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)

Hammerhead ribozyme (type II) (Rfam: RF02276)

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

(RRR()U)
(.NYGRN.)
(.NN.)
((C)AG)N
N(C(G))

100.0
100.0
100.0
91.3
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: 99.7 %
(± 0.0555 %)

Decision tree:

5-fold cross-validation: 94.9 %
(± 5.48 %)

D-ORB structure

D-ORB structure decision tree:

5-fold cross-validation: 96.9 %
(± 5 %)

of EU822883.1/15732-15799

EU822883.1/15732-15799

AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG
(((.(...(((((((....))))))).)))).(..(((((..((...(((.....)))))..))))))
.........1.........2.........3.........4.........5.........6........
12345678901234567890123456789012345678901234567890123456789012345678

abstract shape: `()()`

					Number of sequences
	Structure	ORBs			(out of 23)	(%)
1		(RRR()U)			21	91.3
>FP929062.1/2627211-2627146 AGCCGAAACGCCCUUGUGGGCGUCCACCGUGGGAUGGUCUCCCGGUGCUGAUGAUGGCAGACCAGA ....(...(............).).......................................... >AE017285.1/2805967-2806034 UUGCGAAACCGCCCCCAUGCGGGGCGGUCGUCGGAGCGUGGCGGCUCCGGCCUGACGAGCAGCCGAAG ....(...(.................).)....................................... >EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG ....(...(................).)........................................ >CP001921.1/1469248-1469180 AAGCGAAACACAGGCAUUCGUGCCUGUGUCUGCCGGGUGUCGUGACUCGGUACUGACGAGCAGCGAGAU ....(...(..................).)....................................... >FP929049.1/3216698-3216766 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(...............).).......................................... >CP002457.1/4228190-4228119 AAGCGAAACCCGCCUCAAUCUUGAGGCGUGGUCUAUCCAGCGUAGUGGCUGGGUACUGAUGAGCAGCUAACA ....(...(.....................).)....................................... >FP929050.1/3256692-3256760 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUAAUCGCCCGGCUCUGAUGAUGGCAGAUUAAA ....(...(...............).).......................................... >BX640448.1/37265-37328 AAGCGAAACCGCCCAUGAGGCGGUCUGCCCACCGUGGUGGCUGGGUACUGAUGAGCAGCACCAA ....(...(.............).)....................................... >FM209186.1/1691949-1692020 GAGCGAAACCGCCCCGGCCUGGCCGGGACGGUCUGCCGGACGUGGUGGUCCGGUACUGACGAGCAGCCAACC ....(...(.....................).)....................................... >CP001616.1/802639-802703 CCGCGAAACCGCCUGAAAAGGCGGUCUGCCCGAUGUGGUGAUCGGGCACUGAUGAGCAGCCACGG ....(...(..............).)....................................... >FP929049.1/3976834-3976903 AGCCGAAACGCUCCGAUCUGGAGCGUCAGCUGCGGACCGGUCGCCGCGGCUCUGACGAUGGCAGACCAAC ....(...(...............).)........................................... >AE016825.1/2338135-2338209 AAGCGAAACCGCGCACAUUGAAAUAUGUGCGCGGUCUGCCCGGCGUGGUUGCCGGGUACUGAUGAGCAGCCAACG ....(...(........................).)....................................... >CP001339.1/1761142-1761074 GAGCGAAACGCCCGCCUGCGGGUGGGCGUCUGCCGGGCGUGGUGGCCCGGCACUGAUGAGCAGCCAGAG ....(...(..................).)....................................... >FP885897.1/1749548-1749483 GUGCGAAACGCCCGCGAUGCGGGCGUCUGCCUGGCGUGGUGGCCGGGUACUGAUGAGCAGCCGAAA ....(...(...............).)....................................... >ABBO01000909.1/30753-30820 AUGCGAAACGCCCGCGCAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(................).)........................................ >CP002431.1/2631417-2631481 AAGCGAAACCGCCCUGCGGGGCGGUCGCCGGGGCGUGGCGGCCUCGGCCUGAUGAGCAGCCAAGG ....(...(..............).)....................................... >ABBI01002348.1/74-141 AUGCGAAACGCCCGCGUAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(................).)........................................ >BX640448.1/36812-36876 GUGCGAAACCGCCCUCCGGGGCGGUCUGCCGGGCGUGGUGGCCGGGCACUGAUGAGCAGCCAUAC ....(...(..............).)....................................... >FP929049.1/3977641-3977709 AGCCGAAACGCUCCACCUUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(...............).).......................................... >AECZ01000006.1/72490-72555 AAGCGAAACCGCCCCGCGUGGGCGGUCGUCCGGGCGUGGCGGCCCGGGCCUGAUGAGCAGCCAAAG ....(...(...............).)....................................... >CP000112.1/3331688-3331763 AUGCGAAACCGUCCUCCGUGCGGGAGCGGAGGCGGUCGUCCGGCGGUGGCGCGUCGGACCUGAUGAGCAGCCAAGC ....(...(.........................).).......................................
