1     M         1.589   1.602   1.634   1.890   1.889   1.949   1.715   1.734   1.787
2     C        -0.405  -0.443  -0.391  -0.736  -0.736  -0.629  -0.558  -0.611  -0.545
3     L        -1.070  -1.026  -0.945  -1.199  -1.189  -1.014  -1.012  -0.963  -0.865
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     V         0.511   0.486   0.441   0.054   0.030  -0.035   0.351   0.302   0.200
8     K        -0.405  -0.443  -0.391  -0.374  -0.466  -0.409  -0.558  -0.611  -0.545
9     T         0.511   0.597   0.473   0.603   0.734   0.519   0.351   0.493   0.257
10    T        -0.405  -0.379  -0.364  -0.394  -0.351  -0.358  -0.558  -0.528  -0.510
11    A         0.511   0.597   0.473   0.450   0.563   0.378   0.351   0.493   0.257
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    H         1.589   1.602   1.634   1.864   1.868   1.923   1.715   1.734   1.787
15    L         0.260   0.294   0.354  -0.312  -0.275  -0.176  -0.103  -0.048   0.036
16    L         0.511   0.461   0.426   0.160   0.112   0.096   0.351   0.258   0.171
17    F         0.511   0.461   0.426   0.517   0.439   0.368   0.351   0.258   0.171
18    Y         1.589   1.602   1.634   1.780   1.786   1.843   1.715   1.734   1.787
19    S         1.589   1.602   1.634   1.607   1.624   1.677   1.715   1.734   1.787
20    F        -0.405  -0.366  -0.355  -0.861  -0.790  -0.753  -0.558  -0.508  -0.498
21    V        -0.405  -0.379  -0.364  -0.610  -0.596  -0.588  -0.558  -0.528  -0.510
22    F         1.589   1.602   1.634   1.607   1.621   1.677   1.715   1.734   1.787
23    G         1.589   1.602   1.634   1.575   1.587   1.647   1.715   1.734   1.787
24    G         0.511   0.461   0.426   0.434   0.339   0.264   0.351   0.258   0.171
25    T         0.260   0.294   0.354   0.104   0.176   0.261  -0.103  -0.048   0.036
26    T        -0.405  -0.366  -0.355  -0.483  -0.434  -0.412  -0.558  -0.508  -0.498
27    F         0.511   0.461   0.426   0.538   0.463   0.398   0.351   0.258   0.171
28    Y        -0.405  -0.381  -0.358  -0.171  -0.140  -0.113  -0.558  -0.530  -0.501
29    S         1.589   1.602   1.634   1.607   1.624   1.677   1.715   1.734   1.787
30    Y         0.511   0.486   0.441   0.538   0.501   0.423   0.351   0.302   0.200
31    V        -0.405  -0.443  -0.391  -0.321  -0.377  -0.321  -0.558  -0.611  -0.545
32    A        -0.405  -0.443  -0.391  -0.411  -0.475  -0.408  -0.558  -0.611  -0.545
33    S         0.511   0.461   0.426   0.471   0.389   0.300   0.351   0.258   0.171
34    P         0.511   0.461   0.426   0.623   0.541   0.462   0.351   0.258   0.171
35    I        -0.405  -0.379  -0.364  -0.465  -0.382  -0.438  -0.558  -0.528  -0.510
36    A         0.511   0.597   0.473   0.450   0.563   0.378   0.351   0.493   0.257
37    F         0.511   0.461   0.426   0.538   0.463   0.398   0.351   0.258   0.171
38    K         0.511   0.461   0.426   0.571   0.500   0.446   0.351   0.258   0.171
39    V        -1.070  -1.026  -0.945  -1.026  -0.980  -0.848  -1.012  -0.963  -0.865
40    L         1.589   1.602   1.634   1.156   1.179   1.244   1.715   1.734   1.787
41    E        -0.405  -0.366  -0.355  -0.318  -0.243  -0.259  -0.558  -0.508  -0.498
42    K        -0.405  -0.443  -0.391  -0.171  -0.242  -0.192  -0.558  -0.611  -0.545
43    D        -0.405  -0.366  -0.355  -0.146  -0.078  -0.091  -0.558  -0.508  -0.498
44    Q        -0.405  -0.443  -0.391  -0.127  -0.184  -0.125  -0.558  -0.611  -0.545
45    F         1.589   1.602   1.634   1.607   1.621   1.677   1.715   1.734   1.787
46    S         1.589   1.602   1.634   1.607   1.624   1.677   1.715   1.734   1.787
