1     M         0.644   0.649   0.667   1.065   1.054   1.026   0.666   0.673   0.700
2     P         0.644   0.649   0.667   0.842   0.842   0.846   0.666   0.673   0.700
3     R        -0.682  -0.824  -0.810  -1.021  -1.221  -1.137  -0.800  -1.030  -1.047
4     A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
5     P         0.644   0.649   0.667   0.849   0.853   0.852   0.666   0.673   0.700
6     R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
7     T        -1.363  -1.608  -1.686  -0.943  -1.283  -1.542  -1.285  -1.569  -1.651
8     Y        -0.609  -0.668  -0.795  -0.216  -0.304  -0.586  -0.691  -0.788  -1.022
9     S         0.644   0.649   0.667   0.768   0.779   0.785   0.666   0.673   0.700
10    K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
11    T         0.644   0.649   0.667   0.937   0.937   0.923   0.666   0.673   0.700
12    Y        -0.609  -0.741  -0.822  -0.296  -0.517  -0.811  -0.691  -0.900  -1.067
13    S        -0.885  -0.974  -0.826  -0.947  -1.127  -0.949  -1.115  -1.273  -1.074
14    T        -1.091  -1.011  -0.827  -1.136  -1.024  -0.758  -1.455  -1.335  -1.075
15    P         0.644   0.649   0.667   0.849   0.853   0.852   0.666   0.673   0.700
16    K        -1.604  -1.650  -1.697  -1.821  -1.962  -1.825  -1.624  -1.705  -1.663
17    R        -0.170  -0.146  -0.785  -0.353  -0.315  -1.029  -0.097  -0.071  -1.007
18    P         0.644   0.649   0.667   0.849   0.853   0.852   0.666   0.673   0.700
19    Y        -1.041  -1.036  -0.830  -0.914  -0.921  -0.657  -1.370  -1.376  -1.079
20    E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
21    S        -0.170  -0.401  -0.792   0.103  -0.174  -0.861  -0.097  -0.403  -1.017
22    S        -0.885  -0.678  -0.799  -1.037  -0.699  -0.913  -1.115  -0.802  -1.030
23    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
24    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
25    D         0.644   0.649   0.667   0.800   0.808   0.811   0.666   0.673   0.700
26    A        -0.170  -0.401  -0.792  -0.058  -0.318  -0.901  -0.097  -0.403  -1.017
27    E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
28    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
29    K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
30    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
31    A        -0.956  -1.165  -1.675  -0.696  -0.941  -1.639  -0.776  -1.032  -1.638
32    G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
33    E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
34    F        -1.041  -0.908  -0.822  -0.914  -0.687  -0.641  -1.370  -1.164  -1.066
35    G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
36    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
37    K        -0.885  -0.974  -0.826  -1.256  -1.464  -1.244  -1.115  -1.273  -1.074
38    N         0.644   0.649   0.667   0.999   0.995   0.973   0.666   0.673   0.700
39    K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
40    R        -0.609  -0.668  -0.795  -0.860  -0.925  -1.006  -0.691  -0.788  -1.022
41    E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
42    I        -0.170  -0.401  -0.792   0.149  -0.123  -0.766  -0.097  -0.403  -1.017
43    Y        -0.885  -0.974  -0.826  -0.556  -0.696  -0.533  -1.115  -1.273  -1.074
44    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
45    I        -0.885  -0.974  -0.826  -0.848  -1.020  -0.832  -1.115  -1.273  -1.074
46    S        -2.560  -2.638  -2.322  -2.550  -2.680  -2.299  -2.303  -2.335  -1.966
47    F        -1.041  -1.036  -0.829  -1.243  -1.320  -0.997  -1.370  -1.376  -1.079
48    Q        -0.885  -0.974  -0.826  -0.654  -0.816  -0.651  -1.115  -1.273  -1.074
49    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
50    S         0.644   0.649   0.667   0.768   0.779   0.785   0.666   0.673   0.700
51    K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
52    I         0.644   0.649   0.667   0.796   0.804   0.809   0.666   0.673   0.700
53    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
54    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
55    A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
56    A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
57    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
58    D        -1.604  -1.781  -1.696  -1.475  -1.698  -1.578  -1.624  -1.804  -1.662
59    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
60    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
61    T         0.644   0.649   0.667   0.937   0.937   0.923   0.666   0.673   0.700
62    R        -0.885  -0.974  -0.826  -1.507  -1.689  -1.386  -1.115  -1.273  -1.074
63    D         0.644   0.649   0.667   0.800   0.808   0.811   0.666   0.673   0.700
64    E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
65    K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
66    D         0.644   0.649   0.667   0.800   0.808   0.811   0.666   0.673   0.700
67    P         0.644   0.649   0.667   0.849   0.853   0.852   0.666   0.673   0.700
