1     M         1.562   1.594   1.671   1.870   1.919   2.026   1.693   1.741   1.859
2     S         0.557   0.652   0.574   0.452   0.616   0.446   0.354   0.514   0.323
3     E        -0.814  -0.778  -0.718  -0.718  -0.677  -0.566  -0.886  -0.838  -0.748
4     Y        -1.108  -1.101  -1.073  -1.047  -1.047  -0.992  -0.985  -0.977  -0.900
5     A        -0.606  -0.475  -0.629  -0.592  -0.366  -0.687  -0.650  -0.484  -0.651
6     S        -1.535  -1.516  -1.431  -1.319  -1.280  -1.159  -1.208  -1.182  -1.054
7     S        -0.798  -0.760  -0.715  -0.778  -0.690  -0.673  -0.874  -0.834  -0.746
8     I        -1.108  -1.023  -1.070  -1.243  -1.119  -1.219  -0.985  -0.907  -0.897
9     H        -0.047  -0.043  -0.127   0.130   0.113   0.019  -0.204  -0.220  -0.327
10    S        -1.535  -1.431  -1.418  -1.322  -1.155  -1.140  -1.208  -1.112  -1.045
11    Q        -1.535  -1.515  -1.432  -1.373  -1.334  -1.235  -1.208  -1.181  -1.055
12    M        -0.047  -0.147  -0.147  -0.254  -0.391  -0.333  -0.204  -0.346  -0.354
13    K        -0.798  -0.828  -0.721  -0.804  -0.824  -0.681  -0.874  -0.892  -0.752
14    Q        -1.418  -1.373  -1.378  -1.003  -0.937  -0.949  -1.097  -1.052  -1.010
15    F        -0.179  -0.101  -0.143  -0.627  -0.529  -0.537  -0.427  -0.321  -0.350
16    D         1.562   1.594   1.671   1.759   1.808   1.919   1.693   1.741   1.859
17    T        -0.682  -0.715  -0.677  -0.608  -0.640  -0.540  -0.762  -0.785  -0.706
18    K        -1.108  -1.137  -1.092  -0.808  -0.821  -0.751  -0.985  -1.007  -0.917
19    Y        -0.606  -0.482  -0.627  -0.902  -0.738  -0.900  -0.650  -0.490  -0.645
20    S        -0.720  -0.684  -0.670  -0.765  -0.718  -0.663  -0.785  -0.740  -0.698
21    G        -0.720  -0.774  -0.703  -0.703  -0.793  -0.670  -0.785  -0.838  -0.733
22    N        -0.366  -0.375  -0.249  -0.465  -0.513  -0.320  -0.639  -0.651  -0.488
23    R        -1.108  -0.976  -1.056  -0.780  -0.591  -0.689  -0.985  -0.841  -0.883
24    I        -1.108  -1.177  -1.077  -1.102  -1.174  -1.043  -0.985  -1.036  -0.903
25    L         1.562   1.594   1.671   1.258   1.289   1.433   1.693   1.741   1.859
26    Q        -1.418  -1.274  -1.365  -0.971  -0.765  -0.899  -1.097  -0.950  -0.999
27    Q        -0.915  -1.004  -1.049  -0.502  -0.646  -0.684  -0.762  -0.856  -0.872
28    L        -0.047   0.058  -0.096  -0.395  -0.256  -0.459  -0.204  -0.053  -0.275
29    E         1.562   1.594   1.671   1.773   1.827   1.933   1.693   1.741   1.859
30    N        -1.108  -0.976  -1.055  -1.018  -0.808  -0.962  -0.985  -0.841  -0.883
31    K        -1.225  -1.278  -1.107  -0.971  -1.036  -0.793  -1.097  -1.122  -0.931
32    T        -0.357  -0.412  -0.584  -0.199  -0.294  -0.577  -0.316  -0.389  -0.589
33    N        -0.606  -0.478  -0.623  -0.466  -0.274  -0.465  -0.650  -0.487  -0.639
34    L         0.380   0.360   0.461  -0.110  -0.146   0.037   0.019  -0.035   0.102
35    P         0.888   0.756   0.678   1.135   0.956   0.819   0.912   0.694   0.520
36    K         0.380   0.443   0.492   0.362   0.464   0.529   0.019   0.129   0.163
37    S         0.247   0.051  -0.059   0.303   0.004  -0.226   0.243  -0.036  -0.214
