1     M         0.998   1.015   1.061   1.333   1.340   1.377   1.047   1.074   1.139
2     A        -1.045  -0.913  -0.979  -1.247  -0.924  -1.075  -1.154  -0.935  -1.001
3     R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
4     Y         0.998   1.015   1.061   1.207   1.229   1.272   1.047   1.074   1.139
5     G        -1.397  -1.240  -1.029  -1.798  -1.595  -1.253  -1.536  -1.344  -1.062
6     A         0.238   0.143  -0.171  -0.048  -0.140  -0.519   0.282   0.148  -0.360
7     T        -1.188  -1.287  -1.542  -0.822  -0.970  -1.487  -0.962  -1.071  -1.306
8     S        -1.045  -1.135  -1.013  -0.956  -1.051  -0.875  -1.154  -1.226  -1.045
9     T        -1.651  -1.690  -1.561  -1.838  -1.856  -1.580  -1.536  -1.514  -1.325
10    N        -1.507  -1.701  -1.575  -1.201  -1.552  -1.415  -1.345  -1.527  -1.338
11    P        -0.157  -0.153  -0.185   0.084   0.064  -0.040  -0.292  -0.300  -0.384
12    A        -0.390  -0.388  -0.261  -0.883  -0.861  -0.598  -0.675  -0.693  -0.515
13    K         0.998   1.015   1.061   0.875   0.917   0.994   1.047   1.074   1.139
14    S        -0.852  -0.930  -0.987  -0.615  -0.701  -0.784  -0.867  -0.959  -1.011
15    A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
16    S        -0.852  -1.017  -0.996  -0.823  -1.076  -1.125  -0.867  -1.061  -1.021
17    A         0.238   0.033  -0.178  -0.055  -0.288  -0.551   0.282  -0.012  -0.372
18    R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
19    G         0.998   1.015   1.061   1.068   1.088   1.155   1.047   1.074   1.139
20    S        -0.390  -0.388  -0.261  -0.738  -0.784  -0.621  -0.675  -0.693  -0.515
21    Y         0.998   1.015   1.061   1.207   1.229   1.272   1.047   1.074   1.139
22    L         0.998   1.015   1.061   1.029   1.053   1.123   1.047   1.074   1.139
23    R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
24    V        -0.390  -0.388  -0.261  -0.461  -0.481  -0.300  -0.675  -0.693  -0.515
25    S        -0.157  -0.153  -0.185  -0.091  -0.078  -0.138  -0.292  -0.300  -0.384
26    F        -0.157   0.019  -0.206   0.135   0.359  -0.008  -0.292  -0.033  -0.420
27    K         0.998   1.015   1.061   0.875   0.917   0.994   1.047   1.074   1.139
28    N         0.998   1.015   1.061   1.121   1.144   1.199   1.047   1.074   1.139
29    T        -0.157  -0.153  -0.185  -0.069  -0.071  -0.175  -0.292  -0.300  -0.384
30    R         0.238   0.143  -0.171   0.204   0.115  -0.267   0.282   0.148  -0.360
31    E         0.998   1.015   1.061   1.058   1.079   1.146   1.047   1.074   1.139
32    T        -0.390  -0.388  -0.261  -0.439  -0.465  -0.296  -0.675  -0.693  -0.515
33    A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
34    Q        -0.852  -0.930  -0.987  -0.592  -0.697  -0.798  -0.867  -0.959  -1.011
35    A        -0.157  -0.153  -0.185  -0.540  -0.523  -0.517  -0.292  -0.300  -0.384
36    I         0.998   1.015   1.061   1.121   1.141   1.199   1.047   1.074   1.139
37    N        -0.852  -0.785  -0.979  -0.649  -0.547  -0.944  -0.867  -0.760  -1.002
38    G         0.998   1.015   1.061   1.068   1.088   1.155   1.047   1.074   1.139