47    A         0.511   0.486   0.441   0.641   0.586   0.482   0.351   0.302   0.200
48    L         1.589   1.602   1.634   1.156   1.179   1.244   1.715   1.734   1.787
49    Q         1.589   1.602   1.634   1.811   1.820   1.872   1.715   1.734   1.787
50    N        -0.233  -0.326  -0.327  -0.054  -0.225  -0.258  -0.321  -0.453  -0.460
51    K         1.589   1.602   1.634   1.625   1.638   1.694   1.715   1.734   1.787
52    I        -0.794  -0.765  -0.815  -0.645  -0.643  -0.717  -0.709  -0.676  -0.726
53    F         1.589   1.602   1.634   1.620   1.705   1.690   1.715   1.734   1.787
54    P         1.589   1.602   1.634   1.708   1.707   1.774   1.715   1.734   1.787
55    Y        -1.383  -1.390  -1.333  -1.020  -1.041  -0.959  -1.105  -1.102  -1.021
56    F         0.279   0.346   0.378   0.235   0.434   0.393  -0.066   0.050   0.082
57    F         1.589   1.602   1.634   1.638   1.745   1.706   1.715   1.734   1.787
58    Q        -1.763  -1.761  -1.686  -1.624  -1.663  -1.599  -1.254  -1.243  -1.150
59    M        -1.383  -1.408  -1.339  -1.248  -1.263  -1.242  -1.105  -1.114  -1.026
60    Q         1.589   1.602   1.634   1.820   1.829   1.881   1.715   1.734   1.787
61    A        -0.244  -0.218  -0.288  -0.311  -0.305  -0.376  -0.363  -0.345  -0.419
62    A        -0.860  -0.768  -0.864  -1.239  -1.156  -1.178  -0.808  -0.715  -0.788
63    S        -0.244  -0.339  -0.322  -0.304  -0.440  -0.433  -0.363  -0.485  -0.462
64    P         0.803   0.696   0.569   1.023   0.892   0.672   0.825   0.655   0.428
65    V        -0.860  -0.860  -0.855  -0.874  -0.870  -0.908  -0.808  -0.798  -0.778
66    I         0.279   0.293   0.346   0.165   0.187   0.259  -0.066  -0.049   0.022
67    L         1.589   1.602   1.634   1.177   1.167   1.264   1.715   1.734   1.787
68    A        -0.244  -0.324  -0.322  -0.410  -0.627  -0.607  -0.363  -0.461  -0.463
69    L         1.589   1.602   1.634   1.177   1.167   1.264   1.715   1.734   1.787
70    T         0.803   0.851   0.612   0.966   1.019   0.681   0.825   0.896   0.502
71    A        -1.240  -1.304  -1.311  -0.966  -1.047  -1.029  -0.957  -1.018  -1.000
72    P         1.589   1.602   1.634   1.727   1.747   1.792   1.715   1.734   1.787
73    I        -0.860  -0.837  -0.837  -0.922  -0.802  -0.929  -0.808  -0.769  -0.754
74    A         0.062   0.004  -0.185   0.153   0.045  -0.207   0.082  -0.003  -0.264
75    L        -0.624  -0.750  -0.813  -0.836  -1.043  -1.060  -0.511  -0.662  -0.725
76    T        -1.004  -1.006  -0.913  -0.849  -0.848  -0.744  -0.957  -0.945  -0.835
77    T        -0.860  -0.829  -0.871  -0.737  -0.672  -0.775  -0.808  -0.762  -0.791
78    G        -0.860  -0.834  -0.868  -0.759  -0.657  -0.747  -0.808  -0.767  -0.788
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    P        -1.383  -1.390  -1.333  -1.261  -1.226  -1.178  -1.105  -1.102  -1.021
99    L        -0.244  -0.274  -0.284  -0.587  -0.619  -0.587  -0.363  -0.386  -0.412
100   S        -1.383  -1.401  -1.336  -1.236  -1.249  -1.142  -1.105  -1.110  -1.023
101   S        -0.480  -0.472  -0.401  -0.817  -0.749  -0.683  -0.660  -0.651  -0.559
102   L         0.803   0.703   0.575   0.487   0.334   0.198   0.825   0.666   0.438
103   V        -0.244  -0.247  -0.279  -0.314  -0.333  -0.359  -0.363  -0.347  -0.398
104   V        -1.383  -1.401  -1.336  -1.569  -1.583  -1.451  -1.105  -1.110  -1.023
105   A        -0.860  -0.951  -0.898  -0.810  -0.896  -0.806  -0.808  -0.889  -0.819
106   S         0.062  -0.126  -0.238   0.122  -0.123  -0.408   0.082  -0.175  -0.337
107   V        -1.240  -1.187  -1.252  -1.141  -1.011  -1.225  -0.957  -0.905  -0.947
