D-ORB

The Overrepresented RNA Blocks

M.J. Dupont, F. Major

D-ORB: A Web Server to Extract Structural Features of Related But Unaligned RNA Sequences

J. Mol. Biol., 435 (2023)

SMK box translational riboswitch (Rfam: RF01767)

Options

Negatives sequences: Random sequences of similar lengths
ORBs positions sequence: Best consensus structure-matching sequence
Motifs: 162,498 motifs on the alphabet ACGURYN

Rfam

D-ORB

Augmented

((G)R(U))
(GANA)
(.GGRR.)
((A)U)G
((U)A)A
((C)Y)U

96.0
92.0
96.0
100.0
100.0
100.0

% of positive sequence with ORB

Job*

Email*

Sequence(s)*

Obtain

One structure matching the consensus structure ORBs
Several structures containing instances of most discriminative ORBs

Up to structures per sequence

Position offset nucleotides

Job*

Email*

Wildtype sequence*

Mutant sequences

All SNPs
Submit mutant sequences

Use the mutation generator

Deep neural network:

5-fold cross-validation: 99 %
(± 0.386 %)

Decision tree:

5-fold cross-validation: 87.3 %
(± 9.64 %)

D-ORB structure

D-ORB structure decision tree:

5-fold cross-validation: 86.8 %
(± 9.52 %)

of ACBD01000055.1/1906-1985

ACBD01000055.1/1906-1985

GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG
(((((((((((((.(((....)).(((((...))))..)))).)))).)))))))((((.(((((.....)))))))).)
.........1.........2.........3.........4.........5.........6.........7.........8
12345678901234567890123456789012345678901234567890123456789012345678901234567890

