1     M         1.310   1.318   1.356   1.415   1.443   1.491   1.411   1.424   1.478
2     S         1.310   1.318   1.356   1.278   1.297   1.357   1.411   1.424   1.478
3     F        -1.430  -1.401  -1.336  -1.393  -1.346  -1.247  -1.254  -1.219  -1.122
4     F         0.198   0.218   0.108   0.293   0.330   0.179   0.079   0.110  -0.083
5     L         1.310   1.318   1.356   1.240   1.258   1.320   1.411   1.424   1.478
6     N        -0.745  -0.750  -0.745  -0.702  -0.715  -0.703  -0.810  -0.818  -0.794
7     S        -0.060  -0.048   0.013  -0.194  -0.180  -0.079  -0.366  -0.345  -0.251
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    L        -0.745  -0.769  -0.754  -0.777  -0.829  -0.775  -0.810  -0.841  -0.805
12    R        -0.745  -0.676  -0.727  -0.799  -0.696  -0.772  -0.810  -0.718  -0.771
13    G        -0.745  -0.769  -0.754  -0.756  -0.800  -0.777  -0.810  -0.841  -0.805
14    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    Q         0.198   0.101   0.071   0.209   0.051  -0.006   0.079  -0.085  -0.149
16    E        -0.060  -0.045   0.015  -0.323  -0.277  -0.183  -0.366  -0.339  -0.246
17    V         0.198   0.101   0.071   0.245   0.087   0.026   0.079  -0.085  -0.149
18    S        -0.060  -0.045   0.015  -0.267  -0.235  -0.136  -0.366  -0.339  -0.246
19    Q        -1.430  -1.401  -1.336  -1.421  -1.359  -1.274  -1.254  -1.219  -1.122
20    E         1.310   1.318   1.356   1.163   1.187   1.245   1.411   1.424   1.478
21    K         0.198   0.218   0.108   0.135   0.161  -0.014   0.079   0.110  -0.083
22    L        -0.745  -0.676  -0.727  -0.740  -0.628  -0.720  -0.810  -0.718  -0.771
23    D        -0.745  -0.651  -0.724  -0.821  -0.677  -0.786  -0.810  -0.684  -0.767
24    V        -0.745  -0.651  -0.724  -0.815  -0.678  -0.777  -0.810  -0.684  -0.767
25    A         1.310   1.318   1.356   1.354   1.376   1.430   1.411   1.424   1.478
26    G        -1.430  -1.401  -1.336  -1.528  -1.477  -1.379  -1.254  -1.219  -1.122
27    V         0.198   0.101   0.071   0.245   0.087   0.026   0.079  -0.085  -0.149
28    Q         1.310   1.318   1.356   1.316   1.338   1.394   1.411   1.424   1.478
29    F         1.310   1.318   1.356   1.316   1.344   1.394   1.411   1.424   1.478
30    D        -0.745  -0.789  -0.752  -0.843  -0.929  -0.885  -0.810  -0.864  -0.802
31    A         1.310   1.318   1.356   1.354   1.376   1.430   1.411   1.424   1.478
32    M         1.310   1.318   1.356   1.414   1.463   1.489   1.411   1.424   1.478
33    C        -1.871  -1.846  -1.769  -1.668  -1.599  -1.515  -1.432  -1.404  -1.295
34    S        -0.569  -0.558  -0.681  -0.461  -0.454  -0.653  -0.579  -0.568  -0.713
35    T         1.310   1.318   1.356   1.361   1.347   1.438   1.411   1.424   1.478
36    F         1.310   1.318   1.356   1.329   1.401   1.407   1.411   1.424   1.478
37    N         0.321   0.294   0.138   0.462   0.380   0.175   0.274   0.233  -0.032
38    N        -0.775  -0.728  -0.750  -0.840  -0.859  -0.789  -0.863  -0.805  -0.802
39    I        -1.323  -1.340  -1.316  -1.195  -1.202  -1.187  -1.148  -1.160  -1.103
40    L         0.321   0.325   0.158   0.354   0.408   0.122   0.274   0.281   0.001