38    Y         1.562   1.594   1.671   1.599   1.650   1.764   1.693   1.741   1.859
39    L        -0.798  -0.757  -0.704  -1.134  -1.058  -0.970  -0.874  -0.826  -0.735
40    V        -0.606  -0.636  -0.646  -0.696  -0.722  -0.810  -0.650  -0.672  -0.669
41    A        -0.606  -0.568  -0.638  -0.920  -0.869  -0.952  -0.650  -0.590  -0.659
42    G         0.888   0.756   0.678   0.994   0.830   0.694   0.912   0.694   0.520
43    L        -1.108  -1.030  -1.063  -1.412  -1.325  -1.309  -0.985  -0.914  -0.891
44    G        -1.108  -1.093  -1.059  -1.093  -1.070  -1.026  -0.985  -0.962  -0.887
45    F        -0.606  -0.519  -0.640  -0.628  -0.504  -0.704  -0.650  -0.555  -0.665
46    A        -1.108  -1.099  -1.073  -1.416  -1.426  -1.333  -0.985  -0.965  -0.900
47    Y         1.562   1.594   1.671   1.599   1.650   1.764   1.693   1.741   1.859
48    L        -0.047  -0.101  -0.110  -0.226  -0.303  -0.358  -0.204  -0.259  -0.293
49    L        -0.606  -0.546  -0.644  -0.924  -0.864  -0.957  -0.650  -0.586  -0.669
50    L         0.888   0.756   0.678   0.656   0.460   0.366   0.912   0.694   0.520
51    I         0.888   0.756   0.678   0.883   0.693   0.528   0.912   0.694   0.520
52    F         0.247   0.223  -0.022   0.296   0.254  -0.160   0.243   0.207  -0.159
53    I        -0.179  -0.188  -0.156  -0.627  -0.639  -0.556  -0.427  -0.414  -0.367
54    N         1.562   1.594   1.671   1.717   1.760   1.878   1.693   1.741   1.859
55    V        -1.108  -1.182  -1.099  -1.133  -1.224  -1.134  -0.985  -1.040  -0.922
56    G         1.562   1.594   1.671   1.588   1.649   1.753   1.693   1.741   1.859
57    G         1.562   1.594   1.671   1.588   1.650   1.753   1.693   1.741   1.859
58    V        -0.146  -0.232  -0.164  -0.299  -0.425  -0.333  -0.347  -0.449  -0.374
59    G         1.562   1.594   1.671   1.561   1.611   1.727   1.693   1.741   1.859
60    E         0.341   0.388   0.474   0.302   0.374   0.502  -0.056   0.021   0.128
61    I         0.380   0.454   0.505  -0.142  -0.029   0.060   0.019   0.149   0.189
62    L         1.562   1.594   1.671   1.258   1.289   1.433   1.693   1.741   1.859
63    S        -0.047  -0.072  -0.144  -0.081  -0.152  -0.244  -0.204  -0.279  -0.349
64    N         1.562   1.594   1.671   1.717   1.760   1.878   1.693   1.741   1.859
65    F        -0.372  -0.381  -0.249  -0.803  -0.881  -0.653  -0.650  -0.659  -0.488
66    A         0.247   0.170  -0.034   0.283   0.132  -0.186   0.243   0.123  -0.178
67    G         0.888   0.756   0.678   0.985   0.815   0.673   0.912   0.694   0.520
68    F         0.557   0.632   0.567   0.361   0.477   0.314   0.354   0.480   0.312
69    V         0.247   0.170  -0.034   0.441   0.330   0.067   0.243   0.123  -0.178
70    L        -0.047  -0.171  -0.145  -0.173  -0.340  -0.344  -0.204  -0.367  -0.351
71    P         1.562   1.594   1.671   1.735   1.779   1.895   1.693   1.741   1.859
72    A        -0.179  -0.131  -0.165  -0.338  -0.282  -0.299  -0.427  -0.375  -0.384
73    Y         0.888   0.756   0.678   0.999   0.821   0.690   0.912   0.694   0.520
74    L        -0.047  -0.043  -0.127  -0.111  -0.133  -0.302  -0.204  -0.220  -0.327
