1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    M         1.164   1.245   1.297   1.436   1.531   1.598   1.229   1.336   1.423
12    S         1.164   1.245   1.297   0.863   1.017   1.124   1.229   1.336   1.423
13    R        -0.530  -0.883  -0.854  -0.174  -0.654  -0.637  -0.481  -0.914  -0.878
14    S         1.164   1.245   1.297   0.863   1.017   1.124   1.229   1.336   1.423
15    G         1.164   1.245   1.297   1.184   1.321   1.390   1.229   1.336   1.423
16    V         1.164   1.245   1.297   1.032   1.176   1.263   1.229   1.336   1.423
17    A        -1.308  -1.473  -1.449  -1.110  -1.340  -1.295  -1.139  -1.289  -1.207
18    V         1.164   1.245   1.297   1.032   1.176   1.263   1.229   1.336   1.423
19    A        -1.308  -1.493  -1.454  -1.184  -1.518  -1.452  -1.139  -1.306  -1.212
20    D        -0.131  -0.250  -0.094  -0.189  -0.346  -0.103  -0.350  -0.570  -0.353
21    E         0.296   0.491   0.049   0.230   0.500  -0.154   0.308   0.580  -0.107
22    S        -0.909  -0.859  -0.874  -1.046  -0.874  -0.862  -1.008  -0.961  -0.907
23    L        -0.530  -0.637  -0.827  -0.320  -0.487  -0.728  -0.481  -0.640  -0.844
24    T        -2.277  -2.151  -1.919  -1.912  -1.802  -1.452  -1.929  -1.694  -1.408
25    A         1.164   1.245   1.297   1.043   1.178   1.273   1.229   1.336   1.423
26    F         1.164   1.245   1.297   1.207   1.334   1.408   1.229   1.336   1.423
27    N        -0.530  -0.883  -0.854  -0.115  -0.639  -0.636  -0.481  -0.914  -0.878
28    D        -0.909  -1.081  -0.882  -1.042  -1.340  -1.056  -1.008  -1.159  -0.916
29    L         1.164   1.245   1.297   1.123   1.260   1.339   1.229   1.336   1.423
30    K         1.164   1.245   1.297   1.017   1.130   1.251   1.229   1.336   1.423
31    L         0.296   0.000  -0.002   0.422   0.077   0.063   0.308  -0.146  -0.192
32    G         0.296   0.000  -0.002   0.402  -0.034  -0.121   0.308  -0.146  -0.192
33    K        -0.909  -0.786  -0.861  -0.922  -0.809  -0.771  -1.008  -0.870  -0.893
34    K        -0.530  -0.883  -0.854  -0.464  -0.941  -0.926  -0.481  -0.914  -0.878
35    Y        -0.909  -0.859  -0.874  -0.842  -0.861  -0.882  -1.008  -0.961  -0.907
36    K        -0.909  -0.859  -0.874  -0.967  -0.927  -0.861  -1.008  -0.961  -0.907
37    F        -0.131  -0.250  -0.094  -0.114  -0.339  -0.119  -0.350  -0.570  -0.353
38    I        -0.360  -0.202  -0.086  -0.575  -0.344  -0.190  -0.745  -0.487  -0.340
39    L        -1.080  -0.906  -0.839  -1.165  -0.852  -0.798  -1.271  -0.946  -0.862
40    F        -0.360  -0.264  -0.095  -0.504  -0.365  -0.119  -0.745  -0.594  -0.354
41    G        -2.277  -1.615  -1.868  -2.375  -1.395  -1.780  -1.929  -1.196  -1.368
42    L        -0.530  -0.469  -0.796  -0.289  -0.182  -0.616  -0.481  -0.386  -0.805
43    N         0.296   0.000  -0.002   0.551   0.097  -0.006   0.308  -0.146  -0.192
44    D         1.164   1.245   1.297   1.072   1.203   1.296   1.229   1.336   1.423
45    A        -2.676  -2.430  -2.287  -2.526  -2.232  -2.025  -2.061  -1.756  -1.530
46    K         0.296   0.000  -0.002   0.280  -0.109  -0.111   0.308  -0.146  -0.192
