1     M         1.548   1.574   1.730   2.306   2.323   2.619   1.702   1.752   2.017
2     E         0.371   0.421   0.408   0.394   0.483   0.211   0.183   0.262   0.173
3     K         0.759   0.740   0.542   0.867   0.864   0.595   0.816   0.789   0.425
4     I        -0.492  -0.446  -0.425  -0.417  -0.335  -0.234  -0.704  -0.646  -0.573
5     K         0.371   0.316   0.356   0.327   0.254   0.318   0.183   0.073   0.072
6     E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
7     K         1.548   1.574   1.730   1.568   1.622   1.890   1.702   1.752   2.017
8     L        -0.717  -0.671  -0.500  -0.576  -0.493  -0.232  -0.957  -0.897  -0.664
9     N         0.008   0.098  -0.282   0.630   0.766   0.172   0.056   0.179  -0.354
10    S        -0.991  -1.103  -1.022  -0.566  -0.727  -0.678  -0.957  -1.069  -0.939
11    L         0.759   0.590   0.517   0.867   0.634   0.506   0.816   0.550   0.379
12    K         0.163   0.155   0.321   0.013   0.028   0.307  -0.197  -0.231   0.004
13    L         0.759   0.590   0.517   0.867   0.634   0.506   0.816   0.550   0.379
14    E         0.371   0.554   0.501  -0.365  -0.077  -0.147   0.183   0.491   0.350
15    S        -0.337  -0.389  -0.411   0.024  -0.081  -0.124  -0.451  -0.539  -0.548
16    E         0.163   0.155   0.321  -0.645  -0.581  -0.269  -0.197  -0.231   0.004
17    S        -1.217  -1.119  -1.046  -1.723  -1.663  -1.612  -1.211  -1.108  -0.964
18    W         0.163   0.155   0.321   0.571   0.500   0.726  -0.197  -0.231   0.004
19    Q         0.008  -0.181  -0.335   0.550   0.292   0.039   0.056  -0.209  -0.430
20    E        -0.337  -0.360  -0.414  -1.039  -1.052  -1.024  -0.451  -0.522  -0.554
21    K         0.759   0.590   0.517   0.867   0.662   0.556   0.816   0.550   0.379
22    Y        -1.217  -1.162  -1.046  -0.703  -0.629  -0.489  -1.211  -1.142  -0.964
23    E         0.163   0.292   0.383  -0.645  -0.460  -0.297  -0.197   0.028   0.125
24    E         0.759   0.590   0.517   0.171  -0.047  -0.154   0.816   0.550   0.379
25    L        -0.337  -0.295  -0.396  -0.309  -0.292  -0.349  -0.451  -0.433  -0.527
26    R        -2.079  -2.071  -1.899  -2.312  -2.487  -2.233  -1.591  -1.563  -1.332
27    E        -0.991  -1.022  -0.989  -1.594  -1.613  -1.489  -0.957  -0.968  -0.897
28    Q        -0.717  -0.596  -0.458  -0.848  -0.704  -0.499  -0.957  -0.808  -0.611
29    L        -1.217  -1.173  -1.045  -0.827  -0.838  -0.626  -1.211  -1.161  -0.965
30    K         1.548   1.574   1.730   1.568   1.622   1.890   1.702   1.752   2.017
31    E        -0.991  -0.911  -0.984  -1.520  -1.398  -1.361  -0.957  -0.866  -0.899
32    L         0.008  -0.101  -0.321   0.188   0.052  -0.273   0.056  -0.105  -0.411
33    E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
34    Q         0.759   0.590   0.517   1.169   0.899   0.701   0.816   0.550   0.379
35    S        -0.699  -0.828  -0.961  -1.228  -1.383  -1.488  -0.577  -0.739  -0.864
36    N        -0.337  -0.331  -0.406  -0.159  -0.194  -0.481  -0.451  -0.472  -0.543
37    T        -0.991  -1.063  -1.020  -0.865  -0.935  -0.829  -0.957  -1.029  -0.935
38    E        -1.217  -1.209  -1.042  -1.631  -1.586  -1.489  -1.211  -1.178  -0.960
39    K         0.759   0.842   0.551   0.849   0.978   0.566   0.816   0.942   0.441
40    E         0.163   0.292   0.383  -0.645  -0.460  -0.297  -0.197   0.028   0.125
41    N        -0.337  -0.368  -0.428   0.106   0.012  -0.059  -0.451  -0.531  -0.572