abstract shape: `(()())()`

					Number of sequences
	Structure	ORBs			(out of 25)	(%)
1		((G)R(U))			22	88.0
>ACKZ01000012.1/36527-36446 AAAAGUUAAAAAUGAUAUUCCCGAAAGGAUGCACCAUGUGUAGAUGCCUUGUAACCGGAAUUGAAUGGGGGAAAAAGAAAUG ...................((......).(...........))....................................... >ABHH01000037.1/13513-13426 GAGGUUUGCAAUUCGGAUUCCCGAGAGGAUUCACUUUUAAAGUGGAGAAGCCUUGUAACCGAAAAUUUAAAGGGGGAACAAAGUAAUG ...................((......).(...............))......................................... >ACGH01000133.1/29066-28984 GUAGGUUAUGAGUUCCCGAUAGGAUUCACGCCAGACGUGAAGAAGCCUUGUAACCUAAAAAAUAUAUAGGGGGAAAUAAAAUG ..............((......).(...............))......................................... >CP000413.1/483009-483080 UUCGGUUAAGGUCCCGAAAGGAUUCGCUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............((......).(...............)..).............................. >ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG ..............((......).(.............).)....................................... >ACGU01000017.1/23671-23581 UAUCGGUUCAAGUCCUGAUAGGAUUCAUUACUUAGUUAAUGAAGAUGCCUUGUAACCGGAUAGCCAAUGUCUAUAUAGGGGGACUAAUAUG .............((......).(..................)...)............................................ >AE017198.1/564018-564088 UUCGGUUAAGGUCCCGAAAGGAUUCGUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............((......).(...............).).............................. >ACKR01000001.1/1180-1268 UAUCGGUUCAAGUCCUGAGAGGAUUCACUAUGAUUAGUGAAGAUGCCUUGUAACCGAAUAGCCAAUGUCUAUAUAGGGGGACUAAUAUG .............((......).(................)...)............................................ >ACGV01000186.1/13246-13351 UCUCGUUAUAAAGCAAAUUCCCGAUAGGAUUCACUUUACUGUGAAGAUGCCUUGUAACCACUAAAUGUUUCAAUUGUAACUUGCAUAUGGGGGAAUUAACACACAU ...................((......).(..............))............................................................ >ACIZ01000041.1/43695-43782 UAGAGUUGCAAUACAUUCCCGAUGGGGUUCGUUAGCGAUUAACGAACAUGCCUUGUAACCGAAAAUCAUGAGGGGGAAACAAACGAUG ................(.(......).(.................))......................................... >ACAJ01000030.1/519-601 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAUCGAAAUUUAGGGGGAAUACAAAAAAUG ..............((......).(..............).)......................................... >CP000233.1/487061-487146 AAUAGUUACAAUCCAUUCCCGAAAGGAUUCGUUUUAAACGAAGAUGCCUUGUAACCAAAUUACUUAUAAUAAUGGGGGAAUUAAAU ................(.(......).(.............))........................................... >CP000422.1/681467-681547 GUAAGUUACUAGUGUUCCCGAUAGGAUUAGUUAUCCAAAAGAUCCUUGUAACCGAAAUUAAAUUUAGGGGGAAUUUACAUG ...............(.(......).(.............))....................................... >AF401669.1/1455-1540 UAGAGUUAUAAGAAGUUCCCGAUAGGAUUCACACACCGUGAAGAGGCCUUGUAACCGACACAUAUAUAGGGGGAAACAUAGAAAUG .................((......).(...............))......................................... >ACLN01000012.1/57665-57589 UACGGUUAAGGUCCCGAGAGGAUUCGAAAUUCGAAGAUGCCUUGUAACCGAUUUUUUAAAGGGGGACUUCUAUUAUG ............((......).(.............).)...................................... >CP000517.1/1692576-1692488 UAUCGGUUCAAGUCCUGAAAGGAUUCACUAUUAUUAGUGAAGAUGCCUUGUAACCGAAUAGCUAAUGUCUAUAUGGGGGGACUAUUAUG .............((......).(................)...)............................................ >ADEX01000093.1/3153-3076 AUCGGUUCAAGUCCUGAUAGGAUUCGUUAUACGAAGAUGCCUUGUAACCGAAUAGCUUGUCUAUAGGGGGACAUUAUG ...........(.(......).(...............))...................................... >ACAO01000044.1/534-615 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAACAUAUAUUAGGGGGAAUACAAAAAUG ..............((......).(............))........................................... >CR954253.1/1355763-1355676 AUUUGUUACAAGUCCUGAUAGGAUUCACCAAAUUGGUGAAGAUGCCUUGUAACCGUGUAGCUAGUCUAUAGGGGGACACAUAUAGAUG .............((......).(...............)...)............................................ >CP000033.3/1626537-1626447 UAUCGGUUCAAGUCCUGAAAGGAUUCAUUAAAUAAUUAGUGAAGAUGCCUUGUAACCGAAUAGCCGAUGUCUAUAUAGGGGGACUAAUAUG .............((......).(..................)...)............................................ >FM177140.1/914403-914491 UAGAGUUGCAAAACAUUCCCGAUGGGGUUCGUCAAAGCUAUGACGAACAUGCCUUGUAACCUAAAAUAAUAAGGGGGAAACAAAACAUG ................((.......).(..................))......................................... >CP003032.1/1501869-1501780 AAGCGUUACAACUCAUUCCCGAUAGGAUUCACGCUUUUAGUGAAGAUGCCUUGUAACCACAAAUAUAAUGAAUGGGGGAAUUUUAUUAUG ................(.(......).(...............)).............................................
