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)

PreQ1 riboswitch   (Rfam: RF00522)

Seed sequences
All NCMs (CSV file) (all) positive sequences (all) negative sequences (random) (training) positive sequences (training) negative sequences (testing) positive sequences (testing) negative sequences 

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
(.AANNA.)
(.NANCN.)
(.N.())
100.0
97.1
100.0
(.AANNA.)
(.NANCN.)

% of positive sequence with ORB





Deep neural network:

5-fold cross-validation: 99.7 %
(± 0.101 %)
Decision tree:

5-fold cross-validation: 89.9 %
(± 5.63 %)
D-ORB structure
D-ORB structure decision tree:

5-fold cross-validation: 94.6 %
(± 5.19 %)
of AL009126.3/1439274-1439318
AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
(.(((....(.(......))))))((((((......))))))...
.........1.........2.........3.........4.....
123456789012345678901234567890123456789012345

abstract shape: ()()

Number of sequences
Structure ORBs (out of 35) (%)
1 (.AANNA.)
 35 100.0
>X99978.2/10136-10181
CAAUACGUGGUUCGUAACCAUCCCACGUUAAAAAAACUAGGAGGAA
............................(.....)...........
>AE016827.1/1848390-1848434
UAAUUCGUGGUUCGAAAACCUCCCACGCAAAAAAACUAAGGAAAA
....................................(.....)..
>CP000029.1/370924-370878
AUAACAGAGGUUCCUAGCCGAAACCCUCUAUAAAAAACUAGACAUGA
..................................(.....)......
>AASA01000045.1/1296-1252
UUAUUUGUGGUUCGUAAACCUCCCACACAAAAAAACUAAGGACAC
....................................(......).
>AP006627.1/2249570-2249527
AAAGAAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAACCAAUU
...................................(.....)..
>AL935263.2/2519559-2519515
GCUGGCCUGGUUCGUAAACUUCCCAGGAUAAAAAACCAAGAACUU
...................................(......)..
>AP006716.1/2221258-2221304
UCAAAAGAGGUUCCUAGCUGAAACCCUCUAUAAAAAACUAGACAAUA
..................................(........)...
>AE017355.1/1321429-1321472
ACGGGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAUGGAAAC
............................(......)........
>CP000233.1/1599957-1600001
CUUGGACUGGUUCGUAAACUUCCCAGUAUAAAAAACCAAGAAUCU
..................................(.......)..
>AAXV01000007.1/14855-14899
AGCACCGUGGUUCGUAACCAUCCCACGAAAAAAAACUAAGGAGAA
...........................(......)..........
>AAVO02000002.1/275638-275594
UCAUAACUGGUUCGAAACCCUCCCAGUAUAAAAAACUAGGUCAUG
................................(.......)....
>AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
.............................(......)........
>AL766846.1/39196-39152
CUCGGACUGGUUCGAAAACUUCCCAGAAUAAAAAACUAAGUGACU
............................(.....)..........
>AE002098.2/329220-329176
CCGCCCGUGGUUCGAAAACCUCCCACAUUAAAAAACUAAGGAAAC
.............................(......)........
>ABDX01000003.1/184506-184550
UUGGUAGAGGUUCGUAACCAUCCCUCUAUAAAAAACUAAGGGCUG
.............(.......).......................
>CP000414.1/1235047-1235002
