1     M         1.100   1.124   1.185   1.371   1.412   1.487   1.170   1.202   1.292
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    L         0.213   0.150   0.079   0.254   0.160   0.065   0.091  -0.021  -0.179
33    S        -1.261  -1.268  -1.131  -1.452  -1.461  -1.242  -1.258  -1.252  -1.062
34    R        -1.261  -1.143  -1.124  -1.452  -1.273  -1.236  -1.258  -1.112  -1.056
35    F        -1.261  -1.143  -1.124  -1.273  -1.085  -1.104  -1.258  -1.112  -1.056
36    M        -0.584  -0.580  -0.617  -0.637  -0.647  -0.659  -0.718  -0.713  -0.755
37    S         1.100   1.124   1.185   0.981   1.025   1.126   1.170   1.202   1.292
38    N        -0.693  -0.722  -0.623  -0.877  -0.925  -0.802  -0.891  -0.905  -0.765
39    T        -0.693  -0.709  -0.619  -0.655  -0.680  -0.558  -0.891  -0.886  -0.760
40    W        -1.666  -1.568  -1.500  -1.466  -1.341  -1.226  -1.453  -1.351  -1.217
41    C        -1.666  -1.568  -1.500  -1.383  -1.335  -1.155  -1.453  -1.351  -1.217
42    T        -1.753  -1.652  -1.511  -1.688  -1.532  -1.345  -1.528  -1.423  -1.226
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    P        -0.584  -0.545  -0.604  -0.497  -0.472  -0.527  -0.718  -0.672  -0.739
45    L        -1.261  -1.270  -1.131  -1.069  -1.064  -0.862  -1.258  -1.260  -1.062
46    R        -1.257  -1.118  -1.113  -1.313  -1.099  -1.136  -1.265  -1.120  -1.046
47    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    Q        -1.515  -1.559  -1.480  -1.365  -1.466  -1.407  -1.307  -1.341  -1.200
50    R        -1.515  -1.602  -1.496  -1.396  -1.513  -1.311  -1.307  -1.378  -1.213
51    L        -1.647  -1.636  -1.484  -1.604  -1.593  -1.343  -1.445  -1.415  -1.204
52    F        -0.594  -0.596  -0.611  -0.435  -0.445  -0.542  -0.757  -0.750  -0.751
53    S        -0.312  -0.291  -0.541  -0.270  -0.233  -0.625  -0.344  -0.314  -0.654
54    S        -1.515  -1.445  -1.469  -1.320  -1.232  -1.222  -1.307  -1.224  -1.191
55    T        -1.647  -1.613  -1.490  -1.537  -1.508  -1.315  -1.445  -1.390  -1.209
56    T        -0.813  -0.771  -0.647  -0.934  -0.873  -0.672  -1.032  -0.969  -0.795
57    T        -1.515  -1.269  -1.459  -1.638  -1.287  -1.557  -1.307  -1.044  -1.182
58    M        -1.164  -1.029  -1.098  -1.195  -1.003  -1.075  -1.170  -1.034  -1.031
59    Q        -1.296  -1.238  -1.121  -1.162  -1.086  -0.903  -1.307  -1.232  -1.053
60    A        -0.594  -0.657  -0.619  -0.722  -0.887  -0.820  -0.757  -0.846  -0.762
61    T         0.373   0.363   0.136   0.590   0.575   0.178   0.344   0.326  -0.076
62    L         0.373   0.372   0.142   0.484   0.495   0.149   0.344   0.340  -0.064
63    N         1.100   1.124   1.185   1.202   1.238   1.330   1.170   1.202   1.292
64    Q         1.100   1.124   1.185   1.235   1.274   1.361   1.170   1.202   1.292
65    I         0.373   0.210   0.115   0.598   0.378   0.207   0.344   0.080  -0.113
66    K        -0.594  -0.719  -0.619  -0.712  -0.877  -0.701  -0.757  -0.905  -0.761
67    R        -0.312  -0.300  -0.567  -0.378  -0.359  -0.826  -0.344  -0.325  -0.689
68    G        -0.945  -1.095  -1.088  -0.795  -1.004  -0.951  -0.894  -1.063  -1.018
69    S        -1.998  -1.824  -1.792  -2.273  -1.970  -1.978  -1.583  -1.418  -1.314
