1     M         1.157   1.194   1.258   1.410   1.457   1.541   1.234   1.279   1.381
2     S         0.067  -0.024   0.047  -0.040  -0.249  -0.173  -0.146  -0.322  -0.243
3     Q        -0.887  -0.857  -0.668  -1.142  -1.130  -0.841  -1.122  -1.053  -0.801
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    A        -1.867  -1.818  -1.589  -1.974  -1.883  -1.561  -1.629  -1.546  -1.264
11    A        -1.193  -1.178  -1.153  -1.321  -1.324  -1.255  -1.182  -1.169  -1.061
12    K        -0.923  -1.180  -1.143  -1.000  -1.352  -1.322  -0.836  -1.115  -1.046
13    N        -0.923  -1.072  -1.129  -0.500  -0.735  -0.903  -0.836  -0.999  -1.032
14    V        -1.193  -1.248  -1.158  -1.217  -1.287  -1.139  -1.182  -1.226  -1.065
15    I        -1.193  -1.086  -1.128  -1.240  -1.077  -1.133  -1.182  -1.026  -1.034
16    V         0.427   0.298   0.167   0.414   0.247   0.021   0.429   0.226  -0.025
17    K         1.157   1.194   1.258   0.921   0.995   1.109   1.234   1.279   1.381
18    L         0.427   0.360   0.173   0.448   0.357   0.061   0.429   0.322  -0.014
19    I         0.427   0.510   0.186   0.443   0.558   0.072   0.429   0.544   0.008
20    V         1.157   1.194   1.258   1.070   1.129   1.240   1.234   1.279   1.381
21    G        -0.269  -0.339  -0.563  -0.199  -0.303  -0.639  -0.261  -0.360  -0.661
22    A         1.157   1.194   1.258   1.016   1.081   1.192   1.234   1.279   1.381
23    G         1.157   1.194   1.258   1.080   1.138   1.249   1.234   1.279   1.381
24    Q        -0.587  -0.678  -0.633  -0.514  -0.710  -0.744  -0.721  -0.831  -0.759
25    A         1.157   1.194   1.258   1.016   1.081   1.192   1.234   1.279   1.381
26    A        -0.923  -1.180  -1.143  -0.926  -1.317  -1.300  -0.836  -1.115  -1.046
27    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
28    S        -1.276  -1.340  -1.158  -1.373  -1.417  -1.119  -1.297  -1.305  -1.065
29    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
30    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
31    V         0.427   0.298   0.167   0.414   0.247   0.021   0.429   0.226  -0.025
32    G         1.157   1.194   1.258   1.080   1.138   1.249   1.234   1.279   1.381
33    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
34    A         0.427   0.360   0.173   0.354   0.281  -0.026   0.429   0.322  -0.014
35    L         1.157   1.194   1.258   1.104   1.150   1.270   1.234   1.279   1.381
36    G         1.157   1.194   1.258   1.080   1.138   1.249   1.234   1.279   1.381
37    S         0.427   0.298   0.167   0.513   0.320   0.083   0.429   0.226  -0.025
38    K         0.427   0.298   0.167   0.306   0.172   0.003   0.429   0.226  -0.025
39    G         1.157   1.194   1.258   1.080   1.138   1.249   1.234   1.279   1.381
40    I        -0.731  -0.780  -0.645  -1.014  -1.070  -0.863  -0.951  -0.971  -0.776
41    K         1.157   1.194   1.258   0.921   0.995   1.109   1.234   1.279   1.381
42    A         0.067  -0.033   0.045  -0.148  -0.327  -0.206  -0.146  -0.339  -0.247
43    I         0.427   0.338   0.168   0.493   0.395   0.166   0.429   0.288  -0.023