2		((G)R(U)) (GANA)			17	68.0
>CP000413.1/483009-483080 UUCGGUUAAGGUCCCGAAAGGAUUCGCUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............(((....)).(...............)..).............................. >ACAJ01000030.1/519-601 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAUCGAAAUUUAGGGGGAAUACAAAAAAUG ..............(((....)).(..............).)......................................... >CP003032.1/1501869-1501780 AAGCGUUACAACUCAUUCCCGAUAGGAUUCACGCUUUUAGUGAAGAUGCCUUGUAACCACAAAUAUAAUGAAUGGGGGAAUUUUAUUAUG ................(.((....)).(...............))............................................. >CP000517.1/1692576-1692488 UAUCGGUUCAAGUCCUGAAAGGAUUCACUAUUAUUAGUGAAGAUGCCUUGUAACCGAAUAGCUAAUGUCUAUAUGGGGGGACUAUUAUG .............(((....)).(................)...)............................................ >ADEX01000093.1/3153-3076 AUCGGUUCAAGUCCUGAUAGGAUUCGUUAUACGAAGAUGCCUUGUAACCGAAUAGCUUGUCUAUAGGGGGACAUUAUG ...........(.((....)).(...............))...................................... >ACKR01000001.1/1180-1268 UAUCGGUUCAAGUCCUGAGAGGAUUCACUAUGAUUAGUGAAGAUGCCUUGUAACCGAAUAGCCAAUGUCUAUAUAGGGGGACUAAUAUG .............(((....)).(................)...)............................................ >ABHH01000037.1/13513-13426 GAGGUUUGCAAUUCGGAUUCCCGAGAGGAUUCACUUUUAAAGUGGAGAAGCCUUGUAACCGAAAAUUUAAAGGGGGAACAAAGUAAUG ...................(((....)).(...............))......................................... >ACGH01000133.1/29066-28984 GUAGGUUAUGAGUUCCCGAUAGGAUUCACGCCAGACGUGAAGAAGCCUUGUAACCUAAAAAAUAUAUAGGGGGAAAUAAAAUG ..............(((....)).(...............))......................................... >CP000233.1/487061-487146 AAUAGUUACAAUCCAUUCCCGAAAGGAUUCGUUUUAAACGAAGAUGCCUUGUAACCAAAUUACUUAUAAUAAUGGGGGAAUUAAAU ................(.((....)).(.............))........................................... >AE017198.1/564018-564088 UUCGGUUAAGGUCCCGAAAGGAUUCGUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............(((....)).(...............).).............................. >ACLN01000012.1/57665-57589 UACGGUUAAGGUCCCGAGAGGAUUCGAAAUUCGAAGAUGCCUUGUAACCGAUUUUUUAAAGGGGGACUUCUAUUAUG ............(((....)).(.............).)...................................... >ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG ..............(((....)).(.............).)....................................... >ACGV01000186.1/13246-13351 UCUCGUUAUAAAGCAAAUUCCCGAUAGGAUUCACUUUACUGUGAAGAUGCCUUGUAACCACUAAAUGUUUCAAUUGUAACUUGCAUAUGGGGGAAUUAACACACAU ...................(((....)).(..............))............................................................ >CR954253.1/1355763-1355676 AUUUGUUACAAGUCCUGAUAGGAUUCACCAAAUUGGUGAAGAUGCCUUGUAACCGUGUAGCUAGUCUAUAGGGGGACACAUAUAGAUG .............(((....)).(...............)...)............................................ >ACAO01000044.1/534-615 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAACAUAUAUUAGGGGGAAUACAAAAAUG ..............(((....)).(............))........................................... >CP000422.1/681467-681547 GUAAGUUACUAGUGUUCCCGAUAGGAUUAGUUAUCCAAAAGAUCCUUGUAACCGAAAUUAAAUUUAGGGGGAAUUUACAUG ...............(.((....)).(.............))....................................... >AF401669.1/1455-1540 UAGAGUUAUAAGAAGUUCCCGAUAGGAUUCACACACCGUGAAGAGGCCUUGUAACCGACACAUAUAUAGGGGGAAACAUAGAAAUG .................(((....)).(...............)).........................................
3		((G)R(U)) (GANA) (.GGRR.)			15	60.0