47    T         0.296   0.000  -0.002   0.450   0.012  -0.040   0.308  -0.146  -0.192
48    E         0.296   0.519   0.049   0.310   0.588   0.044   0.308   0.617  -0.107
49    I         1.164   1.245   1.297   1.246   1.334   1.440   1.229   1.336   1.423
50    V         0.296   0.576   0.055   0.303   0.667   0.007   0.308   0.689  -0.096
51    V         0.296   0.000  -0.002   0.303  -0.070  -0.082   0.308  -0.146  -0.192
52    K        -0.360  -0.031  -0.034  -0.792  -0.226  -0.251  -0.745  -0.196  -0.247
53    E        -1.308  -1.473  -1.449  -1.208  -1.579  -1.452  -1.139  -1.289  -1.207
54    T        -0.530  -0.469  -0.796  -0.308  -0.237  -0.787  -0.481  -0.386  -0.805
55    S         0.296   0.491   0.049   0.125   0.415  -0.156   0.308   0.580  -0.107
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    T        -1.629  -1.310  -1.428  -1.560  -1.197  -1.336  -1.534  -1.174  -1.191
59    D        -1.878  -1.533  -1.456  -1.981  -1.483  -1.322  -1.797  -1.377  -1.216
60    P        -2.826  -2.553  -2.294  -2.495  -2.256  -1.916  -2.192  -1.834  -1.534
61    S        -1.727  -1.620  -1.452  -1.990  -1.700  -1.484  -1.666  -1.449  -1.211
62    Y         0.296   0.237   0.031   0.499   0.440   0.109   0.308   0.222  -0.136
63    D         1.164   1.245   1.297   1.072   1.203   1.296   1.229   1.336   1.423
64    A        -1.629  -1.584  -1.459  -1.679  -1.662  -1.454  -1.534  -1.422  -1.218
65    F         1.164   1.245   1.297   1.207   1.334   1.408   1.229   1.336   1.423
66    L         0.296   0.000  -0.002   0.394   0.018  -0.012   0.308  -0.146  -0.192
67    E        -0.131  -0.057  -0.063  -0.316  -0.200  -0.222  -0.350  -0.239  -0.299
68    K        -0.530  -0.393  -0.785  -0.430  -0.278  -0.747  -0.481  -0.301  -0.791
69    L         1.164   1.245   1.297   1.123   1.260   1.339   1.229   1.336   1.423
70    P         0.296   0.000  -0.002   0.639   0.199   0.107   0.308  -0.146  -0.192
71    E         0.296   0.000  -0.002   0.299  -0.064  -0.059   0.308  -0.146  -0.192
72    N        -0.530  -0.883  -0.854  -0.183  -0.744  -0.805  -0.481  -0.914  -0.878
73    D        -0.909  -0.930  -0.857  -0.964  -0.917  -0.848  -1.008  -0.970  -0.883
74    C         0.296   0.000  -0.002   0.753   0.320   0.243   0.308  -0.146  -0.192
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    L        -1.080  -0.624  -0.818  -1.164  -0.459  -0.761  -1.271  -0.640  -0.836
87    Y         1.164   1.245   1.297   1.235   1.350   1.431   1.229   1.336   1.423
88    A         1.164   1.245   1.297   1.043   1.178   1.273   1.229   1.336   1.423
89    I        -0.360  -0.161  -0.074  -0.651  -0.329  -0.195  -0.745  -0.414  -0.317
90    Y         1.164   1.245   1.297   1.235   1.350   1.431   1.229   1.336   1.423
91    D         1.164   1.245   1.297   1.072   1.203   1.296   1.229   1.336   1.423
92    F         1.164   1.245   1.297   1.207   1.334   1.408   1.229   1.336   1.423
93    E         1.164   1.245   1.297   1.014   1.138   1.249   1.229   1.336   1.423
94    Y         0.296   0.237   0.031   0.499   0.440   0.109   0.308   0.222  -0.136
95    E        -2.028  -2.001  -1.912  -1.806  -1.850  -1.629  -1.666  -1.572  -1.403
