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

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General features for molecule TMR_00302
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00302
Molecule name [?]:Leif.xyli._AE016822_1-394
Source [?]:tmRNA Database
Source ID [?]:Leif.xyli._AE016822_1-394
Reference [?]:Zwieb, C., Gorodkin, J., Knudsen B., Burks, J., and Wower, J. (2003) tmRDB (tmRNA database) Nucleic Acids Res, 31, 446-447.
Type [?]:Transfer Messenger 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 [?]:394
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:206
Number of paired bases [?]:188

Click on any header below for additional features.

Stem features

Number of stems [?]:8
Number of base pairs in stems [?]:32
Maximum length of a stem [?]:7
Average length of a stem [?]:4
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.9
Minimum estimated free energy [?]:-13.2

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:23
Average number of free bases in hairpin loops [?]:15
Minimum number of free bases in hairpin loop [?]:7

Bulge loop features
Number of bulge loops [?]:0
Maximum number of free bases in bulge loops [?]:N/A
Average number of free bases in bulge loops [?]:N/A
Minimum number of free bases in bulge loop [?]:N/A

Internal loop features
Number of internal loops [?]:4
Maximum number of free bases in internal loops:8
Average number of free bases in internal loops:4.12
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:2
Average internal loop absolute asymmetry:0.75
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:1
Average internal loop relative asymmetry:1
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:45
Average number of free bases in multi-loops:8.22
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:45
Average multi-loop absolute asymmetry:11.86
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:45
Average multi-loop relative asymmetry:2.57
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:6
Average number of branches in multi-loops:4.5
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 0

Pseudoknot features
Number of pseudoknots [?]:4
Number of bands:8
Number of base pairs in bands:62
Maximum band length:11
Average band length:7.75
Minimum band length:5
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:0
Average number of un-bands:0
Minimum number of un-bands:0
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:24
Average number of unpaired bases:16.25
Minimum number of unpaired bases:11
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:25
Maximum number of base pairs to remove, per pseudoknot:7
Average number of base pairs to remove, per pseudoknot:6.25
Minimum number of base pairs to remove, per pseudoknot:5
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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