1     M         1.289   1.313   1.377   1.459   1.488   1.584   1.374   1.404   1.498
2     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    T        -0.569  -0.555  -0.476  -0.668  -0.658  -0.522  -0.780  -0.760  -0.647
13    H        -1.087  -1.053  -0.958  -1.073  -0.997  -0.847  -1.115  -1.058  -0.919
14    N        -1.346  -1.299  -1.320  -1.329  -1.252  -1.290  -1.158  -1.096  -1.070
15    F        -0.418  -0.516  -0.451  -0.455  -0.583  -0.471  -0.596  -0.710  -0.619
16    Q        -0.993  -1.009  -0.949  -0.943  -0.945  -0.876  -1.018  -1.018  -0.911
17    R         1.289   1.313   1.377   1.380   1.412   1.510   1.374   1.404   1.498
18    K         0.556   0.630   0.376   0.584   0.684   0.344   0.530   0.639   0.202
19    I         0.556   0.678   0.385   0.470   0.636   0.227   0.530   0.708   0.219
20    A         0.556   0.458   0.355   0.629   0.501   0.303   0.530   0.370   0.166
21    L        -0.134  -0.187  -0.361  -0.177  -0.259  -0.549  -0.173  -0.251  -0.490
22    I        -0.418  -0.516  -0.447  -0.643  -0.814  -0.703  -0.596  -0.711  -0.615
23    G         1.289   1.313   1.377   1.287   1.317   1.424   1.374   1.404   1.498
24    A         0.556   0.438   0.347   0.541   0.401   0.246   0.530   0.337   0.151
25    R         1.289   1.313   1.377   1.380   1.412   1.510   1.374   1.404   1.498
26    N        -0.418  -0.424  -0.450  -0.534  -0.552  -0.565  -0.596  -0.625  -0.619
27    V         1.289   1.313   1.377   1.166   1.209   1.310   1.374   1.404   1.498
28    G         1.289   1.313   1.377   1.287   1.317   1.424   1.374   1.404   1.498
29    K         1.289   1.313   1.377   1.225   1.263   1.365   1.374   1.404   1.498
30    T         0.220   0.135   0.209   0.042  -0.099   0.004  -0.033  -0.199  -0.105
31    T         0.220   0.135   0.209   0.042  -0.099   0.004  -0.033  -0.199  -0.105
32    L        -0.418  -0.239  -0.398  -0.479  -0.242  -0.451  -0.596  -0.346  -0.546
33    T        -0.134  -0.169  -0.351  -0.006  -0.068  -0.349  -0.173  -0.226  -0.477
34    V         1.289   1.313   1.377   1.166   1.209   1.310   1.374   1.404   1.498
35    R         0.069   0.097   0.195  -0.032   0.013   0.157  -0.314  -0.272  -0.131
36    F        -0.418  -0.423  -0.409  -0.333  -0.335  -0.335  -0.596  -0.574  -0.562
37    V         0.556   0.458   0.355   0.512   0.391   0.232   0.530   0.370   0.166
38    E         0.556   0.634   0.373   0.517   0.625   0.276   0.530   0.645   0.197
39    S        -1.480  -1.338  -1.342  -1.417  -1.221  -1.210  -1.299  -1.141  -1.090
40    R         0.556   0.438   0.347   0.841   0.687   0.527   0.530   0.337   0.151
41    F         1.289   1.313   1.377   1.391   1.427   1.521   1.374   1.404   1.498
42    V         1.289   1.313   1.377   1.166   1.209   1.310   1.374   1.404   1.498
43    E         1.289   1.313   1.377   1.162   1.203   1.306   1.374   1.404   1.498
44    S         0.556   0.678   0.385   0.526   0.697   0.278   0.530   0.708   0.219
45    Y         1.289   1.313   1.377   1.406   1.448   1.535   1.374   1.404   1.498
46    Y         1.289   1.313   1.377   1.406   1.448   1.535   1.374   1.404   1.498
47    P         1.289   1.313   1.377   1.466   1.502   1.591   1.374   1.404   1.498
48    T         1.289   1.313   1.377   1.303   1.341   1.438   1.374   1.404   1.498
