1     M         1.065   1.069   1.073   1.120   1.147   1.129   1.089   1.092   1.097
2     L         1.065   1.069   1.073   0.804   0.829   0.824   1.089   1.092   1.097
3     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     S         1.065   1.069   1.073   0.896   0.922   0.913   1.089   1.092   1.097
10    S        -0.785  -0.774  -0.743  -0.997  -0.985  -0.920  -0.885  -0.867  -0.822
11    R        -0.785  -0.774  -0.743  -0.997  -0.985  -0.920  -0.885  -0.867  -0.822
12    V         1.065   1.069   1.073   1.207   1.235   1.214   1.089   1.092   1.097
13    T        -0.785  -0.774  -0.743  -0.477  -0.462  -0.417  -0.885  -0.867  -0.822
14    R         1.065   1.069   1.073   1.076   1.103   1.087   1.089   1.092   1.097
15    S         1.065   1.069   1.073   0.896   0.922   0.913   1.089   1.092   1.097
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    I        -0.785  -0.774  -0.743  -1.098  -1.088  -1.019  -0.885  -0.867  -0.822
18    E        -0.785  -0.774  -0.743  -0.881  -0.869  -0.808  -0.885  -0.867  -0.822
19    L        -0.785  -0.774  -0.743  -0.930  -0.918  -0.856  -0.885  -0.867  -0.822
20    S        -0.785  -0.774  -0.743  -0.864  -0.852  -0.792  -0.885  -0.867  -0.822
21    N        -0.785  -0.774  -0.743  -0.612  -0.598  -0.548  -0.885  -0.867  -0.822
22    I        -0.785  -0.774  -0.743  -0.658  -0.645  -0.593  -0.885  -0.867  -0.822
23    S        -0.785  -0.774  -0.743  -0.832  -0.820  -0.761  -0.885  -0.867  -0.822
24    T        -0.785  -0.774  -0.743  -0.582  -0.568  -0.519  -0.885  -0.867  -0.822
25    T        -0.785  -0.774  -0.743  -0.612  -0.598  -0.548  -0.885  -0.867  -0.822
26    N        -0.785  -0.774  -0.743  -0.612  -0.598  -0.548  -0.885  -0.867  -0.822
27    H        -0.785  -0.774  -0.743  -0.536  -0.522  -0.475  -0.885  -0.867  -0.822
28    T        -0.785  -0.774  -0.743  -0.597  -0.583  -0.533  -0.885  -0.867  -0.822
29    R         1.065   1.069   1.073   1.076   1.103   1.087   1.089   1.092   1.097
30    S         1.065   1.069   1.073   0.896   0.922   0.913   1.089   1.092   1.097
31    L        -0.785  -0.774  -0.743  -0.752  -0.739  -0.684  -0.885  -0.867  -0.822
32    R         1.065   1.069   1.073   1.076   1.103   1.087   1.089   1.092   1.097
33    R        -0.785  -0.774  -0.743  -0.705  -0.692  -0.638  -0.885  -0.867  -0.822
34    L        -0.785  -0.774  -0.743  -1.098  -1.088  -1.019  -0.885  -0.867  -0.822
35    S        -0.785  -0.774  -0.743  -1.030  -1.019  -0.953  -0.885  -0.867  -0.822
36    W        -0.785  -0.774  -0.743  -0.536  -0.522  -0.475  -0.885  -0.867  -0.822
37    I        -0.785  -0.774  -0.743  -1.098  -1.088  -1.019  -0.885  -0.867  -0.822
38    S        -0.785  -0.774  -0.743  -1.203  -1.194  -1.120  -0.885  -0.867  -0.822
39    P        -0.785  -0.774  -0.743  -0.658  -0.645  -0.593  -0.885  -0.867  -0.822
40    R        -0.785  -0.774  -0.743  -0.768  -0.755  -0.699  -0.885  -0.867  -0.822
41    R        -0.785  -0.774  -0.743  -1.030  -1.019  -0.953  -0.885  -0.867  -0.822
42    F        -0.785  -0.774  -0.743  -0.628  -0.614  -0.563  -0.885  -0.867  -0.822
43    Y         1.065   1.069   1.073   1.462   1.492   1.460   1.089   1.092   1.097
