1     M         1.680   1.697   1.776   1.893   1.917   2.040   1.850   1.873   1.997
2     K        -0.933  -0.947  -0.881  -0.858  -0.893  -0.801  -0.909  -0.918  -0.821
3     A        -0.184  -0.076  -0.200  -0.392  -0.237  -0.411  -0.296  -0.143  -0.320
4     T        -0.184  -0.169  -0.217  -0.169  -0.138  -0.208  -0.296  -0.276  -0.344
5     I         0.360   0.375   0.442   0.243   0.264   0.357   0.011   0.030   0.118
6     Q        -0.933  -0.914  -0.872  -1.059  -1.022  -0.949  -0.909  -0.882  -0.811
7     R        -1.476  -1.439  -1.350  -1.356  -1.307  -1.176  -1.215  -1.170  -1.048
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    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -0.359  -0.309  -0.295  -0.491  -0.424  -0.412  -0.545  -0.474  -0.455
13    V        -0.359  -0.342  -0.299  -0.699  -0.674  -0.605  -0.545  -0.523  -0.460
14    F         0.577   0.586   0.563   0.634   0.645   0.597   0.413   0.422   0.349
15    G         0.577   0.533   0.545   0.585   0.512   0.513   0.413   0.327   0.315
16    V         0.577   0.633   0.576   0.552   0.634   0.546   0.413   0.505   0.374
17    P         0.577   0.533   0.545   0.294   0.242   0.253   0.413   0.327   0.315
18    R         0.320   0.343   0.430  -0.082  -0.035   0.088  -0.066  -0.032   0.094
19    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    P         1.680   1.697   1.776   1.733   1.764   1.881   1.850   1.873   1.997
25    R        -0.933  -0.914  -0.872  -1.040  -1.009  -0.980  -0.909  -0.882  -0.811
26    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    D        -1.039  -1.010  -0.916  -0.849  -0.804  -0.675  -1.024  -0.984  -0.858
43    L        -0.184  -0.119  -0.201  -0.320  -0.227  -0.327  -0.296  -0.203  -0.322
44    F        -1.476  -1.439  -1.350  -1.605  -1.554  -1.422  -1.215  -1.170  -1.048
45    S        -0.933  -0.947  -0.881  -0.772  -0.805  -0.727  -0.909  -0.918  -0.821
46    K        -1.476  -1.439  -1.350  -1.394  -1.330  -1.214  -1.215  -1.170  -1.048
47    E        -1.476  -1.439  -1.350  -1.378  -1.324  -1.198  -1.215  -1.170  -1.048
48    F        -0.933  -0.947  -0.881  -1.086  -1.106  -0.990  -0.909  -0.918  -0.821
49    H        -0.933  -0.947  -0.881  -0.930  -0.919  -0.810  -0.909  -0.918  -0.821
50    N        -1.476  -1.439  -1.350  -1.316  -1.222  -1.137  -1.215  -1.170  -1.048
51    G        -1.834  -1.780  -1.704  -1.392  -1.372  -1.212  -1.343  -1.288  -1.175
52    R         1.680   1.697   1.776   1.709   1.788   1.858   1.850   1.873   1.997
53    V        -1.381  -1.362  -1.311  -1.041  -1.029  -0.928  -1.130  -1.106  -1.015
54    S        -0.757  -0.700  -0.799  -0.677  -0.600  -0.793  -0.705  -0.640  -0.729
55    K        -0.928  -0.937  -0.878  -0.841  -0.804  -0.773  -0.917  -0.913  -0.819
56    S         0.796   0.702   0.617   0.758   0.642   0.501   0.785   0.624   0.450
57    D        -0.928  -0.913  -0.872  -0.643  -0.601  -0.519  -0.917  -0.889  -0.813
58    L        -1.834  -1.780  -1.704  -1.528  -1.479  -1.346  -1.343  -1.288  -1.175
