1     M         0.785   0.803   0.845   0.973   0.994   1.035   0.819   0.845   0.903
2     Y        -1.800  -1.786  -1.657  -1.881  -1.845  -1.597  -1.765  -1.720  -1.485
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     H        -1.172  -1.308  -1.139  -1.214  -1.460  -1.206  -1.286  -1.461  -1.219
9     A        -1.958  -1.939  -1.668  -1.987  -1.927  -1.532  -1.887  -1.850  -1.494
10    F        -1.773  -1.844  -1.663  -1.617  -1.771  -1.552  -1.687  -1.748  -1.490
11    Q        -2.292  -2.301  -2.067  -2.173  -2.180  -1.875  -2.000  -1.972  -1.650
12    G        -0.577  -0.443  -0.396  -0.816  -0.592  -0.516  -0.943  -0.717  -0.666
13    R         0.785   0.803   0.845   0.707   0.733   0.815   0.819   0.845   0.903
14    K        -2.292  -2.219  -2.067  -2.300  -2.279  -1.966  -2.000  -1.922  -1.650
15    L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
16    T        -0.577  -0.569  -0.413  -0.778  -0.784  -0.533  -0.943  -0.940  -0.697
17    D        -1.426  -1.419  -1.632  -1.195  -1.185  -1.599  -1.295  -1.286  -1.460
18    Q        -1.800  -1.786  -1.657  -1.777  -1.732  -1.496  -1.765  -1.720  -1.485
19    E         0.785   0.803   0.845   0.538   0.566   0.675   0.819   0.845   0.903
20    R         0.785   0.803   0.845   0.707   0.733   0.815   0.819   0.845   0.903
21    A        -0.730  -0.753  -1.090  -0.488  -0.543  -1.138  -0.708  -0.744  -1.158
22    R         0.009   0.115  -0.345   0.027   0.158  -0.468  -0.003   0.143  -0.579
23    V        -1.221  -1.081  -1.127  -1.360  -1.257  -1.220  -1.413  -1.264  -1.205
24    L        -0.577  -0.589  -0.412  -1.204  -1.255  -0.892  -0.943  -0.976  -0.696
25    E         0.009  -0.102  -0.350  -0.162  -0.310  -0.658  -0.003  -0.167  -0.587
26    F         0.785   0.803   0.845   0.966   0.995   1.030   0.819   0.845   0.903
27    Q        -0.373  -0.510  -0.411  -0.368  -0.616  -0.492  -0.591  -0.834  -0.693
28    D        -0.373  -0.289  -0.388  -0.459  -0.315  -0.595  -0.591  -0.459  -0.654
29    S        -1.713  -1.666  -1.644  -1.600  -1.529  -1.470  -1.648  -1.563  -1.472
30    I         0.785   0.803   0.845   0.852   0.883   0.935   0.819   0.845   0.903
31    H         0.785   0.803   0.845   0.825   0.863   0.912   0.819   0.845   0.903
32    Y         0.785   0.803   0.845   0.777   0.811   0.873   0.819   0.845   0.903
33    S         0.785   0.803   0.845   0.804   0.817   0.896   0.819   0.845   0.903
34    P        -0.373  -0.456  -0.406  -0.462  -0.616  -0.540  -0.591  -0.740  -0.683
35    R         0.785   0.803   0.845   0.707   0.733   0.815   0.819   0.845   0.903
36    Y         0.785   0.803   0.845   0.777   0.811   0.873   0.819   0.845   0.903
37    S         0.009  -0.102  -0.350   0.127  -0.027  -0.396  -0.003  -0.167  -0.587
38    D         0.785   0.803   0.845   0.886   0.915   0.963   0.819   0.845   0.903
39    D         0.009  -0.183  -0.361   0.190  -0.076  -0.410  -0.003  -0.291  -0.606
40    N        -1.713  -1.594  -1.650  -1.731  -1.694  -1.642  -1.648  -1.555  -1.479
41    Y        -1.221  -1.102  -1.114  -1.374  -1.156  -1.129  -1.413  -1.235  -1.189
42    E         0.785   0.803   0.845   0.538   0.566   0.675   0.819   0.845   0.903
43    Y         0.785   0.803   0.845   0.777   0.811   0.873   0.819   0.845   0.903
44    R         0.785   0.803   0.845   0.707   0.733   0.815   0.819   0.845   0.903
45    H         0.785   0.803   0.845   0.825   0.863   0.912   0.819   0.845   0.903
46    V         0.785   0.803   0.845   1.019   1.041   1.074   0.819   0.845   0.903
47    M         0.009  -0.183  -0.361   0.287   0.023  -0.315  -0.003  -0.291  -0.606
48    L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
49    P         0.785   0.803   0.845   0.777   0.793   0.873   0.819   0.845   0.903
50    K         0.785   0.803   0.845   0.906   0.922   0.980   0.819   0.845   0.903
51    A        -0.577  -0.470  -0.395  -0.610  -0.429  -0.340  -0.943  -0.764  -0.665
52    M         0.785   0.803   0.845   0.973   0.994   1.035   0.819   0.845   0.903
53    L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
54    K         0.785   0.803   0.845   0.906   0.922   0.980   0.819   0.845   0.903
55    V        -0.577  -0.443  -0.396  -0.613  -0.387  -0.345  -0.943  -0.717  -0.666
56    I         0.785   0.803   0.845   0.852   0.883   0.935   0.819   0.845   0.903
57    P         0.785   0.803   0.845   0.777   0.793   0.873   0.819   0.845   0.903
58    S        -2.070  -1.947  -2.049  -1.880  -1.731  -1.890  -1.765  -1.637  -1.636
59    D         0.785   0.803   0.845   0.886   0.915   0.963   0.819   0.845   0.903
60    Y         0.785   0.803   0.845   0.777   0.811   0.873   0.819   0.845   0.903
61    F         0.009  -0.183  -0.361   0.273   0.012  -0.343  -0.003  -0.291  -0.606
