RNA STRAND v2.0  The RNA secondary STRucture and statistical ANalysis Database
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General features for molecule CRW_00467 (click to expand/contract all tables)



Molecule ID [?]:  CRW_00467 
Molecule name [?]:  d.233.a.H.marismortui.1 
Source [?]:  Gutell Lab CRW Site 
Source ID [?]:  d.233.a.H.marismortui.1 
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 [?]:  Haloarcula marismortui 
Validated by NMR or XRay [?]:  No 
Method for secondary structure determination [?]:  Comparative sequence analysis 
Number of molecules [?]:  1 
Length [?]:  2925 
Fragments used [?]:  No 
Duplicated sequence [?]:  No other molecule in the database has the same sequence 
Number of
domains [?]:  1 
Number of unpaired bases [?]:  1221 
Number of paired bases [?]:  1704 

Click on any header below for additional features.

Number of stems [?]:  158 
Number of base pairs in stems [?]:  675 
Maximum length of a stem [?]:  18 
Average length of a stem [?]:  4.28 
Minimum length of a stem [?]:  1 
Maximum estimated free energy [?]:  0 
Average estimated free energy [?]:  7.37 
Minimum estimated free energy [?]:  30.6 

Number of hairpin loops [?]:  63 
Maximum number of free bases in hairpin loops [?]:  15 
Average number of free bases in hairpin loops [?]:  5.51 
Minimum number of free bases in hairpin loop [?]:  3 
Total number of UUCG hairpin motifs per molecule [?]:  1 

Number of bulge loops [?]:  34 
Maximum number of free bases in bulge loops [?]:  9 
Average number of free bases in bulge loops [?]:  0.82 
Minimum number of free bases in bulge loop [?]:  0 

Number of internal loops [?]:  42 
Maximum number of free bases in internal loops:  9 
Average number of free bases in internal loops:  3.36 
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:  4 
Average internal loop relative asymmetry:  1.74 
Minimum internal loop relative asymmetry:  1 

Number of multiloops [?]:  18 
Maximum number of free bases in multiloops:  9 
Average number of free bases in multiloops:  2.52 
Minimum number of free bases in multiloop:  0 
Maximum multiloop absolute asymmetry:  9 
Average multiloop absolute asymmetry:  2.31 
Minimum multiloop absolute asymmetry:  0 
Maximum multiloop relative asymmetry:  9 
Average multiloop relative asymmetry:  1.17 
Minimum multiloop relative asymmetry:  0 
Maximum number of branches in multiloops:  7 
Average number of branches in multiloops:  3.83 
Minimum number of branches in multiloops:  3 

Noncanonical base pairs features

Total number of noncanonical base pairs [?]: 
29 
Total number of AA noncanonical base pairs:  4 
Total number of AC noncanonical base pairs:  5 
Total number of AG noncanonical base pairs:  7 
Total number of CC noncanonical base pairs:  4 
Total number of CU noncanonical base pairs:  3 
Total number of GG noncanonical base pairs:  1 
Total number of UU noncanonical base pairs:  5 

Number of pseudoknots [?]:  8 
Number of bands:  25 
Number of base pairs in bands:  177 
Maximum band length:  33 
Average band length:  7.08 
Minimum band length:  1 
Maximum number of bands per pseudoknot:  6 
Average number of bands per pseudoknot:  3.13 
Minimum number of bands per pseudoknot:  2 
Maximum number of unbands:  4 
Average number of unbands:  1.38 
Minimum number of unbands:  0 
Maximum number of inbands:  23 
Average number of inbands:  3.25 
Minimum number of inbands:  0 
Maximum number of unpaired bases:  240 
Average number of unpaired bases:  43.63 
Minimum number of unpaired bases:  5 
Several ways to remove minimum number of base pairs, per molecule:  No 
Minimum number of base pairs to remove, per molecule:  28 
Maximum number of base pairs to remove, per pseudoknot:  7 
Average number of base pairs to remove, per pseudoknot:  3.5 
Minimum number of base pairs to remove, per pseudoknot:  1 
Minimum number of bands to remove, per molecule:  13 
Maximum number of bands to remove, per pseudoknot:  3 
Average number of bands to remove, per pseudoknot:  1.63 
Minimum number of bands to remove, per pseudoknot:  1 

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