1     M         1.928   1.929   1.999   2.238   2.242   2.356   2.190   2.192   2.307
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    Q         0.574   0.606   0.601   0.627   0.660   0.670   0.333   0.392   0.358
18    D         0.574   0.606   0.601   0.330   0.392   0.368   0.333   0.392   0.358
19    N         0.574   0.606   0.601   0.439   0.486   0.463   0.333   0.392   0.358
20    S        -0.409  -0.401  -0.349  -0.452  -0.427  -0.358  -0.596  -0.585  -0.510
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    -         0.574   0.593   0.592   0.542   0.555   0.566   0.333   0.368   0.340
38    -        -0.409  -0.402  -0.349  -0.373  -0.345  -0.279  -0.596  -0.587  -0.510
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    S         0.574   0.606   0.603   0.807   0.874   0.841   0.333   0.392   0.361
43    H         0.732   0.744   0.675   0.906   0.913   0.832   0.623   0.643   0.497
44    S        -0.284  -0.262  -0.297  -0.495  -0.408  -0.529  -0.422  -0.391  -0.438
45    R        -0.284  -0.293  -0.275  -0.267  -0.302  -0.256  -0.422  -0.435  -0.407
46    E         0.454   0.455   0.517   0.166   0.152   0.266   0.101   0.102   0.194
47    S        -1.021  -1.019  -0.964  -0.923  -0.902  -0.834  -0.944  -0.942  -0.862
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    A        -0.284  -0.286  -0.268  -0.044  -0.033  -0.026  -0.422  -0.426  -0.397
55    S        -1.495  -1.491  -1.441  -1.460  -1.446  -1.375  -1.153  -1.150  -1.073
56    A        -0.906  -0.929  -0.918  -0.894  -0.975  -0.973  -0.819  -0.845  -0.813
57    G        -0.093  -0.096  -0.182  -0.117  -0.137  -0.234  -0.150  -0.155  -0.275
58    D        -0.906  -0.900  -0.916  -0.939  -0.929  -0.933  -0.819  -0.813  -0.811
59    D         0.864   0.823   0.750   0.728   0.654   0.529   0.853   0.782   0.637
60    P         0.864   0.823   0.750   1.328   1.272   1.149   0.853   0.782   0.637
61    L         0.864   0.883   0.758   0.723   0.736   0.586   0.853   0.884   0.653
62    G        -0.906  -0.900  -0.916  -0.675  -0.680  -0.721  -0.819  -0.813  -0.811
63    I         0.496   0.495   0.533   0.142   0.125   0.166   0.184   0.180   0.226
64    D         0.496   0.495   0.533   0.113   0.135   0.160   0.184   0.180   0.226
65    K        -0.093  -0.110  -0.174  -0.079  -0.058  -0.210  -0.150  -0.175  -0.263
66    L         1.928   1.929   1.999   1.714   1.706   1.827   2.190   2.192   2.307
67    T        -0.906  -0.865  -0.882  -0.646  -0.577  -0.604  -0.819  -0.772  -0.773
68    V         0.864   0.835   0.743   1.015   0.961   0.783   0.853   0.804   0.625
69    D         0.496   0.495   0.533   0.183   0.174   0.240   0.184   0.180   0.226
70    Y         0.864   0.885   0.757   1.155   1.182   1.007   0.853   0.888   0.649
71    D         1.928   1.929   1.999   1.825   1.824   1.939   2.190   2.192   2.307
72    Y         1.928   1.929   1.999   2.156   2.159   2.273   2.190   2.192   2.307
73    L         1.928   1.929   1.999   1.714   1.706   1.827   2.190   2.192   2.307
74    L        -0.316  -0.334  -0.307  -0.446  -0.474  -0.416  -0.485  -0.505  -0.457
75    Y         1.928   1.929   1.999   2.156   2.159   2.273   2.190   2.192   2.307
76    K         0.864   0.823   0.750   0.957   0.954   0.807   0.853   0.782   0.637
77    M         0.864   0.902   0.767   1.007   1.060   0.876   0.853   0.918   0.668
78    R        -1.495  -1.491  -1.441  -1.274  -1.252  -1.188  -1.153  -1.150  -1.073
79    D         1.928   1.929   1.999   1.825   1.824   1.939   2.190   2.192   2.307