49    I         1.289   1.313   1.377   1.138   1.184   1.284   1.374   1.404   1.498
50    E         1.289   1.313   1.377   1.162   1.203   1.306   1.374   1.404   1.498
51    N         1.289   1.313   1.377   1.311   1.350   1.446   1.374   1.404   1.498
52    E        -0.418  -0.455  -0.428  -0.412  -0.454  -0.458  -0.596  -0.619  -0.586
53    F         1.289   1.313   1.377   1.391   1.427   1.521   1.374   1.404   1.498
54    T        -0.134  -0.335  -0.393  -0.132  -0.418  -0.548  -0.173  -0.448  -0.535
55    R        -0.134  -0.335  -0.393  -0.016  -0.278  -0.350  -0.173  -0.448  -0.535
56    I        -1.480  -1.413  -1.335  -1.590  -1.506  -1.381  -1.299  -1.215  -1.085
57    I         0.556   0.458   0.355   0.499   0.386   0.240   0.530   0.370   0.166
58    P        -1.480  -1.414  -1.337  -1.459  -1.346  -1.212  -1.299  -1.215  -1.086
59    Y        -0.772  -0.715  -0.873  -0.447  -0.396  -0.603  -0.736  -0.667  -0.825
60    K         0.556   0.684   0.380   0.572   0.739   0.328   0.530   0.718   0.210
61    S        -0.993  -1.077  -0.955  -1.024  -1.160  -0.988  -1.018  -1.076  -0.916
62    H        -0.772  -0.894  -0.923  -0.499  -0.647  -0.733  -0.736  -0.874  -0.880
63    D        -0.418  -0.441  -0.426  -0.452  -0.462  -0.481  -0.596  -0.601  -0.584
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    C        -0.418  -0.516  -0.447  -0.263  -0.390  -0.295  -0.596  -0.711  -0.615
70    T        -0.993  -1.013  -0.948  -0.990  -1.013  -0.932  -1.018  -1.023  -0.910
71    L        -0.639  -0.586  -0.486  -0.909  -0.842  -0.680  -0.877  -0.803  -0.662
72    E         0.556   0.458   0.355   0.517   0.397   0.248   0.530   0.370   0.166
73    I         1.289   1.313   1.377   1.138   1.184   1.284   1.374   1.404   1.498
74    L        -0.639  -0.594  -0.491  -1.006  -0.946  -0.781  -0.877  -0.808  -0.668
75    D         1.289   1.313   1.377   1.357   1.393   1.489   1.374   1.404   1.498
76    T         1.289   1.313   1.377   1.303   1.341   1.438   1.374   1.404   1.498
77    A         0.556   0.458   0.355   0.638   0.514   0.322   0.530   0.370   0.166
78    G         1.289   1.313   1.377   1.287   1.317   1.424   1.374   1.404   1.498
79    Q         1.289   1.313   1.377   1.368   1.414   1.499   1.374   1.404   1.498
80    D         1.289   1.313   1.377   1.357   1.393   1.489   1.374   1.404   1.498
81    E         1.289   1.313   1.377   1.162   1.203   1.306   1.374   1.404   1.498
82    V        -0.418  -0.455  -0.428  -0.345  -0.395  -0.388  -0.596  -0.619  -0.586
83    S         1.289   1.313   1.377   1.194   1.245   1.336   1.374   1.404   1.498
84    L        -0.418  -0.497  -0.444  -0.592  -0.699  -0.592  -0.596  -0.686  -0.611
85    L        -0.505  -0.528  -0.447  -0.589  -0.656  -0.516  -0.736  -0.734  -0.614
86    N         1.289   1.313   1.377   1.311   1.350   1.446   1.374   1.404   1.498
87    I        -1.480  -1.491  -1.358  -1.605  -1.601  -1.394  -1.299  -1.276  -1.103
88    K         1.289   1.313   1.377   1.225   1.263   1.365   1.374   1.404   1.498
89    S         0.220   0.135   0.209   0.278   0.093   0.165  -0.033  -0.199  -0.105
90    L        -0.772  -0.757  -0.890  -0.651  -0.645  -0.811  -0.736  -0.713  -0.843
