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

General features for molecule TMR_00412 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: TMR_00412 Molecule name [?]: Onio.yell._AP006628_1-423 Source [?]: tmRNA Database Source ID [?]: Onio.yell._AP006628_1-423 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 [?]: 423 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 217 Number of paired bases [?]: 206

Click on any header below for additional features.

Stem features Number of stems [?]: 8 Number of base pairs in stems [?]: 43 Maximum length of a stem [?]: 10 Average length of a stem [?]: 5.38 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.96 Minimum estimated free energy [?]: -12.5

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 [?]: 6.5 Minimum number of free bases in hairpin loop [?]: 6

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: 5 Average number of free bases in internal loops: 2.17 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 1.67 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 5 Average internal loop relative asymmetry: 2.33 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 112 Average number of free bases in multi-loops: 14.56 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 112 Average multi-loop absolute asymmetry: 23 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 112 Average multi-loop relative asymmetry: 5.62 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: 60 Maximum band length: 11 Average band length: 7.5 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: 18 Average number of unpaired bases: 13.75 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: 26 Maximum number of base pairs to remove, per pseudoknot: 9 Average number of base pairs to remove, per pseudoknot: 6.5 Minimum number of base pairs to remove, per pseudoknot: 4 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