108   S        -0.480  -0.430  -0.373  -0.621  -0.551  -0.456  -0.660  -0.596  -0.524
109   G         1.589   1.602   1.634   1.601   1.568   1.671   1.715   1.734   1.787
110   L         0.279   0.326   0.366  -0.354  -0.319  -0.200  -0.066   0.013   0.060
111   T        -0.860  -0.822  -0.871  -1.191  -1.179  -1.165  -0.808  -0.757  -0.791
112   N         1.589   1.602   1.634   1.799   1.822   1.861   1.715   1.734   1.787
113   L        -0.337  -0.382  -0.331  -0.601  -0.659  -0.575  -0.511  -0.550  -0.478
114   F        -0.337  -0.374  -0.318  -0.753  -0.744  -0.713  -0.511  -0.538  -0.463
115   W        -0.337  -0.380  -0.314  -0.155  -0.203  -0.125  -0.511  -0.546  -0.459
116   L         0.803   0.703   0.575   0.487   0.334   0.198   0.825   0.666   0.438
117   L        -0.244  -0.260  -0.328  -0.608  -0.677  -0.643  -0.363  -0.413  -0.470
118   P         1.589   1.602   1.634   1.727   1.747   1.792   1.715   1.734   1.787
119   W        -0.480  -0.466  -0.402  -0.399  -0.429  -0.323  -0.660  -0.644  -0.560
120   T        -0.244  -0.288  -0.297  -0.014  -0.056  -0.072  -0.363  -0.407  -0.422
121   H        -0.860  -0.855  -0.869  -0.452  -0.458  -0.463  -0.808  -0.807  -0.793
122   K        -0.860  -0.787  -0.834  -0.654  -0.569  -0.605  -0.808  -0.738  -0.758
123   V        -0.244  -0.322  -0.321  -0.097  -0.188  -0.195  -0.363  -0.458  -0.462
124   K         0.442   0.353   0.374   0.470   0.344   0.372   0.231   0.063   0.076
125   E        -0.624  -0.748  -0.817  -0.148  -0.343  -0.438  -0.511  -0.660  -0.729
126   Q        -0.244  -0.219  -0.289   0.071   0.094   0.005  -0.363  -0.340  -0.421
127   R         1.589   1.602   1.634   1.861   1.861   1.920   1.715   1.734   1.787
128   K        -0.244  -0.156  -0.261  -0.109   0.011  -0.099  -0.363  -0.247  -0.374
129   N        -1.240  -1.259  -1.288  -0.901  -0.943  -0.955  -0.957  -0.979  -0.980
130   I        -1.004  -0.910  -0.916  -1.140  -0.956  -0.954  -0.957  -0.864  -0.838
131   A        -1.763  -1.761  -1.686  -1.720  -1.782  -1.617  -1.254  -1.243  -1.150
132   K        -1.763  -1.761  -1.686  -1.439  -1.412  -1.325  -1.254  -1.243  -1.150
133   K        -0.244  -0.139  -0.263  -0.096   0.030  -0.103  -0.363  -0.227  -0.376
134   Y        -0.860  -0.951  -0.898  -0.566  -0.653  -0.595  -0.808  -0.889  -0.819
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -0.405  -0.261  -0.353  -0.309  -0.106  -0.225  -0.558  -0.361  -0.495
138   -        -0.405  -0.453  -0.391  -0.627  -0.716  -0.676  -0.558  -0.625  -0.545
139   -        -1.070  -1.015  -0.945  -1.120  -1.020  -0.939  -1.012  -0.953  -0.865
140   -        -1.498  -1.450  -1.360  -1.289  -1.191  -1.100  -1.194  -1.145  -1.042
141   -        -0.966  -0.942  -0.897  -0.531  -0.472  -0.453  -0.903  -0.876  -0.816
142   T        -1.383  -1.323  -1.312  -1.123  -1.054  -1.019  -1.105  -1.049  -1.003
143   G        -1.383  -1.359  -1.312  -1.149  -1.141  -1.010  -1.105  -1.074  -1.003
144   S        -1.404  -1.247  -1.315  -1.047  -0.811  -0.931  -1.114  -0.962  -1.004
145   E        -0.351  -0.324  -0.303  -0.295  -0.250  -0.218  -0.507  -0.453  -0.431
146   L        -0.860  -0.951  -0.898  -1.091  -1.179  -1.059  -0.808  -0.889  -0.819
147   E        -0.337  -0.275  -0.315  -0.302  -0.202  -0.268  -0.511  -0.431  -0.455
148   A        -0.860  -0.867  -0.870  -0.781  -0.799  -0.851  -0.808  -0.815  -0.794
149   K        -0.244  -0.111  -0.273  -0.182   0.045  -0.284  -0.363  -0.176  -0.391
150   D        -0.480  -0.486  -0.410  -0.488  -0.545  -0.444  -0.660  -0.668  -0.570
151   A        -0.860  -0.893  -0.887  -0.880  -0.943  -0.897  -0.808  -0.841  -0.810