75    S         1.562   1.594   1.671   1.548   1.611   1.715   1.693   1.741   1.859
76    L         0.557   0.522   0.516   0.167   0.090   0.079   0.354   0.279   0.211
77    V        -0.798  -0.767  -0.711  -1.058  -0.981  -0.868  -0.874  -0.842  -0.744
78    A         1.562   1.594   1.671   1.519   1.556   1.686   1.693   1.741   1.859
79    L         0.888   0.756   0.678   0.653   0.461   0.360   0.912   0.694   0.520
80    K        -0.179  -0.224  -0.169  -0.146  -0.199  -0.114  -0.427  -0.476  -0.390
81    T         0.888   0.967   0.709   0.986   1.088   0.731   0.912   1.029   0.577
82    P        -0.296  -0.259  -0.217  -0.397  -0.358  -0.291  -0.539  -0.487  -0.444
83    T        -0.357  -0.503  -0.611  -0.151  -0.360  -0.536  -0.316  -0.499  -0.622
84    S        -0.296  -0.189  -0.201  -0.400  -0.207  -0.276  -0.539  -0.385  -0.421
85    T        -1.535  -1.485  -1.421  -1.392  -1.331  -1.205  -1.208  -1.157  -1.047
86    D         1.562   1.594   1.671   1.759   1.808   1.919   1.693   1.741   1.859
87    D         1.562   1.594   1.671   1.759   1.808   1.919   1.693   1.741   1.859
88    T         1.562   1.594   1.671   1.585   1.628   1.750   1.693   1.741   1.859
89    Q         0.888   0.949   0.704   1.106   1.190   0.852   0.912   1.002   0.568
90    L        -0.047  -0.097  -0.156  -0.260  -0.336  -0.348  -0.204  -0.307  -0.365
91    L         1.562   1.594   1.671   1.258   1.289   1.433   1.693   1.741   1.859
92    T         1.562   1.594   1.671   1.585   1.628   1.750   1.693   1.741   1.859
93    Y         1.562   1.594   1.671   1.599   1.650   1.764   1.693   1.741   1.859
94    W         0.888   0.756   0.678   1.229   1.051   0.916   0.912   0.694   0.520
95    I        -0.179  -0.241  -0.169  -0.411  -0.494  -0.418  -0.427  -0.479  -0.384
96    V         1.562   1.594   1.671   1.578   1.639   1.743   1.693   1.741   1.859
97    F         0.888   0.756   0.678   0.947   0.761   0.649   0.912   0.694   0.520
98    S         0.380   0.439   0.495   0.119   0.231   0.289   0.019   0.119   0.170
99    F        -0.047  -0.053  -0.112  -0.151  -0.174  -0.299  -0.204  -0.196  -0.298
100   L        -0.047  -0.017  -0.120  -0.395  -0.379  -0.498  -0.204  -0.171  -0.313
101   S        -0.047  -0.048  -0.111   0.064   0.082  -0.057  -0.204  -0.187  -0.297
102   V         1.562   1.594   1.671   1.578   1.639   1.743   1.693   1.741   1.859
103   I         0.247   0.350  -0.000   0.334   0.485  -0.032   0.243   0.387  -0.128
104   E         1.562   1.594   1.671   1.773   1.827   1.933   1.693   1.741   1.859
105   F         0.247   0.051  -0.059   0.357   0.075  -0.102   0.243  -0.036  -0.214
106   W         0.888   0.832   0.691   1.184   1.101   0.840   0.912   0.820   0.544
107   S         1.562   1.594   1.671   1.546   1.598   1.712   1.693   1.741   1.859
108   K        -0.357  -0.505  -0.610  -0.079  -0.291  -0.457  -0.316  -0.501  -0.620
109   A        -0.357  -0.505  -0.610  -0.308  -0.583  -0.763  -0.316  -0.501  -0.620
110   I         0.247   0.255  -0.006   0.287   0.316  -0.130   0.243   0.249  -0.136
111   L         0.888   0.832   0.691   0.661   0.580   0.400   0.912   0.820   0.544
