1     M         0.673   0.676   0.717   0.903   0.910   0.941   0.705   0.710   0.764
2     N         0.673   0.676   0.717   0.676   0.685   0.743   0.705   0.710   0.764
3     S        -2.225  -2.203  -1.927  -2.200  -2.173  -1.771  -2.128  -2.107  -1.734
4     E         0.673   0.676   0.717   0.707   0.711   0.770   0.705   0.710   0.764
5     Y         0.673   0.676   0.717   0.772   0.780   0.827   0.705   0.710   0.764
6     D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
7     Y         0.673   0.676   0.717   0.772   0.780   0.827   0.705   0.710   0.764
8     L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
9     F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
10    K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
11    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
12    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
13    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
14    I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
15    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
16    N        -0.503  -0.464  -0.569  -0.591  -0.535  -0.712  -0.711  -0.651  -0.837
17    S         0.673   0.676   0.717   0.565   0.571   0.645   0.705   0.710   0.764
18    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
19    V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
20    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
21    K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
22    S         0.673   0.676   0.717   0.565   0.571   0.645   0.705   0.710   0.764
23    C         0.673   0.676   0.717   0.923   0.928   0.959   0.705   0.710   0.764
24    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
25    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
26    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
27    R         0.673   0.676   0.717   0.806   0.812   0.856   0.705   0.710   0.764
28    F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
29    S        -0.503  -0.464  -0.569  -0.546  -0.481  -0.705  -0.711  -0.651  -0.837
30    D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
31    D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
32    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
33    Y         0.673   0.676   0.717   0.772   0.780   0.827   0.705   0.710   0.764
34    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
35    N        -2.089  -2.063  -1.925  -1.907  -1.890  -1.689  -2.010  -1.981  -1.732
36    D        -0.710  -0.717  -0.602  -1.001  -1.023  -0.836  -1.065  -1.081  -0.895
37    Y         0.673   0.676   0.717   0.772   0.780   0.827   0.705   0.710   0.764
38    I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
39    S         0.673   0.676   0.717   0.565   0.571   0.645   0.705   0.710   0.764
40    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
41    I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
42    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
43    V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
44    D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
45    F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
46    K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
47    I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
48    K        -0.710  -0.721  -0.603  -0.799  -0.830  -0.674  -1.065  -1.088  -0.896
49    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
50    V        -1.952  -1.962  -1.920  -1.921  -1.942  -1.836  -1.892  -1.898  -1.728
51    E         0.673   0.676   0.717   0.707   0.711   0.770   0.705   0.710   0.764
52    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
53    D        -0.503  -0.521  -0.584  -0.581  -0.615  -0.721  -0.711  -0.744  -0.863
54    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
55    K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
56    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
57    V        -0.503  -0.418  -0.565  -0.559  -0.437  -0.682  -0.711  -0.577  -0.830
