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)

Small Cajal body specific RNA 11   (Rfam: RF00564)

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
C(U(C))
((R)C)N
(.CNNU.)
C(AG)N
90.5
95.2
90.5
71.4

% of positive sequence with ORB





Deep neural network:

5-fold cross-validation: 99.7 %
(± 0.11 %)
Decision tree:

5-fold cross-validation: 76.8 %
(± 6.22 %)
D-ORB structure
D-ORB structure decision tree:

5-fold cross-validation: 82 %
(± 8.06 %)
of AAQR03127877.1/2089-2226
AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
((((((((((....)))(.((((((((((((((((((((..)))(((((((((((((..)))))))))......)))).)))))))))).))))))((((((..))))))((.((.((...))))).)))))))))).
...................................................................................................1......................................
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3........
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678

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

Number of sequences
Structure ORBs (out of 21) (%)
1 C(U(C))
 17 81.0
>AAQQ01201309.1/4377-4515
UUGUCCUGGCCUGUGCUUUUUUUGCUCCCUGUGCUCAGCUCUAACAGGGUAGUCUGGCAGGACACACAGCAGUUUCCCUCUCAGUUUAGGAGAGCCAUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...............................................................................(.(......)).................................................
>AAGW02051573.1/21026-20891
CUGUCCUGGCCUGUGCCUCUCCUCGCCUGUGCCCAGUUCUCACAGGGGAGUCCGGCGGGACACACAGUACUCUCCCUCUCAGUUUAGGAGGCCGUCCUAAGAAUGGGGCUGGUUCUUAAAGGCACGAGAGGACAAU
.....................(.(...))...........................................................................................................
>AANG01080854.1/423-284
UUGUCCUUGCCUAUGCUUUGUCUGCUCCCUUGUGCUCAGCUCUAACAGGGGAGUCUGGCAGGACACAGAGCAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAC
....................................................................................................................(.(......).)............
>AAPN01410804.1/2610-2752
CCGUCCCGGCCCUUGCAGCUGCCCCCCUGUGCCGAGCUGUGGCGGGGGGGUGUCCGGGCGGGACACACAGUAACCCUAACCCUCUCCAUUUAGGAGGGCCCCCCCGAGGCUGGGGGUGGUCCUUAAAGGCAAGAGAGGACAAA
...................................................................................(.(......)).................................................
>AALT01287000.1/5146-5006
UAGCUUUGUCCCAUGCUUUGCCUGCCCAUUGUGCAUAGCUCCAACAGUGAAGUUUGGUGGAGUACACAACACUCUCUCUCUCUAUGUAUAGGAGAGUUGUUCUGAGCCUAUGGCUGACUCUUAAAGGCAUGAGAGGACAGU
...............................................................................(.(........)).................................................
>AAFC03022303.1/17401-17264
UUGUCCUGGCCUGUGGUUUUUCUGUUCCCCUGUGCUCAGUUCUCAGGGGACUCCGGCAGGACGCACAGCAAGCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAGU
..............................................................................(.(......)).................................................
>AAHX01032860.1/31011-31146
UUGUCCUGUGCCUUUUUCUGCUACCCUGUGCCCAGUCUUAACAGGGUAGUCUGGCAGGACACAUAGCAAUUUACCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
............................................................................(.(......)).................................................
>AAPE02007003.1/20242-20104
UUGUCCUGGCCUAUGGUUUCUCUGCUCACCUGUGCUCAGUAAAACAGGGGAGUCUGGCAGGACACACAGCAACCUCCCUCUCACUUUAGGAGGGCCGUCCUGAGUAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
........................(.(......).).......................................................................................................
>ABDC01192957.1/1309-1171
UUGUCCUAGCCUAUGCUCAUUCUGCUCCCUGUGCUCAGUUCCAACAGGGCAGUCUGGCAGGACACACAGCAAUCUCCCUCUCAGUUUAGGAGAGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................................(.(.....))..............
>AAIY01376073.1/3485-3344
UCGUCCUGGCCCCCGAGUGUCCCUGCUCCCCUGUGCUCAGCUGUGGCAGGGGGGCCUGAGGCAGGACGUACAGCAUCUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGCACGGGGCUGGCUCUUAAAGGCACGAGAGGACAUU
