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

General features for molecule CRW_00546 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_00546 Molecule name [?]: d.233.m.Z.mays Source [?]: Gutell Lab CRW Site Source ID [?]: d.233.m.Z.mays 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 [?]: 23S 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 [?]: 3514 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 3 Number of unpaired bases [?]: 2796 Number of paired bases [?]: 718

Click on any header below for additional features.

Stem features Number of stems [?]: 60 Number of base pairs in stems [?]: 256 Maximum length of a stem [?]: 18 Average length of a stem [?]: 4.27 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.37 Minimum estimated free energy [?]: -15.1

Hairpin loop features Number of hairpin loops [?]: 24 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.83 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 [?]: 17 Maximum number of free bases in bulge loops [?]: 9 Average number of free bases in bulge loops [?]: 1 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 14 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.89 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 1.07 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.57 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 5 Maximum number of free bases in multi-loops: 9 Average number of free bases in multi-loops: 2.39 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 9 Average multi-loop absolute asymmetry: 2.62 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 9 Average multi-loop relative asymmetry: 1.24 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.6 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 18 Total number of AA non-canonical base pairs: 4 Total number of AC non-canonical base pairs: 3 Total number of AG non-canonical base pairs: 5 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 3 Total number of UU non-canonical base pairs: 2

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 17 Number of base pairs in bands: 103 Maximum band length: 32 Average band length: 6.06 Minimum band length: 1 Maximum number of bands per pseudoknot: 13 Average number of bands per pseudoknot: 8.5 Minimum number of bands per pseudoknot: 4 Maximum number of un-bands: 8 Average number of un-bands: 4.5 Minimum number of un-bands: 1 Maximum number of in-bands: 6 Average number of in-bands: 3 Minimum number of in-bands: 0 Maximum number of unpaired bases: 1919 Average number of unpaired bases: 967.5 Minimum number of unpaired bases: 16 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 14 Maximum number of base pairs to remove, per pseudoknot: 11 Average number of base pairs to remove, per pseudoknot: 7 Minimum number of base pairs to remove, per pseudoknot: 3 Minimum number of bands to remove, per molecule: 8 Maximum number of bands to remove, per pseudoknot: 5 Average number of bands to remove, per pseudoknot: 4 Minimum number of bands to remove, per pseudoknot: 3

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