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    G        -0.945  -1.003  -1.080  -0.846  -0.909  -1.027  -0.894  -0.968  -1.010
72    P        -1.164  -1.187  -1.109  -1.261  -1.329  -1.185  -1.170  -1.182  -1.042
73    P         0.373   0.210   0.115   0.437   0.192  -0.010   0.344   0.080  -0.113
74    R        -1.998  -1.912  -1.801  -2.210  -2.055  -1.908  -1.583  -1.499  -1.320
75    R        -1.164  -1.204  -1.102  -1.340  -1.343  -1.185  -1.170  -1.186  -1.034
76    K        -0.594  -0.592  -0.610  -0.749  -0.745  -0.725  -0.757  -0.747  -0.748
77    K        -1.972  -1.994  -1.804  -1.977  -1.992  -1.669  -1.570  -1.558  -1.322
78    I        -1.549  -1.631  -1.493  -1.547  -1.705  -1.524  -1.359  -1.410  -1.211
79    S        -1.241  -1.291  -1.115  -1.373  -1.443  -1.150  -1.254  -1.277  -1.048
80    T        -1.357  -1.190  -1.473  -1.136  -0.955  -1.193  -1.148  -0.973  -1.194
81    A        -0.073   0.032   0.031  -0.329  -0.149  -0.167  -0.410  -0.228  -0.268
82    P         0.432   0.338   0.095   0.513   0.386  -0.079   0.433   0.287  -0.150
83    Q        -1.050  -1.003  -1.087  -0.745  -0.763  -0.811  -1.043  -1.018  -1.019
84    L         1.100   1.124   1.185   1.135   1.181   1.268   1.170   1.202   1.292
85    D        -0.111  -0.069   0.027  -0.026   0.040   0.168  -0.481  -0.414  -0.274
86    Q        -2.349  -2.266  -2.075  -2.327  -2.206  -1.936  -1.720  -1.639  -1.406
87    C        -0.594  -0.707  -0.627  -0.408  -0.605  -0.542  -0.757  -0.887  -0.771
88    P         1.100   1.124   1.185   1.125   1.165   1.259   1.170   1.202   1.292
89    Q        -0.813  -0.701  -0.637  -0.696  -0.510  -0.457  -1.032  -0.876  -0.783
90    R         0.039   0.057   0.054  -0.244  -0.219  -0.265  -0.206  -0.183  -0.226
91    K         0.432   0.338   0.095   0.355   0.225  -0.190   0.433   0.287  -0.150
92    G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
93    V         1.100   1.124   1.185   0.918   0.953   1.068   1.170   1.202   1.292
94    V         0.103  -0.022   0.054  -0.056  -0.235  -0.090  -0.094  -0.326  -0.226
95    L        -0.204  -0.452  -0.561  -0.045  -0.412  -0.618  -0.200  -0.534  -0.680
96    R         0.432   0.267   0.154   0.375   0.143  -0.063   0.433   0.175  -0.042
97    V         0.432   0.456   0.116   0.347   0.379  -0.074   0.433   0.466  -0.111
98    M        -0.803  -0.985  -1.062  -0.342  -0.630  -0.795  -0.727  -0.941  -0.991
99    V        -0.627  -0.620  -0.623  -0.743  -0.654  -0.694  -0.832  -0.780  -0.767
100   L        -0.496  -0.650  -0.606  -0.534  -0.773  -0.743  -0.621  -0.812  -0.746
101   K         0.432   0.267   0.154   0.355   0.119  -0.075   0.433   0.175  -0.042
102   P         1.100   1.124   1.185   1.130   1.174   1.264   1.170   1.202   1.292
103   K         1.100   1.124   1.185   0.964   0.999   1.110   1.170   1.202   1.292
104   K         1.100   1.124   1.185   0.964   0.999   1.110   1.170   1.202   1.292
105   P         1.100   1.124   1.185   1.130   1.174   1.264   1.170   1.202   1.292
106   N         1.100   1.124   1.185   1.218   1.263   1.345   1.170   1.202   1.292
107   S         1.100   1.124   1.185   1.037   1.080   1.178   1.170   1.202   1.292
108   A         0.432   0.267   0.154   0.540   0.299   0.095   0.433   0.175  -0.042