AUAAUAGCGGUUCAUCAACCAUCCCGCUUAAAAAAACUAGGAGAUA
..............................(.....).........
>AAAK03000099.1/1629-1673
CUUGGACUGGUUCGGAAACUUCCCAGAAUAAAAAACUAAGUAUCU
................................(.....)......
>AAYG02000018.1/120313-120357
UCUGGACUGGUUCGUGAACUUCCCAGUAUAAAAAACCAAGUAUCU
................................(.....)......
>AM421808.1/1884627-1884671
CGCCCCGUGGUUCGAAAACCUCCCACACUAAAAAACUAAGGAAAC
.............................(......)........
>AARM02000383.1/1741-1694
CCACACGUGGUUCAUUCAUACCAUCCCACGUAAAAAAACUAAGGAGGA
................................(.....).........
>AE017355.1/1568663-1568707
AAUAACGUGGUUCGAAACCAUCCCACGUAAAAAAACUAAGGAGAU
..............(.....)........................
>AAOX01000006.1/21305-21347
ACGGUAGAGGUUCUAGCUACCCUCUCAAAAAAACUAAGGAAAA
...........................(.....).........
>AE004439.1/209165-209100
UUCAUAGUGGUUCGUAACCCUCCCACUUGAACAACCAACAAUUGUUCGAAACAAAACUAGGAAAAU
................................................(........)........
>BA000004.3/2373342-2373299
GUGAGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAAGGCAAG
...............................(.....)......
>BA000028.3/467676-467632
AUCACCGUGGUUCGUAACCAUCCCACGCAAAAAAACUAGGAAGGA
...........................(......)..........
>ABCF01000001.1/139145-139189
GCAGGAGAGGUUCUAGCUUAACCCUCUAUAAAAAACUAAGGAAAC
.............................(......)........
>CP000746.1/2223340-2223384
UUCAUCGUGGUUCGCAAACCUCCCACGCAAAAAAACUAAGGAAAU
....................................(.....)..
>CP000513.1/859945-859989
CCGCUUGUGGUUCGAAAACUUCCCACACUAAAAAACUAGGAAAAA
............................(.....)..........
>CR936503.1/1598027-1597983
AAAAACGUGGUUCGUAACCAUCCCACGCUAAAAAACUAGGAGGAU
............................(.....)..........
>AE017333.1/1501710-1501754
GCGGGAGAGGUUCUAGCAAAACCCUCUAUAAAAAACUAAGGAAAG
....................................(.....)..
>AL596166.1/191853-191900
CCACACGUGGUUCAUUCAUACCAUCCCACGUAAAAAAACUAGGAGGAA
..............................(.....)...........
>CP000764.1/1180651-1180694
AUGGGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAUGAGAAC
............................(......)........
>AARF01000079.1/5363-5319
AUGGGAGAGGUUCGAGAUCUUCCCUCUAUAAAAAACUAAGGAGCU
.............................(......)........
>AP008934.1/2076124-2076170
UAUAAAGAGGUUCCUAGCUGAUACCCUCUAUAAAAAACUAGACACAU
..................................(........)...
>AAXB02000001.1/142227-142271
CUUGAACUGGUUCGAAAACCUCCCAGUAUAAAAAACUAGGCAAAG
..........................(.......)..........
2 (.AANNA.)
(.NANCN.)
 29 82.9
>AL935263.2/2519559-2519515
GCUGGCCUGGUUCGUAAACUUCCCAGGAUAAAAAACCAAGAACUU
.............(.......).............(......)..
>BA000004.3/2373342-2373299
GUGAGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAAGGCAAG
.............(......)..........(.....)......
>ABDX01000003.1/184506-184550
UUGGUAGAGGUUCGUAACCAUCCCUCUAUAAAAAACUAAGGGCUG
...........(.......)........(.....)..........