62    N         0.009  -0.183  -0.361   0.341   0.077  -0.275  -0.003  -0.291  -0.606
63    S        -2.292  -2.244  -2.065  -2.225  -2.184  -1.855  -2.000  -1.936  -1.649
64    E        -0.730  -0.827  -1.102  -0.830  -0.983  -1.303  -0.708  -0.847  -1.172
65    V        -1.069  -1.095  -1.117  -0.947  -0.960  -1.012  -1.178  -1.181  -1.191
66    G         0.785   0.803   0.845   0.879   0.906   0.957   0.819   0.845   0.903
67    T         0.785   0.803   0.845   0.865   0.904   0.946   0.819   0.845   0.903
68    L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
69    R         0.009  -0.183  -0.361   0.027  -0.231  -0.494  -0.003  -0.291  -0.606
70    I         0.009  -0.183  -0.361   0.122  -0.160  -0.546  -0.003  -0.291  -0.606
71    L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
72    T        -1.713  -1.798  -1.659  -1.631  -1.727  -1.573  -1.648  -1.716  -1.487
73    E         0.785   0.803   0.845   0.538   0.566   0.675   0.819   0.845   0.903
74    D        -0.577  -0.443  -0.396  -1.022  -0.799  -0.674  -0.943  -0.717  -0.666
75    E         0.785   0.803   0.845   0.538   0.566   0.675   0.819   0.845   0.903
76    W         0.785   0.803   0.845   1.045   1.062   1.095   0.819   0.845   0.903
77    R         0.785   0.803   0.845   0.707   0.733   0.815   0.819   0.845   0.903
78    G         0.009  -0.183  -0.361   0.201  -0.053  -0.362  -0.003  -0.291  -0.606
79    L         0.009  -0.183  -0.361  -0.118  -0.354  -0.574  -0.003  -0.291  -0.606
80    G         0.785   0.803   0.845   0.879   0.906   0.957   0.819   0.845   0.903
81    I         0.785   0.803   0.845   0.852   0.883   0.935   0.819   0.845   0.903
82    T         0.785   0.803   0.845   0.865   0.904   0.946   0.819   0.845   0.903
83    Q         0.785   0.803   0.845   0.879   0.914   0.957   0.819   0.845   0.903
84    S         0.785   0.803   0.845   0.804   0.817   0.896   0.819   0.845   0.903
85    L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
86    G         0.785   0.803   0.845   0.879   0.906   0.957   0.819   0.845   0.903
87    W         0.785   0.803   0.845   1.045   1.062   1.095   0.819   0.845   0.903
88    E        -0.373  -0.209  -0.374  -0.672  -0.425  -0.625  -0.591  -0.332  -0.629
89    H         0.009  -0.102  -0.350   0.154   0.026  -0.361  -0.003  -0.167  -0.587
90    Y         0.785   0.803   0.845   0.777   0.811   0.873   0.819   0.845   0.903
91    E         0.785   0.803   0.845   0.538   0.566   0.675   0.819   0.845   0.903
92    C        -1.443  -1.401  -1.149  -1.370  -1.302  -0.946  -1.648  -1.580  -1.230
93    H         0.785   0.803   0.845   0.825   0.863   0.912   0.819   0.845   0.903
94    A        -0.730  -1.009  -1.115  -0.463  -0.888  -1.124  -0.708  -1.069  -1.189
95    P         0.785   0.803   0.845   0.777   0.793   0.873   0.819   0.845   0.903
96    E         0.785   0.803   0.845   0.538   0.566   0.675   0.819   0.845   0.903
97    P         0.785   0.803   0.845   0.777   0.793   0.873   0.819   0.845   0.903
98    H         0.785   0.803   0.845   0.825   0.863   0.912   0.819   0.845   0.903
99    I         0.785   0.803   0.845   0.852   0.883   0.935   0.819   0.845   0.903
100   L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
101   L         0.785   0.803   0.845   0.552   0.591   0.687   0.819   0.845   0.903
102   F         0.785   0.803   0.845   0.966   0.995   1.030   0.819   0.845   0.903
103   K         0.785   0.803   0.845   0.906   0.922   0.980   0.819   0.845   0.903
104   R         0.785   0.803   0.845   0.707   0.733   0.815   0.819   0.845   0.903
105   P        -0.059  -0.179  -0.362  -0.063  -0.262  -0.615  -0.102  -0.285  -0.607
106   L        -0.855  -0.852  -1.109  -0.957  -0.954  -1.267  -0.869  -0.876  -1.181
107   N        -0.059  -0.179  -0.362   0.254   0.084  -0.279  -0.102  -0.285  -0.607
108   Y        -0.059   0.029  -0.354  -0.028   0.098  -0.503  -0.102   0.023  -0.593
109   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   A        -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   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   Q        -0.245  -0.098  -0.360  -0.270  -0.027  -0.460  -0.384  -0.161  -0.604
127   Q        -1.172  -1.144  -1.121  -1.288  -1.235  -1.237  -1.286  -1.258  -1.196
128   Q        -2.529  -2.373  -2.077  -2.675  -2.439  -1.988  -2.188  -2.027  -1.658
129   Q        -1.713  -1.632  -1.644  -1.548  -1.454  -1.425  -1.648  -1.562  -1.473
130   Q        -2.070  -2.177  -2.064  -1.764  -1.900  -1.800  -1.765  -1.859  -1.648
131   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P20486
Output conservation file - output/P20486
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
