1     M         1.520   1.560   1.662   1.616   1.658   1.827   1.653   1.707   1.877
2     G         0.344   0.321   0.424   0.092   0.066   0.213   0.017  -0.045   0.088
3     L        -0.348  -0.433  -0.289  -0.307  -0.439  -0.235  -0.597  -0.696  -0.503
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     F         0.687   0.718   0.560   0.932   0.964   0.766   0.630   0.671   0.353
8     G         0.687   0.718   0.560   0.807   0.862   0.589   0.630   0.671   0.353
9     G        -0.083  -0.037  -0.203   0.042   0.115  -0.216  -0.188  -0.120  -0.376
10    G        -0.775  -0.803  -0.775  -0.867  -0.935  -0.832  -0.801  -0.836  -0.775
11    A         0.687   0.802   0.572   0.415   0.560   0.224   0.630   0.807   0.376
12    P        -0.775  -0.803  -0.775  -0.836  -0.879  -0.790  -0.801  -0.836  -0.775
13    S        -0.083  -0.182  -0.214  -0.317  -0.485  -0.542  -0.188  -0.342  -0.392
14    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    A        -0.348  -0.276  -0.265  -0.721  -0.593  -0.595  -0.597  -0.490  -0.470
19    A        -0.941  -0.928  -0.815  -1.128  -1.092  -0.918  -0.998  -0.977  -0.820
20    T         0.277   0.277   0.413  -0.076  -0.121   0.073  -0.114  -0.132   0.066
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    T         0.277   0.315   0.420   0.217   0.274   0.400  -0.114  -0.058   0.079
33    A        -0.083  -0.203  -0.220  -0.244  -0.488  -0.515  -0.188  -0.379  -0.400
34    K        -0.775  -0.771  -0.766  -0.887  -0.883  -0.847  -0.801  -0.809  -0.765
35    T        -1.363  -1.241  -1.200  -1.485  -1.330  -1.246  -1.210  -1.074  -0.990
36    T        -0.775  -0.634  -0.758  -0.779  -0.581  -0.809  -0.801  -0.622  -0.756
37    P        -0.143   0.032  -0.171  -0.257  -0.044  -0.244  -0.303  -0.045  -0.335
38    N        -1.360  -1.312  -1.213  -1.514  -1.415  -1.335  -1.223  -1.161  -1.004
39    P        -1.680  -1.676  -1.531  -1.443  -1.464  -1.239  -1.338  -1.314  -1.120
40    I        -0.720  -0.784  -0.738  -0.583  -0.670  -0.627  -0.763  -0.809  -0.740
41    A         0.762   0.835   0.627   0.747   0.822   0.540   0.752   0.860   0.478
42    K        -1.240  -1.263  -1.171  -1.227  -1.282  -1.128  -1.108  -1.117  -0.968
43    E        -1.680  -1.673  -1.531  -1.637  -1.622  -1.410  -1.338  -1.309  -1.120
44    L        -0.479  -0.446  -0.315  -0.534  -0.486  -0.289  -0.763  -0.711  -0.536
45    K        -0.720  -0.800  -0.751  -0.687  -0.797  -0.722  -0.763  -0.828  -0.753
46    N        -1.240  -1.044  -1.165  -1.263  -0.970  -1.193  -1.108  -0.896  -0.961
47    Q         0.824   0.762   0.627   0.776   0.716   0.523   0.848   0.743   0.478
48    I         0.824   0.743   0.626   0.867   0.782   0.622   0.848   0.713   0.477
49    A        -0.799  -0.876  -0.761  -1.035  -1.111  -0.907  -0.878  -0.931  -0.768
50    Q         0.161  -0.001  -0.124   0.176  -0.032  -0.252   0.157  -0.069  -0.261
51    E         1.520   1.560   1.662   1.453   1.512   1.669   1.653   1.707   1.877
