1     M         0.975   1.028   1.061   1.133   1.194   1.247   1.016   1.087   1.139
2     T        -1.152  -1.167  -1.013  -1.287  -1.336  -1.077  -1.292  -1.259  -1.057
3     T        -1.152  -1.167  -1.013  -1.375  -1.383  -1.146  -1.292  -1.259  -1.057
4     F         0.975   1.028   1.061   0.944   1.053   1.084   1.016   1.087   1.139
5     R         0.028  -0.214  -0.212  -0.052  -0.392  -0.393  -0.033  -0.426  -0.445
6     F         0.028  -0.214  -0.212   0.084  -0.255  -0.276  -0.033  -0.426  -0.445
7     C         0.975   1.028   1.061   0.893   0.975   1.041   1.016   1.087   1.139
8     R        -1.152  -1.167  -1.013  -1.298  -1.262  -1.014  -1.292  -1.259  -1.057
9     D        -0.483  -0.295  -0.218  -0.863  -0.550  -0.419  -0.872  -0.562  -0.456
10    C         0.975   1.028   1.061   0.893   0.975   1.041   1.016   1.087   1.139
11    N         0.975   1.028   1.061   0.977   1.057   1.113   1.016   1.087   1.139
12    N         0.975   1.028   1.061   0.977   1.057   1.113   1.016   1.087   1.139
13    M         0.975   1.028   1.061   1.133   1.226   1.247   1.016   1.087   1.139
14    L         0.975   1.028   1.061   0.901   0.964   1.048   1.016   1.087   1.139
15    Y         0.975   1.028   1.061   1.097   1.149   1.216   1.016   1.087   1.139
16    P         0.975   1.028   1.061   1.030   1.088   1.158   1.016   1.087   1.139
17    R        -0.283  -0.128  -0.202  -0.492  -0.237  -0.364  -0.525  -0.284  -0.429
18    E         0.975   1.028   1.061   0.840   0.915   0.995   1.016   1.087   1.139
19    D         0.975   1.028   1.061   0.970   1.029   1.106   1.016   1.087   1.139
20    K         0.975   1.028   1.061   1.037   1.095   1.165   1.016   1.087   1.139
21    E        -0.699  -0.845  -0.962  -0.687  -0.957  -1.076  -0.679  -0.879  -0.995
22    N        -1.710  -1.409  -1.531  -1.686  -1.266  -1.423  -1.604  -1.267  -1.310
23    N        -2.284  -1.846  -1.954  -2.186  -1.581  -1.690  -1.913  -1.444  -1.480
24    R        -1.035  -1.114  -0.996  -1.176  -1.297  -1.085  -1.142  -1.193  -1.038
25    L         0.975   1.028   1.061   0.901   0.964   1.048   1.016   1.087   1.139
26    L         0.113  -0.152  -0.180   0.108  -0.311  -0.369   0.091  -0.322  -0.391
27    F        -1.035  -1.104  -0.998  -1.072  -1.159  -1.027  -1.142  -1.180  -1.039
28    E        -1.137  -0.860  -0.952  -1.324  -0.841  -0.983  -1.296  -0.900  -0.982
29    C         0.975   1.028   1.061   0.886   1.027   1.034   1.016   1.087   1.139
30    R         0.975   1.028   1.061   0.840   0.945   0.995   1.016   1.087   1.139
31    T        -0.461  -0.170  -0.183  -0.755  -0.168  -0.283  -0.834  -0.352  -0.396
32    C         0.975   1.028   1.061   0.886   1.027   1.034   1.016   1.087   1.139
33    S        -1.867  -1.577  -1.533  -1.929  -1.512  -1.407  -1.758  -1.406  -1.312
34    Y         0.975   1.028   1.061   1.097   1.149   1.216   1.016   1.087   1.139
35    V        -1.710  -1.488  -1.531  -1.762  -1.505  -1.476  -1.604  -1.334  -1.310
36    E         0.975   1.028   1.061   0.840   0.915   0.995   1.016   1.087   1.139
37    E        -1.710  -1.718  -1.557  -1.836  -1.773  -1.548  -1.604  -1.535  -1.333
38    A         0.975   1.028   1.061   1.067   1.121   1.190   1.016   1.087   1.139
