1     M         1.040   1.058   1.127   1.394   1.408   1.476   1.099   1.130   1.231
2     A        -0.305  -0.231  -0.160  -0.659  -0.535  -0.404  -0.607  -0.500  -0.419
3     P         1.040   1.058   1.127   1.232   1.237   1.338   1.099   1.130   1.231
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    S        -2.504  -2.475  -2.244  -2.188  -2.191  -1.852  -1.934  -1.885  -1.570
18    A        -1.527  -1.392  -1.423  -1.658  -1.472  -1.386  -1.460  -1.314  -1.237
19    K        -0.079  -0.236  -0.166  -0.471  -0.660  -0.450  -0.228  -0.509  -0.429
20    A         0.303   0.376  -0.049   0.208   0.307  -0.210   0.340   0.438  -0.225
21    T        -1.730  -1.612  -1.459  -1.999  -1.838  -1.499  -1.650  -1.502  -1.270
22    A        -1.388  -1.571  -1.460  -1.481  -1.774  -1.604  -1.271  -1.448  -1.270
23    A         1.040   1.058   1.127   0.809   0.850   0.978   1.099   1.130   1.231
24    K        -0.753  -0.865  -0.883  -1.097  -1.252  -1.222  -0.797  -0.928  -0.938
25    K         0.303   0.118  -0.071  -0.006  -0.196  -0.369   0.340   0.068  -0.264
26    A        -0.079  -0.023  -0.093  -0.332  -0.239  -0.346  -0.228  -0.152  -0.301
27    V        -0.412  -0.353  -0.172  -0.895  -0.813  -0.511  -0.797  -0.718  -0.440
28    V        -1.202  -1.021  -0.887  -1.340  -1.053  -0.851  -1.366  -1.131  -0.944
29    K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
30    G         1.040   1.058   1.127   1.296   1.313   1.393   1.099   1.130   1.231
31    T        -1.063  -1.042  -0.913  -1.124  -1.119  -0.961  -1.176  -1.160  -0.977
32    N        -0.305  -0.311  -0.172  -0.219  -0.250  -0.049  -0.607  -0.642  -0.439
33    G        -1.388  -1.432  -1.439  -1.023  -1.105  -1.231  -1.271  -1.314  -1.249
34    K        -0.405  -0.702  -0.865  -0.605  -0.941  -1.054  -0.323  -0.710  -0.916
35    K        -0.079  -0.023  -0.093  -0.584  -0.475  -0.561  -0.228  -0.152  -0.301
36    A        -1.079  -1.293  -1.427  -1.112  -1.475  -1.685  -0.892  -1.147  -1.237
37    L        -1.079  -1.179  -1.423  -0.892  -1.061  -1.518  -0.892  -1.019  -1.233
38    K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
39    V        -0.405  -0.421  -0.832  -0.206  -0.213  -0.789  -0.323  -0.362  -0.873
40    R         1.040   1.058   1.127   1.174   1.193   1.289   1.099   1.130   1.231
41    T        -0.405  -0.702  -0.865  -0.123  -0.499  -0.756  -0.323  -0.710  -0.916
42    S         0.303   0.376  -0.049   0.558   0.646   0.053   0.340   0.438  -0.225
43    A        -0.305  -0.091  -0.101  -0.577  -0.177  -0.266  -0.607  -0.264  -0.314
44    T        -0.753  -0.736  -0.870  -0.626  -0.583  -0.814  -0.797  -0.756  -0.923
45    F         1.040   1.058   1.127   1.359   1.369   1.446   1.099   1.130   1.231
46    R        -0.079  -0.147  -0.159   0.106  -0.012  -0.045  -0.228  -0.356  -0.417
47    L        -0.412  -0.254  -0.139  -0.620  -0.332  -0.180  -0.797  -0.541  -0.382
48    P         1.040   1.058   1.127   1.238   1.250   1.343   1.099   1.130   1.231
49    K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
50    T         0.303   0.172  -0.066   0.446   0.285  -0.116   0.340   0.150  -0.254
51    L         1.040   1.058   1.127   1.021   1.042   1.158   1.099   1.130   1.231
52    K        -1.063  -1.125  -0.941  -1.373  -1.385  -0.972  -1.176  -1.267  -1.011
53    L         1.040   1.058   1.127   1.021   1.042   1.158   1.099   1.130   1.231
54    A        -1.527  -1.483  -1.431  -1.633  -1.515  -1.371  -1.460  -1.407  -1.244
55    R         0.303   0.172  -0.066   0.494   0.297  -0.198   0.340   0.150  -0.254
56    A        -1.202  -1.151  -0.941  -1.703  -1.698  -1.372  -1.366  -1.302  -1.010
57    P         1.040   1.058   1.127   1.238   1.250   1.343   1.099   1.130   1.231
58    K         0.303   0.172  -0.066  -0.054  -0.196  -0.511   0.340   0.150  -0.254
59    Y         1.040   1.058   1.127   1.256   1.283   1.358   1.099   1.130   1.231
60    A        -1.388  -1.472  -1.448  -1.332  -1.425  -1.278  -1.271  -1.364  -1.260
61    S        -0.753  -0.415  -0.834  -0.541  -0.094  -0.705  -0.797  -0.366  -0.876
