1     M         1.354   1.370   1.444   1.580   1.603   1.709   1.455   1.480   1.591
2     V         0.585   0.440   0.432   0.610   0.397   0.353   0.516   0.264   0.206
3     K        -0.308  -0.370  -0.295  -0.566  -0.622  -0.514  -0.552  -0.606  -0.500
4     V        -1.195  -1.224  -1.163  -1.075  -1.115  -1.047  -1.080  -1.102  -0.991
5     Y         0.099   0.011  -0.181   0.260   0.138  -0.147   0.082  -0.047  -0.327
6     I        -0.900  -0.842  -0.794  -0.925  -0.837  -0.773  -0.974  -0.910  -0.819
7     H         0.099  -0.020  -0.192   0.386   0.232  -0.032   0.082  -0.087  -0.343
8     D         1.354   1.370   1.444   1.197   1.211   1.342   1.455   1.480   1.591
9     N         0.394   0.354   0.353   0.323   0.245   0.176   0.188   0.109   0.056
10    K        -1.195  -1.224  -1.164  -1.252  -1.291  -1.204  -1.080  -1.100  -0.992
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    V        -0.915  -0.897  -0.821  -0.914  -0.881  -0.807  -0.986  -0.962  -0.845
13    D        -0.825  -0.801  -0.790  -0.737  -0.707  -0.731  -0.890  -0.866  -0.814
14    S        -0.825  -0.847  -0.795  -0.916  -0.931  -0.835  -0.890  -0.904  -0.816
15    D         0.394   0.453   0.407   0.197   0.278   0.207   0.188   0.288   0.159
16    Y        -0.308  -0.306  -0.302  -0.263  -0.259  -0.240  -0.552  -0.554  -0.512
17    R        -0.182  -0.112  -0.239  -0.136  -0.041  -0.181  -0.340  -0.236  -0.413
18    A        -1.602  -1.607  -1.478  -1.661  -1.665  -1.477  -1.291  -1.287  -1.117
19    P        -0.182  -0.116  -0.259  -0.131  -0.021  -0.300  -0.340  -0.243  -0.447
20    H         0.711   0.589   0.488   0.919   0.760   0.596   0.716   0.520   0.310
21    N         0.171   0.190   0.301  -0.160  -0.145   0.041  -0.235  -0.205  -0.045
22    S         0.711   0.740   0.501   0.935   0.973   0.641   0.716   0.760   0.335
23    G         0.711   0.589   0.488   0.857   0.694   0.524   0.716   0.520   0.310
24    T        -0.788  -0.844  -0.778  -0.968  -1.037  -0.904  -0.869  -0.915  -0.803
25    E        -0.308  -0.276  -0.294  -0.413  -0.409  -0.391  -0.552  -0.524  -0.504
26    L         0.711   0.729   0.500   0.764   0.800   0.449   0.716   0.744   0.333
27    S        -0.182  -0.121  -0.248  -0.032   0.053  -0.147  -0.340  -0.259  -0.429
28    L        -0.900  -0.876  -0.812  -1.027  -0.986  -0.876  -0.974  -0.953  -0.838
29    D        -0.182  -0.150  -0.253  -0.423  -0.370  -0.537  -0.340  -0.288  -0.438
30    E        -0.900  -0.863  -0.799  -1.116  -1.082  -0.955  -0.974  -0.928  -0.824
31    L         1.354   1.370   1.444   1.272   1.300   1.414   1.455   1.480   1.591
32    A        -0.716  -0.628  -0.754  -0.869  -0.742  -0.917  -0.763  -0.656  -0.774
33    K        -0.478  -0.523  -0.695  -0.338  -0.400  -0.674  -0.446  -0.508  -0.701
34    L        -0.716  -0.791  -0.762  -0.730  -0.833  -0.817  -0.763  -0.840  -0.783
35    G         0.711   0.589   0.488   0.857   0.694   0.524   0.716   0.520   0.310
36    V         0.711   0.740   0.501   0.764   0.814   0.452   0.716   0.760   0.335
37    I        -0.716  -0.773  -0.760  -0.708  -0.783  -0.773  -0.763  -0.823  -0.780
38    Y         0.711   0.749   0.508   0.806   0.863   0.521   0.716   0.773   0.347
39    K        -0.492  -0.500  -0.366  -0.677  -0.698  -0.494  -0.763  -0.770  -0.591
40    Y        -0.716  -0.679  -0.744  -0.590  -0.530  -0.662  -0.763  -0.711  -0.763
41    C        -1.602  -1.611  -1.483  -1.343  -1.342  -1.162  -1.291  -1.289  -1.120
42    A        -1.011  -0.991  -0.839  -1.100  -1.087  -0.863  -1.080  -1.053  -0.863
43    N        -1.195  -1.225  -1.156  -1.155  -1.199  -1.055  -1.080  -1.099  -0.986
44    E        -1.195  -1.235  -1.159  -1.076  -1.163  -1.077  -1.080  -1.110  -0.987
45    E        -0.478  -0.515  -0.689  -0.491  -0.559  -0.803  -0.446  -0.498  -0.693