109   Q        -0.803  -1.015  -1.070  -0.485  -0.800  -0.945  -0.727  -0.973  -0.999
110   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
111   K         1.100   1.124   1.185   0.964   0.999   1.110   1.170   1.202   1.292
112   A        -1.050  -1.204  -1.105  -0.899  -1.136  -0.992  -1.043  -1.185  -1.038
113   C        -0.129  -0.068   0.024  -0.178  -0.110   0.051  -0.516  -0.412  -0.281
114   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
115   V         1.100   1.124   1.185   0.918   0.953   1.068   1.170   1.202   1.292
116   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
117   L         1.100   1.124   1.185   1.135   1.181   1.268   1.170   1.202   1.292
118   T        -0.129  -0.077   0.024  -0.337  -0.276  -0.095  -0.516  -0.428  -0.282
119   N         0.103  -0.022   0.054   0.192  -0.025   0.077  -0.094  -0.326  -0.226
120   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
121   N        -0.627  -0.684  -0.612  -0.791  -0.898  -0.781  -0.832  -0.881  -0.754
122   V        -0.204  -0.191  -0.586  -0.247  -0.252  -0.794  -0.200  -0.192  -0.714
123   V        -0.073  -0.081   0.039  -0.380  -0.393  -0.185  -0.410  -0.435  -0.252
124   S        -0.073  -0.095   0.031  -0.265  -0.300  -0.094  -0.410  -0.463  -0.269
125   A         0.432   0.505   0.116   0.592   0.677   0.175   0.433   0.536  -0.111
126   Y         0.103   0.155   0.048   0.238   0.323   0.068  -0.094  -0.012  -0.236
127   I         1.100   1.124   1.185   1.239   1.280   1.365   1.170   1.202   1.292
128   P         1.100   1.124   1.185   1.130   1.174   1.264   1.170   1.202   1.292
129   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
130   E         0.432   0.338   0.095   0.781   0.666   0.252   0.433   0.287  -0.150
131   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
132   H         1.100   1.124   1.185   1.333   1.371   1.452   1.170   1.202   1.292
133   D         0.103   0.247   0.070   0.217   0.434   0.144  -0.094   0.142  -0.196
134   A        -0.496  -0.599  -0.594  -0.449  -0.588  -0.599  -0.621  -0.737  -0.728
135   Q         0.432   0.267   0.154   0.647   0.424   0.195   0.433   0.175  -0.042
136   E         0.432   0.267   0.154   0.782   0.570   0.364   0.433   0.175  -0.042
137   H         1.100   1.124   1.185   1.333   1.371   1.452   1.170   1.202   1.292
138   S        -0.496  -0.544  -0.623  -0.491  -0.553  -0.647  -0.621  -0.667  -0.766
139   I         0.103   0.250   0.070  -0.103   0.109  -0.145  -0.094   0.146  -0.196
140   V         1.100   1.124   1.185   0.918   0.953   1.068   1.170   1.202   1.292
141   Y        -0.129  -0.069   0.025  -0.233  -0.148  -0.000  -0.516  -0.414  -0.278
142   V         0.432   0.338   0.095   0.331   0.209  -0.158   0.433   0.287  -0.150
143   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
144   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
145   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
146   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
147   C        -0.818  -0.809  -0.651  -0.970  -0.995  -0.737  -1.043  -1.020  -0.800
148   Q         1.100   1.124   1.185   1.248   1.294   1.373   1.170   1.202   1.292
