1     M         1.905   1.929   2.047   2.155   2.191   2.392   2.183   2.225   2.443
2     G        -0.027   0.013   0.052  -0.128  -0.074  -0.001  -0.301  -0.227  -0.183
3     I         1.905   1.929   2.047   1.882   1.923   2.117   2.183   2.225   2.443
4     Y         0.831   0.936   0.853   0.864   1.023   0.890   0.659   0.850   0.634
5     S         1.185   1.092   1.009   1.117   1.012   0.895   1.294   1.134   0.947
6     F         1.185   1.156   1.020   1.274   1.235   1.022   1.294   1.243   0.969
7     W        -0.081  -0.098  -0.018  -0.019  -0.072   0.028  -0.357  -0.391  -0.290
8     I         1.905   1.929   2.047   1.882   1.923   2.117   2.183   2.225   2.443
9     F         1.185   1.092   1.009   1.305   1.183   1.067   1.294   1.134   0.947
10    D         1.185   1.092   1.009   1.370   1.239   1.093   1.294   1.134   0.947
11    R         1.905   1.929   2.047   2.078   2.114   2.314   2.183   2.225   2.443
12    H         1.185   1.092   1.009   1.477   1.352   1.228   1.294   1.134   0.947
13    C         0.500   0.502   0.237   0.871   0.879   0.435   0.532   0.533   0.112
14    N         0.641   0.632   0.734   0.394   0.372   0.524   0.278   0.241   0.378
15    C         1.905   1.929   2.047   2.205   2.249   2.442   2.183   2.225   2.443
16    I         1.185   1.092   1.009   1.236   1.117   1.000   1.294   1.134   0.947
17    F         0.641   0.645   0.739   0.449   0.437   0.575   0.278   0.269   0.390
18    D        -0.949  -0.995  -0.971  -0.928  -0.999  -1.000  -0.865  -0.906  -0.846
19    R         0.044  -0.019   0.046   0.014  -0.079   0.038  -0.230  -0.307  -0.211
20    E         0.500   0.390   0.216   0.734   0.573   0.318   0.532   0.363   0.079
21    W         0.641   0.656   0.748   0.672   0.686   0.812   0.278   0.291   0.409
22    T        -0.412  -0.470  -0.483  -0.577  -0.673  -0.753  -0.484  -0.545  -0.555
23    L        -1.074  -1.051  -0.990  -0.977  -0.913  -0.809  -0.992  -0.962  -0.864
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    A        -1.055  -0.947  -0.964  -1.266  -1.133  -1.125  -0.969  -0.868  -0.841
67    S        -1.055  -1.078  -1.002  -1.145  -1.141  -1.035  -0.969  -0.983  -0.874
68    N        -0.146  -0.263  -0.396  -0.039  -0.204  -0.440  -0.103  -0.261  -0.433
69    S        -0.412  -0.427  -0.468  -0.545  -0.578  -0.593  -0.484  -0.516  -0.537
70    A        -0.949  -0.871  -0.929  -1.138  -1.051  -1.093  -0.865  -0.791  -0.804
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    S        -0.913  -0.963  -0.956  -1.032  -1.116  -1.107  -0.803  -0.858  -0.827
75    G         0.044   0.054   0.052  -0.097  -0.120  -0.089  -0.230  -0.228  -0.204
76    T        -0.949  -0.984  -0.952  -0.779  -0.825  -0.743  -0.865  -0.900  -0.830
77    I         0.044  -0.019   0.046  -0.184  -0.286  -0.182  -0.230  -0.307  -0.211
78    N        -0.146  -0.235  -0.409  -0.040  -0.164  -0.464  -0.103  -0.225  -0.450
79    S        -0.493  -0.547  -0.506  -0.664  -0.700  -0.607  -0.611  -0.659  -0.585
80    K        -0.949  -0.967  -0.956  -0.982  -1.014  -1.003  -0.865  -0.882  -0.833
81    Q        -0.412  -0.433  -0.450  -0.418  -0.443  -0.493  -0.484  -0.489  -0.504
82    N        -1.405  -1.427  -1.341  -1.245  -1.266  -1.133  -1.119  -1.128  -1.009
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    E        -0.618  -0.608  -0.541  -0.781  -0.757  -0.628  -0.738  -0.719  -0.628