>CP000764.1/1180651-1180694
AUGGGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAUGAGAAC
.............(......).......(......)........
>CR936503.1/1598027-1597983
AAAAACGUGGUUCGUAACCAUCCCACGCUAAAAAACUAGGAGGAU
..........(........)........(.....)..........
>AARF01000079.1/5363-5319
AUGGGAGAGGUUCGAGAUCUUCCCUCUAUAAAAAACUAAGGAGCU
..............(.....)........(......)........
>AAYG02000018.1/120313-120357
UCUGGACUGGUUCGUGAACUUCCCAGUAUAAAAAACCAAGUAUCU
.............(.......)..........(.....)......
>CP000233.1/1599957-1600001
CUUGGACUGGUUCGUAAACUUCCCAGUAUAAAAAACCAAGAAUCU
.............(.......)............(.......)..
>AAXB02000001.1/142227-142271
CUUGAACUGGUUCGAAAACCUCCCAGUAUAAAAAACUAGGCAAAG
..............(.....).....(.......)..........
>AP006627.1/2249570-2249527
AAAGAAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAACCAAUU
.............(......)..............(.....)..
>AM421808.1/1884627-1884671
CGCCCCGUGGUUCGAAAACCUCCCACACUAAAAAACUAAGGAAAC
..............(.....)........(......)........
>AAOX01000006.1/21305-21347
ACGGUAGAGGUUCUAGCUACCCUCUCAAAAAAACUAAGGAAAA
...........(......)........(.....).........
>AL766846.1/39196-39152
CUCGGACUGGUUCGAAAACUUCCCAGAAUAAAAAACUAAGUGACU
..............(.....).......(.....)..........
>ABCF01000001.1/139145-139189
GCAGGAGAGGUUCUAGCUUAACCCUCUAUAAAAAACUAAGGAAAC
............(.....)..........(......)........
>AAXV01000007.1/14855-14899
AGCACCGUGGUUCGUAACCAUCCCACGAAAAAAAACUAAGGAGAA
..........(........).......(......)..........
>BA000028.3/467676-467632
AUCACCGUGGUUCGUAACCAUCCCACGCAAAAAAACUAGGAAGGA
..........(........).......(......)..........
>CP000746.1/2223340-2223384
UUCAUCGUGGUUCGCAAACCUCCCACGCAAAAAAACUAAGGAAAU
.........(............).............(.....)..
>CP000513.1/859945-859989
CCGCUUGUGGUUCGAAAACUUCCCACACUAAAAAACUAGGAAAAA
..............(.....).......(.....)..........
>AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
...........(......)..........(......)........
>AAAK03000099.1/1629-1673
CUUGGACUGGUUCGGAAACUUCCCAGAAUAAAAAACUAAGUAUCU
.............(.......)..........(.....)......
>CP000414.1/1235047-1235002
AUAAUAGCGGUUCAUCAACCAUCCCGCUUAAAAAAACUAGGAGAUA
...........(.......)..........(.....).........
>AE016827.1/1848390-1848434
UAAUUCGUGGUUCGAAAACCUCCCACGCAAAAAAACUAAGGAAAA
..............(.........)...........(.....)..
>AE017333.1/1501710-1501754
GCGGGAGAGGUUCUAGCAAAACCCUCUAUAAAAAACUAAGGAAAG
...........(........)...............(.....)..
>AE017355.1/1568663-1568707
AAUAACGUGGUUCGAAACCAUCCCACGUAAAAAAACUAAGGAGAU
.........(............)............(......)..
>AP006716.1/2221258-2221304
UCAAAAGAGGUUCCUAGCUGAAACCCUCUAUAAAAAACUAGACAAUA
...........(..........)...........(........)...
>CP000029.1/370924-370878
AUAACAGAGGUUCCUAGCCGAAACCCUCUAUAAAAAACUAGACAUGA
...........(..........)...........(.....)......
>AASA01000045.1/1296-1252
UUAUUUGUGGUUCGUAAACCUCCCACACAAAAAAACUAAGGACAC