44    A         1.065   1.069   1.073   1.250   1.279   1.255   1.089   1.092   1.097
45    Q        -0.785  -0.774  -0.743  -0.881  -0.869  -0.808  -0.885  -0.867  -0.822
46    S         1.065   1.069   1.073   0.896   0.922   0.913   1.089   1.092   1.097
47    W         1.065   1.069   1.073   1.399   1.428   1.399   1.089   1.092   1.097
48    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    D         1.065   1.069   1.073   1.142   1.169   1.150   1.089   1.092   1.097
50    R        -0.785  -0.774  -0.743  -1.030  -1.019  -0.953  -0.885  -0.867  -0.822
51    Q        -0.785  -0.774  -0.743  -0.881  -0.869  -0.808  -0.885  -0.867  -0.822
52    P         1.065   1.069   1.073   1.207   1.235   1.214   1.089   1.092   1.097
53    N        -0.785  -0.774  -0.743  -0.784  -0.771  -0.715  -0.885  -0.867  -0.822
54    D         1.065   1.069   1.073   1.142   1.169   1.150   1.089   1.092   1.097
55    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    I        -0.785  -0.774  -0.743  -1.098  -1.088  -1.019  -0.885  -0.867  -0.822
57    D         1.065   1.069   1.073   1.142   1.169   1.150   1.089   1.092   1.097
58    A         1.065   1.069   1.073   1.250   1.279   1.255   1.089   1.092   1.097
59    H         1.065   1.069   1.073   1.357   1.386   1.359   1.089   1.092   1.097
60    I        -0.785  -0.774  -0.743  -0.800  -0.787  -0.730  -0.885  -0.867  -0.822
61    K         1.065   1.069   1.073   0.851   0.876   0.868   1.089   1.092   1.097
62    V         1.065   1.069   1.073   1.207   1.235   1.214   1.089   1.092   1.097
63    Q         1.065   1.069   1.073   1.229   1.257   1.235   1.089   1.092   1.097
64    K         1.065   1.069   1.073   0.851   0.876   0.868   1.089   1.092   1.097
65    L         1.065   1.069   1.073   0.804   0.829   0.824   1.089   1.092   1.097
66    M         1.065   1.069   1.073   1.071   0.975   1.082   1.089   1.092   1.097
67    D         1.065   1.069   1.073   1.123   1.157   1.132   1.089   1.092   1.097
68    Q        -0.633  -0.709  -0.720  -0.487  -0.649  -0.648  -0.666  -0.772  -0.787
69    I         1.065   1.069   1.073   1.018   1.029   1.031   1.089   1.092   1.097
70    N        -0.633  -0.588  -0.700  -0.289  -0.181  -0.417  -0.666  -0.599  -0.758
71    S        -0.633  -0.544  -0.684  -0.662  -0.331  -0.724  -0.666  -0.538  -0.736
72    R        -1.867  -1.833  -1.805  -1.468  -1.273  -1.377  -1.543  -1.500  -1.461
73    P         1.065   1.069   1.073   1.208   1.222   1.215   1.089   1.092   1.097
74    N        -1.867  -1.833  -1.805  -1.694  -1.515  -1.596  -1.543  -1.500  -1.461
75    V        -0.633  -0.709  -0.720  -0.479  -0.580  -0.652  -0.666  -0.772  -0.787
76    L        -1.867  -1.833  -1.805  -1.835  -1.793  -1.733  -1.543  -1.500  -1.461
77    E         1.065   1.069   1.073   1.071   0.971   1.082   1.089   1.092   1.097
78    K        -0.633  -0.709  -0.720  -0.903  -1.042  -1.036  -0.666  -0.772  -0.787
79    L         1.065   1.069   1.073   0.786   0.813   0.806   1.089   1.092   1.097
80    E         1.065   1.069   1.073   1.071   0.971   1.082   1.089   1.092   1.097
81    K        -0.633  -0.709  -0.720  -0.793  -1.013  -0.891  -0.666  -0.772  -0.787
82    V        -0.633  -0.709  -0.720  -0.581  -0.694  -0.789  -0.666  -0.772  -0.787