62    K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
63    A        -0.305  -0.214  -0.153  -0.493  -0.333  -0.323  -0.607  -0.472  -0.406
64    V         0.303   0.118  -0.071   0.391   0.171  -0.134   0.340   0.068  -0.264
65    P        -0.079  -0.133  -0.155   0.018  -0.116  -0.272  -0.228  -0.333  -0.409
66    H         1.040   1.058   1.127   1.363   1.365   1.450   1.099   1.130   1.231
67    Y        -0.753  -0.865  -0.883  -0.536  -0.679  -0.788  -0.797  -0.928  -0.938
68    N        -0.940  -0.903  -0.896  -0.798  -0.780  -0.727  -1.081  -1.059  -0.958
69    R         1.040   1.058   1.127   1.174   1.193   1.289   1.099   1.130   1.231
70    L         0.303   0.172  -0.066   0.440   0.288  -0.008   0.340   0.150  -0.254
71    D         1.040   1.058   1.127   1.197   1.210   1.308   1.099   1.130   1.231
72    S        -1.202  -1.090  -0.931  -1.268  -1.088  -0.916  -1.366  -1.236  -0.999
73    Y        -0.079  -0.123  -0.153   0.185   0.108   0.020  -0.228  -0.316  -0.406
74    K         0.303   0.172  -0.066  -0.029  -0.161  -0.434   0.340   0.150  -0.254
75    V        -0.412  -0.329  -0.173  -0.686  -0.553  -0.307  -0.797  -0.674  -0.442
76    I         1.040   1.058   1.127   1.128   1.139   1.249   1.099   1.130   1.231
77    E        -0.940  -0.876  -0.872  -0.930  -0.806  -0.805  -1.081  -0.952  -0.925
78    Q        -2.301  -2.104  -1.880  -1.948  -1.713  -1.448  -1.934  -1.754  -1.442
79    P         1.040   1.058   1.127   1.238   1.250   1.343   1.099   1.130   1.231
80    I        -0.079  -0.236  -0.166  -0.034  -0.346  -0.271  -0.228  -0.509  -0.429
81    T        -1.202  -0.972  -0.901  -1.380  -0.968  -0.960  -1.366  -1.069  -0.961
82    S        -0.305  -0.331  -0.178  -0.374  -0.456  -0.244  -0.607  -0.678  -0.450
83    E         1.040   1.058   1.127   1.301   1.314   1.397   1.099   1.130   1.231
84    T        -0.753  -0.865  -0.883  -0.598  -0.729  -0.766  -0.797  -0.928  -0.938
85    A         1.040   1.058   1.127   0.809   0.850   0.978   1.099   1.130   1.231
86    M         0.303   0.118  -0.071   0.765   0.505   0.127   0.340   0.068  -0.264
87    K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
88    K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
89    V        -0.412  -0.345  -0.168  -0.686  -0.567  -0.282  -0.797  -0.703  -0.432
90    E         1.040   1.058   1.127   1.301   1.314   1.397   1.099   1.130   1.231
91    D         0.303   0.118  -0.071   0.603   0.366   0.081   0.340   0.068  -0.264
92    G        -1.388  -1.571  -1.460  -0.924  -1.184  -1.064  -1.271  -1.448  -1.270
93    N         1.040   1.058   1.127   1.192   1.218   1.304   1.099   1.130   1.231
94    I        -0.305  -0.139  -0.130  -0.431  -0.163  -0.183  -0.607  -0.343  -0.366
95    L         1.040   1.058   1.127   1.021   1.042   1.158   1.099   1.130   1.231
96    V         1.040   1.058   1.127   1.007   1.050   1.146   1.099   1.130   1.231
97    F         1.040   1.058   1.127   1.359   1.369   1.446   1.099   1.130   1.231
98    Q        -1.650  -1.539  -1.460  -1.359  -1.299  -1.269  -1.555  -1.468  -1.271
99    V         1.040   1.058   1.127   1.007   1.050   1.146   1.099   1.130   1.231
100   S        -1.730  -1.676  -1.455  -1.500  -1.414  -1.111  -1.650  -1.561  -1.265
101   M        -1.714  -1.714  -1.852  -1.459  -1.599  -1.754  -1.366  -1.392  -1.419
102   K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
103   A        -0.079   0.047  -0.105  -0.305  -0.114  -0.326  -0.228  -0.041  -0.322
104   N         1.040   1.058   1.127   1.192   1.218   1.304   1.099   1.130   1.231
105   K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
106   Y        -2.179  -2.104  -1.885  -1.735  -1.705  -1.421  -1.840  -1.746  -1.446
107   Q        -0.079  -0.023  -0.093   0.206   0.261   0.078  -0.228  -0.152  -0.301
108   I         1.040   1.058   1.127   1.128   1.139   1.249   1.099   1.130   1.231
109   K         0.303   0.172  -0.066  -0.032  -0.165  -0.444   0.340   0.150  -0.254
110   K        -2.504  -2.512  -2.241  -2.436  -2.323  -1.839  -1.934  -1.905  -1.569
