1     M         0.954   0.964   0.970   1.189   1.198   1.204   0.985   0.995   1.002
2     S        -0.544  -0.617  -0.613  -0.546  -0.663  -0.653  -0.657  -0.759  -0.753
3     Q        -0.544  -0.468  -0.583  -0.434  -0.318  -0.480  -0.657  -0.535  -0.706
4     P        -0.544  -0.617  -0.613  -0.508  -0.597  -0.584  -0.657  -0.759  -0.753
5     T        -0.678  -0.661  -0.628  -0.842  -0.806  -0.749  -0.863  -0.827  -0.776
6     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    K        -1.632  -1.586  -1.563  -1.496  -1.394  -1.379  -1.479  -1.407  -1.369
16    P        -0.544  -0.617  -0.613  -0.540  -0.632  -0.626  -0.657  -0.759  -0.753
17    K        -0.544  -0.461  -0.583  -0.610  -0.482  -0.661  -0.657  -0.526  -0.707
18    P        -0.544  -0.617  -0.613  -0.540  -0.632  -0.626  -0.657  -0.759  -0.753
19    K        -1.632  -1.586  -1.563  -1.464  -1.384  -1.347  -1.479  -1.407  -1.369
20    I        -0.544  -0.617  -0.613  -0.701  -0.831  -0.823  -0.657  -0.759  -0.753
21    F        -0.544  -0.617  -0.613  -0.515  -0.640  -0.649  -0.657  -0.759  -0.753
22    N        -0.544  -0.617  -0.613  -0.471  -0.611  -0.621  -0.657  -0.759  -0.753
23    L         0.954   0.964   0.970   0.944   0.952   0.968   0.985   0.995   1.002
24    F        -0.544  -0.617  -0.613  -0.502  -0.631  -0.632  -0.657  -0.759  -0.753
25    R        -1.632  -1.586  -1.563  -1.464  -1.363  -1.347  -1.479  -1.407  -1.369
26    V        -0.544  -0.617  -0.613  -0.695  -0.814  -0.801  -0.657  -0.759  -0.753
27    C        -1.632  -1.586  -1.563  -1.589  -1.536  -1.467  -1.479  -1.407  -1.369
28    F        -1.632  -1.586  -1.563  -1.538  -1.473  -1.419  -1.479  -1.407  -1.369
29    I        -1.632  -1.586  -1.563  -1.701  -1.604  -1.576  -1.479  -1.407  -1.369
30    S        -0.544  -0.617  -0.613  -0.546  -0.663  -0.653  -0.657  -0.759  -0.753
31    L         0.954   0.964   0.970   0.944   0.952   0.968   0.985   0.995   1.002
32    L        -1.632  -1.586  -1.563  -1.657  -1.603  -1.533  -1.479  -1.407  -1.369
33    L         0.954   0.964   0.970   0.944   0.952   0.968   0.985   0.995   1.002
34    I         0.954   0.964   0.970   0.874   0.890   0.901   0.985   0.995   1.002
35    A         0.954   0.964   0.970   1.013   1.017   1.035   0.985   0.995   1.002
36    A         0.954   0.964   0.970   1.013   1.017   1.035   0.985   0.995   1.002
37    V         0.954   0.964   0.970   0.845   0.852   0.874   0.985   0.995   1.002
38    E         0.954   0.964   0.970   0.845   0.861   0.874   0.985   0.995   1.002
39    Y         0.954   0.964   0.970   0.916   0.936   0.941   0.985   0.995   1.002
40    F         0.954   0.964   0.970   1.040   1.054   1.061   0.985   0.995   1.002
41    K         0.954   0.964   0.970   0.888   0.898   0.914   0.985   0.995   1.002
42    Y         0.954   0.964   0.970   0.916   0.936   0.941   0.985   0.995   1.002
43    G        -0.544  -0.617  -0.613  -0.604  -0.728  -0.730  -0.657  -0.759  -0.753
44    T         0.954   0.964   0.970   0.999   1.014   1.021   0.985   0.995   1.002
45    R         0.954   0.964   0.970   1.054   1.071   1.074   0.985   0.995   1.002
