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

General features for molecule TMR_00046 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: TMR_00046 Molecule name [?]: Baci.clau._AP006627_1-355 Source [?]: tmRNA Database Source ID [?]: Baci.clau._AP006627_1-355 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 [?]: 355 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 163 Number of paired bases [?]: 192

Click on any header below for additional features.

Stem features Number of stems [?]: 8 Number of base pairs in stems [?]: 45 Maximum length of a stem [?]: 9 Average length of a stem [?]: 5.62 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -9.95 Minimum estimated free energy [?]: -14.5

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 7 Average number of free bases in hairpin loops [?]: 6 Minimum number of free bases in hairpin loop [?]: 5

Bulge loop features Number of bulge loops [?]: 1 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 3 Maximum number of free bases in internal loops: 4 Average number of free bases in internal loops: 2 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.33 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 34 Average number of free bases in multi-loops: 7 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 34 Average multi-loop absolute asymmetry: 10.07 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 17 Average multi-loop relative asymmetry: 1.74 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: 51 Maximum band length: 11 Average band length: 6.38 Minimum band length: 2 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: 26 Average number of unpaired bases: 17.75 Minimum number of unpaired bases: 11 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 20 Maximum number of base pairs to remove, per pseudoknot: 7 Average number of base pairs to remove, per pseudoknot: 5 Minimum number of base pairs to remove, per pseudoknot: 2 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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