68    K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
69    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
70    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
71    F         0.644   0.649   0.667   0.913   0.910   0.903   0.666   0.673   0.700
72    E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
73    G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
74    N         0.644   0.649   0.667   0.999   0.995   0.973   0.666   0.673   0.700
75    A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
76    L        -0.609  -0.668  -0.795  -0.817  -0.895  -1.040  -0.691  -0.788  -1.022
77    I         0.644   0.649   0.667   0.796   0.804   0.809   0.666   0.673   0.700
78    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
79    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
80    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
81    V         0.644   0.649   0.667   0.750   0.742   0.771   0.666   0.673   0.700
82    R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
83    V        -2.560  -2.525  -2.320  -2.549  -2.538  -2.136  -2.303  -2.259  -1.964
84    G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
85    V        -0.609  -0.668  -0.795  -0.443  -0.540  -0.781  -0.691  -0.788  -1.022
86    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
87    S        -1.604  -1.650  -1.697  -1.420  -1.502  -1.521  -1.624  -1.705  -1.663
88    E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
89    D        -1.363  -1.552  -1.692  -0.999  -1.267  -1.476  -1.285  -1.533  -1.657
90    K        -1.041  -1.036  -0.829  -1.606  -1.641  -1.267  -1.370  -1.376  -1.079
91    K        -1.041  -0.884  -0.811  -1.004  -0.691  -0.712  -1.370  -1.125  -1.048
92    K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
93    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
94    D         0.644   0.649   0.667   0.800   0.808   0.811   0.666   0.673   0.700
95    Y         0.644   0.649   0.667   0.951   0.952   0.934   0.666   0.673   0.700
96    V         0.644   0.649   0.667   0.750   0.742   0.771   0.666   0.673   0.700
97    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
98    A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
99    L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
100   K        -2.082  -2.094  -2.306  -1.984  -2.025  -2.248  -1.794  -1.818  -1.951
101   V        -2.560  -2.561  -2.318  -2.342  -2.318  -2.048  -2.303  -2.265  -1.962
102   E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
103   D         0.644   0.649   0.667   0.800   0.808   0.811   0.666   0.673   0.700
104   F         0.644   0.649   0.667   0.913   0.910   0.903   0.666   0.673   0.700
105   L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
106   E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
107   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
108   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
109   L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
110   Q         0.644   0.649   0.667   0.927   0.921   0.914   0.666   0.673   0.700
111   T         0.644   0.649   0.667   0.937   0.937   0.923   0.666   0.673   0.700
112   Q        -0.170  -0.401  -0.792   0.321   0.059  -0.504  -0.097  -0.403  -1.017
113   V         0.644   0.649   0.667   0.750   0.742   0.771   0.666   0.673   0.700
114   Y        -1.091  -1.034  -0.830  -1.012  -0.920  -0.657  -1.455  -1.374  -1.079
115   K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
116   L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
117   G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
118   L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
119   A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
120   K        -0.609  -0.512  -0.801  -0.751  -0.588  -1.175  -0.691  -0.559  -1.033
121   S         0.644   0.649   0.667   0.768   0.779   0.785   0.666   0.673   0.700
122   V        -1.041  -0.884  -0.811  -1.134  -0.854  -0.802  -1.370  -1.125  -1.048
123   H         0.644   0.649   0.667   0.989   0.981   0.965   0.666   0.673   0.700
124   H         0.644   0.649   0.667   0.989   0.981   0.965   0.666   0.673   0.700
125   A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
126   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
127   V         0.644   0.649   0.667   0.750   0.742   0.771   0.666   0.673   0.700
128   L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
129   I         0.644   0.649   0.667   0.796   0.804   0.809   0.666   0.673   0.700
130   T        -2.412  -2.536  -2.319  -1.998  -2.215  -2.072  -2.133  -2.233  -1.963
131   Q         0.644   0.649   0.667   0.927   0.921   0.914   0.666   0.673   0.700
132   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
133   H         0.644   0.649   0.667   0.989   0.981   0.965   0.666   0.673   0.700
134   I         0.644   0.649   0.667   0.796   0.804   0.809   0.666   0.673   0.700
135   A        -1.041  -1.036  -0.829  -1.590  -1.629  -1.255  -1.370  -1.376  -1.079