>AF401669.1/1455-1540 UAGAGUUAUAAGAAGUUCCCGAUAGGAUUCACACACCGUGAAGAGGCCUUGUAACCGACACAUAUAUAGGGGGAAACAUAGAAAUG .................(((....)).(...............)).........................(....).......... >ACKR01000001.1/1180-1268 UAUCGGUUCAAGUCCUGAGAGGAUUCACUAUGAUUAGUGAAGAUGCCUUGUAACCGAAUAGCCAAUGUCUAUAUAGGGGGACUAAUAUG .............(((....)).(................)...)..............................(.....)....... >ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG ..............(((....)).(.............).).......................(....).......... >ADEX01000093.1/3153-3076 AUCGGUUCAAGUCCUGAUAGGAUUCGUUAUACGAAGAUGCCUUGUAACCGAAUAGCUUGUCUAUAGGGGGACAUUAUG ...........(.((....)).(...............))....................(........)........ >CP000413.1/483009-483080 UUCGGUUAAGGUCCCGAAAGGAUUCGCUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............(((....)).(...............)..)..................(....)...... >ACLN01000012.1/57665-57589 UACGGUUAAGGUCCCGAGAGGAUUCGAAAUUCGAAGAUGCCUUGUAACCGAUUUUUUAAAGGGGGACUUCUAUUAUG ............(((....)).(.............).)......................(....).......... >CP003032.1/1501869-1501780 AAGCGUUACAACUCAUUCCCGAUAGGAUUCACGCUUUUAGUGAAGAUGCCUUGUAACCACAAAUAUAAUGAAUGGGGGAAUUUUAUUAUG ................(.((....)).(...............)).........................(......)............ >AE017198.1/564018-564088 UUCGGUUAAGGUCCCGAAAGGAUUCGUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............(((....)).(...............).)..................(....)...... >ACAJ01000030.1/519-601 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAUCGAAAUUUAGGGGGAAUACAAAAAAUG ..............(((....)).(..............).).........................(.....)......... >CP000517.1/1692576-1692488 UAUCGGUUCAAGUCCUGAAAGGAUUCACUAUUAUUAGUGAAGAUGCCUUGUAACCGAAUAGCUAAUGUCUAUAUGGGGGGACUAUUAUG .............(((....)).(................)...)........................(........).......... >CP000422.1/681467-681547 GUAAGUUACUAGUGUUCCCGAUAGGAUUAGUUAUCCAAAAGAUCCUUGUAACCGAAAUUAAAUUUAGGGGGAAUUUACAUG ...............(.((....)).(.............)).........................(.....)....... >CP000233.1/487061-487146 AAUAGUUACAAUCCAUUCCCGAAAGGAUUCGUUUUAAACGAAGAUGCCUUGUAACCAAAUUACUUAUAAUAAUGGGGGAAUUAAAU ................(.((....)).(.............))..........................(.........)...... >ACGH01000133.1/29066-28984 GUAGGUUAUGAGUUCCCGAUAGGAUUCACGCCAGACGUGAAGAAGCCUUGUAACCUAAAAAAUAUAUAGGGGGAAAUAAAAUG ..............(((....)).(...............)).........................(......)........ >ABHH01000037.1/13513-13426 GAGGUUUGCAAUUCGGAUUCCCGAGAGGAUUCACUUUUAAAGUGGAGAAGCCUUGUAACCGAAAAUUUAAAGGGGGAACAAAGUAAUG ...................(((....)).(...............)).........................(.....)......... >ACAO01000044.1/534-615 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAACAUAUAUUAGGGGGAAUACAAAAAUG ..............(((....)).(............))..........................(.....)..........
4		((G)R(U)) (GANA) (.GGRR.) ((A)U)G			13	52.0
>ACAJ01000030.1/519-601 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAUCGAAAUUUAGGGGGAAUACAAAAAAUG ..............(((....)).(............)).................(..(.......(.....)......).) >AE017198.1/564018-564088 UUCGGUUAAGGUCCCGAAAGGAUUCGUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............(((....)).(.............))................((...(....)...).) >CP000422.1/681467-681547 GUAAGUUACUAGUGUUCCCGAUAGGAUUAGUUAUCCAAAAGAUCCUUGUAACCGAAAUUAAAUUUAGGGGGAAUUUACAUG ...............(.((....)).(.............))...............((........(.....)....).) >ACLN01000012.1/57665-57589 UACGGUUAAGGUCCCGAGAGGAUUCGAAAUUCGAAGAUGCCUUGUAACCGAUUUUUUAAAGGGGGACUUCUAUUAUG ............(((....)).(.............).)...............((.....(....).......).) >CP000517.1/1692576-1692488 UAUCGGUUCAAGUCCUGAAAGGAUUCACUAUUAUUAGUGAAGAUGCCUUGUAACCGAAUAGCUAAUGUCUAUAUGGGGGGACUAUUAUG .............(((....)).(................)...)................((......(........).......).) >ADEX01000093.1/3153-3076 AUCGGUUCAAGUCCUGAUAGGAUUCGUUAUACGAAGAUGCCUUGUAACCGAAUAGCUUGUCUAUAGGGGGACAUUAUG ...........(.((....)).(...............))...............((...(........).....).) >AF401669.1/1455-1540 UAGAGUUAUAAGAAGUUCCCGAUAGGAUUCACACACCGUGAAGAGGCCUUGUAACCGACACAUAUAUAGGGGGAAACAUAGAAAUG .................(((....)).(...............))................((.......(....).......).) >CP000413.1/483009-483080 UUCGGUUAAGGUCCCGAAAGGAUUCGCUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............(((....)).(..............))................((...(....)...).) >ACGH01000133.1/29066-28984 GUAGGUUAUGAGUUCCCGAUAGGAUUCACGCCAGACGUGAAGAAGCCUUGUAACCUAAAAAAUAUAUAGGGGGAAAUAAAAUG ..............(((....)).(...............))................((.......(......).....).) >ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG ..............(((....)).(.............).)..............((.......(....).......).) >ACAO01000044.1/534-615 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAACAUAUAUUAGGGGGAAUACAAAAAUG ..............(((....)).(............)).................(...(......(....)......).) >ACKR01000001.1/1180-1268 UAUCGGUUCAAGUCCUGAGAGGAUUCACUAUGAUUAGUGAAGAUGCCUUGUAACCGAAUAGCCAAUGUCUAUAUAGGGGGACUAAUAUG .............(((....)).(................)...).................(...(........(.....)....).) >ABHH01000037.1/13513-13426 GAGGUUUGCAAUUCGGAUUCCCGAGAGGAUUCACUUUUAAAGUGGAGAAGCCUUGUAACCGAAAAUUUAAAGGGGGAACAAAGUAAUG ...................(((....)).(...............))................(.(......(.....)......).)