46    I         0.954   0.964   0.970   0.874   0.890   0.901   0.985   0.995   1.002
47    N        -0.544  -0.617  -0.613  -0.434  -0.565  -0.571  -0.657  -0.759  -0.753
48    Y         0.954   0.964   0.970   0.916   0.936   0.941   0.985   0.995   1.002
49    E         0.954   0.964   0.970   0.845   0.861   0.874   0.985   0.995   1.002
50    W         0.954   0.964   0.970   1.215   1.226   1.229   0.985   0.995   1.002
51    F         0.954   0.964   0.970   1.040   1.054   1.061   0.985   0.995   1.002
52    H         0.954   0.964   0.970   1.122   1.139   1.139   0.985   0.995   1.002
53    C         0.954   0.964   0.970   1.122   1.135   1.139   0.985   0.995   1.002
54    T         0.954   0.964   0.970   0.999   1.014   1.021   0.985   0.995   1.002
55    P        -0.544  -0.617  -0.613  -0.662  -0.787  -0.790  -0.657  -0.759  -0.753
56    I        -1.632  -1.586  -1.563  -1.597  -1.483  -1.475  -1.479  -1.407  -1.369
57    K        -1.632  -1.586  -1.563  -1.513  -1.444  -1.395  -1.479  -1.407  -1.369
58    E         0.954   0.964   0.970   0.845   0.861   0.874   0.985   0.995   1.002
59    P        -1.632  -1.586  -1.563  -1.649  -1.573  -1.525  -1.479  -1.407  -1.369
60    Q        -1.632  -1.586  -1.563  -1.555  -1.492  -1.435  -1.479  -1.407  -1.369
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    S        -1.632  -1.586  -1.563  -1.623  -1.536  -1.500  -1.479  -1.407  -1.369
63    G        -0.544  -0.617  -0.613  -0.496  -0.589  -0.586  -0.657  -0.759  -0.753
64    -         0.954   0.964   0.970   0.958   0.972   0.982   0.985   0.995   1.002
65    -        -0.678  -0.661  -0.628  -0.895  -0.859  -0.801  -0.863  -0.827  -0.776
66    -        -0.678  -0.661  -0.628  -0.820  -0.784  -0.728  -0.863  -0.827  -0.776
67    S         0.954   0.964   0.970   0.957   0.973   0.982   0.985   0.995   1.002
68    V        -0.544  -0.617  -0.613  -0.695  -0.812  -0.801  -0.657  -0.759  -0.753
69    I        -0.544  -0.468  -0.583  -0.623  -0.493  -0.691  -0.657  -0.535  -0.706
70    K         0.954   0.964   0.970   0.888   0.898   0.914   0.985   0.995   1.002
71    L        -0.544  -0.461  -0.583  -0.623  -0.482  -0.692  -0.657  -0.526  -0.707
72    W         0.954   0.964   0.970   1.215   1.226   1.229   0.985   0.995   1.002
73    A         0.954   0.964   0.970   1.013   1.017   1.035   0.985   0.995   1.002
74    R        -0.544  -0.617  -0.613  -0.521  -0.652  -0.663  -0.657  -0.759  -0.753
75    G         0.954   0.964   0.970   0.957   0.977   0.982   0.985   0.995   1.002
76    G         0.954   0.964   0.970   0.957   0.977   0.982   0.985   0.995   1.002
77    P         0.954   0.964   0.970   0.916   0.940   0.941   0.985   0.995   1.002
78    S         0.954   0.964   0.970   0.957   0.973   0.982   0.985   0.995   1.002
79    C         0.954   0.964   0.970   1.122   1.135   1.139   0.985   0.995   1.002
80    D         0.954   0.964   0.970   0.944   0.956   0.968   0.985   0.995   1.002
81    K         0.954   0.964   0.970   0.888   0.898   0.914   0.985   0.995   1.002
82    R         0.954   0.964   0.970   1.054   1.071   1.074   0.985   0.995   1.002
83    G         0.954   0.964   0.970   0.957   0.977   0.982   0.985   0.995   1.002