58    K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
59    L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
60    Q         0.673   0.676   0.717   0.786   0.793   0.839   0.705   0.710   0.764
61    I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
62    W         0.673   0.676   0.717   0.959   0.964   0.990   0.705   0.710   0.764
63    D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
64    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
65    A         0.673   0.676   0.717   0.683   0.693   0.749   0.705   0.710   0.764
66    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
67    Q         0.673   0.676   0.717   0.786   0.793   0.839   0.705   0.710   0.764
68    E         0.673   0.676   0.717   0.707   0.711   0.770   0.705   0.710   0.764
69    R         0.673   0.676   0.717   0.806   0.812   0.856   0.705   0.710   0.764
70    F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
71    R         0.673   0.676   0.717   0.806   0.812   0.856   0.705   0.710   0.764
72    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
73    I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
74    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
75    S         0.673   0.676   0.717   0.565   0.571   0.645   0.705   0.710   0.764
76    S         0.673   0.676   0.717   0.565   0.571   0.645   0.705   0.710   0.764
77    Y         0.673   0.676   0.717   0.772   0.780   0.827   0.705   0.710   0.764
78    Y         0.673   0.676   0.717   0.772   0.780   0.827   0.705   0.710   0.764
79    R         0.673   0.676   0.717   0.806   0.812   0.856   0.705   0.710   0.764
80    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
81    S        -0.503  -0.464  -0.569  -0.546  -0.481  -0.705  -0.711  -0.651  -0.837
82    H         0.673   0.676   0.717   0.978   0.983   1.008   0.705   0.710   0.764
83    G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
84    I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
85    I        -0.115  -0.120  -0.546   0.047   0.040  -0.504  -0.121  -0.130  -0.798
86    I        -0.503  -0.512  -0.581  -0.537  -0.558  -0.703  -0.711  -0.730  -0.858
87    V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
88    Y         0.673   0.676   0.717   0.772   0.780   0.827   0.705   0.710   0.764
89    D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
90    V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
91    T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
92    D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
93    Q        -0.115  -0.120  -0.546   0.159   0.155  -0.426  -0.121  -0.130  -0.798
94    E        -0.710  -0.717  -0.602  -0.886  -0.910  -0.740  -1.065  -1.081  -0.895
95    S        -0.115  -0.127  -0.546  -0.111  -0.125  -0.755  -0.121  -0.139  -0.798
96    F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
97    N         0.673   0.676   0.717   0.676   0.685   0.743   0.705   0.710   0.764
98    G        -0.503  -0.464  -0.569  -0.536  -0.474  -0.684  -0.711  -0.651  -0.837
99    V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
100   K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
101   M        -1.501  -1.516  -1.372  -1.416  -1.464  -1.276  -1.655  -1.680  -1.449
102   W         0.673   0.676   0.717   0.959   0.964   0.990   0.705   0.710   0.764
103   L        -0.115  -0.127  -0.546  -0.103  -0.115  -0.667  -0.121  -0.139  -0.798
104   Q        -0.115  -0.127  -0.546   0.170   0.159  -0.392  -0.121  -0.139  -0.798
105   E         0.673   0.676   0.717   0.707   0.711   0.770   0.705   0.710   0.764
106   I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
107   D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
108   R         0.673   0.676   0.717   0.806   0.812   0.856   0.705   0.710   0.764
109   Y        -0.115  -0.228  -0.552   0.129  -0.007  -0.501  -0.121  -0.285  -0.809
110   A        -0.115  -0.228  -0.552   0.016  -0.124  -0.648  -0.121  -0.285  -0.809
111   T        -0.115  -0.136  -0.547  -0.104  -0.131  -0.725  -0.121  -0.152  -0.800