39    W        -0.157  -0.153  -0.185   0.273   0.254   0.156  -0.292  -0.300  -0.384
40    E        -1.860  -1.666  -1.551  -1.823  -1.565  -1.384  -1.728  -1.516  -1.318
41    L         0.998   1.015   1.061   1.029   1.053   1.123   1.047   1.074   1.139
42    T        -1.987  -1.740  -1.557  -1.954  -1.617  -1.367  -1.823  -1.565  -1.321
43    K        -0.157  -0.221  -0.248  -0.317  -0.430  -0.532  -0.292  -0.410  -0.492
44    A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
45    Q        -0.852  -0.930  -0.987  -0.598  -0.705  -0.814  -0.867  -0.959  -1.011
46    K        -0.852  -0.930  -0.987  -0.876  -1.000  -1.164  -0.867  -0.959  -1.011
47    Y        -0.390  -0.413  -0.265  -0.232  -0.303  -0.110  -0.675  -0.736  -0.521
48    L         0.998   1.015   1.061   1.029   1.053   1.123   1.047   1.074   1.139
49    E        -0.157  -0.178  -0.245   0.134   0.071  -0.120  -0.292  -0.340  -0.486
50    Q        -0.390  -0.413  -0.265  -0.415  -0.473  -0.262  -0.675  -0.736  -0.521
51    V         0.998   1.015   1.061   1.026   1.052   1.120   1.047   1.074   1.139
52    L        -0.852  -0.930  -0.987  -0.725  -0.846  -0.954  -0.867  -0.959  -1.011
53    D        -0.500  -0.437  -0.265  -0.480  -0.423  -0.178  -0.867  -0.779  -0.522
54    H         0.238   0.033  -0.178   0.609   0.333  -0.074   0.282  -0.012  -0.372
55    Q        -0.500  -0.416  -0.251  -0.762  -0.653  -0.397  -0.867  -0.743  -0.497
56    R        -0.852  -1.017  -0.996  -0.898  -1.109  -1.055  -0.867  -1.061  -1.021
57    A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
58    I        -0.390  -0.413  -0.265  -0.397  -0.484  -0.275  -0.675  -0.736  -0.521
59    P         0.998   1.015   1.061   1.210   1.226   1.274   1.047   1.074   1.139
60    F         0.238   0.033  -0.178   0.644   0.401   0.089   0.282  -0.012  -0.372
61    R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
62    R         0.238   0.143  -0.171   0.161   0.059  -0.407   0.282   0.148  -0.360
63    F        -1.045  -1.065  -1.005  -0.720  -0.746  -0.664  -1.154  -1.155  -1.036
64    N        -0.157  -0.305  -0.260  -0.133  -0.464  -0.515  -0.292  -0.551  -0.513
65    S        -0.500  -0.416  -0.251  -0.701  -0.555  -0.307  -0.867  -0.743  -0.497
66    S        -0.390  -0.413  -0.265  -0.510  -0.563  -0.341  -0.675  -0.736  -0.521
67    I        -0.852  -1.017  -0.996  -0.589  -0.832  -0.846  -0.867  -1.061  -1.021
68    G         0.998   1.015   1.061   1.068   1.088   1.155   1.047   1.074   1.139
69    R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
70    T         0.238   0.033  -0.178   0.407   0.120  -0.322   0.282  -0.012  -0.372
71    A        -0.390  -0.327  -0.256  -0.887  -0.786  -0.602  -0.675  -0.587  -0.506
72    Q         0.998   1.015   1.061   1.054   1.087   1.144   1.047   1.074   1.139
73    G         0.998   1.015   1.061   1.068   1.088   1.155   1.047   1.074   1.139
74    K         0.998   1.015   1.061   0.875   0.917   0.994   1.047   1.074   1.139
75    E         0.238   0.033  -0.178   0.447   0.193  -0.143   0.282  -0.012  -0.372
76    F         0.998   1.015   1.061   1.221   1.237   1.283   1.047   1.074   1.139