2		(RRR()U) (.NYGRN.)			18	78.3
>CP001616.1/802639-802703 CCGCGAAACCGCCUGAAAAGGCGGUCUGCCCGAUGUGGUGAUCGGGCACUGAUGAGCAGCCACGG ....(...(..............).)................(..........)........... >FP929050.1/3256692-3256760 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUAAUCGCCCGGCUCUGAUGAUGGCAGAUUAAA ....(...(...............).).....................(......)............. >ABBI01002348.1/74-141 AUGCGAAACGCCCGCGUAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(................).).....................(.....)............ >FP929049.1/3976834-3976903 AGCCGAAACGCUCCGAUCUGGAGCGUCAGCUGCGGACCGGUCGCCGCGGCUCUGACGAUGGCAGACCAAC ....(...(...............).)..........................(.......)........ >CP002431.1/2631417-2631481 AAGCGAAACCGCCCUGCGGGGCGGUCGCCGGGGCGUGGCGGCCUCGGCCUGAUGAGCAGCCAAGG ....(...(..............).)..................(........)........... >ABBO01000909.1/30753-30820 AUGCGAAACGCCCGCGCAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(................).).....................(.....)............ >CP001921.1/1469248-1469180 AAGCGAAACACAGGCAUUCGUGCCUGUGUCUGCCGGGUGUCGUGACUCGGUACUGACGAGCAGCGAGAU ....(...(..................).).................(.........)........... >BX640448.1/37265-37328 AAGCGAAACCGCCCAUGAGGCGGUCUGCCCACCGUGGUGGCUGGGUACUGAUGAGCAGCACCAA ....(...(.............).).....................(.....)........... >FM209186.1/1691949-1692020 GAGCGAAACCGCCCCGGCCUGGCCGGGACGGUCUGCCGGACGUGGUGGUCCGGUACUGACGAGCAGCCAACC ....(...(.....................).).....................(.....)........... >BX640448.1/36812-36876 GUGCGAAACCGCCCUCCGGGGCGGUCUGCCGGGCGUGGUGGCCGGGCACUGAUGAGCAGCCAUAC ....(...(..............).)....................(......)........... >AE017285.1/2805967-2806034 UUGCGAAACCGCCCCCAUGCGGGGCGGUCGUCGGAGCGUGGCGGCUCCGGCCUGACGAGCAGCCGAAG ....(...(.................).)..................(........)........... >FP929049.1/3977641-3977709 AGCCGAAACGCUCCACCUUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(...............).).....................(......)............. >CP002457.1/4228190-4228119 AAGCGAAACCCGCCUCAAUCUUGAGGCGUGGUCUAUCCAGCGUAGUGGCUGGGUACUGAUGAGCAGCUAACA ....(...(.....................).).....................(.....)........... >FP929062.1/2627211-2627146 AGCCGAAACGCCCUUGUGGGCGUCCACCGUGGGAUGGUCUCCCGGUGCUGAUGAUGGCAGACCAGA ....(...(............).).....................(......)............. >FP929049.1/3216698-3216766 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(...............).).....................(......)............. >EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG ....(...(................).).....................(.....)............ >FP885897.1/1749548-1749483 GUGCGAAACGCCCGCGAUGCGGGCGUCUGCCUGGCGUGGUGGCCGGGUACUGAUGAGCAGCCGAAA ....(...(...............).).....................(.....)........... >AECZ01000006.1/72490-72555 AAGCGAAACCGCCCCGCGUGGGCGGUCGUCCGGGCGUGGCGGCCCGGGCCUGAUGAGCAGCCAAAG ....(...(...............).)........................(.....)........
3		(RRR()U) (.NYGRN.) (.NN.)			14	60.9
>FP929050.1/3256692-3256760 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUAAUCGCCCGGCUCUGAUGAUGGCAGAUUAAA ....(...(.....(...).....).).....................(......)............. >FP929049.1/3216698-3216766 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(.....(...).....).).....................(......)............. >FP929049.1/3977641-3977709 AGCCGAAACGCUCCACCUUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(.....(...).....).).....................(......)............. >ABBO01000909.1/30753-30820 AUGCGAAACGCCCGCGCAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(.....(....).....).).....................(.....)............ >CP002431.1/2631417-2631481 AAGCGAAACCGCCCUGCGGGGCGGUCGCCGGGGCGUGGCGGCCUCGGCCUGAUGAGCAGCCAAGG ....(...(.....(..).....).)..................(........)........... >FP885897.1/1749548-1749483 GUGCGAAACGCCCGCGAUGCGGGCGUCUGCCUGGCGUGGUGGCCGGGUACUGAUGAGCAGCCGAAA ....(...(.....(...).....).).....................(.....)........... >AE017285.1/2805967-2806034 UUGCGAAACCGCCCCCAUGCGGGGCGGUCGUCGGAGCGUGGCGGCUCCGGCCUGACGAGCAGCCGAAG ....(...(.....(.....).....).)..................(........)........... >CP001921.1/1469248-1469180 AAGCGAAACACAGGCAUUCGUGCCUGUGUCUGCCGGGUGUCGUGACUCGGUACUGACGAGCAGCGAGAU ....(...(.....