112   S        -2.089  -2.098  -1.924  -2.118  -2.114  -1.866  -2.010  -2.007  -1.732
113   T        -0.503  -0.464  -0.569  -0.611  -0.555  -0.758  -0.711  -0.651  -0.837
114   V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
115   L        -1.590  -1.547  -1.375  -1.702  -1.659  -1.357  -1.773  -1.728  -1.453
116   K        -0.115  -0.136  -0.547  -0.040  -0.067  -0.614  -0.121  -0.152  -0.800
117   L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
118   L         0.673   0.676   0.717   0.540   0.547   0.623   0.705   0.710   0.764
119   V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
120   G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
121   N         0.673   0.676   0.717   0.676   0.685   0.743   0.705   0.710   0.764
122   K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
123   C        -2.089  -2.098  -1.924  -2.008  -2.018  -1.746  -2.010  -2.007  -1.732
124   D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
125   L        -1.209  -1.232  -1.359  -1.173  -1.205  -1.334  -1.301  -1.334  -1.433
126   K        -2.451  -2.386  -2.343  -2.439  -2.339  -2.256  -2.128  -2.064  -1.894
127   D         0.673   0.676   0.717   0.600   0.603   0.676   0.705   0.710   0.764
128   K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
129   R        -0.503  -0.464  -0.569  -0.548  -0.496  -0.646  -0.711  -0.651  -0.837
130   V        -0.115  -0.052  -0.541  -0.025   0.043  -0.640  -0.121  -0.036  -0.789
131   V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
132   E        -0.115  -0.228  -0.552   0.038  -0.110  -0.637  -0.121  -0.285  -0.809
133   Y        -0.115  -0.228  -0.552   0.097  -0.048  -0.605  -0.121  -0.285  -0.809
134   D        -1.863  -1.933  -1.915  -1.875  -1.971  -1.933  -1.773  -1.839  -1.723
135   V        -0.503  -0.418  -0.565  -0.555  -0.432  -0.675  -0.711  -0.577  -0.830
136   A         0.673   0.676   0.717   0.683   0.693   0.749   0.705   0.710   0.764
137   K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
138   E         0.673   0.676   0.717   0.707   0.711   0.770   0.705   0.710   0.764
139   F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
140   A         0.673   0.676   0.717   0.683   0.693   0.749   0.705   0.710   0.764
141   D        -0.115  -0.072  -0.540  -0.054  -0.007  -0.648  -0.121  -0.062  -0.788
142   A        -0.776  -0.760  -0.606  -1.077  -1.056  -0.794  -1.183  -1.159  -0.901
143   N        -1.209  -1.271  -1.357  -1.263  -1.338  -1.452  -1.301  -1.367  -1.430
144   K        -2.089  -2.045  -1.917  -2.182  -2.111  -1.901  -2.010  -1.959  -1.725
145   M        -0.503  -0.464  -0.569  -0.449  -0.397  -0.546  -0.711  -0.651  -0.837
146   P         0.673   0.676   0.717   0.972   0.978   1.002   0.705   0.710   0.764
147   F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
148   L        -0.115  -0.228  -0.552  -0.120  -0.260  -0.734  -0.121  -0.285  -0.809
149   E         0.673   0.676   0.717   0.707   0.711   0.770   0.705   0.710   0.764
150   T         0.673   0.676   0.717   0.561   0.566   0.642   0.705   0.710   0.764
151   S         0.673   0.676   0.717   0.565   0.571   0.645   0.705   0.710   0.764
152   A         0.673   0.676   0.717   0.683   0.693   0.749   0.705   0.710   0.764
153   L        -0.710  -0.717  -0.602  -1.036  -1.055  -0.856  -1.065  -1.081  -0.895
154   D        -1.501  -1.450  -1.363  -1.674  -1.593  -1.471  -1.655  -1.593  -1.438
155   S        -0.503  -0.512  -0.581  -0.623  -0.638  -0.755  -0.711  -0.730  -0.858
156   T        -0.503  -0.568  -0.596  -0.665  -0.780  -0.850  -0.711  -0.824  -0.884
157   N         0.673   0.676   0.717   0.676   0.685   0.743   0.705   0.710   0.764
158   V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
159   E         0.673   0.676   0.717   0.707   0.711   0.770   0.705   0.710   0.764
160   D        -1.209  -1.225  -1.362  -1.031  -1.072  -1.316  -1.301  -1.336  -1.437
161   A         0.673   0.676   0.717   0.683   0.693   0.749   0.705   0.710   0.764