77    G         0.998   1.015   1.061   1.068   1.088   1.155   1.047   1.074   1.139
78    V         0.998   1.015   1.061   1.026   1.052   1.120   1.047   1.074   1.139
79    T         0.238   0.033  -0.178   0.455   0.204  -0.161   0.282  -0.012  -0.372
80    K        -0.852  -1.017  -0.996  -0.863  -1.103  -1.115  -0.867  -1.061  -1.021
81    A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
82    R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
83    W         0.998   1.015   1.061   1.329   1.342   1.374   1.047   1.074   1.139
84    P         0.998   1.015   1.061   1.210   1.226   1.274   1.047   1.074   1.139
85    A        -0.390  -0.388  -0.261  -0.908  -0.895  -0.629  -0.675  -0.693  -0.515
86    K         0.998   1.015   1.061   0.875   0.917   0.994   1.047   1.074   1.139
87    S         0.998   1.015   1.061   0.976   1.019   1.078   1.047   1.074   1.139
88    V        -0.493  -0.773  -0.979  -0.245  -0.657  -1.042  -0.388  -0.744  -1.000
89    K        -1.045  -1.114  -0.998  -1.092  -1.153  -0.966  -1.154  -1.197  -1.029
90    F         0.998   1.015   1.061   1.221   1.237   1.283   1.047   1.074   1.139
91    V        -1.778  -1.755  -1.566  -1.523  -1.504  -1.256  -1.632  -1.578  -1.330
92    Q        -1.778  -1.787  -1.576  -1.607  -1.608  -1.366  -1.632  -1.609  -1.340
93    G        -0.500  -0.407  -0.258  -0.473  -0.341  -0.144  -0.867  -0.726  -0.509
94    L         0.998   1.015   1.061   1.029   1.053   1.123   1.047   1.074   1.139
95    L         0.998   1.015   1.061   1.029   1.053   1.123   1.047   1.074   1.139
96    Q        -1.315  -1.182  -1.032  -1.538  -1.361  -1.162  -1.441  -1.284  -1.066
97    N         0.998   1.015   1.061   1.121   1.144   1.199   1.047   1.074   1.139
98    A         0.238   0.341  -0.153  -0.042   0.092  -0.475   0.282   0.415  -0.331
99    A        -1.397  -1.230  -1.029  -1.753  -1.413  -1.142  -1.536  -1.332  -1.062
100   A         0.238   0.411  -0.150  -0.055   0.157  -0.509   0.282   0.503  -0.325
101   N         0.998   1.015   1.061   1.121   1.144   1.199   1.047   1.074   1.139
102   A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
103   E         0.238   0.033  -0.178   0.474   0.233  -0.059   0.282  -0.012  -0.372
104   A        -0.493  -0.497  -0.952  -0.658  -0.649  -1.186  -0.388  -0.403  -0.967
105   K         0.998   1.015   1.061   0.875   0.917   0.994   1.047   1.074   1.139
106   G         0.998   1.015   1.061   1.068   1.088   1.155   1.047   1.074   1.139
107   L         0.998   1.015   1.061   1.029   1.053   1.123   1.047   1.074   1.139
108   D         0.998   1.015   1.061   1.262   1.274   1.317   1.047   1.074   1.139
109   A        -2.114  -2.175  -2.010  -2.095  -2.119  -1.855  -1.728  -1.761  -1.514
110   T        -2.323  -2.321  -2.017  -1.953  -1.938  -1.576  -1.919  -1.865  -1.519
111   K        -1.188  -1.305  -1.541  -0.959  -1.112  -1.465  -0.962  -1.112  -1.305
112   L         0.998   1.015   1.061   1.029   1.053   1.123   1.047   1.074   1.139
113   Y        -1.860  -1.665  -1.554  -1.659  -1.432  -1.298  -1.728  -1.514  -1.318