52    L         0.161   0.140  -0.112   0.318   0.279  -0.116   0.157   0.123  -0.244
53    A         0.824   0.743   0.626   0.700   0.598   0.430   0.848   0.713   0.477
54    V        -0.463  -0.424  -0.662  -0.261  -0.241  -0.630  -0.418  -0.371  -0.643
55    A         1.520   1.560   1.662   1.292   1.344   1.512   1.653   1.707   1.877
56    N         0.824   0.776   0.632   0.816   0.784   0.549   0.848   0.766   0.488
57    A         1.520   1.560   1.662   1.292   1.344   1.512   1.653   1.707   1.877
58    T        -0.463  -0.670  -0.710  -0.202  -0.469  -0.545  -0.418  -0.663  -0.700
59    E        -0.463  -0.559  -0.682  -0.233  -0.377  -0.548  -0.418  -0.535  -0.667
60    L         1.520   1.560   1.662   1.506   1.566   1.720   1.653   1.707   1.877
61    V         0.161   0.012  -0.131   0.402   0.206   0.009   0.157  -0.051  -0.270
62    N        -1.040  -1.195  -1.167  -0.850  -1.081  -1.068  -0.878  -1.029  -0.959
63    K         0.824   0.886   0.646   0.845   0.903   0.620   0.848   0.937   0.512
64    I        -0.143  -0.114  -0.183  -0.092  -0.028  -0.123  -0.303  -0.237  -0.351
65    S        -0.720  -0.783  -0.745  -0.721  -0.766  -0.761  -0.763  -0.806  -0.743
66    E         1.520   1.560   1.662   1.453   1.512   1.669   1.653   1.707   1.877
67    N         1.520   1.560   1.662   1.407   1.486   1.624   1.653   1.707   1.877
68    C         1.520   1.560   1.662   1.558   1.608   1.771   1.653   1.707   1.877
69    F         1.520   1.560   1.662   1.648   1.705   1.859   1.653   1.707   1.877
70    E        -0.280  -0.340  -0.248  -0.265  -0.329  -0.188  -0.533  -0.594  -0.454
71    K         0.161  -0.001  -0.124   0.263   0.019  -0.149   0.157  -0.069  -0.261
72    C         1.520   1.560   1.662   1.558   1.608   1.771   1.653   1.707   1.877
73    L        -0.479  -0.449  -0.310  -0.569  -0.531  -0.338  -0.763  -0.715  -0.530
74    T        -1.560  -1.329  -1.496  -1.168  -0.818  -1.141  -1.223  -0.987  -1.090
75    S        -1.680  -1.596  -1.541  -1.796  -1.647  -1.598  -1.338  -1.250  -1.127
76    P         1.520   1.560   1.662   1.616   1.671   1.827   1.653   1.707   1.877
77    Y        -0.799  -0.694  -0.761  -0.599  -0.439  -0.567  -0.878  -0.748  -0.766
78    A        -1.240  -1.069  -1.168  -1.384  -1.142  -1.244  -1.108  -0.912  -0.962
79    T        -1.240  -1.119  -1.164  -1.190  -1.090  -1.080  -1.108  -0.997  -0.961
80    -         0.595   0.604   0.547   0.681   0.703   0.613   0.475   0.478   0.327
81    -        -0.235  -0.199  -0.214  -0.431  -0.384  -0.384  -0.409  -0.355  -0.391
82    -        -0.235  -0.225  -0.230  -0.103  -0.093  -0.160  -0.409  -0.393  -0.416
83    R        -2.000  -1.957  -1.815  -1.919  -1.884  -1.655  -1.453  -1.400  -1.212
84    N        -0.400  -0.245  -0.254  -0.571  -0.301  -0.380  -0.648  -0.421  -0.451
85    D        -0.799  -0.696  -0.757  -0.674  -0.582  -0.608  -0.878  -0.750  -0.763
86    A        -1.680  -1.689  -1.531  -1.713  -1.714  -1.506  -1.338  -1.321  -1.120