44    D         1.157   1.194   1.258   1.368   1.412   1.505   1.234   1.279   1.381
45    F         1.157   1.194   1.258   1.377   1.420   1.513   1.234   1.279   1.381
46    C         1.157   1.194   1.258   1.460   1.495   1.585   1.234   1.279   1.381
47    K         1.157   1.194   1.258   0.921   0.995   1.109   1.234   1.279   1.381
48    E         1.157   1.194   1.258   1.303   1.353   1.447   1.234   1.279   1.381
49    F         1.157   1.194   1.258   1.377   1.420   1.513   1.234   1.279   1.381
50    N         1.157   1.194   1.258   1.391   1.436   1.525   1.234   1.279   1.381
51    A         1.157   1.194   1.258   1.016   1.081   1.192   1.234   1.279   1.381
52    R         0.427   0.360   0.173   0.697   0.587   0.229   0.429   0.322  -0.014
53    S         0.427   0.592   0.192   0.611   0.785   0.250   0.429   0.659   0.019
54    A         0.427   0.556   0.191   0.356   0.537   0.009   0.429   0.608   0.017
55    N        -1.738  -1.656  -1.558  -1.428  -1.351  -1.258  -1.527  -1.425  -1.240
56    Y        -0.923  -0.984  -1.117  -0.374  -0.493  -0.717  -0.836  -0.912  -1.019
57    Q        -0.587  -0.707  -0.639  -0.275  -0.448  -0.376  -0.721  -0.861  -0.767
58    P        -0.923  -1.026  -1.118  -0.733  -0.878  -0.962  -0.836  -0.944  -1.020
59    G         0.067  -0.024   0.047  -0.016  -0.153  -0.037  -0.146  -0.322  -0.243
60    V        -0.940  -0.852  -0.675  -1.221  -1.073  -0.807  -1.182  -1.046  -0.810
61    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
62    V        -0.587  -0.669  -0.633  -0.661  -0.766  -0.721  -0.721  -0.812  -0.759
63    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
64    V         0.067   0.058   0.061  -0.002  -0.011   0.009  -0.146  -0.176  -0.218
65    L        -1.529  -1.693  -1.563  -1.460  -1.757  -1.596  -1.297  -1.430  -1.243
66    I        -0.587  -0.653  -0.626  -0.715  -0.818  -0.817  -0.721  -0.788  -0.749
67    T        -0.269  -0.040  -0.528   0.044   0.288  -0.307  -0.261   0.038  -0.613
68    I        -0.125  -0.120   0.031  -0.465  -0.481  -0.239  -0.491  -0.498  -0.274
69    K        -0.587  -0.669  -0.630  -0.743  -0.834  -0.730  -0.721  -0.805  -0.755
70    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
71    D         0.427   0.298   0.167   0.752   0.585   0.372   0.429   0.226  -0.025
72    R         1.157   1.194   1.258   1.377   1.411   1.513   1.234   1.279   1.381
73    T        -0.125  -0.049   0.042  -0.271  -0.180  -0.038  -0.491  -0.368  -0.252
74    F         1.157   1.194   1.258   1.377   1.420   1.513   1.234   1.279   1.381
75    T        -0.587  -0.628  -0.623  -0.473  -0.546  -0.535  -0.721  -0.751  -0.745
76    F         1.157   1.194   1.258   1.377   1.420   1.513   1.234   1.279   1.381
77    E        -0.269  -0.489  -0.588   0.064  -0.241  -0.418  -0.261  -0.552  -0.694
78    M        -0.923  -1.180  -1.143  -0.550  -0.983  -1.055  -0.836  -1.115  -1.046
79    K        -0.269  -0.489  -0.588  -0.283  -0.531  -0.629  -0.261  -0.552  -0.694
80    S         0.067  -0.033   0.045   0.037  -0.173  -0.044  -0.146  -0.339  -0.247
81    P         1.157   1.194   1.258   1.075   1.128   1.245   1.234   1.279   1.381
