RNA STRAND v2.0  The RNA secondary STRucture and statistical ANalysis Database
[
Home
 Search
 Analyse
 Submit structures
 News
 Help
]
General features for molecule CRW_00088 (click to expand/contract all tables)



Molecule ID [?]:  CRW_00088 
Molecule name [?]:  d.16.b.C.muridarum 
Source [?]:  Gutell Lab CRW Site 
Source ID [?]:  d.16.b.C.muridarum 
Reference [?]:  http://www.rna.ccbb.utexas.edu; Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Muller K.M., Pande N., Shang Z., Yu N., and Gutell R.R. (2002). The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and other RNAs. BioMed Central Bioinformatics, 3:2. [Correction: BioMed Central Bioinformatics. 3:15.] 
Type [?]:  16S Ribosomal RNA  [?]
PS figure
PDF figure Figure from original source 
Organism [?]:  N/A 
Validated by NMR or XRay [?]:  No 
Method for secondary structure determination [?]:  Comparative sequence analysis 
Number of molecules [?]:  1 
Length [?]:  1554 
Fragments used [?]:  No 
Duplicated sequence [?]:  No other molecule in the database has the same sequence 
Number of
domains [?]:  4 
Number of unpaired bases [?]:  590 
Number of paired bases [?]:  964 

Click on any header below for additional features.

Number of stems [?]:  98 
Number of base pairs in stems [?]:  451 
Maximum length of a stem [?]:  13 
Average length of a stem [?]:  4.62 
Minimum length of a stem [?]:  1 
Maximum estimated free energy [?]:  0 
Average estimated free energy [?]:  6.87 
Minimum estimated free energy [?]:  21.7 

Number of hairpin loops [?]:  29 
Maximum number of free bases in hairpin loops [?]:  10 
Average number of free bases in hairpin loops [?]:  5.38 
Minimum number of free bases in hairpin loop [?]:  4 
Total number of UUCG hairpin motifs per molecule [?]:  2 

Number of bulge loops [?]:  25 
Maximum number of free bases in bulge loops [?]:  3 
Average number of free bases in bulge loops [?]:  0.8 
Minimum number of free bases in bulge loop [?]:  0 

Number of internal loops [?]:  27 
Maximum number of free bases in internal loops:  6 
Average number of free bases in internal loops:  3.04 
Minimum number of free bases in internal loop:  1 
Maximum internal loop absolute asymmetry:  4 
Average internal loop absolute asymmetry:  1.26 
Minimum internal loop absolute asymmetry:  0 
Maximum internal loop relative asymmetry:  5 
Average internal loop relative asymmetry:  1.7 
Minimum internal loop relative asymmetry:  1 

Number of multiloops [?]:  15 
Maximum number of free bases in multiloops:  8 
Average number of free bases in multiloops:  2.6 
Minimum number of free bases in multiloop:  0 
Maximum multiloop absolute asymmetry:  6 
Average multiloop absolute asymmetry:  2.32 
Minimum multiloop absolute asymmetry:  0 
Maximum multiloop relative asymmetry:  6 
Average multiloop relative asymmetry:  1.16 
Minimum multiloop relative asymmetry:  0 
Maximum number of branches in multiloops:  5 
Average number of branches in multiloops:  3.47 
Minimum number of branches in multiloops:  3 

Noncanonical base pairs features

Total number of noncanonical base pairs [?]: 
24 
Total number of AA noncanonical base pairs:  2 
Total number of AC noncanonical base pairs:  4 
Total number of AG noncanonical base pairs:  10 
Total number of CC noncanonical base pairs:  1 
Total number of CU noncanonical base pairs:  2 
Total number of GG noncanonical base pairs:  2 
Total number of UU noncanonical base pairs:  3 

Number of pseudoknots [?]:  4 
Number of bands:  8 
Number of base pairs in bands:  31 
Maximum band length:  9 
Average band length:  3.88 
Minimum band length:  1 
Maximum number of bands per pseudoknot:  2 
Average number of bands per pseudoknot:  2 
Minimum number of bands per pseudoknot:  2 
Maximum number of unbands:  3 
Average number of unbands:  1 
Minimum number of unbands:  0 
Maximum number of inbands:  3 
Average number of inbands:  0.75 
Minimum number of inbands:  0 
Maximum number of unpaired bases:  30 
Average number of unpaired bases:  17 
Minimum number of unpaired bases:  3 
Several ways to remove minimum number of base pairs, per molecule:  Yes 
Minimum number of base pairs to remove, per molecule:  9 
Maximum number of base pairs to remove, per pseudoknot:  3 
Average number of base pairs to remove, per pseudoknot:  2.25 
Minimum number of base pairs to remove, per pseudoknot:  1 
Minimum number of bands to remove, per molecule:  4 
Maximum number of bands to remove, per pseudoknot:  1 
Average number of bands to remove, per pseudoknot:  1 
Minimum number of bands to remove, per pseudoknot:  1 

[
Home
 Search
 Analyse
 Submit structures
 News
 Help
]
For questions, comments, suggestions and bug reports, please contact:
Copyright ©
20042008 BETA LAB  University of British Columbia