91    T        -0.418  -0.516  -0.451  -0.630  -0.779  -0.663  -0.596  -0.710  -0.619
92    G         1.289   1.313   1.377   1.287   1.317   1.424   1.374   1.404   1.498
93    V         0.069   0.087   0.196  -0.358  -0.324  -0.147  -0.314  -0.291  -0.130
94    R        -0.134  -0.335  -0.393   0.203  -0.085  -0.215  -0.173  -0.448  -0.535
95    G         1.289   1.313   1.377   1.287   1.317   1.424   1.374   1.404   1.498
96    I        -0.134  -0.335  -0.393   0.120  -0.168  -0.290  -0.173  -0.448  -0.535
97    I        -0.993  -0.924  -0.950  -1.125  -1.076  -1.044  -1.018  -0.940  -0.911
98    L         1.289   1.313   1.377   1.221   1.234   1.362   1.374   1.404   1.498
99    C        -0.772  -0.858  -0.913  -0.687  -0.776  -0.856  -0.736  -0.837  -0.869
100   Y         1.289   1.313   1.377   1.406   1.448   1.535   1.374   1.404   1.498
101   S         1.289   1.313   1.377   1.194   1.245   1.336   1.374   1.404   1.498
102   I         0.220   0.197   0.220  -0.049  -0.094  -0.095  -0.033  -0.084  -0.085
103   I        -0.772  -0.893  -0.921  -0.669  -0.870  -0.959  -0.736  -0.873  -0.878
104   N         0.220   0.135   0.209   0.045  -0.094   0.008  -0.033  -0.199  -0.105
105   R        -0.772  -0.578  -0.858  -0.554  -0.285  -0.720  -0.736  -0.493  -0.807
106   A        -1.126  -1.106  -0.967  -1.140  -1.062  -0.879  -1.158  -1.106  -0.928
107   S         0.556   0.634   0.375   0.539   0.658   0.288   0.530   0.644   0.200
108   F         1.289   1.313   1.377   1.391   1.427   1.521   1.374   1.404   1.498
109   D         0.220   0.198   0.221   0.033  -0.002   0.030  -0.033  -0.082  -0.082
110   L        -1.480  -1.409  -1.339  -1.448  -1.395  -1.274  -1.299  -1.212  -1.088
111   I        -0.418  -0.372  -0.422  -0.663  -0.605  -0.678  -0.596  -0.539  -0.582
112   P        -1.126  -1.050  -0.966  -1.185  -1.057  -0.923  -1.158  -1.061  -0.928
113   I        -0.993  -0.925  -0.920  -1.186  -1.085  -1.044  -1.018  -0.923  -0.880
114   L        -0.134  -0.190  -0.356  -0.200  -0.285  -0.554  -0.173  -0.256  -0.484
115   W        -0.134  -0.187  -0.358   0.168   0.100  -0.117  -0.173  -0.252  -0.486
116   D         1.289   1.313   1.377   1.357   1.393   1.489   1.374   1.404   1.498
117   K         1.289   1.313   1.377   1.225   1.263   1.365   1.374   1.404   1.498
118   L        -0.134  -0.335  -0.393  -0.139  -0.418  -0.494  -0.173  -0.448  -0.535
119   V         0.556   0.438   0.347   0.544   0.356   0.217   0.530   0.337   0.151
120   D         0.220   0.135   0.209   0.174   0.021   0.125  -0.033  -0.199  -0.105
121   Q        -1.480  -1.491  -1.358  -1.275  -1.245  -1.076  -1.299  -1.276  -1.103
122   L        -0.639  -0.511  -0.458  -0.931  -0.722  -0.637  -0.877  -0.694  -0.624
123   G         1.289   1.313   1.377   1.287   1.317   1.424   1.374   1.404   1.498
124   K        -1.346  -1.363  -1.331  -1.254  -1.324  -1.282  -1.158  -1.163  -1.079
125   D        -0.993  -0.958  -0.927  -1.056  -0.990  -0.974  -1.018  -0.954  -0.888
126   N        -1.480  -1.408  -1.337  -1.406  -1.306  -1.169  -1.299  -1.209  -1.086
127   L        -0.639  -0.607  -0.494  -1.029  -0.980  -0.791  -0.877  -0.827  -0.672
128   P         1.289   1.313   1.377   1.466   1.502   1.591   1.374   1.404   1.498
129   V        -0.993  -1.009  -0.946  -1.079  -1.104  -0.991  -1.018  -1.018  -0.908