..................................................................................(.(......)).................................................
>AANN01528625.1/1227-1368
UUGUCCUGGCCUAUGCUUUUGCUGCUCCCCUGUGCUCACUUCUGACAGAGGGAGUCUGGCAGGACGCACAGUAAUUCUCCCUCUCAGUUUAGGAGGGCCAUCCUGAGAAAAGGACUGGCUCUUAAAGGCACGAGAGGACAAC
......................................................................................................................(.(......).)............
>AAFR03037693.1/44000-43864
AAGUCCAUGCUUAUUAUUGCUUUCCUGCUUGCCACUGUAGCAGGAGGGCCAGAGGCAGGACUAAGAGCAAAUCUUCCUCUCAGAUUAGGAGGGCUGUCCUGAGAUGGGGCUGACUCUUAAAGGCACAAGAGGACACU
............................................................................(.(...........)).............................................
>AAKN02051621.1/20436-20572
GUGUCCUGGCCUAUGUUUGUGCUCCCCUGUGCUCAGCUGUGACAGGGUAGUCUGGCAGGACGUACAGCAGUUUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.................................................................................................................(.(.....))..............
>AAWR02029183.1/19489-19348
UUGUCCUGGCCUAUGCUUUCUCUGCUCGCCUGUGCUCAGUUCUAACAGGGGCCUCUGGCAGGACACACAGCAAUCUCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGUCUGGCUCUUAAAGGCACGAGAGGACAAU
......................................................................................................................(.(......).)............
>AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
..................................................................................................................(.(.....))..............
>AADN03001033.1/16904-17044
GUGUCCUGACCUCAUCCUGACUCUUCCCCUCACCGGAGCUGUGGUGGUGGGGUCUGGGGGUGGACACAGAUCAUCUUACCCUCUCAAGUUAGGAGGGUUGCUGAAGAUGUUUGCAAACCCUUAAAGGCAAGAGAGGACAUC
............................(.(............).)...............................................................................................
>AJ609487.1/1-136
UUGUCCUGGCCUAUUUUUCUGCUCCCCUGUGCUCAGUUCUAACAGGGUAGUCUGGCAGGACACACAGCAAUUCCCUCUCAGUUUAGGAGGGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
................................................................................................................(.(......).)............
2 C(U(C))
((R)C)N
 13 61.9
>AALT01287000.1/5146-5006
UAGCUUUGUCCCAUGCUUUGCCUGCCCAUUGUGCAUAGCUCCAACAGUGAAGUUUGGUGGAGUACACAACACUCUCUCUCUCUAUGUAUAGGAGAGUUGUUCUGAGCCUAUGGCUGACUCUUAAAGGCAUGAGAGGACAGU
.....................................((........................................(.(........)).............).).................................
>AAWR02029183.1/19489-19348
UUGUCCUGGCCUAUGCUUUCUCUGCUCGCCUGUGCUCAGUUCUAACAGGGGCCUCUGGCAGGACACACAGCAAUCUCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGUCUGGCUCUUAAAGGCACGAGAGGACAAU
..................................................................................................................((..(.(.....)).).)..........
>AAQQ01201309.1/4377-4515
UUGUCCUGGCCUGUGCUUUUUUUGCUCCCUGUGCUCAGCUCUAACAGGGUAGUCUGGCAGGACACACAGCAGUUUCCCUCUCAGUUUAGGAGAGCCAUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.......................................................(.(.....................(.(......))...).)...........................................
>AAIY01376073.1/3485-3344
UCGUCCUGGCCCCCGAGUGUCCCUGCUCCCCUGUGCUCAGCUGUGGCAGGGGGGCCUGAGGCAGGACGUACAGCAUCUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGCACGGGGCUGGCUCUUAAAGGCACGAGAGGACAUU
.............................................................................((...(.(......))...).)...........................................
>AJ609487.1/1-136
UUGUCCUGGCCUAUUUUUCUGCUCCCCUGUGCUCAGUUCUAACAGGGUAGUCUGGCAGGACACACAGCAAUUCCCUCUCAGUUUAGGAGGGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
............................................................................................................((..(.(.....)).).)..........
>AANN01528625.1/1227-1368
UUGUCCUGGCCUAUGCUUUUGCUGCUCCCCUGUGCUCACUUCUGACAGAGGGAGUCUGGCAGGACGCACAGUAAUUCUCCCUCUCAGUUUAGGAGGGCCAUCCUGAGAAAAGGACUGGCUCUUAAAGGCACGAGAGGACAAC