111   A         1.040   1.058   1.127   0.809   0.850   0.978   1.099   1.130   1.231
112   V        -0.405  -0.702  -0.865  -0.233  -0.629  -0.914  -0.323  -0.710  -0.916
113   K         0.303   0.335  -0.043  -0.032   0.033  -0.412   0.340   0.381  -0.216
114   E        -0.412  -0.345  -0.168  -0.788  -0.791  -0.485  -0.797  -0.703  -0.432
115   L         1.040   1.058   1.127   1.021   1.042   1.158   1.099   1.130   1.231
116   Y         1.040   1.058   1.127   1.256   1.283   1.358   1.099   1.130   1.231
117   E        -1.202  -1.121  -0.918  -1.092  -1.005  -0.727  -1.366  -1.269  -0.984
118   V         0.303   0.118  -0.071   0.391   0.171  -0.134   0.340   0.068  -0.264
119   D        -0.079  -0.133  -0.155   0.111   0.006  -0.055  -0.228  -0.333  -0.409
120   V        -1.976  -2.068  -1.881  -1.929  -2.056  -1.791  -1.650  -1.708  -1.443
121   L        -2.056  -1.921  -1.879  -1.967  -1.810  -1.649  -1.745  -1.599  -1.442
122   K        -1.063  -0.950  -0.909  -1.473  -1.299  -1.136  -1.176  -1.039  -0.972
123   V        -0.305  -0.311  -0.172  -0.496  -0.520  -0.305  -0.607  -0.642  -0.439
124   N         1.040   1.058   1.127   1.192   1.218   1.304   1.099   1.130   1.231
125   T         1.040   1.058   1.127   1.077   1.108   1.206   1.099   1.130   1.231
126   L         1.040   1.058   1.127   1.021   1.042   1.158   1.099   1.130   1.231
127   V        -0.305  -0.118  -0.125  -0.440  -0.128  -0.191  -0.607  -0.308  -0.356
128   R         0.303   0.432  -0.046   0.552   0.696   0.023   0.340   0.510  -0.220
129   P         0.303   0.432  -0.046   0.584   0.728  -0.020   0.340   0.510  -0.220
130   N        -0.753  -0.783  -0.897  -0.588  -0.698  -0.959  -0.797  -0.903  -0.959
131   G         1.040   1.058   1.127   1.296   1.313   1.393   1.099   1.130   1.231
132   T        -1.079  -1.249  -1.422  -0.816  -1.112  -1.432  -0.892  -1.104  -1.232
133   K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
134   K         1.040   1.058   1.127   0.579   0.631   0.782   1.099   1.130   1.231
135   A         1.040   1.058   1.127   0.809   0.850   0.978   1.099   1.130   1.231
136   Y        -0.412  -0.270  -0.147  -0.326  -0.092   0.049  -0.797  -0.569  -0.395
137   V        -0.753  -0.808  -0.879  -0.757  -0.837  -1.015  -0.797  -0.850  -0.934
138   R        -0.079  -0.023  -0.093  -0.105  -0.029  -0.263  -0.228  -0.152  -0.301
139   L         1.040   1.058   1.127   1.021   1.042   1.158   1.099   1.130   1.231
140   T        -0.079  -0.023  -0.093  -0.043   0.039  -0.101  -0.228  -0.152  -0.301
141   A         0.303   0.430  -0.045   0.198   0.359  -0.232   0.340   0.508  -0.218
142   D         1.040   1.058   1.127   1.197   1.210   1.308   1.099   1.130   1.231
143   Y        -2.179  -2.093  -1.884  -1.906  -1.846  -1.490  -1.840  -1.750  -1.446
144   D         1.040   1.058   1.127   1.197   1.210   1.308   1.099   1.130   1.231
145   A         1.040   1.058   1.127   0.809   0.850   0.978   1.099   1.130   1.231
146   L         1.040   1.058   1.127   1.021   1.042   1.158   1.099   1.130   1.231
147   D         1.040   1.058   1.127   1.197   1.210   1.308   1.099   1.130   1.231
148   I        -0.079  -0.023  -0.093  -0.038   0.029  -0.128  -0.228  -0.152  -0.301
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   A         1.040   1.058   1.127   0.809   0.850   0.978   1.099   1.130   1.231
151   N         0.303   0.118  -0.071   0.570   0.331  -0.009   0.340   0.068  -0.264
152   R        -0.079  -0.236  -0.166  -0.105  -0.475  -0.476  -0.228  -0.509  -0.429
153   I         0.303   0.118  -0.071   0.499   0.239  -0.081   0.340   0.068  -0.264
154   G         1.040   1.058   1.127   1.296   1.313   1.393   1.099   1.130   1.231
155   Y        -0.753  -0.865  -0.883  -0.410  -0.578  -0.672  -0.797  -0.928  -0.938
156   I        -0.753  -0.865  -0.883  -0.642  -0.823  -0.908  -0.797  -0.928  -0.938
* 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/P04456
Output conservation file - output/P04456
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