80    Y        -0.906  -0.906  -0.888  -0.601  -0.610  -0.568  -0.819  -0.820  -0.779
81    V        -0.316  -0.306  -0.306  -0.461  -0.454  -0.471  -0.485  -0.473  -0.456
82    Q        -1.495  -1.491  -1.441  -1.500  -1.471  -1.416  -1.153  -1.150  -1.073
83    S        -0.093  -0.100  -0.222   0.137   0.142  -0.065  -0.150  -0.160  -0.331
84    I         0.496   0.515   0.552   0.054   0.071   0.138   0.184   0.219   0.262
85    Q        -0.906  -0.929  -0.918  -0.802  -0.852  -0.825  -0.819  -0.845  -0.813
86    L         0.496   0.495   0.533  -0.039  -0.063   0.006   0.184   0.180   0.226
87    D        -0.906  -0.920  -0.897  -1.104  -1.097  -1.110  -0.819  -0.836  -0.790
88    T         0.864   0.823   0.750   1.233   1.174   1.071   0.853   0.782   0.637
89    T        -0.906  -0.900  -0.916  -0.687  -0.687  -0.725  -0.819  -0.813  -0.811
90    E        -0.906  -0.929  -0.918  -0.985  -1.030  -0.995  -0.819  -0.845  -0.813
91    L        -0.906  -0.900  -0.916  -1.023  -1.025  -1.006  -0.819  -0.813  -0.811
92    C        -0.316  -0.328  -0.294  -0.095  -0.124  -0.071  -0.485  -0.498  -0.440
93    K        -0.906  -0.890  -0.905  -1.009  -0.980  -1.038  -0.819  -0.801  -0.799
94    K        -0.906  -0.929  -0.918  -0.716  -0.704  -0.705  -0.819  -0.845  -0.813
95    Q         0.496   0.495   0.533   0.320   0.340   0.360   0.184   0.180   0.226
96    N         0.496   0.495   0.533   0.387   0.379   0.435   0.184   0.180   0.226
97    E        -0.093  -0.100  -0.222  -0.208  -0.229  -0.430  -0.150  -0.160  -0.331
98    V        -1.495  -1.491  -1.441  -1.414  -1.448  -1.330  -1.153  -1.150  -1.073
99    M        -0.093  -0.086  -0.166   0.149   0.150   0.033  -0.150  -0.141  -0.251
100   V        -0.284  -0.262  -0.297  -0.319  -0.297  -0.354  -0.422  -0.391  -0.438
101   N        -0.906  -0.891  -0.891  -0.510  -0.495  -0.487  -0.819  -0.803  -0.783
102   G        -0.316  -0.334  -0.307  -0.340  -0.388  -0.322  -0.485  -0.505  -0.457
103   I        -0.316  -0.334  -0.307  -0.304  -0.333  -0.278  -0.485  -0.505  -0.457
104   I        -0.316  -0.334  -0.307  -0.631  -0.667  -0.601  -0.485  -0.505  -0.457
105   E        -0.093  -0.100  -0.222  -0.058  -0.076  -0.224  -0.150  -0.160  -0.331
106   N        -1.495  -1.491  -1.441  -1.529  -1.505  -1.446  -1.153  -1.150  -1.073
107   T        -0.316  -0.295  -0.301  -0.242  -0.227  -0.200  -0.485  -0.461  -0.450
108   I         0.496   0.495   0.533   0.142   0.125   0.166   0.184   0.180   0.226
109   D         0.864   0.835   0.743   0.780   0.733   0.595   0.853   0.804   0.625
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   K        -0.906  -0.930  -0.890  -0.999  -1.020  -0.982  -0.819  -0.846  -0.783
113   N         0.864   0.885   0.757   0.965   0.998   0.776   0.853   0.888   0.649
114   I         0.864   0.835   0.743   0.986   0.944   0.808   0.853   0.804   0.625
115   A        -0.906  -0.865  -0.882  -0.806  -0.769  -0.754  -0.819  -0.772  -0.773
116   K        -1.495  -1.491  -1.441  -1.222  -1.191  -1.135  -1.153  -1.150  -1.073
117   F        -0.316  -0.306  -0.306  -0.196  -0.188  -0.161  -0.485  -0.473  -0.456
118   K        -0.316  -0.334  -0.307  -0.531  -0.523  -0.485  -0.485  -0.505  -0.457
119   E        -0.906  -0.906  -0.888  -1.139  -1.146  -1.119  -0.819  -0.820  -0.779
120   L        -0.906  -0.929  -0.918  -1.013  -1.054  -0.997  -0.819  -0.845  -0.813
121   L         1.928   1.929   1.999   1.714   1.706   1.827   2.190   2.192   2.307