42    E        -0.337  -0.123  -0.310  -1.155  -0.809  -1.161  -0.451  -0.142  -0.395
43    I         0.759   0.590   0.517   1.543   1.323   1.212   0.816   0.550   0.379
44    K        -1.080  -1.150  -1.040  -1.364  -1.573  -1.469  -1.084  -1.131  -0.957
45    S         0.371   0.519   0.425   0.709   0.947   0.732   0.183   0.431   0.206
46    L         1.548   1.574   1.730   1.600   1.638   1.921   1.702   1.752   2.017
47    S         0.163   0.148   0.320   0.380   0.328   0.576  -0.197  -0.245   0.002
48    A        -1.580  -1.509  -1.489  -0.822  -0.742  -0.726  -1.337  -1.262  -1.163
49    K         1.548   1.574   1.730   1.568   1.622   1.890   1.702   1.752   2.017
50    N         0.759   0.590   0.517   1.331   1.107   0.954   0.816   0.550   0.379
51    E        -0.628  -0.651  -0.496  -0.911  -1.096  -0.976  -0.831  -0.869  -0.660
52    Q        -1.580  -1.577  -1.501  -1.123  -1.148  -1.118  -1.337  -1.328  -1.173
53    L         0.759   0.590   0.517   0.867   0.634   0.506   0.816   0.550   0.379
54    D         0.371   0.397   0.410  -0.365  -0.309  -0.269   0.183   0.219   0.177
55    S        -0.492  -0.459  -0.420  -1.164  -0.957  -0.859  -0.704  -0.668  -0.567
56    E         0.371   0.335   0.363  -0.399  -0.438  -0.369   0.183   0.107   0.087
57    V         0.759   0.590   0.517   1.414   1.135   0.934   0.816   0.550   0.379
58    E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
59    K         0.008  -0.092  -0.315  -0.038  -0.259  -0.741   0.056  -0.094  -0.402
60    L         1.548   1.574   1.730   1.600   1.638   1.921   1.702   1.752   2.017
61    E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
62    S        -1.942  -1.944  -1.875  -1.481  -1.651  -1.535  -1.464  -1.460  -1.314
63    Q        -0.699  -0.616  -0.929  -0.361  -0.365  -0.927  -0.577  -0.502  -0.827
64    L        -0.991  -1.072  -1.008  -0.799  -0.876  -0.727  -0.957  -1.041  -0.925
65    S        -1.080  -0.871  -0.984  -1.027  -0.779  -0.875  -1.084  -0.879  -0.903
66    D         0.008  -0.156  -0.323  -0.546  -0.757  -0.973   0.056  -0.177  -0.414
67    T        -2.079  -2.045  -1.900  -1.332  -1.346  -1.130  -1.591  -1.545  -1.333
68    K         0.759   0.590   0.517   0.867   0.662   0.556   0.816   0.550   0.379
69    Q        -1.580  -1.598  -1.482  -1.883  -1.883  -1.834  -1.337  -1.338  -1.157
70    L        -1.080  -1.077  -1.021  -1.172  -1.217  -1.105  -1.084  -1.072  -0.939
71    A         1.548   1.574   1.730   1.973   1.990   2.290   1.702   1.752   2.017
72    E         0.163   0.202   0.343  -0.645  -0.566  -0.315  -0.197  -0.140   0.046
73    D        -0.492  -0.580  -0.431  -1.138  -1.142  -0.884  -0.704  -0.792  -0.580
74    S        -0.337  -0.460  -0.426  -0.003  -0.274  -0.338  -0.451  -0.605  -0.567
75    N        -1.716  -1.708  -1.518  -1.153  -1.158  -0.924  -1.464  -1.434  -1.188
76    N        -1.716  -1.718  -1.510  -1.234  -1.179  -0.949  -1.464  -1.441  -1.181
77    L        -0.337  -0.368  -0.428  -0.315  -0.388  -0.390  -0.451  -0.531  -0.572
78    R        -0.337  -0.320  -0.387  -0.212  -0.165  -0.207  -0.451  -0.427  -0.512
79    S        -0.492  -0.412  -0.425  -0.208  -0.090  -0.119  -0.704  -0.605  -0.570
80    N        -2.079  -2.071  -1.899  -1.694  -1.836  -1.600  -1.591  -1.563  -1.332
81    N         0.759   0.590   0.517   1.322   1.090   0.931   0.816   0.550   0.379
