1     M         1.884   1.892   1.954   1.969   1.983   2.081   2.067   2.079   2.172
2     D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    S        -0.717  -0.715  -0.672  -0.858  -0.855  -0.788  -0.776  -0.772  -0.703
11    L        -0.717  -0.715  -0.672  -0.646  -0.643  -0.572  -0.776  -0.772  -0.703
12    V        -0.717  -0.715  -0.672  -0.982  -0.983  -0.913  -0.776  -0.772  -0.703
13    P        -1.398  -1.394  -1.360  -1.144  -1.131  -1.078  -1.132  -1.125  -1.062
14    K         0.553   0.601   0.469   0.395   0.467   0.287   0.468   0.546   0.319
15    R        -1.398  -1.394  -1.360  -1.354  -1.339  -1.291  -1.132  -1.125  -1.062
16    Q        -1.398  -1.394  -1.360  -1.561  -1.541  -1.500  -1.132  -1.125  -1.062
17    L        -0.577  -0.543  -0.596  -0.454  -0.399  -0.477  -0.599  -0.552  -0.607
18    Q        -0.577  -0.543  -0.596  -0.470  -0.406  -0.514  -0.599  -0.552  -0.607
19    Q        -1.398  -1.394  -1.360  -1.492  -1.475  -1.431  -1.132  -1.125  -1.062
20    Q        -0.577  -0.609  -0.595  -0.570  -0.593  -0.563  -0.599  -0.637  -0.605
21    Q        -0.577  -0.586  -0.603  -0.640  -0.643  -0.687  -0.599  -0.609  -0.616
22    Q        -0.577  -0.561  -0.578  -0.711  -0.683  -0.702  -0.599  -0.575  -0.584
23    Q        -0.577  -0.543  -0.596  -0.613  -0.556  -0.652  -0.599  -0.552  -0.607
24    Q         0.553   0.601   0.469   0.556   0.635   0.399   0.468   0.546   0.319
25    E        -0.577  -0.543  -0.596  -0.444  -0.382  -0.491  -0.599  -0.552  -0.607
26    Q         1.884   1.892   1.954   1.587   1.592   1.693   2.067   2.079   2.172
27    Q         0.377   0.364   0.373   0.199   0.163   0.162   0.171   0.148   0.152
28    Q        -0.717  -0.714  -0.672  -1.072  -1.066  -1.005  -0.776  -0.770  -0.703
29    Q        -0.717  -0.714  -0.672  -0.883  -0.885  -0.812  -0.776  -0.770  -0.703
30    Q        -0.717  -0.714  -0.672  -0.862  -0.867  -0.792  -0.776  -0.770  -0.703
31    Q         0.377   0.370   0.375   0.009  -0.011  -0.006   0.171   0.159   0.154
32    Q        -0.717  -0.714  -0.672  -0.783  -0.792  -0.711  -0.776  -0.770  -0.703
33    D         0.377   0.364   0.373   0.408   0.386   0.396   0.171   0.148   0.152
34    F        -0.717  -0.714  -0.672  -0.438  -0.431  -0.361  -0.776  -0.770  -0.703
35    H         0.377   0.370   0.375   0.614   0.603   0.600   0.171   0.159   0.154
36    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    D        -0.577  -0.609  -0.595  -0.470  -0.520  -0.496  -0.599  -0.637  -0.605
38    Q        -1.398  -1.394  -1.360  -1.492  -1.488  -1.431  -1.132  -1.125  -1.062
39    L         1.884   1.892   1.954   1.800   1.808   1.909   2.067   2.079   2.172
40    M        -0.577  -0.586  -0.603  -0.678  -0.691  -0.696  -0.599  -0.609  -0.616
41    T         0.553   0.496   0.459   0.604   0.510   0.426   0.468   0.374   0.301
42    V         0.553   0.574   0.495   0.592   0.623   0.498   0.468   0.502   0.363
43    G         0.553   0.496   0.459   0.685   0.598   0.542   0.468   0.374   0.301
44    M         1.884   1.892   1.954   1.969   1.983   2.081   2.067   2.079   2.172
45    R         1.884   1.892   1.954   1.812   1.827   1.921   2.067   2.079   2.172
46    I         1.884   1.892   1.954   2.040   2.056   2.153   2.067   2.079   2.172
47    R         1.884   1.892   1.954   1.812   1.827   1.921   2.067   2.079   2.172
48    Q         0.553   0.496   0.459   0.395   0.323   0.273   0.468   0.374   0.301
49    R         0.243   0.249   0.297   0.071   0.083   0.157  -0.066  -0.057   0.016
50    V         0.553   0.564   0.476   0.669   0.688   0.568   0.468   0.486   0.330
51    D         0.553   0.496   0.459   0.556   0.464   0.380   0.468   0.374   0.301
