1     M         1.988   2.020   2.182   2.262   2.315   2.562   2.284   2.341   2.647
2     S        -0.828  -0.873  -0.866  -0.870  -0.952  -0.976  -0.744  -0.784  -0.749
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    D        -1.188  -1.163  -1.010  -1.135  -1.093  -0.885  -1.100  -1.071  -0.892
27    L        -0.641  -0.586  -0.519  -0.772  -0.694  -0.604  -0.761  -0.694  -0.612
28    V         0.276   0.318   0.208   0.064   0.118  -0.070   0.169   0.231   0.025
29    N        -0.961  -0.954  -0.911  -0.851  -0.864  -0.809  -0.888  -0.884  -0.800
30    K        -0.828  -0.794  -0.846  -0.731  -0.678  -0.781  -0.744  -0.698  -0.731
31    K        -0.524  -0.495  -0.480  -0.675  -0.664  -0.624  -0.640  -0.636  -0.575
32    F         0.942   0.859   0.889   0.975   0.832   0.829   0.822   0.646   0.614
33    P         1.299   1.351   1.132   1.458   1.531   1.248   1.449   1.532   1.119
34    A        -0.636  -0.640  -0.514  -0.885  -0.896  -0.724  -0.771  -0.771  -0.610
35    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    D        -1.017  -1.079  -0.936  -1.027  -1.116  -0.912  -0.953  -1.000  -0.827
37    Y        -0.828  -0.770  -0.857  -0.855  -0.789  -0.888  -0.744  -0.673  -0.744
38    K        -0.903  -0.842  -0.879  -0.850  -0.739  -0.773  -0.849  -0.780  -0.772
39    F         0.139   0.188   0.149   0.117   0.176   0.143  -0.118  -0.063  -0.100
40    Q        -0.828  -0.883  -0.872  -0.453  -0.489  -0.501  -0.744  -0.787  -0.754
41    Y         1.299   1.169   1.120   1.577   1.429   1.358   1.449   1.228   1.095
42    I         0.620   0.648   0.808   0.239   0.274   0.515   0.169   0.207   0.438
43    A        -0.406  -0.441  -0.462  -0.345  -0.401  -0.451  -0.492  -0.536  -0.551
44    I        -0.961  -0.996  -0.950  -0.688  -0.742  -0.681  -0.888  -0.920  -0.837
45    S        -0.406  -0.406  -0.421  -0.462  -0.450  -0.489  -0.492  -0.482  -0.496
46    Q        -0.619  -0.641  -0.525  -0.636  -0.665  -0.486  -0.756  -0.776  -0.626
47    S        -0.064  -0.057   0.039  -0.278  -0.270  -0.151  -0.359  -0.356  -0.247
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    D        -1.461  -1.412  -1.324  -1.103  -1.022  -0.908  -1.169  -1.119  -0.999
50    A        -1.740  -1.735  -1.624  -1.790  -1.793  -1.643  -1.267  -1.256  -1.109
51    D        -1.740  -1.724  -1.619  -1.605  -1.562  -1.435  -1.267  -1.249  -1.105
52    S        -1.740  -1.732  -1.633  -1.562  -1.533  -1.381  -1.267  -1.253  -1.114
53    E        -1.017  -0.940  -0.928  -1.038  -0.901  -0.908  -0.953  -0.870  -0.818
54    S         0.024   0.046   0.077  -0.343  -0.344  -0.331  -0.222  -0.206  -0.187
55    C         1.299   1.169   1.120   1.652   1.484   1.393   1.449   1.228   1.095
56    K        -1.017  -1.028  -0.937  -1.172  -1.179  -1.077  -0.953  -0.956  -0.830
57    M        -1.321  -1.396  -1.319  -0.931  -1.039  -0.953  -1.058  -1.113  -0.997
58    P         1.988   2.020   2.182   2.040   2.090   2.336   2.284   2.341   2.647
59    Q        -1.017  -1.006  -0.940  -0.938  -0.951  -0.846  -0.953  -0.941  -0.831
