1     M         1.734   1.741   1.784   1.985   1.996   2.062   1.950   1.960   2.024
2     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    A         0.504   0.507   0.505   0.209   0.206   0.190   0.263   0.268   0.245
26    D         0.395   0.398   0.439   0.151   0.165   0.220   0.052   0.057   0.118
27    I        -0.275  -0.246  -0.276  -0.348  -0.307  -0.352  -0.423  -0.380  -0.418
28    P         0.647   0.667   0.596   0.606   0.627   0.525   0.526   0.560   0.419
29    M         1.734   1.741   1.784   1.968   1.980   2.045   1.950   1.960   2.024
30    E         0.504   0.488   0.499   0.286   0.256   0.265   0.263   0.232   0.234
31    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    I        -0.275  -0.277  -0.283  -0.108  -0.111  -0.116  -0.423  -0.425  -0.428
33    Q        -0.275  -0.269  -0.285  -0.200  -0.184  -0.232  -0.423  -0.413  -0.431
34    R        -0.945  -0.944  -0.906  -0.869  -0.862  -0.805  -0.897  -0.894  -0.836
35    E         0.647   0.681   0.577   0.466   0.517   0.364   0.526   0.586   0.382
36    D         1.734   1.741   1.784   1.828   1.838   1.905   1.950   1.960   2.024
37    N        -0.275  -0.293  -0.305  -0.291  -0.323  -0.354  -0.423  -0.447  -0.459
38    K        -0.945  -0.944  -0.906  -0.908  -0.913  -0.844  -0.897  -0.894  -0.836
39    N         0.647   0.628   0.572   0.606   0.576   0.468   0.526   0.491   0.374
40    Y        -0.945  -0.944  -0.906  -0.886  -0.871  -0.822  -0.897  -0.894  -0.836
41    D        -0.275  -0.269  -0.285  -0.535  -0.522  -0.544  -0.423  -0.413  -0.431
42    K         0.395   0.399   0.440   0.142   0.150   0.214   0.052   0.058   0.120
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    H         1.734   1.741   1.784   1.994   2.006   2.072   1.950   1.960   2.024
46    D        -0.389  -0.388  -0.348  -0.344  -0.339  -0.277  -0.581  -0.578  -0.518
47    N         0.504   0.513   0.504   0.402   0.416   0.395   0.263   0.278   0.245
48    E        -0.102  -0.153  -0.207  -0.201  -0.274  -0.363  -0.176  -0.249  -0.321
49    C        -1.376  -1.372  -1.339  -1.080  -1.084  -1.017  -1.087  -1.081  -1.027
50    F        -0.305  -0.290  -0.297  -0.080  -0.050  -0.063  -0.479  -0.461  -0.455
51    D        -0.102  -0.153  -0.207   0.048  -0.040  -0.123  -0.176  -0.249  -0.321
52    M        -1.376  -1.372  -1.339  -1.246  -1.245  -1.184  -1.087  -1.081  -1.027
53    N        -0.305  -0.339  -0.298  -0.525  -0.570  -0.507  -0.479  -0.518  -0.457
54    G        -0.945  -0.943  -0.906  -0.943  -0.948  -0.879  -0.897  -0.893  -0.836
55    N        -0.945  -0.943  -0.906  -0.844  -0.846  -0.780  -0.897  -0.893  -0.836
56    H        -0.945  -0.943  -0.906  -0.988  -0.998  -0.925  -0.897  -0.893  -0.836
57    N        -0.275  -0.246  -0.276  -0.493  -0.443  -0.494  -0.423  -0.380  -0.418
58    N         0.395   0.399   0.439   0.180   0.187   0.249   0.052   0.058   0.118
59    N        -0.945  -0.943  -0.906  -1.100  -1.099  -1.038  -0.897  -0.893  -0.836
60    S        -0.275  -0.285  -0.284  -0.434  -0.450  -0.457  -0.423  -0.437  -0.430
61    D        -0.389  -0.387  -0.348  -0.501  -0.506  -0.435  -0.581  -0.577  -0.518
62    N         0.647   0.601   0.572   0.544   0.475   0.410   0.526   0.442   0.373
63    L        -0.840  -0.847  -0.853  -0.779  -0.801  -0.790  -0.783  -0.790  -0.779
64    Q        -0.102  -0.148  -0.207  -0.207  -0.278  -0.370  -0.176  -0.242  -0.321
65    F        -0.305  -0.293  -0.300  -0.295  -0.295  -0.264  -0.479  -0.463  -0.458
66    D        -0.840  -0.861  -0.847  -0.830  -0.847  -0.856  -0.783  -0.805  -0.773
67    S        -1.376  -1.372  -1.339  -1.463  -1.449  -1.402  -1.087  -1.081  -1.027
68    V        -1.376  -1.372  -1.339  -1.237  -1.239  -1.175  -1.087  -1.081  -1.027
69    P         0.767   0.793   0.663   0.802   0.824   0.657   0.735   0.778   0.542
70    S        -0.840  -0.853  -0.851  -0.804  -0.831  -0.797  -0.783  -0.797  -0.777