5		((G)R(U)) (GANA) (.GGRR.) ((A)U)G ((U)A)A			10	40.0
>CP000413.1/483009-483080 UUCGGUUAAGGUCCCGAAAGGAUUCGCUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG .....((.....(((....)).(..............))........).).....((...(....)...).) >CP000422.1/681467-681547 GUAAGUUACUAGUGUUCCCGAUAGGAUUAGUUAUCCAAAAGAUCCUUGUAACCGAAAUUAAAUUUAGGGGGAAUUUACAUG .....(.(.......(.((....)).(.............))......).)......((........(.....)....).) >ACLN01000012.1/57665-57589 UACGGUUAAGGUCCCGAGAGGAUUCGAAAUUCGAAGAUGCCUUGUAACCGAUUUUUUAAAGGGGGACUUCUAUUAUG .....((.....(((....)).(.............).).....).).......((.....(....).......).) >ACAJ01000030.1/519-601 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAUCGAAAUUUAGGGGGAAUACAAAAAAUG .....(.(......(((....)).(............))........).)......(..(.......(.....)......).) >ADEX01000093.1/3153-3076 AUCGGUUCAAGUCCUGAUAGGAUUCGUUAUACGAAGAUGCCUUGUAACCGAAUAGCUUGUCUAUAGGGGGACAUUAUG .....((....(.((....)).(...............))....).)........((...(........).....).) >ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG ......((......(((....)).(.............).).....).)......((.......(....).......).) >ACGH01000133.1/29066-28984 GUAGGUUAUGAGUUCCCGAUAGGAUUCACGCCAGACGUGAAGAAGCCUUGUAACCUAAAAAAUAUAUAGGGGGAAAUAAAAUG .....(.(......(((....)).(...............))........).).....((.......(......).....).) >ACAO01000044.1/534-615 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAACAUAUAUUAGGGGGAAUACAAAAAUG .....(.(......(((....)).(............))........).)......(...(......(....)......).) >AF401669.1/1455-1540 UAGAGUUAUAAGAAGUUCCCGAUAGGAUUCACACACCGUGAAGAGGCCUUGUAACCGACACAUAUAUAGGGGGAAACAUAGAAAUG .....(.(.........(((....)).(...............))......).).......((.......(....).......).) >CP000517.1/1692576-1692488 UAUCGGUUCAAGUCCUGAAAGGAUUCACUAUUAUUAGUGAAGAUGCCUUGUAACCGAAUAGCUAAUGUCUAUAUGGGGGGACUAUUAUG ......((.....(((....)).(................)...).....).)........((......(........).......).)
6		((G)R(U)) (GANA) (.GGRR.) ((A)U)G ((U)A)A ((C)Y)U			9	36.0
>CP000422.1/681467-681547 GUAAGUUACUAGUGUUCCCGAUAGGAUUAGUUAUCCAAAAGAUCCUUGUAACCGAAAUUAAAUUUAGGGGGAAUUUACAUG .....(.(..(..(.(.((....)).(.............)).).)..).)......((........(.....)....).) >ACLN01000012.1/57665-57589 UACGGUUAAGGUCCCGAGAGGAUUCGAAAUUCGAAGAUGCCUUGUAACCGAUUUUUUAAAGGGGGACUUCUAUUAUG .....((.((..(((....)).(.............).).).).).).......((.....(....).......).) >AF401669.1/1455-1540 UAGAGUUAUAAGAAGUUCCCGAUAGGAUUCACACACCGUGAAGAGGCCUUGUAACCGACACAUAUAUAGGGGGAAACAUAGAAAUG .....(.(..(...(..(((....)).(...............)).).)..).).......((.......(....).......).) >ACAO01000044.1/534-615 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAACAUAUAUUAGGGGGAAUACAAAAAUG .....(.(..((..(((....)).(............))...).)..).)......(...(......(....)......).) >ACGH01000133.1/29066-28984 GUAGGUUAUGAGUUCCCGAUAGGAUUCACGCCAGACGUGAAGAAGCCUUGUAACCUAAAAAAUAUAUAGGGGGAAAUAAAAUG .....(.(..((..(((....)).(...............))...).)..).).....((.......(......).....).) >ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG ......((..((..(((....)).(.............).)).)..).)......((.......(....).......).) >ADEX01000093.1/3153-3076 AUCGGUUCAAGUCCUGAUAGGAUUCGUUAUACGAAGAUGCCUUGUAACCGAAUAGCUUGUCUAUAGGGGGACAUUAUG .....((.((.(.((....)).(...............))).).).)........((...(........).....).) >ACAJ01000030.1/519-601 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAUCGAAAUUUAGGGGGAAUACAAAAAAUG .....(.(..((..(((....)).(............))...).)..).)......(..(.......(.....)......).) >CP000517.1/1692576-1692488 UAUCGGUUCAAGUCCUGAAAGGAUUCACUAUUAUUAGUGAAGAUGCCUUGUAACCGAAUAGCUAAUGUCUAUAUGGGGGGACUAUUAUG ......((..((.(((....)).(................)...)).)..).)........((......(........).......).)