82    P        -0.269  -0.436  -0.578  -0.129  -0.330  -0.499  -0.261  -0.480  -0.680
83    T         1.157   1.194   1.258   1.257   1.276   1.406   1.234   1.279   1.381
84    G        -0.731  -0.650  -0.611  -0.961  -0.779  -0.762  -0.951  -0.788  -0.728
85    Y        -0.731  -0.650  -0.611  -0.406  -0.255  -0.238  -0.951  -0.788  -0.728
86    L         1.157   1.194   1.258   1.104   1.150   1.270   1.234   1.279   1.381
87    L         0.427   0.298   0.167   0.448   0.268   0.050   0.429   0.226  -0.025
88    L        -0.269  -0.339  -0.563  -0.138  -0.251  -0.541  -0.261  -0.360  -0.661
89    K        -0.269  -0.436  -0.578  -0.288  -0.470  -0.629  -0.261  -0.480  -0.680
90    A         0.427   0.298   0.167   0.382   0.225   0.034   0.429   0.226  -0.025
91    L        -0.186  -0.117   0.035  -0.641  -0.524  -0.270  -0.606  -0.493  -0.266
92    K        -2.074  -1.948  -1.878  -1.892  -1.692  -1.620  -1.642  -1.507  -1.351
93    M        -1.193  -1.030  -1.123  -1.322  -1.108  -1.191  -1.182  -0.993  -1.030
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   D        -0.923  -0.803  -1.088  -0.578  -0.419  -0.880  -0.836  -0.693  -0.988
102   K         1.157   1.194   1.258   0.921   0.995   1.109   1.234   1.279   1.381
103   G         1.157   1.194   1.258   1.080   1.138   1.249   1.234   1.279   1.381
104   H        -0.940  -0.873  -0.678  -1.069  -1.037  -0.741  -1.182  -1.075  -0.814
105   G        -1.193  -1.210  -1.157  -1.249  -1.316  -1.186  -1.182  -1.194  -1.065
106   Q        -1.276  -1.335  -1.161  -1.301  -1.382  -1.107  -1.297  -1.296  -1.067
107   P        -0.269  -0.283  -0.555  -0.187  -0.189  -0.592  -0.261  -0.281  -0.649
108   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   P        -2.200  -2.069  -1.894  -2.264  -2.043  -1.815  -1.757  -1.603  -1.363
122   T        -1.865  -1.661  -1.564  -1.717  -1.476  -1.295  -1.642  -1.439  -1.247
123   R        -2.200  -2.071  -1.891  -1.784  -1.592  -1.398  -1.757  -1.609  -1.362
124   A        -1.865  -1.663  -1.565  -2.100  -1.823  -1.644  -1.642  -1.441  -1.247
125   L        -1.193  -1.024  -1.119  -1.293  -1.062  -1.171  -1.182  -0.961  -1.022
126   G         1.157   1.194   1.258   1.080   1.138   1.249   1.234   1.279   1.381
127   E        -0.587  -0.734  -0.646  -0.383  -0.616  -0.494  -0.721  -0.911  -0.777
128   L        -0.125  -0.076   0.039  -0.465  -0.395  -0.220  -0.491  -0.418  -0.259
129   S         1.157   1.194   1.258   1.181   1.218   1.338   1.234   1.279   1.381
130   L         1.157   1.194   1.258   1.104   1.150   1.270   1.234   1.279   1.381
131   K         1.157   1.194   1.258   0.921   0.995   1.109   1.234   1.279   1.381
132   H         1.157   1.194   1.258   1.423   1.463   1.553   1.234   1.279   1.381
133   V        -0.186  -0.118   0.033  -0.601  -0.477  -0.233  -0.606  -0.494  -0.269
134   Y         0.427   0.510   0.186   0.854   0.950   0.511   0.429   0.544   0.008
135   E         1.157   1.194   1.258   1.303   1.353   1.447   1.234   1.279   1.381
136   I         0.427   0.360   0.173   0.448   0.363   0.061   0.429   0.322  -0.014