52    Q        -1.398  -1.394  -1.360  -1.397  -1.378  -1.334  -1.132  -1.125  -1.062
53    G         1.884   1.892   1.954   1.945   1.957   2.056   2.067   2.079   2.172
54    Y         1.884   1.892   1.954   2.087   2.098   2.200   2.067   2.079   2.172
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    A         0.553   0.496   0.459   0.681   0.598   0.550   0.468   0.374   0.301
70    S        -1.398  -1.394  -1.360  -1.250  -1.242  -1.185  -1.132  -1.125  -1.062
71    R        -0.577  -0.586  -0.603  -0.751  -0.759  -0.780  -0.599  -0.609  -0.616
72    T         0.553   0.601   0.469   0.700   0.770   0.579   0.468   0.546   0.319
73    P        -1.398  -1.394  -1.360  -1.271  -1.261  -1.206  -1.132  -1.125  -1.062
74    S         0.553   0.601   0.469   0.497   0.569   0.340   0.468   0.546   0.319
75    T        -0.577  -0.561  -0.578  -0.398  -0.370  -0.396  -0.599  -0.575  -0.584
76    S         0.553   0.496   0.459   0.362   0.283   0.228   0.468   0.374   0.301
77    D        -1.398  -1.394  -1.360  -1.333  -1.344  -1.269  -1.132  -1.125  -1.062
78    A        -1.398  -1.394  -1.360  -1.455  -1.457  -1.393  -1.132  -1.125  -1.062
79    S        -0.577  -0.609  -0.595  -0.837  -0.888  -0.867  -0.599  -0.637  -0.605
80    L        -1.398  -1.394  -1.360  -1.042  -1.024  -0.974  -1.132  -1.125  -1.062
81    Q        -0.577  -0.603  -0.605  -0.866  -0.911  -0.917  -0.599  -0.630  -0.618
82    P        -0.577  -0.543  -0.596  -0.429  -0.376  -0.458  -0.599  -0.552  -0.607
83    G        -1.398  -1.394  -1.360  -1.177  -1.182  -1.111  -1.132  -1.125  -1.062
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    I         0.377   0.376   0.365   0.465   0.462   0.431   0.171   0.169   0.137
91    R         0.377   0.376   0.365   0.084   0.080   0.028   0.171   0.169   0.137
92    D         1.884   1.892   1.954   1.947   1.960   2.058   2.067   2.079   2.172
93    Y        -0.717  -0.715  -0.672  -0.585  -0.585  -0.510  -0.776  -0.772  -0.703
94    S        -0.717  -0.715  -0.672  -0.836  -0.832  -0.765  -0.776  -0.772  -0.703
95    S         0.377   0.376   0.365   0.008   0.004  -0.021   0.171   0.169   0.137
96    V        -0.717  -0.715  -0.672  -0.545  -0.540  -0.469  -0.776  -0.772  -0.703
97    I         0.377   0.376   0.365   0.495   0.493   0.467   0.171   0.169   0.137
98    V         0.377   0.376   0.365   0.389   0.387   0.374   0.171   0.169   0.137
99    P         1.884   1.892   1.954   1.930   1.944   2.041   2.067   2.079   2.172
100   Q         0.377   0.376   0.365   0.076   0.076   0.067   0.171   0.169   0.137
101   F         0.553   0.574   0.495   0.887   0.916   0.815   0.468   0.502   0.363
102   T        -1.398  -1.394  -1.360  -1.291  -1.299  -1.227  -1.132  -1.125  -1.062
103   R         0.553   0.564   0.476   0.572   0.592   0.464   0.468   0.486   0.330
104   S        -0.577  -0.543  -0.596  -0.723  -0.651  -0.785  -0.599  -0.552  -0.607
105   P        -0.577  -0.561  -0.578  -0.465  -0.442  -0.462  -0.599  -0.575  -0.584
106   L         1.884   1.892   1.954   1.800   1.808   1.909   2.067   2.079   2.172
107   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   P         1.884   1.892   1.954   1.843   1.853   1.953   2.067   2.079   2.172
120   T        -0.717  -0.712  -0.672  -0.797  -0.800  -0.725  -0.776  -0.768  -0.703
121   A        -0.717  -0.712  -0.672  -0.797  -0.800  -0.725  -0.776  -0.768  -0.703
122   N         0.377   0.343   0.365   0.407   0.343   0.382   0.171   0.112   0.137
123   S        -0.717  -0.712  -0.672  -0.763  -0.745  -0.691  -0.776  -0.768  -0.703
124   L        -0.717  -0.712  -0.672  -0.730  -0.722  -0.657  -0.776  -0.768  -0.703
125   P         0.553   0.564   0.476   0.639   0.652   0.524   0.468   0.486   0.330