59    W        -0.928  -0.913  -0.872  -1.237  -1.177  -1.103  -0.917  -0.889  -0.813
60    S         0.432   0.432   0.468   0.207   0.218   0.245   0.147   0.140   0.169
61    S        -0.928  -0.866  -0.866  -0.721  -0.625  -0.609  -0.917  -0.848  -0.808
62    N        -0.928  -0.866  -0.866  -0.879  -0.806  -0.775  -0.917  -0.848  -0.808
63    K        -0.928  -0.973  -0.881  -0.523  -0.580  -0.435  -0.917  -0.947  -0.823
64    E         0.432   0.474   0.477   0.373   0.440   0.386   0.147   0.217   0.187
65    E        -1.381  -1.403  -1.334  -1.118  -1.167  -1.091  -1.130  -1.141  -1.035
66    E        -0.757  -0.758  -0.831  -0.430  -0.474  -0.590  -0.705  -0.703  -0.765
67    L        -0.757  -0.754  -0.806  -0.633  -0.659  -0.749  -0.705  -0.701  -0.737
68    L         1.680   1.697   1.776   1.405   1.418   1.556   1.850   1.873   1.997
69    V        -0.304  -0.267  -0.295  -0.479  -0.443  -0.460  -0.492  -0.452  -0.463
70    S        -0.475  -0.435  -0.350  -0.701  -0.589  -0.490  -0.705  -0.650  -0.530
71    Q         1.680   1.697   1.776   1.804   1.850   1.951   1.850   1.873   1.997
72    R         1.680   1.697   1.776   1.709   1.788   1.858   1.850   1.873   1.997
73    K        -0.757  -0.758  -0.831  -0.641  -0.668  -0.859  -0.705  -0.703  -0.765
74    K        -0.757  -0.774  -0.826  -0.356  -0.396  -0.495  -0.705  -0.723  -0.760
75    R         1.680   1.697   1.776   1.709   1.788   1.858   1.850   1.873   1.997
76    P         1.680   1.697   1.776   1.744   1.787   1.892   1.850   1.873   1.997
77    I        -0.757  -0.859  -0.848  -0.624  -0.775  -0.732  -0.705  -0.820  -0.785
78    S         1.680   1.697   1.776   1.634   1.682   1.783   1.850   1.873   1.997
79    P         1.680   1.697   1.776   1.744   1.787   1.892   1.850   1.873   1.997
80    H         1.680   1.697   1.776   1.838   1.848   1.985   1.850   1.873   1.997
81    L         1.680   1.697   1.776   1.405   1.418   1.556   1.850   1.873   1.997
82    T        -0.757  -0.682  -0.794  -0.511  -0.423  -0.520  -0.705  -0.617  -0.724
83    V         0.796   0.702   0.617   0.900   0.759   0.631   0.785   0.624   0.450
84    Y         1.680   1.697   1.776   1.764   1.760   1.912   1.850   1.873   1.997
85    E        -0.304  -0.304  -0.268  -0.028  -0.021   0.042  -0.492  -0.474  -0.425
86    P         0.796   0.895   0.676   0.911   1.062   0.713   0.785   0.940   0.557
87    E        -0.022  -0.167  -0.220   0.337   0.150   0.068  -0.066  -0.272  -0.349
88    M        -0.022  -0.167  -0.220  -0.036  -0.214  -0.252  -0.066  -0.272  -0.349
89    S         0.796   0.702   0.617   0.758   0.642   0.501   0.785   0.624   0.450
90    W         0.796   0.895   0.676   1.133   1.238   0.988   0.785   0.940   0.557
91    Y        -0.757  -0.661  -0.786  -0.482  -0.376  -0.544  -0.705  -0.593  -0.714
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    L        -0.304  -0.285  -0.259  -0.423  -0.427  -0.354  -0.492  -0.446  -0.408
94    S         1.680   1.697   1.776   1.634   1.682   1.783   1.850   1.873   1.997