46    E        -0.716  -0.777  -0.762  -0.886  -0.959  -0.920  -0.763  -0.820  -0.783
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    V        -0.182  -0.244  -0.255  -0.235  -0.295  -0.355  -0.340  -0.409  -0.436
50    N         0.225   0.244   0.315  -0.085  -0.063   0.056  -0.129  -0.100  -0.019
51    E        -2.194  -2.167  -1.988  -2.000  -1.950  -1.717  -1.502  -1.477  -1.278
52    I        -0.182  -0.143  -0.259  -0.257  -0.197  -0.368  -0.340  -0.284  -0.448
53    A         0.711   0.589   0.488   0.843   0.711   0.563   0.716   0.520   0.310
54    R        -1.195  -1.160  -1.149  -1.079  -1.022  -0.999  -1.080  -1.035  -0.976
55    Q        -0.478  -0.429  -0.685  -0.490  -0.426  -0.795  -0.446  -0.382  -0.688
56    R         0.711   0.589   0.488   0.763   0.597   0.446   0.716   0.520   0.310
57    E        -1.307  -1.272  -1.183  -1.416  -1.351  -1.240  -1.185  -1.148  -1.009
58    Y         0.711   0.589   0.488   0.814   0.662   0.505   0.716   0.520   0.310
59    K         0.711   0.749   0.508   0.771   0.824   0.501   0.716   0.773   0.347
60    N         1.354   1.370   1.444   1.401   1.432   1.538   1.455   1.480   1.591
61    R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
62    D         1.354   1.370   1.444   1.197   1.211   1.342   1.455   1.480   1.591
63    V        -0.420  -0.362  -0.333  -0.723  -0.633  -0.591  -0.657  -0.575  -0.545
64    V         0.394   0.419   0.362   0.318   0.363   0.229   0.188   0.227   0.073
65    N        -0.716  -0.795  -0.770  -0.595  -0.708  -0.700  -0.763  -0.845  -0.791
66    I        -0.420  -0.427  -0.333  -0.602  -0.619  -0.494  -0.657  -0.671  -0.546
67    C        -0.900  -0.900  -0.816  -0.774  -0.769  -0.622  -0.974  -0.973  -0.841
68    E        -1.307  -1.333  -1.193  -1.364  -1.395  -1.210  -1.185  -1.196  -1.016
69    G        -1.602  -1.606  -1.487  -1.675  -1.692  -1.463  -1.291  -1.286  -1.123
70    S        -1.195  -1.216  -1.147  -0.993  -1.016  -0.934  -1.080  -1.092  -0.977
71    F        -0.182  -0.273  -0.273  -0.052  -0.185  -0.202  -0.340  -0.452  -0.464
72    K        -0.716  -0.636  -0.747  -0.603  -0.483  -0.646  -0.763  -0.665  -0.765
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    S        -0.126  -0.171  -0.269  -0.169  -0.235  -0.364  -0.235  -0.299  -0.453
75    E        -1.309  -1.279  -1.192  -1.394  -1.349  -1.205  -1.174  -1.140  -1.014
76    A        -0.900  -0.851  -0.807  -1.182  -1.115  -1.019  -0.974  -0.921  -0.832
77    E        -1.491  -1.532  -1.474  -1.326  -1.396  -1.348  -1.185  -1.218  -1.112
78    F        -0.716  -0.646  -0.746  -0.614  -0.512  -0.648  -0.763  -0.679  -0.766
79    N        -0.788  -0.839  -0.779  -0.968  -1.055  -0.952  -0.869  -0.910  -0.804
80    E        -1.602  -1.626  -1.492  -1.493  -1.510  -1.332  -1.291  -1.300  -1.126
81    K         0.099   0.032  -0.181   0.270   0.189  -0.076   0.082  -0.019  -0.327
82    L        -0.420  -0.427  -0.333  -0.535  -0.557  -0.412  -0.657  -0.671  -0.546
83    A        -1.491  -1.415  -1.444  -1.266  -1.158  -1.202  -1.185  -1.109  -1.088
84    T        -1.195  -1.218  -1.159  -0.998  -1.033  -0.971  -1.080  -1.095  -0.987
85    F         1.354   1.370   1.444   1.429   1.451   1.564   1.455   1.480   1.591
86    Y         0.394   0.328   0.352   0.370   0.260   0.272   0.188   0.061   0.054
87    Q        -1.195  -1.197  -1.164  -1.264  -1.293  -1.220  -1.080  -1.081  -0.992
88    E         1.354   1.370   1.444   1.175   1.196   1.321   1.455   1.480   1.591
89    H         1.354   1.370   1.444   1.476   1.499   1.610   1.455   1.480   1.591
90    L         0.394   0.453   0.407   0.258   0.355   0.259   0.188   0.288   0.159
91    H         1.354   1.370   1.444   1.476   1.499   1.610   1.455   1.480   1.591
92    E         1.354   1.370   1.444   1.175   1.196   1.321   1.455   1.480   1.591