..................................................................................................................((..(.(.....)).).)..........
>AAPE02007003.1/20242-20104
UUGUCCUGGCCUAUGGUUUCUCUGCUCACCUGUGCUCAGUAAAACAGGGGAGUCUGGCAGGACACACAGCAACCUCCCUCUCACUUUAGGAGGGCCGUCCUGAGUAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
....................(.(.(.(......).).............................).).......................................................................
>AAKN02051621.1/20436-20572
GUGUCCUGGCCUAUGUUUGUGCUCCCCUGUGCUCAGCUGUGACAGGGUAGUCUGGCAGGACGUACAGCAGUUUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.............................................................................................................((..(.(.....)).).)..........
>AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
..............................................................................................................((..(.(.....)).).)..........
>AAHX01032860.1/31011-31146
UUGUCCUGUGCCUUUUUCUGCUACCCUGUGCCCAGUCUUAACAGGGUAGUCUGGCAGGACACAUAGCAAUUUACCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
........................................................................(.(.(.(......))...).)...........................................
>AANG01080854.1/423-284
UUGUCCUUGCCUAUGCUUUGUCUGCUCCCUUGUGCUCAGCUCUAACAGGGGAGUCUGGCAGGACACAGAGCAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAC
................................................................................................................((..(.(.....)).).)..........
>ABDC01192957.1/1309-1171
UUGUCCUAGCCUAUGCUCAUUCUGCUCCCUGUGCUCAGUUCCAACAGGGCAGUCUGGCAGGACACACAGCAAUCUCCCUCUCAGUUUAGGAGAGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...............................................................................................................((..(.(.....)).).)..........
>AAFC03022303.1/17401-17264
UUGUCCUGGCCUGUGGUUUUUCUGUUCCCCUGUGCUCAGUUCUCAGGGGACUCCGGCAGGACGCACAGCAAGCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAGU
..............................................................(..(............(.(......))...).)...........................................
3 C(U(C))
((R)C)N
(.CNNU.)
 11 52.4
>ABDC01192957.1/1309-1171
UUGUCCUAGCCUAUGCUCAUUCUGCUCCCUGUGCUCAGUUCCAACAGGGCAGUCUGGCAGGACACACAGCAAUCUCCCUCUCAGUUUAGGAGAGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
....................................................................(....).....................................((..(.(.....)).).)..........
>AJ609487.1/1-136
UUGUCCUGGCCUAUUUUUCUGCUCCCCUGUGCUCAGUUCUAACAGGGUAGUCUGGCAGGACACACAGCAAUUCCCUCUCAGUUUAGGAGGGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.......................(....)...............................................................................((..(.(.....)).).)..........
>AAHX01032860.1/31011-31146
UUGUCCUGUGCCUUUUUCUGCUACCCUGUGCCCAGUCUUAACAGGGUAGUCUGGCAGGACACAUAGCAAUUUACCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
..............................(.....)...................................(.(.(.(......))...).)...........................................
>AAKN02051621.1/20436-20572
GUGUCCUGGCCUAUGUUUGUGCUCCCCUGUGCUCAGCUGUGACAGGGUAGUCUGGCAGGACGUACAGCAGUUUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.......................(....)................................................................................((..(.(.....)).).)..........
>AAQQ01201309.1/4377-4515
UUGUCCUGGCCUGUGCUUUUUUUGCUCCCUGUGCUCAGCUCUAACAGGGUAGUCUGGCAGGACACACAGCAGUUUCCCUCUCAGUUUAGGAGAGCCAUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
................................(.........)............(.(.....................(.(......))...).)...........................................
>AAWR02029183.1/19489-19348
UUGUCCUGGCCUAUGCUUUCUCUGCUCGCCUGUGCUCAGUUCUAACAGGGGCCUCUGGCAGGACACACAGCAAUCUCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGUCUGGCUCUUAAAGGCACGAGAGGACAAU
