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

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General features for molecule CRW_00028
(click to expand/contract all tables)

Format:
Molecule ID [?]:CRW_00028
Molecule name [?]:d.16.a.M.thermautotrophicus.1
Source [?]:Gutell Lab CRW Site
Source ID [?]:d.16.a.M.thermautotrophicus.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 [?]: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 [?]:1481
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:4
Number of unpaired bases [?]:555
Number of paired bases [?]:926

Click on any header below for additional features.

Stem features

Number of stems [?]:92
Number of base pairs in stems [?]:433
Maximum length of a stem [?]:25
Average length of a stem [?]:4.73
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.98
Minimum estimated free energy [?]:-35.2

Hairpin loop features

Number of hairpin loops [?]:28
Maximum number of free bases in hairpin loops [?]:10
Average number of free bases in hairpin loops [?]:5.43
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 [?]:23
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.8
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:25
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.88
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:4
Average internal loop absolute asymmetry:1.28
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:5
Average internal loop relative asymmetry:1.76
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:14
Maximum number of free bases in multi-loops:8
Average number of free bases in multi-loops:2.71
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:6
Average multi-loop absolute asymmetry:2.29
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:6
Average multi-loop relative asymmetry:1.14
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.5
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 20
Total number of AA non-canonical base pairs:1
Total number of AC non-canonical base pairs:4
Total number of AG non-canonical base pairs:9
Total number of CU non-canonical base pairs:2
Total number of GG non-canonical base pairs:1
Total number of UU non-canonical base pairs:3

Pseudoknot features
Number of pseudoknots [?]:4
Number of bands:8
Number of base pairs in bands:30
Maximum band length:9
Average band length:3.75
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
Minimum number of un-bands:0
Maximum number of in-bands:3
Average number of in-bands:0.75
Minimum number of in-bands:0
Maximum number of unpaired bases:30
Average number of unpaired bases:17.25
Minimum number of unpaired bases:3
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:9
Maximum number of base pairs to remove, per pseudoknot:3
Average number of base pairs to remove, per pseudoknot:2.25
Minimum number of base pairs to remove, per pseudoknot:1
Minimum number of bands to remove, per molecule:4
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



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