152   I        -0.860  -0.711  -0.836  -0.754  -0.579  -0.694  -0.808  -0.641  -0.756
153   L         0.803   0.696   0.569   0.487   0.325   0.190   0.825   0.655   0.428
154   R         0.279   0.346   0.378   0.373   0.490   0.518  -0.066   0.050   0.082
155   K         1.589   1.602   1.634   1.606   1.609   1.676   1.715   1.734   1.787
156   E        -0.860  -0.844  -0.861  -0.511  -0.466  -0.516  -0.808  -0.785  -0.780
157   F         1.589   1.602   1.634   1.638   1.745   1.706   1.715   1.734   1.787
158   G         0.062  -0.126  -0.238   0.191  -0.126  -0.288   0.082  -0.175  -0.337
159   K         0.442   0.431   0.388   0.446   0.423   0.358   0.231   0.204   0.102
160   S        -0.860  -0.951  -0.898  -0.859  -0.979  -0.966  -0.808  -0.889  -0.819
161   H         1.589   1.602   1.634   1.876   1.905   1.935   1.715   1.734   1.787
162   G         1.589   1.602   1.634   1.601   1.568   1.671   1.715   1.734   1.787
163   L        -0.337  -0.377  -0.343  -0.729  -0.764  -0.682  -0.511  -0.541  -0.490
164   S         1.589   1.602   1.634   1.590   1.633   1.660   1.715   1.734   1.787
165   L        -0.860  -0.897  -0.884  -1.201  -1.199  -1.140  -0.808  -0.845  -0.807
166   L         1.589   1.602   1.634   1.177   1.167   1.264   1.715   1.734   1.787
167   F        -0.480  -0.430  -0.395  -0.801  -0.675  -0.724  -0.660  -0.595  -0.551
168   N         1.589   1.602   1.634   1.799   1.822   1.861   1.715   1.734   1.787
169   L        -0.860  -0.741  -0.837  -1.072  -0.948  -0.986  -0.808  -0.676  -0.755
170   S        -1.240  -1.266  -1.270  -1.124  -1.190  -1.246  -0.957  -0.985  -0.964
171   N        -0.860  -0.861  -0.863  -0.647  -0.628  -0.645  -0.808  -0.802  -0.782
172   V        -0.480  -0.451  -0.394  -0.536  -0.433  -0.418  -0.660  -0.626  -0.550
173   C        -1.240  -1.259  -1.288  -1.332  -1.411  -1.313  -0.957  -0.979  -0.980
174   G        -0.480  -0.472  -0.401  -0.700  -0.732  -0.594  -0.660  -0.651  -0.559
175   M        -0.480  -0.475  -0.407  -0.787  -0.749  -0.607  -0.660  -0.653  -0.567
176   L        -0.860  -0.951  -0.898  -1.194  -1.314  -1.169  -0.808  -0.889  -0.819
177   A        -0.244  -0.342  -0.322  -0.305  -0.428  -0.416  -0.363  -0.488  -0.464
178   Y         1.589   1.602   1.634   1.794   1.824   1.856   1.715   1.734   1.787
179   G         1.589   1.602   1.634   1.601   1.568   1.671   1.715   1.734   1.787
180   V        -0.860  -0.942  -0.882  -0.769  -0.853  -0.817  -0.808  -0.878  -0.804
181   C        -1.383  -1.251  -1.304  -1.040  -0.873  -0.916  -1.105  -0.984  -0.998
182   L         1.589   1.602   1.634   1.177   1.167   1.264   1.715   1.734   1.787
183   S        -0.244  -0.342  -0.322  -0.305  -0.442  -0.439  -0.363  -0.488  -0.464
184   G        -0.860  -0.879  -0.872  -0.790  -0.844  -0.791  -0.808  -0.826  -0.796
185   G        -0.244  -0.218  -0.297  -0.116  -0.121  -0.168  -0.363  -0.344  -0.431
186   L         0.442   0.522   0.441  -0.018   0.078  -0.001   0.231   0.365   0.200
187   L        -0.966  -0.908  -0.896  -1.420  -1.288  -1.283  -0.903  -0.839  -0.814
188   R         0.298   0.379   0.392   0.227   0.331   0.367  -0.030   0.110   0.108
189   K        -0.405  -0.387  -0.378  -0.317  -0.259  -0.314  -0.558  -0.548  -0.528
190   I         1.589   1.602   1.634   1.707   1.685   1.772   1.715   1.734   1.787
191   P         0.629   0.579   0.492   0.787   0.707   0.542   0.552   0.462   0.292
192   K        -0.624  -0.636  -0.797  -0.475  -0.463  -0.774  -0.511  -0.529  -0.706
* 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/Q06089
Output conservation file - output/Q06089
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
