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)

SAM riboswitch (alpha-proteobacteria)   (Rfam: RF00521)

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
((U)AA)A
U(URN)R
((R)G)G
((A)NA)A
97.5
87.5
97.5
87.5
U(URN)R
U(URN)R

% of positive sequence with ORB





Deep neural network:

5-fold cross-validation: 99.4 %
(± 0.285 %)
Decision tree:

5-fold cross-validation: 87.7 %
(± 7.3 %)
D-ORB structure
D-ORB structure decision tree:

5-fold cross-validation: 88.7 %
(± 4.09 %)
of CU234118.1/6715248-6715169
CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
(..(((((((((((((....)))((((((((....(((((((((...)..)))))))..)))))))).))))))))))))
.........1.........2.........3.........4.........5.........6.........7.........8
12345678901234567890123456789012345678901234567890123456789012345678901234567890

abstract shape: ()()

Number of sequences
Structure ORBs (out of 40) (%)
1 ((U)AA)A
 35 87.5
>CP000133.1/4272024-4272101
AAGGCACUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAAAAGUCGCUAAAGGGCCGCGUGCGGACCGGU
.................................(.(...................)..)...................
>AAMY01000002.1/143789-143710
GACGCGCUCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAGCGCGAU
...................................((...................)..)....................
>CP000158.1/3446494-3446417
AUCCUCGUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAAGGGCCGAGAUGCAGGAAAC
.................................(.(...................)..)...................
>BX572607.1/122628-122549
ACCAGAACUCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUCCGA
...................................((...................)..)....................
>CP000774.1/443091-443012
GCCCGAACUCGUGGUGAUUUGAGCCGACCGGCUUGCGGCCACGUUAAAUAAUUCGCUAAAAAGGUCGGGACGCGAGCCCC
.....................(...(..................)..)................................
>CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
...................................((...................)..)....................
>AAMV01000014.1/88367-88291
AUGCGCGACUGUGGCGAUUUGUUACCGGAUUGCGGGCCACGUUAAACAAACCGCUAAAAGGUCAGGAUGAAAGGCCC
.....................((...................)..)...............................
>AAUW01000005.1/136978-137057
GGCGCACUUCGUGGUGAUUUGGGCCGGCCGGCUUGCAGCCACGUUAAACAAGUUGCUAAAAAGGCCGGAGGUGAGAACCC
...................................((...................)..)....................
>CP000250.1/4839177-4839098
GCCAGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUUCUG
...................................((...................)..)....................
>CP000230.1/3707118-3707042
CCCCAGAUUCGUGGGGAUUUGAGACCGGCUUGCGCCCACGUUAAACAAACAGCUAAAAGGGUCGUGUGACGAAAGUC
.....................((..................)..)................................
>AE007869.2/429434-429356
AGCUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUGCUAGGAACC
.................................(.(...................)..)....................
>CP000758.1/425473-425394
AAUGUGUUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAUUCGCUAAAAAAGGCCGCGGUUCGUUACCG
................................(..(...................)..).....................
>CP001389.1/177149-177071
GCUUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUAGCUAAAAAGGCCGGGUGUCAAACCGG
.....................((....................)..)................................
>ABCL01000002.1/530718-530642
AGUCGCAACCGUGGCGAUUUGUUACCGGAUUGCGGGCCACGUUAAACAAACCGCUAAAAGGUCAGGAUGAAAGGCCC
.....................((...................)..)...............................
>CP000738.1/3178367-3178444
CAAACAAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACGAUAGA
.................................(.(...................)..)...................
>AE007869.2/2703451-2703527
AAACGCCUCAGUGGUGAUUUGCCGACCGGCUUGCAGCCACUUUAAAGAAGUCGCUAAAGGGUCGAGGAAAAGGGCAA
................................(.(...................)..)...................
>CP000115.1/164818-164739
UACGUCUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAAUGUGAU
...................................((...................)..)....................