130   I        -0.134  -0.187  -0.361  -0.117  -0.204  -0.434  -0.173  -0.251  -0.490
131   L        -0.418  -0.304  -0.414  -0.623  -0.452  -0.633  -0.596  -0.430  -0.568
132   V         0.556   0.678   0.385   0.484   0.655   0.225   0.530   0.708   0.219
133   G         1.289   1.313   1.377   1.287   1.317   1.424   1.374   1.404   1.498
134   T         0.556   0.438   0.347   0.656   0.502   0.347   0.530   0.337   0.151
135   K         1.289   1.313   1.377   1.225   1.263   1.365   1.374   1.404   1.498
136   A        -0.772  -0.858  -0.913  -0.748  -0.884  -0.981  -0.736  -0.837  -0.869
137   D         1.289   1.313   1.377   1.357   1.393   1.489   1.374   1.404   1.498
138   L         1.289   1.313   1.377   1.221   1.234   1.362   1.374   1.404   1.498
139   G        -1.834  -1.712  -1.655  -1.520  -1.367  -1.274  -1.440  -1.316  -1.203
140   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   V        -1.499  -1.468  -1.365  -1.417  -1.405  -1.263  -1.307  -1.256  -1.108
146   K         0.484   0.309   0.295   0.599   0.337   0.271   0.417   0.117   0.056
147   R         1.289   1.313   1.377   1.380   1.412   1.510   1.374   1.404   1.498
148   C        -0.134  -0.190  -0.356   0.115   0.054  -0.199  -0.173  -0.256  -0.484
149   V         1.289   1.313   1.377   1.166   1.209   1.310   1.374   1.404   1.498
150   T        -0.639  -0.564  -0.475  -0.911  -0.772  -0.661  -0.877  -0.771  -0.648
151   K        -1.834  -1.808  -1.677  -1.628  -1.590  -1.407  -1.440  -1.389  -1.218
152   A        -0.772  -0.858  -0.913  -0.760  -0.898  -0.973  -0.736  -0.837  -0.869
153   E        -0.134   0.036  -0.319  -0.106   0.120  -0.349  -0.173   0.059  -0.433
154   G         0.556   0.634   0.375   0.634   0.733   0.375   0.530   0.644   0.200
155   E        -0.639  -0.586  -0.486  -0.880  -0.822  -0.655  -0.877  -0.803  -0.662
156   K        -0.505  -0.545  -0.446  -0.721  -0.764  -0.613  -0.736  -0.755  -0.614
157   L         1.289   1.313   1.377   1.221   1.234   1.362   1.374   1.404   1.498
158   A         1.289   1.313   1.377   1.311   1.356   1.446   1.374   1.404   1.498
159   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   K        -0.772  -0.620  -0.871  -0.711  -0.487  -0.879  -0.736  -0.542  -0.823
167   R        -1.126  -1.023  -0.969  -1.294  -1.090  -1.044  -1.158  -1.029  -0.931
168   N        -1.480  -1.491  -1.353  -1.172  -1.221  -1.013  -1.299  -1.276  -1.099
169   Q        -0.993  -0.937  -0.930  -1.023  -0.930  -0.904  -1.018  -0.937  -0.890
170   A        -0.772  -0.736  -0.877  -0.387  -0.361  -0.586  -0.736  -0.693  -0.829
171   A        -0.772  -0.681  -0.874  -0.602  -0.482  -0.774  -0.736  -0.629  -0.825
172   F         0.220   0.302   0.267   0.322   0.446   0.385  -0.033   0.105   0.004
173   I        -1.126  -1.113  -0.970  -1.361  -1.355  -1.126  -1.158  -1.113  -0.931
174   E         1.289   1.313   1.377   1.162   1.203   1.306   1.374   1.404   1.498
175   C        -0.993  -1.077  -0.959  -0.952  -1.053  -0.889  -1.018  -1.076  -0.920
176   S         0.556   0.458   0.355   0.575   0.473   0.333   0.530   0.370   0.166
177   A         0.069   0.110   0.204  -0.212  -0.130   0.001  -0.314  -0.246  -0.114
178   E        -0.134  -0.335  -0.393   0.042  -0.275  -0.415  -0.173  -0.448  -0.535