112   Y         1.562   1.594   1.671   1.599   1.650   1.764   1.693   1.741   1.859
113   L        -0.606  -0.552  -0.644  -0.437  -0.385  -0.574  -0.650  -0.605  -0.669
114   I        -0.179  -0.188  -0.146  -0.354  -0.326  -0.280  -0.427  -0.414  -0.355
115   P         1.562   1.594   1.671   1.735   1.779   1.895   1.693   1.741   1.859
116   F         0.888   0.756   0.678   0.946   0.763   0.647   0.912   0.694   0.520
117   Y         1.562   1.594   1.671   1.599   1.650   1.764   1.693   1.741   1.859
118   W        -0.179  -0.198  -0.160  -0.105  -0.115  -0.071  -0.427  -0.430  -0.374
119   F        -0.179  -0.188  -0.156  -0.604  -0.628  -0.528  -0.427  -0.414  -0.367
120   L        -0.179  -0.144  -0.158  -0.556  -0.543  -0.516  -0.427  -0.389  -0.375
121   K         1.562   1.594   1.671   1.642   1.695   1.806   1.693   1.741   1.859
122   T         0.247   0.051  -0.059   0.386   0.093  -0.094   0.243  -0.036  -0.214
123   V        -0.606  -0.577  -0.640  -0.626  -0.588  -0.697  -0.650  -0.626  -0.665
124   F         1.562   1.594   1.671   1.541   1.578   1.707   1.693   1.741   1.859
125   L         1.562   1.594   1.671   1.258   1.289   1.433   1.693   1.741   1.859
126   I        -0.179  -0.135  -0.149  -0.618  -0.564  -0.526  -0.427  -0.381  -0.366
127   Y         0.557   0.457   0.503   0.600   0.445   0.512   0.354   0.156   0.186
128   I         0.380   0.360   0.461  -0.044  -0.136   0.018   0.019  -0.036   0.103
129   A        -0.296  -0.264  -0.211  -0.506  -0.457  -0.390  -0.539  -0.494  -0.435
130   L         0.493   0.569   0.532   0.047   0.160   0.097   0.236   0.365   0.243
131   P         1.562   1.594   1.671   1.729   1.774   1.890   1.693   1.741   1.859
132   Q        -0.682  -0.787  -0.674  -0.660  -0.785  -0.624  -0.762  -0.851  -0.705
133   T        -0.179  -0.099  -0.140  -0.333  -0.218  -0.243  -0.427  -0.311  -0.346
134   G         0.247   0.051  -0.059   0.440   0.191   0.014   0.243  -0.036  -0.214
135   G         1.562   1.594   1.671   1.588   1.649   1.753   1.693   1.741   1.859
136   A         0.888   0.949   0.704   0.920   0.993   0.661   0.912   1.002   0.568
137   R        -1.108  -1.018  -1.056  -0.862  -0.747  -0.761  -0.985  -0.896  -0.884
138   M        -0.798  -0.845  -0.705  -0.998  -1.081  -0.841  -0.874  -0.905  -0.735
139   I         0.323   0.356   0.462   0.020   0.085   0.237  -0.092  -0.044   0.103
140   Y         0.888   0.832   0.691   0.999   0.931   0.712   0.912   0.820   0.544
141   Q        -1.108  -1.050  -1.073  -0.780  -0.700  -0.727  -0.985  -0.934  -0.901
142   K        -1.225  -1.233  -1.114  -1.057  -1.035  -0.865  -1.097  -1.090  -0.935
143   I        -1.225  -1.173  -1.096  -1.551  -1.511  -1.345  -1.097  -1.043  -0.922
144   V        -0.047  -0.055  -0.118  -0.171  -0.169  -0.329  -0.204  -0.199  -0.310
145   A        -0.798  -0.845  -0.717  -0.831  -0.864  -0.690  -0.874  -0.905  -0.748
146   P         1.562   1.594   1.671   1.735   1.779   1.895   1.693   1.741   1.859
147   L        -0.606  -0.716  -0.658  -0.902  -1.068  -0.941  -0.650  -0.757  -0.683