114   V        -0.500  -0.436  -0.266  -0.627  -0.540  -0.278  -0.867  -0.778  -0.523
115   S        -0.390  -0.413  -0.265  -0.599  -0.668  -0.455  -0.675  -0.736  -0.521
116   H         0.998   1.015   1.061   1.241   1.257   1.300   1.047   1.074   1.139
117   I        -0.157  -0.153  -0.185  -0.011  -0.026  -0.120  -0.292  -0.300  -0.384
118   Q         0.998   1.015   1.061   1.054   1.087   1.144   1.047   1.074   1.139
119   V         0.998   1.015   1.061   1.026   1.052   1.120   1.047   1.074   1.139
120   N         0.998   1.015   1.061   1.121   1.144   1.199   1.047   1.074   1.139
121   Q        -1.172  -0.994  -0.988  -1.188  -0.971  -0.968  -1.249  -1.033  -1.012
122   A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
123   P         0.998   1.015   1.061   1.210   1.226   1.274   1.047   1.074   1.139
124   K         0.998   1.015   1.061   0.875   0.917   0.994   1.047   1.074   1.139
125   Q         0.998   1.015   1.061   1.054   1.087   1.144   1.047   1.074   1.139
126   R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
127   R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
128   R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
129   T         0.998   1.015   1.061   1.075   1.105   1.161   1.047   1.074   1.139
130   Y         0.238   0.411  -0.150   0.617   0.796   0.079   0.282   0.503  -0.325
131   R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
132   A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
133   H         0.998   1.015   1.061   1.241   1.257   1.300   1.047   1.074   1.139
134   G         0.998   1.015   1.061   1.068   1.088   1.155   1.047   1.074   1.139
135   R         0.998   1.015   1.061   0.794   0.834   0.926   1.047   1.074   1.139
136   I        -0.157  -0.153  -0.185  -0.011  -0.026  -0.120  -0.292  -0.300  -0.384
137   N        -0.157  -0.153  -0.185   0.002  -0.006  -0.100  -0.292  -0.300  -0.384
138   K        -1.045  -1.001  -0.984  -1.479  -1.319  -1.213  -1.154  -1.039  -1.007
139   Y         0.998   1.015   1.061   1.207   1.229   1.272   1.047   1.074   1.139
140   E        -1.860  -1.835  -1.572  -1.679  -1.601  -1.232  -1.728  -1.656  -1.336
141   S         0.998   1.015   1.061   0.976   1.019   1.078   1.047   1.074   1.139
142   S        -0.493  -0.580  -0.961  -0.224  -0.333  -0.851  -0.388  -0.520  -0.978
143   P         0.998   1.015   1.061   1.210   1.226   1.274   1.047   1.074   1.139
144   S        -0.157  -0.221  -0.248  -0.054  -0.129  -0.157  -0.292  -0.410  -0.492
145   H         0.998   1.015   1.061   1.241   1.257   1.300   1.047   1.074   1.139
146   I         0.998   1.015   1.061   1.121   1.141   1.199   1.047   1.074   1.139
147   E         0.998   1.015   1.061   1.058   1.079   1.146   1.047   1.074   1.139
148   L        -0.157  -0.153  -0.185  -0.074  -0.083  -0.149  -0.292  -0.300  -0.384
149   V        -1.045  -0.730  -0.961  -0.925  -0.463  -0.790  -1.154  -0.733  -0.979
150   V        -0.500  -0.436  -0.262  -0.686  -0.602  -0.328  -0.867  -0.777  -0.516
151   T        -0.852  -0.930  -0.987  -0.791  -0.927  -1.089  -0.867  -0.959  -1.011