84    E         0.954   0.964   0.970   0.845   0.861   0.874   0.985   0.995   1.002
85    Y        -0.544  -0.617  -0.613  -0.616  -0.733  -0.728  -0.657  -0.759  -0.753
86    K         0.954   0.964   0.970   0.888   0.898   0.914   0.985   0.995   1.002
87    T         0.954   0.964   0.970   0.999   1.014   1.021   0.985   0.995   1.002
88    I         0.954   0.964   0.970   0.874   0.890   0.901   0.985   0.995   1.002
89    V        -1.632  -1.586  -1.563  -1.546  -1.435  -1.427  -1.479  -1.407  -1.369
90    K         0.954   0.964   0.970   0.888   0.898   0.914   0.985   0.995   1.002
91    R         0.954   0.964   0.970   1.054   1.071   1.074   0.985   0.995   1.002
92    I         0.954   0.964   0.970   0.874   0.890   0.901   0.985   0.995   1.002
93    T        -0.544  -0.461  -0.583  -0.534  -0.390  -0.600  -0.657  -0.526  -0.707
94    R        -0.544  -0.617  -0.613  -0.379  -0.477  -0.472  -0.657  -0.759  -0.753
95    D         0.954   0.964   0.970   0.944   0.956   0.968   0.985   0.995   1.002
96    Y        -0.544  -0.617  -0.613  -0.572  -0.673  -0.668  -0.657  -0.759  -0.753
97    E        -0.544  -0.617  -0.613  -0.681  -0.795  -0.783  -0.657  -0.759  -0.753
98    P         0.954   0.964   0.970   0.916   0.940   0.941   0.985   0.995   1.002
99    N         0.954   0.964   0.970   1.108   1.119   1.126   0.985   0.995   1.002
100   D        -0.544  -0.617  -0.613  -0.636  -0.773  -0.768  -0.657  -0.759  -0.753
101   E         0.954   0.964   0.970   0.845   0.861   0.874   0.985   0.995   1.002
102   H        -0.544  -0.617  -0.613  -0.440  -0.566  -0.585  -0.657  -0.759  -0.753
103   L        -0.544  -0.617  -0.613  -0.636  -0.777  -0.768  -0.657  -0.759  -0.753
104   S        -0.544  -0.617  -0.613  -0.604  -0.732  -0.730  -0.657  -0.759  -0.753
105   F         0.954   0.964   0.970   1.040   1.054   1.061   0.985   0.995   1.002
106   C         0.954   0.964   0.970   1.122   1.135   1.139   0.985   0.995   1.002
107   I         0.954   0.964   0.970   0.874   0.890   0.901   0.985   0.995   1.002
108   I        -1.632  -1.586  -1.563  -1.782  -1.705  -1.653  -1.479  -1.407  -1.369
109   E         0.954   0.964   0.970   0.845   0.861   0.874   0.985   0.995   1.002
110   N        -0.544  -0.617  -0.613  -0.440  -0.574  -0.579  -0.657  -0.759  -0.753
111   D        -1.632  -1.586  -1.563  -1.455  -1.384  -1.339  -1.479  -1.407  -1.369
112   N        -1.632  -1.586  -1.563  -1.563  -1.500  -1.443  -1.479  -1.407  -1.369
113   V         0.954   0.964   0.970   0.845   0.852   0.874   0.985   0.995   1.002
114   P        -1.632  -1.586  -1.563  -1.692  -1.609  -1.567  -1.479  -1.407  -1.369
115   P        -0.544  -0.617  -0.613  -0.610  -0.717  -0.720  -0.657  -0.759  -0.753
116   V        -0.544  -0.617  -0.613  -0.714  -0.841  -0.828  -0.657  -0.759  -0.753
117   H         0.954   0.964   0.970   1.122   1.139   1.139   0.985   0.995   1.002
118   Y         0.954   0.964   0.970   0.916   0.936   0.941   0.985   0.995   1.002
119   P         0.954   0.964   0.970   0.916   0.940   0.941   0.985   0.995   1.002
120   I         0.954   0.964   0.970   0.874   0.890   0.901   0.985   0.995   1.002
