| Output for Srna |
Job ID: 7351
Folded seq.: NM_008874_CD300 |
|
Ensemble centroid in comparison with the minimum free energy structure  |
| Ensemble centroid (EC) structure diagram |
| Minimum free energy (MFE) structure diagram |
| Number of common base pairs between MFE and EC (BP in green) |
106
|
| Number of base pairs only in MFE (BP in blue) |
111
|
| Number of base pairs only in EC (BP in red) |
67
|
| Base pair distance between MFE and EC |
178 |
|
| Comparison of MFE and EC in circle diagram format |
|
|
|
| Cluster representation of the Boltzmann ensemble |
| |
Cluster # |
Size |
Cluster centroid |
Cluster 2Dhist |
| |
1 |
0.887 |
| * |
2 |
0.085 |
| |
3 |
0.028 |
(* marks the cluster in which the
MFE structure is located)
|
|
|
| Two-dimensional histograms for all clusters in panel format |
| Circle diagrams for all cluster centroids in panel format |
Multi-dimensional scaling (MDS) plot of the sampled
ensemble and representative structures |
Energy landscape of the sampled ensemble and
representative structures |
|
|
|
| Base pair frequencies in the sample |
| Two-dimensional histogram of base pairs in the sample |
|
|
|
| Ad hoc representation based on free energy intervals |
| Structure # |
Free energy interval |
Sample frequency |
Lowest free energy |
Structure diagram |
| 1 |
[ -247.80, -244.52) |
0.027 |
-247.80 |
| 2 |
[ -244.52, -241.24) |
0.076 |
-244.40 |
| 3 |
[ -241.24, -237.96) |
0.188 |
-241.20 |
| 4 |
[ -237.96, -234.68) |
0.233 |
-237.90 |
| 5 |
[ -234.68, -231.40) |
0.194 |
-234.60 |
| 6 |
[ -231.40, -228.12) |
0.148 |
-231.30 |
| 7 |
[ -228.12, -224.84) |
0.077 |
-228.10 |
| 8 |
[ -224.84, -221.56) |
0.034 |
-224.80 |
| 9 |
[ -221.56, -218.28) |
0.017 |
-221.50 |
| 10 |
[ -218.28, -215.00] |
0.006 |
-217.30 |
|
Cumulative free energy distribution for sampled structures |
View |
|
|
|
| Text files |
| Full clustering output |
sclass.out |
| Base pair frequencies for two-dimensional histogram |
2dhist.out |
| Free energies of sampled structures |
fe.out |
| Cumulative free energy distribution |
cdf.out |
| Free energy density distribution |
pdf.out |
|
|
|
| Output from other application modules |
| Select application module |
|
|
|
| Download all output files |
| Choose the compressed file format for general output |
| Choose the compressed file format for all sampled structures |
|
|
|
| Job and system information |
| Job information |
View |
| System information |
View |
|
|
|
|