82    E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
83    N        -0.699  -0.823  -0.979  -0.007  -0.194  -0.438  -0.577  -0.734  -0.885
84    Y        -0.717  -0.639  -0.488  -0.512  -0.456  -0.203  -0.957  -0.854  -0.648
85    T        -0.492  -0.457  -0.417  -0.192  -0.143  -0.085  -0.704  -0.665  -0.564
86    K         0.371   0.274   0.358   0.327   0.188   0.321   0.183  -0.005   0.076
87    K         0.759   0.740   0.542   0.867   0.864   0.595   0.816   0.789   0.425
88    N        -0.991  -1.016  -1.009  -0.619  -0.654  -0.658  -0.957  -0.988  -0.924
89    Q         0.008  -0.101  -0.321   0.340   0.084  -0.423   0.056  -0.105  -0.411
90    D        -2.079  -1.957  -1.884  -1.555  -1.464  -1.302  -1.591  -1.473  -1.320
91    L         1.548   1.574   1.730   1.600   1.638   1.921   1.702   1.752   2.017
92    E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
93    Q         0.759   0.768   0.545   0.168   0.200  -0.119   0.816   0.832   0.430
94    Q         0.008   0.062  -0.284  -0.546  -0.453  -0.924   0.056   0.130  -0.358
95    L         0.759   0.740   0.542   0.867   0.848   0.549   0.816   0.789   0.425
96    E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
97    D        -0.699  -0.801  -0.952  -1.189  -1.289  -1.409  -0.577  -0.709  -0.854
98    S        -1.217  -1.182  -1.053  -0.929  -0.871  -0.698  -1.211  -1.170  -0.973
99    E         0.759   0.768   0.545   1.165   1.169   0.623   0.816   0.832   0.430
100   A        -0.991  -0.906  -0.996  -0.911  -0.784  -0.872  -0.957  -0.854  -0.911
101   K        -1.080  -1.150  -1.040  -1.123  -1.236  -1.109  -1.084  -1.131  -0.957
102   L         1.548   1.574   1.730   1.600   1.638   1.921   1.702   1.752   2.017
103   K         0.163   0.155   0.321   0.013   0.028   0.307  -0.197  -0.231   0.004
104   E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
105   A         0.759   0.768   0.545   1.346   1.356   1.006   0.816   0.832   0.430
106   M        -0.699  -0.711  -0.934   0.017   0.007  -0.348  -0.577  -0.590  -0.833
107   D         0.371   0.397   0.410  -0.365  -0.309  -0.269   0.183   0.219   0.177
108   K         0.759   0.797   0.546   0.867   0.935   0.601   0.816   0.875   0.432
109   L         0.759   0.590   0.517   0.919   0.714   0.640   0.816   0.550   0.379
110   K         0.371   0.397   0.410   0.715   0.731   0.635   0.183   0.219   0.177
111   E         0.163   0.155   0.321  -0.700  -0.644  -0.339  -0.197  -0.231   0.004
112   A        -0.337  -0.278  -0.395   0.119   0.207   0.005  -0.451  -0.369  -0.523
113   D         0.759   0.797   0.546   1.165   1.216   0.626   0.816   0.875   0.432
114   L        -0.492  -0.372  -0.413  -0.311  -0.142  -0.153  -0.704  -0.564  -0.554
115   N         0.371   0.397   0.410   0.287   0.351   0.331   0.183   0.219   0.177
116   S        -0.337  -0.261  -0.391   0.039   0.125  -0.051  -0.451  -0.358  -0.517
117   E         0.759   0.740   0.542   0.240   0.242   0.055   0.816   0.789   0.425
118   Q        -0.492  -0.460  -0.433  -0.119  -0.048   0.006  -0.704  -0.670  -0.583
119   M        -0.492  -0.479  -0.435  -0.326  -0.232  -0.108  -0.704  -0.688  -0.584
120   G         0.759   0.768   0.545   0.240   0.275   0.058   0.816   0.832   0.430
121   R         1.548   1.574   1.730   2.170   2.178   2.484   1.702   1.752   2.017
122   R         0.371   0.285   0.347   0.327   0.206   0.309   0.183   0.016   0.054