>ACGH01000133.1/29066-28984 GUAGGUUAUGAGUUCCCGAUAGGAUUCACGCCAGACGUGAAGAAGCCUUGUAACCUAAAAAAUAUAUAGGGGGAAAUAAAAUG ..............((......).(...............))......................................... ..............(((....)).(...............))......................................... ..............(((....)).(...............)).........................(......)........ ..............(((....)).(...............))................((.......(......).....).) .....(.(......(((....)).(...............))........).).....((.......(......).....).) .....(.(..((..(((....)).(...............))...).)..).).....((.......(......).....).) >ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG ..............((......).(.............).)....................................... ..............(((....)).(.............).)....................................... ..............(((....)).(.............).).......................(....).......... ..............(((....)).(.............).)..............((.......(....).......).) ......((......(((....)).(.............).).....).)......((.......(....).......).) ......((..((..(((....)).(.............).)).)..).)......((.......(....).......).) >ACAJ01000030.1/519-601 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAUCGAAAUUUAGGGGGAAUACAAAAAAUG ..............((......).(..............).)......................................... ..............(((....)).(..............).)......................................... ..............(((....)).(..............).).........................(.....)......... ..............(((....)).(............)).................(..(.......(.....)......).) .....(.(......(((....)).(............))........).)......(..(.......(.....)......).) .....(.(..((..(((....)).(............))...).)..).)......(..(.......(.....)......).) >CP000422.1/681467-681547 GUAAGUUACUAGUGUUCCCGAUAGGAUUAGUUAUCCAAAAGAUCCUUGUAACCGAAAUUAAAUUUAGGGGGAAUUUACAUG ...............(.(......).(.............))....................................... ...............(.((....)).(.............))....................................... ...............(.((....)).(.............)).........................(.....)....... ...............(.((....)).(.............))...............((........(.....)....).) .....(.(.......(.((....)).(.............))......).)......((........(.....)....).) .....(.(..(..(.(.((....)).(.............)).).)..).)......((........(.....)....).) >AF401669.1/1455-1540 UAGAGUUAUAAGAAGUUCCCGAUAGGAUUCACACACCGUGAAGAGGCCUUGUAACCGACACAUAUAUAGGGGGAAACAUAGAAAUG .................((......).(...............))......................................... .................(((....)).(...............))......................................... .................(((....)).(...............)).........................(....).......... .................(((....)).(...............))................((.......(....).......).) .....(.(.........(((....)).(...............))......).).......((.......(....).......).) .....(.(..(...(..(((....)).(...............)).).)..).).......((.......(....).......).) >ACLN01000012.1/57665-57589 UACGGUUAAGGUCCCGAGAGGAUUCGAAAUUCGAAGAUGCCUUGUAACCGAUUUUUUAAAGGGGGACUUCUAUUAUG ............((......).(.............).)...................................... ............(((....)).(.............).)...................................... ............(((....)).(.............).)......................(....).......... ............(((....)).(.............).)...............((.....(....).......).) .....((.....(((....)).(.............).).....).).......((.....(....).......).) .....((.((..(((....)).(.............).).).).).).......((.....(....).......).) >CP000517.1/1692576-1692488 UAUCGGUUCAAGUCCUGAAAGGAUUCACUAUUAUUAGUGAAGAUGCCUUGUAACCGAAUAGCUAAUGUCUAUAUGGGGGGACUAUUAUG .............((......).(................)...)............................................ .............(((....)).(................)...)............................................ .............(((....)).(................)...)........................(........).......... .............(((....)).(................)...)................((......(........).......).) ......((.....(((....)).(................)...).....).)........((......(........).......).) ......((..((.(((....)).(................)...)).)..).)........((......(........).......).) >ADEX01000093.1/3153-3076 AUCGGUUCAAGUCCUGAUAGGAUUCGUUAUACGAAGAUGCCUUGUAACCGAAUAGCUUGUCUAUAGGGGGACAUUAUG ...........(.(......).(...............))...................................... ...........(.((....)).(...............))...................................... ...........(.((....)).(...............))....................(........)........ ...........(.((....)).(...............))...............((...(........).....).) .....((....(.((....)).(...............))....).)........((...(........).....).) .....((.((.(.((....)).(...............))).).).)........((...