41    S        -1.323  -1.287  -1.291  -1.305  -1.263  -1.266  -1.148  -1.105  -1.080
42    T         0.321   0.243   0.124   0.425   0.261   0.111   0.274   0.152  -0.057
43    C         1.310   1.318   1.356   1.372   1.331   1.448   1.411   1.424   1.478
44    L        -0.775  -0.799  -0.745  -0.944  -1.009  -0.897  -0.863  -0.881  -0.796
45    E        -1.323  -1.367  -1.314  -1.384  -1.472  -1.347  -1.148  -1.186  -1.101
46    K         1.310   1.318   1.356   1.232   1.218   1.312   1.411   1.424   1.478
47    C         1.310   1.318   1.356   1.372   1.331   1.448   1.411   1.424   1.478
48    I         0.321   0.243   0.124   0.402   0.297   0.078   0.274   0.152  -0.057
49    P         0.321   0.243   0.124   0.485   0.375   0.154   0.274   0.152  -0.057
50    H        -0.775  -0.773  -0.741  -0.693  -0.724  -0.646  -0.863  -0.851  -0.792
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    E         1.310   1.318   1.356   1.156   1.170   1.237   1.411   1.424   1.478
53    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    F        -0.021   0.015   0.042  -0.054   0.008   0.042  -0.295  -0.234  -0.200
55    G         0.321   0.325   0.158   0.397   0.418   0.138   0.274   0.281   0.001
56    E         1.310   1.318   1.356   1.156   1.170   1.237   1.411   1.424   1.478
57    P        -0.569  -0.558  -0.681  -0.481  -0.428  -0.644  -0.579  -0.568  -0.713
58    D        -0.021  -0.040   0.013  -0.214  -0.236  -0.193  -0.295  -0.330  -0.251
59    L         1.310   1.318   1.356   1.265   1.323   1.344   1.411   1.424   1.478
60    T        -0.021  -0.005   0.022  -0.098  -0.132  -0.034  -0.295  -0.269  -0.234
61    K         0.321   0.294   0.138   0.309   0.229   0.039   0.274   0.233  -0.032
62    G         1.310   1.318   1.356   1.340   1.359   1.417   1.411   1.424   1.478
63    E         1.310   1.318   1.356   1.156   1.170   1.237   1.411   1.424   1.478
64    Q        -0.021   0.005   0.036  -0.104  -0.011  -0.014  -0.295  -0.250  -0.210
65    C        -0.569  -0.629  -0.690  -0.481  -0.666  -0.702  -0.579  -0.656  -0.724
66    C         1.310   1.318   1.356   1.372   1.331   1.448   1.411   1.424   1.478
67    I         0.321   0.325   0.158   0.423   0.439   0.174   0.274   0.281   0.001
68    D         1.310   1.318   1.356   1.382   1.454   1.459   1.411   1.424   1.478
69    R         1.310   1.318   1.356   1.319   1.285   1.396   1.411   1.424   1.478
70    C         1.310   1.318   1.356   1.372   1.331   1.448   1.411   1.424   1.478
71    V         1.310   1.318   1.356   1.351   1.402   1.428   1.411   1.424   1.478
72    A         0.321   0.243   0.124   0.397   0.382   0.078   0.274   0.152  -0.057
73    K         1.310   1.318   1.356   1.232   1.218   1.312   1.411   1.424   1.478
74    M        -0.775  -0.728  -0.750  -0.675  -0.616  -0.631  -0.863  -0.805  -0.802
75    H        -0.021  -0.040   0.013   0.019  -0.023   0.045  -0.295  -0.330  -0.251
76    Y        -0.775  -0.728  -0.750  -0.829  -0.815  -0.793  -0.863  -0.805  -0.802
77    S        -0.021  -0.040   0.013  -0.192  -0.129  -0.141  -0.295  -0.330  -0.251
78    N         1.310   1.318   1.356   1.393   1.368   1.469   1.411   1.424   1.478
