1     M         1.308   1.323   1.388   1.597   1.610   1.706   1.413   1.435   1.540
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -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     S         0.608   0.518   0.338   0.780   0.657   0.330   0.638   0.495   0.165
9     A        -0.685  -0.790  -0.929  -0.300  -0.457  -0.691  -0.581  -0.708  -0.860
10    -        -0.456  -0.598  -0.523  -0.356  -0.637  -0.564  -0.573  -0.774  -0.681
11    T        -0.569  -0.550  -0.505  -0.690  -0.669  -0.632  -0.754  -0.725  -0.660
12    R        -0.998  -1.141  -1.029  -0.937  -1.148  -0.990  -0.951  -1.115  -0.967
13    A        -1.936  -1.934  -1.751  -1.624  -1.617  -1.372  -1.482  -1.467  -1.259
14    N        -0.501  -0.423  -0.487  -0.361  -0.272  -0.345  -0.692  -0.613  -0.638
15    K         0.608   0.744   0.366   0.679   0.849   0.361   0.638   0.827   0.216
16    D        -0.058  -0.193  -0.401  -0.038  -0.225  -0.547  -0.027  -0.215  -0.515
17    I         0.080   0.087   0.187   0.016   0.010   0.154  -0.249  -0.250  -0.114
18    F         1.308   1.323   1.388   1.423   1.448   1.544   1.413   1.435   1.540
19    T        -0.701  -0.594  -0.508  -0.797  -0.650  -0.515  -0.914  -0.788  -0.664
20    L         1.308   1.323   1.388   1.173   1.197   1.312   1.413   1.435   1.540
21    F         1.308   1.323   1.388   1.423   1.448   1.544   1.413   1.435   1.540
22    D         1.308   1.323   1.388   1.193   1.222   1.331   1.413   1.435   1.540
23    K         0.608   0.561   0.342   0.679   0.634   0.324   0.638   0.561   0.173
24    K        -0.685  -0.859  -0.948  -0.436  -0.653  -0.752  -0.581  -0.789  -0.880
25    G         0.608   0.546   0.341   0.600   0.521   0.235   0.638   0.538   0.171
26    Q        -0.944  -1.037  -1.001  -0.807  -0.941  -0.910  -0.914  -1.005  -0.939
27    G         1.308   1.323   1.388   1.208   1.231   1.344   1.413   1.435   1.540
28    A        -1.144  -1.139  -1.027  -1.142  -1.108  -0.931  -1.136  -1.125  -0.966
29    I         0.608   0.518   0.338   0.796   0.686   0.372   0.638   0.495   0.165
30    A        -0.363  -0.455  -0.464  -0.120  -0.279  -0.329  -0.471  -0.600  -0.610
31    K        -0.944  -0.828  -0.951  -1.014  -0.829  -1.042  -0.914  -0.765  -0.884
32    D        -1.022  -1.044  -0.985  -1.220  -1.232  -1.108  -1.025  -1.023  -0.923
33    S        -1.465  -1.340  -1.356  -1.131  -0.975  -1.018  -1.246  -1.108  -1.081
34    L        -0.363  -0.418  -0.445  -0.527  -0.610  -0.640  -0.471  -0.545  -0.578
35    G         1.308   1.323   1.388   1.208   1.231   1.344   1.413   1.435   1.540
36    D         1.308   1.323   1.388   1.193   1.222   1.331   1.413   1.435   1.540
37    Y         0.080   0.087   0.187  -0.168  -0.154   0.013  -0.249  -0.250  -0.114
38    L         1.308   1.323   1.388   1.173   1.197   1.312   1.413   1.435   1.540
39    R         1.308   1.323   1.388   1.534   1.548   1.647   1.413   1.435   1.540
40    A         0.608   0.744   0.366   0.847   1.000   0.486   0.638   0.827   0.216
41    I        -0.701  -0.672  -0.534  -0.731  -0.647  -0.447  -0.914  -0.875  -0.696
42    G         1.308   1.323   1.388   1.208   1.231   1.344   1.413   1.435   1.540