126   P         1.884   1.892   1.954   1.897   1.906   2.008   2.067   2.079   2.172
127   M         0.553   0.496   0.459   0.708   0.624   0.564   0.468   0.374   0.301
128   L         1.884   1.892   1.954   1.800   1.808   1.909   2.067   2.079   2.172
129   I         0.553   0.601   0.469   0.669   0.739   0.558   0.468   0.546   0.319
130   N         1.884   1.892   1.954   1.849   1.854   1.959   2.067   2.079   2.172
131   Q         0.553   0.496   0.459   0.375   0.301   0.245   0.468   0.374   0.301
132   R         0.553   0.496   0.459   0.461   0.370   0.285   0.468   0.374   0.301
133   T         0.553   0.496   0.459   0.604   0.510   0.426   0.468   0.374   0.301
134   M        -1.398  -1.394  -1.360  -1.099  -1.092  -1.032  -1.132  -1.125  -1.062
135   S         0.553   0.496   0.459   0.329   0.247   0.182   0.468   0.374   0.301
136   T        -0.577  -0.561  -0.578  -0.501  -0.470  -0.509  -0.599  -0.575  -0.584
137   E        -0.577  -0.586  -0.603  -0.496  -0.519  -0.529  -0.599  -0.609  -0.616
138   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   S         0.553   0.564   0.476   0.362   0.382   0.253   0.468   0.486   0.330
140   S        -0.577  -0.543  -0.596  -0.485  -0.431  -0.507  -0.599  -0.552  -0.607
141   L         0.553   0.564   0.476   0.564   0.577   0.458   0.468   0.486   0.330
142   E         0.553   0.564   0.476   0.580   0.596   0.435   0.468   0.486   0.330
143   K        -0.577  -0.536  -0.575  -0.506  -0.442  -0.506  -0.599  -0.543  -0.579
144   W         1.884   1.892   1.954   2.196   2.210   2.311   2.067   2.079   2.172
145   D         0.377   0.413   0.390   0.401   0.461   0.419   0.171   0.232   0.181
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   V         0.377   0.364   0.373   0.078   0.050   0.073   0.171   0.148   0.152
152   A         0.377   0.364   0.373   0.323   0.305   0.313   0.171   0.148   0.152
153   E        -0.717  -0.714  -0.672  -0.724  -0.715  -0.651  -0.776  -0.770  -0.703
154   P         0.377   0.413   0.390   0.352   0.406   0.369   0.171   0.232   0.181
155   A        -0.717  -0.714  -0.672  -0.945  -0.935  -0.875  -0.776  -0.770  -0.703
156   A        -0.717  -0.714  -0.672  -0.883  -0.885  -0.812  -0.776  -0.770  -0.703
157   E        -0.717  -0.714  -0.672  -0.705  -0.696  -0.632  -0.776  -0.770  -0.703
158   H        -0.717  -0.714  -0.672  -0.783  -0.761  -0.711  -0.776  -0.770  -0.703
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -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   E        -0.577  -0.603  -0.605  -0.548  -0.602  -0.609  -0.599  -0.630  -0.618
180   T        -1.398  -1.394  -1.360  -0.908  -0.897  -0.838  -1.132  -1.125  -1.062
181   M        -0.577  -0.586  -0.603  -0.640  -0.669  -0.687  -0.599  -0.609  -0.616
182   V        -0.577  -0.586  -0.603  -0.711  -0.721  -0.735  -0.599  -0.609  -0.616
183   N        -0.577  -0.603  -0.605  -0.439  -0.481  -0.466  -0.599  -0.630  -0.618
184   G        -0.577  -0.603  -0.605  -0.338  -0.372  -0.367  -0.599  -0.630  -0.618
185   S        -0.577  -0.609  -0.595  -0.640  -0.679  -0.643  -0.599  -0.637  -0.605
186   K        -0.577  -0.609  -0.595  -0.393  -0.447  -0.424  -0.599  -0.637  -0.605
187   R         0.553   0.496   0.459   0.521   0.434   0.368   0.468   0.374   0.301
188   R        -1.398  -1.394  -1.360  -1.333  -1.312  -1.269  -1.132  -1.125  -1.062
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   L         0.553   0.601   0.469   0.798   0.871   0.657   0.468   0.546   0.319
* 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/O13577
Output conservation file - output/O13577
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