..............(.........)...........(......).
>AAVO02000002.1/275638-275594
UCAUAACUGGUUCGAAACCCUCCCAGUAUAAAAAACUAGGUCAUG
.............(.......)..........(.......)....
>AP008934.1/2076124-2076170
UAUAAAGAGGUUCCUAGCUGAUACCCUCUAUAAAAAACUAGACACAU
...........(..........)...........(........)...
3 (.AANNA.)
(.NANCN.)
(.N.())
 21 60.0
>CP000414.1/1235047-1235002
AUAAUAGCGGUUCAUCAACCAUCCCGCUUAAAAAAACUAGGAGAUA
(.(........(.......)..))......(.....).........
>CP000029.1/370924-370878
AUAACAGAGGUUCCUAGCCGAAACCCUCUAUAAAAAACUAGACAUGA
..(...(......(.....).....)..).....(.....)......
>AE017333.1/1501710-1501754
GCGGGAGAGGUUCUAGCAAAACCCUCUAUAAAAAACUAAGGAAAG
.(.(.......(........).....)...).....(.....)..
>AE017355.1/1568663-1568707
AAUAACGUGGUUCGAAACCAUCCCACGUAAAAAAACUAAGGAGAU
(.(......(............).....).)....(......)..
>AAOX01000006.1/21305-21347
ACGGUAGAGGUUCUAGCUACCCUCUCAAAAAAACUAAGGAAAA
(.(........(......)..))....(.....).........
>CP000513.1/859945-859989
CCGCUUGUGGUUCGAAAACUUCCCACACUAAAAAACUAGGAAAAA
..(..(........(.....).))....(.....)..........
>CP000764.1/1180651-1180694
AUGGGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAUGAGAAC
...(.(.......(......)..))...(......)........
>AAXV01000007.1/14855-14899
AGCACCGUGGUUCGUAACCAUCCCACGAAAAAAAACUAAGGAGAA
.(..(.....(........)..))...(......)..........
>AP006716.1/2221258-2221304
UCAAAAGAGGUUCCUAGCUGAAACCCUCUAUAAAAAACUAGACAAUA
..(.(......(..........)....)).....(........)...
>AM421808.1/1884627-1884671
CGCCCCGUGGUUCGAAAACCUCCCACACUAAAAAACUAAGGAAAC
.(....(.......(.....)..))....(......)........
>CP000233.1/1599957-1600001
CUUGGACUGGUUCGUAAACUUCCCAGUAUAAAAAACCAAGAAUCU
..(..(.......(.......)....)..)....(.......)..
>AAYG02000018.1/120313-120357
UCUGGACUGGUUCGUGAACUUCCCAGUAUAAAAAACCAAGUAUCU
..(..(.......(.......)....))....(.....)......
>ABCF01000001.1/139145-139189
GCAGGAGAGGUUCUAGCUUAACCCUCUAUAAAAAACUAAGGAAAC
(..(........(.....)...).)....(......)........
>AE016827.1/1848390-1848434
UAAUUCGUGGUUCGAAAACCUCCCACGCAAAAAAACUAAGGAAAA
.(..(.........(.........)..)...)....(.....)..
>AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
(..(.......(......)...).)....(......)........
>AASA01000045.1/1296-1252
UUAUUUGUGGUUCGUAAACCUCCCACACAAAAAAACUAAGGACAC
.....(.(......(.........)...).).....(......).
>CP000746.1/2223340-2223384
UUCAUCGUGGUUCGCAAACCUCCCACGCAAAAAAACUAAGGAAAU
(.(......(............)...)...).....(.....)..
>AARF01000079.1/5363-5319
AUGGGAGAGGUUCGAGAUCUUCCCUCUAUAAAAAACUAAGGAGCU
....(.(.......(.....)..))....(......)........
>AAVO02000002.1/275638-275594
UCAUAACUGGUUCGAAACCCUCCCAGUAUAAAAAACUAGGUCAUG
...(.(.......(.......)....))....(.......)....
>AL935263.2/2519559-2519515
GCUGGCCUGGUUCGUAAACUUCCCAGGAUAAAAAACCAAGAACUU
..(..(.......(.......)....)...)....(......)..
>BA000004.3/2373342-2373299
GUGAGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAAGGCAAG
...(.(.......(......)....).)...(.....)......