136   V         0.644   0.649   0.667   0.750   0.742   0.771   0.666   0.673   0.700
137   G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
138   K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
139   Q         0.644   0.649   0.667   0.927   0.921   0.914   0.666   0.673   0.700
140   I         0.644   0.649   0.667   0.796   0.804   0.809   0.666   0.673   0.700
141   V         0.644   0.649   0.667   0.750   0.742   0.771   0.666   0.673   0.700
142   N         0.644   0.649   0.667   0.999   0.995   0.973   0.666   0.673   0.700
143   I        -1.091  -0.995  -0.823  -1.238  -1.077  -0.829  -1.455  -1.308  -1.068
144   P         0.644   0.649   0.667   0.849   0.853   0.852   0.666   0.673   0.700
145   S         0.644   0.649   0.667   0.768   0.779   0.785   0.666   0.673   0.700
146   F         0.644   0.649   0.667   0.913   0.910   0.903   0.666   0.673   0.700
147   M        -1.604  -1.566  -1.692  -1.164  -1.221  -1.345  -1.624  -1.634  -1.658
148   V         0.644   0.649   0.667   0.750   0.742   0.771   0.666   0.673   0.700
149   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
150   L         0.644   0.649   0.667   0.370   0.378   0.463   0.666   0.673   0.700
151   D        -0.609  -0.544  -0.814  -0.445  -0.346  -0.889  -0.691  -0.604  -1.054
152   S        -0.956  -1.059  -1.670  -0.518  -0.625  -1.532  -0.776  -0.898  -1.632
153   E        -1.041  -0.884  -0.811  -1.113  -0.810  -0.796  -1.370  -1.125  -1.048
154   K         0.644   0.649   0.667   0.568   0.586   0.624   0.666   0.673   0.700
155   H         0.644   0.649   0.667   0.989   0.981   0.965   0.666   0.673   0.700
156   I         0.644   0.649   0.667   0.796   0.804   0.809   0.666   0.673   0.700
157   D         0.644   0.649   0.667   0.800   0.808   0.811   0.666   0.673   0.700
158   F         0.644   0.649   0.667   0.913   0.910   0.903   0.666   0.673   0.700
159   A         0.644   0.649   0.667   0.587   0.601   0.639   0.666   0.673   0.700
160   P        -2.560  -2.311  -2.315  -2.634  -2.311  -2.287  -2.303  -2.040  -1.959
161   T        -1.934  -1.903  -1.695  -1.627  -1.581  -1.366  -1.964  -1.921  -1.661
162   S         0.644   0.649   0.667   0.768   0.779   0.785   0.666   0.673   0.700
163   P         0.644   0.649   0.667   0.849   0.853   0.852   0.666   0.673   0.700
164   F        -1.091  -1.034  -0.830  -1.012  -0.918  -0.656  -1.455  -1.374  -1.079
165   G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
166   G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
167   A        -1.041  -0.884  -0.811  -1.300  -0.999  -0.941  -1.370  -1.125  -1.048
168   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
169   P        -0.609  -0.512  -0.801  -0.396  -0.255  -0.825  -0.691  -0.559  -1.033
170   G         0.644   0.649   0.667   0.710   0.715   0.739   0.666   0.673   0.700
171   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
172   V        -0.609  -0.668  -0.795  -0.360  -0.447  -0.623  -0.691  -0.788  -1.022
173   A        -1.718  -1.770  -1.689  -2.019  -2.031  -1.985  -1.794  -1.788  -1.655
174   R         0.644   0.649   0.667   0.274   0.289   0.385   0.666   0.673   0.700
175   R        -0.609  -0.520  -0.813  -0.751  -0.601  -1.207  -0.691  -0.570  -1.053
176   N        -1.604  -1.766  -1.691  -1.479  -1.740  -1.770  -1.624  -1.782  -1.657
177   A        -2.691  -2.505  -2.310  -2.745  -2.497  -2.197  -2.388  -2.203  -1.955
178   A        -3.601  -3.579  -3.201  -3.437  -3.446  -2.790  -2.727  -2.673  -2.266
179   R        -2.412  -2.403  -2.315  -2.457  -2.458  -2.410  -2.133  -2.145  -1.959
180   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   A        -2.106  -2.000  -1.696  -2.170  -2.011  -1.598  -2.162  -2.036  -1.662
182   E         0.644   0.649   0.667   0.590   0.600   0.642   0.666   0.673   0.700
183   A        -1.363  -1.224  -1.674  -1.159  -0.950  -1.649  -1.285  -1.110  -1.637
184   S        -0.956  -0.846  -1.666  -0.597  -0.468  -1.633  -0.776  -0.656  -1.627
185   G        -2.412  -2.205  -2.308  -2.290  -1.976  -2.114  -2.133  -1.905  -1.954
186   E        -2.393  -2.451  -2.315  -2.300  -2.408  -2.209  -2.118  -2.159  -1.960
187   A        -2.553  -2.461  -2.324  -2.554  -2.383  -2.214  -2.277  -2.188  -1.967
188   A        -0.609  -0.668  -0.795  -0.625  -0.704  -0.934  -0.691  -0.788  -1.022
189   E        -0.229  -0.088  -0.783  -0.124   0.037  -0.874  -0.172   0.001  -1.002
190   E         0.644   0.649   0.667   0.577   0.586   0.631   0.666   0.673   0.700
191   A        -0.854  -0.916  -0.827  -1.063  -1.177  -1.064  -1.065  -1.177  -1.075
192   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   D        -1.041  -1.002  -0.828  -1.223  -1.159  -0.923  -1.370  -1.319  -1.076
194   E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
195   E         0.644   0.649   0.667   0.587   0.594   0.639   0.666   0.673   0.700
* 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/P05755
Output conservation file - output/P05755
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
