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

General features for molecule CRW_00423 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_00423 Molecule name [?]: d.16.m.C.elegans Source [?]: Gutell Lab CRW Site Source ID [?]: d.16.m.C.elegans 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 [?]: 697 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 319 Number of paired bases [?]: 378

Click on any header below for additional features.

Stem features Number of stems [?]: 41 Number of base pairs in stems [?]: 168 Maximum length of a stem [?]: 10 Average length of a stem [?]: 4.15 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -3.75 Minimum estimated free energy [?]: -15.5

Hairpin loop features Number of hairpin loops [?]: 12 Maximum number of free bases in hairpin loops [?]: 44 Average number of free bases in hairpin loops [?]: 8.08 Minimum number of free bases in hairpin loop [?]: 3

Bulge loop features Number of bulge loops [?]: 12 Maximum number of free bases in bulge loops [?]: 4 Average number of free bases in bulge loops [?]: 0.79 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 10 Maximum number of free bases in internal loops: 16 Average number of free bases in internal loops: 3.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 15 Average internal loop absolute asymmetry: 2.8 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 16 Average internal loop relative asymmetry: 3.4 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 5 Maximum number of free bases in multi-loops: 10 Average number of free bases in multi-loops: 3.62 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 9 Average multi-loop absolute asymmetry: 2.93 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 10 Average multi-loop relative asymmetry: 1.39 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 4 Average number of branches in multi-loops: 3.2 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 19 Total number of AA non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 5 Total number of CU non-canonical base pairs: 4 Total number of GG non-canonical base pairs: 2 Total number of UU non-canonical base pairs: 6

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 21 Maximum band length: 7 Average band length: 3.5 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 un-bands: 3 Average number of un-bands: 1.67 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: 13.33 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: 7 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.33 Minimum number of base pairs to remove, per pseudoknot: 1 Minimum number of bands to remove, per molecule: 3 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