95    S        -0.304  -0.304  -0.268  -0.452  -0.447  -0.422  -0.492  -0.474  -0.425
96    L        -0.022   0.016  -0.164  -0.062  -0.027  -0.224  -0.066  -0.021  -0.270
97    H         0.796   0.727   0.631   1.080   0.982   0.858   0.785   0.667   0.475
98    R         1.680   1.697   1.776   1.709   1.788   1.858   1.850   1.873   1.997
99    I         0.432   0.513   0.508   0.332   0.460   0.436   0.147   0.290   0.246
100   S         0.796   0.702   0.617   0.758   0.642   0.501   0.785   0.624   0.450
101   G         1.680   1.697   1.776   1.639   1.632   1.788   1.850   1.873   1.997
102   V        -0.022  -0.076  -0.197   0.071  -0.010  -0.192  -0.066  -0.144  -0.316
103   L        -1.381  -1.392  -1.319  -1.574  -1.583  -1.472  -1.130  -1.132  -1.022
104   L        -0.928  -0.927  -0.867  -0.886  -0.912  -0.826  -0.917  -0.902  -0.808
105   A        -0.022  -0.033  -0.189  -0.194  -0.191  -0.431  -0.066  -0.085  -0.305
106   L        -0.022  -0.029  -0.169   0.030  -0.038  -0.228  -0.066  -0.085  -0.277
107   G        -0.304  -0.292  -0.282  -0.641  -0.626  -0.596  -0.492  -0.477  -0.445
108   F         0.320   0.343   0.431  -0.030  -0.002   0.131  -0.066  -0.031   0.097
109   Y         1.680   1.697   1.776   1.764   1.760   1.912   1.850   1.873   1.997
110   A         1.680   1.697   1.776   1.356   1.408   1.508   1.850   1.873   1.997
111   F        -0.304  -0.357  -0.303  -0.529  -0.578  -0.490  -0.492  -0.556  -0.473
112   T        -0.304  -0.267  -0.295  -0.685  -0.635  -0.720  -0.492  -0.452  -0.463
113   I        -0.757  -0.859  -0.848  -0.262  -0.441  -0.435  -0.705  -0.820  -0.785
114   T        -0.304  -0.362  -0.301  -0.557  -0.681  -0.590  -0.492  -0.559  -0.470
115   L        -0.022  -0.006  -0.187   0.173   0.134  -0.115  -0.066  -0.054  -0.302
116   G        -0.304  -0.368  -0.304  -0.759  -0.860  -0.749  -0.492  -0.569  -0.474
117   V         0.432   0.405   0.448   0.017  -0.006   0.036   0.147   0.088   0.130
118   T        -0.304  -0.252  -0.278  -0.670  -0.589  -0.615  -0.492  -0.427  -0.439
119   T        -0.304  -0.303  -0.275  -0.307  -0.266  -0.271  -0.492  -0.469  -0.430
120   I        -0.304  -0.267  -0.295  -0.534  -0.515  -0.584  -0.492  -0.452  -0.463
121   M        -0.757  -0.859  -0.848  -0.870  -0.999  -1.002  -0.705  -0.820  -0.785
122   G        -0.022   0.166  -0.136   0.150   0.358   0.002  -0.066   0.196  -0.229
123   M        -0.757  -0.859  -0.848  -0.392  -0.539  -0.485  -0.705  -0.820  -0.785
124   D        -0.928  -0.937  -0.878  -0.624  -0.620  -0.538  -0.917  -0.913  -0.819
125   T        -0.928  -0.913  -0.872  -1.041  -1.058  -0.970  -0.917  -0.889  -0.813
126   T        -0.022  -0.167  -0.220   0.367   0.133   0.051  -0.066  -0.272  -0.349
127   F        -0.928  -0.907  -0.865  -1.058  -0.974  -0.974  -0.917  -0.888  -0.807
128   Q        -0.304  -0.313  -0.276  -0.618  -0.570  -0.542  -0.492  -0.484  -0.436
129   D        -0.022  -0.167  -0.220   0.062  -0.123  -0.196  -0.066  -0.272  -0.349
130   L         0.796   0.814   0.644   0.629   0.639   0.431   0.785   0.811   0.499