79    R        -0.569  -0.651  -0.717  -0.478  -0.619  -0.713  -0.579  -0.685  -0.758
80    L        -1.323  -1.367  -1.314  -1.265  -1.277  -1.241  -1.148  -1.186  -1.101
81    I         1.310   1.318   1.356   1.351   1.372   1.428   1.411   1.424   1.478
82    G         1.310   1.318   1.356   1.340   1.359   1.417   1.411   1.424   1.478
83    G        -1.323  -1.367  -1.314  -1.274  -1.355  -1.274  -1.148  -1.186  -1.101
84    F        -1.323  -1.367  -1.314  -1.072  -1.137  -1.035  -1.148  -1.186  -1.101
85    V        -1.323  -1.340  -1.316  -1.225  -1.198  -1.223  -1.148  -1.160  -1.103
86    Q         0.321   0.294   0.138   0.365   0.366   0.049   0.274   0.233  -0.032
87    T        -1.323  -1.340  -1.316  -1.265  -1.362  -1.273  -1.148  -1.160  -1.103
88    R        -0.775  -0.773  -0.741  -0.863  -0.874  -0.806  -0.863  -0.851  -0.792
89    G        -0.021  -0.034   0.014  -0.159  -0.228  -0.112  -0.295  -0.320  -0.248
90    F         0.321   0.243   0.124   0.381   0.325   0.059   0.274   0.152  -0.057
91    G        -1.871  -1.846  -1.769  -1.652  -1.610  -1.500  -1.432  -1.404  -1.295
92    P         1.310   1.318   1.356   1.435   1.452   1.510   1.411   1.424   1.478
93    E        -0.569  -0.651  -0.717  -0.622  -0.753  -0.825  -0.579  -0.685  -0.758
94    N        -0.775  -0.781  -0.740  -0.747  -0.837  -0.672  -0.863  -0.863  -0.791
95    Q        -0.775  -0.728  -0.750  -0.780  -0.661  -0.709  -0.863  -0.805  -0.802
96    L        -0.021  -0.040   0.013  -0.168  -0.152  -0.107  -0.295  -0.330  -0.251
97    R         0.321   0.417   0.158   0.498   0.620   0.239   0.274   0.421   0.002
98    H        -0.060  -0.049   0.012  -0.194  -0.197  -0.086  -0.366  -0.346  -0.252
99    Y         1.310   1.318   1.356   1.456   1.445   1.530   1.411   1.424   1.478
100   S        -1.871  -1.846  -1.769  -1.795  -1.737  -1.639  -1.432  -1.404  -1.295
101   R        -0.021   0.039   0.038  -0.251  -0.209  -0.155  -0.295  -0.190  -0.207
102   F        -0.021  -0.040   0.013  -0.150  -0.131  -0.102  -0.295  -0.330  -0.251
103   V        -1.323  -1.367  -1.314  -1.131  -1.200  -1.109  -1.148  -1.186  -1.101
104   A        -1.323  -1.287  -1.291  -1.156  -1.021  -1.112  -1.148  -1.105  -1.080
105   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   E        -1.430  -1.415  -1.336  -1.481  -1.473  -1.333  -1.254  -1.232  -1.122
107   I        -0.060  -0.047   0.012  -0.297  -0.256  -0.178  -0.366  -0.343  -0.253
108   A         0.198   0.244   0.122   0.243   0.367   0.119   0.079   0.153  -0.060
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   D        -0.745  -0.747  -0.735  -0.906  -0.892  -0.880  -0.810  -0.810  -0.780
122   D        -1.430  -1.415  -1.336  -1.488  -1.452  -1.340  -1.254  -1.232  -1.122
123   S        -1.430  -1.415  -1.336  -1.565  -1.520  -1.415  -1.254  -1.232  -1.122
124   K        -0.060  -0.050   0.011  -0.317  -0.291  -0.199  -0.366  -0.348  -0.254
125   K        -0.569  -0.581  -0.691  -0.580  -0.608  -0.770  -0.579  -0.596  -0.725
* 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/P32830
Output conservation file - output/P32830
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