43    Y         0.080   0.087   0.187   0.099   0.102   0.240  -0.249  -0.250  -0.114
44    N         1.308   1.323   1.388   1.511   1.530   1.626   1.413   1.435   1.540
45    P         1.308   1.323   1.388   1.552   1.575   1.664   1.413   1.435   1.540
46    T         1.308   1.323   1.388   1.385   1.409   1.509   1.413   1.435   1.540
47    N         0.080   0.087   0.187  -0.186  -0.178  -0.007  -0.249  -0.250  -0.114
48    Q        -0.058  -0.031  -0.366   0.230   0.255  -0.261  -0.027   0.004  -0.466
49    L        -0.363  -0.363  -0.473  -0.486  -0.523  -0.673  -0.471  -0.488  -0.617
50    V         0.080   0.087   0.187  -0.066  -0.060   0.071  -0.249  -0.250  -0.114
51    Q        -2.230  -2.119  -1.997  -1.962  -1.824  -1.666  -1.579  -1.491  -1.324
52    D         0.080   0.156   0.195  -0.278  -0.136  -0.111  -0.249  -0.121  -0.099
53    I        -0.501  -0.531  -0.487  -0.734  -0.757  -0.667  -0.692  -0.720  -0.640
54    I        -1.908  -1.830  -1.735  -1.877  -1.790  -1.688  -1.468  -1.390  -1.248
55    N        -1.908  -1.809  -1.717  -1.753  -1.610  -1.484  -1.468  -1.384  -1.236
56    A        -1.465  -1.473  -1.387  -1.321  -1.330  -1.223  -1.246  -1.241  -1.112
57    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    D        -1.465  -1.526  -1.419  -1.423  -1.541  -1.457  -1.246  -1.288  -1.137
63    A        -1.144  -1.043  -0.987  -1.258  -1.098  -0.995  -1.136  -1.015  -0.926
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    S        -1.908  -1.858  -1.721  -1.791  -1.786  -1.573  -1.468  -1.418  -1.239
66    S        -0.685  -0.742  -0.923  -0.571  -0.679  -0.958  -0.581  -0.654  -0.853
67    L        -0.501  -0.522  -0.499  -0.681  -0.730  -0.684  -0.692  -0.712  -0.654
68    T         0.080   0.087   0.187  -0.239  -0.230  -0.070  -0.249  -0.250  -0.114
69    L        -1.022  -0.972  -1.004  -1.042  -0.988  -0.928  -1.025  -0.968  -0.944
70    D        -1.022  -1.006  -0.987  -1.241  -1.211  -1.145  -1.025  -0.992  -0.928
71    Q        -0.944  -0.978  -0.991  -0.881  -0.954  -1.011  -0.914  -0.954  -0.932
72    I        -1.465  -1.401  -1.387  -1.293  -1.209  -1.246  -1.246  -1.164  -1.109
73    T        -1.465  -1.438  -1.406  -1.379  -1.385  -1.350  -1.246  -1.217  -1.126
74    G        -1.465  -1.499  -1.374  -1.487  -1.508  -1.346  -1.246  -1.259  -1.101
75    L        -0.701  -0.672  -0.534  -1.000  -0.977  -0.757  -0.914  -0.875  -0.696
76    I        -0.701  -0.684  -0.530  -0.965  -0.965  -0.729  -0.914  -0.891  -0.690
77    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    E         0.021   0.052   0.174  -0.181  -0.138   0.052  -0.360  -0.317  -0.139
81    K        -0.685  -0.721  -0.954  -0.322  -0.400  -0.832  -0.581  -0.627  -0.888
82    E        -0.685  -0.721  -0.954  -0.277  -0.346  -0.766  -0.581  -0.627  -0.888
83    L        -1.465  -1.410  -1.407  -1.645  -1.547  -1.515  -1.246  -1.176  -1.126
84    D        -0.363  -0.401  -0.468  -0.579  -0.641  -0.783  -0.471  -0.516  -0.608
85    A        -0.363  -0.401  -0.468  -0.229  -0.283  -0.397  -0.471  -0.516  -0.608
86    T        -1.022  -1.060  -1.013  -1.098  -1.113  -1.062  -1.025  -1.038  -0.952