>AE016827.1/1848390-1848434
UAAUUCGUGGUUCGAAAACCUCCCACGCAAAAAAACUAAGGAAAA
....................................(.....)..
..............(.........)...........(.....)..
.(..(.........(.........)..)...)....(.....)..
>CP000029.1/370924-370878
AUAACAGAGGUUCCUAGCCGAAACCCUCUAUAAAAAACUAGACAUGA
..................................(.....)......
...........(..........)...........(.....)......
..(...(......(.....).....)..).....(.....)......
>AASA01000045.1/1296-1252
UUAUUUGUGGUUCGUAAACCUCCCACACAAAAAAACUAAGGACAC
....................................(......).
..............(.........)...........(......).
.....(.(......(.........)...).).....(......).
>AL935263.2/2519559-2519515
GCUGGCCUGGUUCGUAAACUUCCCAGGAUAAAAAACCAAGAACUU
...................................(......)..
.............(.......).............(......)..
..(..(.......(.......)....)...)....(......)..
>AP006716.1/2221258-2221304
UCAAAAGAGGUUCCUAGCUGAAACCCUCUAUAAAAAACUAGACAAUA
..................................(........)...
...........(..........)...........(........)...
..(.(......(..........)....)).....(........)...
>CP000233.1/1599957-1600001
CUUGGACUGGUUCGUAAACUUCCCAGUAUAAAAAACCAAGAAUCU
..................................(.......)..
.............(.......)............(.......)..
..(..(.......(.......)....)..)....(.......)..
>AAXV01000007.1/14855-14899
AGCACCGUGGUUCGUAACCAUCCCACGAAAAAAAACUAAGGAGAA
...........................(......)..........
..........(........).......(......)..........
.(..(.....(........)..))...(......)..........
>AAVO02000002.1/275638-275594
UCAUAACUGGUUCGAAACCCUCCCAGUAUAAAAAACUAGGUCAUG
................................(.......)....
.............(.......)..........(.......)....
...(.(.......(.......)....))....(.......)....
>AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
.............................(......)........
...........(......)..........(......)........
(..(.......(......)...).)....(......)........
>CP000414.1/1235047-1235002
AUAAUAGCGGUUCAUCAACCAUCCCGCUUAAAAAAACUAGGAGAUA
..............................(.....).........
...........(.......)..........(.....).........
(.(........(.......)..))......(.....).........
>AAYG02000018.1/120313-120357
UCUGGACUGGUUCGUGAACUUCCCAGUAUAAAAAACCAAGUAUCU
................................(.....)......
.............(.......)..........(.....)......
..(..(.......(.......)....))....(.....)......
>AM421808.1/1884627-1884671
CGCCCCGUGGUUCGAAAACCUCCCACACUAAAAAACUAAGGAAAC
.............................(......)........
..............(.....)........(......)........
.(....(.......(.....)..))....(......)........
>AE017355.1/1568663-1568707
AAUAACGUGGUUCGAAACCAUCCCACGUAAAAAAACUAAGGAGAU
..............(.....)........................
.........(............)............(......)..
(.(......(............).....).)....(......)..
>AAOX01000006.1/21305-21347
ACGGUAGAGGUUCUAGCUACCCUCUCAAAAAAACUAAGGAAAA
...........................(.....).........
...........(......)........(.....).........
(.(........(......)..))....(.....).........
>BA000004.3/2373342-2373299
GUGAGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAAGGCAAG
...............................(.....)......
.............(......)..........(.....)......
...(.(.......(......)....).)...(.....)......
>ABCF01000001.1/139145-139189
GCAGGAGAGGUUCUAGCUUAACCCUCUAUAAAAAACUAAGGAAAC
.............................(......)........
............(.....)..........(......)........
(..(........(.....)...).)....(......)........
>CP000746.1/2223340-2223384
UUCAUCGUGGUUCGCAAACCUCCCACGCAAAAAAACUAAGGAAAU
....................................(.....)..
.........(............).............(.....)..
(.(......(............)...)...).....(.....)..
>CP000513.1/859945-859989
CCGCUUGUGGUUCGAAAACUUCCCACACUAAAAAACUAGGAAAAA
............................(.....)..........
..............(.....).......(.....)..........
