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

General features for molecule CRW_01349 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_01349 Molecule name [?]: d.16.e.W.palustris Source [?]: Gutell Lab CRW Site Source ID [?]: d.16.e.W.palustris 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 [?]: 1402 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 548 Number of paired bases [?]: 854

Click on any header below for additional features.

Stem features Number of stems [?]: 87 Number of base pairs in stems [?]: 400 Maximum length of a stem [?]: 22 Average length of a stem [?]: 4.61 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.17 Minimum estimated free energy [?]: -23.5

Hairpin loop features Number of hairpin loops [?]: 27 Maximum number of free bases in hairpin loops [?]: 10 Average number of free bases in hairpin loops [?]: 5.3 Minimum number of free bases in hairpin loop [?]: 3 Total number of UUCG hairpin motifs per molecule [?]: 1

Bulge loop features Number of bulge loops [?]: 21 Maximum number of free bases in bulge loops [?]: 4 Average number of free bases in bulge loops [?]: 0.86 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 23 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.74 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 1.13 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

Multi-loop features Number of multi-loops [?]: 15 Maximum number of free bases in multi-loops: 12 Average number of free bases in multi-loops: 3.1 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 11 Average multi-loop absolute asymmetry: 2.75 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 12 Average multi-loop relative asymmetry: 1.27 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.33 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 33 Total number of AA non-canonical base pairs: 2 Total number of AC non-canonical base pairs: 7 Total number of AG non-canonical base pairs: 10 Total number of CC non-canonical base pairs: 1 Total number of CU non-canonical base pairs: 3 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 7

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 27 Maximum band length: 8 Average band length: 4.5 Minimum band length: 2 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: 1 Average number of in-bands: 0.33 Minimum number of in-bands: 0 Maximum number of unpaired bases: 31 Average number of unpaired bases: 22 Minimum number of unpaired bases: 17 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 8 Maximum number of base pairs to remove, per pseudoknot: 3 Average number of base pairs to remove, per pseudoknot: 2.67 Minimum number of base pairs to remove, per pseudoknot: 2 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