122   E        -1.495  -1.491  -1.441  -1.376  -1.339  -1.291  -1.153  -1.150  -1.073
123   K        -0.093  -0.148  -0.186   0.052   0.024  -0.062  -0.150  -0.228  -0.280
124   C        -0.093  -0.148  -0.186   0.222   0.114   0.016  -0.150  -0.228  -0.280
125   D        -0.093  -0.100  -0.222  -0.176  -0.188  -0.371  -0.150  -0.160  -0.331
126   T        -0.906  -0.891  -0.891  -1.009  -1.008  -0.983  -0.819  -0.803  -0.783
127   L         1.928   1.929   1.999   1.714   1.706   1.827   2.190   2.192   2.307
128   E         1.928   1.929   1.999   1.858   1.855   1.973   2.190   2.192   2.307
129   N        -1.495  -1.491  -1.441  -1.620  -1.599  -1.537  -1.153  -1.150  -1.073
130   H        -0.906  -0.929  -0.918  -0.696  -0.754  -0.766  -0.819  -0.845  -0.813
131   Y         0.496   0.515   0.552   0.607   0.640   0.692   0.184   0.219   0.262
132   E        -1.495  -1.491  -1.441  -1.577  -1.590  -1.494  -1.153  -1.150  -1.073
133   M        -0.316  -0.306  -0.306  -0.318  -0.274  -0.298  -0.485  -0.473  -0.456
134   L         0.864   0.823   0.750   0.717   0.648   0.566   0.853   0.782   0.637
135   N        -0.093  -0.096  -0.182  -0.262  -0.283  -0.420  -0.150  -0.155  -0.275
136   Q         0.864   0.883   0.758   1.061   1.082   0.917   0.853   0.884   0.653
137   L        -0.093  -0.111  -0.174  -0.291  -0.337  -0.409  -0.150  -0.177  -0.263
138   A        -0.906  -0.896  -0.886  -0.767  -0.767  -0.716  -0.819  -0.809  -0.777
139   I        -1.495  -1.491  -1.441  -1.305  -1.304  -1.220  -1.153  -1.150  -1.073
140   I         0.496   0.495   0.533   0.456   0.450   0.519   0.184   0.180   0.226
141   T        -0.316  -0.329  -0.297  -0.199  -0.225  -0.173  -0.485  -0.499  -0.444
142   D        -0.316  -0.306  -0.306  -0.652  -0.656  -0.617  -0.485  -0.473  -0.456
143   T        -0.316  -0.295  -0.301  -0.427  -0.398  -0.377  -0.485  -0.461  -0.450
144   F         1.928   1.929   1.999   2.259   2.264   2.377   2.190   2.192   2.307
145   K         1.928   1.929   1.999   1.945   2.005   2.060   2.190   2.192   2.307
146   E        -0.316  -0.329  -0.297  -0.469  -0.491  -0.425  -0.485  -0.499  -0.444
147   R         1.928   1.929   1.999   2.289   2.290   2.407   2.190   2.192   2.307
148   I         0.864   0.902   0.767   0.656   0.700   0.505   0.853   0.918   0.668
149   A        -0.906  -0.897  -0.918  -0.881  -0.863  -0.916  -0.819  -0.810  -0.813
150   E        -0.906  -0.891  -0.891  -0.725  -0.693  -0.702  -0.819  -0.803  -0.783
151   A        -0.316  -0.306  -0.306  -0.438  -0.439  -0.407  -0.485  -0.473  -0.456
152   V        -0.906  -0.897  -0.918  -0.894  -0.894  -0.890  -0.819  -0.810  -0.813
153   N        -1.495  -1.491  -1.441  -1.137  -1.124  -1.049  -1.153  -1.150  -1.073
154   N        -1.495  -1.491  -1.441  -1.248  -1.258  -1.161  -1.153  -1.150  -1.073
155   Y        -0.316  -0.334  -0.307  -0.275  -0.321  -0.288  -0.485  -0.505  -0.457
156   N        -0.284  -0.293  -0.275  -0.551  -0.535  -0.553  -0.422  -0.435  -0.407
157   S        -0.284  -0.278  -0.263  -0.495  -0.438  -0.470  -0.422  -0.414  -0.389
158   L        -0.284  -0.271  -0.265  -0.573  -0.581  -0.541  -0.422  -0.404  -0.392
159   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   S         0.574   0.614   0.598   0.488   0.571   0.503   0.333   0.406   0.352
166   K         1.928   1.929   1.999   1.936   1.943   2.051   2.190   2.192   2.307
* 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/Q06333
Output conservation file - output/Q06333
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