>AAMT01000001.1/270050-270128
CGCGAUUGCCGUGGCGAUUUGUCUUCCGGAUUGCGGGCCACGUUAAUCACUCCGCUAAAGAGGUCUGGGACGAUGAACG
..................................((...................)..)....................
>CP000781.1/516361-516281
CCGCUCACUCGUGGUGAAUUUGAGCCGGCCCGCUUGCAGCCACGUUAAACAACCUUGCUAAAAGGCCGGGGACGAACAGAC
...................................(.(....................)..)...................
>BA000040.2/1515209-1515288
UGCCUGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGCUUCCGA
....................((......................)..)................................
>CP000463.1/5459740-5459819
AACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAAUCGCUAAACAGGCCGGGGAUAUGUGUCC
...................................((...................)..)....................
>CP000390.1/128049-128127
CUUUAUCCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAAAGGCCGUGCUCGAAGCUCG
..................................((...................)..)....................
>CP000394.1/99101-99022
AGUCCUCUCCCUCGCGAUUUGUCCGGCCAGCUUGCGGCGAGGUUAAAUAAUCGCGCUAAAGAGGCCUGGGGAGCGUUGUU
....................(...(..................)..).................................
>CP000577.1/522526-522602
GGCAAAUGCCGUGGUGCUUUGUGCCGGAUUGCGGGCCACGUUAAAGAAACCGCUAAAGAGGCGAGGGCCCGCCGCCC
.........................................((..........)..)....................
>CP000494.1/790440-790361
CACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUCGCUAAACAGGCCGGGGACGAAUGUGA
...................................((...................)..)....................
>BA000012.4/2853663-2853740
CAACAGUUCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAUUCGCUAAAGGGCCGUUUGCGUGACGUA
.....................(.(...................)..)...............................
>AL591688.1/3461766-3461843
CAAAUGAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACAAUGGA
.................................(.(...................)..)...................
>CP000301.1/5473167-5473246
GACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAAUCGCUAAACAGGCCGGGGACAGUGUGAU
......(...(.................................)..)................................
>BX572608.1/148770-148849
GACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACGUUGUGGU
...................................((...................)..)....................
>CP000319.1/239336-239415
GACCUGUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUUGCUAAACAGGCCGGGGACAAUGUGAU
...................................((...................)..)....................
>AJ012295.1/100-178
GAAUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUUGAAACCGGU
.................................(.(...................)..)....................
>AATP01000002.1/342466-342543
GCAAAGGACAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAAGGGCCGAUCCGAUCGUGGA
.................................(.(...................)..)...................
>AAAP01003864.1/43186-43108
GUCUUGGUCCGUGGUGAUUUGUCCGACCGGAUUGCGGCCACGUUAAACAUCCCGCUAAAGAGGUCCGAGCGCUCCGCUA
.....................(..(..................)..)................................
>CP000283.1/4563959-4563880
CCGCGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAUUCGCUAAACAGGCCGGGGAUAGUUUCGA
...................................((...................)..)....................
>AAPJ01000002.1/433486-433409
CAAAGCAGAAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGUUCUGACGAUAUG
.................................(.(...................)..)...................
2 ((U)AA)A
U(URN)R
 29 72.5
>AAMV01000014.1/88367-88291
AUGCGCGACUGUGGCGAUUUGUUACCGGAUUGCGGGCCACGUUAAACAAACCGCUAAAAGGUCAGGAUGAAAGGCCC
.....................((......(...)........)..)...............................
>CP001389.1/177149-177071
GCUUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUAGCUAAAAAGGCCGGGUGUCAAACCGG
.....................((........(...).......)..)................................
>AAUW01000005.1/136978-137057
GGCGCACUUCGUGGUGAUUUGGGCCGGCCGGCUUGCAGCCACGUUAAACAAGUUGCUAAAAAGGCCGGAGGUGAGAACCC
.....................((.........(...).......)..)................................
>CP000758.1/425473-425394
AAUGUGUUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAUUCGCUAAAAAAGGCCGCGGUUCGUUACCG
................................(..(......(...)........)..).....................