87    T        -1.465  -1.410  -1.407  -1.240  -1.182  -1.181  -1.246  -1.176  -1.126
88    K        -1.144  -1.160  -1.027  -1.278  -1.244  -1.035  -1.136  -1.141  -0.966
89    A         0.608   0.609   0.349   0.600   0.602   0.249   0.638   0.634   0.186
90    K        -1.144  -1.084  -1.015  -1.491  -1.369  -1.312  -1.136  -1.059  -0.955
91    T        -0.685  -0.721  -0.954  -0.325  -0.388  -0.861  -0.581  -0.627  -0.888
92    E         1.308   1.323   1.388   1.266   1.286   1.398   1.413   1.435   1.540
93    D         0.264   0.194   0.213   0.039  -0.093  -0.091   0.083  -0.052  -0.064
94    F         0.021   0.060   0.182  -0.046   0.011   0.188  -0.360  -0.301  -0.124
95    V        -0.501  -0.548  -0.479  -0.512  -0.555  -0.430  -0.692  -0.738  -0.631
96    K         0.264   0.263   0.227   0.209   0.211   0.141   0.083   0.071  -0.038
97    A         0.080   0.087   0.187  -0.184  -0.185  -0.013  -0.249  -0.250  -0.114
98    F         1.308   1.323   1.388   1.423   1.448   1.544   1.413   1.435   1.540
99    Q         1.308   1.323   1.388   1.483   1.505   1.600   1.413   1.435   1.540
100   V         1.308   1.323   1.388   1.328   1.355   1.456   1.413   1.435   1.540
101   F         1.308   1.323   1.388   1.423   1.448   1.544   1.413   1.435   1.540
102   D         1.308   1.323   1.388   1.193   1.222   1.331   1.413   1.435   1.540
103   K         1.308   1.323   1.388   1.276   1.311   1.407   1.413   1.435   1.540
104   E         0.264   0.351   0.226   0.039   0.183  -0.065   0.083   0.223  -0.040
105   S        -1.908  -1.816  -1.722  -1.434  -1.342  -1.182  -1.468  -1.390  -1.239
106   T         1.308   1.323   1.388   1.385   1.409   1.509   1.413   1.435   1.540
107   G         1.308   1.323   1.388   1.208   1.231   1.344   1.413   1.435   1.540
108   K        -1.144  -1.084  -1.015  -1.101  -1.014  -0.882  -1.136  -1.059  -0.955
109   V         0.021   0.052   0.175  -0.201  -0.147   0.036  -0.360  -0.316  -0.136
110   S         0.080   0.087   0.187  -0.205  -0.198  -0.035  -0.249  -0.250  -0.114
111   V         0.608   0.546   0.341   0.734   0.664   0.374   0.638   0.538   0.171
112   G         1.308   1.323   1.388   1.208   1.231   1.344   1.413   1.435   1.540
113   D        -0.501  -0.549  -0.499  -0.770  -0.835  -0.715  -0.692  -0.740  -0.654
114   L        -0.058  -0.038  -0.370  -0.010   0.005  -0.413  -0.027  -0.011  -0.470
115   R         0.608   0.518   0.338   0.900   0.769   0.452   0.638   0.495   0.165
116   Y         1.308   1.323   1.388   1.543   1.569   1.656   1.413   1.435   1.540
117   M        -0.944  -1.010  -1.001  -0.785  -0.894  -0.939  -0.914  -0.978  -0.939
118   L         1.308   1.323   1.388   1.173   1.197   1.312   1.413   1.435   1.540
119   T         1.308   1.323   1.388   1.385   1.409   1.509   1.413   1.435   1.540
120   G        -0.501  -0.549  -0.499  -0.622  -0.694  -0.588  -0.692  -0.740  -0.654
121   L         0.264   0.440   0.319   0.073   0.338   0.156   0.083   0.370   0.132
122   G         1.308   1.323   1.388   1.208   1.231   1.344   1.413   1.435   1.540
123   E         1.308   1.323   1.388   1.266   1.286   1.398   1.413   1.435   1.540