85    E        -0.412  -0.370  -0.433  -0.363  -0.284  -0.424  -0.484  -0.410  -0.482
86    D        -1.280  -1.284  -1.276  -0.995  -1.013  -1.012  -0.992  -0.998  -0.952
87    A        -0.146  -0.281  -0.387   0.141  -0.059  -0.258  -0.103  -0.284  -0.421
88    K         1.905   1.929   2.047   1.938   1.979   2.174   2.183   2.225   2.443
89    L         1.905   1.929   2.047   1.771   1.810   2.005   2.183   2.225   2.443
90    L         0.581   0.615   0.732   0.103   0.171   0.350   0.151   0.206   0.375
91    Y         0.641   0.703   0.781   0.436   0.540   0.654   0.278   0.390   0.481
92    G         1.905   1.929   2.047   2.078   2.121   2.314   2.183   2.225   2.443
93    M        -0.743  -0.834  -0.909  -0.375  -0.538  -0.683  -0.611  -0.716  -0.778
94    I         0.185   0.307   0.153   0.123   0.291   0.047   0.024   0.186  -0.031
95    F         0.044   0.047   0.077  -0.057  -0.041   0.030  -0.230  -0.212  -0.166
96    S         1.905   1.929   2.047   1.752   1.800   1.985   2.183   2.225   2.443
97    L         1.905   1.929   2.047   1.771   1.810   2.005   2.183   2.225   2.443
98    R         0.641   0.656   0.748   0.519   0.530   0.661   0.278   0.291   0.409
99    S        -0.412  -0.329  -0.451  -0.504  -0.359  -0.581  -0.484  -0.382  -0.517
100   I         0.641   0.712   0.774   0.558   0.696   0.759   0.278   0.409   0.466
101   T        -0.743  -0.702  -0.585  -0.977  -0.928  -0.744  -0.865  -0.819  -0.672
102   Q        -1.405  -1.411  -1.336  -1.311  -1.343  -1.258  -1.119  -1.115  -1.005
103   K         1.905   1.929   2.047   1.938   1.979   2.174   2.183   2.225   2.443
104   L         0.185   0.141   0.086   0.013  -0.084  -0.129   0.024  -0.068  -0.145
105   S        -0.618  -0.605  -0.514  -0.708  -0.648  -0.521  -0.738  -0.709  -0.592
106   K        -1.736  -1.684  -1.642  -1.340  -1.270  -1.206  -1.246  -1.204  -1.116
107   G        -0.081  -0.111  -0.033  -0.091  -0.160  -0.048  -0.357  -0.410  -0.313
108   S        -1.055  -1.080  -0.983  -1.126  -1.120  -0.966  -0.969  -0.985  -0.855
109   V        -0.640  -0.644  -0.557  -0.465  -0.498  -0.361  -0.743  -0.755  -0.637
110   K        -0.110  -0.057  -0.007  -0.384  -0.294  -0.237  -0.418  -0.343  -0.275
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   N         0.641   0.632   0.734   0.414   0.398   0.549   0.278   0.241   0.378
114   D        -1.736  -1.716  -1.632  -1.584  -1.554  -1.449  -1.246  -1.227  -1.109
115   I        -0.162  -0.087  -0.002  -0.580  -0.462  -0.335  -0.484  -0.389  -0.273
116   R        -0.949  -0.995  -0.971  -0.805  -0.877  -0.843  -0.865  -0.906  -0.846
117   S         0.831   0.871   0.841   0.568   0.637   0.556   0.659   0.726   0.608
118   I        -0.618  -0.603  -0.531  -0.826  -0.803  -0.703  -0.738  -0.716  -0.612
119   S        -0.949  -0.843  -0.900  -1.012  -0.833  -0.919  -0.865  -0.744  -0.776
120   T         1.185   1.180   1.021   1.271   1.258   1.037   1.294   1.284   0.972
121   G        -0.412  -0.430  -0.481  -0.382  -0.424  -0.544  -0.484  -0.513  -0.555
122   K         0.500   0.470   0.245   0.641   0.606   0.262   0.532   0.485   0.126
123   Y         1.185   1.180   1.021   1.337   1.334   1.113   1.294   1.284   0.972
124   R         0.044   0.151   0.077  -0.088   0.062  -0.038  -0.230  -0.092  -0.167