83    S        -0.633  -0.709  -0.720  -0.678  -0.654  -0.792  -0.666  -0.772  -0.787
84    N        -1.867  -1.833  -1.805  -1.937  -1.844  -1.831  -1.543  -1.500  -1.461
85    I         1.065   1.069   1.073   1.018   1.029   1.031   1.089   1.092   1.097
86    M         1.065   1.069   1.073   1.071   0.975   1.082   1.089   1.092   1.097
87    I        -0.633  -0.709  -0.720  -0.621  -0.632  -0.747  -0.666  -0.772  -0.787
88    E         1.065   1.069   1.073   1.071   0.971   1.082   1.089   1.092   1.097
89    K         1.065   1.069   1.073   0.823   0.729   0.841   1.089   1.092   1.097
90    K        -0.633  -0.544  -0.684  -0.793  -0.784  -0.848  -0.666  -0.538  -0.736
91    L         1.065   1.069   1.073   0.786   0.813   0.806   1.089   1.092   1.097
92    V        -0.633  -0.588  -0.700  -0.581  -0.504  -0.668  -0.666  -0.599  -0.758
93    N        -0.633  -0.709  -0.720  -0.495  -0.632  -0.645  -0.666  -0.772  -0.787
94    L        -1.867  -1.833  -1.805  -1.937  -1.781  -1.831  -1.543  -1.500  -1.461
95    D        -0.633  -0.709  -0.720  -0.566  -0.763  -0.717  -0.666  -0.772  -0.787
96    G        -1.867  -1.833  -1.805  -1.641  -1.547  -1.545  -1.543  -1.500  -1.461
97    T        -1.867  -1.833  -1.805  -1.370  -1.272  -1.282  -1.543  -1.500  -1.461
98    S        -1.867  -1.833  -1.805  -1.813  -1.766  -1.711  -1.543  -1.500  -1.461
99    A        -0.633  -0.709  -0.720  -0.425  -0.464  -0.567  -0.666  -0.772  -0.787
100   N        -0.633  -0.709  -0.720  -0.456  -0.596  -0.593  -0.666  -0.772  -0.787
101   E        -0.785  -0.774  -0.743  -0.698  -0.791  -0.632  -0.885  -0.867  -0.822
102   E        -0.785  -0.774  -0.743  -0.774  -0.817  -0.705  -0.885  -0.867  -0.822
103   N        -0.785  -0.774  -0.743  -0.774  -0.610  -0.705  -0.885  -0.867  -0.822
104   T        -0.785  -0.774  -0.743  -0.717  -0.511  -0.650  -0.885  -0.867  -0.822
105   M        -0.785  -0.774  -0.743  -0.605  -0.636  -0.542  -0.885  -0.867  -0.822
106   K        -0.633  -0.709  -0.720  -0.903  -1.042  -1.036  -0.666  -0.772  -0.787
107   P        -0.633  -0.709  -0.720  -0.510  -0.673  -0.679  -0.666  -0.772  -0.787
108   W        -0.633  -0.588  -0.700  -0.441  -0.457  -0.511  -0.666  -0.599  -0.758
109   Q         1.065   1.069   1.073   1.208   1.286   1.215   1.089   1.092   1.097
110   M         1.065   1.069   1.073   1.071   0.975   1.082   1.089   1.092   1.097
111   I        -0.633  -0.709  -0.720  -0.581  -0.673  -0.694  -0.666  -0.772  -0.787
112   K         1.065   1.069   1.073   0.823   0.729   0.841   1.089   1.092   1.097
113   I        -0.633  -0.709  -0.720  -0.793  -0.965  -0.975  -0.666  -0.772  -0.787
114   L        -0.633  -0.709  -0.720  -0.878  -1.067  -0.986  -0.666  -0.772  -0.787
115   M         1.065   1.069   1.073   1.071   0.975   1.082   1.089   1.092   1.097
116   D         1.065   1.069   1.073   1.123   1.157   1.132   1.089   1.092   1.097
117   R        -0.633  -0.588  -0.700  -0.802  -0.746  -0.877  -0.666  -0.599  -0.758
118   D         1.065   1.069   1.073   1.123   1.157   1.132   1.089   1.092   1.097
119   L        -0.633  -0.709  -0.720  -0.903  -1.035  -1.020  -0.666  -0.772  -0.787
120   R         1.065   1.069   1.073   1.157   1.401   1.165   1.089   1.092   1.097