71    S        -0.102  -0.153  -0.207  -0.219  -0.281  -0.386  -0.176  -0.249  -0.321
72    A        -0.102  -0.148  -0.207  -0.225  -0.308  -0.393  -0.176  -0.242  -0.321
73    T        -1.376  -1.372  -1.339  -1.292  -1.293  -1.230  -1.087  -1.081  -1.027
74    K        -0.389  -0.387  -0.348  -0.486  -0.492  -0.421  -0.581  -0.577  -0.518
75    D        -0.389  -0.387  -0.348  -0.587  -0.590  -0.522  -0.581  -0.577  -0.518
76    L         0.504   0.528   0.509   0.448   0.494   0.444   0.263   0.307   0.254
77    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    K         0.504   0.527   0.511   0.317   0.353   0.317   0.263   0.305   0.257
89    I        -0.389  -0.387  -0.348  -0.426  -0.424  -0.360  -0.581  -0.577  -0.518
90    E         0.504   0.495   0.504   0.266   0.245   0.252   0.263   0.245   0.245
91    E        -0.389  -0.387  -0.348  -0.459  -0.448  -0.393  -0.581  -0.577  -0.518
92    S        -0.840  -0.850  -0.849  -0.819  -0.849  -0.840  -0.783  -0.794  -0.775
93    S        -0.305  -0.291  -0.295  -0.505  -0.479  -0.480  -0.479  -0.463  -0.453
94    S        -1.376  -1.372  -1.339  -1.339  -1.355  -1.277  -1.087  -1.081  -1.027
95    T        -0.305  -0.283  -0.296  -0.485  -0.465  -0.477  -0.479  -0.453  -0.454
96    N        -1.376  -1.372  -1.339  -1.388  -1.379  -1.326  -1.087  -1.081  -1.027
97    S        -0.102  -0.076  -0.179  -0.195  -0.157  -0.311  -0.176  -0.137  -0.281
98    V        -0.102  -0.071  -0.180   0.037   0.082  -0.077  -0.176  -0.130  -0.282
99    I        -0.840  -0.808  -0.842  -0.887  -0.833  -0.877  -0.783  -0.744  -0.768
100   E        -0.102  -0.131  -0.202  -0.254  -0.290  -0.423  -0.176  -0.219  -0.313
101   E        -1.376  -1.372  -1.339  -1.210  -1.215  -1.148  -1.087  -1.081  -1.027
102   S        -1.376  -1.372  -1.339  -1.417  -1.416  -1.356  -1.087  -1.081  -1.027
103   S        -1.376  -1.372  -1.339  -1.278  -1.275  -1.216  -1.087  -1.081  -1.027
104   E        -0.102  -0.063  -0.193  -0.254  -0.186  -0.409  -0.176  -0.119  -0.302
105   P         1.734   1.741   1.784   1.702   1.697   1.778   1.950   1.960   2.024
106   K        -0.840  -0.847  -0.853  -0.742  -0.740  -0.755  -0.783  -0.790  -0.779
107   I        -0.275  -0.252  -0.277  -0.331  -0.293  -0.338  -0.423  -0.388  -0.420
108   S        -0.945  -0.943  -0.906  -1.070  -1.038  -1.007  -0.897  -0.893  -0.836
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   K        -1.376  -1.372  -1.339  -1.315  -1.308  -1.254  -1.087  -1.081  -1.027
113   L        -1.376  -1.372  -1.339  -1.131  -1.120  -1.068  -1.087  -1.081  -1.027
114   E        -1.376  -1.372  -1.339  -1.448  -1.433  -1.386  -1.087  -1.081  -1.027
115   N        -1.376  -1.372  -1.339  -1.311  -1.306  -1.249  -1.087  -1.081  -1.027
116   V         0.434   0.444   0.458   0.265   0.287   0.300   0.128   0.147   0.155
117   N        -0.102  -0.081  -0.200  -0.081  -0.058  -0.232  -0.176  -0.144  -0.311
118   L        -1.376  -1.372  -1.339  -1.219  -1.220  -1.157  -1.087  -1.081  -1.027
119   A        -0.840  -0.864  -0.868  -0.610  -0.673  -0.677  -0.783  -0.809  -0.796
120   A         0.434   0.455   0.474   0.184   0.211   0.243   0.128   0.169   0.186
121   T        -1.376  -1.372  -1.339  -1.166  -1.176  -1.103  -1.087  -1.081  -1.027
122   V        -0.102  -0.153  -0.207   0.043  -0.035  -0.121  -0.176  -0.249  -0.321
123   G         0.767   0.694   0.643   1.016   0.921   0.850   0.735   0.609   0.505
124   G         1.734   1.741   1.784   1.884   1.897   1.961   1.950   1.960   2.024
125   S         0.767   0.694   0.643   0.667   0.560   0.479   0.735   0.609   0.505
126   Q        -0.840  -0.864  -0.868  -0.894  -0.936  -0.916  -0.783  -0.809  -0.796
127   T         0.434   0.455   0.474   0.325   0.362   0.387   0.128   0.169   0.186
128   R         1.734   1.741   1.784   1.926   1.939   2.003   1.950   1.960   2.024
129   K        -0.840  -0.858  -0.849  -0.627  -0.660  -0.646  -0.783  -0.802  -0.775