121   H        -0.544  -0.617  -0.613  -0.471  -0.610  -0.627  -0.657  -0.759  -0.753
122   E        -0.544  -0.617  -0.613  -0.681  -0.795  -0.783  -0.657  -0.759  -0.753
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   D        -0.544  -0.617  -0.613  -0.515  -0.618  -0.605  -0.657  -0.759  -0.753
125   K         0.954   0.964   0.970   0.888   0.898   0.914   0.985   0.995   1.002
126   G         0.954   0.964   0.970   0.957   0.977   0.982   0.985   0.995   1.002
127   E        -0.544  -0.617  -0.613  -0.681  -0.795  -0.783  -0.657  -0.759  -0.753
128   P         0.954   0.964   0.970   0.916   0.940   0.941   0.985   0.995   1.002
129   G         0.954   0.964   0.970   0.957   0.977   0.982   0.985   0.995   1.002
130   Y         0.954   0.964   0.970   0.916   0.936   0.941   0.985   0.995   1.002
131   V        -0.544  -0.468  -0.583  -0.701  -0.567  -0.765  -0.657  -0.535  -0.706
132   A        -0.544  -0.617  -0.613  -0.521  -0.651  -0.644  -0.657  -0.759  -0.753
133   Y        -0.544  -0.617  -0.613  -0.572  -0.673  -0.668  -0.657  -0.759  -0.753
134   V         0.954   0.964   0.970   0.845   0.852   0.874   0.985   0.995   1.002
135   G         0.954   0.964   0.970   0.957   0.977   0.982   0.985   0.995   1.002
136   Y         0.954   0.964   0.970   0.916   0.936   0.941   0.985   0.995   1.002
137   D        -0.544  -0.617  -0.613  -0.636  -0.768  -0.768  -0.657  -0.759  -0.753
138   T        -1.632  -1.586  -1.563  -1.530  -1.432  -1.411  -1.479  -1.407  -1.369
139   D         0.954   0.964   0.970   0.944   0.956   0.968   0.985   0.995   1.002
140   S        -0.544  -0.461  -0.583  -0.604  -0.459  -0.673  -0.657  -0.526  -0.707
141   E        -1.632  -1.586  -1.563  -1.631  -1.546  -1.508  -1.479  -1.407  -1.369
142   L        -1.632  -1.586  -1.563  -1.666  -1.605  -1.542  -1.479  -1.407  -1.369
143   V         0.954   0.964   0.970   0.845   0.852   0.874   0.985   0.995   1.002
144   Q        -1.632  -1.586  -1.563  -1.555  -1.503  -1.435  -1.479  -1.407  -1.369
145   E        -0.544  -0.617  -0.613  -0.572  -0.663  -0.637  -0.657  -0.759  -0.753
146   L        -0.544  -0.617  -0.613  -0.559  -0.681  -0.664  -0.657  -0.759  -0.753
147   C         0.954   0.964   0.970   1.122   1.135   1.139   0.985   0.995   1.002
148   A        -0.544  -0.461  -0.583  -0.572  -0.431  -0.650  -0.657  -0.526  -0.707
149   D        -1.632  -1.586  -1.563  -1.623  -1.533  -1.500  -1.479  -1.407  -1.369
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   S        -1.632  -1.586  -1.563  -1.555  -1.472  -1.435  -1.479  -1.407  -1.369
153   T         0.954   0.964   0.970   0.999   1.014   1.021   0.985   0.995   1.002
154   I        -0.544  -0.468  -0.583  -0.714  -0.588  -0.773  -0.657  -0.535  -0.706
155   Y        -0.544  -0.468  -0.583  -0.515  -0.378  -0.588  -0.657  -0.535  -0.706
156   H        -0.544  -0.617  -0.613  -0.355  -0.466  -0.470  -0.657  -0.759  -0.753
157   M        -1.632  -1.586  -1.563  -1.431  -1.375  -1.316  -1.479  -1.407  -1.369
* 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/Q03579
Output conservation file - output/Q03579
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
