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

General features for molecule TMR_00028 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: TMR_00028 Molecule name [?]: Alka.meta._TRW-293826_1-355 Source [?]: tmRNA Database Source ID [?]: Alka.meta._TRW-293826_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 [?]: 161 Number of paired bases [?]: 194

Click on any header below for additional features.

Stem features Number of stems [?]: 6 Number of base pairs in stems [?]: 40 Maximum length of a stem [?]: 9 Average length of a stem [?]: 6.67 Minimum length of a stem [?]: 5 Maximum estimated free energy [?]: -9.7 Average estimated free energy [?]: -11.93 Minimum estimated free energy [?]: -16

Hairpin loop features Number of hairpin loops [?]: 2 Maximum number of free bases in hairpin loops [?]: 13 Average number of free bases in hairpin loops [?]: 10 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 [?]: 2 Maximum number of free bases in internal loops: 5 Average number of free bases in internal loops: 3.25 Minimum number of free bases in internal loop: 2 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.5 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 1.5 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 35 Average number of free bases in multi-loops: 6.33 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 35 Average multi-loop absolute asymmetry: 10.14 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 17.5 Average multi-loop relative asymmetry: 1.86 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: 57 Maximum band length: 14 Average band length: 7.12 Minimum band length: 3 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: 29 Average number of unpaired bases: 16.75 Minimum number of unpaired bases: 9 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 23 Maximum number of base pairs to remove, per pseudoknot: 7 Average number of base pairs to remove, per pseudoknot: 5.75 Minimum number of base pairs to remove, per pseudoknot: 3 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