>CP000781.1/516361-516281
CCGCUCACUCGUGGUGAAUUUGAGCCGGCCCGCUUGCAGCCACGUUAAACAACCUUGCUAAAAGGCCGGGGACGAACAGAC
...................................(.(......(...).........)..)...................
>CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
...................................((......(...)........)..)....................
>BA000012.4/2853663-2853740
CAACAGUUCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAUUCGCUAAAGGGCCGUUUGCGUGACGUA
.....................(.(.......(...).......)..)...............................
>CP000774.1/443091-443012
GCCCGAACUCGUGGUGAUUUGAGCCGACCGGCUUGCGGCCACGUUAAAUAAUUCGCUAAAAAGGUCGGGACGCGAGCCCC
.....................(...(......(...).......)..)................................
>CP000283.1/4563959-4563880
CCGCGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAUUCGCUAAACAGGCCGGGGAUAGUUUCGA
...................................((......(...)........)..)....................
>CP000394.1/99101-99022
AGUCCUCUCCCUCGCGAUUUGUCCGGCCAGCUUGCGGCGAGGUUAAAUAAUCGCGCUAAAGAGGCCUGGGGAGCGUUGUU
....................(...(......(...).......)..).................................
>CP000115.1/164818-164739
UACGUCUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAAUGUGAU
...................................((......(...)........)..)....................
>CP000230.1/3707118-3707042
CCCCAGAUUCGUGGGGAUUUGAGACCGGCUUGCGCCCACGUUAAACAAACAGCUAAAAGGGUCGUGUGACGAAAGUC
.....................((......(...).......)..)................................
>AAAP01003864.1/43186-43108
GUCUUGGUCCGUGGUGAUUUGUCCGACCGGAUUGCGGCCACGUUAAACAUCCCGCUAAAGAGGUCCGAGCGCUCCGCUA
.....................(..(......(...).......)..)................................
>AJ012295.1/100-178
GAAUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUUGAAACCGGU
.................................(.(......(...)........)..)....................
>AE007869.2/2703451-2703527
AAACGCCUCAGUGGUGAUUUGCCGACCGGCUUGCAGCCACUUUAAAGAAGUCGCUAAAGGGUCGAGGAAAAGGGCAA
................................(.(......(...)........)..)...................
>BX572608.1/148770-148849
GACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACGUUGUGGU
...................................((......(...)........)..)....................
>BX572607.1/122628-122549
ACCAGAACUCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUCCGA
...................................((......(...)........)..)....................
>AAMY01000002.1/143789-143710
GACGCGCUCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAGCGCGAU
...................................((......(...)........)..)....................
>AL591688.1/3461766-3461843
CAAAUGAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACAAUGGA
.................................(.(......(...)........)..)...................
>AE007869.2/429434-429356
AGCUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUGCUAGGAACC
.................................(.(......(...)........)..)....................
>CP000738.1/3178367-3178444
CAAACAAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACGAUAGA
.................................(.(......(...)........)..)...................
>CP000319.1/239336-239415
GACCUGUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUUGCUAAACAGGCCGGGGACAAUGUGAU
...................................((......(...)........)..)....................
>CP000463.1/5459740-5459819
AACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAAUCGCUAAACAGGCCGGGGAUAUGUGUCC
...................................((......(...)........)..)....................
>BA000040.2/1515209-1515288
UGCCUGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGCUUCCGA
....................((..........(...).......)..)................................
>AAPJ01000002.1/433486-433409
CAAAGCAGAAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGUUCUGACGAUAUG
.................................(.(......(...)........)..)...................
>CP000494.1/790440-790361
CACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUCGCUAAACAGGCCGGGGACGAAUGUGA
...................................((......(...)........)..)....................
>AATP01000002.1/342466-342543
GCAAAGGACAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAAGGGCCGAUCCGAUCGUGGA
.....................((........(...).......)..)...............................
>CP000133.1/4272024-4272101
AAGGCACUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAAAAGUCGCUAAAGGGCCGCGUGCGGACCGGU
.................................(.(......(...)........)..)...................
