RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

General features for molecule CRW_00429 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_00429 Molecule name [?]: d.16.m.D.virilis Source [?]: Gutell Lab CRW Site Source ID [?]: d.16.m.D.virilis 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 X-Ray [?]: No Method for secondary structure determination [?]: Comparative sequence analysis Number of molecules [?]: 1 Length [?]: 784 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 318 Number of paired bases [?]: 466

Click on any header below for additional features.

Stem features Number of stems [?]: 49 Number of base pairs in stems [?]: 215 Maximum length of a stem [?]: 11 Average length of a stem [?]: 4.41 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 1.3 Average estimated free energy [?]: -3.87 Minimum estimated free energy [?]: -11.9

Hairpin loop features Number of hairpin loops [?]: 14 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 5.36 Minimum number of free bases in hairpin loop [?]: 3

Bulge loop features Number of bulge loops [?]: 13 Maximum number of free bases in bulge loops [?]: 8 Average number of free bases in bulge loops [?]: 1.15 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 13 Maximum number of free bases in internal loops: 10 Average number of free bases in internal loops: 3.12 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 6 Average internal loop absolute asymmetry: 1.62 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 1.54 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 8 Maximum number of free bases in multi-loops: 13 Average number of free bases in multi-loops: 3.4 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 10 Average multi-loop absolute asymmetry: 3.08 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 8 Average multi-loop relative asymmetry: 1.43 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.13 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 11 Total number of AA non-canonical base pairs: 1 Total number of AC non-canonical base pairs: 1 Total number of AG non-canonical base pairs: 4 Total number of CU non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 4

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 4 Number of base pairs in bands: 18 Maximum band length: 7 Average band length: 4.5 Minimum band length: 3 Maximum number of bands per pseudoknot: 2 Average number of bands per pseudoknot: 2 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 3 Average number of un-bands: 1.5 Minimum number of un-bands: 0 Maximum number of in-bands: 0 Average number of in-bands: 0 Minimum number of in-bands: 0 Maximum number of unpaired bases: 16 Average number of unpaired bases: 14 Minimum number of unpaired bases: 12 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 6 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 3 Minimum number of base pairs to remove, per pseudoknot: 3 Minimum number of bands to remove, per molecule: 2 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