.....................................................................(....).......................................((..(.(.....)).).)..........
>AANG01080854.1/423-284
UUGUCCUUGCCUAUGCUUUGUCUGCUCCCUUGUGCUCAGCUCUAACAGGGGAGUCUGGCAGGACACAGAGCAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAC
.....................................................................(....).....................................((..(.(.....)).).)..........
>AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.................................(......).....................................................................((..(.(.....)).).)..........
>AAFC03022303.1/17401-17264
UUGUCCUGGCCUGUGGUUUUUCUGUUCCCCUGUGCUCAGUUCUCAGGGGACUCCGGCAGGACGCACAGCAAGCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAGU
..................................(.....).....................((..............(.(......))...).)...........................................
>AAIY01376073.1/3485-3344
UCGUCCUGGCCCCCGAGUGUCCCUGCUCCCCUGUGCUCAGCUGUGGCAGGGGGGCCUGAGGCAGGACGUACAGCAUCUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGCACGGGGCUGGCUCUUAAAGGCACGAGAGGACAUU
...................................................................................(....).........................((..(.(.....)).).)..........
>AANN01528625.1/1227-1368
UUGUCCUGGCCUAUGCUUUUGCUGCUCCCCUGUGCUCACUUCUGACAGAGGGAGUCUGGCAGGACGCACAGUAAUUCUCCCUCUCAGUUUAGGAGGGCCAUCCUGAGAAAAGGACUGGCUCUUAAAGGCACGAGAGGACAAC
...................................................................(.......)......................................((..(.(.....)).).)..........
4 C(U(C))
((R)C)N
(.CNNU.)
C(AG)N
 8 38.1
>AAWR02029183.1/19489-19348
UUGUCCUGGCCUAUGCUUUCUCUGCUCGCCUGUGCUCAGUUCUAACAGGGGCCUCUGGCAGGACACACAGCAAUCUCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGUCUGGCUCUUAAAGGCACGAGAGGACAAU
.....................................................................(....).........(..)..........................((..(.(.....)).).)..........
>AANN01528625.1/1227-1368
UUGUCCUGGCCUAUGCUUUUGCUGCUCCCCUGUGCUCACUUCUGACAGAGGGAGUCUGGCAGGACGCACAGUAAUUCUCCCUCUCAGUUUAGGAGGGCCAUCCUGAGAAAAGGACUGGCUCUUAAAGGCACGAGAGGACAAC
..........................(....)...........................(..)...................................................((..(.(.....)).).)..........
>AAKN02051621.1/20436-20572
GUGUCCUGGCCUAUGUUUGUGCUCCCCUGUGCUCAGCUGUGACAGGGUAGUCUGGCAGGACGUACAGCAGUUUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.......................(....)..........................(..)..................................................((..(.(.....)).).)..........
>AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.................................(......)...............(..)..................................................((..(.(.....)).).)..........
>AAFC03022303.1/17401-17264
UUGUCCUGGCCUGUGGUUUUUCUGUUCCCCUGUGCUCAGUUCUCAGGGGACUCCGGCAGGACGCACAGCAAGCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAGU
..................................(.....)...............(..)..((..............(.(......))...).)...........................................
>AANG01080854.1/423-284
UUGUCCUUGCCUAUGCUUUGUCUGCUCCCUUGUGCUCAGCUCUAACAGGGGAGUCUGGCAGGACACAGAGCAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAC
.................................(.........)..............(..)..................................................((..(.(.....)).).)..........
>AJ609487.1/1-136
UUGUCCUGGCCUAUUUUUCUGCUCCCCUGUGCUCAGUUCUAACAGGGUAGUCUGGCAGGACACACAGCAAUUCCCUCUCAGUUUAGGAGGGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.......................(....)..........................(..).................................................((..(.(.....)).).)..........
>AAHX01032860.1/31011-31146
UUGUCCUGUGCCUUUUUCUGCUACCCUGUGCCCAGUCUUAACAGGGUAGUCUGGCAGGACACAUAGCAAUUUACCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
..............................(.....).................(..)..............(.(.(.(......))...).)...........................................