>CP000250.1/4839177-4839098
GCCAGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUUCUG
...................................((......(...)........)..)....................
3 ((U)AA)A
U(URN)R
((R)G)G
 23 57.5
>AJ012295.1/100-178
GAAUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUUGAAACCGGU
......................((.........(.(......(...)........)..)......).)...........
>CP000319.1/239336-239415
GACCUGUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUUGCUAAACAGGCCGGGGACAAUGUGAU
.......................((..........((......(...)........)..)......).)...........
>BX572607.1/122628-122549
ACCAGAACUCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUCCGA
.......................((..........((......(...)........)..)......).)...........
>CP000738.1/3178367-3178444
CAAACAAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACGAUAGA
.......................(.(.......(.(......(...)........)..)......).)..........
>BA000012.4/2853663-2853740
CAACAGUUCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAUUCGCUAAAGGGCCGUUUGCGUGACGUA
.......(.(...........(.(.......(...).......)..)...........).).................
>CP000133.1/4272024-4272101
AAGGCACUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAAAAGUCGCUAAAGGGCCGCGUGCGGACCGGU
..............................((.(.(......(...)........)..)).)................
>AL591688.1/3461766-3461843
CAAAUGAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACAAUGGA
.................(....(..........(.(......(...)........)..)......).)..........
>CP000283.1/4563959-4563880
CCGCGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAUUCGCUAAACAGGCCGGGGAUAGUUUCGA
.......................((..........((......(...)........)..)......).)...........
>CP000494.1/790440-790361
CACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUCGCUAAACAGGCCGGGGACGAAUGUGA
.......................((..........((......(...)........)..)......).)...........
>AAMV01000014.1/88367-88291
AUGCGCGACUGUGGCGAUUUGUUACCGGAUUGCGGGCCACGUUAAACAAACCGCUAAAAGGUCAGGAUGAAAGGCCC
........((...........((......(...)........)..)............).)................
>CP000250.1/4839177-4839098
GCCAGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUUCUG
.......................((..........((......(...)........)..)......).)...........
>CP000115.1/164818-164739
UACGUCUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAAUGUGAU
.......................((..........((......(...)........)..)......).)...........
>AAAP01003864.1/43186-43108
GUCUUGGUCCGUGGUGAUUUGUCCGACCGGAUUGCGGCCACGUUAAACAUCCCGCUAAAGAGGUCCGAGCGCUCCGCUA
..(.(................(..(......(...).......)..).............).)................
>AATP01000002.1/342466-342543
GCAAAGGACAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAAGGGCCGAUCCGAUCGUGGA
........(.(..........((........(...).......)..)...........).).................
>CP000230.1/3707118-3707042
CCCCAGAUUCGUGGGGAUUUGAGACCGGCUUGCGCCCACGUUAAACAAACAGCUAAAAGGGUCGUGUGACGAAAGUC
.......(.(...........((......(...).......)..).............).)................
>AAMY01000002.1/143789-143710
GACGCGCUCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAGCGCGAU
.......................((..........((......(...)........)..)......).)...........
>AE007869.2/2703451-2703527
AAACGCCUCAGUGGUGAUUUGCCGACCGGCUUGCAGCCACUUUAAAGAAGUCGCUAAAGGGUCGAGGAAAAGGGCAA
........................((......(.(......(...)........)..)......).)..........
>AAPJ01000002.1/433486-433409
CAAAGCAGAAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGUUCUGACGAUAUG
..............................((.(.(......(...)........)..)).)................
>BX572608.1/148770-148849
GACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACGUUGUGGU
.................(.....(...........((......(...)........)..).......).)..........
>CP001389.1/177149-177071
GCUUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUAGCUAAAAAGGCCGGGUGUCAAACCGG
.(.(.................((........(...).......)..).............).)................
>AE007869.2/429434-429356
AGCUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUGCUAGGAACC
......................((.........(.(......(...)........)..)......).)...........
>CP000463.1/5459740-5459819
AACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAAUCGCUAAACAGGCCGGGGAUAUGUGUCC
.......................((..........((......(...)........)..)......).)...........
>CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.......................((..........((......(...)........)..)......).)...........
4 ((U)AA)A
U(URN)R
((R)G)G
((A)NA)A
 15 37.5
>AJ012295.1/100-178
GAAUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUUGAAACCGGU
......................((.........(.(.....((...)..).....)..)......).)...........
>CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.......................((..........((.....((...)..).....)..)......).)...........
>AE007869.2/429434-429356
AGCUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUGCUAGGAACC
......................((.........(.(.....((...)..).....)..)......).)...........
>BX572608.1/148770-148849
GACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACGUUGUGGU
.................(.....(...........((.....((...)..).....)..).......).)..........
>CP000319.1/239336-239415
GACCUGUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUUGCUAAACAGGCCGGGGACAAUGUGAU
.......................((..........((.....((...)..).....)..)......).)...........
>CP000115.1/164818-164739
UACGUCUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAAUGUGAU
.......................((..........((.....((...)..).....)..)......).)...........
>CP000738.1/3178367-3178444
CAAACAAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACGAUAGA
.......................(.(.......(.(.....((...)..).....)..)......).)..........
>AAMY01000002.1/143789-143710
GACGCGCUCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAGCGCGAU
.......................((..........((.....((...)..).....)..)......).)...........
>CP000494.1/790440-790361
CACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUCGCUAAACAGGCCGGGGACGAAUGUGA
.......................((..........((.....((...)..).....)..)......).)...........
>CP000463.1/5459740-5459819
AACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAAUCGCUAAACAGGCCGGGGAUAUGUGUCC
.......................((..........((.....((...)..).....)..)......).)...........
>AE007869.2/2703451-2703527
AAACGCCUCAGUGGUGAUUUGCCGACCGGCUUGCAGCCACUUUAAAGAAGUCGCUAAAGGGUCGAGGAAAAGGGCAA
........................((......(.(.....((...)..).....)..)......).)..........
>CP000283.1/4563959-4563880
CCGCGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAUUCGCUAAACAGGCCGGGGAUAGUUUCGA
.......................((..........((.....((...)..).....)..)......).)...........
>AL591688.1/3461766-3461843
CAAAUGAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACAAUGGA
.................(....(..........(.(.....((...)..).....)..)......).)..........
>BX572607.1/122628-122549
ACCAGAACUCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUCCGA
.......................((..........((.....((...)..).....)..)......).)...........
>CP000250.1/4839177-4839098
GCCAGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUUCUG
.......................((..........((.....((...)..).....)..)......).)...........

>AAMY01000002.1/143789-143710
GACGCGCUCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAGCGCGAU
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>BX572607.1/122628-122549
ACCAGAACUCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUCCGA
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>CP000250.1/4839177-4839098
GCCAGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAACAGGCCGGGGACAGUUUCUG
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>AE007869.2/429434-429356
AGCUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUGCUAGGAACC
.................................(.(...................)..)....................
.................................(.(......(...)........)..)....................
......................((.........(.(......(...)........)..)......).)...........
......................((.........(.(.....((...)..).....)..)......).)...........
>CP000738.1/3178367-3178444
CAAACAAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACGAUAGA
.................................(.(...................)..)...................
.................................(.(......(...)........)..)...................
.......................(.(.......(.(......(...)........)..)......).)..........
.......................(.(.......(.(.....((...)..).....)..)......).)..........
>AE007869.2/2703451-2703527
AAACGCCUCAGUGGUGAUUUGCCGACCGGCUUGCAGCCACUUUAAAGAAGUCGCUAAAGGGUCGAGGAAAAGGGCAA
................................(.(...................)..)...................
................................(.(......(...)........)..)...................
........................((......(.(......(...)........)..)......).)..........
........................((......(.(.....((...)..).....)..)......).)..........