131   N        -0.757  -0.774  -0.826  -0.662  -0.655  -0.785  -0.705  -0.723  -0.760
132   K        -1.381  -1.362  -1.311  -1.208  -1.226  -1.113  -1.130  -1.106  -1.015
133   W        -0.757  -0.774  -0.826  -0.925  -0.923  -1.023  -0.705  -0.723  -0.760
134   Y        -0.757  -0.859  -0.848  -0.589  -0.765  -0.771  -0.705  -0.820  -0.785
135   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   E        -0.757  -0.735  -0.817  -0.796  -0.729  -0.839  -0.705  -0.681  -0.750
137   K        -1.381  -1.314  -1.311  -1.374  -1.256  -1.243  -1.130  -1.060  -1.015
138   M        -0.304  -0.343  -0.294  -0.514  -0.545  -0.451  -0.492  -0.530  -0.460
139   P         1.680   1.697   1.776   1.744   1.787   1.892   1.850   1.873   1.997
140   K        -0.928  -0.922  -0.862  -1.026  -0.996  -0.926  -0.917  -0.901  -0.804
141   W        -0.928  -0.826  -0.857  -0.921  -0.771  -0.808  -0.917  -0.810  -0.800
142   S        -0.928  -0.941  -0.867  -1.120  -1.091  -1.005  -0.917  -0.917  -0.810
143   Q         0.432   0.442   0.464   0.515   0.529   0.546   0.147   0.158   0.160
144   W        -1.381  -1.381  -1.320  -1.291  -1.321  -1.167  -1.130  -1.123  -1.023
145   V        -0.928  -0.897  -0.865  -1.047  -1.002  -0.955  -0.917  -0.880  -0.808
146   A        -0.304  -0.216  -0.274  -0.741  -0.628  -0.680  -0.492  -0.390  -0.435
147   K         1.680   1.697   1.776   1.799   1.818   1.946   1.850   1.873   1.997
148   G        -0.304  -0.368  -0.304  -0.569  -0.622  -0.526  -0.492  -0.569  -0.474
149   S        -1.381  -1.314  -1.311  -1.559  -1.454  -1.457  -1.130  -1.060  -1.015
150   A        -1.381  -1.314  -1.311  -1.126  -1.089  -1.016  -1.130  -1.060  -1.015
151   A         0.796   0.814   0.644   0.567   0.623   0.361   0.785   0.811   0.499
152   Y        -0.022  -0.033  -0.189   0.284   0.239   0.055  -0.066  -0.085  -0.305
153   L         0.796   0.702   0.617   0.911   0.780   0.605   0.785   0.624   0.450
154   F         0.796   0.814   0.644   0.876   0.917   0.622   0.785   0.811   0.499
155   A        -0.304  -0.343  -0.294  -0.529  -0.587  -0.552  -0.492  -0.530  -0.460
156   F         0.432   0.542   0.532   0.416   0.594   0.565   0.147   0.343   0.290
157   H         1.680   1.697   1.776   1.838   1.848   1.985   1.850   1.873   1.997
158   F        -0.304  -0.329  -0.288  -0.557  -0.562  -0.498  -0.492  -0.509  -0.454
159   G        -0.304  -0.343  -0.292  -0.293  -0.363  -0.277  -0.492  -0.535  -0.458
160   N         1.680   1.697   1.776   1.891   1.914   2.038   1.850   1.873   1.997
161   G         1.680   1.697   1.776   1.639   1.632   1.788   1.850   1.873   1.997
162   I         0.320   0.343   0.431   0.107   0.135   0.278  -0.066  -0.033   0.097
163   R         1.680   1.697   1.776   1.709   1.788   1.858   1.850   1.873   1.997
164   H         1.680   1.697   1.776   1.838   1.848   1.985   1.850   1.873   1.997
165   L         0.796   0.895   0.676   0.629   0.740   0.479   0.785   0.940   0.557
166   I        -0.304  -0.295  -0.273  -0.417  -0.400  -0.398  -0.492  -0.461  -0.431