(......).....).).................(.........)........... >BX640448.1/36812-36876 GUGCGAAACCGCCCUCCGGGGCGGUCUGCCGGGCGUGGUGGCCGGGCACUGAUGAGCAGCCAUAC ....(...(.....(..).....).)....................(......)........... >FP929062.1/2627211-2627146 AGCCGAAACGCCCUUGUGGGCGUCCACCGUGGGAUGGUCUCCCGGUGCUGAUGAUGGCAGACCAGA ....(...(....(..)....).).....................(......)............. >EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG ....(...(.....(....).....).).....................(.....)............ >AECZ01000006.1/72490-72555 AAGCGAAACCGCCCCGCGUGGGCGGUCGUCCGGGCGUGGCGGCCCGGGCCUGAUGAGCAGCCAAAG ....(...(.....(...).....).)........................(.....)........ >BX640448.1/37265-37328 AAGCGAAACCGCCCAUGAGGCGGUCUGCCCACCGUGGUGGCUGGGUACUGAUGAGCAGCACCAA ....(...(....(..).....).).....................(.....)........... >ABBI01002348.1/74-141 AUGCGAAACGCCCGCGUAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(.....(....).....).).....................(.....)............
4		(RRR()U) (.NYGRN.) (.NN.) ((C)AG)N			11	47.8
>FP929049.1/3216698-3216766 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(.....(...).....).).............(.(.....(......)....)..)..... >FP929050.1/3256692-3256760 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUAAUCGCCCGGCUCUGAUGAUGGCAGAUUAAA ....(...(.....(...).....).).............(.(.....(......)....)..)..... >BX640448.1/36812-36876 GUGCGAAACCGCCCUCCGGGGCGGUCUGCCGGGCGUGGUGGCCGGGCACUGAUGAGCAGCCAUAC ....(...(.....(..).....).)..............(..(..(......)..)..)..... >ABBI01002348.1/74-141 AUGCGAAACGCCCGCGUAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(.....(....).....).)......(.(............(.....)...)..)..... >FP885897.1/1749548-1749483 GUGCGAAACGCCCGCGAUGCGGGCGUCUGCCUGGCGUGGUGGCCGGGUACUGAUGAGCAGCCGAAA ....(...(.....(...).....).)..........((.........(.....)..)..)..... >ABBO01000909.1/30753-30820 AUGCGAAACGCCCGCGCAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(.....(....).....).)......(.(............(.....)...)..)..... >CP002431.1/2631417-2631481 AAGCGAAACCGCCCUGCGGGGCGGUCGCCGGGGCGUGGCGGCCUCGGCCUGAUGAGCAGCCAAGG ....(...(.....(..).....).).....((...........(........)..)..)..... >CP001921.1/1469248-1469180 AAGCGAAACACAGGCAUUCGUGCCUGUGUCUGCCGGGUGUCGUGACUCGGUACUGACGAGCAGCGAGAU ....(...(.....(......).....).)...........(..(..(.........)..)..)..... >FP929049.1/3977641-3977709 AGCCGAAACGCUCCACCUUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(.....(...).....).).............(.(.....(......)....)..)..... >EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG ....(...(.....(....).....).)...........(..(......(.....)...)..)..... >AE017285.1/2805967-2806034 UUGCGAAACCGCCCCCAUGCGGGGCGGUCGUCGGAGCGUGGCGGCUCCGGCCUGACGAGCAGCCGAAG ....(...(.....(.....).....).).............((...(........)..)..).....
5		(RRR()U) (.NYGRN.) (.NN.) ((C)AG)N N(C(G))			9	39.1
>ABBI01002348.1/74-141 AUGCGAAACGCCCGCGUAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ..(.(...(.....(....).....).)).....(.(............(.....)...)..)..... >CP001921.1/1469248-1469180 AAGCGAAACACAGGCAUUCGUGCCUGUGUCUGCCGGGUGUCGUGACUCGGUACUGACGAGCAGCGAGAU ..(.(...(.....(......).....).)....)......(..(..(.........)..)..)..... >CP002431.1/2631417-2631481 AAGCGAAACCGCCCUGCGGGGCGGUCGCCGGGGCGUGGCGGCCUCGGCCUGAUGAGCAGCCAAGG ..(.(...(.....(..).....).))....((...........(........)..)..)..... >FP929049.1/3977641-3977709 AGCCGAAACGCUCCACCUUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ..(.(...(.....(...).....).)....)........(.(.....(......)....)..)..... >FP929049.1/3216698-3216766 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ..(.(...(.....(...).....).)....)........(.(.....(......)....)..)..... >EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG ..(.(...(.....(....).....).)..)........(..(......(.....)...)..)..... >FP929050.1/3256692-3256760 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUAAUCGCCCGGCUCUGAUGAUGGCAGAUUAAA ..(.(...(.....(...).....).)....)........(.(.....(......)....)..)..... >FP885897.1/1749548-1749483 GUGCGAAACGCCCGCGAUGCGGGCGUCUGCCUGGCGUGGUGGCCGGGUACUGAUGAGCAGCCGAAA ..(.(...(.....(...).....).))........((..........(.....)..)..)..... >ABBO01000909.1/30753-30820 AUGCGAAACGCCCGCGCAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ..(.(...(.....(....).....).)).....(.(............(.....)...)..).....

>EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG ....(...(................).)........................................ ....(...(................).).....................(.....)............ ....(...(.....(....).....).).....................(.....)............ ....(...(.....(....).....).)...........(..(......(.....)...)..)..... ..(.(...(.....(....).....).)..)........(..(......(.....)...)..)..... >CP001921.1/1469248-1469180 AAGCGAAACACAGGCAUUCGUGCCUGUGUCUGCCGGGUGUCGUGACUCGGUACUGACGAGCAGCGAGAU ....(...(..................).)....................................... ....(...(..................).).................(.........)........... ....(...(.....(......).....).).................(.........)........... ....(...(.....(......).....).)...........(..(..(.........)..)..)..... ..(.(...(.....(......).....).)....)......(..(..(.........)..)..)..... >FP929049.1/3216698-3216766 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(...............).).......................................... ....(...(...............).).....................(......)............. ....(...(.....(...).....).).....................(......)............. ....(...(.....(...).....).).............(.(.....(......)....)..)..... ..(.(...(.....(...).....).)....)........(.(.....(......)....)..)..... >FP929050.1/3256692-3256760 AGCCGAAACGCUCCACCCUGGAGCGUCAGCCGCGGGAUAAUCGCCCGGCUCUGAUGAUGGCAGAUUAAA ....(...(...............).).......................................... ....(...(...............).).....................(......)............. ....(...(.....(...).....).).....................(......)............. ....(...(.....(...).....).).............(.(.....(......)....)..)..... ..(.(...(.....(...).....).)....)........(.(.....(......)....)..)..... >FP885897.1/1749548-1749483 GUGCGAAACGCCCGCGAUGCGGGCGUCUGCCUGGCGUGGUGGCCGGGUACUGAUGAGCAGCCGAAA ....(...(...............).)....................................... ....(...(...............).).....................(.....)........... ....(...(.....(...).....).).....................(.....)........... ....(...(.....(...).....).)..........((.........(.....)..)..)..... ..(.(...(.....(...).....).))........((..........(.....)..)..)..... >ABBO01000909.1/30753-30820 AUGCGAAACGCCCGCGCAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(................).)........................................ ....(...(................).).....................(.....)............ ....(...(.....(....).....).).....................(.....)............ ....(...(.....(....).....).)......(.(............(.....)...)..)..... ..(.(...(.....(....).....).)).....(.(............(.....)...)..)..... >CP002431.1/2631417-2631481 AAGCGAAACCGCCCUGCGGGGCGGUCGCCGGGGCGUGGCGGCCUCGGCCUGAUGAGCAGCCAAGG ....(...(..............).)....................................... ....(...(..............).)..................(........)........... ....(...(.....(..).....).)..................(........)........... ....(...(.....(..).....).).....((...........(........)..)..)..... ..(.(...(.....(..).....).))....((...........(........)..)..)..... >ABBI01002348.1/74-141 AUGCGAAACGCCCGCGUAAGCGGGCGUCUAUUCGGCGUGGCGGCCGAGUACUGACGAUGCAGCCGAGG ....(...(................).)........................................ ....(...(................).).....................(.....)............ ....(...(.....(....).....).).....................(.....)............ ....(...(.....(....).....).)......(.(............(.....)...)..)..... ..(.(...(.....(....).....).)).....(.(............(.....)...)..)