130   Y         0.767   0.694   0.643   1.174   1.079   1.012   0.735   0.609   0.505
131   L         1.734   1.741   1.784   1.719   1.733   1.795   1.950   1.960   2.024
132   N         1.734   1.741   1.784   1.754   1.774   1.831   1.950   1.960   2.024
133   T        -1.376  -1.372  -1.339  -1.210  -1.206  -1.148  -1.087  -1.081  -1.027
134   N        -0.102  -0.148  -0.207   0.128   0.050  -0.074  -0.176  -0.242  -0.321
135   V         0.434   0.455   0.474   0.293   0.340   0.354   0.128   0.169   0.186
136   T         0.767   0.694   0.643   0.817   0.699   0.604   0.735   0.609   0.505
137   P        -0.305  -0.290  -0.297  -0.390  -0.381  -0.362  -0.479  -0.461  -0.455
138   H        -0.102  -0.131  -0.202   0.190   0.134   0.018  -0.176  -0.219  -0.313
139   L         1.734   1.741   1.784   1.719   1.733   1.795   1.950   1.960   2.024
140   L         1.734   1.741   1.784   1.719   1.733   1.795   1.950   1.960   2.024
141   A         0.434   0.420   0.452   0.132   0.097   0.160   0.128   0.099   0.144
142   G         1.734   1.741   1.784   1.884   1.897   1.961   1.950   1.960   2.024
143   M         0.434   0.455   0.474   0.440   0.489   0.500   0.128   0.169   0.186
144   R         0.434   0.451   0.458   0.408   0.447   0.434   0.128   0.160   0.155
145   L        -0.840  -0.847  -0.853  -0.812  -0.801  -0.826  -0.783  -0.790  -0.779
146   I         0.434   0.455   0.474   0.413   0.458   0.475   0.128   0.169   0.186
147   A         0.767   0.793   0.663   0.800   0.817   0.624   0.735   0.778   0.542
148   V        -0.840  -0.808  -0.842  -0.658  -0.607  -0.648  -0.783  -0.744  -0.768
149   Q        -1.376  -1.372  -1.339  -1.201  -1.181  -1.139  -1.087  -1.081  -1.027
150   Q         0.767   0.787   0.656   0.865   0.897   0.712   0.735   0.768   0.529
151   P         1.734   1.741   1.784   1.702   1.697   1.778   1.950   1.960   2.024
152   E         1.734   1.741   1.784   1.594   1.611   1.670   1.950   1.960   2.024
153   D         1.734   1.741   1.784   1.841   1.855   1.918   1.950   1.960   2.024
154   P         1.734   1.741   1.784   1.702   1.697   1.778   1.950   1.960   2.024
155   L         0.767   0.694   0.643   0.802   0.700   0.616   0.735   0.609   0.505
156   R         0.434   0.455   0.474   0.408   0.456   0.469   0.128   0.169   0.186
157   V        -0.305  -0.339  -0.305  -0.174  -0.237  -0.178  -0.479  -0.518  -0.465
158   L         1.734   1.741   1.784   1.719   1.733   1.795   1.950   1.960   2.024
159   G         1.734   1.741   1.784   1.884   1.897   1.961   1.950   1.960   2.024
160   E         0.767   0.780   0.650   0.708   0.734   0.549   0.735   0.757   0.517
161   Y         0.434   0.453   0.462   0.676   0.711   0.718   0.128   0.165   0.162
162   L         1.734   1.741   1.784   1.719   1.733   1.795   1.950   1.960   2.024
163   I         1.734   1.741   1.784   1.892   1.905   1.969   1.950   1.960   2.024
164   E        -0.945  -0.944  -0.906  -1.109  -1.107  -1.046  -0.897  -0.894  -0.836
165   Q        -0.945  -0.944  -0.906  -0.735  -0.728  -0.670  -0.897  -0.894  -0.836
166   S         1.734   1.741   1.784   1.570   1.579   1.645   1.950   1.960   2.024
167   N         0.647   0.642   0.572   0.518   0.508   0.360   0.526   0.517   0.373
168   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   S        -0.275  -0.260  -0.287  -0.449  -0.424  -0.458  -0.423  -0.400  -0.434
202   N        -0.840  -0.804  -0.847  -0.964  -0.878  -0.992  -0.783  -0.740  -0.773
203   A        -1.376  -1.372  -1.339  -1.114  -1.104  -1.051  -1.087  -1.081  -1.027
204   S        -0.305  -0.291  -0.295  -0.498  -0.469  -0.469  -0.479  -0.463  -0.453
205   K        -0.840  -0.804  -0.847  -0.964  -0.882  -0.992  -0.783  -0.740  -0.773
* 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/Q03323
Output conservation file - output/Q03323
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