..(..(........(.....).))....(.....)..........
>AE017333.1/1501710-1501754
GCGGGAGAGGUUCUAGCAAAACCCUCUAUAAAAAACUAAGGAAAG
....................................(.....)..
...........(........)...............(.....)..
.(.(.......(........).....)...).....(.....)..
>CP000764.1/1180651-1180694
AUGGGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAUGAGAAC
............................(......)........
.............(......).......(......)........
...(.(.......(......)..))...(......)........
>AARF01000079.1/5363-5319
AUGGGAGAGGUUCGAGAUCUUCCCUCUAUAAAAAACUAAGGAGCU
.............................(......)........
..............(.....)........(......)........
....(.(.......(.....)..))....(......)........
>AP006627.1/2249570-2249527
AAAGAAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAACCAAUU
...................................(.....)..
.............(......)..............(.....)..
>AL766846.1/39196-39152
CUCGGACUGGUUCGAAAACUUCCCAGAAUAAAAAACUAAGUGACU
............................(.....)..........
..............(.....).......(.....)..........
>ABDX01000003.1/184506-184550
UUGGUAGAGGUUCGUAACCAUCCCUCUAUAAAAAACUAAGGGCUG
.............(.......).......................
...........(.......)........(.....)..........
>AAAK03000099.1/1629-1673
CUUGGACUGGUUCGGAAACUUCCCAGAAUAAAAAACUAAGUAUCU
................................(.....)......
.............(.......)..........(.....)......
>BA000028.3/467676-467632
AUCACCGUGGUUCGUAACCAUCCCACGCAAAAAAACUAGGAAGGA
...........................(......)..........
..........(........).......(......)..........
>CR936503.1/1598027-1597983
AAAAACGUGGUUCGUAACCAUCCCACGCUAAAAAACUAGGAGGAU
............................(.....)..........
..........(........)........(.....)..........
>AP008934.1/2076124-2076170
UAUAAAGAGGUUCCUAGCUGAUACCCUCUAUAAAAAACUAGACACAU
..................................(........)...
...........(..........)...........(........)...
>AAXB02000001.1/142227-142271
CUUGAACUGGUUCGAAAACCUCCCAGUAUAAAAAACUAGGCAAAG
..........................(.......)..........
..............(.....).....(.......)..........
>X99978.2/10136-10181
CAAUACGUGGUUCGUAACCAUCCCACGUUAAAAAAACUAGGAGGAA
............................(.....)...........
>AE017355.1/1321429-1321472
ACGGGAGAGGUUCGCGAACUCCCUCUAUAAAAAACUAUGGAAAC
............................(......)........
>AE002098.2/329220-329176
CCGCCCGUGGUUCGAAAACCUCCCACAUUAAAAAACUAAGGAAAC
.............................(......)........
>AARM02000383.1/1741-1694
CCACACGUGGUUCAUUCAUACCAUCCCACGUAAAAAAACUAAGGAGGA
................................(.....).........
>AE004439.1/209165-209100
UUCAUAGUGGUUCGUAACCCUCCCACUUGAACAACCAACAAUUGUUCGAAACAAAACUAGGAAAAU
................................................(........)........
>AL596166.1/191853-191900
CCACACGUGGUUCAUUCAUACCAUCCCACGUAAAAAAACUAGGAGGAA
..............................(.....)...........

ORB p-value ORB frequency
(per structure per nucleotide) 		Means
ratio
1 (.AANNA.) < 0.001 12.2
AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
.........1.........2.........3.........4.....
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2 (.NANCN.) < 0.001 9.28
AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
.........1.........2.........3.........4.....
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3 (.N.()) < 0.001 1.47
AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
.........1.........2.........3.........4.....
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ORB p-value ORB frequency
(per structure per nucleotide) 		Means
ratio

NCM p-value NCM frequency
(per structure per nucleotide) 		Means
ratio
1 .RNAAC. < 0.001 30.9
AL009126.3/1439274-1439318
GCGGGAGAGGUUCUAGCUACACCCUCUAUAAAAAACUAAGGACGA
.........1.........2.........3.........4.....
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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).