60    T        -0.961  -0.958  -0.914  -0.813  -0.801  -0.726  -0.888  -0.885  -0.802
61    V        -0.961  -0.950  -0.941  -0.847  -0.835  -0.835  -0.888  -0.879  -0.827
62    E        -0.961  -0.938  -0.934  -0.841  -0.813  -0.761  -0.888  -0.866  -0.820
63    W        -0.961  -1.021  -0.955  -0.792  -0.883  -0.812  -0.888  -0.940  -0.840
64    S        -1.302  -1.250  -1.280  -1.264  -1.177  -1.282  -1.020  -0.967  -0.960
65    K        -0.131  -0.132  -0.350  -0.031  -0.026  -0.377  -0.095  -0.098  -0.394
66    L        -0.961  -0.998  -0.930  -0.828  -0.875  -0.797  -0.888  -0.916  -0.818
67    I         0.102   0.110   0.120   0.065   0.080   0.080  -0.133  -0.129  -0.131
68    S         0.006   0.037   0.096  -0.264  -0.236  -0.150  -0.305  -0.260  -0.170
69    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    N        -0.409  -0.488  -0.420  -0.332  -0.406  -0.309  -0.536  -0.606  -0.505
71    K         0.313   0.279   0.179   0.274   0.189   0.063   0.196   0.106  -0.041
72    K         0.732   0.770   0.839   0.462   0.526   0.584   0.404   0.465   0.506
73    V         0.313   0.279   0.233   0.191   0.153   0.088   0.196   0.168   0.057
74    I         0.942   0.904   0.911   0.731   0.654   0.648   0.822   0.735   0.662
75    I        -0.409  -0.345  -0.428  -0.407  -0.299  -0.430  -0.536  -0.452  -0.516
76    T         0.732   0.698   0.828   0.452   0.354   0.514   0.404   0.315   0.482
77    G        -0.106  -0.053   0.030  -0.473  -0.384  -0.300  -0.431  -0.356  -0.261
78    A         0.632   0.648   0.808   0.078   0.076   0.318   0.196   0.208   0.436
79    P         1.299   1.362   1.129   1.466   1.552   1.260   1.449   1.551   1.113
80    A         0.732   0.776   0.871   0.434   0.500   0.601   0.404   0.477   0.575
81    A         1.988   2.020   2.182   1.796   1.844   2.089   2.284   2.341   2.647
82    F         1.988   2.020   2.182   2.040   2.084   2.336   2.284   2.341   2.647
83    S         0.732   0.776   0.871   0.501   0.580   0.675   0.404   0.477   0.575
84    P         1.988   2.020   2.182   2.040   2.090   2.336   2.284   2.341   2.647
85    T         0.942   0.891   0.898   0.918   0.842   0.807   0.822   0.710   0.635
86    C         1.988   2.020   2.182   2.255   2.308   2.555   2.284   2.341   2.647
87    T         0.139   0.103   0.135   0.030  -0.033   0.045  -0.118  -0.181  -0.123
88    V        -0.961  -0.996  -0.950  -0.912  -0.977  -0.917  -0.888  -0.920  -0.837
89    S        -0.828  -0.710  -0.876  -0.636  -0.485  -0.672  -0.744  -0.618  -0.762
90    H         1.299   1.169   1.120   1.701   1.558   1.506   1.449   1.228   1.095
91    I         0.313   0.270   0.185   0.340   0.225   0.086   0.196   0.094  -0.030
92    P         1.988   2.020   2.182   2.040   2.090   2.336   2.284   2.341   2.647
93    G        -1.132  -1.012  -1.233  -0.858  -0.699  -1.028  -0.849  -0.722  -0.916
94    Y         1.988   2.020   2.182   2.150   2.205   2.448   2.284   2.341   2.647
95    I         0.084   0.093   0.128  -0.059  -0.032   0.011  -0.222  -0.203  -0.133
96    N        -1.436  -1.402  -1.315  -1.377  -1.337  -1.181  -1.162  -1.123  -0.997