96    I        -0.360  -0.270  -0.086  -0.528  -0.444  -0.154  -0.745  -0.605  -0.339
97    N        -1.777  -1.601  -1.470  -1.904  -1.716  -1.462  -1.693  -1.439  -1.227
98    G        -1.777  -1.409  -1.450  -1.904  -1.472  -1.457  -1.693  -1.249  -1.209
99    N        -0.909  -0.418  -0.796  -0.839  -0.123  -0.733  -1.008  -0.327  -0.806
100   E         1.164   1.245   1.297   1.014   1.138   1.249   1.229   1.336   1.423
101   G         1.164   1.245   1.297   1.184   1.321   1.390   1.229   1.336   1.423
102   K        -0.530  -0.883  -0.854  -0.530  -1.101  -1.094  -0.481  -0.914  -0.878
103   R         1.164   1.245   1.297   1.251   1.357   1.445   1.229   1.336   1.423
104   S        -0.131  -0.250  -0.094  -0.412  -0.530  -0.267  -0.350  -0.570  -0.353
105   K         1.164   1.245   1.297   1.014   1.135   1.249   1.229   1.336   1.423
106   I        -0.530  -0.678  -0.828  -0.255  -0.545  -0.776  -0.481  -0.684  -0.845
107   V        -0.530  -0.883  -0.854  -0.417  -0.884  -0.842  -0.481  -0.914  -0.878
108   F         1.164   1.245   1.297   1.207   1.334   1.408   1.229   1.336   1.423
109   F        -0.131  -0.250  -0.094  -0.110  -0.349  -0.112  -0.350  -0.570  -0.353
110   T        -0.530  -0.883  -0.854  -0.328  -0.893  -0.949  -0.481  -0.914  -0.878
111   W         1.164   1.245   1.297   1.495   1.592   1.647   1.229   1.336   1.423
112   S         1.164   1.245   1.297   0.863   1.017   1.124   1.229   1.336   1.423
113   P         1.164   1.245   1.297   1.399   1.509   1.567   1.229   1.336   1.423
114   D         1.164   1.245   1.297   1.072   1.203   1.296   1.229   1.336   1.423
115   T        -0.530  -0.883  -0.854  -0.296  -0.839  -0.868  -0.481  -0.914  -0.878
116   A         1.164   1.245   1.297   1.043   1.178   1.273   1.229   1.336   1.423
117   P        -0.530  -0.637  -0.827  -0.119  -0.310  -0.706  -0.481  -0.640  -0.844
118   V        -0.360  -0.270  -0.086  -0.651  -0.498  -0.188  -0.745  -0.606  -0.339
119   R        -0.360  -0.270  -0.086  -0.579  -0.520  -0.220  -0.745  -0.606  -0.339
120   S        -0.530  -0.161  -0.771  -0.588  -0.091  -0.851  -0.481   0.005  -0.773
121   K         1.164   1.245   1.297   1.014   1.135   1.249   1.229   1.336   1.423
122   M         1.164   1.245   1.297   1.436   1.531   1.598   1.229   1.336   1.423
123   V        -0.131   0.156  -0.026  -0.279   0.158  -0.121  -0.350   0.100  -0.234
124   Y         1.164   1.245   1.297   1.235   1.350   1.431   1.229   1.336   1.423
125   A         0.296   0.237   0.031   0.259   0.203  -0.165   0.308   0.222  -0.136
126   S         1.164   1.245   1.297   0.863   1.017   1.124   1.229   1.336   1.423
127   S         1.164   1.245   1.297   0.863   1.017   1.124   1.229   1.336   1.423
128   K         1.164   1.245   1.297   1.014   1.135   1.249   1.229   1.336   1.423
129   D         0.296   0.000  -0.002   0.309  -0.109  -0.147   0.308  -0.146  -0.192
130   A        -0.909  -0.794  -0.840  -1.089  -0.849  -0.993  -1.008  -0.792  -0.864
131   L         1.164   1.245   1.297   1.123   1.260   1.339   1.229   1.336   1.423