149   D         1.100   1.124   1.185   1.338   1.381   1.456   1.170   1.202   1.292
150   L        -1.050  -1.069  -1.096  -0.906  -0.926  -0.983  -1.043  -1.076  -1.028
151   P         1.100   1.124   1.185   1.130   1.174   1.264   1.170   1.202   1.292
152   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
153   V         1.100   1.124   1.185   0.918   0.953   1.068   1.170   1.202   1.292
154   K        -0.204  -0.452  -0.561  -0.208  -0.569  -0.734  -0.200  -0.534  -0.680
155   Y         1.100   1.124   1.185   1.308   1.348   1.429   1.170   1.202   1.292
156   H         0.432   0.505   0.116   0.726   0.823   0.172   0.433   0.536  -0.111
157   V        -0.129  -0.093   0.025  -0.519  -0.445  -0.266  -0.516  -0.458  -0.278
158   I         0.103   0.207   0.049  -0.103   0.048  -0.173  -0.094   0.076  -0.234
159   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
160   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
161   A         0.432   0.338   0.095   0.526   0.387  -0.068   0.433   0.287  -0.150
162   G        -1.050  -1.204  -1.105  -0.949  -1.147  -0.963  -1.043  -1.185  -1.038
163   D         1.100   1.124   1.185   1.338   1.381   1.456   1.170   1.202   1.292
164   L         0.432   0.338   0.095   0.563   0.456   0.072   0.433   0.287  -0.150
165   S        -1.050  -0.911  -1.083  -1.112  -0.879  -1.236  -1.043  -0.858  -1.014
166   G         0.432   0.497   0.113   0.428   0.509  -0.040   0.433   0.525  -0.116
167   V         1.100   1.124   1.185   0.918   0.953   1.068   1.170   1.202   1.292
168   V        -0.627  -0.497  -0.615  -0.853  -0.607  -0.801  -0.832  -0.639  -0.756
169   N        -0.204  -0.452  -0.561   0.052  -0.298  -0.514  -0.200  -0.534  -0.680
170   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
171   I        -1.549  -1.628  -1.491  -1.338  -1.471  -1.269  -1.359  -1.408  -1.210
172   S        -0.073  -0.042   0.024  -0.265  -0.221  -0.092  -0.410  -0.363  -0.281
173   S         1.100   1.124   1.185   1.037   1.080   1.178   1.170   1.202   1.292
174   R         1.100   1.124   1.185   0.987   1.030   1.131   1.170   1.202   1.292
175   S         1.100   1.124   1.185   1.037   1.080   1.178   1.170   1.202   1.292
176   K         1.100   1.124   1.185   0.964   0.999   1.110   1.170   1.202   1.292
177   Y         1.100   1.124   1.185   1.308   1.348   1.429   1.170   1.202   1.292
178   G         1.100   1.124   1.185   1.014   1.048   1.157   1.170   1.202   1.292
179   A        -0.743  -0.734  -0.635  -0.986  -0.977  -0.796  -0.937  -0.923  -0.779
180   K         1.100   1.124   1.185   0.964   0.999   1.110   1.170   1.202   1.292
181   K         1.100   1.124   1.185   0.964   0.999   1.110   1.170   1.202   1.292
182   P         1.100   1.124   1.185   1.130   1.174   1.264   1.170   1.202   1.292
183   S        -1.050  -0.830  -1.091  -1.116  -0.811  -1.162  -1.043  -0.769  -1.023
184   K        -0.594  -0.603  -0.629  -0.740  -0.766  -0.725  -0.757  -0.767  -0.775
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   S        -1.664  -1.663  -1.490  -1.575  -1.612  -1.339  -1.464  -1.434  -1.210
* 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/P53732
Output conservation file - output/P53732
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