124   K         0.608   0.546   0.341   0.679   0.615   0.322   0.638   0.538   0.171
125   L         0.264   0.263   0.227   0.133   0.126   0.092   0.083   0.071  -0.038
126   T         0.080   0.145   0.206  -0.049   0.063   0.134  -0.249  -0.142  -0.078
127   D         0.608   0.561   0.342   0.593   0.542   0.243   0.638   0.561   0.173
128   A        -0.501  -0.408  -0.444  -0.629  -0.479  -0.506  -0.692  -0.545  -0.577
129   E         1.308   1.323   1.388   1.266   1.286   1.398   1.413   1.435   1.540
130   V         0.608   0.561   0.342   0.741   0.689   0.392   0.638   0.561   0.173
131   D         1.308   1.323   1.388   1.193   1.222   1.331   1.413   1.435   1.540
132   E         1.308   1.323   1.388   1.266   1.286   1.398   1.413   1.435   1.540
133   L         1.308   1.323   1.388   1.173   1.197   1.312   1.413   1.435   1.540
134   L         0.608   0.546   0.341   0.587   0.513   0.256   0.638   0.538   0.171
135   K         1.308   1.323   1.388   1.276   1.311   1.407   1.413   1.435   1.540
136   G         0.608   0.518   0.338   0.600   0.484   0.230   0.638   0.495   0.165
137   V         0.264   0.252   0.256   0.223   0.202   0.181   0.083   0.051   0.017
138   E        -1.022  -1.060  -1.013  -1.008  -1.082  -1.000  -1.025  -1.038  -0.952
139   V        -0.058  -0.207  -0.394   0.107  -0.094  -0.400  -0.027  -0.233  -0.504
140   D         0.021   0.058   0.178  -0.342  -0.295  -0.096  -0.360  -0.305  -0.131
141   S        -0.058  -0.024  -0.372   0.202   0.237  -0.285  -0.027   0.009  -0.474
142   N        -0.685  -0.742  -0.923  -0.619  -0.700  -0.970  -0.581  -0.654  -0.853
143   G         1.308   1.323   1.388   1.208   1.231   1.344   1.413   1.435   1.540
144   E        -1.465  -1.517  -1.398  -1.223  -1.331  -1.188  -1.246  -1.281  -1.120
145   I         0.080   0.087   0.187  -0.099  -0.089   0.055  -0.249  -0.250  -0.114
146   D         0.080   0.081   0.179  -0.169  -0.165   0.001  -0.249  -0.261  -0.128
147   Y         1.308   1.323   1.388   1.543   1.569   1.656   1.413   1.435   1.540
148   K        -1.022  -1.060  -1.013  -1.057  -1.069  -0.961  -1.025  -1.038  -0.952
149   K        -1.144  -1.097  -1.017  -1.476  -1.384  -1.308  -1.136  -1.069  -0.956
150   F         0.608   0.518   0.338   0.835   0.726   0.467   0.638   0.495   0.165
151   I        -0.363  -0.423  -0.441  -0.343  -0.418  -0.466  -0.471  -0.543  -0.572
152   E        -1.022  -1.060  -1.013  -1.134  -1.154  -1.048  -1.025  -1.038  -0.952
153   D        -0.501  -0.522  -0.499  -0.612  -0.645  -0.560  -0.692  -0.712  -0.654
154   V        -0.501  -0.549  -0.499  -0.559  -0.622  -0.537  -0.692  -0.740  -0.654
155   L         1.308   1.323   1.388   1.173   1.197   1.312   1.413   1.435   1.540
156   R        -0.701  -0.594  -0.508  -0.789  -0.617  -0.513  -0.914  -0.788  -0.664
157   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   Q        -0.058  -0.193  -0.401   0.287   0.100  -0.228  -0.027  -0.215  -0.515
* 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/P53141
Output conservation file - output/P53141
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