97    Y        -0.409  -0.323  -0.406  -0.299  -0.198  -0.240  -0.536  -0.445  -0.494
98    L         0.009  -0.081  -0.296   0.253   0.138  -0.205   0.091  -0.036  -0.321
99    D        -1.017  -0.974  -0.924  -1.036  -0.962  -0.894  -0.953  -0.900  -0.815
100   E        -1.132  -1.084  -0.976  -1.034  -0.938  -0.794  -1.058  -1.009  -0.864
101   L         0.632   0.664   0.813   0.415   0.466   0.674   0.196   0.242   0.449
102   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   K         0.009  -0.109  -0.312   0.111  -0.071  -0.406   0.091  -0.072  -0.342
104   E        -0.599  -0.535  -0.490  -0.875  -0.797  -0.705  -0.744  -0.677  -0.590
105   K         1.299   1.297   1.124   1.284   1.291   1.035   1.449   1.446   1.103
106   E         1.299   1.388   1.140   1.369   1.476   1.184   1.449   1.592   1.135
107   V         0.639   0.489   0.315   0.606   0.399   0.142   0.718   0.490   0.199
108   D         0.313   0.279   0.179   0.297   0.213   0.040   0.196   0.106  -0.041
109   Q        -0.409  -0.403  -0.427  -0.252  -0.262  -0.241  -0.536  -0.529  -0.515
110   V         0.632   0.650   0.809   0.228   0.248   0.488   0.196   0.211   0.438
111   I        -0.409  -0.490  -0.410  -0.457  -0.536  -0.422  -0.536  -0.609  -0.497
112   V         1.299   1.294   1.135   1.210   1.196   1.019   1.449   1.440   1.125
113   V         0.024   0.064   0.089  -0.225  -0.177  -0.149  -0.222  -0.167  -0.167
114   T         0.024  -0.015   0.058  -0.174  -0.265  -0.211  -0.222  -0.294  -0.217
115   V        -0.409  -0.397  -0.414  -0.729  -0.735  -0.725  -0.536  -0.524  -0.501
116   D         0.732   0.776   0.871   0.640   0.717   0.816   0.404   0.477   0.575
117   N         0.732   0.776   0.871   0.583   0.658   0.772   0.404   0.477   0.575
118   P         0.639   0.486   0.325   0.833   0.619   0.340   0.718   0.485   0.215
119   F         1.299   1.294   1.135   1.495   1.497   1.335   1.449   1.440   1.125
120   A         0.732   0.776   0.871   0.282   0.337   0.452   0.404   0.477   0.575
121   N        -0.280  -0.379  -0.394   0.026  -0.101  -0.129  -0.327  -0.446  -0.465
122   Q        -1.017  -1.050  -0.947  -1.068  -1.120  -0.951  -0.953  -0.976  -0.836
123   A         1.299   1.297   1.124   1.246   1.252   1.065   1.449   1.446   1.103
124   W         1.988   2.020   2.182   2.252   2.301   2.551   2.284   2.341   2.647
125   A         0.084   0.009   0.121  -0.244  -0.340  -0.176  -0.222  -0.299  -0.144
126   K         1.299   1.319   1.125   1.342   1.379   1.169   1.449   1.482   1.104
127   S        -0.280  -0.310  -0.421  -0.370  -0.431  -0.579  -0.327  -0.379  -0.501
128   L         0.639   0.486   0.325   0.859   0.681   0.455   0.718   0.485   0.215
129   G         0.639   0.509   0.327   0.772   0.599   0.327   0.718   0.519   0.217
130   V        -0.828  -0.813  -0.878  -0.861  -0.866  -0.953  -0.744  -0.727  -0.761
131   K        -0.584  -0.638  -0.791  -0.342  -0.428  -0.623  -0.431  -0.501  -0.658
132   D         0.009  -0.090  -0.292   0.251   0.124  -0.173   0.091  -0.048  -0.315
133   T        -0.409  -0.485  -0.452  -0.343  -0.414  -0.355  -0.536  -0.610  -0.541