..... >FP929049.1/3977641-3977709 AGCCGAAACGCUCCACCUUGGAGCGUCAGCCGCGGGAUGAUCGCCCGGCUCUGAUGAUGGCAGAUCAAA ....(...(...............).).......................................... ....(...(...............).).....................(......)............. ....(...(.....(...).....).).....................(......)............. ....(...(.....(...).....).).............(.(.....(......)....)..)..... ..(.(...(.....(...).....).)....)........(.(.....(......)....)..)..... >AE017285.1/2805967-2806034 UUGCGAAACCGCCCCCAUGCGGGGCGGUCGUCGGAGCGUGGCGGCUCCGGCCUGACGAGCAGCCGAAG ....(...(.................).)....................................... ....(...(.................).)..................(........)........... ....(...(.....(.....).....).)..................(........)........... ....(...(.....(.....).....).).............((...(........)..)..)..... >BX640448.1/36812-36876 GUGCGAAACCGCCCUCCGGGGCGGUCUGCCGGGCGUGGUGGCCGGGCACUGAUGAGCAGCCAUAC ....(...(..............).)....................................... ....(...(..............).)....................(......)........... ....(...(.....(..).....).)....................(......)........... ....(...(.....(..).....).)..............(..(..(......)..)..)..... >FP929062.1/2627211-2627146 AGCCGAAACGCCCUUGUGGGCGUCCACCGUGGGAUGGUCUCCCGGUGCUGAUGAUGGCAGACCAGA ....(...(............).).......................................... ....(...(............).).....................(......)............. ....(...(....(..)....).).....................(......)............. >BX640448.1/37265-37328 AAGCGAAACCGCCCAUGAGGCGGUCUGCCCACCGUGGUGGCUGGGUACUGAUGAGCAGCACCAA ....(...(.............).)....................................... ....(...(.............).).....................(.....)........... ....(...(....(..).....).).....................(.....)........... >AECZ01000006.1/72490-72555 AAGCGAAACCGCCCCGCGUGGGCGGUCGUCCGGGCGUGGCGGCCCGGGCCUGAUGAGCAGCCAAAG ....(...(...............).)....................................... ....(...(...............).)........................(.....)........ ....(...(.....(...).....).)........................(.....)........ >CP002457.1/4228190-4228119 AAGCGAAACCCGCCUCAAUCUUGAGGCGUGGUCUAUCCAGCGUAGUGGCUGGGUACUGAUGAGCAGCUAACA ....(...(.....................).)....................................... ....(...(.....................).).....................(.....)........... >FM209186.1/1691949-1692020 GAGCGAAACCGCCCCGGCCUGGCCGGGACGGUCUGCCGGACGUGGUGGUCCGGUACUGACGAGCAGCCAACC ....(...(.....................).)....................................... ....(...(.....................).).....................(.....)........... >CP001616.1/802639-802703 CCGCGAAACCGCCUGAAAAGGCGGUCUGCCCGAUGUGGUGAUCGGGCACUGAUGAGCAGCCACGG ....(...(..............).)....................................... ....(...(..............).)................(..........)........... >FP929049.1/3976834-3976903 AGCCGAAACGCUCCGAUCUGGAGCGUCAGCUGCGGACCGGUCGCCGCGGCUCUGACGAUGGCAGACCAAC ....(...(...............).)........................................... ....(...(...............).)..........................(.......)........ >AE016825.1/2338135-2338209 AAGCGAAACCGCGCACAUUGAAAUAUGUGCGCGGUCUGCCCGGCGUGGUUGCCGGGUACUGAUGAGCAGCCAACG ....(...(........................).)....................................... >CP001339.1/1761142-1761074 GAGCGAAACGCCCGCCUGCGGGUGGGCGUCUGCCGGGCGUGGUGGCCCGGCACUGAUGAGCAGCCAGAG ....(...(..................).)....................................... >CP000112.1/3331688-3331763 AUGCGAAACCGUCCUCCGUGCGGGAGCGGAGGCGGUCGUCCGGCGGUGGCGCGUCGGACCUGAUGAGCAGCCAAGC ....(...(.........................).).......................................