125   V        -0.493  -0.463  -0.499  -0.706  -0.689  -0.715  -0.611  -0.572  -0.578
126   H         1.905   1.929   2.047   2.132   2.169   2.370   2.183   2.225   2.443
127   T        -0.949  -0.845  -0.927  -0.920  -0.779  -0.890  -0.865  -0.766  -0.804
128   Y        -0.618  -0.591  -0.530  -0.753  -0.707  -0.605  -0.738  -0.700  -0.614
129   C         0.185   0.263   0.165   0.312   0.426   0.289   0.024   0.161  -0.004
130   T         0.831   0.865   0.849   0.687   0.734   0.662   0.659   0.715   0.625
131   A         0.185   0.135   0.091   0.330   0.247   0.161   0.024  -0.064  -0.134
132   S         0.641   0.647   0.735   0.227   0.229   0.359   0.278   0.274   0.382
133   G         0.044   0.097   0.081  -0.064   0.038   0.027  -0.230  -0.133  -0.153
134   L         1.185   1.180   1.021   1.118   1.117   0.897   1.294   1.284   0.972
135   W        -0.162  -0.162  -0.042  -0.192  -0.206  -0.025  -0.484  -0.487  -0.327
136   F        -0.146  -0.253  -0.388   0.015  -0.167  -0.381  -0.103  -0.249  -0.422
137   V         0.831   0.831   0.799   0.793   0.780   0.675   0.659   0.649   0.518
138   L        -0.493  -0.543  -0.503  -0.720  -0.772  -0.683  -0.611  -0.654  -0.583
139   L        -0.412  -0.469  -0.480  -0.612  -0.711  -0.718  -0.484  -0.557  -0.554
140   S         0.581   0.613   0.731   0.128   0.189   0.378   0.151   0.201   0.373
141   D         0.831   0.775   0.787   0.845   0.736   0.701   0.659   0.537   0.494
142   F        -1.074  -1.066  -0.977  -1.036  -1.020  -0.885  -0.992  -0.975  -0.853
143   K        -1.405  -1.386  -1.310  -1.427  -1.407  -1.269  -1.119  -1.098  -0.986
144   Q        -1.405  -1.407  -1.329  -1.189  -1.218  -1.090  -1.119  -1.111  -0.999
145   Q        -1.405  -1.407  -1.329  -1.173  -1.195  -1.088  -1.119  -1.111  -0.999
146   S        -0.146  -0.148  -0.368  -0.136  -0.127  -0.450  -0.103  -0.109  -0.395
147   Y         0.185   0.282   0.182   0.041   0.203   0.075   0.024   0.189   0.022
148   T        -1.074  -1.050  -0.973  -1.094  -1.061  -0.924  -0.992  -0.966  -0.851
149   Q        -1.074  -1.096  -0.975  -0.946  -0.971  -0.801  -0.992  -1.001  -0.852
150   V         0.500   0.481   0.245   0.743   0.714   0.395   0.532   0.501   0.125
151   L         1.185   1.179   1.018   1.149   1.148   0.955   1.294   1.282   0.966
152   Q        -0.949  -0.948  -0.918  -0.606  -0.616  -0.548  -0.865  -0.863  -0.797
153   Y        -1.074  -1.051  -0.990  -0.957  -0.912  -0.815  -0.992  -0.962  -0.864
154   I         0.831   0.865   0.849   0.642   0.699   0.621   0.659   0.715   0.625
155   Y         1.905   1.929   2.047   1.990   2.027   2.226   2.183   2.225   2.443
156   S        -0.913  -0.932  -0.936  -1.020  -1.067  -1.059  -0.803  -0.828  -0.807
157   H        -0.412  -0.433  -0.450  -0.384  -0.407  -0.434  -0.484  -0.489  -0.504
158   I        -0.081   0.030   0.057  -0.440  -0.258  -0.230  -0.357  -0.195  -0.175
159   Y         0.185   0.174   0.098   0.247   0.227   0.119   0.024   0.004  -0.123
160   V        -0.412  -0.432  -0.469  -0.417  -0.456  -0.517  -0.484  -0.506  -0.537
161   K         0.641   0.632   0.734   0.436   0.401   0.562   0.278   0.241   0.378
162   Y         0.500   0.462   0.247   0.683   0.625   0.295   0.532   0.467   0.128
163   V         1.185   1.259   1.037   1.337   1.432   1.130   1.294   1.413   1.003
164   S        -0.743  -0.532  -0.813  -0.580  -0.270  -0.728  -0.611  -0.365  -0.672