(........).....).) >ACAO01000044.1/534-615 GUCCGUUGCAAGUUCCCGAAAGGAUUCGCAGCUGCGAAGAUGCCUUGUAACCGAAACAUAUAUUAGGGGGAAUACAAAAAUG ..............((......).(............))........................................... ..............(((....)).(............))........................................... ..............(((....)).(............))..........................(.....).......... ..............(((....)).(............)).................(...(......(....)......).) .....(.(......(((....)).(............))........).)......(...(......(....)......).) .....(.(..((..(((....)).(............))...).)..).)......(...(......(....)......).) >CP000413.1/483009-483080 UUCGGUUAAGGUCCCGAAAGGAUUCGCUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............((......).(...............)..).............................. ............(((....)).(...............)..).............................. ............(((....)).(...............)..)..................(....)...... ............(((....)).(..............))................((...(....)...).) .....((.....(((....)).(..............))........).).....((...(....)...).) >ABHH01000037.1/13513-13426 GAGGUUUGCAAUUCGGAUUCCCGAGAGGAUUCACUUUUAAAGUGGAGAAGCCUUGUAACCGAAAAUUUAAAGGGGGAACAAAGUAAUG ...................((......).(...............))......................................... ...................(((....)).(...............))......................................... ...................(((....)).(...............)).........................(.....)......... ...................(((....)).(...............))................(.(......(.....)......).) >AE017198.1/564018-564088 UUCGGUUAAGGUCCCGAAAGGAUUCGUUUUUAACGAAGAUGCCUUGUAACCGAAAGAUGGGGGACUCUAUG ............((......).(...............).).............................. ............(((....)).(...............).).............................. ............(((....)).(...............).)..................(....)...... ............(((....)).(.............))................((...(....)...).) >ACKR01000001.1/1180-1268 UAUCGGUUCAAGUCCUGAGAGGAUUCACUAUGAUUAGUGAAGAUGCCUUGUAACCGAAUAGCCAAUGUCUAUAUAGGGGGACUAAUAUG .............((......).(................)...)............................................ .............(((....)).(................)...)............................................ .............(((....)).(................)...)..............................(.....)....... .............(((....)).(................)...).................(...(........(.....)....).) >CP000233.1/487061-487146 AAUAGUUACAAUCCAUUCCCGAAAGGAUUCGUUUUAAACGAAGAUGCCUUGUAACCAAAUUACUUAUAAUAAUGGGGGAAUUAAAU ................(.(......).(.............))........................................... ................(.((....)).(.............))........................................... ................(.((....)).(.............))..........................(.........)...... >CP003032.1/1501869-1501780 AAGCGUUACAACUCAUUCCCGAUAGGAUUCACGCUUUUAGUGAAGAUGCCUUGUAACCACAAAUAUAAUGAAUGGGGGAAUUUUAUUAUG ................(.(......).(...............))............................................. ................(.((....)).(...............))............................................. ................(.((....)).(...............)).........................(......)............ >ACGV01000186.1/13246-13351 UCUCGUUAUAAAGCAAAUUCCCGAUAGGAUUCACUUUACUGUGAAGAUGCCUUGUAACCACUAAAUGUUUCAAUUGUAACUUGCAUAUGGGGGAAUUAACACACAU ...................((......).(..............))............................................................ ...................(((....)).(..............))............................................................ >CR954253.1/1355763-1355676 AUUUGUUACAAGUCCUGAUAGGAUUCACCAAAUUGGUGAAGAUGCCUUGUAACCGUGUAGCUAGUCUAUAGGGGGACACAUAUAGAUG .............((......).(...............)...)............................................ .............(((....)).(...............)...)............................................ >ACKZ01000012.1/36527-36446 AAAAGUUAAAAAUGAUAUUCCCGAAAGGAUGCACCAUGUGUAGAUGCCUUGUAACCGGAAUUGAAUGGGGGAAAAAGAAAUG ...................((......).(...........))....................................... >ACGU01000017.1/23671-23581 UAUCGGUUCAAGUCCUGAUAGGAUUCAUUACUUAGUUAAUGAAGAUGCCUUGUAACCGGAUAGCCAAUGUCUAUAUAGGGGGACUAAUAUG .............((......).(..................)...)............................................ >ACIZ01000041.1/43695-43782 UAGAGUUGCAAUACAUUCCCGAUGGGGUUCGUUAGCGAUUAACGAACAUGCCUUGUAACCGAAAAUCAUGAGGGGGAAACAAACGAUG ................(.(......).(.................))......................................... >CP000033.3/1626537-1626447 UAUCGGUUCAAGUCCUGAAAGGAUUCAUUAAAUAAUUAGUGAAGAUGCCUUGUAACCGAAUAGCCGAUGUCUAUAUAGGGGGACUAAUAUG .............((......).(..................)...)............................................ >FM177140.1/914403-914491 UAGAGUUGCAAAACAUUCCCGAUGGGGUUCGUCAAAGCUAUGACGAACAUGCCUUGUAACCUAAAAUAAUAAGGGGGAAACAAAACAUG ................((.......).(..................)).........................................