>CP000115.1/164818-164739
UACGUCUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACAAUGUGAU
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>CP000463.1/5459740-5459819
AACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAAUCGCUAAACAGGCCGGGGAUAUGUGUCC
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>CP000494.1/790440-790361
CACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUCGCUAAACAGGCCGGGGACGAAUGUGA
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>AL591688.1/3461766-3461843
CAAAUGAUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGAGGGAACAAUGGA
.................................(.(...................)..)...................
.................................(.(......(...)........)..)...................
.................(....(..........(.(......(...)........)..)......).)..........
.................(....(..........(.(.....((...)..).....)..)......).)..........
>BX572608.1/148770-148849
GACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAACAGGCCGGGGACGUUGUGGU
...................................((...................)..)....................
...................................((......(...)........)..)....................
.................(.....(...........((......(...)........)..).......).)..........
.................(.....(...........((.....((...)..).....)..).......).)..........
>CP000319.1/239336-239415
GACCUGUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAGUUGCUAAACAGGCCGGGGACAAUGUGAU
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>AJ012295.1/100-178
GAAUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUGGCUAAAAAGACCGGGUUGAAACCGGU
.................................(.(...................)..)....................
.................................(.(......(...)........)..)....................
......................((.........(.(......(...)........)..)......).)...........
......................((.........(.(.....((...)..).....)..)......).)...........
>CP000283.1/4563959-4563880
CCGCGAUCCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAACAAUUCGCUAAACAGGCCGGGGAUAGUUUCGA
...................................((...................)..)....................
...................................((......(...)........)..)....................
.......................((..........((......(...)........)..)......).)...........
.......................((..........((.....((...)..).....)..)......).)...........
>CP000133.1/4272024-4272101
AAGGCACUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAAAAGUCGCUAAAGGGCCGCGUGCGGACCGGU
.................................(.(...................)..)...................
.................................(.(......(...)........)..)...................
..............................((.(.(......(...)........)..)).)................
>AAMV01000014.1/88367-88291
AUGCGCGACUGUGGCGAUUUGUUACCGGAUUGCGGGCCACGUUAAACAAACCGCUAAAAGGUCAGGAUGAAAGGCCC
.....................((...................)..)...............................
.....................((......(...)........)..)...............................
........((...........((......(...)........)..)............).)................
>CP000230.1/3707118-3707042
CCCCAGAUUCGUGGGGAUUUGAGACCGGCUUGCGCCCACGUUAAACAAACAGCUAAAAGGGUCGUGUGACGAAAGUC
.....................((..................)..)................................
.....................((......(...).......)..)................................
.......(.(...........((......(...).......)..).............).)................
>CP001389.1/177149-177071
GCUUUAUCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAGUAGCUAAAAAGGCCGGGUGUCAAACCGG
.....................((....................)..)................................
.....................((........(...).......)..)................................
.(.(.................((........(...).......)..).............).)................
>BA000012.4/2853663-2853740
CAACAGUUCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAACAAUUCGCUAAAGGGCCGUUUGCGUGACGUA
.....................(.(...................)..)...............................
.....................(.(.......(...).......)..)...............................
.......(.(...........(.(.......(...).......)..)...........).).................
>AATP01000002.1/342466-342543
GCAAAGGACAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAACAACUCGCUAAAGGGCCGAUCCGAUCGUGGA
.................................(.(...................)..)...................
.....................((........(...).......)..)...............................
........(.(..........((........(...).......)..)...........).).................
>AAAP01003864.1/43186-43108
GUCUUGGUCCGUGGUGAUUUGUCCGACCGGAUUGCGGCCACGUUAAACAUCCCGCUAAAGAGGUCCGAGCGCUCCGCUA
.....................(..(..................)..)................................
.....................(..(......(...).......)..)................................
..(.(................(..(......(...).......)..).............).)................
>AAPJ01000002.1/433486-433409
CAAAGCAGAAGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAGGGCCGUUCUGACGAUAUG
.................................(.(...................)..)...................
.................................(.(......(...)........)..)...................
..............................((.(.(......(...)........)..)).)................
