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

General features for molecule TMR_00198 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: TMR_00198 Molecule name [?]: envi.sequ._TRW-351057-2_1-343 Source [?]: tmRNA Database Source ID [?]: envi.sequ._TRW-351057-2_1-343 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 [?]: 343 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 5 Number of unpaired bases [?]: 243 Number of paired bases [?]: 100

Click on any header below for additional features.

Stem features Number of stems [?]: 5 Number of base pairs in stems [?]: 17 Maximum length of a stem [?]: 5 Average length of a stem [?]: 3.4 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: 0.3 Average estimated free energy [?]: -2.18 Minimum estimated free energy [?]: -4.8

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 9 Average number of free bases in hairpin loops [?]: 6 Minimum number of free bases in hairpin loop [?]: 3

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 [?]: 3 Maximum number of free bases in internal loops: 3 Average number of free bases in internal loops: 1.67 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 0.67 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 1.33 Minimum internal loop relative asymmetry: 1

Multi-loop features

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

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 6 Number of base pairs in bands: 33 Maximum band length: 10 Average band length: 5.5 Minimum band length: 4 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: 16.67 Minimum number of unpaired bases: 10 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 13 Maximum number of base pairs to remove, per pseudoknot: 5 Average number of base pairs to remove, per pseudoknot: 4.33 Minimum number of base pairs to remove, per pseudoknot: 4 Minimum number of bands to remove, per molecule: 3 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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