132   R        -0.131  -0.178  -0.091  -0.141  -0.293  -0.207  -0.350  -0.444  -0.347
133   R         1.164   1.245   1.297   1.251   1.357   1.445   1.229   1.336   1.423
134   A         0.296   0.000  -0.002   0.259  -0.175  -0.230   0.308  -0.146  -0.192
135   L         0.296   0.237   0.031   0.388   0.351   0.024   0.308   0.222  -0.136
136   N        -0.909  -1.081  -0.882  -0.745  -1.084  -0.849  -1.008  -1.159  -0.916
137   G         1.164   1.245   1.297   1.184   1.321   1.390   1.229   1.336   1.423
138   V        -0.360  -0.266  -0.083  -0.651  -0.484  -0.180  -0.745  -0.597  -0.333
139   S        -1.080  -1.008  -0.857  -1.505  -1.287  -1.044  -1.271  -1.092  -0.886
140   T        -2.277  -2.012  -1.902  -2.286  -1.906  -1.770  -1.929  -1.583  -1.395
141   D        -0.360  -0.266  -0.094  -0.740  -0.615  -0.334  -0.745  -0.598  -0.353
142   V        -1.080  -1.069  -0.864  -1.202  -1.130  -0.857  -1.271  -1.144  -0.893
143   Q         1.164   1.245   1.297   1.409   1.489   1.576   1.229   1.336   1.423
144   G        -0.131  -0.250  -0.094  -0.197  -0.456  -0.245  -0.350  -0.570  -0.353
145   T         0.296   0.000  -0.002   0.495   0.117   0.087   0.308  -0.146  -0.192
146   D         0.296   0.000  -0.002   0.309  -0.109  -0.147   0.308  -0.146  -0.192
147   F         0.296   0.000  -0.002   0.501   0.133   0.113   0.308  -0.146  -0.192
148   S         0.296   0.000  -0.002   0.108  -0.270  -0.283   0.308  -0.146  -0.192
149   E         0.296   0.000  -0.002   0.260  -0.151  -0.167   0.308  -0.146  -0.192
150   V         0.296   0.000  -0.002   0.303  -0.070  -0.082   0.308  -0.146  -0.192
151   S        -0.909  -0.896  -0.847  -1.128  -1.076  -1.074  -1.008  -0.930  -0.870
152   Y         1.164   1.245   1.297   1.235   1.350   1.431   1.229   1.336   1.423
153   D        -0.131   0.205  -0.009  -0.353   0.158  -0.181  -0.350   0.174  -0.205
154   S        -1.629  -1.695  -1.464  -1.784  -1.734  -1.412  -1.534  -1.493  -1.222
155   V         0.296   0.000  -0.002   0.303  -0.070  -0.082   0.308  -0.146  -0.192
156   L        -0.530  -0.655  -0.828  -0.278  -0.474  -0.633  -0.481  -0.659  -0.845
157   E        -0.530  -0.597  -0.823  -0.498  -0.661  -0.958  -0.481  -0.600  -0.839
158   R        -1.080  -1.076  -0.863  -1.238  -1.186  -0.860  -1.271  -1.153  -0.892
159   V         1.164   1.245   1.297   1.032   1.176   1.263   1.229   1.336   1.423
160   S         0.296   0.237   0.031   0.129   0.108  -0.172   0.308   0.222  -0.136
161   R        -0.131  -0.165  -0.089  -0.141  -0.267  -0.201  -0.350  -0.422  -0.344
162   G         0.126   0.403   0.009   0.199   0.596  -0.038   0.060   0.461  -0.175
163   A         0.126  -0.155  -0.051   0.075  -0.334  -0.168   0.060  -0.404  -0.277
164   G         0.219  -0.121  -0.039   0.318  -0.216  -0.139   0.198  -0.347  -0.256
165   S         0.126   0.188  -0.051  -0.101   0.020  -0.304   0.060   0.149  -0.277
166   H        -0.530  -0.883  -0.854  -0.018  -0.605  -0.693  -0.481  -0.914  -0.878
* 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/Q03048
Output conservation file - output/Q03048
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