93    D         1.354   1.370   1.444   1.197   1.211   1.342   1.455   1.480   1.591
94    E         1.354   1.370   1.444   1.175   1.196   1.321   1.455   1.480   1.591
95    E         1.354   1.370   1.444   1.175   1.196   1.321   1.455   1.480   1.591
96    I         1.354   1.370   1.444   1.353   1.375   1.491   1.455   1.480   1.591
97    R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
98    Y         0.711   0.589   0.488   0.792   0.631   0.453   0.716   0.520   0.310
99    C         0.225   0.258   0.321   0.166   0.212   0.313  -0.129  -0.073  -0.006
100   L        -0.716  -0.643  -0.740  -0.771  -0.657  -0.805  -0.763  -0.670  -0.759
101   E         0.225   0.269   0.324  -0.210  -0.140  -0.066  -0.129  -0.052  -0.001
102   G         1.354   1.370   1.444   1.425   1.448   1.561   1.455   1.480   1.591
103   A        -0.716  -0.763  -0.764  -0.805  -0.869  -0.831  -0.763  -0.816  -0.786
104   G         1.354   1.370   1.444   1.425   1.448   1.561   1.455   1.480   1.591
105   Y         0.711   0.740   0.501   0.814   0.858   0.528   0.716   0.760   0.335
106   F         1.354   1.370   1.444   1.429   1.451   1.564   1.455   1.480   1.591
107   D         1.354   1.370   1.444   1.197   1.211   1.342   1.455   1.480   1.591
108   V         1.354   1.370   1.444   1.339   1.372   1.478   1.455   1.480   1.591
109   R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
110   D        -0.182  -0.261  -0.270  -0.298  -0.400  -0.399  -0.340  -0.434  -0.463
111   A        -1.491  -1.518  -1.471  -1.343  -1.391  -1.337  -1.185  -1.206  -1.109
112   S        -1.602  -1.563  -1.487  -1.420  -1.396  -1.261  -1.291  -1.252  -1.123
113   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   E         0.394   0.419   0.373   0.121   0.148   0.039   0.188   0.227   0.094
116   N        -0.716  -0.663  -0.752  -0.794  -0.724  -0.862  -0.763  -0.701  -0.772
117   W         1.354   1.370   1.444   1.590   1.616   1.719   1.455   1.480   1.591
118   I         0.394   0.354   0.353   0.327   0.255   0.216   0.188   0.109   0.056
119   R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
120   C        -0.492  -0.503  -0.366  -0.505  -0.523  -0.334  -0.763  -0.773  -0.591
121   L        -1.011  -1.064  -1.117  -0.832  -0.911  -0.998  -0.869  -0.925  -0.944
122   V         0.171   0.188   0.301  -0.152  -0.115   0.056  -0.235  -0.210  -0.046
123   E        -1.602  -1.534  -1.471  -1.500  -1.432  -1.286  -1.291  -1.231  -1.112
124   S        -0.788  -0.753  -0.772  -0.728  -0.685  -0.682  -0.869  -0.826  -0.796
125   G        -0.478  -0.408  -0.684  -0.258  -0.164  -0.606  -0.446  -0.357  -0.687
126   D         1.354   1.370   1.444   1.197   1.211   1.342   1.455   1.480   1.591
127   L         0.711   0.752   0.507   0.742   0.798   0.499   0.716   0.778   0.345
128   L         0.394   0.328   0.352   0.254   0.140   0.153   0.188   0.061   0.054
129   I         0.394   0.432   0.365   0.327   0.387   0.240   0.188   0.250   0.080
130   L         1.354   1.370   1.444   1.272   1.300   1.414   1.455   1.480   1.591
131   P         1.354   1.370   1.444   1.483   1.509   1.616   1.455   1.480   1.591
132   P        -0.182  -0.211  -0.275  -0.100  -0.146  -0.226  -0.340  -0.400  -0.471
133   G         1.354   1.370   1.444   1.425   1.448   1.561   1.455   1.480   1.591
134   I         1.354   1.370   1.444   1.353   1.375   1.491   1.455   1.480   1.591
135   Y         1.354   1.370   1.444   1.367   1.395   1.505   1.455   1.480   1.591
136   H         1.354   1.370   1.444   1.476   1.499   1.610   1.455   1.480   1.591
137   R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
138   F         1.354   1.370   1.444   1.429   1.451   1.564   1.455   1.480   1.591
139   T         1.354   1.370   1.444   1.442   1.470   1.577   1.455   1.480   1.591