>CP000774.1/443091-443012
GCCCGAACUCGUGGUGAUUUGAGCCGACCGGCUUGCGGCCACGUUAAAUAAUUCGCUAAAAAGGUCGGGACGCGAGCCCC
.....................(...(..................)..)................................
.....................(...(......(...).......)..)................................
>AAUW01000005.1/136978-137057
GGCGCACUUCGUGGUGAUUUGGGCCGGCCGGCUUGCAGCCACGUUAAACAAGUUGCUAAAAAGGCCGGAGGUGAGAACCC
...................................((...................)..)....................
.....................((.........(...).......)..)................................
>CP000758.1/425473-425394
AAUGUGUUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAAGAAUUCGCUAAAAAAGGCCGCGGUUCGUUACCG
................................(..(...................)..).....................
................................(..(......(...)........)..).....................
>CP000781.1/516361-516281
CCGCUCACUCGUGGUGAAUUUGAGCCGGCCCGCUUGCAGCCACGUUAAACAACCUUGCUAAAAGGCCGGGGACGAACAGAC
...................................(.(....................)..)...................
...................................(.(......(...).........)..)...................
>BA000040.2/1515209-1515288
UGCCUGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGCUUCCGA
....................((......................)..)................................
....................((..........(...).......)..)................................
>CP000394.1/99101-99022
AGUCCUCUCCCUCGCGAUUUGUCCGGCCAGCUUGCGGCGAGGUUAAAUAAUCGCGCUAAAGAGGCCUGGGGAGCGUUGUU
....................(...(..................)..).................................
....................(...(......(...).......)..).................................
>CP000158.1/3446494-3446417
AUCCUCGUCCGUGGUGAUUUGGCCGGCCGGCUUGCAGCCACGUUAAACAAGUCGCUAAAGGGCCGAGAUGCAGGAAAC
.................................(.(...................)..)...................
>ABCL01000002.1/530718-530642
AGUCGCAACCGUGGCGAUUUGUUACCGGAUUGCGGGCCACGUUAAACAAACCGCUAAAAGGUCAGGAUGAAAGGCCC
.....................((...................)..)...............................
>AAMT01000001.1/270050-270128
CGCGAUUGCCGUGGCGAUUUGUCUUCCGGAUUGCGGGCCACGUUAAUCACUCCGCUAAAGAGGUCUGGGACGAUGAACG
..................................((...................)..)....................
>CP000390.1/128049-128127
CUUUAUCCCCGUGGUGAUUUGGCCGGUCGGCUUGCAGCCACGUUAAAGAAGUCGCUAAAAAGGCCGUGCUCGAAGCUCG
..................................((...................)..)....................
>CP000577.1/522526-522602
GGCAAAUGCCGUGGUGCUUUGUGCCGGAUUGCGGGCCACGUUAAAGAAACCGCUAAAGAGGCGAGGGCCCGCCGCCC
.........................................((..........)..)....................
>CP000301.1/5473167-5473246
GACUUAUCCCGUGGUGAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAUAAAUCGCUAAACAGGCCGGGGACAGUGUGAU
......(...(.................................)..)................................

ORB p-value ORB frequency
(per structure per nucleotide) 		Means
ratio
1 ((U)AA)A < 0.001 16.2
CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.........1.........2.........3.........4.........5.........6.........7.........8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
2 ((A)NA)A < 0.001 16.5
CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.........1.........2.........3.........4.........5.........6.........7.........8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
3 U(URN)R < 0.001 3.67
CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.........1.........2.........3.........4.........5.........6.........7.........8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
4 ((R)G)G < 0.001 3.32
CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.........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 .UAAAN. < 0.001 19
CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.........1.........2.........3.........4.........5.........6.........7.........8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
2 G(NUU)G < 0.001 21.3
CU234118.1/6715248-6715169
UGCCCGUUCCGUGGUCAUUUGAGCCGGCCGGCUUGCAGCCACGUUAAAAAACUCGCUAAACAGGCCGGGGACGUUAUCGA
.........1.........2.........3.........4.........5.........6.........7.........8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
3 R(U(A)) (URB) < 0.001 3.47e-05
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).