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

General features for molecule CRW_00527 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_00527 Molecule name [?]: d.233.e.P.falciparum.A Source [?]: Gutell Lab CRW Site Source ID [?]: d.233.e.P.falciparum.A 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 [?]: 3946 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 2988 Number of paired bases [?]: 958

Click on any header below for additional features.

Stem features Number of stems [?]: 77 Number of base pairs in stems [?]: 375 Maximum length of a stem [?]: 14 Average length of a stem [?]: 4.87 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.38 Minimum estimated free energy [?]: -17.9

Hairpin loop features Number of hairpin loops [?]: 28 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 6 Minimum number of free bases in hairpin loop [?]: 3 Total number of UUCG hairpin motifs per molecule [?]: 2

Bulge loop features Number of bulge loops [?]: 22 Maximum number of free bases in bulge loops [?]: 9 Average number of free bases in bulge loops [?]: 0.95 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 19 Maximum number of free bases in internal loops: 7 Average number of free bases in internal loops: 2.97 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 6 Average internal loop absolute asymmetry: 1.42 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 7 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 8 Maximum number of free bases in multi-loops: 54 Average number of free bases in multi-loops: 5.56 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 52 Average multi-loop absolute asymmetry: 8.47 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 27 Average multi-loop relative asymmetry: 2.23 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.38 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 27 Total number of AA non-canonical base pairs: 3 Total number of AC non-canonical base pairs: 4 Total number of AG non-canonical base pairs: 6 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 12

Pseudoknot features Number of pseudoknots [?]: 2 Number of bands: 17 Number of base pairs in bands: 104 Maximum band length: 31 Average band length: 6.12 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: 1989 Average number of unpaired bases: 1002.5 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: 16 Maximum number of base pairs to remove, per pseudoknot: 13 Average number of base pairs to remove, per pseudoknot: 8 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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