165   N        -0.412  -0.311  -0.421  -0.420  -0.236  -0.401  -0.484  -0.340  -0.467
166   N         1.185   1.092   1.009   1.265   1.165   1.051   1.294   1.134   0.947
167   L        -1.405  -1.373  -1.340  -1.253  -1.146  -1.110  -1.119  -1.083  -1.008
168   L         1.905   1.929   2.047   1.771   1.810   2.005   2.183   2.225   2.443
169   S        -0.743  -0.872  -0.893  -0.694  -0.876  -0.890  -0.611  -0.758  -0.761
170   P         0.500   0.462   0.247   0.908   0.839   0.534   0.532   0.467   0.128
171   Y        -0.949  -0.918  -0.933  -0.836  -0.794  -0.787  -0.865  -0.834  -0.810
172   D         0.044  -0.017   0.047   0.009  -0.088   0.027  -0.230  -0.304  -0.210
173   F        -0.146  -0.282  -0.397   0.073  -0.126  -0.295  -0.103  -0.285  -0.433
174   A        -1.405  -1.435  -1.334  -1.259  -1.296  -1.165  -1.119  -1.134  -1.003
175   E        -0.412  -0.465  -0.495  -0.399  -0.512  -0.547  -0.484  -0.556  -0.570
176   N        -1.405  -1.435  -1.352  -1.372  -1.405  -1.289  -1.119  -1.135  -1.018
177   E        -0.743  -0.692  -0.840  -0.487  -0.418  -0.649  -0.611  -0.554  -0.702
178   N         0.619   0.605   0.723   0.390   0.348   0.542   0.232   0.184   0.356
179   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   R        -0.640  -0.700  -0.594  -0.646  -0.763  -0.624  -0.743  -0.817  -0.680
187   K         0.185   0.149   0.077   0.240   0.169   0.101   0.024  -0.053  -0.154
188   I         1.185   1.179   1.018   1.236   1.234   1.016   1.294   1.282   0.966
189   T        -0.949  -0.933  -0.954  -0.993  -0.987  -1.012  -0.865  -0.855  -0.831
190   N         0.500   0.370   0.227   0.605   0.445   0.206   0.532   0.333   0.097
191   R        -1.405  -1.373  -1.340  -1.130  -1.089  -1.024  -1.119  -1.083  -1.008
192   N        -0.949  -1.029  -0.965  -1.193  -1.338  -1.272  -0.865  -0.939  -0.841
193   F         1.905   1.929   2.047   1.952   1.989   2.188   2.183   2.225   2.443
194   I        -0.146  -0.235  -0.409  -0.021  -0.148  -0.421  -0.103  -0.225  -0.450
195   S        -1.736  -1.709  -1.640  -1.822  -1.789  -1.718  -1.246  -1.222  -1.115
196   V        -1.405  -1.362  -1.336  -1.273  -1.221  -1.189  -1.119  -1.083  -1.006
197   L        -0.081  -0.067  -0.008  -0.412  -0.405  -0.308  -0.357  -0.343  -0.275
198   E         0.185   0.282   0.182   0.263   0.428   0.259   0.024   0.189   0.022
199   S        -1.736  -1.662  -1.627  -1.507  -1.370  -1.372  -1.246  -1.186  -1.105
200   F         0.185   0.155   0.104   0.183   0.131   0.045   0.024  -0.021  -0.115
201   L         0.185   0.104   0.080  -0.033  -0.155  -0.208   0.024  -0.091  -0.147
202   A        -1.405  -1.435  -1.352  -1.068  -1.102  -0.987  -1.119  -1.135  -1.018
203   P        -0.677  -0.688  -0.573  -0.763  -0.801  -0.626  -0.803  -0.806  -0.659
204   M         0.762   0.874   0.885   0.569   0.736   0.761   0.524   0.731   0.698
205   V        -0.677  -0.650  -0.553  -0.816  -0.792  -0.625  -0.803  -0.768  -0.637
206   N        -1.169  -1.108  -1.027  -1.129  -1.010  -0.921  -1.068  -1.009  -0.897
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     *
209   Q        -0.640  -0.643  -0.559  -0.815  -0.884  -0.759  -0.743  -0.754  -0.640
* 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/Q03630
Output conservation file - output/Q03630
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