	ORB			p-value	ORB frequency (per structure per nucleotide)	Means ratio
1	(RRR()U)			< 0.001		47.3

EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG .........1.........2.........3.........4.........5.........6........ 12345678901234567890123456789012345678901234567890123456789012345678
2	(.NYGRN.)			< 0.001		12.5

EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG .........1.........2.........3.........4.........5.........6........ 12345678901234567890123456789012345678901234567890123456789012345678
3	(.NN.)			< 0.001		1.76

EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG .........1.........2.........3.........4.........5.........6........ 12345678901234567890123456789012345678901234567890123456789012345678
4	((C)AG)N			< 0.001		1.91

EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG .........1.........2.........3.........4.........5.........6........ 12345678901234567890123456789012345678901234567890123456789012345678
5	N(C(G))			< 0.001		1.86

EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG .........1.........2.........3.........4.........5.........6........ 12345678901234567890123456789012345678901234567890123456789012345678
	ORB			p-value	ORB frequency (per structure per nucleotide)	Means ratio

	NCM			p-value	NCM frequency (per structure per nucleotide)	Means ratio
1	(RRR()U)			< 0.001		47.3

EU822883.1/15732-15799 AUGCGAAACGCCCGCGCGAGCGGGUGUCUAUCCGGCGUGGUGGCCGGGUACUGACGAUGCAGCCGAGG .........1.........2.........3.........4.........5.........6........ 12345678901234567890123456789012345678901234567890123456789012345678
	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).