134   T        -1.321  -1.260  -1.271  -1.202  -1.106  -1.130  -1.058  -0.992  -0.956
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   H        -0.961  -1.032  -0.955  -0.618  -0.736  -0.640  -0.888  -0.950  -0.840
137   I         0.084   0.103   0.128  -0.164  -0.145  -0.065  -0.222  -0.195  -0.136
138   K        -0.409  -0.501  -0.457  -0.382  -0.466  -0.389  -0.536  -0.625  -0.548
139   F         1.988   2.020   2.182   2.040   2.084   2.336   2.284   2.341   2.647
140   A         0.009  -0.155  -0.312   0.099  -0.134  -0.333   0.091  -0.132  -0.342
141   S         0.084   0.009   0.136  -0.171  -0.262  -0.087  -0.222  -0.298  -0.125
142   D         1.988   2.020   2.182   1.960   2.014   2.255   2.284   2.341   2.647
143   P        -0.409  -0.493  -0.423  -0.432  -0.533  -0.423  -0.536  -0.622  -0.513
144   G         0.139   0.150   0.152   0.117   0.145   0.147  -0.118  -0.094  -0.085
145   C         0.313   0.216   0.195   0.270   0.143   0.129   0.196   0.063  -0.013
146   A        -0.524  -0.535  -0.488  -0.750  -0.777  -0.707  -0.640  -0.669  -0.586
147   F         0.139   0.245   0.160   0.114   0.283   0.157  -0.118   0.044  -0.083
148   T         0.313   0.300   0.190   0.237   0.202   0.007   0.196   0.154  -0.021
149   K         0.639   0.656   0.338   0.804   0.836   0.473   0.718   0.745   0.235
150   S        -0.828  -0.817  -0.859  -0.696  -0.692  -0.713  -0.744  -0.720  -0.740
151   I         0.139   0.049   0.143   0.090  -0.009   0.111  -0.118  -0.226  -0.110
152   G         1.299   1.169   1.120   1.360   1.196   1.131   1.449   1.228   1.095
153   F        -1.740  -1.754  -1.644  -1.371  -1.403  -1.213  -1.267  -1.267  -1.122
154   -        -0.641  -0.508  -0.504  -0.853  -0.649  -0.679  -0.761  -0.598  -0.594
155   -         1.000   1.012   0.975   1.000   0.999   0.904   0.931   0.943   0.799
156   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   E         0.211   0.259   0.178   0.179   0.265   0.097   0.037   0.119  -0.031
159   L         0.536   0.430   0.286   0.727   0.577   0.383   0.566   0.393   0.152
160   A        -0.961  -1.014  -0.943  -1.034  -1.122  -1.049  -0.888  -0.937  -0.830
161   V        -1.432  -1.417  -1.329  -1.559  -1.544  -1.402  -1.152  -1.137  -1.006
162   G        -1.432  -1.461  -1.343  -1.515  -1.555  -1.396  -1.152  -1.168  -1.017
163   D        -1.132  -1.200  -1.266  -0.883  -0.995  -1.120  -0.849  -0.920  -0.947
164   G        -0.828  -0.715  -0.877  -0.577  -0.438  -0.592  -0.744  -0.622  -0.762
165   V         0.139   0.057   0.123  -0.080  -0.190  -0.095  -0.118  -0.212  -0.131
166   Y        -1.740  -1.686  -1.628  -1.427  -1.354  -1.294  -1.267  -1.219  -1.111
167   W         0.732   0.776   0.871   0.915   0.985   1.109   0.404   0.477   0.575
168   S        -0.409  -0.389  -0.436  -0.522  -0.500  -0.569  -0.536  -0.516  -0.527
169   G        -1.132  -1.080  -0.976  -1.319  -1.254  -1.077  -1.058  -1.006  -0.863
170   R         1.988   2.020   2.182   2.245   2.297   2.544   2.284   2.341   2.647
171   W         0.942   1.021   0.977   1.154   1.272   1.203   0.822   0.959   0.803
