -1.092  -1.075  -1.077  -1.075  -1.100  -1.114  -1.041
151   S        -1.165  -1.022  -1.085  -1.204  -1.018  -1.080  -1.207  -1.057  -1.036
152   M        -1.283  -1.188  -1.106  -1.210  -1.087  -0.946  -1.314  -1.187  -1.055
153   D         0.079   0.218   0.082   0.080   0.294   0.031  -0.134   0.095  -0.178
154   L        -0.232  -0.454  -0.553  -0.391  -0.679  -0.786  -0.241  -0.538  -0.681
155   L         0.412   0.296   0.152   0.206   0.072  -0.096   0.402   0.221  -0.050
156   K        -0.156  -0.112   0.018  -0.412  -0.348  -0.135  -0.563  -0.490  -0.296
157   T        -1.594  -1.643  -1.478  -1.509  -1.557  -1.318  -1.422  -1.444  -1.219
158   Y         1.089   1.116   1.169   1.200   1.234   1.306   1.153   1.190   1.265
159   I         0.079   0.217   0.102  -0.298  -0.080  -0.245  -0.134   0.094  -0.141
160   Q        -1.089  -1.187  -1.098  -0.877  -1.053  -0.924  -1.100  -1.200  -1.048
161   Q         1.089   1.116   1.169   1.276   1.311   1.375   1.153   1.190   1.265
162   F         0.412   0.304   0.148   0.459   0.331   0.097   0.402   0.234  -0.058
163   R         1.089   1.116   1.169   1.107   1.137   1.223   1.153   1.190   1.265
164   Q         1.089   1.116   1.169   1.276   1.311   1.375   1.153   1.190   1.265
165   E         1.089   1.116   1.169   1.181   1.212   1.290   1.153   1.190   1.265
166   L         1.089   1.116   1.169   0.783   0.828   0.932   1.153   1.190   1.265
167   A         0.412   0.426   0.157   0.491   0.503   0.092   0.402   0.421  -0.041
168   M        -2.333  -2.323  -2.072  -1.948  -1.939  -1.636  -1.743  -1.710  -1.424
169   R         1.089   1.116   1.169   1.107   1.137   1.223   1.153   1.190   1.265
170   L         1.089   1.116   1.169   0.783   0.828   0.932   1.153   1.190   1.265
171   L        -0.099  -0.053   0.026  -0.591  -0.515  -0.357  -0.456  -0.379  -0.281
172   E        -1.089  -1.223  -1.100  -1.026  -1.238  -1.081  -1.100  -1.219  -1.048
173   R        -0.232  -0.328  -0.540  -0.054  -0.182  -0.485  -0.241  -0.371  -0.663
174   V        -0.156  -0.121   0.014  -0.293  -0.231  -0.031  -0.563  -0.508  -0.303
175   Y         1.089   1.116   1.169   1.200   1.234   1.306   1.153   1.190   1.265
176   S        -2.022  -1.963  -1.793  -1.858  -1.787  -1.522  -1.636  -1.569  -1.335
177   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   D        -0.232  -0.270  -0.530  -0.065  -0.120  -0.509  -0.241  -0.299  -0.650
180   S        -1.283  -1.202  -1.118  -1.400  -1.275  -1.151  -1.314  -1.227  -1.067
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   K        -1.594  -1.560  -1.478  -1.518  -1.492  -1.329  -1.422  -1.379  -1.218
183   E        -1.283  -1.178  -1.101  -1.404  -1.224  -1.130  -1.314  -1.179  -1.049
184   Y        -2.022  -1.887  -1.789  -1.692  -1.521  -1.381  -1.636  -1.515  -1.332
185   P         1.089   1.116   1.169   1.092   1.122   1.210   1.153   1.190   1.265
186   S         0.412   0.448   0.160   0.462   0.519   0.070   0.402   0.454  -0.036
187   K         1.089   1.116   1.169   1.148   1.189   1.260   1.153   1.190   1.265
188   F        -1.089  -1.134  -1.100  -0.958  -0.995  -0.905  -1.100  -1.154  -1.049
189   W         1.089   1.116   1.169   1.383   1.415   1.471   1.153   1.190   1.265
190   L         0.412   0.296   0.152   0.186   0.043  -0.148   0.402   0.221  -0.050
191   A        -0.232  -0.454  -0.553  -0.065  -0.372  -0.524  -0.241  -0.538  -0.681
192   F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
193   T         0.412   0.296   0.152   0.576   0.419   0.156   0.402   0.221  -0.050
194   R        -0.099  -0.124   0.013  -0.303  -0.369  -0.142  -0.456  -0.512  -0.305
195   R         1.089   1.116   1.169   1.107   1.137   1.223   1.153   1.190   1.265
196   R        -0.660  -0.637  -0.608  -0.746  -0.723  -0.611  -0.885  -0.852  -0.764
197   F         1.089   1.116   1.169   1.043   1.088   1.166   1.153   1.190   1.265
198   M         1.089   1.116   1.169   1.319   1.357   1.414   1.153   1.190   1.265
199   N         0.412   0.304   0.148   0.470   0.340   0.093   0.402   0.234  -0.058
200   K         1.089   1.116   1.169   1.148   1.189   1.260   1.153   1.190   1.265
201   S        -0.232  -0.454  -0.553  -0.113  -0.424  -0.593  -0.241  -0.538  -0.681
202   L         1.089   1.116   1.169   0.783   0.828   0.932   1.153   1.190   1.265
* 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/Q05933
Output conservation file - output/Q05933
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