121   H        -1.867  -1.833  -1.805  -1.748  -1.768  -1.648  -1.543  -1.500  -1.461
122   A         1.065   1.069   1.073   1.208   1.344   1.215   1.089   1.092   1.097
123   M         1.065   1.069   1.073   1.071   0.975   1.082   1.089   1.092   1.097
124   K        -1.867  -1.833  -1.805  -1.769  -1.753  -1.669  -1.543  -1.500  -1.461
125   E        -0.633  -0.709  -0.720  -0.727  -1.066  -0.909  -0.666  -0.772  -0.787
126   F         1.065   1.069   1.073   1.392   1.474   1.393   1.089   1.092   1.097
127   K         1.065   1.069   1.073   0.823   0.729   0.841   1.089   1.092   1.097
128   L        -0.633  -0.588  -0.700  -0.861  -0.619  -0.991  -0.666  -0.599  -0.758
129   E        -0.633  -0.544  -0.684  -0.670  -0.574  -0.765  -0.666  -0.538  -0.736
130   L        -0.633  -0.709  -0.720  -0.878  -1.067  -0.986  -0.666  -0.772  -0.787
131   E        -0.633  -0.588  -0.700  -0.566  -0.540  -0.681  -0.666  -0.599  -0.758
132   K         1.065   1.069   1.073   0.823   0.729   0.841   1.089   1.092   1.097
133   S        -0.633  -0.544  -0.684  -0.662  -0.331  -0.724  -0.666  -0.538  -0.736
134   G         1.065   1.069   1.073   1.292   1.280   1.296   1.089   1.092   1.097
135   I         1.065   1.069   1.073   1.018   1.029   1.031   1.089   1.092   1.097
136   Q        -0.633  -0.709  -0.720  -0.441  -0.531  -0.587  -0.666  -0.772  -0.787
137   L         1.065   1.069   1.073   0.786   0.813   0.806   1.089   1.092   1.097
138   G         1.065   1.069   1.073   1.292   1.280   1.296   1.089   1.092   1.097
139   P         1.065   1.069   1.073   1.208   1.222   1.215   1.089   1.092   1.097
140   E        -0.633  -0.588  -0.700  -0.566  -0.540  -0.681  -0.666  -0.599  -0.758
141   Q         1.065   1.069   1.073   1.208   1.286   1.215   1.089   1.092   1.097
142   L         1.065   1.069   1.073   0.786   0.813   0.806   1.089   1.092   1.097
143   A        -0.633  -0.709  -0.720  -0.387  -0.433  -0.516  -0.666  -0.772  -0.787
144   P         1.065   1.069   1.073   1.208   1.222   1.215   1.089   1.092   1.097
145   L         1.065   1.069   1.073   0.786   0.813   0.806   1.089   1.092   1.097
146   M         1.065   1.069   1.073   1.071   0.975   1.082   1.089   1.092   1.097
147   T        -0.633  -0.709  -0.720  -0.487  -0.604  -0.699  -0.666  -0.772  -0.787
148   V         1.065   1.069   1.073   1.242   1.329   1.247   1.089   1.092   1.097
149   L         1.065   1.069   1.073   0.786   0.813   0.806   1.089   1.092   1.097
150   G         1.065   1.069   1.073   1.292   1.280   1.296   1.089   1.092   1.097
151   L        -0.633  -0.588  -0.700  -0.793  -0.729  -0.931  -0.666  -0.599  -0.758
152   E         1.065   1.069   1.073   1.071   0.971   1.082   1.089   1.092   1.097
153   K         1.065   1.069   1.073   0.771   0.696   0.791   1.089   1.092   1.097
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   K         1.065   1.069   1.073   0.823   0.729   0.841   1.089   1.092   1.097
156   K         1.065   1.069   1.073   0.823   0.729   0.841   1.089   1.092   1.097
* 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/P0C5N3
Output conservation file - output/P0C5N3
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