39    G        -1.710  -1.718  -1.557  -1.674  -1.715  -1.485  -1.604  -1.535  -1.333
40    S        -1.294  -0.966  -0.965  -1.577  -1.019  -1.059  -1.450  -1.011  -0.999
41    P         0.113  -0.152  -0.180   0.245  -0.179  -0.245   0.091  -0.322  -0.391
42    L        -0.461  -0.355  -0.246  -0.740  -0.582  -0.376  -0.834  -0.668  -0.504
43    V         0.975   1.028   1.061   0.962   1.003   1.100   1.016   1.087   1.139
44    Y         0.113   0.095  -0.153   0.319   0.288  -0.123   0.091   0.062  -0.346
45    R         0.113   0.095  -0.153   0.080   0.088  -0.284   0.091   0.062  -0.346
46    H         0.975   1.028   1.061   1.111   1.148   1.228   1.016   1.087   1.139
47    E         0.113   0.095  -0.153   0.086   0.068  -0.269   0.091   0.062  -0.346
48    L         0.975   1.028   1.061   0.901   0.964   1.048   1.016   1.087   1.139
49    I        -1.451  -1.366  -1.517  -1.084  -1.041  -1.221  -1.296  -1.210  -1.296
50    T         0.113  -0.152  -0.180   0.117  -0.284  -0.345   0.091  -0.322  -0.391
51    N         0.113  -0.152  -0.180   0.200  -0.135  -0.280   0.091  -0.322  -0.391
52    I         0.113  -0.152  -0.180   0.327  -0.047  -0.155   0.091  -0.322  -0.391
53    G        -0.699  -0.957  -0.980  -0.458  -0.916  -0.988  -0.679  -1.004  -1.017
54    E         0.113   0.253  -0.137   0.085   0.265  -0.245   0.091   0.288  -0.318
55    T         0.113  -0.152  -0.180   0.132  -0.227  -0.304   0.091  -0.322  -0.391
56    A         0.113  -0.152  -0.180   0.284  -0.148  -0.213   0.091  -0.322  -0.391
57    G         0.113  -0.152  -0.180   0.313  -0.104  -0.191   0.091  -0.322  -0.391
58    V         0.975   1.028   1.061   0.962   1.003   1.100   1.016   1.087   1.139
59    V        -0.699  -0.957  -0.980  -0.593  -1.057  -1.083  -0.679  -1.004  -1.017
60    Q        -1.451  -1.559  -1.541  -1.196  -1.430  -1.428  -1.296  -1.389  -1.318
61    D         0.113   0.095  -0.153   0.219   0.188  -0.159   0.091   0.062  -0.346
62    I         0.113  -0.152  -0.180   0.340  -0.052  -0.120   0.091  -0.322  -0.391
63    G         0.113  -0.152  -0.180   0.312  -0.104  -0.194   0.091  -0.322  -0.391
64    S        -1.451  -1.559  -1.541  -1.346  -1.544  -1.493  -1.296  -1.389  -1.318
65    D         0.975   1.028   1.061   0.970   1.029   1.106   1.016   1.087   1.139
66    P         0.975   1.028   1.061   1.030   1.088   1.158   1.016   1.087   1.139
67    T         0.975   1.028   1.061   0.901   0.978   1.048   1.016   1.087   1.139
68    L         0.975   1.028   1.061   0.901   0.964   1.048   1.016   1.087   1.139
69    P         0.975   1.028   1.061   1.030   1.088   1.158   1.016   1.087   1.139
70    R         0.975   1.028   1.061   0.840   0.945   0.995   1.016   1.087   1.139
71    S         0.975   1.028   1.061   0.894   0.980   1.041   1.016   1.087   1.139
72    D         0.113   0.240  -0.135   0.185   0.342  -0.208   0.091   0.270  -0.315
73    R        -0.283   0.060  -0.137  -0.379   0.156  -0.178  -0.525   0.011  -0.318
74    E         0.975   1.028   1.061   0.840   0.915   0.995   1.016   1.087   1.139
75    C         0.975   1.028   1.061   0.886   1.027   1.034   1.016   1.087   1.139
76    P         0.975   1.028   1.061   1.030   1.088   1.158   1.016   1.087   1.139
77    K        -1.035  -1.104  -0.998  -1.055  -1.217  -1.059  -1.142  -1.180  -1.039