137   A         1.157   1.194   1.258   1.016   1.081   1.192   1.234   1.279   1.381
138   K         1.157   1.194   1.258   0.921   0.995   1.109   1.234   1.279   1.381
139   I         0.427   0.298   0.167   0.448   0.275   0.050   0.429   0.226  -0.025
140   K         1.157   1.194   1.258   0.921   0.995   1.109   1.234   1.279   1.381
141   K        -0.269  -0.489  -0.588  -0.323  -0.596  -0.721  -0.261  -0.552  -0.694
142   S        -0.587  -0.633  -0.625  -0.476  -0.564  -0.547  -0.721  -0.763  -0.749
143   D         0.427   0.338   0.168   0.740   0.623   0.343   0.429   0.288  -0.023
144   E        -2.200  -2.091  -1.895  -2.032  -1.940  -1.657  -1.757  -1.626  -1.364
145   R         0.427   0.298   0.167   0.732   0.539   0.305   0.429   0.226  -0.025
146   H         0.067  -0.033   0.045   0.222  -0.011   0.048  -0.146  -0.339  -0.247
147   S        -1.402  -1.345  -1.169  -1.733  -1.569  -1.302  -1.412  -1.304  -1.076
148   L        -2.536  -2.234  -2.166  -2.317  -1.891  -1.811  -1.872  -1.600  -1.443
149   L        -1.193  -1.272  -1.155  -1.253  -1.347  -1.181  -1.182  -1.223  -1.060
150   E        -0.940  -0.892  -0.687  -1.000  -0.966  -0.672  -1.182  -1.098  -0.825
151   M         0.067   0.284   0.134   0.014   0.316   0.115  -0.146   0.203  -0.084
152   E        -1.529  -1.381  -1.516  -1.259  -1.075  -1.364  -1.297  -1.133  -1.202
153   G        -1.193  -1.272  -1.155  -1.282  -1.355  -1.194  -1.182  -1.223  -1.060
154   I         0.067  -0.033   0.045  -0.088  -0.289  -0.186  -0.146  -0.339  -0.247
155   V        -0.186  -0.079   0.051  -0.335  -0.097   0.072  -0.606  -0.422  -0.236
156   K        -0.587  -0.580  -0.610  -0.840  -0.771  -0.816  -0.721  -0.681  -0.726
157   S         0.067   0.082   0.068  -0.040  -0.041  -0.125  -0.146  -0.134  -0.205
158   I        -0.731  -0.650  -0.611  -1.021  -0.836  -0.802  -0.951  -0.788  -0.728
159   V        -0.269  -0.208  -0.546  -0.148  -0.058  -0.536  -0.261  -0.189  -0.638
160   G        -1.529  -1.353  -1.517  -1.413  -1.141  -1.429  -1.297  -1.100  -1.203
161   V        -0.731  -0.666  -0.620  -0.825  -0.662  -0.589  -0.951  -0.808  -0.740
162   A         1.157   1.194   1.258   1.016   1.081   1.192   1.234   1.279   1.381
163   K        -0.923  -0.990  -1.112  -0.932  -1.012  -1.150  -0.836  -0.907  -1.014
164   S        -0.269  -0.103  -0.535  -0.146   0.068  -0.613  -0.261  -0.040  -0.622
165   M        -0.731  -0.756  -0.644  -0.756  -0.793  -0.661  -0.951  -0.945  -0.774
166   G         1.157   1.194   1.258   1.080   1.138   1.249   1.234   1.279   1.381
167   I        -0.125  -0.113   0.031  -0.465  -0.466  -0.237  -0.491  -0.485  -0.273
168   K        -0.269  -0.436  -0.578  -0.302  -0.484  -0.659  -0.261  -0.480  -0.680
169   V         0.067   0.096   0.077  -0.121  -0.076  -0.148  -0.146  -0.110  -0.187
170   V         0.427   0.338   0.168   0.414   0.304   0.023   0.429   0.288  -0.023
171   P         0.427   0.360   0.173   0.461   0.388   0.143   0.429   0.322  -0.014
* 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/P53875
Output conservation file - output/P53875
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