123   I         0.008   0.030  -0.298   0.800   0.824   0.332   0.056   0.087  -0.378
124   V        -1.217  -1.187  -1.060  -0.928  -0.896  -0.696  -1.211  -1.173  -0.979
125   A         0.163   0.185   0.331   0.310   0.329   0.530  -0.197  -0.173   0.024
126   L         1.548   1.574   1.730   1.600   1.638   1.921   1.702   1.752   2.017
127   E         0.759   0.797   0.546   0.168   0.238  -0.117   0.816   0.875   0.432
128   E        -1.716  -1.716  -1.515  -1.925  -1.903  -1.590  -1.464  -1.440  -1.185
129   E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
130   R         0.371   0.554   0.501   0.715   1.029   0.861   0.183   0.491   0.350
131   D         0.371   0.554   0.501   0.394   0.776   0.504   0.183   0.491   0.350
132   E        -0.492  -0.494  -0.425  -1.164  -1.070  -0.883  -0.704  -0.703  -0.573
133   W         0.008  -0.092  -0.315   0.875   0.738   0.290   0.056  -0.094  -0.402
134   E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
135   K        -0.699  -0.780  -0.944  -0.546  -0.651  -0.900  -0.577  -0.688  -0.844
136   K         1.548   1.574   1.730   1.568   1.622   1.890   1.702   1.752   2.017
137   C        -1.580  -1.559  -1.475  -0.698  -0.728  -0.602  -1.337  -1.298  -1.148
138   E         0.759   0.842   0.551   0.183   0.308  -0.073   0.816   0.942   0.441
139   E         0.008   0.181  -0.261  -0.546  -0.298  -0.895   0.056   0.290  -0.325
140   F        -0.991  -1.024  -1.019  -0.695  -0.682  -0.585  -0.957  -1.008  -0.936
141   Q        -1.217  -1.145  -1.053  -1.045  -0.936  -0.890  -1.211  -1.132  -0.972
142   S        -1.942  -1.988  -1.887  -2.519  -2.465  -2.195  -1.464  -1.496  -1.323
143   K         0.008   0.276  -0.263   0.135   0.501  -0.259   0.056   0.415  -0.327
144   Y         0.759   0.885   0.559   1.617   1.763   1.353   0.816   1.005   0.456
145   E        -1.580  -1.621  -1.511  -1.653  -1.741  -1.603  -1.337  -1.364  -1.181
146   E        -0.991  -1.091  -1.018  -1.199  -1.503  -1.545  -0.957  -1.066  -0.935
147   A         0.371   0.274   0.358   0.721   0.539   0.665   0.183  -0.005   0.076
148   Q         0.371   0.366   0.374   0.251   0.256   0.215   0.183   0.163   0.107
149   K         0.097   0.139   0.321  -0.174  -0.107   0.163  -0.324  -0.262   0.003
150   E         0.759   0.740   0.542   0.183   0.180  -0.087   0.816   0.789   0.425
151   L         1.548   1.574   1.730   1.600   1.638   1.921   1.702   1.752   2.017
152   D         0.097   0.140   0.321  -0.592  -0.478  -0.223  -0.324  -0.260   0.003
153   E         1.548   1.574   1.730   0.913   0.964   1.242   1.702   1.752   2.017
154   I        -0.337  -0.473  -0.417   0.380   0.193   0.249  -0.451  -0.625  -0.557
155   A        -1.580  -1.626  -1.510  -1.064  -1.102  -0.963  -1.337  -1.368  -1.181
156   N        -0.628  -0.590  -0.480  -0.474  -0.414  -0.297  -0.831  -0.782  -0.637
157   S        -1.080  -1.150  -1.040  -0.793  -0.870  -0.737  -1.084  -1.131  -0.957
158   L         0.759   0.740   0.542   0.908   0.895   0.648   0.816   0.789   0.425
159   E         0.759   0.740   0.542   0.171   0.164  -0.115   0.816   0.789   0.425
160   N        -0.991  -0.958  -0.981  -0.561  -0.475  -0.573  -0.957  -0.900  -0.888
161   L         0.097   0.149   0.328   0.046   0.097   0.364  -0.324  -0.242   0.017
* 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/P40414
Output conservation file - output/P40414
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