172   A         0.313   0.383   0.209   0.179   0.298   0.016   0.196   0.317   0.010
173   M        -1.132  -1.077  -0.980  -1.311  -1.264  -1.067  -1.058  -1.006  -0.867
174   V         0.732   0.714   0.836   0.503   0.437   0.583   0.404   0.349   0.500
175   V         0.139   0.167   0.166  -0.138  -0.102  -0.100  -0.118  -0.063  -0.069
176   E        -0.524  -0.511  -0.492  -0.627  -0.617  -0.618  -0.640  -0.636  -0.588
177   N         0.084   0.088   0.148   0.050   0.078   0.199  -0.222  -0.211  -0.111
178   G         1.988   2.020   2.182   1.942   1.984   2.236   2.284   2.341   2.647
179   I        -0.280  -0.149  -0.362  -0.324  -0.139  -0.468  -0.327  -0.158  -0.427
180   V         0.732   0.774   0.836   0.391   0.441   0.522   0.404   0.473   0.498
181   T        -0.409  -0.307  -0.405  -0.594  -0.494  -0.596  -0.536  -0.441  -0.492
182   Y         0.639   0.619   0.351   0.992   0.956   0.594   0.718   0.671   0.258
183   A        -0.903  -0.974  -0.909  -0.925  -1.034  -0.903  -0.849  -0.905  -0.798
184   A        -0.280  -0.347  -0.420  -0.190  -0.282  -0.438  -0.327  -0.408  -0.495
185   K        -2.044  -2.046  -1.927  -1.795  -1.788  -1.626  -1.371  -1.364  -1.214
186   E         1.299   1.294   1.135   1.451   1.457   1.246   1.449   1.440   1.125
187   T        -0.532  -0.471  -0.461  -0.578  -0.477  -0.495  -0.651  -0.576  -0.546
188   N        -0.406  -0.340  -0.433  -0.349  -0.238  -0.445  -0.492  -0.397  -0.509
189   P        -0.280  -0.281  -0.374  -0.113  -0.091  -0.255  -0.327  -0.313  -0.432
190   G        -0.280  -0.404  -0.402  -0.340  -0.555  -0.594  -0.327  -0.477  -0.470
191   T        -0.599  -0.573  -0.503  -0.716  -0.678  -0.598  -0.744  -0.709  -0.604
192   D        -0.828  -0.756  -0.878  -0.727  -0.589  -0.797  -0.744  -0.648  -0.760
193   V         1.988   2.020   2.182   1.672   1.713   1.963   2.284   2.341   2.647
194   T        -0.828  -0.855  -0.880  -0.740  -0.766  -0.856  -0.744  -0.759  -0.763
195   V        -0.409  -0.390  -0.423  -0.538  -0.517  -0.510  -0.536  -0.513  -0.512
196   S         0.942   0.969   0.928   0.822   0.864   0.753   0.822   0.861   0.698
197   S         0.313   0.345   0.201   0.278   0.311   0.109   0.196   0.229  -0.000
198   V         0.139   0.169   0.152  -0.213  -0.172  -0.170  -0.118  -0.070  -0.086
199   E        -0.409  -0.260  -0.394  -0.400  -0.192  -0.352  -0.536  -0.360  -0.476
200   S        -2.044  -2.048  -1.926  -1.873  -1.895  -1.737  -1.371  -1.366  -1.214
201   V        -0.280  -0.201  -0.375  -0.430  -0.343  -0.574  -0.327  -0.232  -0.435
202   L         1.299   1.319   1.125   1.432   1.477   1.241   1.449   1.482   1.104
203   A        -0.599  -0.637  -0.495  -0.877  -0.926  -0.718  -0.744  -0.769  -0.597
204   H        -1.017  -1.039  -0.941  -0.748  -0.793  -0.614  -0.953  -0.956  -0.828
205   L         1.299   1.371   1.134   1.415   1.521   1.218   1.449   1.565   1.123
206   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P38013
Output conservation file - output/P38013
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