167   W         0.796   0.727   0.631   1.100   0.992   0.862   0.785   0.667   0.475
168   D         1.680   1.697   1.776   1.896   1.912   2.043   1.850   1.873   1.997
169   M        -0.757  -0.859  -0.848  -0.583  -0.734  -0.762  -0.705  -0.820  -0.785
170   G         0.432   0.474   0.477   0.252   0.292   0.294   0.147   0.217   0.187
171   Y        -0.022  -0.167  -0.220   0.286   0.056  -0.012  -0.066  -0.272  -0.349
172   E         0.796   0.727   0.631   1.068   0.946   0.819   0.785   0.667   0.475
173   L         0.796   0.727   0.631   0.632   0.535   0.417   0.785   0.667   0.475
174   T         0.432   0.415   0.454   0.207   0.188   0.220   0.147   0.107   0.141
175   N        -1.381  -1.403  -1.334  -1.169  -1.180  -1.118  -1.130  -1.141  -1.035
176   R        -0.757  -0.791  -0.823  -0.508  -0.576  -0.655  -0.705  -0.748  -0.756
177   G         0.796   0.727   0.631   0.833   0.704   0.580   0.785   0.667   0.475
178   V         0.796   0.727   0.631   0.832   0.745   0.605   0.785   0.667   0.475
179   I         0.432   0.379   0.439   0.434   0.295   0.406   0.147   0.038   0.112
180   K         0.432   0.379   0.439   0.432   0.380   0.430   0.147   0.038   0.112
181   T         1.680   1.697   1.776   1.547   1.580   1.696   1.850   1.873   1.997
182   G         1.680   1.697   1.776   1.639   1.632   1.788   1.850   1.873   1.997
183   S        -0.022  -0.167  -0.220   0.266   0.031  -0.020  -0.066  -0.272  -0.349
184   I        -1.381  -1.373  -1.308  -1.454  -1.418  -1.328  -1.130  -1.115  -1.012
185   V         0.796   0.727   0.631   0.835   0.756   0.610   0.785   0.667   0.475
186   L        -0.022  -0.007  -0.155  -0.104  -0.094  -0.274  -0.066  -0.052  -0.257
187   A         0.432   0.433   0.464   0.032   0.036   0.078   0.147   0.142   0.160
188   G        -0.304  -0.352  -0.290  -0.744  -0.825  -0.727  -0.492  -0.545  -0.458
189   T         0.320   0.343   0.431   0.017   0.072   0.188  -0.066  -0.031   0.097
190   L        -0.928  -0.973  -0.881  -1.208  -1.259  -1.124  -0.917  -0.947  -0.823
191   V        -0.304  -0.210  -0.257  -0.512  -0.378  -0.431  -0.492  -0.369  -0.410
192   L        -1.834  -1.780  -1.704  -1.743  -1.729  -1.559  -1.343  -1.288  -1.175
193   G        -0.022   0.043  -0.170   0.019   0.091  -0.246  -0.066   0.024  -0.277
194   T        -1.381  -1.403  -1.334  -1.417  -1.458  -1.395  -1.130  -1.141  -1.035
195   Y         0.796   0.866   0.654   0.969   1.033   0.759   0.785   0.893   0.516
196   L         0.796   0.814   0.644   0.632   0.649   0.436   0.785   0.811   0.499
197   L        -0.022  -0.029  -0.169  -0.279  -0.289  -0.534  -0.066  -0.085  -0.277
198   A        -0.022  -0.097  -0.208   0.151   0.046  -0.149  -0.066  -0.175  -0.331
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   Q        -1.381  -1.349  -1.315  -0.923  -0.878  -0.813  -1.130  -1.095  -1.018
* 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/Q04487
Output conservation file - output/Q04487
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