140   L         0.394   0.328   0.352   0.283   0.179   0.200   0.188   0.061   0.054
141   T         0.099   0.126  -0.170   0.319   0.357  -0.093   0.082   0.121  -0.311
142   T        -1.307  -1.271  -1.177  -1.326  -1.267  -1.135  -1.185  -1.148  -1.005
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   S        -1.602  -1.548  -1.474  -1.548  -1.489  -1.364  -1.291  -1.241  -1.114
145   N        -0.478  -0.514  -0.702  -0.305  -0.376  -0.702  -0.446  -0.497  -0.709
146   H        -0.308  -0.258  -0.293  -0.352  -0.276  -0.317  -0.552  -0.480  -0.500
147   I         0.225   0.268   0.328   0.019   0.097   0.166  -0.129  -0.054   0.006
148   K        -0.182  -0.229  -0.279  -0.144  -0.217  -0.261  -0.340  -0.417  -0.476
149   A         0.711   0.749   0.508   0.823   0.888   0.549   0.716   0.773   0.347
150   L        -0.492  -0.458  -0.350  -0.598  -0.522  -0.385  -0.763  -0.716  -0.570
151   R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
152   L         1.354   1.370   1.444   1.272   1.300   1.414   1.455   1.480   1.591
153   F         1.354   1.370   1.444   1.429   1.451   1.564   1.455   1.480   1.591
154   K         0.099   0.008  -0.182   0.252   0.136  -0.113   0.082  -0.050  -0.329
155   D        -0.308  -0.294  -0.300  -0.674  -0.679  -0.630  -0.552  -0.541  -0.510
156   E         0.711   0.589   0.488   0.619   0.460   0.320   0.716   0.520   0.310
157   P         1.354   1.370   1.444   1.483   1.509   1.616   1.455   1.480   1.591
158   K         1.354   1.370   1.444   1.321   1.349   1.461   1.455   1.480   1.591
159   W         1.354   1.370   1.444   1.590   1.616   1.719   1.455   1.480   1.591
160   Q        -1.602  -1.620  -1.495  -1.519  -1.539  -1.359  -1.291  -1.296  -1.129
161   A         0.711   0.718   0.502   0.829   0.857   0.553   0.716   0.726   0.337
162   I        -0.492  -0.460  -0.360  -0.744  -0.698  -0.543  -0.763  -0.720  -0.582
163   N         0.099   0.008  -0.182   0.325   0.211  -0.056   0.082  -0.050  -0.329
164   R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
165   S        -1.195  -1.163  -1.158  -1.044  -1.006  -1.034  -1.080  -1.053  -0.987
166   N        -0.825  -0.797  -0.779  -0.989  -0.961  -0.925  -0.890  -0.848  -0.799
167   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   A        -1.195  -1.230  -1.166  -1.081  -1.107  -1.044  -1.080  -1.103  -0.993
170   D        -0.478  -0.514  -0.702  -0.516  -0.603  -0.890  -0.446  -0.497  -0.709
171   S        -0.900  -0.892  -0.814  -1.009  -1.032  -0.912  -0.974  -0.965  -0.839
172   L        -0.788  -0.730  -0.768  -0.805  -0.734  -0.734  -0.869  -0.808  -0.793
173   P        -0.716  -0.760  -0.754  -0.695  -0.770  -0.801  -0.763  -0.802  -0.771
174   V        -0.492  -0.467  -0.358  -0.678  -0.621  -0.479  -0.763  -0.728  -0.581
175   R         1.354   1.370   1.444   1.325   1.342   1.465   1.455   1.480   1.591
176   K        -1.195  -1.136  -1.154  -1.011  -0.949  -0.985  -1.080  -1.029  -0.984
177   D        -0.478  -0.532  -0.702  -0.510  -0.588  -0.856  -0.446  -0.518  -0.709
178   Y         1.354   1.370   1.444   1.367   1.395   1.505   1.455   1.480   1.591
179   I        -0.716  -0.659  -0.739  -0.771  -0.682  -0.799  -0.763  -0.695  -0.756
180   A        -1.307  -1.269  -1.178  -1.203  -1.143  -1.004  -1.185  -1.148  -1.005
181   L        -1.307  -1.281  -1.183  -1.110  -1.065  -0.945  -1.185  -1.156  -1.008
182   I         0.099   0.118  -0.174   0.244   0.270  -0.152   0.082   0.111  -0.316
183   N        -1.628  -1.639  -1.506  -1.469  -1.497  -1.304  -1.304  -1.306  -1.136
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   Y        -0.825  -0.803  -0.787  -0.882  -0.842  -0.835  -0.890  -0.858  -0.809
* 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/Q03677
Output conservation file - output/Q03677
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