87    C         1.520   1.560   1.662   1.558   1.608   1.771   1.653   1.707   1.877
88    I        -0.143  -0.145  -0.193  -0.068  -0.061  -0.162  -0.303  -0.284  -0.370
89    D        -1.240  -1.298  -1.196  -1.145  -1.290  -1.170  -1.108  -1.147  -0.989
90    Q         0.824   0.776   0.632   0.771   0.724   0.520   0.848   0.766   0.488
91    C         1.520   1.560   1.662   1.558   1.608   1.771   1.653   1.707   1.877
92    L        -1.040  -1.195  -1.167  -0.697  -0.938  -0.897  -0.878  -1.029  -0.959
93    A        -0.280  -0.274  -0.230  -0.498  -0.449  -0.408  -0.533  -0.490  -0.425
94    K         0.824   0.776   0.632   0.866   0.796   0.647   0.848   0.766   0.488
95    Y         1.520   1.560   1.662   1.641   1.699   1.852   1.653   1.707   1.877
96    M         0.824   0.762   0.627   1.036   0.950   0.763   0.848   0.743   0.478
97    R        -0.463  -0.670  -0.710  -0.064  -0.354  -0.431  -0.418  -0.663  -0.700
98    S         0.298   0.276   0.415  -0.208  -0.281  -0.052  -0.073  -0.134   0.068
99    W         1.520   1.560   1.662   1.704   1.763   1.914   1.653   1.707   1.877
100   N         1.520   1.560   1.662   1.407   1.486   1.624   1.653   1.707   1.877
101   V        -0.463  -0.499  -0.671  -0.205  -0.264  -0.545  -0.418  -0.463  -0.654
102   I         0.240   0.290   0.418   0.022   0.104   0.292  -0.188  -0.107   0.075
103   S         0.824   0.743   0.626   0.631   0.531   0.375   0.848   0.713   0.477
104   K        -0.143  -0.279  -0.232  -0.100  -0.311  -0.216  -0.303  -0.493  -0.427
105   A        -0.799  -0.778  -0.747  -0.939  -0.887  -0.848  -0.878  -0.838  -0.753
106   Y         1.520   1.560   1.662   1.641   1.699   1.852   1.653   1.707   1.877
107   I         0.824   0.743   0.626   0.864   0.780   0.615   0.848   0.713   0.477
108   S        -1.360  -1.360  -1.206  -1.368  -1.340  -1.123  -1.223  -1.199  -0.998
109   R         0.824   0.762   0.627   1.028   0.951   0.753   0.848   0.743   0.478
110   I         0.161   0.028  -0.115   0.323   0.167  -0.024   0.157  -0.028  -0.247
111   Q         1.520   1.560   1.662   1.353   1.421   1.571   1.653   1.707   1.877
112   N        -0.463  -0.390  -0.660  -0.292  -0.187  -0.532  -0.418  -0.325  -0.641
113   A        -0.479  -0.444  -0.308  -0.869  -0.809  -0.628  -0.763  -0.708  -0.527
114   S        -0.245  -0.384  -0.261  -0.533  -0.723  -0.517  -0.451  -0.629  -0.467
115   A        -1.789  -1.733  -1.570  -1.532  -1.447  -1.240  -1.415  -1.350  -1.147
116   S        -0.941  -0.860  -0.794  -0.946  -0.818  -0.745  -0.998  -0.894  -0.797
117   G         0.687   0.650   0.578   0.809   0.759   0.644   0.630   0.557   0.387
118   E        -0.348  -0.381  -0.285  -0.482  -0.560  -0.410  -0.597  -0.638  -0.498
119   I        -0.235  -0.347  -0.276  -0.192  -0.365  -0.270  -0.409  -0.569  -0.481
* 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/P53299
Output conservation file - output/P53299
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