148   T        -1.108  -1.174  -1.085  -1.219  -1.345  -1.233  -0.985  -1.032  -0.908
149   D        -0.915  -1.004  -1.048  -0.480  -0.634  -0.695  -0.762  -0.856  -0.871
150   R        -0.179  -0.264  -0.160  -0.078  -0.171  -0.011  -0.427  -0.516  -0.379
151   Y         0.247   0.156  -0.038   0.416   0.315  -0.012   0.243   0.106  -0.183
152   I        -0.682  -0.673  -0.664  -0.868  -0.828  -0.855  -0.762  -0.741  -0.694
153   L        -1.844  -1.843  -1.722  -1.790  -1.780  -1.534  -1.320  -1.307  -1.154
154   R        -0.854  -0.808  -0.721  -0.782  -0.691  -0.579  -0.930  -0.878  -0.753
155   D        -1.314  -1.279  -1.143  -1.114  -1.085  -0.867  -1.164  -1.122  -0.959
156   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   S        -1.314  -1.271  -1.143  -1.048  -0.929  -0.803  -1.164  -1.115  -0.959
158   K        -0.819  -0.739  -0.702  -0.720  -0.599  -0.547  -0.878  -0.780  -0.727
159   T        -0.819  -0.780  -0.718  -0.850  -0.791  -0.713  -0.878  -0.835  -0.745
160   E        -0.819  -0.841  -0.732  -0.727  -0.771  -0.595  -0.878  -0.900  -0.760
161   K        -0.136   0.020  -0.131  -0.153   0.097  -0.167  -0.307  -0.079  -0.319
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   D        -1.225  -1.240  -1.111  -1.083  -1.121  -0.918  -1.097  -1.094  -0.933
166   E        -1.535  -1.485  -1.421  -1.309  -1.264  -1.149  -1.208  -1.157  -1.047
167   I        -1.844  -1.831  -1.704  -1.783  -1.728  -1.580  -1.320  -1.300  -1.142
168   R         0.247   0.377   0.008   0.398   0.551   0.103   0.243   0.424  -0.116
169   A        -0.606  -0.680  -0.660  -0.475  -0.584  -0.574  -0.650  -0.734  -0.686
170   S        -1.108  -1.173  -1.078  -1.006  -1.089  -0.938  -0.985  -1.033  -0.904
171   V        -0.798  -0.828  -0.721  -1.045  -1.112  -0.968  -0.874  -0.892  -0.752
172   N        -1.844  -1.837  -1.708  -1.388  -1.381  -1.198  -1.320  -1.304  -1.145
173   E        -1.108  -1.133  -1.079  -0.864  -0.934  -0.830  -0.985  -1.004  -0.905
174   A        -0.357  -0.505  -0.610  -0.233  -0.471  -0.621  -0.316  -0.501  -0.620
175   S         0.557   0.650   0.592   0.433   0.574   0.466   0.354   0.511   0.359
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   K        -1.844  -1.833  -1.716  -1.230  -1.188  -1.033  -1.320  -1.301  -1.150
182   A        -0.682  -0.717  -0.676  -0.739  -0.794  -0.689  -0.762  -0.788  -0.706
183   T        -0.682  -0.614  -0.663  -0.675  -0.585  -0.600  -0.762  -0.689  -0.693
184   G        -1.108  -1.166  -1.093  -1.005  -1.058  -0.942  -0.985  -1.026  -0.916
185   A        -0.179  -0.088  -0.145  -0.348  -0.204  -0.268  -0.427  -0.298  -0.352
186   S        -0.798  -0.760  -0.712  -0.838  -0.751  -0.695  -0.874  -0.837  -0.743
187   -        -0.136  -0.226  -0.182  -0.213  -0.371  -0.330  -0.307  -0.440  -0.393
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   V        -1.074  -0.955  -1.044  -0.936  -0.756  -0.892  -0.930  -0.796  -0.867
192   H        -1.074  -1.110  -1.077  -0.675  -0.778  -0.741  -0.930  -0.966  -0.899
* 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/Q12402
Output conservation file - output/Q12402
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