162   F         0.673   0.676   0.717   0.786   0.789   0.839   0.705   0.710   0.764
163   L        -0.503  -0.418  -0.565  -0.617  -0.494  -0.702  -0.711  -0.577  -0.830
164   T        -0.115  -0.228  -0.552  -0.098  -0.241  -0.717  -0.121  -0.285  -0.809
165   M         0.673   0.676   0.717   0.903   0.910   0.941   0.705   0.710   0.764
166   A        -0.865  -0.990  -1.337  -0.662  -0.832  -1.422  -0.829  -0.992  -1.405
167   R        -0.115  -0.228  -0.552   0.136  -0.009  -0.561  -0.121  -0.285  -0.809
168   Q         0.673   0.676   0.717   0.786   0.793   0.839   0.705   0.710   0.764
169   I         0.673   0.676   0.717   0.669   0.674   0.737   0.705   0.710   0.764
170   K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
171   E        -0.503  -0.418  -0.565  -0.484  -0.358  -0.620  -0.711  -0.577  -0.830
172   S        -1.590  -1.547  -1.375  -1.651  -1.600  -1.326  -1.773  -1.728  -1.453
173   M        -0.115  -0.228  -0.552   0.238   0.094  -0.470  -0.121  -0.285  -0.809
174   S        -1.952  -1.990  -1.919  -2.034  -2.079  -1.941  -1.892  -1.922  -1.727
175   Q        -2.451  -2.505  -2.351  -2.251  -2.340  -2.157  -2.128  -2.170  -1.900
176   Q        -1.952  -1.954  -1.920  -1.826  -1.822  -1.785  -1.892  -1.891  -1.728
177   N        -2.587  -2.615  -2.350  -2.483  -2.507  -2.113  -2.246  -2.262  -1.900
178   L        -3.674  -3.645  -3.256  -3.204  -3.177  -2.658  -2.600  -2.582  -2.156
179   N        -2.451  -2.459  -2.345  -2.325  -2.345  -2.218  -2.128  -2.136  -1.896
180   E        -2.587  -2.580  -2.351  -2.535  -2.528  -2.213  -2.246  -2.236  -1.900
181   T        -2.107  -2.093  -1.923  -2.209  -2.206  -1.940  -2.023  -2.008  -1.730
182   T        -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   K        -1.533  -1.592  -1.382  -1.645  -1.713  -1.373  -1.712  -1.778  -1.460
185   K        -0.734  -0.690  -0.599  -0.962  -0.878  -0.757  -1.108  -1.034  -0.890
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   E        -2.451  -2.391  -2.341  -2.277  -2.206  -2.146  -2.128  -2.086  -1.893
188   D        -2.089  -2.060  -1.924  -2.173  -2.133  -1.923  -2.010  -1.979  -1.732
189   K         0.673   0.676   0.717   0.600   0.602   0.676   0.705   0.710   0.764
190   G        -1.501  -1.481  -1.364  -1.679  -1.650  -1.467  -1.655  -1.632  -1.439
191   N        -0.503  -0.517  -0.584  -0.552  -0.577  -0.742  -0.711  -0.738  -0.863
192   V         0.673   0.676   0.717   0.635   0.635   0.706   0.705   0.710   0.764
193   N        -0.115  -0.136  -0.547   0.007  -0.017  -0.651  -0.121  -0.152  -0.800
194   L        -0.503  -0.517  -0.584  -0.663  -0.690  -0.805  -0.711  -0.738  -0.863
195   K        -1.952  -1.959  -1.920  -1.881  -1.905  -1.843  -1.892  -1.895  -1.728
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   G         0.673   0.676   0.717   0.617   0.620   0.691   0.705   0.710   0.764
198   Q        -1.571  -1.545  -1.892  -1.117  -1.088  -1.597  -1.419  -1.393  -1.701
199   S        -1.209  -1.230  -1.359  -1.249  -1.285  -1.462  -1.301  -1.333  -1.433
200   L        -0.710  -0.717  -0.602  -1.017  -1.036  -0.835  -1.065  -1.081  -0.895
201   T        -0.710  -0.717  -0.602  -1.036  -1.055  -0.863  -1.065  -1.081  -0.895
202   N        -2.089  -2.109  -1.915  -2.042  -2.058  -1.802  -2.010  -2.020  -1.724
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   T        -1.209  -1.118  -1.339  -1.217  -1.086  -1.407  -1.301  -1.177  -1.409
205   G        -1.863  -1.861  -1.910  -1.843  -1.842  -1.877  -1.773  -1.771  -1.719
206   G        -1.590  -1.546  -1.366  -1.833  -1.776  -1.477  -1.773  -1.727  -1.443
207   G        -1.364  -1.386  -1.360  -1.540  -1.578  -1.469  -1.537  -1.566  -1.435
208   C         0.673   0.676   0.717   0.923   0.928   0.959   0.705   0.710   0.764
209   C         0.673   0.676   0.717   0.923   0.928   0.959   0.705   0.710   0.764
* 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/P01123
Output conservation file - output/P01123
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