179   L        -1.834  -1.790  -1.669  -1.563  -1.524  -1.338  -1.440  -1.378  -1.213
180   D        -0.639  -0.625  -0.498  -0.756  -0.742  -0.545  -0.877  -0.849  -0.676
181   Y        -1.834  -1.773  -1.672  -1.891  -1.760  -1.648  -1.440  -1.366  -1.215
182   N         0.556   0.458   0.355   0.654   0.525   0.355   0.530   0.370   0.166
183   V         0.220   0.226   0.233  -0.049  -0.037  -0.065  -0.033  -0.030  -0.058
184   E        -0.505  -0.394  -0.435  -0.688  -0.542  -0.550  -0.736  -0.596  -0.601
185   E        -1.480  -1.476  -1.351  -1.393  -1.390  -1.199  -1.299  -1.267  -1.097
186   T        -0.134  -0.335  -0.393   0.049  -0.219  -0.321  -0.173  -0.448  -0.535
187   F         1.289   1.313   1.377   1.391   1.427   1.521   1.374   1.404   1.498
188   M        -0.134  -0.335  -0.393  -0.114  -0.388  -0.473  -0.173  -0.448  -0.535
189   L        -0.418  -0.327  -0.418  -0.540  -0.434  -0.544  -0.596  -0.483  -0.577
190   L         0.556   0.630   0.376   0.539   0.620   0.258   0.530   0.639   0.202
191   L        -0.134  -0.187  -0.358  -0.200  -0.281  -0.557  -0.173  -0.252  -0.486
192   K        -1.834  -1.808  -1.677  -1.718  -1.684  -1.526  -1.440  -1.389  -1.218
193   Q        -0.134  -0.335  -0.393  -0.133  -0.412  -0.511  -0.173  -0.448  -0.535
194   M        -0.134  -0.187  -0.361  -0.150  -0.204  -0.468  -0.173  -0.251  -0.490
195   E         1.289   1.313   1.377   1.162   1.203   1.306   1.374   1.404   1.498
196   R        -0.772  -0.863  -0.907  -0.664  -0.805  -0.860  -0.736  -0.842  -0.863
197   V        -1.834  -1.808  -1.677  -1.813  -1.746  -1.557  -1.440  -1.389  -1.218
198   E        -0.993  -0.924  -0.950  -0.989  -0.931  -0.940  -1.018  -0.940  -0.911
199   G        -0.134  -0.335  -0.393   0.024  -0.263  -0.370  -0.173  -0.448  -0.535
200   T        -0.772  -0.894  -0.923  -0.472  -0.678  -0.772  -0.736  -0.874  -0.880
201   L        -1.346  -1.366  -1.325  -1.179  -1.250  -1.171  -1.158  -1.165  -1.074
202   G        -1.834  -1.808  -1.677  -1.697  -1.651  -1.429  -1.440  -1.389  -1.218
203   L        -1.499  -1.472  -1.353  -1.324  -1.331  -1.149  -1.307  -1.259  -1.099
204   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
205   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
206   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
207   E        -1.480  -1.428  -1.339  -1.506  -1.438  -1.287  -1.299  -1.224  -1.087
208   N        -0.772  -0.771  -0.897  -0.562  -0.560  -0.791  -0.736  -0.732  -0.851
209   N        -1.346  -1.227  -1.295  -1.169  -1.015  -1.113  -1.158  -1.026  -1.047
210   N        -1.480  -1.419  -1.340  -1.533  -1.450  -1.300  -1.299  -1.221  -1.089
211   K        -0.418  -0.378  -0.430  -0.516  -0.473  -0.527  -0.596  -0.549  -0.593
212   C         1.289   1.313   1.377   1.511   1.538   1.633   1.374   1.404   1.498
213   S        -1.126  -1.007  -0.969  -1.434  -1.225  -1.163  -1.158  -1.018  -0.931
214   I         0.220   0.304   0.255  -0.065   0.088  -0.032  -0.033   0.109  -0.019
215   M         0.556   0.630   0.376   0.804   0.899   0.529   0.530   0.639   0.202
* 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/P25378
Output conservation file - output/P25378
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