>AANG01080854.1/423-284
UUGUCCUUGCCUAUGCUUUGUCUGCUCCCUUGUGCUCAGCUCUAACAGGGGAGUCUGGCAGGACACAGAGCAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAC
....................................................................................................................(.(......).)............
................................................................................................................((..(.(.....)).).)..........
.....................................................................(....).....................................((..(.(.....)).).)..........
.................................(.........)..............(..)..................................................((..(.(.....)).).)..........
>AAFC03022303.1/17401-17264
UUGUCCUGGCCUGUGGUUUUUCUGUUCCCCUGUGCUCAGUUCUCAGGGGACUCCGGCAGGACGCACAGCAAGCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAGU
..............................................................................(.(......)).................................................
..............................................................(..(............(.(......))...).)...........................................
..................................(.....).....................((..............(.(......))...).)...........................................
..................................(.....)...............(..)..((..............(.(......))...).)...........................................
>AAHX01032860.1/31011-31146
UUGUCCUGUGCCUUUUUCUGCUACCCUGUGCCCAGUCUUAACAGGGUAGUCUGGCAGGACACAUAGCAAUUUACCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
............................................................................(.(......)).................................................
........................................................................(.(.(.(......))...).)...........................................
..............................(.....)...................................(.(.(.(......))...).)...........................................
..............................(.....).................(..)..............(.(.(.(......))...).)...........................................
>AANN01528625.1/1227-1368
UUGUCCUGGCCUAUGCUUUUGCUGCUCCCCUGUGCUCACUUCUGACAGAGGGAGUCUGGCAGGACGCACAGUAAUUCUCCCUCUCAGUUUAGGAGGGCCAUCCUGAGAAAAGGACUGGCUCUUAAAGGCACGAGAGGACAAC
......................................................................................................................(.(......).)............
..................................................................................................................((..(.(.....)).).)..........
...................................................................(.......)......................................((..(.(.....)).).)..........
..........................(....)...........................(..)...................................................((..(.(.....)).).)..........
>AAKN02051621.1/20436-20572
GUGUCCUGGCCUAUGUUUGUGCUCCCCUGUGCUCAGCUGUGACAGGGUAGUCUGGCAGGACGUACAGCAGUUUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
.................................................................................................................(.(.....))..............
.............................................................................................................((..(.(.....)).).)..........
.......................(....)................................................................................((..(.(.....)).).)..........
.......................(....)..........................(..)..................................................((..(.(.....)).).)..........
>AAWR02029183.1/19489-19348
UUGUCCUGGCCUAUGCUUUCUCUGCUCGCCUGUGCUCAGUUCUAACAGGGGCCUCUGGCAGGACACACAGCAAUCUCUCCCUCUCAGUUUAGGAGGGCCGUCCUGAGAAUAGGUCUGGCUCUUAAAGGCACGAGAGGACAAU
......................................................................................................................(.(......).)............
..................................................................................................................((..(.(.....)).).)..........
.....................................................................(....).......................................((..(.(.....)).).)..........
.....................................................................(....).........(..)..........................((..(.(.....)).).)..........
>AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
..................................................................................................................(.(.....))..............
..............................................................................................................((..(.(.....)).).)..........
.................................(......).....................................................................((..(.(.....)).).)..........
.................................(......)...............(..)..................................................((..(.(.....)).).)..........
>AJ609487.1/1-136
UUGUCCUGGCCUAUUUUUCUGCUCCCCUGUGCUCAGUUCUAACAGGGUAGUCUGGCAGGACACACAGCAAUUCCCUCUCAGUUUAGGAGGGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
................................................................................................................(.(......).)............
............................................................................................................((..(.(.....)).).)..........
.......................(....)...............................................................................((..(.(.....)).).)..........
.......................(....)..........................(..).................................................((..(.(.....)).).)..........
>AAQQ01201309.1/4377-4515