152   E         0.998   1.015   1.061   1.058   1.079   1.146   1.047   1.074   1.139
153   K        -1.651  -1.690  -1.561  -1.629  -1.668  -1.516  -1.536  -1.514  -1.325
154   E        -1.507  -1.531  -1.562  -1.199  -1.296  -1.359  -1.345  -1.378  -1.327
155   E         0.998   1.015   1.061   1.058   1.079   1.146   1.047   1.074   1.139
156   A        -1.188  -1.345  -1.545  -1.235  -1.449  -1.580  -0.962  -1.150  -1.309
157   V         0.238   0.143  -0.171   0.424   0.316  -0.129   0.282   0.148  -0.360
158   A        -1.860  -1.853  -1.576  -1.982  -1.932  -1.522  -1.728  -1.675  -1.340
159   K         0.998   1.015   1.061   0.875   0.917   0.994   1.047   1.074   1.139
160   A        -0.493  -0.580  -0.961  -0.636  -0.754  -1.138  -0.388  -0.520  -0.978
161   A        -3.121  -2.923  -2.665  -2.882  -2.559  -2.224  -2.206  -2.029  -1.711
162   E        -1.045  -1.138  -1.013  -0.940  -1.112  -0.977  -1.154  -1.230  -1.045
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   K        -2.218  -2.232  -2.019  -2.124  -2.232  -1.904  -1.800  -1.805  -1.520
166   K        -1.507  -1.701  -1.575  -1.382  -1.637  -1.460  -1.345  -1.527  -1.338
167   V        -2.114  -2.039  -1.993  -1.809  -1.745  -1.699  -1.728  -1.647  -1.501
168   V        -1.860  -1.668  -1.554  -2.107  -1.905  -1.619  -1.728  -1.522  -1.320
169   R        -0.157  -0.305  -0.260  -0.267  -0.468  -0.352  -0.292  -0.551  -0.513
170   L        -0.852  -0.930  -0.987  -0.670  -0.787  -0.873  -0.867  -0.959  -1.011
171   T        -0.852  -0.550  -0.959  -0.697  -0.315  -0.847  -0.867  -0.503  -0.976
172   S        -0.852  -0.766  -0.966  -0.735  -0.636  -0.913  -0.867  -0.779  -0.984
173   R        -0.157  -0.153  -0.185  -0.375  -0.369  -0.432  -0.292  -0.300  -0.384
174   Q         0.998   1.015   1.061   1.054   1.087   1.144   1.047   1.074   1.139
175   R        -0.157  -0.153  -0.185  -0.318  -0.312  -0.348  -0.292  -0.300  -0.384
176   G        -0.157  -0.153  -0.185  -0.185  -0.211  -0.345  -0.292  -0.300  -0.384
177   R        -0.852  -1.017  -0.996  -1.041  -1.322  -1.358  -0.867  -1.061  -1.021
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   I        -0.444  -0.356  -0.256  -0.529  -0.405  -0.266  -0.769  -0.637  -0.506
182   A         0.238   0.033  -0.178  -0.079  -0.332  -0.633   0.282  -0.012  -0.372
183   A        -1.778  -1.652  -1.561  -2.052  -1.858  -1.644  -1.632  -1.465  -1.326
184   Q        -0.390  -0.413  -0.265  -0.563  -0.660  -0.451  -0.675  -0.736  -0.521
185   K         0.238   0.033  -0.178   0.232  -0.024  -0.389   0.282  -0.012  -0.372
186   R        -0.390  -0.413  -0.265  -0.916  -1.021  -0.764  -0.675  -0.736  -0.521
187   I        -0.493  -0.292  -0.939  -0.101   0.121  -0.767  -0.388  -0.149  -0.950
188   A        -0.493  -0.405  -0.946  -0.216  -0.108  -0.999  -0.388  -0.301  -0.960
189   -        -0.093   0.034  -0.193  -0.470  -0.282  -0.555  -0.193  -0.011  -0.397
190   A         0.998   1.015   1.061   0.568   0.612   0.736   1.047   1.074   1.139
* 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/P05740
Output conservation file - output/P05740
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