	ORB			p-value	ORB frequency (per structure per nucleotide)	Means ratio
1	((G)R(U))			< 0.001		26

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
2	(GANA)			< 0.001		6.32

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
3	(.GGRR.)			< 0.001		6.34

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
4	((A)U)G			< 0.001		2.53

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
5	((U)A)A			< 0.001		1.16

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
6	((C)Y)U			0.00234		1.15

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
	ORB			p-value	ORB frequency (per structure per nucleotide)	Means ratio

	NCM			p-value	NCM frequency (per structure per nucleotide)	Means ratio
1	((G)R(U))			< 0.001		26

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
2	U(C(C)())			< 0.001		31.5

ACBD01000055.1/1906-1985 GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG GUUCGUUGCAAGUUCCCGAAAGGAUCCGUAGGACGGAGAUGCCUUGUAACCGAAUUUAACUAGGGGGAAUCAUUAUAAUG .........1.........2.........3.........4.........5.........6.........7.........8 12345678901234567890123456789012345678901234567890123456789012345678901234567890
3	((A)CU)A			0.622		6.64
	NCM			p-value	NCM frequency (per structure per nucleotide)	Means ratio

Structure is visualized using R2R 1.0.6 (Zasha Weinberg).
LOGOS are generated with ggseqlogo (Omar Wagih).