78    C         0.975   1.028   1.061   0.886   1.027   1.034   1.016   1.087   1.139
79    H        -0.283  -0.128  -0.202  -0.214  -0.018  -0.136  -0.525  -0.284  -0.429
80    S        -2.127  -2.084  -1.981  -1.986  -1.932  -1.773  -1.758  -1.657  -1.501
81    R        -1.137  -0.860  -0.952  -1.256  -0.779  -0.896  -1.296  -0.900  -0.982
82    E        -0.283  -0.213  -0.232  -0.519  -0.430  -0.448  -0.525  -0.423  -0.481
83    N        -2.127  -2.084  -1.981  -1.965  -1.888  -1.817  -1.758  -1.657  -1.501
84    V         0.975   1.028   1.061   0.962   1.003   1.100   1.016   1.087   1.139
85    F         0.975   1.028   1.061   0.939   1.086   1.080   1.016   1.087   1.139
86    F         0.113  -0.152  -0.180   0.189  -0.120  -0.225   0.091  -0.322  -0.391
87    Q         0.975   1.028   1.061   1.074   1.135   1.197   1.016   1.087   1.139
88    S         0.113  -0.152  -0.180   0.111  -0.283  -0.348   0.091  -0.322  -0.391
89    Q         0.113  -0.152  -0.180   0.325  -0.074  -0.117   0.091  -0.322  -0.391
90    Q         0.113  -0.152  -0.180   0.290  -0.134  -0.211   0.091  -0.322  -0.391
91    R         0.113   0.095  -0.153   0.080   0.088  -0.284   0.091   0.062  -0.346
92    R         0.975   1.028   1.061   0.840   0.945   0.995   1.016   1.087   1.139
93    K        -0.699  -0.957  -0.980  -0.447  -0.849  -0.871  -0.679  -1.004  -1.017
94    D         0.113   0.095  -0.153   0.177   0.134  -0.263   0.091   0.062  -0.346
95    T         0.975   1.028   1.061   0.901   0.978   1.048   1.016   1.087   1.139
96    S        -0.699  -0.957  -0.980  -0.613  -0.964  -1.020  -0.679  -1.004  -1.017
97    M         0.975   1.028   1.061   1.133   1.226   1.247   1.016   1.087   1.139
98    V        -1.137  -1.125  -0.987  -1.213  -1.194  -0.976  -1.296  -1.207  -1.026
99    L         0.975   1.028   1.061   0.901   0.964   1.048   1.016   1.087   1.139
100   F         0.113  -0.152  -0.180   0.189  -0.112  -0.225   0.091  -0.322  -0.391
101   F        -0.461  -0.361  -0.248  -0.672  -0.473  -0.321  -0.834  -0.678  -0.508
102   V         0.975   1.028   1.061   0.962   1.003   1.100   1.016   1.087   1.139
103   C         0.975   1.028   1.061   0.886   1.027   1.034   1.016   1.087   1.139
104   L        -0.699  -0.957  -0.980  -0.623  -1.036  -1.055  -0.679  -1.004  -1.017
105   S        -2.284  -1.864  -1.953  -2.156  -1.572  -1.710  -1.913  -1.498  -1.481
106   C         0.975   1.028   1.061   0.886   1.027   1.034   1.016   1.087   1.139
107   S        -1.710  -1.718  -1.557  -1.701  -1.644  -1.432  -1.604  -1.535  -1.333
108   H        -1.451  -1.567  -1.540  -1.136  -1.366  -1.361  -1.296  -1.396  -1.318
109   I        -1.035  -1.104  -0.998  -0.955  -1.084  -0.928  -1.142  -1.180  -1.039
110   F         0.975   1.028   1.061   0.939   1.086   1.080   1.016   1.087   1.139
111   T        -1.710  -1.660  -1.543  -1.853  -1.826  -1.590  -1.604  -1.491  -1.321
112   S        -0.208  -0.355  -0.247  -0.427  -0.726  -0.533  -0.400  -0.667  -0.507
113   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   S        -1.035  -1.104  -0.998  -1.088  -1.175  -0.995  -1.142  -1.180  -1.039
* 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/P27999
Output conservation file - output/P27999
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