UUGUCCUGGCCUGUGCUUUUUUUGCUCCCUGUGCUCAGCUCUAACAGGGUAGUCUGGCAGGACACACAGCAGUUUCCCUCUCAGUUUAGGAGAGCCAUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...............................................................................(.(......)).................................................
.......................................................(.(.....................(.(......))...).)...........................................
................................(.........)............(.(.....................(.(......))...).)...........................................
>ABDC01192957.1/1309-1171
UUGUCCUAGCCUAUGCUCAUUCUGCUCCCUGUGCUCAGUUCCAACAGGGCAGUCUGGCAGGACACACAGCAAUCUCCCUCUCAGUUUAGGAGAGCUGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................................(.(.....))..............
...............................................................................................................((..(.(.....)).).)..........
....................................................................(....).....................................((..(.(.....)).).)..........
>AAIY01376073.1/3485-3344
UCGUCCUGGCCCCCGAGUGUCCCUGCUCCCCUGUGCUCAGCUGUGGCAGGGGGGCCUGAGGCAGGACGUACAGCAUCUCCCUCUCAGUUUAGGAGGGCUGUCCUAAGCACGGGGCUGGCUCUUAAAGGCACGAGAGGACAUU
..................................................................................(.(......)).................................................
.............................................................................((...(.(......))...).)...........................................
...................................................................................(....).........................((..(.(.....)).).)..........
>AALT01287000.1/5146-5006
UAGCUUUGUCCCAUGCUUUGCCUGCCCAUUGUGCAUAGCUCCAACAGUGAAGUUUGGUGGAGUACACAACACUCUCUCUCUCUAUGUAUAGGAGAGUUGUUCUGAGCCUAUGGCUGACUCUUAAAGGCAUGAGAGGACAGU
...............................................................................(.(........)).................................................
.....................................((........................................(.(........)).............).).................................
>AAPE02007003.1/20242-20104
UUGUCCUGGCCUAUGGUUUCUCUGCUCACCUGUGCUCAGUAAAACAGGGGAGUCUGGCAGGACACACAGCAACCUCCCUCUCACUUUAGGAGGGCCGUCCUGAGUAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
........................(.(......).).......................................................................................................
....................(.(.(.(......).).............................).).......................................................................
>AAGW02051573.1/21026-20891
CUGUCCUGGCCUGUGCCUCUCCUCGCCUGUGCCCAGUUCUCACAGGGGAGUCCGGCGGGACACACAGUACUCUCCCUCUCAGUUUAGGAGGCCGUCCUAAGAAUGGGGCUGGUUCUUAAAGGCACGAGAGGACAAU
.....................(.(...))...........................................................................................................
>AAPN01410804.1/2610-2752
CCGUCCCGGCCCUUGCAGCUGCCCCCCUGUGCCGAGCUGUGGCGGGGGGGUGUCCGGGCGGGACACACAGUAACCCUAACCCUCUCCAUUUAGGAGGGCCCCCCCGAGGCUGGGGGUGGUCCUUAAAGGCAAGAGAGGACAAA
...................................................................................(.(......)).................................................
>AAFR03037693.1/44000-43864
AAGUCCAUGCUUAUUAUUGCUUUCCUGCUUGCCACUGUAGCAGGAGGGCCAGAGGCAGGACUAAGAGCAAAUCUUCCUCUCAGAUUAGGAGGGCUGUCCUGAGAUGGGGCUGACUCUUAAAGGCACAAGAGGACACU
............................................................................(.(...........)).............................................
>AADN03001033.1/16904-17044
GUGUCCUGACCUCAUCCUGACUCUUCCCCUCACCGGAGCUGUGGUGGUGGGGUCUGGGGGUGGACACAGAUCAUCUUACCCUCUCAAGUUAGGAGGGUUGCUGAAGAUGUUUGCAAACCCUUAAAGGCAAGAGAGGACAUC
............................(.(............).)...............................................................................................

ORB p-value ORB frequency
(per structure per nucleotide) 		Means
ratio
1 C(U(C)) < 0.001 2.42
AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................1......................................
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3........
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
2 ((R)C)N < 0.001 2.44
AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................1......................................
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3........
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
3 C(AG)N < 0.001 5.92
AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................1......................................
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3........
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
4 (.CNNU.) < 0.001 2.98
AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................1......................................
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3........
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
ORB p-value ORB frequency
(per structure per nucleotide) 		Means
ratio

NCM p-value NCM frequency
(per structure per nucleotide) 		Means
ratio
1 .CYCU. < 0.001 6.83
AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................1......................................
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3........
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
2 U(N(G)) 0.111 1.48
AAQR03127877.1/2089-2226
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
UUGUCCUGGCCUAUGCUCUUCUGCUCCCUGUGCUCAGUUCAAACAGGGUAGUCUGGCAGGACACACAAUAAUCUCCCUCUCAGUUUAGGAGAGCCGUCCUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
...................................................................................................1......................................
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3........
123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678
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).